From d9f92faf40f2970ed86943d120a41982c391af44 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 27 Aug 2014 16:17:57 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12365
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/KOKKOS/Install.sh | 10 +-
src/KOKKOS/atom_kokkos.cpp | 108 +-
src/KOKKOS/atom_kokkos.h | 24 +-
src/KOKKOS/atom_vec_angle_kokkos.cpp | 1886 +++++++++++++++
src/KOKKOS/atom_vec_angle_kokkos.h | 153 ++
src/KOKKOS/atom_vec_atomic_kokkos.cpp | 142 +-
src/KOKKOS/atom_vec_bond_kokkos.cpp | 1717 ++++++++++++++
src/KOKKOS/atom_vec_bond_kokkos.h | 141 ++
src/KOKKOS/atom_vec_charge_kokkos.cpp | 1517 ++++++++++++
src/KOKKOS/atom_vec_charge_kokkos.h | 126 +
src/KOKKOS/atom_vec_full_kokkos.cpp | 2321 +++++++++++++++++++
src/KOKKOS/atom_vec_full_kokkos.h | 183 ++
src/KOKKOS/atom_vec_kokkos.h | 28 +-
src/KOKKOS/atom_vec_molecular_kokkos.cpp | 2236 ++++++++++++++++++
src/KOKKOS/atom_vec_molecular_kokkos.h | 178 ++
src/KOKKOS/comm_kokkos.cpp | 164 +-
src/KOKKOS/comm_kokkos.h | 12 +
src/KOKKOS/fix_langevin_kokkos.cpp | 810 +++++++
src/KOKKOS/fix_langevin_kokkos.h | 266 +++
src/KOKKOS/fix_nve_kokkos.cpp | 2 +-
src/KOKKOS/kokkos.cpp | 8 +-
src/KOKKOS/kokkos_type.h | 157 +-
src/KOKKOS/neigh_full_kokkos.h | 295 ++-
src/KOKKOS/neigh_list_kokkos.cpp | 2 +-
src/KOKKOS/neigh_list_kokkos.h | 2 +-
src/KOKKOS/neighbor_kokkos.cpp | 61 +-
src/KOKKOS/neighbor_kokkos.h | 138 +-
src/KOKKOS/pair_coul_cut_kokkos.cpp | 266 +++
src/KOKKOS/pair_coul_cut_kokkos.h | 137 ++
src/KOKKOS/pair_kokkos.h | 462 ++--
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp | 347 +++
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h | 131 ++
src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp | 496 ++++
src/KOKKOS/pair_lj_cut_coul_long_kokkos.h | 147 ++
src/KOKKOS/pair_lj_cut_kokkos.cpp | 14 +-
src/KOKKOS/pair_lj_cut_kokkos.h | 11 +-
src/KOKKOS/pair_table_kokkos.cpp | 141 +-
src/KOKKOS/pair_table_kokkos.h | 60 +-
src/KOKKOS/verlet_kokkos.cpp | 132 +-
39 files changed, 14362 insertions(+), 669 deletions(-)
create mode 100644 src/KOKKOS/atom_vec_angle_kokkos.cpp
create mode 100644 src/KOKKOS/atom_vec_angle_kokkos.h
create mode 100644 src/KOKKOS/atom_vec_bond_kokkos.cpp
create mode 100644 src/KOKKOS/atom_vec_bond_kokkos.h
create mode 100644 src/KOKKOS/atom_vec_charge_kokkos.cpp
create mode 100644 src/KOKKOS/atom_vec_charge_kokkos.h
create mode 100644 src/KOKKOS/atom_vec_full_kokkos.cpp
create mode 100644 src/KOKKOS/atom_vec_full_kokkos.h
create mode 100644 src/KOKKOS/atom_vec_molecular_kokkos.cpp
create mode 100644 src/KOKKOS/atom_vec_molecular_kokkos.h
create mode 100644 src/KOKKOS/fix_langevin_kokkos.cpp
create mode 100644 src/KOKKOS/fix_langevin_kokkos.h
create mode 100644 src/KOKKOS/pair_coul_cut_kokkos.cpp
create mode 100644 src/KOKKOS/pair_coul_cut_kokkos.h
create mode 100644 src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
create mode 100644 src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h
create mode 100644 src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
create mode 100644 src/KOKKOS/pair_lj_cut_coul_long_kokkos.h
diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh
index 9378eccfc7..8f6e21bf8b 100644
--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@@ -40,12 +40,12 @@ if (test $1 = 1) then
if (test -e ../Makefile.package) then
sed -i -e 's/[^ \t]*kokkos[^ \t]* //g' ../Makefile.package
sed -i -e 's/[^ \t]*KOKKOS[^ \t]* //g' ../Makefile.package
- sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/kokkos\/core\/src -I../../lib/kokkos/containers/src -DLMP_KOKKOS |' ../Makefile.package
- sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/kokkos\/core\/src |' ../Makefile.package
+ sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_KOKKOS |' ../Makefile.package
+# sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/kokkos\/core\/src |' ../Makefile.package
sed -i -e 's|^PKG_LIB =[ \t]*|&-lkokkoscore |' ../Makefile.package
- sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(kokkos_SYSINC) |' ../Makefile.package
- sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(kokkos_SYSLIB) |' ../Makefile.package
- sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(kokkos_SYSPATH) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(KOKKOS_INC) |' ../Makefile.package
+ sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(KOKKOS_LINK) |' ../Makefile.package
+# sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(kokkos_SYSPATH) |' ../Makefile.package
fi
if (test -e ../Makefile.package.settings) then
diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp
index 14dbd7e10e..89c7eea007 100644
--- a/src/KOKKOS/atom_kokkos.cpp
+++ b/src/KOKKOS/atom_kokkos.cpp
@@ -37,31 +37,43 @@ AtomKokkos::AtomKokkos(LAMMPS *lmp) : Atom(lmp)
AtomKokkos::~AtomKokkos()
{
- k_tag = DAT::tdual_tagint_1d();
- k_mask = DAT::tdual_int_1d();
- k_type = DAT::tdual_int_1d();
- k_image = DAT::tdual_imageint_1d();
- k_molecule = DAT::tdual_tagint_1d();
-
- k_x = DAT::tdual_x_array();
- k_v = DAT::tdual_v_array();
- k_f = DAT::tdual_f_array();
-
- k_mass = DAT::tdual_float_1d();
-
- tag = NULL;
- mask = NULL;
- type = NULL;
- image = NULL;
- molecule = NULL;
- mass = NULL;
-
- memory->sfree(x);
- memory->sfree(v);
- memory->sfree(f);
- x = NULL;
- v = NULL;
- f = NULL;
+ memory->destroy_kokkos(k_tag, tag);
+ memory->destroy_kokkos(k_mask, mask);
+ memory->destroy_kokkos(k_type, type);
+ memory->destroy_kokkos(k_image, image);
+ memory->destroy_kokkos(k_molecule, molecule);
+
+ memory->destroy_kokkos(k_x, x);
+ memory->destroy_kokkos(k_v, v);
+ memory->destroy_kokkos(k_f, f);
+
+ memory->destroy_kokkos(k_mass, mass);
+
+ memory->destroy_kokkos(k_q,q);
+
+ memory->destroy_kokkos(k_nspecial, nspecial);
+ memory->destroy_kokkos(k_special, special);
+ memory->destroy_kokkos(k_num_bond, num_bond);
+ memory->destroy_kokkos(k_bond_type, bond_type);
+ memory->destroy_kokkos(k_bond_atom, bond_atom);
+ memory->destroy_kokkos(k_num_angle, num_angle);
+ memory->destroy_kokkos(k_angle_type, angle_type);
+ memory->destroy_kokkos(k_angle_atom1, angle_atom1);
+ memory->destroy_kokkos(k_angle_atom2, angle_atom2);
+ memory->destroy_kokkos(k_angle_atom3, angle_atom3);
+ memory->destroy_kokkos(k_num_dihedral, num_dihedral);
+ memory->destroy_kokkos(k_dihedral_type, dihedral_type);
+ memory->destroy_kokkos(k_dihedral_atom1, dihedral_atom1);
+ memory->destroy_kokkos(k_dihedral_atom2, dihedral_atom2);
+ memory->destroy_kokkos(k_dihedral_atom3, dihedral_atom3);
+ memory->destroy_kokkos(k_dihedral_atom4, dihedral_atom4);
+ memory->destroy_kokkos(k_num_improper, num_improper);
+ memory->destroy_kokkos(k_improper_type, improper_type);
+ memory->destroy_kokkos(k_improper_atom1, improper_atom1);
+ memory->destroy_kokkos(k_improper_atom2, improper_atom2);
+ memory->destroy_kokkos(k_improper_atom3, improper_atom3);
+ memory->destroy_kokkos(k_improper_atom4, improper_atom4);
+
}
/* ---------------------------------------------------------------------- */
@@ -96,9 +108,6 @@ void AtomKokkos::sort()
{
int i,m,n,ix,iy,iz,ibin,empty;
- sync(Host,ALL_MASK);
- modified(Host,ALL_MASK);
-
// set next timestep for sorting to take place
nextsort = (update->ntimestep/sortfreq)*sortfreq + sortfreq;
@@ -122,6 +131,9 @@ void AtomKokkos::sort()
if (nlocal == nmax) avec->grow(0);
+ sync(Host,ALL_MASK);
+ modified(Host,ALL_MASK);
+
// bin atoms in reverse order so linked list will be in forward order
for (i = 0; i < nbins; i++) binhead[i] = -1;
@@ -188,3 +200,43 @@ void AtomKokkos::sort()
//MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
//if (flagall) error->all(FLERR,"Atom sort did not operate correctly");
}
+
+/* ----------------------------------------------------------------------
+ reallocate memory to the pointer selected by the mask
+------------------------------------------------------------------------- */
+void AtomKokkos::grow(unsigned int mask){
+
+ if (mask && SPECIAL_MASK){
+ memory->destroy_kokkos(k_special, special);
+ sync(Device, mask);
+ modified(Device, mask);
+ memory->grow_kokkos(k_special,special,nmax,maxspecial,"atom:special");
+ avec->grow_reset();
+ sync(Host, mask);
+ }
+
+}
+
+void AtomKokkos::deallocate_topology()
+{
+ memory->destroy_kokkos(k_bond_type, bond_type);
+ memory->destroy_kokkos(k_bond_atom, bond_atom);
+
+ memory->destroy_kokkos(k_angle_type, angle_type);
+ memory->destroy_kokkos(k_angle_atom1, angle_atom1);
+ memory->destroy_kokkos(k_angle_atom2, angle_atom2);
+ memory->destroy_kokkos(k_angle_atom3, angle_atom3);
+
+ memory->destroy_kokkos(k_dihedral_type, dihedral_type);
+ memory->destroy_kokkos(k_dihedral_atom1, dihedral_atom1);
+ memory->destroy_kokkos(k_dihedral_atom2, dihedral_atom2);
+ memory->destroy_kokkos(k_dihedral_atom3, dihedral_atom3);
+ memory->destroy_kokkos(k_dihedral_atom4, dihedral_atom4);
+
+ memory->destroy_kokkos(k_improper_type, improper_type);
+ memory->destroy_kokkos(k_improper_atom1, improper_atom1);
+ memory->destroy_kokkos(k_improper_atom2, improper_atom2);
+ memory->destroy_kokkos(k_improper_atom3, improper_atom3);
+ memory->destroy_kokkos(k_improper_atom4, improper_atom4);
+}
+
diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h
index 6d75f7edd4..2abf288793 100644
--- a/src/KOKKOS/atom_kokkos.h
+++ b/src/KOKKOS/atom_kokkos.h
@@ -21,15 +21,33 @@ namespace LAMMPS_NS {
class AtomKokkos : public Atom {
public:
- DAT::tdual_tagint_1d k_tag, k_molecule;
- DAT::tdual_imageint_1d k_image;
+ DAT::tdual_tagint_1d k_tag;
DAT::tdual_int_1d k_type, k_mask;
+ DAT::tdual_imageint_1d k_image;
DAT::tdual_x_array k_x;
DAT::tdual_v_array k_v;
DAT::tdual_f_array k_f;
+
DAT::tdual_float_1d k_mass;
+ DAT::tdual_float_1d k_q;
+ DAT::tdual_tagint_1d k_molecule;
+ DAT::tdual_int_2d k_nspecial;
+ DAT::tdual_tagint_2d k_special;
+ DAT::tdual_int_1d k_num_bond;
+ DAT::tdual_int_2d k_bond_type;
+ DAT::tdual_tagint_2d k_bond_atom;
+ DAT::tdual_int_1d k_num_angle;
+ DAT::tdual_int_2d k_angle_type;
+ DAT::tdual_tagint_2d k_angle_atom1, k_angle_atom2, k_angle_atom3;
+ DAT::tdual_int_1d k_num_dihedral;
+ DAT::tdual_int_2d k_dihedral_type;
+ DAT::tdual_tagint_2d k_dihedral_atom1, k_dihedral_atom2, k_dihedral_atom3, k_dihedral_atom4;
+ DAT::tdual_int_1d k_num_improper;
+ DAT::tdual_int_2d k_improper_type;
+ DAT::tdual_tagint_2d k_improper_atom1, k_improper_atom2, k_improper_atom3, k_improper_atom4;
+
AtomKokkos(class LAMMPS *);
~AtomKokkos();
@@ -37,6 +55,8 @@ class AtomKokkos : public Atom {
void sync(const ExecutionSpace space, unsigned int mask);
void modified(const ExecutionSpace space, unsigned int mask);
virtual void sort();
+ virtual void grow(unsigned int mask);
+ virtual void deallocate_topology();
};
template<class ViewType, class IndexView>
diff --git a/src/KOKKOS/atom_vec_angle_kokkos.cpp b/src/KOKKOS/atom_vec_angle_kokkos.cpp
new file mode 100644
index 0000000000..86ef5509a5
--- /dev/null
+++ b/src/KOKKOS/atom_vec_angle_kokkos.cpp
@@ -0,0 +1,1886 @@
+/* ----------------------------------------------------------------------
+ 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 "stdlib.h"
+#include "atom_vec_angle_kokkos.h"
+#include "atom_kokkos.h"
+#include "comm_kokkos.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "atom_masks.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecAngleKokkos::AtomVecAngleKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
+{
+ molecular = 1;
+ bonds_allow = angles_allow = 1;
+ mass_type = 1;
+
+ comm_x_only = comm_f_only = 1;
+ size_forward = 3;
+ size_reverse = 3;
+ size_border = 7;
+ size_velocity = 3;
+ size_data_atom = 6;
+ size_data_vel = 4;
+ xcol_data = 4;
+
+ atom->molecule_flag = 1;
+
+ k_count = DAT::tdual_int_1d("atom::k_count",1);
+ atomKK = (AtomKokkos *) atom;
+ commKK = (CommKokkos *) comm;
+}
+
+/* ----------------------------------------------------------------------
+ grow atom arrays
+ n = 0 grows arrays by DELTA
+ n > 0 allocates arrays to size n
+------------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::grow(int n)
+{
+ if (n == 0) nmax += DELTA;
+ else nmax = n;
+ atomKK->nmax = nmax;
+ if (nmax < 0 || nmax > MAXSMALLINT)
+ error->one(FLERR,"Per-processor system is too big");
+
+ sync(Device,ALL_MASK);
+ modified(Device,ALL_MASK);
+
+ memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
+ memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
+ memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
+ memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
+
+ memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
+ memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
+ memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
+
+ memory->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
+ memory->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
+ memory->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
+ "atom:special");
+ memory->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
+ memory->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
+ "atom:bond_type");
+ memory->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
+ "atom:bond_atom");
+
+ memory->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
+ memory->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
+ "atom:angle_type");
+ memory->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
+ "atom:angle_atom1");
+ memory->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
+ "atom:angle_atom2");
+ memory->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
+ "atom:angle_atom3");
+
+ grow_reset();
+ sync(Host,ALL_MASK);
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
+}
+
+/* ----------------------------------------------------------------------
+ reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::grow_reset()
+{
+ tag = atomKK->tag;
+ d_tag = atomKK->k_tag.d_view;
+ h_tag = atomKK->k_tag.h_view;
+
+ type = atomKK->type;
+ d_type = atomKK->k_type.d_view;
+ h_type = atomKK->k_type.h_view;
+ mask = atomKK->mask;
+ d_mask = atomKK->k_mask.d_view;
+ h_mask = atomKK->k_mask.h_view;
+ image = atomKK->image;
+ d_image = atomKK->k_image.d_view;
+ h_image = atomKK->k_image.h_view;
+
+ x = atomKK->x;
+ d_x = atomKK->k_x.d_view;
+ h_x = atomKK->k_x.h_view;
+ v = atomKK->v;
+ d_v = atomKK->k_v.d_view;
+ h_v = atomKK->k_v.h_view;
+ f = atomKK->f;
+ d_f = atomKK->k_f.d_view;
+ h_f = atomKK->k_f.h_view;
+
+ molecule = atomKK->molecule;
+ d_molecule = atomKK->k_molecule.d_view;
+ h_molecule = atomKK->k_molecule.h_view;
+ nspecial = atomKK->nspecial;
+ d_nspecial = atomKK->k_nspecial.d_view;
+ h_nspecial = atomKK->k_nspecial.h_view;
+ special = atomKK->special;
+ d_special = atomKK->k_special.d_view;
+ h_special = atomKK->k_special.h_view;
+ num_bond = atomKK->num_bond;
+ d_num_bond = atomKK->k_num_bond.d_view;
+ h_num_bond = atomKK->k_num_bond.h_view;
+ bond_type = atomKK->bond_type;
+ d_bond_type = atomKK->k_bond_type.d_view;
+ h_bond_type = atomKK->k_bond_type.h_view;
+ bond_atom = atomKK->bond_atom;
+ d_bond_atom = atomKK->k_bond_atom.d_view;
+ h_bond_atom = atomKK->k_bond_atom.h_view;
+
+ num_angle = atomKK->num_angle;
+ d_num_angle = atomKK->k_num_angle.d_view;
+ h_num_angle = atomKK->k_num_angle.h_view;
+ angle_type = atomKK->angle_type;
+ d_angle_type = atomKK->k_angle_type.d_view;
+ h_angle_type = atomKK->k_angle_type.h_view;
+ angle_atom1 = atomKK->angle_atom1;
+ d_angle_atom1 = atomKK->k_angle_atom1.d_view;
+ h_angle_atom1 = atomKK->k_angle_atom1.h_view;
+ angle_atom2 = atomKK->angle_atom2;
+ d_angle_atom2 = atomKK->k_angle_atom2.d_view;
+ h_angle_atom2 = atomKK->k_angle_atom2.h_view;
+ angle_atom3 = atomKK->angle_atom3;
+ d_angle_atom3 = atomKK->k_angle_atom3.d_view;
+ h_angle_atom3 = atomKK->k_angle_atom3.h_view;
+}
+
+/* ----------------------------------------------------------------------
+ copy atom I info to atom J
+------------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::copy(int i, int j, int delflag)
+{
+ int k;
+
+ h_tag[j] = h_tag[i];
+ h_type[j] = h_type[i];
+ mask[j] = mask[i];
+ h_image[j] = h_image[i];
+ h_x(j,0) = h_x(i,0);
+ h_x(j,1) = h_x(i,1);
+ h_x(j,2) = h_x(i,2);
+ h_v(j,0) = h_v(i,0);
+ h_v(j,1) = h_v(i,1);
+ h_v(j,2) = h_v(i,2);
+
+ h_molecule(j) = h_molecule(i);
+
+ h_num_bond(j) = h_num_bond(i);
+ for (k = 0; k < h_num_bond(j); k++) {
+ h_bond_type(j,k) = h_bond_type(i,k);
+ h_bond_atom(j,k) = h_bond_atom(i,k);
+ }
+
+ h_nspecial(j,0) = h_nspecial(i,0);
+ h_nspecial(j,1) = h_nspecial(i,1);
+ h_nspecial(j,2) = h_nspecial(i,2);
+ for (k = 0; k < h_nspecial(j,2); k++)
+ h_special(j,k) = h_special(i,k);
+
+ h_num_angle(j) = h_num_angle(i);
+ for (k = 0; k < h_num_angle(j); k++) {
+ h_angle_type(j,k) = h_angle_type(i,k);
+ h_angle_atom1(j,k) = h_angle_atom1(i,k);
+ h_angle_atom2(j,k) = h_angle_atom2(i,k);
+ h_angle_atom3(j,k) = h_angle_atom3(i,k);
+ }
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecAngleKokkos_PackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_um _buf;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecAngleKokkos_PackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ const size_t maxsend = (buf.view<DeviceType>().dimension_0()
+ *buf.view<DeviceType>().dimension_1())/3;
+ const size_t elements = 3;
+ buffer_view<DeviceType>(_buf,buf,maxsend,elements);
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_comm_kokkos(const int &n,
+ const DAT::tdual_int_2d &list,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag,
+ const int* const pbc)
+{
+ // Check whether to always run forward communication on the host
+ // Choose correct forward PackComm kernel
+
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecAngleKokkos_PackComm<LMPHostType,1,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecAngleKokkos_PackComm<LMPHostType,1,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecAngleKokkos_PackComm<LMPHostType,0,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecAngleKokkos_PackComm<LMPHostType,0,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecAngleKokkos_PackComm<LMPDeviceType,1,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecAngleKokkos_PackComm<LMPDeviceType,1,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecAngleKokkos_PackComm<LMPDeviceType,0,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecAngleKokkos_PackComm<LMPDeviceType,0,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+
+ return n*size_forward;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecAngleKokkos_PackCommSelf {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_x_array _xw;
+ int _nfirst;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecAngleKokkos_PackCommSelf(
+ const typename DAT::tdual_x_array &x,
+ const int &nfirst,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_xw(x.view<DeviceType>()),_nfirst(nfirst),_list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _xw(i+_nfirst,0) = _x(j,0);
+ _xw(i+_nfirst,1) = _x(j,1);
+ _xw(i+_nfirst,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap,
+ const int nfirst, const int &pbc_flag,
+ const int* const pbc) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecAngleKokkos_PackCommSelf<LMPHostType,1,1>
+ f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecAngleKokkos_PackCommSelf<LMPHostType,1,0>
+ f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecAngleKokkos_PackCommSelf<LMPHostType,0,1>
+ f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecAngleKokkos_PackCommSelf<LMPHostType,0,0>
+ f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecAngleKokkos_PackCommSelf<LMPDeviceType,1,1>
+ f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecAngleKokkos_PackCommSelf<LMPDeviceType,1,0>
+ f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecAngleKokkos_PackCommSelf<LMPDeviceType,0,1>
+ f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecAngleKokkos_PackCommSelf<LMPDeviceType,0,0>
+ f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+ return n*3;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecAngleKokkos_UnpackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
+ int _first;
+
+ AtomVecAngleKokkos_UnpackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const int& first):_x(x.view<DeviceType>()),_buf(buf.view<DeviceType>()),
+ _first(first) {};
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::unpack_comm_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf ) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ struct AtomVecAngleKokkos_UnpackComm<LMPHostType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ struct AtomVecAngleKokkos_UnpackComm<LMPDeviceType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_comm_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::unpack_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::unpack_comm_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_reverse(int n, int first, double *buf)
+{
+ if(n > 0)
+ sync(Host,F_MASK);
+
+ int m = 0;
+ const int last = first + n;
+ for (int i = first; i < last; i++) {
+ buf[m++] = h_f(i,0);
+ buf[m++] = h_f(i,1);
+ buf[m++] = h_f(i,2);
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::unpack_reverse(int n, int *list, double *buf)
+{
+ if(n > 0)
+ modified(Host,F_MASK);
+
+ int m = 0;
+ for (int i = 0; i < n; i++) {
+ const int j = list[i];
+ h_f(j,0) += buf[m++];
+ h_f(j,1) += buf[m++];
+ h_f(j,2) += buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG>
+struct AtomVecAngleKokkos_PackBorder {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+
+ typename AT::t_xfloat_2d _buf;
+ const typename AT::t_int_2d_const _list;
+ const int _iswap;
+ const typename AT::t_x_array_randomread _x;
+ const typename AT::t_tagint_1d _tag;
+ const typename AT::t_int_1d _type;
+ const typename AT::t_int_1d _mask;
+ const typename AT::t_tagint_1d _molecule;
+ X_FLOAT _dx,_dy,_dz;
+
+ AtomVecAngleKokkos_PackBorder(
+ const typename AT::t_xfloat_2d &buf,
+ const typename AT::t_int_2d_const &list,
+ const int & iswap,
+ const typename AT::t_x_array &x,
+ const typename AT::t_tagint_1d &tag,
+ const typename AT::t_int_1d &type,
+ const typename AT::t_int_1d &mask,
+ const typename AT::t_tagint_1d &molecule,
+ const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz):
+ _buf(buf),_list(list),_iswap(iswap),
+ _x(x),_tag(tag),_type(type),_mask(mask),_molecule(molecule),
+ _dx(dx),_dy(dy),_dz(dz) {}
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ _buf(i,3) = _tag(j);
+ _buf(i,4) = _type(j);
+ _buf(i,5) = _mask(j);
+ _buf(i,6) = _molecule(j);
+ } else {
+ _buf(i,0) = _x(j,0) + _dx;
+ _buf(i,1) = _x(j,1) + _dy;
+ _buf(i,2) = _x(j,2) + _dz;
+ _buf(i,3) = _tag(j);
+ _buf(i,4) = _type(j);
+ _buf(i,5) = _mask(j);
+ _buf(i,6) = _molecule(j);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::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)
+{
+ X_FLOAT dx,dy,dz;
+
+ if (pbc_flag != 0) {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if(space==Host) {
+ AtomVecAngleKokkos_PackBorder<LMPHostType,1> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecAngleKokkos_PackBorder<LMPDeviceType,1> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+
+ } else {
+ dx = dy = dz = 0;
+ if(space==Host) {
+ AtomVecAngleKokkos_PackBorder<LMPHostType,0> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecAngleKokkos_PackBorder<LMPDeviceType,0> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+ }
+ return n*size_border;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_border(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_border_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_border_hybrid(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_molecule(j);
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecAngleKokkos_UnpackBorder {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+
+ const typename AT::t_xfloat_2d_const _buf;
+ typename AT::t_x_array _x;
+ typename AT::t_tagint_1d _tag;
+ typename AT::t_int_1d _type;
+ typename AT::t_int_1d _mask;
+ typename AT::t_tagint_1d _molecule;
+ int _first;
+
+
+ AtomVecAngleKokkos_UnpackBorder(
+ const typename AT::t_xfloat_2d_const &buf,
+ typename AT::t_x_array &x,
+ typename AT::t_tagint_1d &tag,
+ typename AT::t_int_1d &type,
+ typename AT::t_int_1d &mask,
+ typename AT::t_tagint_1d &molecule,
+ const int& first):
+ _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_molecule(molecule),
+ _first(first){
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ _tag(i+_first) = static_cast<int> (_buf(i,3));
+ _type(i+_first) = static_cast<int> (_buf(i,4));
+ _mask(i+_first) = static_cast<int> (_buf(i,5));
+ _molecule(i+_first) = static_cast<int> (_buf(i,6));
+
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::unpack_border_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf,
+ ExecutionSpace space) {
+ modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
+ while (first+n >= nmax) grow(0);
+ modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
+ if(space==Host) {
+ struct AtomVecAngleKokkos_UnpackBorder<LMPHostType>
+ f(buf.view<LMPHostType>(),h_x,h_tag,h_type,h_mask,h_molecule,first);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ struct AtomVecAngleKokkos_UnpackBorder<LMPDeviceType>
+ f(buf.view<LMPDeviceType>(),d_x,d_tag,d_type,d_mask,d_molecule,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::unpack_border(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax) grow(0);
+ modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::unpack_border_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax) grow(0);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::unpack_border_hybrid(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecAngleKokkos_PackExchangeFunctor {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array_randomread _x;
+ typename AT::t_v_array_randomread _v;
+ typename AT::t_tagint_1d_randomread _tag;
+ typename AT::t_int_1d_randomread _type;
+ typename AT::t_int_1d_randomread _mask;
+ typename AT::t_imageint_1d_randomread _image;
+ typename AT::t_tagint_1d_randomread _molecule;
+ typename AT::t_int_2d_randomread _nspecial;
+ typename AT::t_tagint_2d_randomread _special;
+ typename AT::t_int_1d_randomread _num_bond;
+ typename AT::t_int_2d_randomread _bond_type;
+ typename AT::t_tagint_2d_randomread _bond_atom;
+ typename AT::t_int_1d_randomread _num_angle;
+ typename AT::t_int_2d_randomread _angle_type;
+ typename AT::t_tagint_2d_randomread _angle_atom1,_angle_atom2,_angle_atom3;
+ typename AT::t_x_array _xw;
+ typename AT::t_v_array _vw;
+ typename AT::t_tagint_1d _tagw;
+ typename AT::t_int_1d _typew;
+ typename AT::t_int_1d _maskw;
+ typename AT::t_imageint_1d _imagew;
+ typename AT::t_tagint_1d _moleculew;
+ typename AT::t_int_2d _nspecialw;
+ typename AT::t_tagint_2d _specialw;
+ typename AT::t_int_1d _num_bondw;
+ typename AT::t_int_2d _bond_typew;
+ typename AT::t_tagint_2d _bond_atomw;
+ typename AT::t_int_1d _num_anglew;
+ typename AT::t_int_2d _angle_typew;
+ typename AT::t_tagint_2d _angle_atom1w,_angle_atom2w,_angle_atom3w;
+
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d_const _sendlist;
+ typename AT::t_int_1d_const _copylist;
+ int _nlocal,_dim;
+ X_FLOAT _lo,_hi;
+ size_t elements;
+
+ AtomVecAngleKokkos_PackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d sendlist,
+ typename AT::tdual_int_1d copylist,int nlocal, int dim,
+ X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _num_angle(atom->k_num_angle.view<DeviceType>()),
+ _angle_type(atom->k_angle_type.view<DeviceType>()),
+ _angle_atom1(atom->k_angle_atom1.view<DeviceType>()),
+ _angle_atom2(atom->k_angle_atom2.view<DeviceType>()),
+ _angle_atom3(atom->k_angle_atom3.view<DeviceType>()),
+ _xw(atom->k_x.view<DeviceType>()),
+ _vw(atom->k_v.view<DeviceType>()),
+ _tagw(atom->k_tag.view<DeviceType>()),
+ _typew(atom->k_type.view<DeviceType>()),
+ _maskw(atom->k_mask.view<DeviceType>()),
+ _imagew(atom->k_image.view<DeviceType>()),
+ _moleculew(atom->k_molecule.view<DeviceType>()),
+ _nspecialw(atom->k_nspecial.view<DeviceType>()),
+ _specialw(atom->k_special.view<DeviceType>()),
+ _num_bondw(atom->k_num_bond.view<DeviceType>()),
+ _bond_typew(atom->k_bond_type.view<DeviceType>()),
+ _bond_atomw(atom->k_bond_atom.view<DeviceType>()),
+ _num_anglew(atom->k_num_angle.view<DeviceType>()),
+ _angle_typew(atom->k_angle_type.view<DeviceType>()),
+ _angle_atom1w(atom->k_angle_atom1.view<DeviceType>()),
+ _angle_atom2w(atom->k_angle_atom2.view<DeviceType>()),
+ _angle_atom3w(atom->k_angle_atom3.view<DeviceType>()),
+ _sendlist(sendlist.template view<DeviceType>()),
+ _copylist(copylist.template view<DeviceType>()),
+ _nlocal(nlocal),_dim(dim),
+ _lo(lo),_hi(hi){
+ // 3 comp of x, 3 comp of v, 1 tag, 1 type, 1 mask, 1 image, 1 molecule, 3 nspecial,
+ // maxspecial special, 1 num_bond, bond_per_atom bond_type, bond_per_atom bond_atom,
+ // 1 num_angle, angle_per_atom angle_type, angle_per_atom angle_atom1, angle_atom2,
+ // and angle_atom3
+ // 1 to store buffer length
+ elements = 17+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
+ buf.template view<DeviceType>().dimension_1())/elements;
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &mysend) const {
+ int k;
+ const int i = _sendlist(mysend);
+ _buf(mysend,0) = elements;
+ int m = 1;
+ _buf(mysend,m++) = _x(i,0);
+ _buf(mysend,m++) = _x(i,1);
+ _buf(mysend,m++) = _x(i,2);
+ _buf(mysend,m++) = _v(i,0);
+ _buf(mysend,m++) = _v(i,1);
+ _buf(mysend,m++) = _v(i,2);
+ _buf(mysend,m++) = _tag(i);
+ _buf(mysend,m++) = _type(i);
+ _buf(mysend,m++) = _mask(i);
+ _buf(mysend,m++) = _image(i);
+ _buf(mysend,m++) = _molecule(i);
+ _buf(mysend,m++) = _num_bond(i);
+ for (k = 0; k < _num_bond(i); k++) {
+ _buf(mysend,m++) = _bond_type(i,k);
+ _buf(mysend,m++) = _bond_atom(i,k);
+ }
+ _buf(mysend,m++) = _num_angle(i);
+ for (k = 0; k < _num_angle(i); k++) {
+ _buf(mysend,m++) = _angle_type(i,k);
+ _buf(mysend,m++) = _angle_atom1(i,k);
+ _buf(mysend,m++) = _angle_atom2(i,k);
+ _buf(mysend,m++) = _angle_atom3(i,k);
+ }
+ _buf(mysend,m++) = _nspecial(i,0);
+ _buf(mysend,m++) = _nspecial(i,1);
+ _buf(mysend,m++) = _nspecial(i,2);
+ for (k = 0; k < _nspecial(i,2); k++)
+ _buf(mysend,m++) = _special(i,k);
+
+ const int j = _copylist(mysend);
+
+ if(j>-1) {
+ _xw(i,0) = _x(j,0);
+ _xw(i,1) = _x(j,1);
+ _xw(i,2) = _x(j,2);
+ _vw(i,0) = _v(j,0);
+ _vw(i,1) = _v(j,1);
+ _vw(i,2) = _v(j,2);
+ _tagw(i) = _tag(j);
+ _typew(i) = _type(j);
+ _maskw(i) = _mask(j);
+ _imagew(i) = _image(j);
+ _moleculew(i) = _molecule(j);
+ _num_bondw(i) = _num_bond(j);
+ for (k = 0; k < _num_bond(j); k++) {
+ _bond_typew(i,k) = _bond_type(j,k);
+ _bond_atomw(i,k) = _bond_atom(j,k);
+ }
+ _num_anglew(i) = _num_angle(j);
+ for (k = 0; k < _num_angle(j); k++) {
+ _angle_typew(i,k) = _angle_type(j,k);
+ _angle_atom1w(i,k) = _angle_atom1(j,k);
+ _angle_atom2w(i,k) = _angle_atom2(j,k);
+ _angle_atom3w(i,k) = _angle_atom3(j,k);
+ }
+ _nspecialw(i,0) = _nspecial(j,0);
+ _nspecialw(i,1) = _nspecial(j,1);
+ _nspecialw(i,2) = _nspecial(j,2);
+ for (k = 0; k < _nspecial(j,2); k++)
+ _specialw(i,k) = _special(j,k);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space,int dim,X_FLOAT lo,
+ X_FLOAT hi )
+{
+ const int elements = 17+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom;
+ if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*
+ k_buf.view<LMPHostType>().dimension_1())/elements) {
+ int newsize = nsend*elements/k_buf.view<LMPHostType>().dimension_1()+1;
+ k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
+ }
+ if(space == Host) {
+ AtomVecAngleKokkos_PackExchangeFunctor<LMPHostType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPHostType::fence();
+ return nsend*elements;
+ } else {
+ AtomVecAngleKokkos_PackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPDeviceType::fence();
+ return nsend*elements;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_exchange(int i, double *buf)
+{
+ int k;
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = ubuf(h_molecule(i)).d;
+
+ buf[m++] = ubuf(h_num_bond(i)).d;
+ for (k = 0; k < h_num_bond(i); k++) {
+ buf[m++] = ubuf(h_bond_type(i,k)).d;
+ buf[m++] = ubuf(h_bond_atom(i,k)).d;
+ }
+ buf[m++] = ubuf(h_num_angle(i)).d;
+ for (k = 0; k < h_num_angle(i); k++) {
+ buf[m++] = ubuf(h_angle_type(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom1(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom2(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom3(i,k)).d;
+ }
+ buf[m++] = ubuf(h_nspecial(i,0)).d;
+ buf[m++] = ubuf(h_nspecial(i,1)).d;
+ buf[m++] = ubuf(h_nspecial(i,2)).d;
+ for (k = 0; k < h_nspecial(i,2); k++)
+ buf[m++] = ubuf(h_special(i,k)).d;
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecAngleKokkos_UnpackExchangeFunctor {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array _x;
+ typename AT::t_v_array _v;
+ typename AT::t_tagint_1d _tag;
+ typename AT::t_int_1d _type;
+ typename AT::t_int_1d _mask;
+ typename AT::t_imageint_1d _image;
+ typename AT::t_tagint_1d _molecule;
+ typename AT::t_int_2d _nspecial;
+ typename AT::t_tagint_2d _special;
+ typename AT::t_int_1d _num_bond;
+ typename AT::t_int_2d _bond_type;
+ typename AT::t_tagint_2d _bond_atom;
+ typename AT::t_int_1d _num_angle;
+ typename AT::t_int_2d _angle_type;
+ typename AT::t_tagint_2d _angle_atom1,_angle_atom2,_angle_atom3;
+
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d _nlocal;
+ int _dim;
+ X_FLOAT _lo,_hi;
+ size_t elements;
+
+ AtomVecAngleKokkos_UnpackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d nlocal,
+ int dim, X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _num_angle(atom->k_num_angle.view<DeviceType>()),
+ _angle_type(atom->k_angle_type.view<DeviceType>()),
+ _angle_atom1(atom->k_angle_atom1.view<DeviceType>()),
+ _angle_atom2(atom->k_angle_atom2.view<DeviceType>()),
+ _angle_atom3(atom->k_angle_atom3.view<DeviceType>()),
+ _nlocal(nlocal.template view<DeviceType>()),_dim(dim),
+ _lo(lo),_hi(hi){
+ elements =17+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
+ buf.template view<DeviceType>().dimension_1())/elements;
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &myrecv) const {
+ X_FLOAT x = _buf(myrecv,_dim+1);
+ if (x >= _lo && x < _hi) {
+ int i = Kokkos::atomic_fetch_add(&_nlocal(0),1);
+ int m = 1;
+ _x(i,0) = _buf(myrecv,m++);
+ _x(i,1) = _buf(myrecv,m++);
+ _x(i,2) = _buf(myrecv,m++);
+ _v(i,0) = _buf(myrecv,m++);
+ _v(i,1) = _buf(myrecv,m++);
+ _v(i,2) = _buf(myrecv,m++);
+ _tag(i) = _buf(myrecv,m++);
+ _type(i) = _buf(myrecv,m++);
+ _mask(i) = _buf(myrecv,m++);
+ _image(i) = _buf(myrecv,m++);
+
+ _molecule(i) = _buf(myrecv,m++);
+ _num_bond(i) = _buf(myrecv,m++);
+ int k;
+ for (k = 0; k < _num_bond(i); k++) {
+ _bond_type(i,k) = _buf(myrecv,m++);
+ _bond_atom(i,k) = _buf(myrecv,m++);
+ }
+ _num_angle(i) = _buf(myrecv,m++);
+ for (k = 0; k < _num_angle(i); k++) {
+ _angle_type(i,k) = _buf(myrecv,m++);
+ _angle_atom1(i,k) = _buf(myrecv,m++);
+ _angle_atom2(i,k) = _buf(myrecv,m++);
+ _angle_atom3(i,k) = _buf(myrecv,m++);
+ }
+ _nspecial(i,0) = _buf(myrecv,m++);
+ _nspecial(i,1) = _buf(myrecv,m++);
+ _nspecial(i,2) = _buf(myrecv,m++);
+ for (k = 0; k < _nspecial(i,2); k++)
+ _special(i,k) = _buf(myrecv,m++);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,
+ int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,
+ ExecutionSpace space) {
+ const size_t elements = 17+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom;
+ if(space == Host) {
+ k_count.h_view(0) = nlocal;
+ AtomVecAngleKokkos_UnpackExchangeFunctor<LMPHostType>
+ f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/elements,f);
+ LMPHostType::fence();
+ return k_count.h_view(0);
+ } else {
+ k_count.h_view(0) = nlocal;
+ k_count.modify<LMPHostType>();
+ k_count.sync<LMPDeviceType>();
+ AtomVecAngleKokkos_UnpackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/elements,f);
+ LMPDeviceType::fence();
+ k_count.modify<LMPDeviceType>();
+ k_count.sync<LMPHostType>();
+
+ return k_count.h_view(0);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::unpack_exchange(double *buf)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) grow(0);
+ modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
+ MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK |
+ ANGLE_MASK | SPECIAL_MASK);
+
+ int k;
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
+
+ h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_bond(nlocal); k++) {
+ h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_num_angle(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_angle(nlocal); k++) {
+ h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i;
+ h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i;
+ h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_nspecial(nlocal,2); k++)
+ h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->
+ unpack_exchange(nlocal,&buf[m]);
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ size of restart data for all atoms owned by this proc
+ include extra data stored by fixes
+------------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::size_restart()
+{
+ int i;
+
+ int nlocal = atom->nlocal;
+ int n = 0;
+ for (i = 0; i < nlocal; i++)
+ n += 14 + 2*h_num_bond(i) + 4*h_num_angle(i);
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (i = 0; i < nlocal; i++)
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom I's data for restart file including extra quantities
+ xyz must be 1st 3 values, so that read_restart can test on them
+ molecular types may be negative, but write as positive
+------------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_restart(int i, double *buf)
+{
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+
+ buf[m++] = ubuf(h_molecule(i)).d;
+
+ buf[m++] = ubuf(h_num_bond(i)).d;
+ for (int k = 0; k < h_num_bond(i); k++) {
+ buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d;
+ buf[m++] = ubuf(h_bond_atom(i,k)).d;
+ }
+
+ buf[m++] = ubuf(h_num_angle(i)).d;
+ for (int k = 0; k < h_num_angle(i); k++) {
+ buf[m++] = ubuf(MAX(h_angle_type(i,k),-h_angle_type(i,k))).d;
+ buf[m++] = ubuf(h_angle_atom1(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom2(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom3(i,k)).d;
+ }
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ unpack data for one atom from restart file including extra quantities
+------------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::unpack_restart(double *buf)
+{
+ int k;
+
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ grow(0);
+ if (atom->nextra_store)
+ memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
+ }
+
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+
+ h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
+
+ h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_bond(nlocal); k++) {
+ h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_num_angle(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_angle(nlocal); k++) {
+ h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
+
+ double **extra = atom->extra;
+ if (atom->nextra_store) {
+ int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+ for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
+ }
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ create one atom of itype at coord
+ set other values to defaults
+------------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::create_atom(int itype, double *coord)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ atomKK->modified(Host,ALL_MASK);
+ grow(0);
+ }
+ atomKK->modified(Host,ALL_MASK);
+
+ tag[nlocal] = 0;
+ type[nlocal] = itype;
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+ h_mask(nlocal) = 1;
+ h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) |
+ ((imageint) IMGMAX << IMGBITS) | IMGMAX;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+
+ h_molecule(nlocal) = 0;
+ h_num_bond(nlocal) = 0;
+ h_num_angle(nlocal) = 0;
+ h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack one line from Atoms section of data file
+ initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp,
+ char **values)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) grow(0);
+
+ h_tag(nlocal) = atoi(values[0]);
+ if (h_tag(nlocal) <= 0)
+ error->one(FLERR,"Invalid atom ID in Atoms section of data file");
+
+ h_molecule(nlocal) = atoi(values[1]);
+ if (h_molecule(nlocal) <= 0)
+ error->one(FLERR,"Invalid molecule ID in Atoms section of data file");
+
+ h_type(nlocal) = atoi(values[2]);
+ if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
+ error->one(FLERR,"Invalid atom type in Atoms section of data file");
+
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+
+ h_image(nlocal) = imagetmp;
+
+ h_mask(nlocal) = 1;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+ h_num_bond(nlocal) = 0;
+ h_num_angle(nlocal) = 0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack hybrid quantities from one line in Atoms section of data file
+ initialize other atom quantities for this sub-style
+------------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::data_atom_hybrid(int nlocal, char **values)
+{
+ h_molecule(nlocal) = atoi(values[0]);
+ h_num_bond(nlocal) = 0;
+ h_num_angle(nlocal) = 0;
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom info for data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::pack_data(double **buf)
+{
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ buf[i][0] = h_tag(i);
+ buf[i][1] = h_molecule(i);
+ buf[i][2] = h_type(i);
+ buf[i][3] = h_x(i,0);
+ buf[i][4] = h_x(i,1);
+ buf[i][5] = h_x(i,2);
+ buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX;
+ buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+ buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ pack hybrid atom info for data file
+------------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::pack_data_hybrid(int i, double *buf)
+{
+ buf[0] = h_molecule(i);
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ write atom info to data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::write_data(FILE *fp, int n, double **buf)
+{
+ for (int i = 0; i < n; i++)
+ fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
+ (int) buf[i][0],(int) buf[i][1], (int) buf[i][2],
+ buf[i][3],buf[i][4],buf[i][5],
+ (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
+}
+
+/* ----------------------------------------------------------------------
+ write hybrid atom info to data file
+------------------------------------------------------------------------- */
+
+int AtomVecAngleKokkos::write_data_hybrid(FILE *fp, double *buf)
+{
+ fprintf(fp," " TAGINT_FORMAT, (tagint) (buf[0]));
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ return # of bytes of allocated memory
+------------------------------------------------------------------------- */
+
+bigint AtomVecAngleKokkos::memory_usage()
+{
+ bigint bytes = 0;
+
+ if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
+ if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
+ if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
+ if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
+ if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
+ if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
+ if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
+
+ if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
+ if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
+ if (atom->memcheck("special"))
+ bytes += memory->usage(special,nmax,atom->maxspecial);
+
+ if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
+ if (atom->memcheck("bond_type"))
+ bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
+ if (atom->memcheck("bond_atom"))
+ bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
+
+ if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax);
+ if (atom->memcheck("angle_type"))
+ bytes += memory->usage(angle_type,nmax,atom->angle_per_atom);
+ if (atom->memcheck("angle_atom1"))
+ bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom);
+ if (atom->memcheck("angle_atom2"))
+ bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom);
+ if (atom->memcheck("angle_atom3"))
+ bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom);
+
+ return bytes;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::sync(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPDeviceType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.sync<LMPDeviceType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.sync<LMPDeviceType>();
+ atomKK->k_special.sync<LMPDeviceType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.sync<LMPDeviceType>();
+ atomKK->k_bond_type.sync<LMPDeviceType>();
+ atomKK->k_bond_atom.sync<LMPDeviceType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.sync<LMPDeviceType>();
+ atomKK->k_angle_type.sync<LMPDeviceType>();
+ atomKK->k_angle_atom1.sync<LMPDeviceType>();
+ atomKK->k_angle_atom2.sync<LMPDeviceType>();
+ atomKK->k_angle_atom3.sync<LMPDeviceType>();
+ }
+ } else {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPHostType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.sync<LMPHostType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.sync<LMPHostType>();
+ atomKK->k_special.sync<LMPHostType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.sync<LMPHostType>();
+ atomKK->k_bond_type.sync<LMPHostType>();
+ atomKK->k_bond_atom.sync<LMPHostType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.sync<LMPHostType>();
+ atomKK->k_angle_type.sync<LMPHostType>();
+ atomKK->k_angle_atom1.sync<LMPHostType>();
+ atomKK->k_angle_atom2.sync<LMPHostType>();
+ atomKK->k_angle_atom3.sync<LMPHostType>();
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecAngleKokkos::modified(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPDeviceType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.modify<LMPDeviceType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.modify<LMPDeviceType>();
+ atomKK->k_special.modify<LMPDeviceType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.modify<LMPDeviceType>();
+ atomKK->k_bond_type.modify<LMPDeviceType>();
+ atomKK->k_bond_atom.modify<LMPDeviceType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.modify<LMPDeviceType>();
+ atomKK->k_angle_type.modify<LMPDeviceType>();
+ atomKK->k_angle_atom1.modify<LMPDeviceType>();
+ atomKK->k_angle_atom2.modify<LMPDeviceType>();
+ atomKK->k_angle_atom3.modify<LMPDeviceType>();
+ }
+ } else {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPHostType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.modify<LMPHostType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.modify<LMPHostType>();
+ atomKK->k_special.modify<LMPHostType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.modify<LMPHostType>();
+ atomKK->k_bond_type.modify<LMPHostType>();
+ atomKK->k_bond_atom.modify<LMPHostType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.modify<LMPHostType>();
+ atomKK->k_angle_type.modify<LMPHostType>();
+ atomKK->k_angle_atom1.modify<LMPHostType>();
+ atomKK->k_angle_atom2.modify<LMPHostType>();
+ atomKK->k_angle_atom3.modify<LMPHostType>();
+ }
+ }
+}
diff --git a/src/KOKKOS/atom_vec_angle_kokkos.h b/src/KOKKOS/atom_vec_angle_kokkos.h
new file mode 100644
index 0000000000..b542761073
--- /dev/null
+++ b/src/KOKKOS/atom_vec_angle_kokkos.h
@@ -0,0 +1,153 @@
+/* ----------------------------------------------------------------------
+ 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 ATOM_CLASS
+
+AtomStyle(angle/kk,AtomVecAngleKokkos)
+
+#else
+
+#ifndef LMP_ATOM_VEC_ANGLE_KOKKOS_H
+#define LMP_ATOM_VEC_ANGLE_KOKKOS_H
+
+#include "atom_vec_kokkos.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecAngleKokkos : public AtomVecKokkos {
+ public:
+ AtomVecAngleKokkos(class LAMMPS *);
+ virtual ~AtomVecAngleKokkos() {}
+ void grow(int);
+ void copy(int, int, int);
+ int pack_comm(int, int *, double *, int, int *);
+ int pack_comm_vel(int, int *, double *, int, int *);
+ void unpack_comm(int, int, double *);
+ void unpack_comm_vel(int, int, double *);
+ int pack_reverse(int, int, double *);
+ void unpack_reverse(int, int *, double *);
+ int pack_border(int, int *, double *, int, int *);
+ int pack_border_vel(int, int *, double *, int, int *);
+ int pack_border_hybrid(int, int *, double *);
+ void unpack_border(int, int, double *);
+ void unpack_border_vel(int, int, double *);
+ int unpack_border_hybrid(int, int, double *);
+ int pack_exchange(int, double *);
+ int unpack_exchange(double *);
+ int size_restart();
+ int pack_restart(int, double *);
+ int unpack_restart(double *);
+ void create_atom(int, double *);
+ void data_atom(double *, tagint, char **);
+ int data_atom_hybrid(int, char **);
+ void pack_data(double **);
+ int pack_data_hybrid(int, double *);
+ void write_data(FILE *, int, double **);
+ int write_data_hybrid(FILE *, double *);
+ bigint memory_usage();
+
+ void grow_reset();
+ int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag, const int pbc[]);
+ void unpack_comm_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf);
+ int pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap, const int nfirst,
+ const int &pbc_flag, const int pbc[]);
+ int 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);
+ void unpack_border_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf,
+ ExecutionSpace space);
+ int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space, int dim,
+ X_FLOAT lo, X_FLOAT hi);
+ int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
+ int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
+ ExecutionSpace space);
+
+ void sync(ExecutionSpace space, unsigned int mask);
+ void modified(ExecutionSpace space, unsigned int mask);
+
+ protected:
+
+ tagint *tag;
+ int *type,*mask;
+ imageint *image;
+ double **x,**v,**f;
+
+ tagint *molecule;
+ int **nspecial;
+ tagint **special;
+ int *num_bond;
+ int **bond_type;
+ tagint **bond_atom;
+
+ int *num_angle;
+ int **angle_type;
+ tagint **angle_atom1,**angle_atom2,**angle_atom3;
+
+ DAT::t_tagint_1d d_tag;
+ DAT::t_int_1d d_type, d_mask;
+ HAT::t_tagint_1d h_tag;
+ HAT::t_int_1d h_type, h_mask;
+
+ DAT::t_imageint_1d d_image;
+ HAT::t_imageint_1d h_image;
+
+ DAT::t_x_array d_x;
+ DAT::t_v_array d_v;
+ DAT::t_f_array d_f;
+ HAT::t_x_array h_x;
+ HAT::t_v_array h_v;
+ HAT::t_f_array h_f;
+
+ DAT::t_tagint_1d d_molecule;
+ DAT::t_int_2d d_nspecial;
+ DAT::t_tagint_2d d_special;
+ DAT::t_int_1d d_num_bond;
+ DAT::t_int_2d d_bond_type;
+ DAT::t_tagint_2d d_bond_atom;
+
+ HAT::t_tagint_1d h_molecule;
+ HAT::t_int_2d h_nspecial;
+ HAT::t_tagint_2d h_special;
+ HAT::t_int_1d h_num_bond;
+ HAT::t_int_2d h_bond_type;
+ HAT::t_tagint_2d h_bond_atom;
+
+ DAT::t_int_1d d_num_angle;
+ DAT::t_int_2d d_angle_type;
+ DAT::t_tagint_2d d_angle_atom1,d_angle_atom2,d_angle_atom3;
+
+ HAT::t_int_1d h_num_angle;
+ HAT::t_int_2d h_angle_type;
+ HAT::t_tagint_2d h_angle_atom1,h_angle_atom2,h_angle_atom3;
+
+ DAT::tdual_int_1d k_count;
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/atom_vec_atomic_kokkos.cpp b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
index 2125519129..9b06a49149 100644
--- a/src/KOKKOS/atom_vec_atomic_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_atomic_kokkos.cpp
@@ -553,14 +553,15 @@ void AtomVecAtomicKokkos::unpack_comm_vel(int n, int first, double *buf)
int AtomVecAtomicKokkos::pack_reverse(int n, int first, double *buf)
{
- int i,m,last;
-
- m = 0;
- last = first + n;
- for (i = first; i < last; i++) {
- buf[m++] = f[i][0];
- buf[m++] = f[i][1];
- buf[m++] = f[i][2];
+ if(n > 0)
+ sync(Host,F_MASK);
+
+ int m = 0;
+ const int last = first + n;
+ for (int i = first; i < last; i++) {
+ buf[m++] = h_f(i,0);
+ buf[m++] = h_f(i,1);
+ buf[m++] = h_f(i,2);
}
return m;
}
@@ -569,14 +570,17 @@ int AtomVecAtomicKokkos::pack_reverse(int n, int first, double *buf)
void AtomVecAtomicKokkos::unpack_reverse(int n, int *list, double *buf)
{
- int i,j,m;
+ if(n > 0) {
+ sync(Host,F_MASK);
+ modified(Host,F_MASK);
+ }
- m = 0;
- for (i = 0; i < n; i++) {
- j = list[i];
- f[j][0] += buf[m++];
- f[j][1] += buf[m++];
- f[j][2] += buf[m++];
+ int m = 0;
+ for (int i = 0; i < n; i++) {
+ const int j = list[i];
+ h_f(j,0) += buf[m++];
+ h_f(j,1) += buf[m++];
+ h_f(j,2) += buf[m++];
}
}
@@ -588,11 +592,11 @@ struct AtomVecAtomicKokkos_PackBorder {
typename ArrayTypes<DeviceType>::t_xfloat_2d _buf;
const typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
const typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
const typename ArrayTypes<DeviceType>::t_tagint_1d _tag;
const typename ArrayTypes<DeviceType>::t_int_1d _type;
const typename ArrayTypes<DeviceType>::t_int_1d _mask;
- const int _iswap;
X_FLOAT _dx,_dy,_dz;
AtomVecAtomicKokkos_PackBorder(
@@ -694,9 +698,9 @@ int AtomVecAtomicKokkos::pack_border(int n, int *list, double *buf,
buf[m++] = h_x(j,0);
buf[m++] = h_x(j,1);
buf[m++] = h_x(j,2);
- buf[m++] = h_tag[j];
- buf[m++] = h_type[j];
- buf[m++] = h_mask[j];
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
}
} else {
if (domain->triclinic == 0) {
@@ -713,11 +717,16 @@ int AtomVecAtomicKokkos::pack_border(int n, int *list, double *buf,
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
- buf[m++] = h_tag[j];
- buf[m++] = h_type[j];
- buf[m++] = h_mask[j];
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
}
}
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
return m;
}
@@ -736,9 +745,9 @@ int AtomVecAtomicKokkos::pack_border_vel(int n, int *list, double *buf,
buf[m++] = h_x(j,0);
buf[m++] = h_x(j,1);
buf[m++] = h_x(j,2);
- buf[m++] = h_tag[j];
- buf[m++] = h_type[j];
- buf[m++] = h_mask[j];
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
@@ -759,9 +768,9 @@ int AtomVecAtomicKokkos::pack_border_vel(int n, int *list, double *buf,
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
- buf[m++] = h_tag[j];
- buf[m++] = h_type[j];
- buf[m++] = h_mask[j];
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
buf[m++] = h_v(j,0);
buf[m++] = h_v(j,1);
buf[m++] = h_v(j,2);
@@ -775,9 +784,9 @@ int AtomVecAtomicKokkos::pack_border_vel(int n, int *list, double *buf,
buf[m++] = h_x(j,0) + dx;
buf[m++] = h_x(j,1) + dy;
buf[m++] = h_x(j,2) + dz;
- buf[m++] = h_tag[j];
- buf[m++] = h_type[j];
- buf[m++] = h_mask[j];
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
if (mask[i] & deform_groupbit) {
buf[m++] = h_v(j,0) + dvx;
buf[m++] = h_v(j,1) + dvy;
@@ -790,6 +799,11 @@ int AtomVecAtomicKokkos::pack_border_vel(int n, int *list, double *buf,
}
}
}
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
return m;
}
@@ -861,10 +875,15 @@ void AtomVecAtomicKokkos::unpack_border(int n, int first, double *buf)
h_x(i,0) = buf[m++];
h_x(i,1) = buf[m++];
h_x(i,2) = buf[m++];
- h_tag[i] = static_cast<int> (buf[m++]);
- h_type[i] = static_cast<int> (buf[m++]);
- h_mask[i] = static_cast<int> (buf[m++]);
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
}
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
@@ -880,13 +899,18 @@ void AtomVecAtomicKokkos::unpack_border_vel(int n, int first, double *buf)
h_x(i,0) = buf[m++];
h_x(i,1) = buf[m++];
h_x(i,2) = buf[m++];
- h_tag[i] = static_cast<int> (buf[m++]);
- h_type[i] = static_cast<int> (buf[m++]);
- h_mask[i] = static_cast<int> (buf[m++]);
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
h_v(i,0) = buf[m++];
h_v(i,1) = buf[m++];
h_v(i,2) = buf[m++];
}
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
@@ -895,7 +919,6 @@ template<class DeviceType>
struct AtomVecAtomicKokkos_PackExchangeFunctor {
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
- X_FLOAT _lo,_hi;
typename AT::t_x_array_randomread _x;
typename AT::t_v_array_randomread _v;
typename AT::t_tagint_1d_randomread _tag;
@@ -910,9 +933,10 @@ struct AtomVecAtomicKokkos_PackExchangeFunctor {
typename AT::t_imageint_1d _imagew;
typename AT::t_xfloat_2d_um _buf;
- int _nlocal,_dim;
typename AT::t_int_1d_const _sendlist;
typename AT::t_int_1d_const _copylist;
+ int _nlocal,_dim;
+ X_FLOAT _lo,_hi;
AtomVecAtomicKokkos_PackExchangeFunctor(
const AtomKokkos* atom,
@@ -977,7 +1001,7 @@ struct AtomVecAtomicKokkos_PackExchangeFunctor {
int AtomVecAtomicKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf, DAT::tdual_int_1d k_sendlist,DAT::tdual_int_1d k_copylist,ExecutionSpace space,int dim,X_FLOAT lo,X_FLOAT hi )
{
- if(nsend > (k_buf.view<LMPHostType>().dimension_0()*k_buf.view<LMPHostType>().dimension_1())/11) {
+ if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*k_buf.view<LMPHostType>().dimension_1())/11) {
int newsize = nsend*11/k_buf.view<LMPHostType>().dimension_1()+1;
k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
}
@@ -1005,10 +1029,10 @@ int AtomVecAtomicKokkos::pack_exchange(int i, double *buf)
buf[m++] = h_v(i,0);
buf[m++] = h_v(i,1);
buf[m++] = h_v(i,2);
- buf[m++] = h_tag[i];
- buf[m++] = h_type[i];
- buf[m++] = h_mask[i];
- *((tagint *) &buf[m++]) = h_image[i];
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@@ -1024,7 +1048,6 @@ template<class DeviceType>
struct AtomVecAtomicKokkos_UnpackExchangeFunctor {
typedef DeviceType device_type;
typedef ArrayTypes<DeviceType> AT;
- X_FLOAT _lo,_hi;
typename AT::t_x_array _x;
typename AT::t_v_array _v;
typename AT::t_tagint_1d _tag;
@@ -1033,8 +1056,9 @@ struct AtomVecAtomicKokkos_UnpackExchangeFunctor {
typename AT::t_imageint_1d _image;
typename AT::t_xfloat_2d_um _buf;
- int _dim;
typename AT::t_int_1d _nlocal;
+ int _dim;
+ X_FLOAT _lo,_hi;
AtomVecAtomicKokkos_UnpackExchangeFunctor(
const AtomKokkos* atom,
@@ -1113,10 +1137,10 @@ int AtomVecAtomicKokkos::unpack_exchange(double *buf)
h_v(nlocal,0) = buf[m++];
h_v(nlocal,1) = buf[m++];
h_v(nlocal,2) = buf[m++];
- h_tag[nlocal] = static_cast<int> (buf[m++]);
- h_type[nlocal] = static_cast<int> (buf[m++]);
- h_mask[nlocal] = static_cast<int> (buf[m++]);
- h_image[nlocal] = static_cast<int> (buf[m++]);
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@@ -1159,10 +1183,10 @@ int AtomVecAtomicKokkos::pack_restart(int i, double *buf)
buf[m++] = h_x(i,0);
buf[m++] = h_x(i,1);
buf[m++] = h_x(i,2);
- buf[m++] = h_tag[i];
- buf[m++] = h_type[i];
- buf[m++] = h_mask[i];
- buf[m++] = h_image[i];
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
buf[m++] = h_v(i,0);
buf[m++] = h_v(i,1);
buf[m++] = h_v(i,2);
@@ -1192,17 +1216,17 @@ int AtomVecAtomicKokkos::unpack_restart(double *buf)
h_x(nlocal,0) = buf[m++];
h_x(nlocal,1) = buf[m++];
h_x(nlocal,2) = buf[m++];
- h_tag[nlocal] = static_cast<int> (buf[m++]);
- h_type[nlocal] = static_cast<int> (buf[m++]);
- h_mask[nlocal] = static_cast<int> (buf[m++]);
- h_image[nlocal] = *((tagint *) &buf[m++]);
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
h_v(nlocal,0) = buf[m++];
h_v(nlocal,1) = buf[m++];
h_v(nlocal,2) = buf[m++];
double **extra = atom->extra;
if (atom->nextra_store) {
- int size = static_cast<int> (buf[0]) - m;
+ int size = static_cast<int> (ubuf(buf[m++]).i) - m;
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
}
diff --git a/src/KOKKOS/atom_vec_bond_kokkos.cpp b/src/KOKKOS/atom_vec_bond_kokkos.cpp
new file mode 100644
index 0000000000..a1b2c7823c
--- /dev/null
+++ b/src/KOKKOS/atom_vec_bond_kokkos.cpp
@@ -0,0 +1,1717 @@
+/* ----------------------------------------------------------------------
+ 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 "stdlib.h"
+#include "atom_vec_bond_kokkos.h"
+#include "atom_kokkos.h"
+#include "comm_kokkos.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "atom_masks.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecBondKokkos::AtomVecBondKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
+{
+ molecular = 1;
+ bonds_allow = 1;
+ mass_type = 1;
+
+ comm_x_only = comm_f_only = 1;
+ size_forward = 3;
+ size_reverse = 3;
+ size_border = 7;
+ size_velocity = 3;
+ size_data_atom = 6;
+ size_data_vel = 4;
+ xcol_data = 4;
+
+ k_count = DAT::tdual_int_1d("atom::k_count",1);
+ atomKK = (AtomKokkos *) atom;
+ commKK = (CommKokkos *) comm;
+}
+
+/* ----------------------------------------------------------------------
+ grow atom arrays
+ n = 0 grows arrays by DELTA
+ n > 0 allocates arrays to size n
+------------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::grow(int n)
+{
+ if (n == 0) nmax += DELTA;
+ else nmax = n;
+ atomKK->nmax = nmax;
+ if (nmax < 0 || nmax > MAXSMALLINT)
+ error->one(FLERR,"Per-processor system is too big");
+
+ sync(Device,ALL_MASK);
+ modified(Device,ALL_MASK);
+
+ memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
+ memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
+ memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
+ memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
+
+ memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
+ memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
+ memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
+
+ memory->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
+ memory->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
+ memory->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,"atom:special");
+ memory->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
+ memory->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,"atom:bond_type");
+ memory->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,"atom:bond_atom");
+
+ grow_reset();
+ sync(Host,ALL_MASK);
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atomKK->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
+}
+
+/* ----------------------------------------------------------------------
+ reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::grow_reset()
+{
+ tag = atomKK->tag;
+ d_tag = atomKK->k_tag.d_view;
+ h_tag = atomKK->k_tag.h_view;
+
+ type = atomKK->type;
+ d_type = atomKK->k_type.d_view;
+ h_type = atomKK->k_type.h_view;
+ mask = atomKK->mask;
+ d_mask = atomKK->k_mask.d_view;
+ h_mask = atomKK->k_mask.h_view;
+ image = atomKK->image;
+ d_image = atomKK->k_image.d_view;
+ h_image = atomKK->k_image.h_view;
+
+ x = atomKK->x;
+ d_x = atomKK->k_x.d_view;
+ h_x = atomKK->k_x.h_view;
+ v = atomKK->v;
+ d_v = atomKK->k_v.d_view;
+ h_v = atomKK->k_v.h_view;
+ f = atomKK->f;
+ d_f = atomKK->k_f.d_view;
+ h_f = atomKK->k_f.h_view;
+
+ molecule = atomKK->molecule;
+ d_molecule = atomKK->k_molecule.d_view;
+ h_molecule = atomKK->k_molecule.h_view;
+ nspecial = atomKK->nspecial;
+ d_nspecial = atomKK->k_nspecial.d_view;
+ h_nspecial = atomKK->k_nspecial.h_view;
+ special = atomKK->special;
+ d_special = atomKK->k_special.d_view;
+ h_special = atomKK->k_special.h_view;
+ num_bond = atomKK->num_bond;
+ d_num_bond = atomKK->k_num_bond.d_view;
+ h_num_bond = atomKK->k_num_bond.h_view;
+ bond_type = atomKK->bond_type;
+ d_bond_type = atomKK->k_bond_type.d_view;
+ h_bond_type = atomKK->k_bond_type.h_view;
+ bond_atom = atomKK->bond_atom;
+ d_bond_atom = atomKK->k_bond_atom.d_view;
+ h_bond_atom = atomKK->k_bond_atom.h_view;
+}
+
+/* ----------------------------------------------------------------------
+ copy atom I info to atom J
+------------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::copy(int i, int j, int delflag)
+{
+ int k;
+
+ h_tag[j] = h_tag[i];
+ h_type[j] = h_type[i];
+ mask[j] = mask[i];
+ h_image[j] = h_image[i];
+ h_x(j,0) = h_x(i,0);
+ h_x(j,1) = h_x(i,1);
+ h_x(j,2) = h_x(i,2);
+ h_v(j,0) = h_v(i,0);
+ h_v(j,1) = h_v(i,1);
+ h_v(j,2) = h_v(i,2);
+
+ h_molecule(j) = h_molecule(i);
+
+ h_num_bond(j) = h_num_bond(i);
+ for (k = 0; k < h_num_bond(j); k++) {
+ h_bond_type(j,k) = h_bond_type(i,k);
+ h_bond_atom(j,k) = h_bond_atom(i,k);
+ }
+
+ h_nspecial(j,0) = h_nspecial(i,0);
+ h_nspecial(j,1) = h_nspecial(i,1);
+ h_nspecial(j,2) = h_nspecial(i,2);
+ for (k = 0; k < h_nspecial(j,2); k++) h_special(j,k) = h_special(i,k);
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecBondKokkos_PackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_um _buf;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecBondKokkos_PackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ const size_t maxsend = (buf.view<DeviceType>().dimension_0()*buf.view<DeviceType>().dimension_1())/3;
+ const size_t elements = 3;
+ buffer_view<DeviceType>(_buf,buf,maxsend,elements);
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_comm_kokkos(const int &n,
+ const DAT::tdual_int_2d &list,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag,
+ const int* const pbc)
+{
+ // Check whether to always run forward communication on the host
+ // Choose correct forward PackComm kernel
+
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecBondKokkos_PackComm<LMPHostType,1,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecBondKokkos_PackComm<LMPHostType,1,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecBondKokkos_PackComm<LMPHostType,0,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecBondKokkos_PackComm<LMPHostType,0,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecBondKokkos_PackComm<LMPDeviceType,1,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecBondKokkos_PackComm<LMPDeviceType,1,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecBondKokkos_PackComm<LMPDeviceType,0,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecBondKokkos_PackComm<LMPDeviceType,0,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+
+ return n*size_forward;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecBondKokkos_PackCommSelf {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_x_array _xw;
+ int _nfirst;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecBondKokkos_PackCommSelf(
+ const typename DAT::tdual_x_array &x,
+ const int &nfirst,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_xw(x.view<DeviceType>()),_nfirst(nfirst),_list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _xw(i+_nfirst,0) = _x(j,0);
+ _xw(i+_nfirst,1) = _x(j,1);
+ _xw(i+_nfirst,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list, const int & iswap,
+ const int nfirst, const int &pbc_flag, const int* const pbc) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecBondKokkos_PackCommSelf<LMPHostType,1,1> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecBondKokkos_PackCommSelf<LMPHostType,1,0> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecBondKokkos_PackCommSelf<LMPHostType,0,1> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecBondKokkos_PackCommSelf<LMPHostType,0,0> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecBondKokkos_PackCommSelf<LMPDeviceType,1,1> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecBondKokkos_PackCommSelf<LMPDeviceType,1,0> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecBondKokkos_PackCommSelf<LMPDeviceType,0,1> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecBondKokkos_PackCommSelf<LMPDeviceType,0,0> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+ return n*3;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecBondKokkos_UnpackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
+ int _first;
+
+ AtomVecBondKokkos_UnpackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const int& first):_x(x.view<DeviceType>()),_buf(buf.view<DeviceType>()),
+ _first(first) {};
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::unpack_comm_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf ) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ struct AtomVecBondKokkos_UnpackComm<LMPHostType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ struct AtomVecBondKokkos_UnpackComm<LMPDeviceType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_comm_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::unpack_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::unpack_comm_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_reverse(int n, int first, double *buf)
+{
+ if(n > 0)
+ sync(Host,F_MASK);
+
+ int m = 0;
+ const int last = first + n;
+ for (int i = first; i < last; i++) {
+ buf[m++] = h_f(i,0);
+ buf[m++] = h_f(i,1);
+ buf[m++] = h_f(i,2);
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::unpack_reverse(int n, int *list, double *buf)
+{
+ if(n > 0)
+ modified(Host,F_MASK);
+
+ int m = 0;
+ for (int i = 0; i < n; i++) {
+ const int j = list[i];
+ h_f(j,0) += buf[m++];
+ h_f(j,1) += buf[m++];
+ h_f(j,2) += buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG>
+struct AtomVecBondKokkos_PackBorder {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+
+ typename AT::t_xfloat_2d _buf;
+ const typename AT::t_int_2d_const _list;
+ const int _iswap;
+ const typename AT::t_x_array_randomread _x;
+ const typename AT::t_tagint_1d _tag;
+ const typename AT::t_int_1d _type;
+ const typename AT::t_int_1d _mask;
+ const typename AT::t_tagint_1d _molecule;
+ X_FLOAT _dx,_dy,_dz;
+
+ AtomVecBondKokkos_PackBorder(
+ const typename AT::t_xfloat_2d &buf,
+ const typename AT::t_int_2d_const &list,
+ const int & iswap,
+ const typename AT::t_x_array &x,
+ const typename AT::t_tagint_1d &tag,
+ const typename AT::t_int_1d &type,
+ const typename AT::t_int_1d &mask,
+ const typename AT::t_tagint_1d &molecule,
+ const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz):
+ _buf(buf),_list(list),_iswap(iswap),
+ _x(x),_tag(tag),_type(type),_mask(mask),_molecule(molecule),
+ _dx(dx),_dy(dy),_dz(dz) {}
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ _buf(i,3) = _tag(j);
+ _buf(i,4) = _type(j);
+ _buf(i,5) = _mask(j);
+ _buf(i,6) = _molecule(j);
+ } else {
+ _buf(i,0) = _x(j,0) + _dx;
+ _buf(i,1) = _x(j,1) + _dy;
+ _buf(i,2) = _x(j,2) + _dz;
+ _buf(i,3) = _tag(j);
+ _buf(i,4) = _type(j);
+ _buf(i,5) = _mask(j);
+ _buf(i,6) = _molecule(j);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::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)
+{
+ X_FLOAT dx,dy,dz;
+
+ if (pbc_flag != 0) {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if(space==Host) {
+ AtomVecBondKokkos_PackBorder<LMPHostType,1> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecBondKokkos_PackBorder<LMPDeviceType,1> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+
+ } else {
+ dx = dy = dz = 0;
+ if(space==Host) {
+ AtomVecBondKokkos_PackBorder<LMPHostType,0> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecBondKokkos_PackBorder<LMPDeviceType,0> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+ }
+ return n*size_border;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_border(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_border_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_border_hybrid(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_molecule(j);
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecBondKokkos_UnpackBorder {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+
+ const typename AT::t_xfloat_2d_const _buf;
+ typename AT::t_x_array _x;
+ typename AT::t_tagint_1d _tag;
+ typename AT::t_int_1d _type;
+ typename AT::t_int_1d _mask;
+ typename AT::t_tagint_1d _molecule;
+ int _first;
+
+
+ AtomVecBondKokkos_UnpackBorder(
+ const typename AT::t_xfloat_2d_const &buf,
+ typename AT::t_x_array &x,
+ typename AT::t_tagint_1d &tag,
+ typename AT::t_int_1d &type,
+ typename AT::t_int_1d &mask,
+ typename AT::t_tagint_1d &molecule,
+ const int& first):
+ _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_molecule(molecule),
+ _first(first){
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ _tag(i+_first) = static_cast<int> (_buf(i,3));
+ _type(i+_first) = static_cast<int> (_buf(i,4));
+ _mask(i+_first) = static_cast<int> (_buf(i,5));
+ _molecule(i+_first) = static_cast<int> (_buf(i,6));
+
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::unpack_border_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf,
+ ExecutionSpace space) {
+ modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
+ while (first+n >= nmax) grow(0);
+ modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
+ if(space==Host) {
+ struct AtomVecBondKokkos_UnpackBorder<LMPHostType>
+ f(buf.view<LMPHostType>(),h_x,h_tag,h_type,h_mask,h_molecule,first);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ struct AtomVecBondKokkos_UnpackBorder<LMPDeviceType>
+ f(buf.view<LMPDeviceType>(),d_x,d_tag,d_type,d_mask,d_molecule,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::unpack_border(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax) grow(0);
+ modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::unpack_border_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax) grow(0);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::unpack_border_hybrid(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecBondKokkos_PackExchangeFunctor {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array_randomread _x;
+ typename AT::t_v_array_randomread _v;
+ typename AT::t_tagint_1d_randomread _tag;
+ typename AT::t_int_1d_randomread _type;
+ typename AT::t_int_1d_randomread _mask;
+ typename AT::t_imageint_1d_randomread _image;
+ typename AT::t_tagint_1d_randomread _molecule;
+ typename AT::t_int_2d_randomread _nspecial;
+ typename AT::t_tagint_2d_randomread _special;
+ typename AT::t_int_1d_randomread _num_bond;
+ typename AT::t_int_2d_randomread _bond_type;
+ typename AT::t_tagint_2d_randomread _bond_atom;
+ typename AT::t_x_array _xw;
+ typename AT::t_v_array _vw;
+ typename AT::t_tagint_1d _tagw;
+ typename AT::t_int_1d _typew;
+ typename AT::t_int_1d _maskw;
+ typename AT::t_imageint_1d _imagew;
+ typename AT::t_tagint_1d _moleculew;
+ typename AT::t_int_2d _nspecialw;
+ typename AT::t_tagint_2d _specialw;
+ typename AT::t_int_1d _num_bondw;
+ typename AT::t_int_2d _bond_typew;
+ typename AT::t_tagint_2d _bond_atomw;
+
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d_const _sendlist;
+ typename AT::t_int_1d_const _copylist;
+ int _nlocal,_dim;
+ X_FLOAT _lo,_hi;
+ size_t elements;
+
+ AtomVecBondKokkos_PackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d sendlist,
+ typename AT::tdual_int_1d copylist,int nlocal, int dim,
+ X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _xw(atom->k_x.view<DeviceType>()),
+ _vw(atom->k_v.view<DeviceType>()),
+ _tagw(atom->k_tag.view<DeviceType>()),
+ _typew(atom->k_type.view<DeviceType>()),
+ _maskw(atom->k_mask.view<DeviceType>()),
+ _imagew(atom->k_image.view<DeviceType>()),
+ _moleculew(atom->k_molecule.view<DeviceType>()),
+ _nspecialw(atom->k_nspecial.view<DeviceType>()),
+ _specialw(atom->k_special.view<DeviceType>()),
+ _num_bondw(atom->k_num_bond.view<DeviceType>()),
+ _bond_typew(atom->k_bond_type.view<DeviceType>()),
+ _bond_atomw(atom->k_bond_atom.view<DeviceType>()),
+ _sendlist(sendlist.template view<DeviceType>()),
+ _copylist(copylist.template view<DeviceType>()),
+ _nlocal(nlocal),_dim(dim),
+ _lo(lo),_hi(hi){
+ // 3 comp of x, 3 comp of v, 1 tag, 1 type, 1 mask, 1 image, 1 molecule, 3 nspecial,
+ // maxspecial special, 1 num_bond, bond_per_atom bond_type, bond_per_atom bond_atom,
+ // 1 to store buffer lenght
+ elements = 16+atom->maxspecial+atom->bond_per_atom+atom->bond_per_atom;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
+ buf.template view<DeviceType>().dimension_1())/elements;
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &mysend) const {
+ int k;
+ const int i = _sendlist(mysend);
+ _buf(mysend,0) = elements;
+ int m = 1;
+ _buf(mysend,m++) = _x(i,0);
+ _buf(mysend,m++) = _x(i,1);
+ _buf(mysend,m++) = _x(i,2);
+ _buf(mysend,m++) = _v(i,0);
+ _buf(mysend,m++) = _v(i,1);
+ _buf(mysend,m++) = _v(i,2);
+ _buf(mysend,m++) = _tag(i);
+ _buf(mysend,m++) = _type(i);
+ _buf(mysend,m++) = _mask(i);
+ _buf(mysend,m++) = _image(i);
+ _buf(mysend,m++) = _molecule(i);
+ _buf(mysend,m++) = _num_bond(i);
+ for (k = 0; k < _num_bond(i); k++) {
+ _buf(mysend,m++) = _bond_type(i,k);
+ _buf(mysend,m++) = _bond_atom(i,k);
+ }
+ _buf(mysend,m++) = _nspecial(i,0);
+ _buf(mysend,m++) = _nspecial(i,1);
+ _buf(mysend,m++) = _nspecial(i,2);
+ for (k = 0; k < _nspecial(i,2); k++)
+ _buf(mysend,m++) = _special(i,k);
+
+ const int j = _copylist(mysend);
+
+ if(j>-1) {
+ _xw(i,0) = _x(j,0);
+ _xw(i,1) = _x(j,1);
+ _xw(i,2) = _x(j,2);
+ _vw(i,0) = _v(j,0);
+ _vw(i,1) = _v(j,1);
+ _vw(i,2) = _v(j,2);
+ _tagw(i) = _tag(j);
+ _typew(i) = _type(j);
+ _maskw(i) = _mask(j);
+ _imagew(i) = _image(j);
+ _moleculew(i) = _molecule(j);
+ _num_bondw(i) = _num_bond(j);
+ for (k = 0; k < _num_bond(j); k++) {
+ _bond_typew(i,k) = _bond_type(j,k);
+ _bond_atomw(i,k) = _bond_atom(j,k);
+ }
+ _nspecialw(i,0) = _nspecial(j,0);
+ _nspecialw(i,1) = _nspecial(j,1);
+ _nspecialw(i,2) = _nspecial(j,2);
+ for (k = 0; k < _nspecial(j,2); k++)
+ _specialw(i,k) = _special(j,k);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space,int dim,X_FLOAT lo,
+ X_FLOAT hi )
+{
+ const int elements = 16+atomKK->maxspecial+atomKK->bond_per_atom+atomKK->bond_per_atom;
+ if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*
+ k_buf.view<LMPHostType>().dimension_1())/elements) {
+ int newsize = nsend*elements/k_buf.view<LMPHostType>().dimension_1()+1;
+ k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
+ }
+ if(space == Host) {
+ AtomVecBondKokkos_PackExchangeFunctor<LMPHostType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPHostType::fence();
+ return nsend*elements;
+ } else {
+ AtomVecBondKokkos_PackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPDeviceType::fence();
+ return nsend*elements;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_exchange(int i, double *buf)
+{
+ int k;
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = ubuf(h_molecule(i)).d;
+
+ buf[m++] = ubuf(h_num_bond(i)).d;
+ for (k = 0; k < h_num_bond(i); k++) {
+ buf[m++] = ubuf(h_bond_type(i,k)).d;
+ buf[m++] = ubuf(h_bond_atom(i,k)).d;
+ }
+ buf[m++] = ubuf(h_nspecial(i,0)).d;
+ buf[m++] = ubuf(h_nspecial(i,1)).d;
+ buf[m++] = ubuf(h_nspecial(i,2)).d;
+ for (k = 0; k < h_nspecial(i,2); k++)
+ buf[m++] = ubuf(h_special(i,k)).d;
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecBondKokkos_UnpackExchangeFunctor {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array _x;
+ typename AT::t_v_array _v;
+ typename AT::t_tagint_1d _tag;
+ typename AT::t_int_1d _type;
+ typename AT::t_int_1d _mask;
+ typename AT::t_imageint_1d _image;
+ typename AT::t_tagint_1d _molecule;
+ typename AT::t_int_2d _nspecial;
+ typename AT::t_tagint_2d _special;
+ typename AT::t_int_1d _num_bond;
+ typename AT::t_int_2d _bond_type;
+ typename AT::t_tagint_2d _bond_atom;
+
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d _nlocal;
+ int _dim;
+ X_FLOAT _lo,_hi;
+ size_t elements;
+
+ AtomVecBondKokkos_UnpackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d nlocal,
+ int dim, X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _nlocal(nlocal.template view<DeviceType>()),_dim(dim),
+ _lo(lo),_hi(hi){
+ elements = 16+atom->maxspecial+atom->bond_per_atom+atom->bond_per_atom;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
+ buf.template view<DeviceType>().dimension_1())/elements;
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &myrecv) const {
+ X_FLOAT x = _buf(myrecv,_dim+1);
+ if (x >= _lo && x < _hi) {
+ int i = Kokkos::atomic_fetch_add(&_nlocal(0),1);
+ int m = 1;
+ _x(i,0) = _buf(myrecv,m++);
+ _x(i,1) = _buf(myrecv,m++);
+ _x(i,2) = _buf(myrecv,m++);
+ _v(i,0) = _buf(myrecv,m++);
+ _v(i,1) = _buf(myrecv,m++);
+ _v(i,2) = _buf(myrecv,m++);
+ _tag(i) = _buf(myrecv,m++);
+ _type(i) = _buf(myrecv,m++);
+ _mask(i) = _buf(myrecv,m++);
+ _image(i) = _buf(myrecv,m++);
+
+ _molecule(i) = _buf(myrecv,m++);
+ _num_bond(i) = _buf(myrecv,m++);
+ int k;
+ for (k = 0; k < _num_bond(i); k++) {
+ _bond_type(i,k) = _buf(myrecv,m++);
+ _bond_atom(i,k) = _buf(myrecv,m++);
+ }
+ _nspecial(i,0) = _buf(myrecv,m++);
+ _nspecial(i,1) = _buf(myrecv,m++);
+ _nspecial(i,2) = _buf(myrecv,m++);
+ for (k = 0; k < _nspecial(i,2); k++)
+ _special(i,k) = _buf(myrecv,m++);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,
+ int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,
+ ExecutionSpace space) {
+ const size_t elements = 16+atomKK->maxspecial+atomKK->bond_per_atom+atomKK->bond_per_atom;
+ if(space == Host) {
+ k_count.h_view(0) = nlocal;
+ AtomVecBondKokkos_UnpackExchangeFunctor<LMPHostType>
+ f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/elements,f);
+ LMPHostType::fence();
+ return k_count.h_view(0);
+ } else {
+ k_count.h_view(0) = nlocal;
+ k_count.modify<LMPHostType>();
+ k_count.sync<LMPDeviceType>();
+ AtomVecBondKokkos_UnpackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/elements,f);
+ LMPDeviceType::fence();
+ k_count.modify<LMPDeviceType>();
+ k_count.sync<LMPHostType>();
+
+ return k_count.h_view(0);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::unpack_exchange(double *buf)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) grow(0);
+ modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
+ MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | SPECIAL_MASK);
+
+ int k;
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
+
+ h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_bond(nlocal); k++) {
+ h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i;
+ h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i;
+ h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_nspecial(nlocal,2); k++)
+ h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->
+ unpack_exchange(nlocal,&buf[m]);
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ size of restart data for all atoms owned by this proc
+ include extra data stored by fixes
+------------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::size_restart()
+{
+ int i;
+
+ int nlocal = atom->nlocal;
+ int n = 0;
+ for (i = 0; i < nlocal; i++)
+ n += 13 + 2*h_num_bond[i];
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (i = 0; i < nlocal; i++)
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom I's data for restart file including extra quantities
+ xyz must be 1st 3 values, so that read_restart can test on them
+ molecular types may be negative, but write as positive
+------------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_restart(int i, double *buf)
+{
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+
+ buf[m++] = ubuf(h_molecule(i)).d;
+
+ buf[m++] = ubuf(h_num_bond(i)).d;
+ for (int k = 0; k < h_num_bond(i); k++) {
+ buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d;
+ buf[m++] = ubuf(h_bond_atom(i,k)).d;
+ }
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ unpack data for one atom from restart file including extra quantities
+------------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::unpack_restart(double *buf)
+{
+ int k;
+
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ grow(0);
+ if (atom->nextra_store)
+ memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
+ }
+
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+
+ h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
+
+ h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_bond(nlocal); k++) {
+ h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
+
+ double **extra = atom->extra;
+ if (atom->nextra_store) {
+ int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+ for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
+ }
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ create one atom of itype at coord
+ set other values to defaults
+------------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::create_atom(int itype, double *coord)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ atomKK->modified(Host,ALL_MASK);
+ grow(0);
+ }
+ atomKK->modified(Host,ALL_MASK);
+
+ tag[nlocal] = 0;
+ type[nlocal] = itype;
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+ h_mask(nlocal) = 1;
+ h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) |
+ ((imageint) IMGMAX << IMGBITS) | IMGMAX;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+
+ h_molecule(nlocal) = 0;
+ h_num_bond(nlocal) = 0;
+ h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack one line from Atoms section of data file
+ initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp,
+ char **values)
+{
+ int nlocal = atomKK->nlocal;
+ if (nlocal == nmax) grow(0);
+
+ h_tag(nlocal) = atoi(values[0]);
+ if (h_tag(nlocal) <= 0)
+ error->one(FLERR,"Invalid atom ID in Atoms section of data file");
+
+ h_molecule(nlocal) = atoi(values[1]);
+ if (h_molecule(nlocal) <= 0)
+ error->one(FLERR,"Invalid molecule ID in Atoms section of data file");
+
+ h_type(nlocal) = atoi(values[2]);
+ if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
+ error->one(FLERR,"Invalid atom type in Atoms section of data file");
+
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+
+ h_image(nlocal) = imagetmp;
+
+ h_mask(nlocal) = 1;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+ h_num_bond(nlocal) = 0;
+
+ atomKK->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack hybrid quantities from one line in Atoms section of data file
+ initialize other atom quantities for this sub-style
+------------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::data_atom_hybrid(int nlocal, char **values)
+{
+ h_molecule(nlocal) = atoi(values[0]);
+ h_num_bond(nlocal) = 0;
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom info for data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::pack_data(double **buf)
+{
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ buf[i][0] = h_tag(i);
+ buf[i][1] = h_molecule(i);
+ buf[i][2] = h_type(i);
+ buf[i][3] = h_x(i,0);
+ buf[i][4] = h_x(i,1);
+ buf[i][5] = h_x(i,2);
+ buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX;
+ buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+ buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ pack hybrid atom info for data file
+------------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::pack_data_hybrid(int i, double *buf)
+{
+ buf[0] = h_molecule(i);
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ write atom info to data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::write_data(FILE *fp, int n, double **buf)
+{
+ for (int i = 0; i < n; i++)
+ fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
+ (int) buf[i][0],(int) buf[i][1], (int) buf[i][2],
+ buf[i][3],buf[i][4],buf[i][5],
+ (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
+}
+
+/* ----------------------------------------------------------------------
+ write hybrid atom info to data file
+------------------------------------------------------------------------- */
+
+int AtomVecBondKokkos::write_data_hybrid(FILE *fp, double *buf)
+{
+ fprintf(fp," " TAGINT_FORMAT, (tagint) (buf[0]));
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ return # of bytes of allocated memory
+------------------------------------------------------------------------- */
+
+bigint AtomVecBondKokkos::memory_usage()
+{
+ bigint bytes = 0;
+
+ if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
+ if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
+ if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
+ if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
+ if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
+ if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
+ if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
+
+ if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
+ if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
+ if (atom->memcheck("special"))
+ bytes += memory->usage(special,nmax,atom->maxspecial);
+
+ if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
+ if (atom->memcheck("bond_type"))
+ bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
+ if (atom->memcheck("bond_atom"))
+ bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
+
+ return bytes;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::sync(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPDeviceType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.sync<LMPDeviceType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.sync<LMPDeviceType>();
+ atomKK->k_special.sync<LMPDeviceType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.sync<LMPDeviceType>();
+ atomKK->k_bond_type.sync<LMPDeviceType>();
+ atomKK->k_bond_atom.sync<LMPDeviceType>();
+ }
+ } else {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPHostType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.sync<LMPHostType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.sync<LMPHostType>();
+ atomKK->k_special.sync<LMPHostType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.sync<LMPHostType>();
+ atomKK->k_bond_type.sync<LMPHostType>();
+ atomKK->k_bond_atom.sync<LMPHostType>();
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecBondKokkos::modified(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPDeviceType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.modify<LMPDeviceType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.modify<LMPDeviceType>();
+ atomKK->k_special.modify<LMPDeviceType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.modify<LMPDeviceType>();
+ atomKK->k_bond_type.modify<LMPDeviceType>();
+ atomKK->k_bond_atom.modify<LMPDeviceType>();
+ }
+ } else {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPHostType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.modify<LMPHostType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.modify<LMPHostType>();
+ atomKK->k_special.modify<LMPHostType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.modify<LMPHostType>();
+ atomKK->k_bond_type.modify<LMPHostType>();
+ atomKK->k_bond_atom.modify<LMPHostType>();
+ }
+ }
+}
diff --git a/src/KOKKOS/atom_vec_bond_kokkos.h b/src/KOKKOS/atom_vec_bond_kokkos.h
new file mode 100644
index 0000000000..676cd1202c
--- /dev/null
+++ b/src/KOKKOS/atom_vec_bond_kokkos.h
@@ -0,0 +1,141 @@
+/* ----------------------------------------------------------------------
+ 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 ATOM_CLASS
+
+AtomStyle(bond/kk,AtomVecBondKokkos)
+
+#else
+
+#ifndef LMP_ATOM_VEC_BOND_KOKKOS_H
+#define LMP_ATOM_VEC_BOND_KOKKOS_H
+
+#include "atom_vec_kokkos.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecBondKokkos : public AtomVecKokkos {
+ public:
+ AtomVecBondKokkos(class LAMMPS *);
+ virtual ~AtomVecBondKokkos() {}
+ void grow(int);
+ void copy(int, int, int);
+ int pack_comm(int, int *, double *, int, int *);
+ int pack_comm_vel(int, int *, double *, int, int *);
+ void unpack_comm(int, int, double *);
+ void unpack_comm_vel(int, int, double *);
+ int pack_reverse(int, int, double *);
+ void unpack_reverse(int, int *, double *);
+ int pack_border(int, int *, double *, int, int *);
+ int pack_border_vel(int, int *, double *, int, int *);
+ int pack_border_hybrid(int, int *, double *);
+ void unpack_border(int, int, double *);
+ void unpack_border_vel(int, int, double *);
+ int unpack_border_hybrid(int, int, double *);
+ int pack_exchange(int, double *);
+ int unpack_exchange(double *);
+ int size_restart();
+ int pack_restart(int, double *);
+ int unpack_restart(double *);
+ void create_atom(int, double *);
+ void data_atom(double *, tagint, char **);
+ int data_atom_hybrid(int, char **);
+ void pack_data(double **);
+ int pack_data_hybrid(int, double *);
+ void write_data(FILE *, int, double **);
+ int write_data_hybrid(FILE *, double *);
+ bigint memory_usage();
+
+ void grow_reset();
+ int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag, const int pbc[]);
+ void unpack_comm_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf);
+ int pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap, const int nfirst,
+ const int &pbc_flag, const int pbc[]);
+ int 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);
+ void unpack_border_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf,
+ ExecutionSpace space);
+ int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space, int dim,
+ X_FLOAT lo, X_FLOAT hi);
+ int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
+ int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
+ ExecutionSpace space);
+
+ void sync(ExecutionSpace space, unsigned int mask);
+ void modified(ExecutionSpace space, unsigned int mask);
+
+ protected:
+
+ tagint *tag;
+ int *type,*mask;
+ imageint *image;
+ double **x,**v,**f;
+
+ tagint *molecule;
+ int **nspecial;
+ tagint **special;
+ int *num_bond;
+ int **bond_type;
+ tagint **bond_atom;
+
+ DAT::t_tagint_1d d_tag;
+ DAT::t_int_1d d_type, d_mask;
+ HAT::t_tagint_1d h_tag;
+ HAT::t_int_1d h_type, h_mask;
+
+ DAT::t_imageint_1d d_image;
+ HAT::t_imageint_1d h_image;
+
+ DAT::t_x_array d_x;
+ DAT::t_v_array d_v;
+ DAT::t_f_array d_f;
+ HAT::t_x_array h_x;
+ HAT::t_v_array h_v;
+ HAT::t_f_array h_f;
+
+ DAT::t_tagint_1d d_molecule;
+ DAT::t_int_2d d_nspecial;
+ DAT::t_tagint_2d d_special;
+ DAT::t_int_1d d_num_bond;
+ DAT::t_int_2d d_bond_type;
+ DAT::t_tagint_2d d_bond_atom;
+
+ HAT::t_tagint_1d h_molecule;
+ HAT::t_int_2d h_nspecial;
+ HAT::t_tagint_2d h_special;
+ HAT::t_int_1d h_num_bond;
+ HAT::t_int_2d h_bond_type;
+ HAT::t_tagint_2d h_bond_atom;
+
+ DAT::tdual_int_1d k_count;
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/atom_vec_charge_kokkos.cpp b/src/KOKKOS/atom_vec_charge_kokkos.cpp
new file mode 100644
index 0000000000..97f489fb58
--- /dev/null
+++ b/src/KOKKOS/atom_vec_charge_kokkos.cpp
@@ -0,0 +1,1517 @@
+/* ----------------------------------------------------------------------
+ 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 "stdlib.h"
+#include "atom_vec_charge_kokkos.h"
+#include "atom_kokkos.h"
+#include "comm_kokkos.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "atom_masks.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecChargeKokkos::AtomVecChargeKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
+{
+ molecular = 0;
+ mass_type = 1;
+
+ comm_x_only = comm_f_only = 1;
+ size_forward = 3;
+ size_reverse = 3;
+ size_border = 7;
+ size_velocity = 3;
+ size_data_atom = 6;
+ size_data_vel = 4;
+ xcol_data = 4;
+
+ atom->q_flag = 1;
+
+ k_count = DAT::tdual_int_1d("atom::k_count",1);
+ atomKK = (AtomKokkos *) atom;
+ commKK = (CommKokkos *) comm;
+
+}
+
+/* ----------------------------------------------------------------------
+ grow atom arrays
+ n = 0 grows arrays by DELTA
+ n > 0 allocates arrays to size n
+------------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::grow(int n)
+{
+ if (n == 0) nmax += DELTA;
+ else nmax = n;
+ atomKK->nmax = nmax;
+ if (nmax < 0 || nmax > MAXSMALLINT)
+ error->one(FLERR,"Per-processor system is too big");
+
+ sync(Device,ALL_MASK);
+ modified(Device,ALL_MASK);
+
+ memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
+ memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
+ memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
+ memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
+
+ memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
+ memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
+ memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
+
+ memory->grow_kokkos(atomKK->k_q,atomKK->q,nmax,"atom:q");
+
+ grow_reset();
+ sync(Host,ALL_MASK);
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
+}
+
+/* ----------------------------------------------------------------------
+ reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::grow_reset()
+{
+ tag = atomKK->tag;
+ d_tag = atomKK->k_tag.d_view;
+ h_tag = atomKK->k_tag.h_view;
+
+ type = atomKK->type;
+ d_type = atomKK->k_type.d_view;
+ h_type = atomKK->k_type.h_view;
+ mask = atomKK->mask;
+ d_mask = atomKK->k_mask.d_view;
+ h_mask = atomKK->k_mask.h_view;
+ image = atomKK->image;
+ d_image = atomKK->k_image.d_view;
+ h_image = atomKK->k_image.h_view;
+
+ x = atomKK->x;
+ d_x = atomKK->k_x.d_view;
+ h_x = atomKK->k_x.h_view;
+ v = atomKK->v;
+ d_v = atomKK->k_v.d_view;
+ h_v = atomKK->k_v.h_view;
+ f = atomKK->f;
+ d_f = atomKK->k_f.d_view;
+ h_f = atomKK->k_f.h_view;
+
+ q = atomKK->q;
+ d_q = atomKK->k_q.d_view;
+ h_q = atomKK->k_q.h_view;
+
+}
+
+/* ----------------------------------------------------------------------
+ copy atom I info to atom J
+------------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::copy(int i, int j, int delflag)
+{
+ h_tag[j] = h_tag[i];
+ h_type[j] = h_type[i];
+ mask[j] = mask[i];
+ h_image[j] = h_image[i];
+ h_x(j,0) = h_x(i,0);
+ h_x(j,1) = h_x(i,1);
+ h_x(j,2) = h_x(i,2);
+ h_v(j,0) = h_v(i,0);
+ h_v(j,1) = h_v(i,1);
+ h_v(j,2) = h_v(i,2);
+
+ h_q[j] = h_q[i];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecChargeKokkos_PackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_um _buf;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecChargeKokkos_PackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ const size_t maxsend = (buf.view<DeviceType>().dimension_0()*buf.view<DeviceType>().dimension_1())/3;
+ const size_t elements = 3;
+ buffer_view<DeviceType>(_buf,buf,maxsend,elements);
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_comm_kokkos(const int &n,
+ const DAT::tdual_int_2d &list,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag,
+ const int* const pbc)
+{
+ // Check whether to always run forward communication on the host
+ // Choose correct forward PackComm kernel
+
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecChargeKokkos_PackComm<LMPHostType,1,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecChargeKokkos_PackComm<LMPHostType,1,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecChargeKokkos_PackComm<LMPHostType,0,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecChargeKokkos_PackComm<LMPHostType,0,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecChargeKokkos_PackComm<LMPDeviceType,1,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecChargeKokkos_PackComm<LMPDeviceType,1,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecChargeKokkos_PackComm<LMPDeviceType,0,1> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecChargeKokkos_PackComm<LMPDeviceType,0,0> f(atomKK->k_x,buf,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+
+ return n*size_forward;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecChargeKokkos_PackCommSelf {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_x_array _xw;
+ int _nfirst;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecChargeKokkos_PackCommSelf(
+ const typename DAT::tdual_x_array &x,
+ const int &nfirst,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_xw(x.view<DeviceType>()),_nfirst(nfirst),_list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _xw(i+_nfirst,0) = _x(j,0);
+ _xw(i+_nfirst,1) = _x(j,1);
+ _xw(i+_nfirst,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list, const int & iswap,
+ const int nfirst, const int &pbc_flag, const int* const pbc) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecChargeKokkos_PackCommSelf<LMPHostType,1,1> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecChargeKokkos_PackCommSelf<LMPHostType,1,0> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecChargeKokkos_PackCommSelf<LMPHostType,0,1> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecChargeKokkos_PackCommSelf<LMPHostType,0,0> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecChargeKokkos_PackCommSelf<LMPDeviceType,1,1> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecChargeKokkos_PackCommSelf<LMPDeviceType,1,0> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecChargeKokkos_PackCommSelf<LMPDeviceType,0,1> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecChargeKokkos_PackCommSelf<LMPDeviceType,0,0> f(atomKK->k_x,nfirst,list,iswap,
+ domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+ return n*3;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecChargeKokkos_UnpackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
+ int _first;
+
+ AtomVecChargeKokkos_UnpackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const int& first):_x(x.view<DeviceType>()),_buf(buf.view<DeviceType>()),
+ _first(first) {};
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::unpack_comm_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf ) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ struct AtomVecChargeKokkos_UnpackComm<LMPHostType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ struct AtomVecChargeKokkos_UnpackComm<LMPDeviceType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_comm_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::unpack_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::unpack_comm_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_reverse(int n, int first, double *buf)
+{
+ if(n > 0)
+ sync(Host,F_MASK);
+
+ int m = 0;
+ const int last = first + n;
+ for (int i = first; i < last; i++) {
+ buf[m++] = h_f(i,0);
+ buf[m++] = h_f(i,1);
+ buf[m++] = h_f(i,2);
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::unpack_reverse(int n, int *list, double *buf)
+{
+ if(n > 0)
+ modified(Host,F_MASK);
+
+ int m = 0;
+ for (int i = 0; i < n; i++) {
+ const int j = list[i];
+ h_f(j,0) += buf[m++];
+ h_f(j,1) += buf[m++];
+ h_f(j,2) += buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG>
+struct AtomVecChargeKokkos_PackBorder {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_xfloat_2d _buf;
+ const typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ const typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ const typename ArrayTypes<DeviceType>::t_tagint_1d _tag;
+ const typename ArrayTypes<DeviceType>::t_int_1d _type;
+ const typename ArrayTypes<DeviceType>::t_int_1d _mask;
+ const typename ArrayTypes<DeviceType>::t_float_1d _q;
+ X_FLOAT _dx,_dy,_dz;
+
+ AtomVecChargeKokkos_PackBorder(
+ const typename ArrayTypes<DeviceType>::t_xfloat_2d &buf,
+ const typename ArrayTypes<DeviceType>::t_int_2d_const &list,
+ const int & iswap,
+ const typename ArrayTypes<DeviceType>::t_x_array &x,
+ const typename ArrayTypes<DeviceType>::t_tagint_1d &tag,
+ const typename ArrayTypes<DeviceType>::t_int_1d &type,
+ const typename ArrayTypes<DeviceType>::t_int_1d &mask,
+ const typename ArrayTypes<DeviceType>::t_float_1d &q,
+ const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz):
+ _buf(buf),_list(list),_iswap(iswap),
+ _x(x),_tag(tag),_type(type),_mask(mask),_q(q),
+ _dx(dx),_dy(dy),_dz(dz) {}
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ _buf(i,3) = _tag(j);
+ _buf(i,4) = _type(j);
+ _buf(i,5) = _mask(j);
+ _buf(i,6) = _q(j);
+ } else {
+ _buf(i,0) = _x(j,0) + _dx;
+ _buf(i,1) = _x(j,1) + _dy;
+ _buf(i,2) = _x(j,2) + _dz;
+ _buf(i,3) = _tag(j);
+ _buf(i,4) = _type(j);
+ _buf(i,5) = _mask(j);
+ _buf(i,6) = _q(j);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::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)
+{
+ X_FLOAT dx,dy,dz;
+
+ if (pbc_flag != 0) {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if(space==Host) {
+ AtomVecChargeKokkos_PackBorder<LMPHostType,1> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_q,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecChargeKokkos_PackBorder<LMPDeviceType,1> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_q,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+
+ } else {
+ dx = dy = dz = 0;
+ if(space==Host) {
+ AtomVecChargeKokkos_PackBorder<LMPHostType,0> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_q,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecChargeKokkos_PackBorder<LMPDeviceType,0> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_q,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+ }
+ return n*size_border;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_border(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q(j);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q(j);
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_border_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q[j];
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q[j];
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q[j];
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_border_hybrid(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_q[j];
+ }
+ return m;
+}
+
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecChargeKokkos_UnpackBorder {
+ typedef DeviceType device_type;
+
+ const typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
+ typename ArrayTypes<DeviceType>::t_x_array _x;
+ typename ArrayTypes<DeviceType>::t_tagint_1d _tag;
+ typename ArrayTypes<DeviceType>::t_int_1d _type;
+ typename ArrayTypes<DeviceType>::t_int_1d _mask;
+ typename ArrayTypes<DeviceType>::t_float_1d _q;
+ int _first;
+
+
+ AtomVecChargeKokkos_UnpackBorder(
+ const typename ArrayTypes<DeviceType>::t_xfloat_2d_const &buf,
+ typename ArrayTypes<DeviceType>::t_x_array &x,
+ typename ArrayTypes<DeviceType>::t_tagint_1d &tag,
+ typename ArrayTypes<DeviceType>::t_int_1d &type,
+ typename ArrayTypes<DeviceType>::t_int_1d &mask,
+ typename ArrayTypes<DeviceType>::t_float_1d &q,
+ const int& first):
+ _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_q(q),_first(first){
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ _tag(i+_first) = static_cast<int> (_buf(i,3));
+ _type(i+_first) = static_cast<int> (_buf(i,4));
+ _mask(i+_first) = static_cast<int> (_buf(i,5));
+ _q(i+_first) = _buf(i,6);
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::unpack_border_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) {
+ if (first+n >= nmax) {
+ grow(first+n+100);
+ }
+ if(space==Host) {
+ struct AtomVecChargeKokkos_UnpackBorder<LMPHostType>
+ f(buf.view<LMPHostType>(),h_x,h_tag,h_type,h_mask,h_q,first);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ struct AtomVecChargeKokkos_UnpackBorder<LMPDeviceType>
+ f(buf.view<LMPDeviceType>(),d_x,d_tag,d_type,d_mask,d_q,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+ modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::unpack_border(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+
+ for (i = first; i < last; i++) {
+ if (i == nmax) {
+ grow(0);
+ }
+ modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_q[i] = buf[m++];
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::unpack_border_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax) grow(0);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_q[i] = buf[m++];
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::unpack_border_hybrid(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ h_q[i] = buf[m++];
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecChargeKokkos_PackExchangeFunctor {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array_randomread _x;
+ typename AT::t_v_array_randomread _v;
+ typename AT::t_tagint_1d_randomread _tag;
+ typename AT::t_int_1d_randomread _type;
+ typename AT::t_int_1d_randomread _mask;
+ typename AT::t_imageint_1d_randomread _image;
+ typename AT::t_float_1d_randomread _q;
+ typename AT::t_x_array _xw;
+ typename AT::t_v_array _vw;
+ typename AT::t_tagint_1d _tagw;
+ typename AT::t_int_1d _typew;
+ typename AT::t_int_1d _maskw;
+ typename AT::t_imageint_1d _imagew;
+ typename AT::t_float_1d _qw;
+
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d_const _sendlist;
+ typename AT::t_int_1d_const _copylist;
+ int _nlocal,_dim;
+ X_FLOAT _lo,_hi;
+
+ AtomVecChargeKokkos_PackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d sendlist,
+ typename AT::tdual_int_1d copylist,int nlocal, int dim,
+ X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _q(atom->k_q.view<DeviceType>()),
+ _xw(atom->k_x.view<DeviceType>()),
+ _vw(atom->k_v.view<DeviceType>()),
+ _tagw(atom->k_tag.view<DeviceType>()),
+ _typew(atom->k_type.view<DeviceType>()),
+ _maskw(atom->k_mask.view<DeviceType>()),
+ _imagew(atom->k_image.view<DeviceType>()),
+ _qw(atom->k_q.view<DeviceType>()),
+ _sendlist(sendlist.template view<DeviceType>()),
+ _copylist(copylist.template view<DeviceType>()),
+ _nlocal(nlocal),_dim(dim),
+ _lo(lo),_hi(hi){
+ const size_t elements = 12;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
+ buf.template view<DeviceType>().dimension_1())/elements;
+
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &mysend) const {
+ const int i = _sendlist(mysend);
+ _buf(mysend,0) = 12;
+ _buf(mysend,1) = _x(i,0);
+ _buf(mysend,2) = _x(i,1);
+ _buf(mysend,3) = _x(i,2);
+ _buf(mysend,4) = _v(i,0);
+ _buf(mysend,5) = _v(i,1);
+ _buf(mysend,6) = _v(i,2);
+ _buf(mysend,7) = _tag[i];
+ _buf(mysend,8) = _type[i];
+ _buf(mysend,9) = _mask[i];
+ _buf(mysend,10) = _image[i];
+ _buf(mysend,11) = _q[i];
+ const int j = _copylist(mysend);
+
+ if(j>-1) {
+ _xw(i,0) = _x(j,0);
+ _xw(i,1) = _x(j,1);
+ _xw(i,2) = _x(j,2);
+ _vw(i,0) = _v(j,0);
+ _vw(i,1) = _v(j,1);
+ _vw(i,2) = _v(j,2);
+ _tagw(i) = _tag(j);
+ _typew(i) = _type(j);
+ _maskw(i) = _mask(j);
+ _imagew(i) = _image(j);
+ _qw(i) = _q(j);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space,int dim,
+ X_FLOAT lo,X_FLOAT hi )
+{
+ if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*k_buf.view<LMPHostType>().dimension_1())/12) {
+ int newsize = nsend*12/k_buf.view<LMPHostType>().dimension_1()+1;
+ k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
+ }
+ if(space == Host) {
+ AtomVecChargeKokkos_PackExchangeFunctor<LMPHostType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPHostType::fence();
+ return nsend*12;
+ } else {
+ AtomVecChargeKokkos_PackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPDeviceType::fence();
+ return nsend*12;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_exchange(int i, double *buf)
+{
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = h_q[i];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecChargeKokkos_UnpackExchangeFunctor {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array _x;
+ typename AT::t_v_array _v;
+ typename AT::t_tagint_1d _tag;
+ typename AT::t_int_1d _type;
+ typename AT::t_int_1d _mask;
+ typename AT::t_imageint_1d _image;
+ typename AT::t_float_1d _q;
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d _nlocal;
+ int _dim;
+ X_FLOAT _lo,_hi;
+
+ AtomVecChargeKokkos_UnpackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d nlocal,
+ int dim, X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _q(atom->k_q.view<DeviceType>()),
+ _nlocal(nlocal.template view<DeviceType>()),_dim(dim),
+ _lo(lo),_hi(hi){
+ const size_t elements = 12;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*buf.template view<DeviceType>().dimension_1())/elements;
+
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &myrecv) const {
+ X_FLOAT x = _buf(myrecv,_dim+1);
+ if (x >= _lo && x < _hi) {
+ int i = Kokkos::atomic_fetch_add(&_nlocal(0),1);
+ _x(i,0) = _buf(myrecv,1);
+ _x(i,1) = _buf(myrecv,2);
+ _x(i,2) = _buf(myrecv,3);
+ _v(i,0) = _buf(myrecv,4);
+ _v(i,1) = _buf(myrecv,5);
+ _v(i,2) = _buf(myrecv,6);
+ _tag[i] = _buf(myrecv,7);
+ _type[i] = _buf(myrecv,8);
+ _mask[i] = _buf(myrecv,9);
+ _image[i] = _buf(myrecv,10);
+ _q[i] = _buf(myrecv,11);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,
+ int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,
+ ExecutionSpace space) {
+ if(space == Host) {
+ k_count.h_view(0) = nlocal;
+ AtomVecChargeKokkos_UnpackExchangeFunctor<LMPHostType> f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/12,f);
+ LMPHostType::fence();
+ return k_count.h_view(0);
+ } else {
+ k_count.h_view(0) = nlocal;
+ k_count.modify<LMPHostType>();
+ k_count.sync<LMPDeviceType>();
+ AtomVecChargeKokkos_UnpackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/12,f);
+ LMPDeviceType::fence();
+ k_count.modify<LMPDeviceType>();
+ k_count.sync<LMPHostType>();
+
+ return k_count.h_view(0);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::unpack_exchange(double *buf)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) grow(0);
+ modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
+ MASK_MASK | IMAGE_MASK | Q_MASK);
+
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_q[nlocal] = buf[m++];
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->
+ unpack_exchange(nlocal,&buf[m]);
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ size of restart data for all atoms owned by this proc
+ include extra data stored by fixes
+------------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::size_restart()
+{
+ int i;
+
+ int nlocal = atom->nlocal;
+ int n = 12 * nlocal;
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (i = 0; i < nlocal; i++)
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom I's data for restart file including extra quantities
+ xyz must be 1st 3 values, so that read_restart can test on them
+ molecular types may be negative, but write as positive
+------------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_restart(int i, double *buf)
+{
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+
+ buf[m++] = h_q[i];
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ unpack data for one atom from restart file including extra quantities
+------------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::unpack_restart(double *buf)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ grow(0);
+ if (atom->nextra_store)
+ memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
+ }
+
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+
+ h_q[nlocal] = buf[m++];
+
+ double **extra = atom->extra;
+ if (atom->nextra_store) {
+ int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+ for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
+ }
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ create one atom of itype at coord
+ set other values to defaults
+------------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::create_atom(int itype, double *coord)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ //if(nlocal>2) printf("typeA: %i %i\n",type[0],type[1]);
+ atomKK->modified(Host,ALL_MASK);
+ grow(0);
+ //if(nlocal>2) printf("typeB: %i %i\n",type[0],type[1]);
+ }
+ atomKK->modified(Host,ALL_MASK);
+
+ tag[nlocal] = 0;
+ type[nlocal] = itype;
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+ h_mask[nlocal] = 1;
+ h_image[nlocal] = ((imageint) IMGMAX << IMG2BITS) |
+ ((imageint) IMGMAX << IMGBITS) | IMGMAX;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+
+ h_q[nlocal] = 0.0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack one line from Atoms section of data file
+ initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp,
+ char **values)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) grow(0);
+
+ h_tag[nlocal] = atoi(values[0]);
+ if (tag[nlocal] <= 0)
+ error->one(FLERR,"Invalid atom ID in Atoms section of data file");
+
+ h_type[nlocal] = atoi(values[1]);
+ if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
+ error->one(FLERR,"Invalid atom type in Atoms section of data file");
+
+ h_q[nlocal] = atof(values[2]);
+
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+
+ h_image[nlocal] = imagetmp;
+
+ h_mask[nlocal] = 1;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+
+ atom->nlocal++;
+}
+/* ----------------------------------------------------------------------
+ unpack hybrid quantities from one line in Atoms section of data file
+ initialize other atom quantities for this sub-style
+------------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::data_atom_hybrid(int nlocal, char **values)
+{
+ h_q[nlocal] = atof(values[0]);
+
+ return 1;
+}
+/* ----------------------------------------------------------------------
+ pack atom info for data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::pack_data(double **buf)
+{
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ buf[i][0] = h_tag[i];
+ buf[i][1] = h_type[i];
+ buf[i][2] = h_q[i];
+ buf[i][3] = h_x(i,0);
+ buf[i][4] = h_x(i,1);
+ buf[i][5] = h_x(i,2);
+ buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX;
+ buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+ buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ pack hybrid atom info for data file
+------------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::pack_data_hybrid(int i, double *buf)
+{
+ buf[0] = h_q[i];
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ write atom info to data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::write_data(FILE *fp, int n, double **buf)
+{
+ for (int i = 0; i < n; i++)
+ fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
+ (int) buf[i][0],(int) buf[i][1],buf[i][2],buf[i][3],buf[i][4],buf[i][5],
+ (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
+}
+
+/* ----------------------------------------------------------------------
+ write hybrid atom info to data file
+------------------------------------------------------------------------- */
+
+int AtomVecChargeKokkos::write_data_hybrid(FILE *fp, double *buf)
+{
+ fprintf(fp," %-1.16e",buf[0]);
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ return # of bytes of allocated memory
+------------------------------------------------------------------------- */
+
+bigint AtomVecChargeKokkos::memory_usage()
+{
+ bigint bytes = 0;
+
+ if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
+ if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
+ if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
+ if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
+ if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
+ if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
+ if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
+
+ if (atom->memcheck("q")) bytes += memory->usage(q,nmax);
+
+ return bytes;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::sync(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPDeviceType>();
+ if (mask && Q_MASK) atomKK->k_q.sync<LMPDeviceType>();
+ } else {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPHostType>();
+ if (mask && Q_MASK) atomKK->k_q.sync<LMPHostType>();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecChargeKokkos::modified(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPDeviceType>();
+ if (mask && Q_MASK) atomKK->k_q.modify<LMPDeviceType>();
+ } else {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPHostType>();
+ if (mask && Q_MASK) atomKK->k_q.modify<LMPHostType>();
+ }
+}
diff --git a/src/KOKKOS/atom_vec_charge_kokkos.h b/src/KOKKOS/atom_vec_charge_kokkos.h
new file mode 100644
index 0000000000..98f0f363b9
--- /dev/null
+++ b/src/KOKKOS/atom_vec_charge_kokkos.h
@@ -0,0 +1,126 @@
+/* ----------------------------------------------------------------------
+ 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 ATOM_CLASS
+
+AtomStyle(charge/kk,AtomVecChargeKokkos)
+
+#else
+
+#ifndef LMP_ATOM_VEC_CHARGE_KOKKOS_H
+#define LMP_ATOM_VEC_CHARGE_KOKKOS_H
+
+#include "atom_vec_kokkos.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecChargeKokkos : public AtomVecKokkos {
+ public:
+ AtomVecChargeKokkos(class LAMMPS *);
+ virtual ~AtomVecChargeKokkos() {}
+ void grow(int);
+ void copy(int, int, int);
+ int pack_comm(int, int *, double *, int, int *);
+ int pack_comm_vel(int, int *, double *, int, int *);
+ void unpack_comm(int, int, double *);
+ void unpack_comm_vel(int, int, double *);
+ int pack_reverse(int, int, double *);
+ void unpack_reverse(int, int *, double *);
+ int pack_border(int, int *, double *, int, int *);
+ int pack_border_vel(int, int *, double *, int, int *);
+ int pack_border_hybrid(int, int *, double *);
+ void unpack_border(int, int, double *);
+ void unpack_border_vel(int, int, double *);
+ int unpack_border_hybrid(int, int, double *);
+ int pack_exchange(int, double *);
+ int unpack_exchange(double *);
+ int size_restart();
+ int pack_restart(int, double *);
+ int unpack_restart(double *);
+ void create_atom(int, double *);
+ void data_atom(double *, tagint, char **);
+ int data_atom_hybrid(int , char **);
+ void pack_data(double **);
+ int pack_data_hybrid(int, double *);
+ void write_data(FILE *, int, double **);
+ int write_data_hybrid(FILE *, double *);
+ bigint memory_usage();
+
+ void grow_reset();
+ int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag, const int pbc[]);
+ void unpack_comm_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf);
+ int pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap, const int nfirst,
+ const int &pbc_flag, const int pbc[]);
+ int 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);
+ void unpack_border_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf,
+ ExecutionSpace space);
+ int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space, int dim,
+ X_FLOAT lo, X_FLOAT hi);
+ int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
+ int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
+ ExecutionSpace space);
+
+ void sync(ExecutionSpace space, unsigned int mask);
+ void modified(ExecutionSpace space, unsigned int mask);
+
+ protected:
+ tagint *tag;
+ int *type,*mask;
+ imageint *image;
+ double **x,**v,**f;
+
+ double *q;
+
+ DAT::t_tagint_1d d_tag;
+ HAT::t_tagint_1d h_tag;
+
+ DAT::t_int_1d d_type, d_mask;
+ HAT::t_int_1d h_type, h_mask;
+
+ DAT::t_imageint_1d d_image;
+ HAT::t_imageint_1d h_image;
+
+ DAT::t_x_array d_x;
+ DAT::t_v_array d_v;
+ DAT::t_f_array d_f;
+ HAT::t_x_array h_x;
+ HAT::t_v_array h_v;
+ HAT::t_f_array h_f;
+
+ DAT::t_float_1d d_q;
+
+ HAT::t_float_1d h_q;
+
+ DAT::tdual_int_1d k_count;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/atom_vec_full_kokkos.cpp b/src/KOKKOS/atom_vec_full_kokkos.cpp
new file mode 100644
index 0000000000..684c81c616
--- /dev/null
+++ b/src/KOKKOS/atom_vec_full_kokkos.cpp
@@ -0,0 +1,2321 @@
+/* ----------------------------------------------------------------------
+ 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 "stdlib.h"
+#include "atom_vec_full_kokkos.h"
+#include "atom_kokkos.h"
+#include "comm_kokkos.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "atom_masks.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecFullKokkos::AtomVecFullKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
+{
+ molecular = 1;
+ bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 1;
+ mass_type = 1;
+
+ comm_x_only = comm_f_only = 1;
+ size_forward = 3;
+ size_reverse = 3;
+ size_border = 8;
+ size_velocity = 3;
+ size_data_atom = 7;
+ size_data_vel = 4;
+ xcol_data = 5;
+
+ atom->molecule_flag = atom->q_flag = 1;
+
+ k_count = DAT::tdual_int_1d("atom::k_count",1);
+ atomKK = (AtomKokkos *) atom;
+ commKK = (CommKokkos *) comm;
+}
+
+/* ----------------------------------------------------------------------
+ grow atom arrays
+ n = 0 grows arrays by DELTA
+ n > 0 allocates arrays to size n
+------------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::grow(int n)
+{
+ if (n == 0) nmax += DELTA;
+ else nmax = n;
+ atomKK->nmax = nmax;
+ if (nmax < 0 || nmax > MAXSMALLINT)
+ error->one(FLERR,"Per-processor system is too big");
+
+ sync(Device,ALL_MASK);
+ modified(Device,ALL_MASK);
+
+ memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
+ memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
+ memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
+ memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
+
+ memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
+ memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
+ memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
+
+ memory->grow_kokkos(atomKK->k_q,atomKK->q,nmax,"atom:q");
+ memory->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
+
+ memory->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
+ memory->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
+ "atom:special");
+ memory->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
+ memory->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
+ "atom:bond_type");
+ memory->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
+ "atom:bond_atom");
+
+ memory->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
+ memory->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
+ "atom:angle_type");
+ memory->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
+ "atom:angle_atom1");
+ memory->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
+ "atom:angle_atom2");
+ memory->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
+ "atom:angle_atom3");
+
+ memory->grow_kokkos(atomKK->k_num_dihedral,atomKK->num_dihedral,nmax,"atom:num_dihedral");
+ memory->grow_kokkos(atomKK->k_dihedral_type,atomKK->dihedral_type,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_type");
+ memory->grow_kokkos(atomKK->k_dihedral_atom1,atomKK->dihedral_atom1,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_atom1");
+ memory->grow_kokkos(atomKK->k_dihedral_atom2,atomKK->dihedral_atom2,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_atom2");
+ memory->grow_kokkos(atomKK->k_dihedral_atom3,atomKK->dihedral_atom3,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_atom3");
+ memory->grow_kokkos(atomKK->k_dihedral_atom4,atomKK->dihedral_atom4,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_atom4");
+
+ memory->grow_kokkos(atomKK->k_num_improper,atomKK->num_improper,nmax,"atom:num_improper");
+ memory->grow_kokkos(atomKK->k_improper_type,atomKK->improper_type,nmax,
+ atomKK->improper_per_atom,"atom:improper_type");
+ memory->grow_kokkos(atomKK->k_improper_atom1,atomKK->improper_atom1,nmax,
+ atomKK->improper_per_atom,"atom:improper_atom1");
+ memory->grow_kokkos(atomKK->k_improper_atom2,atomKK->improper_atom2,nmax,
+ atomKK->improper_per_atom,"atom:improper_atom2");
+ memory->grow_kokkos(atomKK->k_improper_atom3,atomKK->improper_atom3,nmax,
+ atomKK->improper_per_atom,"atom:improper_atom3");
+ memory->grow_kokkos(atomKK->k_improper_atom4,atomKK->improper_atom4,nmax,
+ atomKK->improper_per_atom,"atom:improper_atom4");
+
+ grow_reset();
+ sync(Host,ALL_MASK);
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
+}
+
+/* ----------------------------------------------------------------------
+ reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::grow_reset()
+{
+ tag = atomKK->tag;
+ d_tag = atomKK->k_tag.d_view;
+ h_tag = atomKK->k_tag.h_view;
+
+ type = atomKK->type;
+ d_type = atomKK->k_type.d_view;
+ h_type = atomKK->k_type.h_view;
+ mask = atomKK->mask;
+ d_mask = atomKK->k_mask.d_view;
+ h_mask = atomKK->k_mask.h_view;
+ image = atomKK->image;
+ d_image = atomKK->k_image.d_view;
+ h_image = atomKK->k_image.h_view;
+
+ x = atomKK->x;
+ d_x = atomKK->k_x.d_view;
+ h_x = atomKK->k_x.h_view;
+ v = atomKK->v;
+ d_v = atomKK->k_v.d_view;
+ h_v = atomKK->k_v.h_view;
+ f = atomKK->f;
+ d_f = atomKK->k_f.d_view;
+ h_f = atomKK->k_f.h_view;
+
+ q = atomKK->q;
+ d_q = atomKK->k_q.d_view;
+ h_q = atomKK->k_q.h_view;
+
+ molecule = atomKK->molecule;
+ d_molecule = atomKK->k_molecule.d_view;
+ h_molecule = atomKK->k_molecule.h_view;
+
+ nspecial = atomKK->nspecial;
+ d_nspecial = atomKK->k_nspecial.d_view;
+ h_nspecial = atomKK->k_nspecial.h_view;
+ special = atomKK->special;
+ d_special = atomKK->k_special.d_view;
+ h_special = atomKK->k_special.h_view;
+
+ num_bond = atomKK->num_bond;
+ d_num_bond = atomKK->k_num_bond.d_view;
+ h_num_bond = atomKK->k_num_bond.h_view;
+ bond_type = atomKK->bond_type;
+ d_bond_type = atomKK->k_bond_type.d_view;
+ h_bond_type = atomKK->k_bond_type.h_view;
+ bond_atom = atomKK->bond_atom;
+ d_bond_atom = atomKK->k_bond_atom.d_view;
+ h_bond_atom = atomKK->k_bond_atom.h_view;
+
+ num_angle = atomKK->num_angle;
+ d_num_angle = atomKK->k_num_angle.d_view;
+ h_num_angle = atomKK->k_num_angle.h_view;
+ angle_type = atomKK->angle_type;
+ d_angle_type = atomKK->k_angle_type.d_view;
+ h_angle_type = atomKK->k_angle_type.h_view;
+ angle_atom1 = atomKK->angle_atom1;
+ d_angle_atom1 = atomKK->k_angle_atom1.d_view;
+ h_angle_atom1 = atomKK->k_angle_atom1.h_view;
+ angle_atom2 = atomKK->angle_atom2;
+ d_angle_atom2 = atomKK->k_angle_atom2.d_view;
+ h_angle_atom2 = atomKK->k_angle_atom2.h_view;
+ angle_atom3 = atomKK->angle_atom3;
+ d_angle_atom3 = atomKK->k_angle_atom3.d_view;
+ h_angle_atom3 = atomKK->k_angle_atom3.h_view;
+
+ num_dihedral = atomKK->num_dihedral;
+ d_num_dihedral = atomKK->k_num_dihedral.d_view;
+ h_num_dihedral = atomKK->k_num_dihedral.h_view;
+ dihedral_type = atomKK->dihedral_type;
+ d_dihedral_type = atomKK->k_dihedral_type.d_view;
+ h_dihedral_type = atomKK->k_dihedral_type.h_view;
+ dihedral_atom1 = atomKK->dihedral_atom1;
+ d_dihedral_atom1 = atomKK->k_dihedral_atom1.d_view;
+ h_dihedral_atom1 = atomKK->k_dihedral_atom1.h_view;
+ dihedral_atom2 = atomKK->dihedral_atom2;
+ d_dihedral_atom2 = atomKK->k_dihedral_atom2.d_view;
+ h_dihedral_atom2 = atomKK->k_dihedral_atom2.h_view;
+ dihedral_atom3 = atomKK->dihedral_atom3;
+ d_dihedral_atom3 = atomKK->k_dihedral_atom3.d_view;
+ h_dihedral_atom3 = atomKK->k_dihedral_atom3.h_view;
+ dihedral_atom4 = atomKK->dihedral_atom4;
+ d_dihedral_atom4 = atomKK->k_dihedral_atom4.d_view;
+ h_dihedral_atom4 = atomKK->k_dihedral_atom4.h_view;
+
+ num_improper = atomKK->num_improper;
+ d_num_improper = atomKK->k_num_improper.d_view;
+ h_num_improper = atomKK->k_num_improper.h_view;
+ improper_type = atomKK->improper_type;
+ d_improper_type = atomKK->k_improper_type.d_view;
+ h_improper_type = atomKK->k_improper_type.h_view;
+ improper_atom1 = atomKK->improper_atom1;
+ d_improper_atom1 = atomKK->k_improper_atom1.d_view;
+ h_improper_atom1 = atomKK->k_improper_atom1.h_view;
+ improper_atom2 = atomKK->improper_atom2;
+ d_improper_atom2 = atomKK->k_improper_atom2.d_view;
+ h_improper_atom2 = atomKK->k_improper_atom2.h_view;
+ improper_atom3 = atomKK->improper_atom3;
+ d_improper_atom3 = atomKK->k_improper_atom3.d_view;
+ h_improper_atom3 = atomKK->k_improper_atom3.h_view;
+ improper_atom4 = atomKK->improper_atom4;
+ d_improper_atom4 = atomKK->k_improper_atom4.d_view;
+ h_improper_atom4 = atomKK->k_improper_atom4.h_view;
+}
+
+/* ----------------------------------------------------------------------
+ copy atom I info to atom J
+------------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::copy(int i, int j, int delflag)
+{
+ int k;
+
+ h_tag[j] = h_tag[i];
+ h_type[j] = h_type[i];
+ mask[j] = mask[i];
+ h_image[j] = h_image[i];
+ h_x(j,0) = h_x(i,0);
+ h_x(j,1) = h_x(i,1);
+ h_x(j,2) = h_x(i,2);
+ h_v(j,0) = h_v(i,0);
+ h_v(j,1) = h_v(i,1);
+ h_v(j,2) = h_v(i,2);
+
+ h_q[j] = h_q[i];
+ h_molecule(j) = h_molecule(i);
+
+ h_num_bond(j) = h_num_bond(i);
+ for (k = 0; k < h_num_bond(j); k++) {
+ h_bond_type(j,k) = h_bond_type(i,k);
+ h_bond_atom(j,k) = h_bond_atom(i,k);
+ }
+
+ h_nspecial(j,0) = h_nspecial(i,0);
+ h_nspecial(j,1) = h_nspecial(i,1);
+ h_nspecial(j,2) = h_nspecial(i,2);
+ for (k = 0; k < h_nspecial(j,2); k++)
+ h_special(j,k) = h_special(i,k);
+
+ h_num_angle(j) = h_num_angle(i);
+ for (k = 0; k < h_num_angle(j); k++) {
+ h_angle_type(j,k) = h_angle_type(i,k);
+ h_angle_atom1(j,k) = h_angle_atom1(i,k);
+ h_angle_atom2(j,k) = h_angle_atom2(i,k);
+ h_angle_atom3(j,k) = h_angle_atom3(i,k);
+ }
+
+ h_num_dihedral(j) = h_num_dihedral(i);
+ for (k = 0; k < h_num_dihedral(j); k++) {
+ h_dihedral_type(j,k) = h_dihedral_type(i,k);
+ h_dihedral_atom1(j,k) = h_dihedral_atom1(i,k);
+ h_dihedral_atom2(j,k) = h_dihedral_atom2(i,k);
+ h_dihedral_atom3(j,k) = h_dihedral_atom3(i,k);
+ h_dihedral_atom4(j,k) = h_dihedral_atom4(i,k);
+ }
+
+ h_num_improper(j) = h_num_improper(i);
+ for (k = 0; k < h_num_improper(j); k++) {
+ h_improper_type(j,k) = h_improper_type(i,k);
+ h_improper_atom1(j,k) = h_improper_atom1(i,k);
+ h_improper_atom2(j,k) = h_improper_atom2(i,k);
+ h_improper_atom3(j,k) = h_improper_atom3(i,k);
+ h_improper_atom4(j,k) = h_improper_atom4(i,k);
+ }
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecFullKokkos_PackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_um _buf;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecFullKokkos_PackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ const size_t maxsend = (buf.view<DeviceType>().dimension_0()
+ *buf.view<DeviceType>().dimension_1())/3;
+ const size_t elements = 3;
+ buffer_view<DeviceType>(_buf,buf,maxsend,elements);
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_comm_kokkos(const int &n,
+ const DAT::tdual_int_2d &list,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag,
+ const int* const pbc)
+{
+ // Check whether to always run forward communication on the host
+ // Choose correct forward PackComm kernel
+
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecFullKokkos_PackComm<LMPHostType,1,1>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecFullKokkos_PackComm<LMPHostType,1,0>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecFullKokkos_PackComm<LMPHostType,0,1>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecFullKokkos_PackComm<LMPHostType,0,0>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecFullKokkos_PackComm<LMPDeviceType,1,1>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecFullKokkos_PackComm<LMPDeviceType,1,0>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecFullKokkos_PackComm<LMPDeviceType,0,1>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecFullKokkos_PackComm<LMPDeviceType,0,0>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+
+ return n*size_forward;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecFullKokkos_PackCommSelf {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_x_array _xw;
+ int _nfirst;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecFullKokkos_PackCommSelf(
+ const typename DAT::tdual_x_array &x,
+ const int &nfirst,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_xw(x.view<DeviceType>()),_nfirst(nfirst),
+ _list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _xw(i+_nfirst,0) = _x(j,0);
+ _xw(i+_nfirst,1) = _x(j,1);
+ _xw(i+_nfirst,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap,
+ const int nfirst, const int &pbc_flag,
+ const int* const pbc) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecFullKokkos_PackCommSelf<LMPHostType,1,1>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecFullKokkos_PackCommSelf<LMPHostType,1,0>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecFullKokkos_PackCommSelf<LMPHostType,0,1>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecFullKokkos_PackCommSelf<LMPHostType,0,0>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecFullKokkos_PackCommSelf<LMPDeviceType,1,1>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecFullKokkos_PackCommSelf<LMPDeviceType,1,0>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecFullKokkos_PackCommSelf<LMPDeviceType,0,1>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecFullKokkos_PackCommSelf<LMPDeviceType,0,0>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+ return n*3;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecFullKokkos_UnpackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
+ int _first;
+
+ AtomVecFullKokkos_UnpackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const int& first):_x(x.view<DeviceType>()),_buf(buf.view<DeviceType>()),
+ _first(first) {};
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::unpack_comm_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf ) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ struct AtomVecFullKokkos_UnpackComm<LMPHostType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ struct AtomVecFullKokkos_UnpackComm<LMPDeviceType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_comm_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::unpack_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::unpack_comm_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_reverse(int n, int first, double *buf)
+{
+ if(n > 0)
+ sync(Host,F_MASK);
+
+ int m = 0;
+ const int last = first + n;
+ for (int i = first; i < last; i++) {
+ buf[m++] = h_f(i,0);
+ buf[m++] = h_f(i,1);
+ buf[m++] = h_f(i,2);
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::unpack_reverse(int n, int *list, double *buf)
+{
+ if(n > 0)
+ modified(Host,F_MASK);
+
+ int m = 0;
+ for (int i = 0; i < n; i++) {
+ const int j = list[i];
+ h_f(j,0) += buf[m++];
+ h_f(j,1) += buf[m++];
+ h_f(j,2) += buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG>
+struct AtomVecFullKokkos_PackBorder {
+ union ubuf {
+ double d;
+ int64_t i;
+ ubuf(double arg) : d(arg) {}
+ ubuf(int64_t arg) : i(arg) {}
+ ubuf(int arg) : i(arg) {}
+ };
+
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+
+ typename AT::t_xfloat_2d _buf;
+ const typename AT::t_int_2d_const _list;
+ const int _iswap;
+ const typename AT::t_x_array_randomread _x;
+ const typename AT::t_tagint_1d _tag;
+ const typename AT::t_int_1d _type;
+ const typename AT::t_int_1d _mask;
+ const typename AT::t_float_1d _q;
+ const typename AT::t_tagint_1d _molecule;
+ X_FLOAT _dx,_dy,_dz;
+
+ AtomVecFullKokkos_PackBorder(
+ const typename AT::t_xfloat_2d &buf,
+ const typename AT::t_int_2d_const &list,
+ const int & iswap,
+ const typename AT::t_x_array &x,
+ const typename AT::t_tagint_1d &tag,
+ const typename AT::t_int_1d &type,
+ const typename AT::t_int_1d &mask,
+ const typename AT::t_float_1d &q,
+ const typename AT::t_tagint_1d &molecule,
+ const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz):
+ _buf(buf),_list(list),_iswap(iswap),
+ _x(x),_tag(tag),_type(type),_mask(mask),_q(q),_molecule(molecule),
+ _dx(dx),_dy(dy),_dz(dz) {}
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ _buf(i,3) = ubuf(_tag(j)).d;
+ _buf(i,4) = ubuf(_type(j)).d;
+ _buf(i,5) = ubuf(_mask(j)).d;
+ _buf(i,6) = _q(j);
+ _buf(i,7) = ubuf(_molecule(j)).d;
+ } else {
+ _buf(i,0) = _x(j,0) + _dx;
+ _buf(i,1) = _x(j,1) + _dy;
+ _buf(i,2) = _x(j,2) + _dz;
+ _buf(i,3) = ubuf(_tag(j)).d;
+ _buf(i,4) = ubuf(_type(j)).d;
+ _buf(i,5) = ubuf(_mask(j)).d;
+ _buf(i,6) = _q(j);
+ _buf(i,7) = ubuf(_molecule(j)).d;
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::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)
+{
+ X_FLOAT dx,dy,dz;
+
+ if (pbc_flag != 0) {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if(space==Host) {
+ AtomVecFullKokkos_PackBorder<LMPHostType,1> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_q,h_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecFullKokkos_PackBorder<LMPDeviceType,1> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_q,d_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+
+ } else {
+ dx = dy = dz = 0;
+ if(space==Host) {
+ AtomVecFullKokkos_PackBorder<LMPHostType,0> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_q,h_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecFullKokkos_PackBorder<LMPDeviceType,0> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_q,d_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+ }
+ return n*size_border;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_border(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q(j);
+ buf[m++] = ubuf(h_molecule(j)).d;
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q(j);
+ buf[m++] = ubuf(h_molecule(j)).d;
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_border_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q(j);
+ buf[m++] = ubuf(h_molecule(j)).d;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q(j);
+ buf[m++] = ubuf(h_molecule(j)).d;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = h_q(j);
+ buf[m++] = ubuf(h_molecule(j)).d;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_border_hybrid(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_q(j);
+ buf[m++] = ubuf(h_molecule(j)).d;
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecFullKokkos_UnpackBorder {
+ union ubuf {
+ double d;
+ int64_t i;
+ ubuf(double arg) : d(arg) {}
+ ubuf(int64_t arg) : i(arg) {}
+ ubuf(int arg) : i(arg) {}
+ };
+
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+
+ const typename AT::t_xfloat_2d_const _buf;
+ typename AT::t_x_array _x;
+ typename AT::t_tagint_1d _tag;
+ typename AT::t_int_1d _type;
+ typename AT::t_int_1d _mask;
+ typename AT::t_float_1d _q;
+ typename AT::t_tagint_1d _molecule;
+ int _first;
+
+
+ AtomVecFullKokkos_UnpackBorder(
+ const typename AT::t_xfloat_2d_const &buf,
+ typename AT::t_x_array &x,
+ typename AT::t_tagint_1d &tag,
+ typename AT::t_int_1d &type,
+ typename AT::t_int_1d &mask,
+ typename AT::t_float_1d &q,
+ typename AT::t_tagint_1d &molecule,
+ const int& first):
+ _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_q(q),_molecule(molecule),
+ _first(first){
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ _tag(i+_first) = (tagint) ubuf(_buf(i,3)).i;
+ _type(i+_first) = (int) ubuf(_buf(i,4)).i;
+ _mask(i+_first) = (int) ubuf(_buf(i,5)).i;
+ _q(i+_first) = _buf(i,6);
+ _molecule(i+_first) = (tagint) ubuf(_buf(i,7)).i;
+
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::unpack_border_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf,
+ ExecutionSpace space) {
+ modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK|MOLECULE_MASK);
+ while (first+n >= nmax) grow(0);
+ modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK|MOLECULE_MASK);
+ if(space==Host) {
+ struct AtomVecFullKokkos_UnpackBorder<LMPHostType>
+ f(buf.view<LMPHostType>(),h_x,h_tag,h_type,h_mask,h_q,h_molecule,first);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ struct AtomVecFullKokkos_UnpackBorder<LMPDeviceType>
+ f(buf.view<LMPDeviceType>(),d_x,d_tag,d_type,d_mask,d_q,d_molecule,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::unpack_border(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ if(n > 0)
+ modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK|MOLECULE_MASK);
+ for (i = first; i < last; i++) {
+ if (i == nmax) grow(0);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_q(i) = buf[m++];
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::unpack_border_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax) grow(0);
+ modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK|MOLECULE_MASK);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_q(i) = buf[m++];
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::unpack_border_hybrid(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_q(i) = buf[m++];
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecFullKokkos_PackExchangeFunctor {
+
+ union ubuf {
+ double d;
+ int64_t i;
+ ubuf(double arg) : d(arg) {}
+ ubuf(int64_t arg) : i(arg) {}
+ ubuf(int arg) : i(arg) {}
+ };
+
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array_randomread _x;
+ typename AT::t_v_array_randomread _v;
+ typename AT::t_tagint_1d_randomread _tag;
+ typename AT::t_int_1d_randomread _type;
+ typename AT::t_int_1d_randomread _mask;
+ typename AT::t_imageint_1d_randomread _image;
+ typename AT::t_float_1d_randomread _q;
+ typename AT::t_tagint_1d_randomread _molecule;
+ typename AT::t_int_2d_randomread _nspecial;
+ typename AT::t_tagint_2d_randomread _special;
+ typename AT::t_int_1d_randomread _num_bond;
+ typename AT::t_int_2d_randomread _bond_type;
+ typename AT::t_tagint_2d_randomread _bond_atom;
+ typename AT::t_int_1d_randomread _num_angle;
+ typename AT::t_int_2d_randomread _angle_type;
+ typename AT::t_tagint_2d_randomread _angle_atom1,_angle_atom2,_angle_atom3;
+ typename AT::t_int_1d_randomread _num_dihedral;
+ typename AT::t_int_2d_randomread _dihedral_type;
+ typename AT::t_tagint_2d_randomread _dihedral_atom1,_dihedral_atom2,
+ _dihedral_atom3,_dihedral_atom4;
+ typename AT::t_int_1d_randomread _num_improper;
+ typename AT::t_int_2d_randomread _improper_type;
+ typename AT::t_tagint_2d_randomread _improper_atom1,_improper_atom2,
+ _improper_atom3,_improper_atom4;
+ typename AT::t_x_array _xw;
+ typename AT::t_v_array _vw;
+ typename AT::t_tagint_1d _tagw;
+ typename AT::t_int_1d _typew;
+ typename AT::t_int_1d _maskw;
+ typename AT::t_imageint_1d _imagew;
+ typename AT::t_float_1d _qw;
+ typename AT::t_tagint_1d _moleculew;
+ typename AT::t_int_2d _nspecialw;
+ typename AT::t_tagint_2d _specialw;
+ typename AT::t_int_1d _num_bondw;
+ typename AT::t_int_2d _bond_typew;
+ typename AT::t_tagint_2d _bond_atomw;
+ typename AT::t_int_1d _num_anglew;
+ typename AT::t_int_2d _angle_typew;
+ typename AT::t_tagint_2d _angle_atom1w,_angle_atom2w,_angle_atom3w;
+ typename AT::t_int_1d _num_dihedralw;
+ typename AT::t_int_2d _dihedral_typew;
+ typename AT::t_tagint_2d _dihedral_atom1w,_dihedral_atom2w,
+ _dihedral_atom3w,_dihedral_atom4w;
+ typename AT::t_int_1d _num_improperw;
+ typename AT::t_int_2d _improper_typew;
+ typename AT::t_tagint_2d _improper_atom1w,_improper_atom2w,
+ _improper_atom3w,_improper_atom4w;
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d_const _sendlist;
+ typename AT::t_int_1d_const _copylist;
+ int _nlocal,_dim;
+ X_FLOAT _lo,_hi;
+ size_t elements;
+
+ AtomVecFullKokkos_PackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d sendlist,
+ typename AT::tdual_int_1d copylist,int nlocal, int dim,
+ X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _q(atom->k_q.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _num_angle(atom->k_num_angle.view<DeviceType>()),
+ _angle_type(atom->k_angle_type.view<DeviceType>()),
+ _angle_atom1(atom->k_angle_atom1.view<DeviceType>()),
+ _angle_atom2(atom->k_angle_atom2.view<DeviceType>()),
+ _angle_atom3(atom->k_angle_atom3.view<DeviceType>()),
+ _num_dihedral(atom->k_num_dihedral.view<DeviceType>()),
+ _dihedral_type(atom->k_dihedral_type.view<DeviceType>()),
+ _dihedral_atom1(atom->k_dihedral_atom1.view<DeviceType>()),
+ _dihedral_atom2(atom->k_dihedral_atom2.view<DeviceType>()),
+ _dihedral_atom3(atom->k_dihedral_atom3.view<DeviceType>()),
+ _dihedral_atom4(atom->k_dihedral_atom4.view<DeviceType>()),
+ _num_improper(atom->k_num_improper.view<DeviceType>()),
+ _improper_type(atom->k_improper_type.view<DeviceType>()),
+ _improper_atom1(atom->k_improper_atom1.view<DeviceType>()),
+ _improper_atom2(atom->k_improper_atom2.view<DeviceType>()),
+ _improper_atom3(atom->k_improper_atom3.view<DeviceType>()),
+ _improper_atom4(atom->k_improper_atom4.view<DeviceType>()),
+ _xw(atom->k_x.view<DeviceType>()),
+ _vw(atom->k_v.view<DeviceType>()),
+ _tagw(atom->k_tag.view<DeviceType>()),
+ _typew(atom->k_type.view<DeviceType>()),
+ _maskw(atom->k_mask.view<DeviceType>()),
+ _imagew(atom->k_image.view<DeviceType>()),
+ _qw(atom->k_q.view<DeviceType>()),
+ _moleculew(atom->k_molecule.view<DeviceType>()),
+ _nspecialw(atom->k_nspecial.view<DeviceType>()),
+ _specialw(atom->k_special.view<DeviceType>()),
+ _num_bondw(atom->k_num_bond.view<DeviceType>()),
+ _bond_typew(atom->k_bond_type.view<DeviceType>()),
+ _bond_atomw(atom->k_bond_atom.view<DeviceType>()),
+ _num_anglew(atom->k_num_angle.view<DeviceType>()),
+ _angle_typew(atom->k_angle_type.view<DeviceType>()),
+ _angle_atom1w(atom->k_angle_atom1.view<DeviceType>()),
+ _angle_atom2w(atom->k_angle_atom2.view<DeviceType>()),
+ _angle_atom3w(atom->k_angle_atom3.view<DeviceType>()),
+ _num_dihedralw(atom->k_num_dihedral.view<DeviceType>()),
+ _dihedral_typew(atom->k_dihedral_type.view<DeviceType>()),
+ _dihedral_atom1w(atom->k_dihedral_atom1.view<DeviceType>()),
+ _dihedral_atom2w(atom->k_dihedral_atom2.view<DeviceType>()),
+ _dihedral_atom3w(atom->k_dihedral_atom3.view<DeviceType>()),
+ _dihedral_atom4w(atom->k_dihedral_atom4.view<DeviceType>()),
+ _num_improperw(atom->k_num_improper.view<DeviceType>()),
+ _improper_typew(atom->k_improper_type.view<DeviceType>()),
+ _improper_atom1w(atom->k_improper_atom1.view<DeviceType>()),
+ _improper_atom2w(atom->k_improper_atom2.view<DeviceType>()),
+ _improper_atom3w(atom->k_improper_atom3.view<DeviceType>()),
+ _improper_atom4w(atom->k_improper_atom4.view<DeviceType>()),
+ _sendlist(sendlist.template view<DeviceType>()),
+ _copylist(copylist.template view<DeviceType>()),
+ _nlocal(nlocal),_dim(dim),
+ _lo(lo),_hi(hi){
+ // 3 comp of x, 3 comp of v, 1 tag, 1 type, 1 mask, 1 image, 1 molecule, 3 nspecial,
+ // maxspecial special, 1 num_bond, bond_per_atom bond_type, bond_per_atom bond_atom,
+ // 1 num_angle, angle_per_atom angle_type, angle_per_atom angle_atom1, angle_atom2,
+ // and angle_atom3
+ // 1 num_dihedral, dihedral_per_atom dihedral_type, 4*dihedral_per_atom
+ // 1 num_improper, 5*improper_per_atom
+ // 1 charge
+ // 1 to store buffer length
+ elements = 20+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
+ buf.template view<DeviceType>().dimension_1())/elements;
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &mysend) const {
+ int k;
+ const int i = _sendlist(mysend);
+ _buf(mysend,0) = elements;
+ int m = 1;
+ _buf(mysend,m++) = _x(i,0);
+ _buf(mysend,m++) = _x(i,1);
+ _buf(mysend,m++) = _x(i,2);
+ _buf(mysend,m++) = _v(i,0);
+ _buf(mysend,m++) = _v(i,1);
+ _buf(mysend,m++) = _v(i,2);
+ _buf(mysend,m++) = ubuf(_tag(i)).d;
+ _buf(mysend,m++) = ubuf(_type(i)).d;
+ _buf(mysend,m++) = ubuf(_mask(i)).d;
+ _buf(mysend,m++) = ubuf(_image(i)).d;
+ _buf(mysend,m++) = _q(i);
+ _buf(mysend,m++) = ubuf(_molecule(i)).d;
+ _buf(mysend,m++) = ubuf(_num_bond(i)).d;
+ for (k = 0; k < _num_bond(i); k++) {
+ _buf(mysend,m++) = ubuf(_bond_type(i,k)).d;
+ _buf(mysend,m++) = ubuf(_bond_atom(i,k)).d;
+ }
+ _buf(mysend,m++) = ubuf(_num_angle(i)).d;
+ for (k = 0; k < _num_angle(i); k++) {
+ _buf(mysend,m++) = ubuf(_angle_type(i,k)).d;
+ _buf(mysend,m++) = ubuf(_angle_atom1(i,k)).d;
+ _buf(mysend,m++) = ubuf(_angle_atom2(i,k)).d;
+ _buf(mysend,m++) = ubuf(_angle_atom3(i,k)).d;
+ }
+ _buf(mysend,m++) = ubuf(_num_dihedral(i)).d;
+ for (k = 0; k < _num_dihedral(i); k++) {
+ _buf(mysend,m++) = ubuf(_dihedral_type(i,k)).d;
+ _buf(mysend,m++) = ubuf(_dihedral_atom1(i,k)).d;
+ _buf(mysend,m++) = ubuf(_dihedral_atom2(i,k)).d;
+ _buf(mysend,m++) = ubuf(_dihedral_atom3(i,k)).d;
+ _buf(mysend,m++) = ubuf(_dihedral_atom4(i,k)).d;
+ }
+ _buf(mysend,m++) = ubuf(_num_improper(i)).d;
+ for (k = 0; k < _num_improper(i); k++) {
+ _buf(mysend,m++) = ubuf(_improper_type(i,k)).d;
+ _buf(mysend,m++) = ubuf(_improper_atom1(i,k)).d;
+ _buf(mysend,m++) = ubuf(_improper_atom2(i,k)).d;
+ _buf(mysend,m++) = ubuf(_improper_atom3(i,k)).d;
+ _buf(mysend,m++) = ubuf(_improper_atom4(i,k)).d;
+ }
+
+ _buf(mysend,m++) = ubuf(_nspecial(i,0)).d;
+ _buf(mysend,m++) = ubuf(_nspecial(i,1)).d;
+ _buf(mysend,m++) = ubuf(_nspecial(i,2)).d;
+ for (k = 0; k < _nspecial(i,2); k++)
+ _buf(mysend,m++) = ubuf(_special(i,k)).d;
+
+ const int j = _copylist(mysend);
+
+ if(j>-1) {
+ _xw(i,0) = _x(j,0);
+ _xw(i,1) = _x(j,1);
+ _xw(i,2) = _x(j,2);
+ _vw(i,0) = _v(j,0);
+ _vw(i,1) = _v(j,1);
+ _vw(i,2) = _v(j,2);
+ _tagw(i) = _tag(j);
+ _typew(i) = _type(j);
+ _maskw(i) = _mask(j);
+ _imagew(i) = _image(j);
+ _qw(i) = _q(j);
+ _moleculew(i) = _molecule(j);
+ _num_bondw(i) = _num_bond(j);
+ for (k = 0; k < _num_bond(j); k++) {
+ _bond_typew(i,k) = _bond_type(j,k);
+ _bond_atomw(i,k) = _bond_atom(j,k);
+ }
+ _num_anglew(i) = _num_angle(j);
+ for (k = 0; k < _num_angle(j); k++) {
+ _angle_typew(i,k) = _angle_type(j,k);
+ _angle_atom1w(i,k) = _angle_atom1(j,k);
+ _angle_atom2w(i,k) = _angle_atom2(j,k);
+ _angle_atom3w(i,k) = _angle_atom3(j,k);
+ }
+ _num_dihedralw(i) = _num_dihedral(j);
+ for (k = 0; k < _num_dihedral(j); k++) {
+ _dihedral_typew(i,k) = _dihedral_type(j,k);
+ _dihedral_atom1w(i,k) = _dihedral_atom1(j,k);
+ _dihedral_atom2w(i,k) = _dihedral_atom2(j,k);
+ _dihedral_atom3w(i,k) = _dihedral_atom3(j,k);
+ _dihedral_atom4w(i,k) = _dihedral_atom4(j,k);
+ }
+ _num_improperw(i) = _num_improper(j);
+ for (k = 0; k < _num_improper(j); k++) {
+ _improper_typew(i,k) = _improper_type(j,k);
+ _improper_atom1w(i,k) = _improper_atom1(j,k);
+ _improper_atom2w(i,k) = _improper_atom2(j,k);
+ _improper_atom3w(i,k) = _improper_atom3(j,k);
+ _improper_atom4w(i,k) = _improper_atom4(j,k);
+ }
+ _nspecialw(i,0) = _nspecial(j,0);
+ _nspecialw(i,1) = _nspecial(j,1);
+ _nspecialw(i,2) = _nspecial(j,2);
+ for (k = 0; k < _nspecial(j,2); k++)
+ _specialw(i,k) = _special(j,k);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space,int dim,X_FLOAT lo,
+ X_FLOAT hi )
+{
+ const int elements = 20+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
+ if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*
+ k_buf.view<LMPHostType>().dimension_1())/elements) {
+ int newsize = nsend*elements/k_buf.view<LMPHostType>().dimension_1()+1;
+ k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
+ }
+ if(space == Host) {
+ AtomVecFullKokkos_PackExchangeFunctor<LMPHostType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPHostType::fence();
+ return nsend*elements;
+ } else {
+ AtomVecFullKokkos_PackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPDeviceType::fence();
+ return nsend*elements;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_exchange(int i, double *buf)
+{
+ int k;
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = h_q(i);
+ buf[m++] = ubuf(h_molecule(i)).d;
+ buf[m++] = ubuf(h_num_bond(i)).d;
+ for (k = 0; k < h_num_bond(i); k++) {
+ buf[m++] = ubuf(h_bond_type(i,k)).d;
+ buf[m++] = ubuf(h_bond_atom(i,k)).d;
+ }
+ buf[m++] = ubuf(h_num_angle(i)).d;
+ for (k = 0; k < h_num_angle(i); k++) {
+ buf[m++] = ubuf(h_angle_type(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom1(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom2(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom3(i,k)).d;
+ }
+ buf[m++] = ubuf(h_num_dihedral(i)).d;
+ for (k = 0; k < h_num_dihedral(i); k++) {
+ buf[m++] = ubuf(h_dihedral_type(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom1(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom2(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom3(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom4(i,k)).d;
+ }
+ buf[m++] = ubuf(h_num_improper(i)).d;
+ for (k = 0; k < h_num_improper(i); k++) {
+ buf[m++] = ubuf(h_improper_type(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom1(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom2(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom3(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom4(i,k)).d;
+ }
+ buf[m++] = ubuf(h_nspecial(i,0)).d;
+ buf[m++] = ubuf(h_nspecial(i,1)).d;
+ buf[m++] = ubuf(h_nspecial(i,2)).d;
+ for (k = 0; k < h_nspecial(i,2); k++)
+ buf[m++] = ubuf(h_special(i,k)).d;
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecFullKokkos_UnpackExchangeFunctor {
+
+ union ubuf {
+ double d;
+ int64_t i;
+ ubuf(double arg) : d(arg) {}
+ ubuf(int64_t arg) : i(arg) {}
+ ubuf(int arg) : i(arg) {}
+ };
+
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array _x;
+ typename AT::t_v_array _v;
+ typename AT::t_tagint_1d _tag;
+ typename AT::t_int_1d _type;
+ typename AT::t_int_1d _mask;
+ typename AT::t_imageint_1d _image;
+ typename AT::t_float_1d _q;
+ typename AT::t_tagint_1d _molecule;
+ typename AT::t_int_2d _nspecial;
+ typename AT::t_tagint_2d _special;
+ typename AT::t_int_1d _num_bond;
+ typename AT::t_int_2d _bond_type;
+ typename AT::t_tagint_2d _bond_atom;
+ typename AT::t_int_1d _num_angle;
+ typename AT::t_int_2d _angle_type;
+ typename AT::t_tagint_2d _angle_atom1,_angle_atom2,_angle_atom3;
+ typename AT::t_int_1d _num_dihedral;
+ typename AT::t_int_2d _dihedral_type;
+ typename AT::t_tagint_2d _dihedral_atom1,_dihedral_atom2,
+ _dihedral_atom3,_dihedral_atom4;
+ typename AT::t_int_1d _num_improper;
+ typename AT::t_int_2d _improper_type;
+ typename AT::t_tagint_2d _improper_atom1,_improper_atom2,
+ _improper_atom3,_improper_atom4;
+
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d _nlocal;
+ int _dim;
+ X_FLOAT _lo,_hi;
+ size_t elements;
+
+ AtomVecFullKokkos_UnpackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d nlocal,
+ int dim, X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _q(atom->k_q.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _num_angle(atom->k_num_angle.view<DeviceType>()),
+ _angle_type(atom->k_angle_type.view<DeviceType>()),
+ _angle_atom1(atom->k_angle_atom1.view<DeviceType>()),
+ _angle_atom2(atom->k_angle_atom2.view<DeviceType>()),
+ _angle_atom3(atom->k_angle_atom3.view<DeviceType>()),
+ _num_dihedral(atom->k_num_dihedral.view<DeviceType>()),
+ _dihedral_type(atom->k_dihedral_type.view<DeviceType>()),
+ _dihedral_atom1(atom->k_dihedral_atom1.view<DeviceType>()),
+ _dihedral_atom2(atom->k_dihedral_atom2.view<DeviceType>()),
+ _dihedral_atom3(atom->k_dihedral_atom3.view<DeviceType>()),
+ _dihedral_atom4(atom->k_dihedral_atom4.view<DeviceType>()),
+ _num_improper(atom->k_num_improper.view<DeviceType>()),
+ _improper_type(atom->k_improper_type.view<DeviceType>()),
+ _improper_atom1(atom->k_improper_atom1.view<DeviceType>()),
+ _improper_atom2(atom->k_improper_atom2.view<DeviceType>()),
+ _improper_atom3(atom->k_improper_atom3.view<DeviceType>()),
+ _improper_atom4(atom->k_improper_atom4.view<DeviceType>()),
+ _nlocal(nlocal.template view<DeviceType>()),_dim(dim),
+ _lo(lo),_hi(hi){
+
+ elements = 20+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
+ buf.template view<DeviceType>().dimension_1())/elements;
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &myrecv) const {
+ X_FLOAT x = _buf(myrecv,_dim+1);
+ if (x >= _lo && x < _hi) {
+ int i = Kokkos::atomic_fetch_add(&_nlocal(0),1);
+ int m = 1;
+ _x(i,0) = _buf(myrecv,m++);
+ _x(i,1) = _buf(myrecv,m++);
+ _x(i,2) = _buf(myrecv,m++);
+ _v(i,0) = _buf(myrecv,m++);
+ _v(i,1) = _buf(myrecv,m++);
+ _v(i,2) = _buf(myrecv,m++);
+ _tag(i) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _type(i) = (int) ubuf(_buf(myrecv,m++)).i;
+ _mask(i) = (int) ubuf(_buf(myrecv,m++)).i;
+ _image(i) = (imageint) ubuf(_buf(myrecv,m++)).i;
+ _q(i) = _buf(myrecv,m++);
+ _molecule(i) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _num_bond(i) = (int) ubuf(_buf(myrecv,m++)).i;
+ int k;
+ for (k = 0; k < _num_bond(i); k++) {
+ _bond_type(i,k) = (int) ubuf(_buf(myrecv,m++)).i;
+ _bond_atom(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ }
+ _num_angle(i) = (int) ubuf(_buf(myrecv,m++)).i;
+ for (k = 0; k < _num_angle(i); k++) {
+ _angle_type(i,k) = (int) ubuf(_buf(myrecv,m++)).i;
+ _angle_atom1(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _angle_atom2(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _angle_atom3(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ }
+ _num_dihedral(i) = (int) ubuf(_buf(myrecv,m++)).i;
+ for (k = 0; k < _num_dihedral(i); k++) {
+ _dihedral_type(i,k) = (int) ubuf(_buf(myrecv,m++)).i;
+ _dihedral_atom1(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _dihedral_atom2(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _dihedral_atom3(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _dihedral_atom4(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ }
+ _num_improper(i) = (int) ubuf(_buf(myrecv,m++)).i;
+ for (k = 0; k < _num_improper(i); k++) {
+ _improper_type(i,k) = (int) ubuf(_buf(myrecv,m++)).i;
+ _improper_atom1(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _improper_atom2(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _improper_atom3(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ _improper_atom4(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ }
+ _nspecial(i,0) = (int) ubuf(_buf(myrecv,m++)).i;
+ _nspecial(i,1) = (int) ubuf(_buf(myrecv,m++)).i;
+ _nspecial(i,2) = (int) ubuf(_buf(myrecv,m++)).i;
+ for (k = 0; k < _nspecial(i,2); k++)
+ _special(i,k) = (tagint) ubuf(_buf(myrecv,m++)).i;
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,
+ int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,
+ ExecutionSpace space) {
+ const size_t elements = 20+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
+ if(space == Host) {
+ k_count.h_view(0) = nlocal;
+ AtomVecFullKokkos_UnpackExchangeFunctor<LMPHostType>
+ f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/elements,f);
+ LMPHostType::fence();
+ return k_count.h_view(0);
+ } else {
+ k_count.h_view(0) = nlocal;
+ k_count.modify<LMPHostType>();
+ k_count.sync<LMPDeviceType>();
+ AtomVecFullKokkos_UnpackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/elements,f);
+ LMPDeviceType::fence();
+ k_count.modify<LMPDeviceType>();
+ k_count.sync<LMPHostType>();
+
+ return k_count.h_view(0);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::unpack_exchange(double *buf)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) grow(0);
+ modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
+ MASK_MASK | IMAGE_MASK | Q_MASK | MOLECULE_MASK | BOND_MASK |
+ ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK);
+
+ int k;
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_q(nlocal) = buf[m++];
+ h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
+
+ h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_bond(nlocal); k++) {
+ h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_num_angle(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_angle(nlocal); k++) {
+ h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_num_dihedral(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_dihedral(nlocal); k++) {
+ h_dihedral_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_dihedral_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_num_improper(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_improper(nlocal); k++) {
+ h_improper_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_improper_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i;
+ h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i;
+ h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_nspecial(nlocal,2); k++)
+ h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->
+ unpack_exchange(nlocal,&buf[m]);
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ size of restart data for all atoms owned by this proc
+ include extra data stored by fixes
+------------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::size_restart()
+{
+ int i;
+
+ int nlocal = atom->nlocal;
+ int n = 0;
+ for (i = 0; i < nlocal; i++)
+ n += 17 + 2*num_bond[i] + 4*num_angle[i] +
+ 5*num_dihedral[i] + 5*num_improper[i];
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (i = 0; i < nlocal; i++)
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom I's data for restart file including extra quantities
+ xyz must be 1st 3 values, so that read_restart can test on them
+ molecular types may be negative, but write as positive
+------------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_restart(int i, double *buf)
+{
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+
+ buf[m++] = h_q(i);
+ buf[m++] = ubuf(h_molecule(i)).d;
+
+ buf[m++] = ubuf(h_num_bond(i)).d;
+ for (int k = 0; k < h_num_bond(i); k++) {
+ buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d;
+ buf[m++] = ubuf(h_bond_atom(i,k)).d;
+ }
+
+ buf[m++] = ubuf(h_num_angle(i)).d;
+ for (int k = 0; k < h_num_angle(i); k++) {
+ buf[m++] = ubuf(MAX(h_angle_type(i,k),-h_angle_type(i,k))).d;
+ buf[m++] = ubuf(h_angle_atom1(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom2(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom3(i,k)).d;
+ }
+
+ buf[m++] = ubuf(h_num_dihedral(i)).d;
+ for (int k = 0; k < h_num_dihedral(i); k++) {
+ buf[m++] = ubuf(MAX(h_dihedral_type(i,k),-h_dihedral_type(i,k))).d;
+ buf[m++] = ubuf(h_dihedral_atom1(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom2(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom3(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom4(i,k)).d;
+ }
+
+ buf[m++] = ubuf(h_num_improper(i)).d;
+ for (int k = 0; k < h_num_improper(i); k++) {
+ buf[m++] = ubuf(MAX(h_improper_type(i,k),-h_improper_type(i,k))).d;
+ buf[m++] = ubuf(h_improper_atom1(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom2(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom3(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom4(i,k)).d;
+ }
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ unpack data for one atom from restart file including extra quantities
+------------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::unpack_restart(double *buf)
+{
+ int k;
+
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ grow(0);
+ if (atom->nextra_store)
+ memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
+ }
+
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+
+ h_q(nlocal) = buf[m++];
+ h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
+
+ h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_bond(nlocal); k++) {
+ h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_num_angle(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_angle(nlocal); k++) {
+ h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_num_dihedral(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_dihedral(nlocal); k++) {
+ h_dihedral_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_dihedral_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_num_improper(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_improper(nlocal); k++) {
+ h_improper_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_improper_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
+
+ double **extra = atom->extra;
+ if (atom->nextra_store) {
+ int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+ for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
+ }
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ create one atom of itype at coord
+ set other values to defaults
+------------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::create_atom(int itype, double *coord)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ atomKK->modified(Host,ALL_MASK);
+ grow(0);
+ }
+ atomKK->modified(Host,ALL_MASK);
+
+ tag[nlocal] = 0;
+ type[nlocal] = itype;
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+ h_mask(nlocal) = 1;
+ h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) |
+ ((imageint) IMGMAX << IMGBITS) | IMGMAX;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+
+ h_q(nlocal) = 0.0;
+ h_molecule(nlocal) = 0;
+ h_num_bond(nlocal) = 0;
+ h_num_angle(nlocal) = 0;
+ h_num_dihedral(nlocal) = 0;
+ h_num_improper(nlocal) = 0;
+ h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack one line from Atoms section of data file
+ initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::data_atom(double *coord, imageint imagetmp,
+ char **values)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) grow(0);
+
+ h_tag(nlocal) = atoi(values[0]);
+ if (h_tag(nlocal) <= 0)
+ error->one(FLERR,"Invalid atom ID in Atoms section of data file");
+
+ h_molecule(nlocal) = atoi(values[1]);
+ if (h_molecule(nlocal) <= 0)
+ error->one(FLERR,"Invalid molecule ID in Atoms section of data file");
+
+ h_type(nlocal) = atoi(values[2]);
+ if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
+ error->one(FLERR,"Invalid atom type in Atoms section of data file");
+
+ h_q(nlocal) = atof(values[3]);
+
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+
+ h_image(nlocal) = imagetmp;
+
+ h_mask(nlocal) = 1;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+ h_num_bond(nlocal) = 0;
+ h_num_angle(nlocal) = 0;
+ h_num_dihedral(nlocal) = 0;
+ h_num_improper(nlocal) = 0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack hybrid quantities from one line in Atoms section of data file
+ initialize other atom quantities for this sub-style
+------------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::data_atom_hybrid(int nlocal, char **values)
+{
+ h_molecule(nlocal) = atoi(values[0]);
+ h_q(nlocal) = atof(values[1]);
+ h_num_bond(nlocal) = 0;
+ h_num_angle(nlocal) = 0;
+ h_num_dihedral(nlocal) = 0;
+ h_num_improper(nlocal) = 0;
+ return 2;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom info for data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::pack_data(double **buf)
+{
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ buf[i][0] = h_tag(i);
+ buf[i][1] = h_molecule(i);
+ buf[i][2] = h_type(i);
+ buf[i][3] = h_q(i);
+ buf[i][4] = h_x(i,0);
+ buf[i][5] = h_x(i,1);
+ buf[i][6] = h_x(i,2);
+ buf[i][7] = (h_image[i] & IMGMASK) - IMGMAX;
+ buf[i][8] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+ buf[i][9] = (h_image[i] >> IMG2BITS) - IMGMAX;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ pack hybrid atom info for data file
+------------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::pack_data_hybrid(int i, double *buf)
+{
+ buf[0] = h_molecule(i);
+ buf[1] = h_q(i);
+ return 2;
+}
+
+/* ----------------------------------------------------------------------
+ write atom info to data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::write_data(FILE *fp, int n, double **buf)
+{
+ for (int i = 0; i < n; i++)
+ fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
+ (int) buf[i][0],(int) buf[i][1], (int) buf[i][2], buf[i][3],
+ buf[i][4],buf[i][5],buf[i][6],
+ (int) buf[i][7],(int) buf[i][8],(int) buf[i][9]);
+}
+
+/* ----------------------------------------------------------------------
+ write hybrid atom info to data file
+------------------------------------------------------------------------- */
+
+int AtomVecFullKokkos::write_data_hybrid(FILE *fp, double *buf)
+{
+ fprintf(fp," " TAGINT_FORMAT " %-1.16e",(tagint) ubuf(buf[0]).i,buf[1]);
+ return 2;
+}
+
+/* ----------------------------------------------------------------------
+ return # of bytes of allocated memory
+------------------------------------------------------------------------- */
+
+bigint AtomVecFullKokkos::memory_usage()
+{
+ bigint bytes = 0;
+
+ if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
+ if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
+ if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
+ if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
+ if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
+ if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
+ if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
+
+ if (atom->memcheck("q")) bytes += memory->usage(q,nmax);
+ if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
+ if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
+ if (atom->memcheck("special"))
+ bytes += memory->usage(special,nmax,atom->maxspecial);
+
+ if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
+ if (atom->memcheck("bond_type"))
+ bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
+ if (atom->memcheck("bond_atom"))
+ bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
+
+ if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax);
+ if (atom->memcheck("angle_type"))
+ bytes += memory->usage(angle_type,nmax,atom->angle_per_atom);
+ if (atom->memcheck("angle_atom1"))
+ bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom);
+ if (atom->memcheck("angle_atom2"))
+ bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom);
+ if (atom->memcheck("angle_atom3"))
+ bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom);
+
+ if (atom->memcheck("num_dihedral")) bytes += memory->usage(num_dihedral,nmax);
+ if (atom->memcheck("dihedral_type"))
+ bytes += memory->usage(dihedral_type,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("dihedral_atom1"))
+ bytes += memory->usage(dihedral_atom1,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("dihedral_atom2"))
+ bytes += memory->usage(dihedral_atom2,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("dihedral_atom3"))
+ bytes += memory->usage(dihedral_atom3,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("dihedral_atom4"))
+ bytes += memory->usage(dihedral_atom4,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("num_improper")) bytes += memory->usage(num_improper,nmax);
+ if (atom->memcheck("improper_type"))
+ bytes += memory->usage(improper_type,nmax,atom->improper_per_atom);
+ if (atom->memcheck("improper_atom1"))
+ bytes += memory->usage(improper_atom1,nmax,atom->improper_per_atom);
+ if (atom->memcheck("improper_atom2"))
+ bytes += memory->usage(improper_atom2,nmax,atom->improper_per_atom);
+ if (atom->memcheck("improper_atom3"))
+ bytes += memory->usage(improper_atom3,nmax,atom->improper_per_atom);
+ if (atom->memcheck("improper_atom4"))
+ bytes += memory->usage(improper_atom4,nmax,atom->improper_per_atom);
+
+ return bytes;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::sync(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPDeviceType>();
+ if (mask && Q_MASK) atomKK->k_q.sync<LMPDeviceType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.sync<LMPDeviceType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.sync<LMPDeviceType>();
+ atomKK->k_special.sync<LMPDeviceType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.sync<LMPDeviceType>();
+ atomKK->k_bond_type.sync<LMPDeviceType>();
+ atomKK->k_bond_atom.sync<LMPDeviceType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.sync<LMPDeviceType>();
+ atomKK->k_angle_type.sync<LMPDeviceType>();
+ atomKK->k_angle_atom1.sync<LMPDeviceType>();
+ atomKK->k_angle_atom2.sync<LMPDeviceType>();
+ atomKK->k_angle_atom3.sync<LMPDeviceType>();
+ }
+ if (mask && DIHEDRAL_MASK) {
+ atomKK->k_num_dihedral.sync<LMPDeviceType>();
+ atomKK->k_dihedral_type.sync<LMPDeviceType>();
+ atomKK->k_dihedral_atom1.sync<LMPDeviceType>();
+ atomKK->k_dihedral_atom2.sync<LMPDeviceType>();
+ atomKK->k_dihedral_atom3.sync<LMPDeviceType>();
+ atomKK->k_dihedral_atom4.sync<LMPDeviceType>();
+ }
+ if (mask && IMPROPER_MASK) {
+ atomKK->k_num_improper.sync<LMPDeviceType>();
+ atomKK->k_improper_type.sync<LMPDeviceType>();
+ atomKK->k_improper_atom1.sync<LMPDeviceType>();
+ atomKK->k_improper_atom2.sync<LMPDeviceType>();
+ atomKK->k_improper_atom3.sync<LMPDeviceType>();
+ atomKK->k_improper_atom3.sync<LMPDeviceType>();
+ }
+ } else {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPHostType>();
+ if (mask && Q_MASK) atomKK->k_q.sync<LMPHostType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.sync<LMPHostType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.sync<LMPHostType>();
+ atomKK->k_special.sync<LMPHostType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.sync<LMPHostType>();
+ atomKK->k_bond_type.sync<LMPHostType>();
+ atomKK->k_bond_atom.sync<LMPHostType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.sync<LMPHostType>();
+ atomKK->k_angle_type.sync<LMPHostType>();
+ atomKK->k_angle_atom1.sync<LMPHostType>();
+ atomKK->k_angle_atom2.sync<LMPHostType>();
+ atomKK->k_angle_atom3.sync<LMPHostType>();
+ }
+ if (mask && DIHEDRAL_MASK) {
+ atomKK->k_num_dihedral.sync<LMPHostType>();
+ atomKK->k_dihedral_type.sync<LMPHostType>();
+ atomKK->k_dihedral_atom1.sync<LMPHostType>();
+ atomKK->k_dihedral_atom2.sync<LMPHostType>();
+ atomKK->k_dihedral_atom3.sync<LMPHostType>();
+ atomKK->k_dihedral_atom4.sync<LMPHostType>();
+ }
+ if (mask && IMPROPER_MASK) {
+ atomKK->k_num_improper.sync<LMPHostType>();
+ atomKK->k_improper_type.sync<LMPHostType>();
+ atomKK->k_improper_atom1.sync<LMPHostType>();
+ atomKK->k_improper_atom2.sync<LMPHostType>();
+ atomKK->k_improper_atom3.sync<LMPHostType>();
+ atomKK->k_improper_atom3.sync<LMPHostType>();
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecFullKokkos::modified(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPDeviceType>();
+ if (mask && Q_MASK) atomKK->k_q.modify<LMPDeviceType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.modify<LMPDeviceType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.modify<LMPDeviceType>();
+ atomKK->k_special.modify<LMPDeviceType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.modify<LMPDeviceType>();
+ atomKK->k_bond_type.modify<LMPDeviceType>();
+ atomKK->k_bond_atom.modify<LMPDeviceType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.modify<LMPDeviceType>();
+ atomKK->k_angle_type.modify<LMPDeviceType>();
+ atomKK->k_angle_atom1.modify<LMPDeviceType>();
+ atomKK->k_angle_atom2.modify<LMPDeviceType>();
+ atomKK->k_angle_atom3.modify<LMPDeviceType>();
+ }
+ if (mask && DIHEDRAL_MASK) {
+ atomKK->k_num_dihedral.modify<LMPDeviceType>();
+ atomKK->k_dihedral_type.modify<LMPDeviceType>();
+ atomKK->k_dihedral_atom1.modify<LMPDeviceType>();
+ atomKK->k_dihedral_atom2.modify<LMPDeviceType>();
+ atomKK->k_dihedral_atom3.modify<LMPDeviceType>();
+ atomKK->k_dihedral_atom4.modify<LMPDeviceType>();
+ }
+ if (mask && IMPROPER_MASK) {
+ atomKK->k_num_improper.modify<LMPDeviceType>();
+ atomKK->k_improper_type.modify<LMPDeviceType>();
+ atomKK->k_improper_atom1.modify<LMPDeviceType>();
+ atomKK->k_improper_atom2.modify<LMPDeviceType>();
+ atomKK->k_improper_atom3.modify<LMPDeviceType>();
+ atomKK->k_improper_atom3.modify<LMPDeviceType>();
+ }
+ } else {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPHostType>();
+ if (mask && Q_MASK) atomKK->k_q.modify<LMPHostType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.modify<LMPHostType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.modify<LMPHostType>();
+ atomKK->k_special.modify<LMPHostType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.modify<LMPHostType>();
+ atomKK->k_bond_type.modify<LMPHostType>();
+ atomKK->k_bond_atom.modify<LMPHostType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.modify<LMPHostType>();
+ atomKK->k_angle_type.modify<LMPHostType>();
+ atomKK->k_angle_atom1.modify<LMPHostType>();
+ atomKK->k_angle_atom2.modify<LMPHostType>();
+ atomKK->k_angle_atom3.modify<LMPHostType>();
+ }
+ if (mask && DIHEDRAL_MASK) {
+ atomKK->k_num_dihedral.modify<LMPHostType>();
+ atomKK->k_dihedral_type.modify<LMPHostType>();
+ atomKK->k_dihedral_atom1.modify<LMPHostType>();
+ atomKK->k_dihedral_atom2.modify<LMPHostType>();
+ atomKK->k_dihedral_atom3.modify<LMPHostType>();
+ atomKK->k_dihedral_atom4.modify<LMPHostType>();
+ }
+ if (mask && IMPROPER_MASK) {
+ atomKK->k_num_improper.modify<LMPHostType>();
+ atomKK->k_improper_type.modify<LMPHostType>();
+ atomKK->k_improper_atom1.modify<LMPHostType>();
+ atomKK->k_improper_atom2.modify<LMPHostType>();
+ atomKK->k_improper_atom3.modify<LMPHostType>();
+ atomKK->k_improper_atom3.modify<LMPHostType>();
+ }
+ }
+}
diff --git a/src/KOKKOS/atom_vec_full_kokkos.h b/src/KOKKOS/atom_vec_full_kokkos.h
new file mode 100644
index 0000000000..43290bb219
--- /dev/null
+++ b/src/KOKKOS/atom_vec_full_kokkos.h
@@ -0,0 +1,183 @@
+/* ----------------------------------------------------------------------
+ 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 ATOM_CLASS
+
+AtomStyle(full/kk,AtomVecFullKokkos)
+
+#else
+
+#ifndef LMP_ATOM_VEC_FULL_KOKKOS_H
+#define LMP_ATOM_VEC_FULL_KOKKOS_H
+
+#include "atom_vec_kokkos.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecFullKokkos : public AtomVecKokkos {
+ public:
+ AtomVecFullKokkos(class LAMMPS *);
+ virtual ~AtomVecFullKokkos() {}
+ void grow(int);
+ void copy(int, int, int);
+ int pack_comm(int, int *, double *, int, int *);
+ int pack_comm_vel(int, int *, double *, int, int *);
+ void unpack_comm(int, int, double *);
+ void unpack_comm_vel(int, int, double *);
+ int pack_reverse(int, int, double *);
+ void unpack_reverse(int, int *, double *);
+ int pack_border(int, int *, double *, int, int *);
+ int pack_border_vel(int, int *, double *, int, int *);
+ int pack_border_hybrid(int, int *, double *);
+ void unpack_border(int, int, double *);
+ void unpack_border_vel(int, int, double *);
+ int unpack_border_hybrid(int, int, double *);
+ int pack_exchange(int, double *);
+ int unpack_exchange(double *);
+ int size_restart();
+ int pack_restart(int, double *);
+ int unpack_restart(double *);
+ void create_atom(int, double *);
+ void data_atom(double *, tagint, char **);
+ int data_atom_hybrid(int, char **);
+ void pack_data(double **);
+ int pack_data_hybrid(int, double *);
+ void write_data(FILE *, int, double **);
+ int write_data_hybrid(FILE *, double *);
+ bigint memory_usage();
+
+ void grow_reset();
+ int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag, const int pbc[]);
+ void unpack_comm_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf);
+ int pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap, const int nfirst,
+ const int &pbc_flag, const int pbc[]);
+ int 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);
+ void unpack_border_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf,
+ ExecutionSpace space);
+ int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space, int dim,
+ X_FLOAT lo, X_FLOAT hi);
+ int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
+ int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
+ ExecutionSpace space);
+
+ void sync(ExecutionSpace space, unsigned int mask);
+ void modified(ExecutionSpace space, unsigned int mask);
+
+ protected:
+
+ tagint *tag;
+ int *type,*mask;
+ imageint *image;
+ double **x,**v,**f;
+
+ double *q;
+
+ tagint *molecule;
+ int **nspecial;
+ tagint **special;
+ int *num_bond;
+ int **bond_type;
+ tagint **bond_atom;
+
+ int *num_angle;
+ int **angle_type;
+ tagint **angle_atom1,**angle_atom2,**angle_atom3;
+
+ int *num_dihedral;
+ int **dihedral_type;
+ tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
+ int *num_improper;
+ int **improper_type;
+ tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
+
+ DAT::t_tagint_1d d_tag;
+ DAT::t_int_1d d_type, d_mask;
+ HAT::t_tagint_1d h_tag;
+ HAT::t_int_1d h_type, h_mask;
+
+ DAT::t_imageint_1d d_image;
+ HAT::t_imageint_1d h_image;
+
+ DAT::t_x_array d_x;
+ DAT::t_v_array d_v;
+ DAT::t_f_array d_f;
+ HAT::t_x_array h_x;
+ HAT::t_v_array h_v;
+ HAT::t_f_array h_f;
+
+ DAT::t_float_1d d_q;
+ HAT::t_float_1d h_q;
+
+ DAT::t_tagint_1d d_molecule;
+ DAT::t_int_2d d_nspecial;
+ DAT::t_tagint_2d d_special;
+ DAT::t_int_1d d_num_bond;
+ DAT::t_int_2d d_bond_type;
+ DAT::t_tagint_2d d_bond_atom;
+
+ HAT::t_tagint_1d h_molecule;
+ HAT::t_int_2d h_nspecial;
+ HAT::t_tagint_2d h_special;
+ HAT::t_int_1d h_num_bond;
+ HAT::t_int_2d h_bond_type;
+ HAT::t_tagint_2d h_bond_atom;
+
+ DAT::t_int_1d d_num_angle;
+ DAT::t_int_2d d_angle_type;
+ DAT::t_tagint_2d d_angle_atom1,d_angle_atom2,d_angle_atom3;
+
+ HAT::t_int_1d h_num_angle;
+ HAT::t_int_2d h_angle_type;
+ HAT::t_tagint_2d h_angle_atom1,h_angle_atom2,h_angle_atom3;
+
+ DAT::t_int_1d d_num_dihedral;
+ DAT::t_int_2d d_dihedral_type;
+ DAT::t_tagint_2d d_dihedral_atom1,d_dihedral_atom2,
+ d_dihedral_atom3,d_dihedral_atom4;
+ DAT::t_int_1d d_num_improper;
+ DAT::t_int_2d d_improper_type;
+ DAT::t_tagint_2d d_improper_atom1,d_improper_atom2,
+ d_improper_atom3,d_improper_atom4;
+
+ HAT::t_int_1d h_num_dihedral;
+ HAT::t_int_2d h_dihedral_type;
+ HAT::t_tagint_2d h_dihedral_atom1,h_dihedral_atom2,
+ h_dihedral_atom3,h_dihedral_atom4;
+ HAT::t_int_1d h_num_improper;
+ HAT::t_int_2d h_improper_type;
+ HAT::t_tagint_2d h_improper_atom1,h_improper_atom2,
+ h_improper_atom3,h_improper_atom4;
+
+ HAT::tdual_int_1d k_count;
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h
index ac651b0b5a..e555f587e5 100644
--- a/src/KOKKOS/atom_vec_kokkos.h
+++ b/src/KOKKOS/atom_vec_kokkos.h
@@ -24,43 +24,43 @@ class AtomVecKokkos : public AtomVec {
AtomVecKokkos(class LAMMPS *);
virtual ~AtomVecKokkos() {}
- virtual void sync(ExecutionSpace space, unsigned int mask) {};
- virtual void modified(ExecutionSpace space, unsigned int mask) {};
+ virtual void sync(ExecutionSpace space, unsigned int mask) = 0;
+ virtual void modified(ExecutionSpace space, unsigned int mask) = 0;
virtual int
pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
const int & iswap, const int nfirst,
- const int &pbc_flag, const int pbc[])
- {return 0;}
+ const int &pbc_flag, const int pbc[]) = 0;
+ //{return 0;}
virtual int
pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &list,
const int & iswap, const DAT::tdual_xfloat_2d &buf,
- const int &pbc_flag, const int pbc[])
- {return 0;}
+ const int &pbc_flag, const int pbc[]) = 0;
+ //{return 0;}
virtual void
unpack_comm_kokkos(const int &n, const int &nfirst,
- const DAT::tdual_xfloat_2d &buf) {};
+ const DAT::tdual_xfloat_2d &buf) = 0;
virtual int
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)
- {return 0;};
+ int pbc_flag, int *pbc, ExecutionSpace space) = 0;
+ //{return 0;};
virtual void
unpack_border_kokkos(const int &n, const int &nfirst,
const DAT::tdual_xfloat_2d &buf,
- ExecutionSpace space) {};
+ ExecutionSpace space) = 0;
virtual int
pack_exchange_kokkos(const int &nsend, DAT::tdual_xfloat_2d &buf,
DAT::tdual_int_1d k_sendlist,
DAT::tdual_int_1d k_copylist,
- ExecutionSpace space, int dim, X_FLOAT lo, X_FLOAT hi)
- {return 0;};
+ ExecutionSpace space, int dim, X_FLOAT lo, X_FLOAT hi) = 0;
+ //{return 0;};
virtual int
unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
- ExecutionSpace space)
- {return 0;};
+ ExecutionSpace space) = 0;
+ //{return 0;};
protected:
class AtomKokkos *atomKK;
diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.cpp b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
new file mode 100644
index 0000000000..b75023cd37
--- /dev/null
+++ b/src/KOKKOS/atom_vec_molecular_kokkos.cpp
@@ -0,0 +1,2236 @@
+/* ----------------------------------------------------------------------
+ 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 "stdlib.h"
+#include "atom_vec_molecular_kokkos.h"
+#include "atom_kokkos.h"
+#include "comm_kokkos.h"
+#include "domain.h"
+#include "modify.h"
+#include "fix.h"
+#include "atom_masks.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define DELTA 10000
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecMolecularKokkos::AtomVecMolecularKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
+{
+ molecular = 1;
+ bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 1;
+ mass_type = 1;
+
+ comm_x_only = comm_f_only = 1;
+ size_forward = 3;
+ size_reverse = 3;
+ size_border = 7;
+ size_velocity = 3;
+ size_data_atom = 6;
+ size_data_vel = 4;
+ xcol_data = 4;
+
+ atom->molecule_flag = 1;
+
+ k_count = DAT::tdual_int_1d("atom::k_count",1);
+ atomKK = (AtomKokkos *) atom;
+ commKK = (CommKokkos *) comm;
+}
+
+/* ----------------------------------------------------------------------
+ grow atom arrays
+ n = 0 grows arrays by DELTA
+ n > 0 allocates arrays to size n
+------------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::grow(int n)
+{
+ if (n == 0) nmax += DELTA;
+ else nmax = n;
+ atomKK->nmax = nmax;
+ if (nmax < 0 || nmax > MAXSMALLINT)
+ error->one(FLERR,"Per-processor system is too big");
+
+ sync(Device,ALL_MASK);
+ modified(Device,ALL_MASK);
+
+ memory->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag");
+ memory->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type");
+ memory->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask");
+ memory->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image");
+
+ memory->grow_kokkos(atomKK->k_x,atomKK->x,nmax,3,"atom:x");
+ memory->grow_kokkos(atomKK->k_v,atomKK->v,nmax,3,"atom:v");
+ memory->grow_kokkos(atomKK->k_f,atomKK->f,nmax,3,"atom:f");
+
+ memory->grow_kokkos(atomKK->k_molecule,atomKK->molecule,nmax,"atom:molecule");
+ memory->grow_kokkos(atomKK->k_nspecial,atomKK->nspecial,nmax,3,"atom:nspecial");
+ memory->grow_kokkos(atomKK->k_special,atomKK->special,nmax,atomKK->maxspecial,
+ "atom:special");
+ memory->grow_kokkos(atomKK->k_num_bond,atomKK->num_bond,nmax,"atom:num_bond");
+ memory->grow_kokkos(atomKK->k_bond_type,atomKK->bond_type,nmax,atomKK->bond_per_atom,
+ "atom:bond_type");
+ memory->grow_kokkos(atomKK->k_bond_atom,atomKK->bond_atom,nmax,atomKK->bond_per_atom,
+ "atom:bond_atom");
+
+ memory->grow_kokkos(atomKK->k_num_angle,atomKK->num_angle,nmax,"atom:num_angle");
+ memory->grow_kokkos(atomKK->k_angle_type,atomKK->angle_type,nmax,atomKK->angle_per_atom,
+ "atom:angle_type");
+ memory->grow_kokkos(atomKK->k_angle_atom1,atomKK->angle_atom1,nmax,atomKK->angle_per_atom,
+ "atom:angle_atom1");
+ memory->grow_kokkos(atomKK->k_angle_atom2,atomKK->angle_atom2,nmax,atomKK->angle_per_atom,
+ "atom:angle_atom2");
+ memory->grow_kokkos(atomKK->k_angle_atom3,atomKK->angle_atom3,nmax,atomKK->angle_per_atom,
+ "atom:angle_atom3");
+
+ memory->grow_kokkos(atomKK->k_num_dihedral,atomKK->num_dihedral,nmax,"atom:num_dihedral");
+ memory->grow_kokkos(atomKK->k_dihedral_type,atomKK->dihedral_type,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_type");
+ memory->grow_kokkos(atomKK->k_dihedral_atom1,atomKK->dihedral_atom1,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_atom1");
+ memory->grow_kokkos(atomKK->k_dihedral_atom2,atomKK->dihedral_atom2,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_atom2");
+ memory->grow_kokkos(atomKK->k_dihedral_atom3,atomKK->dihedral_atom3,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_atom3");
+ memory->grow_kokkos(atomKK->k_dihedral_atom4,atomKK->dihedral_atom4,nmax,
+ atomKK->dihedral_per_atom,"atom:dihedral_atom4");
+
+ memory->grow_kokkos(atomKK->k_num_improper,atomKK->num_improper,nmax,"atom:num_improper");
+ memory->grow_kokkos(atomKK->k_improper_type,atomKK->improper_type,nmax,
+ atomKK->improper_per_atom,"atom:improper_type");
+ memory->grow_kokkos(atomKK->k_improper_atom1,atomKK->improper_atom1,nmax,
+ atomKK->improper_per_atom,"atom:improper_atom1");
+ memory->grow_kokkos(atomKK->k_improper_atom2,atomKK->improper_atom2,nmax,
+ atomKK->improper_per_atom,"atom:improper_atom2");
+ memory->grow_kokkos(atomKK->k_improper_atom3,atomKK->improper_atom3,nmax,
+ atomKK->improper_per_atom,"atom:improper_atom3");
+ memory->grow_kokkos(atomKK->k_improper_atom4,atomKK->improper_atom4,nmax,
+ atomKK->improper_per_atom,"atom:improper_atom4");
+
+ grow_reset();
+ sync(Host,ALL_MASK);
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
+}
+
+/* ----------------------------------------------------------------------
+ reset local array ptrs
+------------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::grow_reset()
+{
+ tag = atomKK->tag;
+ d_tag = atomKK->k_tag.d_view;
+ h_tag = atomKK->k_tag.h_view;
+
+ type = atomKK->type;
+ d_type = atomKK->k_type.d_view;
+ h_type = atomKK->k_type.h_view;
+ mask = atomKK->mask;
+ d_mask = atomKK->k_mask.d_view;
+ h_mask = atomKK->k_mask.h_view;
+ image = atomKK->image;
+ d_image = atomKK->k_image.d_view;
+ h_image = atomKK->k_image.h_view;
+
+ x = atomKK->x;
+ d_x = atomKK->k_x.d_view;
+ h_x = atomKK->k_x.h_view;
+ v = atomKK->v;
+ d_v = atomKK->k_v.d_view;
+ h_v = atomKK->k_v.h_view;
+ f = atomKK->f;
+ d_f = atomKK->k_f.d_view;
+ h_f = atomKK->k_f.h_view;
+
+ molecule = atomKK->molecule;
+ d_molecule = atomKK->k_molecule.d_view;
+ h_molecule = atomKK->k_molecule.h_view;
+ nspecial = atomKK->nspecial;
+ d_nspecial = atomKK->k_nspecial.d_view;
+ h_nspecial = atomKK->k_nspecial.h_view;
+ special = atomKK->special;
+ d_special = atomKK->k_special.d_view;
+ h_special = atomKK->k_special.h_view;
+ num_bond = atomKK->num_bond;
+ d_num_bond = atomKK->k_num_bond.d_view;
+ h_num_bond = atomKK->k_num_bond.h_view;
+ bond_type = atomKK->bond_type;
+ d_bond_type = atomKK->k_bond_type.d_view;
+ h_bond_type = atomKK->k_bond_type.h_view;
+ bond_atom = atomKK->bond_atom;
+ d_bond_atom = atomKK->k_bond_atom.d_view;
+ h_bond_atom = atomKK->k_bond_atom.h_view;
+
+ num_angle = atomKK->num_angle;
+ d_num_angle = atomKK->k_num_angle.d_view;
+ h_num_angle = atomKK->k_num_angle.h_view;
+ angle_type = atomKK->angle_type;
+ d_angle_type = atomKK->k_angle_type.d_view;
+ h_angle_type = atomKK->k_angle_type.h_view;
+ angle_atom1 = atomKK->angle_atom1;
+ d_angle_atom1 = atomKK->k_angle_atom1.d_view;
+ h_angle_atom1 = atomKK->k_angle_atom1.h_view;
+ angle_atom2 = atomKK->angle_atom2;
+ d_angle_atom2 = atomKK->k_angle_atom2.d_view;
+ h_angle_atom2 = atomKK->k_angle_atom2.h_view;
+ angle_atom3 = atomKK->angle_atom3;
+ d_angle_atom3 = atomKK->k_angle_atom3.d_view;
+ h_angle_atom3 = atomKK->k_angle_atom3.h_view;
+
+ num_dihedral = atomKK->num_dihedral;
+ d_num_dihedral = atomKK->k_num_dihedral.d_view;
+ h_num_dihedral = atomKK->k_num_dihedral.h_view;
+ dihedral_type = atomKK->dihedral_type;
+ d_dihedral_type = atomKK->k_dihedral_type.d_view;
+ h_dihedral_type = atomKK->k_dihedral_type.h_view;
+ dihedral_atom1 = atomKK->dihedral_atom1;
+ d_dihedral_atom1 = atomKK->k_dihedral_atom1.d_view;
+ h_dihedral_atom1 = atomKK->k_dihedral_atom1.h_view;
+ dihedral_atom2 = atomKK->dihedral_atom2;
+ d_dihedral_atom2 = atomKK->k_dihedral_atom2.d_view;
+ h_dihedral_atom2 = atomKK->k_dihedral_atom2.h_view;
+ dihedral_atom3 = atomKK->dihedral_atom3;
+ d_dihedral_atom3 = atomKK->k_dihedral_atom3.d_view;
+ h_dihedral_atom3 = atomKK->k_dihedral_atom3.h_view;
+ dihedral_atom4 = atomKK->dihedral_atom4;
+ d_dihedral_atom4 = atomKK->k_dihedral_atom4.d_view;
+ h_dihedral_atom4 = atomKK->k_dihedral_atom4.h_view;
+
+ num_improper = atomKK->num_improper;
+ d_num_improper = atomKK->k_num_improper.d_view;
+ h_num_improper = atomKK->k_num_improper.h_view;
+ improper_type = atomKK->improper_type;
+ d_improper_type = atomKK->k_improper_type.d_view;
+ h_improper_type = atomKK->k_improper_type.h_view;
+ improper_atom1 = atomKK->improper_atom1;
+ d_improper_atom1 = atomKK->k_improper_atom1.d_view;
+ h_improper_atom1 = atomKK->k_improper_atom1.h_view;
+ improper_atom2 = atomKK->improper_atom2;
+ d_improper_atom2 = atomKK->k_improper_atom2.d_view;
+ h_improper_atom2 = atomKK->k_improper_atom2.h_view;
+ improper_atom3 = atomKK->improper_atom3;
+ d_improper_atom3 = atomKK->k_improper_atom3.d_view;
+ h_improper_atom3 = atomKK->k_improper_atom3.h_view;
+ improper_atom4 = atomKK->improper_atom4;
+ d_improper_atom4 = atomKK->k_improper_atom4.d_view;
+ h_improper_atom4 = atomKK->k_improper_atom4.h_view;
+}
+
+/* ----------------------------------------------------------------------
+ copy atom I info to atom J
+------------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::copy(int i, int j, int delflag)
+{
+ int k;
+
+ h_tag[j] = h_tag[i];
+ h_type[j] = h_type[i];
+ mask[j] = mask[i];
+ h_image[j] = h_image[i];
+ h_x(j,0) = h_x(i,0);
+ h_x(j,1) = h_x(i,1);
+ h_x(j,2) = h_x(i,2);
+ h_v(j,0) = h_v(i,0);
+ h_v(j,1) = h_v(i,1);
+ h_v(j,2) = h_v(i,2);
+
+ h_molecule(j) = h_molecule(i);
+
+ h_num_bond(j) = h_num_bond(i);
+ for (k = 0; k < h_num_bond(j); k++) {
+ h_bond_type(j,k) = h_bond_type(i,k);
+ h_bond_atom(j,k) = h_bond_atom(i,k);
+ }
+
+ h_nspecial(j,0) = h_nspecial(i,0);
+ h_nspecial(j,1) = h_nspecial(i,1);
+ h_nspecial(j,2) = h_nspecial(i,2);
+ for (k = 0; k < h_nspecial(j,2); k++)
+ h_special(j,k) = h_special(i,k);
+
+ h_num_angle(j) = h_num_angle(i);
+ for (k = 0; k < h_num_angle(j); k++) {
+ h_angle_type(j,k) = h_angle_type(i,k);
+ h_angle_atom1(j,k) = h_angle_atom1(i,k);
+ h_angle_atom2(j,k) = h_angle_atom2(i,k);
+ h_angle_atom3(j,k) = h_angle_atom3(i,k);
+ }
+
+ h_num_dihedral(j) = h_num_dihedral(i);
+ for (k = 0; k < h_num_dihedral(j); k++) {
+ h_dihedral_type(j,k) = h_dihedral_type(i,k);
+ h_dihedral_atom1(j,k) = h_dihedral_atom1(i,k);
+ h_dihedral_atom2(j,k) = h_dihedral_atom2(i,k);
+ h_dihedral_atom3(j,k) = h_dihedral_atom3(i,k);
+ h_dihedral_atom4(j,k) = h_dihedral_atom4(i,k);
+ }
+
+ h_num_improper(j) = h_num_improper(i);
+ for (k = 0; k < h_num_improper(j); k++) {
+ h_improper_type(j,k) = h_improper_type(i,k);
+ h_improper_atom1(j,k) = h_improper_atom1(i,k);
+ h_improper_atom2(j,k) = h_improper_atom2(i,k);
+ h_improper_atom3(j,k) = h_improper_atom3(i,k);
+ h_improper_atom4(j,k) = h_improper_atom4(i,k);
+ }
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecMolecularKokkos_PackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_um _buf;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecMolecularKokkos_PackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ const size_t maxsend = (buf.view<DeviceType>().dimension_0()
+ *buf.view<DeviceType>().dimension_1())/3;
+ const size_t elements = 3;
+ buffer_view<DeviceType>(_buf,buf,maxsend,elements);
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _buf(i,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_comm_kokkos(const int &n,
+ const DAT::tdual_int_2d &list,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag,
+ const int* const pbc)
+{
+ // Check whether to always run forward communication on the host
+ // Choose correct forward PackComm kernel
+
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecMolecularKokkos_PackComm<LMPHostType,1,1>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecMolecularKokkos_PackComm<LMPHostType,1,0>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecMolecularKokkos_PackComm<LMPHostType,0,1>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecMolecularKokkos_PackComm<LMPHostType,0,0>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecMolecularKokkos_PackComm<LMPDeviceType,1,1>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecMolecularKokkos_PackComm<LMPDeviceType,1,0>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecMolecularKokkos_PackComm<LMPDeviceType,0,1>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecMolecularKokkos_PackComm<LMPDeviceType,0,0>
+ f(atomKK->k_x,buf,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+
+ return n*size_forward;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG,int TRICLINIC>
+struct AtomVecMolecularKokkos_PackCommSelf {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array_randomread _x;
+ typename ArrayTypes<DeviceType>::t_x_array _xw;
+ int _nfirst;
+ typename ArrayTypes<DeviceType>::t_int_2d_const _list;
+ const int _iswap;
+ X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz;
+ X_FLOAT _pbc[6];
+
+ AtomVecMolecularKokkos_PackCommSelf(
+ const typename DAT::tdual_x_array &x,
+ const int &nfirst,
+ const typename DAT::tdual_int_2d &list,
+ const int & iswap,
+ const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd,
+ const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc):
+ _x(x.view<DeviceType>()),_xw(x.view<DeviceType>()),_nfirst(nfirst),
+ _list(list.view<DeviceType>()),_iswap(iswap),
+ _xprd(xprd),_yprd(yprd),_zprd(zprd),
+ _xy(xy),_xz(xz),_yz(yz) {
+ _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2];
+ _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5];
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _xw(i+_nfirst,0) = _x(j,0);
+ _xw(i+_nfirst,1) = _x(j,1);
+ _xw(i+_nfirst,2) = _x(j,2);
+ } else {
+ if (TRICLINIC == 0) {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ } else {
+ _xw(i+_nfirst,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz;
+ _xw(i+_nfirst,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz;
+ _xw(i+_nfirst,2) = _x(j,2) + _pbc[2]*_zprd;
+ }
+ }
+
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap,
+ const int nfirst, const int &pbc_flag,
+ const int* const pbc) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecMolecularKokkos_PackCommSelf<LMPHostType,1,1>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecMolecularKokkos_PackCommSelf<LMPHostType,1,0>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecMolecularKokkos_PackCommSelf<LMPHostType,0,1>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecMolecularKokkos_PackCommSelf<LMPHostType,0,0>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPHostType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ if(pbc_flag) {
+ if(domain->triclinic) {
+ struct AtomVecMolecularKokkos_PackCommSelf<LMPDeviceType,1,1>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecMolecularKokkos_PackCommSelf<LMPDeviceType,1,0>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ } else {
+ if(domain->triclinic) {
+ struct AtomVecMolecularKokkos_PackCommSelf<LMPDeviceType,0,1>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ } else {
+ struct AtomVecMolecularKokkos_PackCommSelf<LMPDeviceType,0,0>
+ f(atomKK->k_x,nfirst,list,iswap,domain->xprd,domain->yprd,domain->zprd,
+ domain->xy,domain->xz,domain->yz,pbc);
+ Kokkos::parallel_for(n,f);
+ }
+ }
+ LMPDeviceType::fence();
+ }
+ return n*3;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecMolecularKokkos_UnpackComm {
+ typedef DeviceType device_type;
+
+ typename ArrayTypes<DeviceType>::t_x_array _x;
+ typename ArrayTypes<DeviceType>::t_xfloat_2d_const _buf;
+ int _first;
+
+ AtomVecMolecularKokkos_UnpackComm(
+ const typename DAT::tdual_x_array &x,
+ const typename DAT::tdual_xfloat_2d &buf,
+ const int& first):_x(x.view<DeviceType>()),_buf(buf.view<DeviceType>()),
+ _first(first) {};
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::unpack_comm_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf ) {
+ if(commKK->forward_comm_on_host) {
+ sync(Host,X_MASK);
+ modified(Host,X_MASK);
+ struct AtomVecMolecularKokkos_UnpackComm<LMPHostType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ } else {
+ sync(Device,X_MASK);
+ modified(Device,X_MASK);
+ struct AtomVecMolecularKokkos_UnpackComm<LMPDeviceType> f(atomKK->k_x,buf,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_comm(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_comm_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
+ dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
+ dz = pbc[2]*domain->zprd;
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::unpack_comm(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::unpack_comm_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_reverse(int n, int first, double *buf)
+{
+ if(n > 0)
+ sync(Host,F_MASK);
+
+ int m = 0;
+ const int last = first + n;
+ for (int i = first; i < last; i++) {
+ buf[m++] = h_f(i,0);
+ buf[m++] = h_f(i,1);
+ buf[m++] = h_f(i,2);
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::unpack_reverse(int n, int *list, double *buf)
+{
+ if(n > 0)
+ modified(Host,F_MASK);
+
+ int m = 0;
+ for (int i = 0; i < n; i++) {
+ const int j = list[i];
+ h_f(j,0) += buf[m++];
+ h_f(j,1) += buf[m++];
+ h_f(j,2) += buf[m++];
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType,int PBC_FLAG>
+struct AtomVecMolecularKokkos_PackBorder {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+
+ typename AT::t_xfloat_2d _buf;
+ const typename AT::t_int_2d_const _list;
+ const int _iswap;
+ const typename AT::t_x_array_randomread _x;
+ const typename AT::t_tagint_1d _tag;
+ const typename AT::t_int_1d _type;
+ const typename AT::t_int_1d _mask;
+ const typename AT::t_tagint_1d _molecule;
+ X_FLOAT _dx,_dy,_dz;
+
+ AtomVecMolecularKokkos_PackBorder(
+ const typename AT::t_xfloat_2d &buf,
+ const typename AT::t_int_2d_const &list,
+ const int & iswap,
+ const typename AT::t_x_array &x,
+ const typename AT::t_tagint_1d &tag,
+ const typename AT::t_int_1d &type,
+ const typename AT::t_int_1d &mask,
+ const typename AT::t_tagint_1d &molecule,
+ const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz):
+ _buf(buf),_list(list),_iswap(iswap),
+ _x(x),_tag(tag),_type(type),_mask(mask),_molecule(molecule),
+ _dx(dx),_dy(dy),_dz(dz) {}
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ const int j = _list(_iswap,i);
+ if (PBC_FLAG == 0) {
+ _buf(i,0) = _x(j,0);
+ _buf(i,1) = _x(j,1);
+ _buf(i,2) = _x(j,2);
+ _buf(i,3) = _tag(j);
+ _buf(i,4) = _type(j);
+ _buf(i,5) = _mask(j);
+ _buf(i,6) = _molecule(j);
+ } else {
+ _buf(i,0) = _x(j,0) + _dx;
+ _buf(i,1) = _x(j,1) + _dy;
+ _buf(i,2) = _x(j,2) + _dz;
+ _buf(i,3) = _tag(j);
+ _buf(i,4) = _type(j);
+ _buf(i,5) = _mask(j);
+ _buf(i,6) = _molecule(j);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::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)
+{
+ X_FLOAT dx,dy,dz;
+
+ if (pbc_flag != 0) {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if(space==Host) {
+ AtomVecMolecularKokkos_PackBorder<LMPHostType,1> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecMolecularKokkos_PackBorder<LMPDeviceType,1> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+
+ } else {
+ dx = dy = dz = 0;
+ if(space==Host) {
+ AtomVecMolecularKokkos_PackBorder<LMPHostType,0> f(
+ buf.view<LMPHostType>(), k_sendlist.view<LMPHostType>(),
+ iswap,h_x,h_tag,h_type,h_mask,h_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ AtomVecMolecularKokkos_PackBorder<LMPDeviceType,0> f(
+ buf.view<LMPDeviceType>(), k_sendlist.view<LMPDeviceType>(),
+ iswap,d_x,d_tag,d_type,d_mask,d_molecule,dx,dy,dz);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+ }
+ return n*size_border;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_border(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_border_vel(int n, int *list, double *buf,
+ int pbc_flag, int *pbc)
+{
+ int i,j,m;
+ double dx,dy,dz,dvx,dvy,dvz;
+
+ m = 0;
+ if (pbc_flag == 0) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0);
+ buf[m++] = h_x(j,1);
+ buf[m++] = h_x(j,2);
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ if (domain->triclinic == 0) {
+ dx = pbc[0]*domain->xprd;
+ dy = pbc[1]*domain->yprd;
+ dz = pbc[2]*domain->zprd;
+ } else {
+ dx = pbc[0];
+ dy = pbc[1];
+ dz = pbc[2];
+ }
+ if (!deform_vremap) {
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ } else {
+ dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
+ dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
+ dvz = pbc[2]*h_rate[2];
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_x(j,0) + dx;
+ buf[m++] = h_x(j,1) + dy;
+ buf[m++] = h_x(j,2) + dz;
+ buf[m++] = ubuf(h_tag(j)).d;
+ buf[m++] = ubuf(h_type(j)).d;
+ buf[m++] = ubuf(h_mask(j)).d;
+ buf[m++] = ubuf(h_molecule(j)).d;
+ if (mask[i] & deform_groupbit) {
+ buf[m++] = h_v(j,0) + dvx;
+ buf[m++] = h_v(j,1) + dvy;
+ buf[m++] = h_v(j,2) + dvz;
+ } else {
+ buf[m++] = h_v(j,0);
+ buf[m++] = h_v(j,1);
+ buf[m++] = h_v(j,2);
+ }
+ }
+ }
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
+
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_border_hybrid(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = h_molecule(j);
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecMolecularKokkos_UnpackBorder {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+
+ const typename AT::t_xfloat_2d_const _buf;
+ typename AT::t_x_array _x;
+ typename AT::t_tagint_1d _tag;
+ typename AT::t_int_1d _type;
+ typename AT::t_int_1d _mask;
+ typename AT::t_tagint_1d _molecule;
+ int _first;
+
+
+ AtomVecMolecularKokkos_UnpackBorder(
+ const typename AT::t_xfloat_2d_const &buf,
+ typename AT::t_x_array &x,
+ typename AT::t_tagint_1d &tag,
+ typename AT::t_int_1d &type,
+ typename AT::t_int_1d &mask,
+ typename AT::t_tagint_1d &molecule,
+ const int& first):
+ _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_molecule(molecule),
+ _first(first){
+ };
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int& i) const {
+ _x(i+_first,0) = _buf(i,0);
+ _x(i+_first,1) = _buf(i,1);
+ _x(i+_first,2) = _buf(i,2);
+ _tag(i+_first) = static_cast<int> (_buf(i,3));
+ _type(i+_first) = static_cast<int> (_buf(i,4));
+ _mask(i+_first) = static_cast<int> (_buf(i,5));
+ _molecule(i+_first) = static_cast<int> (_buf(i,6));
+
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::unpack_border_kokkos(const int &n, const int &first,
+ const DAT::tdual_xfloat_2d &buf,
+ ExecutionSpace space) {
+ modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
+ while (first+n >= nmax) grow(0);
+ modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
+ if(space==Host) {
+ struct AtomVecMolecularKokkos_UnpackBorder<LMPHostType>
+ f(buf.view<LMPHostType>(),h_x,h_tag,h_type,h_mask,h_molecule,first);
+ Kokkos::parallel_for(n,f);
+ LMPHostType::fence();
+ } else {
+ struct AtomVecMolecularKokkos_UnpackBorder<LMPDeviceType>
+ f(buf.view<LMPDeviceType>(),d_x,d_tag,d_type,d_mask,d_molecule,first);
+ Kokkos::parallel_for(n,f);
+ LMPDeviceType::fence();
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::unpack_border(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax) grow(0);
+ modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::unpack_border_vel(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ if (i == nmax) grow(0);
+ h_x(i,0) = buf[m++];
+ h_x(i,1) = buf[m++];
+ h_x(i,2) = buf[m++];
+ h_tag(i) = (tagint) ubuf(buf[m++]).i;
+ h_type(i) = (int) ubuf(buf[m++]).i;
+ h_mask(i) = (int) ubuf(buf[m++]).i;
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ h_v(i,0) = buf[m++];
+ h_v(i,1) = buf[m++];
+ h_v(i,2) = buf[m++];
+ }
+
+ if (atom->nextra_border)
+ for (int iextra = 0; iextra < atom->nextra_border; iextra++)
+ m += modify->fix[atom->extra_border[iextra]]->
+ unpack_border(n,first,&buf[m]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::unpack_border_hybrid(int n, int first, double *buf)
+{
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ h_molecule(i) = (tagint) ubuf(buf[m++]).i;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecMolecularKokkos_PackExchangeFunctor {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array_randomread _x;
+ typename AT::t_v_array_randomread _v;
+ typename AT::t_tagint_1d_randomread _tag;
+ typename AT::t_int_1d_randomread _type;
+ typename AT::t_int_1d_randomread _mask;
+ typename AT::t_imageint_1d_randomread _image;
+ typename AT::t_tagint_1d_randomread _molecule;
+ typename AT::t_int_2d_randomread _nspecial;
+ typename AT::t_tagint_2d_randomread _special;
+ typename AT::t_int_1d_randomread _num_bond;
+ typename AT::t_int_2d_randomread _bond_type;
+ typename AT::t_tagint_2d_randomread _bond_atom;
+ typename AT::t_int_1d_randomread _num_angle;
+ typename AT::t_int_2d_randomread _angle_type;
+ typename AT::t_tagint_2d_randomread _angle_atom1,_angle_atom2,_angle_atom3;
+ typename AT::t_int_1d_randomread _num_dihedral;
+ typename AT::t_int_2d_randomread _dihedral_type;
+ typename AT::t_tagint_2d_randomread _dihedral_atom1,_dihedral_atom2,
+ _dihedral_atom3,_dihedral_atom4;
+ typename AT::t_int_1d_randomread _num_improper;
+ typename AT::t_int_2d_randomread _improper_type;
+ typename AT::t_tagint_2d_randomread _improper_atom1,_improper_atom2,
+ _improper_atom3,_improper_atom4;
+ typename AT::t_x_array _xw;
+ typename AT::t_v_array _vw;
+ typename AT::t_tagint_1d _tagw;
+ typename AT::t_int_1d _typew;
+ typename AT::t_int_1d _maskw;
+ typename AT::t_imageint_1d _imagew;
+ typename AT::t_tagint_1d _moleculew;
+ typename AT::t_int_2d _nspecialw;
+ typename AT::t_tagint_2d _specialw;
+ typename AT::t_int_1d _num_bondw;
+ typename AT::t_int_2d _bond_typew;
+ typename AT::t_tagint_2d _bond_atomw;
+ typename AT::t_int_1d _num_anglew;
+ typename AT::t_int_2d _angle_typew;
+ typename AT::t_tagint_2d _angle_atom1w,_angle_atom2w,_angle_atom3w;
+ typename AT::t_int_1d _num_dihedralw;
+ typename AT::t_int_2d _dihedral_typew;
+ typename AT::t_tagint_2d _dihedral_atom1w,_dihedral_atom2w,
+ _dihedral_atom3w,_dihedral_atom4w;
+ typename AT::t_int_1d _num_improperw;
+ typename AT::t_int_2d _improper_typew;
+ typename AT::t_tagint_2d _improper_atom1w,_improper_atom2w,
+ _improper_atom3w,_improper_atom4w;
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d_const _sendlist;
+ typename AT::t_int_1d_const _copylist;
+ int _nlocal,_dim;
+ X_FLOAT _lo,_hi;
+ size_t elements;
+
+ AtomVecMolecularKokkos_PackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d sendlist,
+ typename AT::tdual_int_1d copylist,int nlocal, int dim,
+ X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _num_angle(atom->k_num_angle.view<DeviceType>()),
+ _angle_type(atom->k_angle_type.view<DeviceType>()),
+ _angle_atom1(atom->k_angle_atom1.view<DeviceType>()),
+ _angle_atom2(atom->k_angle_atom2.view<DeviceType>()),
+ _angle_atom3(atom->k_angle_atom3.view<DeviceType>()),
+ _num_dihedral(atom->k_num_dihedral.view<DeviceType>()),
+ _dihedral_type(atom->k_dihedral_type.view<DeviceType>()),
+ _dihedral_atom1(atom->k_dihedral_atom1.view<DeviceType>()),
+ _dihedral_atom2(atom->k_dihedral_atom2.view<DeviceType>()),
+ _dihedral_atom3(atom->k_dihedral_atom3.view<DeviceType>()),
+ _dihedral_atom4(atom->k_dihedral_atom4.view<DeviceType>()),
+ _num_improper(atom->k_num_improper.view<DeviceType>()),
+ _improper_type(atom->k_improper_type.view<DeviceType>()),
+ _improper_atom1(atom->k_improper_atom1.view<DeviceType>()),
+ _improper_atom2(atom->k_improper_atom2.view<DeviceType>()),
+ _improper_atom3(atom->k_improper_atom3.view<DeviceType>()),
+ _improper_atom4(atom->k_improper_atom4.view<DeviceType>()),
+ _xw(atom->k_x.view<DeviceType>()),
+ _vw(atom->k_v.view<DeviceType>()),
+ _tagw(atom->k_tag.view<DeviceType>()),
+ _typew(atom->k_type.view<DeviceType>()),
+ _maskw(atom->k_mask.view<DeviceType>()),
+ _imagew(atom->k_image.view<DeviceType>()),
+ _moleculew(atom->k_molecule.view<DeviceType>()),
+ _nspecialw(atom->k_nspecial.view<DeviceType>()),
+ _specialw(atom->k_special.view<DeviceType>()),
+ _num_bondw(atom->k_num_bond.view<DeviceType>()),
+ _bond_typew(atom->k_bond_type.view<DeviceType>()),
+ _bond_atomw(atom->k_bond_atom.view<DeviceType>()),
+ _num_anglew(atom->k_num_angle.view<DeviceType>()),
+ _angle_typew(atom->k_angle_type.view<DeviceType>()),
+ _angle_atom1w(atom->k_angle_atom1.view<DeviceType>()),
+ _angle_atom2w(atom->k_angle_atom2.view<DeviceType>()),
+ _angle_atom3w(atom->k_angle_atom3.view<DeviceType>()),
+ _num_dihedralw(atom->k_num_dihedral.view<DeviceType>()),
+ _dihedral_typew(atom->k_dihedral_type.view<DeviceType>()),
+ _dihedral_atom1w(atom->k_dihedral_atom1.view<DeviceType>()),
+ _dihedral_atom2w(atom->k_dihedral_atom2.view<DeviceType>()),
+ _dihedral_atom3w(atom->k_dihedral_atom3.view<DeviceType>()),
+ _dihedral_atom4w(atom->k_dihedral_atom4.view<DeviceType>()),
+ _num_improperw(atom->k_num_improper.view<DeviceType>()),
+ _improper_typew(atom->k_improper_type.view<DeviceType>()),
+ _improper_atom1w(atom->k_improper_atom1.view<DeviceType>()),
+ _improper_atom2w(atom->k_improper_atom2.view<DeviceType>()),
+ _improper_atom3w(atom->k_improper_atom3.view<DeviceType>()),
+ _improper_atom4w(atom->k_improper_atom4.view<DeviceType>()),
+ _sendlist(sendlist.template view<DeviceType>()),
+ _copylist(copylist.template view<DeviceType>()),
+ _nlocal(nlocal),_dim(dim),
+ _lo(lo),_hi(hi){
+ // 3 comp of x, 3 comp of v, 1 tag, 1 type, 1 mask, 1 image, 1 molecule, 3 nspecial,
+ // maxspecial special, 1 num_bond, bond_per_atom bond_type, bond_per_atom bond_atom,
+ // 1 num_angle, angle_per_atom angle_type, angle_per_atom angle_atom1, angle_atom2,
+ // and angle_atom3
+ // 1 num_dihedral, dihedral_per_atom dihedral_type, 4*dihedral_per_atom
+ // 1 num_improper, 5*improper_per_atom
+ // 1 to store buffer length
+ elements = 19+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
+ buf.template view<DeviceType>().dimension_1())/elements;
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &mysend) const {
+ int k;
+ const int i = _sendlist(mysend);
+ _buf(mysend,0) = elements;
+ int m = 1;
+ _buf(mysend,m++) = _x(i,0);
+ _buf(mysend,m++) = _x(i,1);
+ _buf(mysend,m++) = _x(i,2);
+ _buf(mysend,m++) = _v(i,0);
+ _buf(mysend,m++) = _v(i,1);
+ _buf(mysend,m++) = _v(i,2);
+ _buf(mysend,m++) = _tag(i);
+ _buf(mysend,m++) = _type(i);
+ _buf(mysend,m++) = _mask(i);
+ _buf(mysend,m++) = _image(i);
+ _buf(mysend,m++) = _molecule(i);
+ _buf(mysend,m++) = _num_bond(i);
+ for (k = 0; k < _num_bond(i); k++) {
+ _buf(mysend,m++) = _bond_type(i,k);
+ _buf(mysend,m++) = _bond_atom(i,k);
+ }
+ _buf(mysend,m++) = _num_angle(i);
+ for (k = 0; k < _num_angle(i); k++) {
+ _buf(mysend,m++) = _angle_type(i,k);
+ _buf(mysend,m++) = _angle_atom1(i,k);
+ _buf(mysend,m++) = _angle_atom2(i,k);
+ _buf(mysend,m++) = _angle_atom3(i,k);
+ }
+ _buf(mysend,m++) = _num_dihedral(i);
+ for (k = 0; k < _num_dihedral(i); k++) {
+ _buf(mysend,m++) = _dihedral_type(i,k);
+ _buf(mysend,m++) = _dihedral_atom1(i,k);
+ _buf(mysend,m++) = _dihedral_atom2(i,k);
+ _buf(mysend,m++) = _dihedral_atom3(i,k);
+ _buf(mysend,m++) = _dihedral_atom4(i,k);
+ }
+ _buf(mysend,m++) = _num_improper(i);
+ for (k = 0; k < _num_improper(i); k++) {
+ _buf(mysend,m++) = _improper_type(i,k);
+ _buf(mysend,m++) = _improper_atom1(i,k);
+ _buf(mysend,m++) = _improper_atom2(i,k);
+ _buf(mysend,m++) = _improper_atom3(i,k);
+ _buf(mysend,m++) = _improper_atom4(i,k);
+ }
+
+ _buf(mysend,m++) = _nspecial(i,0);
+ _buf(mysend,m++) = _nspecial(i,1);
+ _buf(mysend,m++) = _nspecial(i,2);
+ for (k = 0; k < _nspecial(i,2); k++)
+ _buf(mysend,m++) = _special(i,k);
+
+ const int j = _copylist(mysend);
+
+ if(j>-1) {
+ _xw(i,0) = _x(j,0);
+ _xw(i,1) = _x(j,1);
+ _xw(i,2) = _x(j,2);
+ _vw(i,0) = _v(j,0);
+ _vw(i,1) = _v(j,1);
+ _vw(i,2) = _v(j,2);
+ _tagw(i) = _tag(j);
+ _typew(i) = _type(j);
+ _maskw(i) = _mask(j);
+ _imagew(i) = _image(j);
+ _moleculew(i) = _molecule(j);
+ _num_bondw(i) = _num_bond(j);
+ for (k = 0; k < _num_bond(j); k++) {
+ _bond_typew(i,k) = _bond_type(j,k);
+ _bond_atomw(i,k) = _bond_atom(j,k);
+ }
+ _num_anglew(i) = _num_angle(j);
+ for (k = 0; k < _num_angle(j); k++) {
+ _angle_typew(i,k) = _angle_type(j,k);
+ _angle_atom1w(i,k) = _angle_atom1(j,k);
+ _angle_atom2w(i,k) = _angle_atom2(j,k);
+ _angle_atom3w(i,k) = _angle_atom3(j,k);
+ }
+ _num_dihedralw(i) = _num_dihedral(j);
+ for (k = 0; k < _num_dihedral(j); k++) {
+ _dihedral_typew(i,k) = _dihedral_type(j,k);
+ _dihedral_atom1w(i,k) = _dihedral_atom1(j,k);
+ _dihedral_atom2w(i,k) = _dihedral_atom2(j,k);
+ _dihedral_atom3w(i,k) = _dihedral_atom3(j,k);
+ _dihedral_atom4w(i,k) = _dihedral_atom4(j,k);
+ }
+ _num_improperw(i) = _num_improper(j);
+ for (k = 0; k < _num_improper(j); k++) {
+ _improper_typew(i,k) = _improper_type(j,k);
+ _improper_atom1w(i,k) = _improper_atom1(j,k);
+ _improper_atom2w(i,k) = _improper_atom2(j,k);
+ _improper_atom3w(i,k) = _improper_atom3(j,k);
+ _improper_atom4w(i,k) = _improper_atom4(j,k);
+ }
+ _nspecialw(i,0) = _nspecial(j,0);
+ _nspecialw(i,1) = _nspecial(j,1);
+ _nspecialw(i,2) = _nspecial(j,2);
+ for (k = 0; k < _nspecial(j,2); k++)
+ _specialw(i,k) = _special(j,k);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space,int dim,X_FLOAT lo,
+ X_FLOAT hi )
+{
+ const int elements = 19+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
+ if(nsend > (int) (k_buf.view<LMPHostType>().dimension_0()*
+ k_buf.view<LMPHostType>().dimension_1())/elements) {
+ int newsize = nsend*elements/k_buf.view<LMPHostType>().dimension_1()+1;
+ k_buf.resize(newsize,k_buf.view<LMPHostType>().dimension_1());
+ }
+ if(space == Host) {
+ AtomVecMolecularKokkos_PackExchangeFunctor<LMPHostType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPHostType::fence();
+ return nsend*elements;
+ } else {
+ AtomVecMolecularKokkos_PackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi);
+ Kokkos::parallel_for(nsend,f);
+ LMPDeviceType::fence();
+ return nsend*elements;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_exchange(int i, double *buf)
+{
+ int k;
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = ubuf(h_molecule(i)).d;
+
+ buf[m++] = ubuf(h_num_bond(i)).d;
+ for (k = 0; k < h_num_bond(i); k++) {
+ buf[m++] = ubuf(h_bond_type(i,k)).d;
+ buf[m++] = ubuf(h_bond_atom(i,k)).d;
+ }
+ buf[m++] = ubuf(h_num_angle(i)).d;
+ for (k = 0; k < h_num_angle(i); k++) {
+ buf[m++] = ubuf(h_angle_type(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom1(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom2(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom3(i,k)).d;
+ }
+ buf[m++] = ubuf(h_num_dihedral(i)).d;
+ for (k = 0; k < h_num_dihedral(i); k++) {
+ buf[m++] = ubuf(h_dihedral_type(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom1(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom2(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom3(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom4(i,k)).d;
+ }
+ buf[m++] = ubuf(h_num_improper(i)).d;
+ for (k = 0; k < h_num_improper(i); k++) {
+ buf[m++] = ubuf(h_improper_type(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom1(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom2(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom3(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom4(i,k)).d;
+ }
+ buf[m++] = ubuf(h_nspecial(i,0)).d;
+ buf[m++] = ubuf(h_nspecial(i,1)).d;
+ buf[m++] = ubuf(h_nspecial(i,2)).d;
+ for (k = 0; k < h_nspecial(i,2); k++)
+ buf[m++] = ubuf(h_special(i,k)).d;
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+struct AtomVecMolecularKokkos_UnpackExchangeFunctor {
+ typedef DeviceType device_type;
+ typedef ArrayTypes<DeviceType> AT;
+ typename AT::t_x_array _x;
+ typename AT::t_v_array _v;
+ typename AT::t_tagint_1d _tag;
+ typename AT::t_int_1d _type;
+ typename AT::t_int_1d _mask;
+ typename AT::t_imageint_1d _image;
+ typename AT::t_tagint_1d _molecule;
+ typename AT::t_int_2d _nspecial;
+ typename AT::t_tagint_2d _special;
+ typename AT::t_int_1d _num_bond;
+ typename AT::t_int_2d _bond_type;
+ typename AT::t_tagint_2d _bond_atom;
+ typename AT::t_int_1d _num_angle;
+ typename AT::t_int_2d _angle_type;
+ typename AT::t_tagint_2d _angle_atom1,_angle_atom2,_angle_atom3;
+ typename AT::t_int_1d _num_dihedral;
+ typename AT::t_int_2d _dihedral_type;
+ typename AT::t_tagint_2d _dihedral_atom1,_dihedral_atom2,
+ _dihedral_atom3,_dihedral_atom4;
+ typename AT::t_int_1d _num_improper;
+ typename AT::t_int_2d _improper_type;
+ typename AT::t_tagint_2d _improper_atom1,_improper_atom2,
+ _improper_atom3,_improper_atom4;
+
+ typename AT::t_xfloat_2d_um _buf;
+ typename AT::t_int_1d _nlocal;
+ int _dim;
+ X_FLOAT _lo,_hi;
+ size_t elements;
+
+ AtomVecMolecularKokkos_UnpackExchangeFunctor(
+ const AtomKokkos* atom,
+ const typename AT::tdual_xfloat_2d buf,
+ typename AT::tdual_int_1d nlocal,
+ int dim, X_FLOAT lo, X_FLOAT hi):
+ _x(atom->k_x.view<DeviceType>()),
+ _v(atom->k_v.view<DeviceType>()),
+ _tag(atom->k_tag.view<DeviceType>()),
+ _type(atom->k_type.view<DeviceType>()),
+ _mask(atom->k_mask.view<DeviceType>()),
+ _image(atom->k_image.view<DeviceType>()),
+ _molecule(atom->k_molecule.view<DeviceType>()),
+ _nspecial(atom->k_nspecial.view<DeviceType>()),
+ _special(atom->k_special.view<DeviceType>()),
+ _num_bond(atom->k_num_bond.view<DeviceType>()),
+ _bond_type(atom->k_bond_type.view<DeviceType>()),
+ _bond_atom(atom->k_bond_atom.view<DeviceType>()),
+ _num_angle(atom->k_num_angle.view<DeviceType>()),
+ _angle_type(atom->k_angle_type.view<DeviceType>()),
+ _angle_atom1(atom->k_angle_atom1.view<DeviceType>()),
+ _angle_atom2(atom->k_angle_atom2.view<DeviceType>()),
+ _angle_atom3(atom->k_angle_atom3.view<DeviceType>()),
+ _num_dihedral(atom->k_num_dihedral.view<DeviceType>()),
+ _dihedral_type(atom->k_dihedral_type.view<DeviceType>()),
+ _dihedral_atom1(atom->k_dihedral_atom1.view<DeviceType>()),
+ _dihedral_atom2(atom->k_dihedral_atom2.view<DeviceType>()),
+ _dihedral_atom3(atom->k_dihedral_atom3.view<DeviceType>()),
+ _dihedral_atom4(atom->k_dihedral_atom4.view<DeviceType>()),
+ _num_improper(atom->k_num_improper.view<DeviceType>()),
+ _improper_type(atom->k_improper_type.view<DeviceType>()),
+ _improper_atom1(atom->k_improper_atom1.view<DeviceType>()),
+ _improper_atom2(atom->k_improper_atom2.view<DeviceType>()),
+ _improper_atom3(atom->k_improper_atom3.view<DeviceType>()),
+ _improper_atom4(atom->k_improper_atom4.view<DeviceType>()),
+ _nlocal(nlocal.template view<DeviceType>()),_dim(dim),
+ _lo(lo),_hi(hi){
+
+ elements = 19+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
+ const int maxsendlist = (buf.template view<DeviceType>().dimension_0()*
+ buf.template view<DeviceType>().dimension_1())/elements;
+ buffer_view<DeviceType>(_buf,buf,maxsendlist,elements);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator() (const int &myrecv) const {
+ X_FLOAT x = _buf(myrecv,_dim+1);
+ if (x >= _lo && x < _hi) {
+ int i = Kokkos::atomic_fetch_add(&_nlocal(0),1);
+ int m = 1;
+ _x(i,0) = _buf(myrecv,m++);
+ _x(i,1) = _buf(myrecv,m++);
+ _x(i,2) = _buf(myrecv,m++);
+ _v(i,0) = _buf(myrecv,m++);
+ _v(i,1) = _buf(myrecv,m++);
+ _v(i,2) = _buf(myrecv,m++);
+ _tag(i) = _buf(myrecv,m++);
+ _type(i) = _buf(myrecv,m++);
+ _mask(i) = _buf(myrecv,m++);
+ _image(i) = _buf(myrecv,m++);
+
+ _molecule(i) = _buf(myrecv,m++);
+ _num_bond(i) = _buf(myrecv,m++);
+ int k;
+ for (k = 0; k < _num_bond(i); k++) {
+ _bond_type(i,k) = _buf(myrecv,m++);
+ _bond_atom(i,k) = _buf(myrecv,m++);
+ }
+ _num_angle(i) = _buf(myrecv,m++);
+ for (k = 0; k < _num_angle(i); k++) {
+ _angle_type(i,k) = _buf(myrecv,m++);
+ _angle_atom1(i,k) = _buf(myrecv,m++);
+ _angle_atom2(i,k) = _buf(myrecv,m++);
+ _angle_atom3(i,k) = _buf(myrecv,m++);
+ }
+ _num_dihedral(i) = _buf(myrecv,m++);
+ for (k = 0; k < _num_dihedral(i); k++) {
+ _dihedral_type(i,k) = _buf(myrecv,m++);
+ _dihedral_atom1(i,k) = _buf(myrecv,m++);
+ _dihedral_atom2(i,k) = _buf(myrecv,m++);
+ _dihedral_atom3(i,k) = _buf(myrecv,m++);
+ _dihedral_atom4(i,k) = _buf(myrecv,m++);
+ }
+ _num_improper(i) = _buf(myrecv,m++);
+ for (k = 0; k < _num_improper(i); k++) {
+ _improper_type(i,k) = _buf(myrecv,m++);
+ _improper_atom1(i,k) = _buf(myrecv,m++);
+ _improper_atom2(i,k) = _buf(myrecv,m++);
+ _improper_atom3(i,k) = _buf(myrecv,m++);
+ _improper_atom4(i,k) = _buf(myrecv,m++);
+ }
+ _nspecial(i,0) = _buf(myrecv,m++);
+ _nspecial(i,1) = _buf(myrecv,m++);
+ _nspecial(i,2) = _buf(myrecv,m++);
+ for (k = 0; k < _nspecial(i,2); k++)
+ _special(i,k) = _buf(myrecv,m++);
+ }
+ }
+};
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv,
+ int nlocal,int dim,X_FLOAT lo,X_FLOAT hi,
+ ExecutionSpace space) {
+ const size_t elements = 19+atom->maxspecial+2*atom->bond_per_atom+4*atom->angle_per_atom+
+ 5*atom->dihedral_per_atom + 5*atom->improper_per_atom;
+ if(space == Host) {
+ k_count.h_view(0) = nlocal;
+ AtomVecMolecularKokkos_UnpackExchangeFunctor<LMPHostType>
+ f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/elements,f);
+ LMPHostType::fence();
+ return k_count.h_view(0);
+ } else {
+ k_count.h_view(0) = nlocal;
+ k_count.modify<LMPHostType>();
+ k_count.sync<LMPDeviceType>();
+ AtomVecMolecularKokkos_UnpackExchangeFunctor<LMPDeviceType>
+ f(atomKK,k_buf,k_count,dim,lo,hi);
+ Kokkos::parallel_for(nrecv/elements,f);
+ LMPDeviceType::fence();
+ k_count.modify<LMPDeviceType>();
+ k_count.sync<LMPHostType>();
+
+ return k_count.h_view(0);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::unpack_exchange(double *buf)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) grow(0);
+ modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
+ MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK |
+ ANGLE_MASK | DIHEDRAL_MASK | IMPROPER_MASK | SPECIAL_MASK);
+
+ int k;
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
+
+ h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_bond(nlocal); k++) {
+ h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_num_angle(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_angle(nlocal); k++) {
+ h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_num_dihedral(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_dihedral(nlocal); k++) {
+ h_dihedral_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_dihedral_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_num_improper(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_improper(nlocal); k++) {
+ h_improper_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_improper_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+ h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i;
+ h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i;
+ h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_nspecial(nlocal,2); k++)
+ h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+
+ if (atom->nextra_grow)
+ for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
+ m += modify->fix[atom->extra_grow[iextra]]->
+ unpack_exchange(nlocal,&buf[m]);
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ size of restart data for all atoms owned by this proc
+ include extra data stored by fixes
+------------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::size_restart()
+{
+ int i;
+
+ int nlocal = atom->nlocal;
+ int n = 0;
+ for (i = 0; i < nlocal; i++)
+ n += 16 + 2*num_bond[i] + 4*num_angle[i] +
+ 5*num_dihedral[i] + 5*num_improper[i];
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ for (i = 0; i < nlocal; i++)
+ n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom I's data for restart file including extra quantities
+ xyz must be 1st 3 values, so that read_restart can test on them
+ molecular types may be negative, but write as positive
+------------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_restart(int i, double *buf)
+{
+ int m = 1;
+ buf[m++] = h_x(i,0);
+ buf[m++] = h_x(i,1);
+ buf[m++] = h_x(i,2);
+ buf[m++] = ubuf(h_tag(i)).d;
+ buf[m++] = ubuf(h_type(i)).d;
+ buf[m++] = ubuf(h_mask(i)).d;
+ buf[m++] = ubuf(h_image(i)).d;
+ buf[m++] = h_v(i,0);
+ buf[m++] = h_v(i,1);
+ buf[m++] = h_v(i,2);
+
+ buf[m++] = ubuf(h_molecule(i)).d;
+
+ buf[m++] = ubuf(h_num_bond(i)).d;
+ for (int k = 0; k < h_num_bond(i); k++) {
+ buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d;
+ buf[m++] = ubuf(h_bond_atom(i,k)).d;
+ }
+
+ buf[m++] = ubuf(h_num_angle(i)).d;
+ for (int k = 0; k < h_num_angle(i); k++) {
+ buf[m++] = ubuf(MAX(h_angle_type(i,k),-h_angle_type(i,k))).d;
+ buf[m++] = ubuf(h_angle_atom1(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom2(i,k)).d;
+ buf[m++] = ubuf(h_angle_atom3(i,k)).d;
+ }
+
+ buf[m++] = ubuf(h_num_dihedral(i)).d;
+ for (int k = 0; k < h_num_dihedral(i); k++) {
+ buf[m++] = ubuf(MAX(h_dihedral_type(i,k),-h_dihedral_type(i,k))).d;
+ buf[m++] = ubuf(h_dihedral_atom1(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom2(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom3(i,k)).d;
+ buf[m++] = ubuf(h_dihedral_atom4(i,k)).d;
+ }
+
+ buf[m++] = ubuf(h_num_improper(i)).d;
+ for (int k = 0; k < h_num_improper(i); k++) {
+ buf[m++] = ubuf(MAX(h_improper_type(i,k),-h_improper_type(i,k))).d;
+ buf[m++] = ubuf(h_improper_atom1(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom2(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom3(i,k)).d;
+ buf[m++] = ubuf(h_improper_atom4(i,k)).d;
+ }
+
+ if (atom->nextra_restart)
+ for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
+ m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
+
+ buf[0] = m;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ unpack data for one atom from restart file including extra quantities
+------------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::unpack_restart(double *buf)
+{
+ int k;
+
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ grow(0);
+ if (atom->nextra_store)
+ memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
+ }
+
+ int m = 1;
+ h_x(nlocal,0) = buf[m++];
+ h_x(nlocal,1) = buf[m++];
+ h_x(nlocal,2) = buf[m++];
+ h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
+ h_type(nlocal) = (int) ubuf(buf[m++]).i;
+ h_mask(nlocal) = (int) ubuf(buf[m++]).i;
+ h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
+ h_v(nlocal,0) = buf[m++];
+ h_v(nlocal,1) = buf[m++];
+ h_v(nlocal,2) = buf[m++];
+
+ h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
+
+ h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_bond(nlocal); k++) {
+ h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_num_angle(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_angle(nlocal); k++) {
+ h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_num_dihedral(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_dihedral(nlocal); k++) {
+ h_dihedral_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_dihedral_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_dihedral_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_num_improper(nlocal) = (int) ubuf(buf[m++]).i;
+ for (k = 0; k < h_num_improper(nlocal); k++) {
+ h_improper_type(nlocal,k) = (int) ubuf(buf[m++]).i;
+ h_improper_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ h_improper_atom4(nlocal,k) = (tagint) ubuf(buf[m++]).i;
+ }
+
+ h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
+
+ double **extra = atom->extra;
+ if (atom->nextra_store) {
+ int size = static_cast<int> (ubuf(buf[m++]).i) - m;
+ for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
+ }
+
+ atom->nlocal++;
+ return m;
+}
+
+/* ----------------------------------------------------------------------
+ create one atom of itype at coord
+ set other values to defaults
+------------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::create_atom(int itype, double *coord)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) {
+ atomKK->modified(Host,ALL_MASK);
+ grow(0);
+ }
+ atomKK->modified(Host,ALL_MASK);
+
+ tag[nlocal] = 0;
+ type[nlocal] = itype;
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+ h_mask(nlocal) = 1;
+ h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) |
+ ((imageint) IMGMAX << IMGBITS) | IMGMAX;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+
+ h_molecule(nlocal) = 0;
+ h_num_bond(nlocal) = 0;
+ h_num_angle(nlocal) = 0;
+ h_num_dihedral(nlocal) = 0;
+ h_num_improper(nlocal) = 0;
+ h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack one line from Atoms section of data file
+ initialize other atom quantities
+------------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::data_atom(double *coord, imageint imagetmp,
+ char **values)
+{
+ int nlocal = atom->nlocal;
+ if (nlocal == nmax) grow(0);
+
+ h_tag(nlocal) = atoi(values[0]);
+ if (h_tag(nlocal) <= 0)
+ error->one(FLERR,"Invalid atom ID in Atoms section of data file");
+
+ h_molecule(nlocal) = atoi(values[1]);
+ if (h_molecule(nlocal) <= 0)
+ error->one(FLERR,"Invalid molecule ID in Atoms section of data file");
+
+ h_type(nlocal) = atoi(values[2]);
+ if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
+ error->one(FLERR,"Invalid atom type in Atoms section of data file");
+
+ h_x(nlocal,0) = coord[0];
+ h_x(nlocal,1) = coord[1];
+ h_x(nlocal,2) = coord[2];
+
+ h_image(nlocal) = imagetmp;
+
+ h_mask(nlocal) = 1;
+ h_v(nlocal,0) = 0.0;
+ h_v(nlocal,1) = 0.0;
+ h_v(nlocal,2) = 0.0;
+ h_num_bond(nlocal) = 0;
+ h_num_angle(nlocal) = 0;
+ h_num_dihedral(nlocal) = 0;
+ h_num_improper(nlocal) = 0;
+
+ atom->nlocal++;
+}
+
+/* ----------------------------------------------------------------------
+ unpack hybrid quantities from one line in Atoms section of data file
+ initialize other atom quantities for this sub-style
+------------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::data_atom_hybrid(int nlocal, char **values)
+{
+ h_molecule(nlocal) = atoi(values[0]);
+ h_num_bond(nlocal) = 0;
+ h_num_angle(nlocal) = 0;
+ h_num_dihedral(nlocal) = 0;
+ h_num_improper(nlocal) = 0;
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ pack atom info for data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::pack_data(double **buf)
+{
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) {
+ buf[i][0] = h_tag(i);
+ buf[i][1] = h_molecule(i);
+ buf[i][2] = h_type(i);
+ buf[i][3] = h_x(i,0);
+ buf[i][4] = h_x(i,1);
+ buf[i][5] = h_x(i,2);
+ buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX;
+ buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+ buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ pack hybrid atom info for data file
+------------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::pack_data_hybrid(int i, double *buf)
+{
+ buf[0] = h_molecule(i);
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ write atom info to data file including 3 image flags
+------------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::write_data(FILE *fp, int n, double **buf)
+{
+ for (int i = 0; i < n; i++)
+ fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
+ (int) buf[i][0],(int) buf[i][1], (int) buf[i][2],
+ buf[i][3],buf[i][4],buf[i][5],
+ (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
+}
+
+/* ----------------------------------------------------------------------
+ write hybrid atom info to data file
+------------------------------------------------------------------------- */
+
+int AtomVecMolecularKokkos::write_data_hybrid(FILE *fp, double *buf)
+{
+ fprintf(fp," " TAGINT_FORMAT, (tagint) (buf[0]));
+ return 1;
+}
+
+/* ----------------------------------------------------------------------
+ return # of bytes of allocated memory
+------------------------------------------------------------------------- */
+
+bigint AtomVecMolecularKokkos::memory_usage()
+{
+ bigint bytes = 0;
+
+ if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
+ if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
+ if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
+ if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
+ if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
+ if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
+ if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
+
+ if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
+ if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
+ if (atom->memcheck("special"))
+ bytes += memory->usage(special,nmax,atom->maxspecial);
+
+ if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
+ if (atom->memcheck("bond_type"))
+ bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
+ if (atom->memcheck("bond_atom"))
+ bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
+
+ if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax);
+ if (atom->memcheck("angle_type"))
+ bytes += memory->usage(angle_type,nmax,atom->angle_per_atom);
+ if (atom->memcheck("angle_atom1"))
+ bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom);
+ if (atom->memcheck("angle_atom2"))
+ bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom);
+ if (atom->memcheck("angle_atom3"))
+ bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom);
+
+ if (atom->memcheck("num_dihedral")) bytes += memory->usage(num_dihedral,nmax);
+ if (atom->memcheck("dihedral_type"))
+ bytes += memory->usage(dihedral_type,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("dihedral_atom1"))
+ bytes += memory->usage(dihedral_atom1,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("dihedral_atom2"))
+ bytes += memory->usage(dihedral_atom2,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("dihedral_atom3"))
+ bytes += memory->usage(dihedral_atom3,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("dihedral_atom4"))
+ bytes += memory->usage(dihedral_atom4,nmax,atom->dihedral_per_atom);
+ if (atom->memcheck("num_improper")) bytes += memory->usage(num_improper,nmax);
+ if (atom->memcheck("improper_type"))
+ bytes += memory->usage(improper_type,nmax,atom->improper_per_atom);
+ if (atom->memcheck("improper_atom1"))
+ bytes += memory->usage(improper_atom1,nmax,atom->improper_per_atom);
+ if (atom->memcheck("improper_atom2"))
+ bytes += memory->usage(improper_atom2,nmax,atom->improper_per_atom);
+ if (atom->memcheck("improper_atom3"))
+ bytes += memory->usage(improper_atom3,nmax,atom->improper_per_atom);
+ if (atom->memcheck("improper_atom4"))
+ bytes += memory->usage(improper_atom4,nmax,atom->improper_per_atom);
+
+ return bytes;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::sync(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPDeviceType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.sync<LMPDeviceType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.sync<LMPDeviceType>();
+ atomKK->k_special.sync<LMPDeviceType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.sync<LMPDeviceType>();
+ atomKK->k_bond_type.sync<LMPDeviceType>();
+ atomKK->k_bond_atom.sync<LMPDeviceType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.sync<LMPDeviceType>();
+ atomKK->k_angle_type.sync<LMPDeviceType>();
+ atomKK->k_angle_atom1.sync<LMPDeviceType>();
+ atomKK->k_angle_atom2.sync<LMPDeviceType>();
+ atomKK->k_angle_atom3.sync<LMPDeviceType>();
+ }
+ if (mask && DIHEDRAL_MASK) {
+ atomKK->k_num_dihedral.sync<LMPDeviceType>();
+ atomKK->k_dihedral_type.sync<LMPDeviceType>();
+ atomKK->k_dihedral_atom1.sync<LMPDeviceType>();
+ atomKK->k_dihedral_atom2.sync<LMPDeviceType>();
+ atomKK->k_dihedral_atom3.sync<LMPDeviceType>();
+ atomKK->k_dihedral_atom4.sync<LMPDeviceType>();
+ }
+ if (mask && IMPROPER_MASK) {
+ atomKK->k_num_improper.sync<LMPDeviceType>();
+ atomKK->k_improper_type.sync<LMPDeviceType>();
+ atomKK->k_improper_atom1.sync<LMPDeviceType>();
+ atomKK->k_improper_atom2.sync<LMPDeviceType>();
+ atomKK->k_improper_atom3.sync<LMPDeviceType>();
+ atomKK->k_improper_atom3.sync<LMPDeviceType>();
+ }
+ } else {
+ if (mask & X_MASK) atomKK->k_x.sync<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.sync<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.sync<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.sync<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.sync<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.sync<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.sync<LMPHostType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.sync<LMPHostType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.sync<LMPHostType>();
+ atomKK->k_special.sync<LMPHostType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.sync<LMPHostType>();
+ atomKK->k_bond_type.sync<LMPHostType>();
+ atomKK->k_bond_atom.sync<LMPHostType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.sync<LMPHostType>();
+ atomKK->k_angle_type.sync<LMPHostType>();
+ atomKK->k_angle_atom1.sync<LMPHostType>();
+ atomKK->k_angle_atom2.sync<LMPHostType>();
+ atomKK->k_angle_atom3.sync<LMPHostType>();
+ }
+ if (mask && DIHEDRAL_MASK) {
+ atomKK->k_num_dihedral.sync<LMPHostType>();
+ atomKK->k_dihedral_type.sync<LMPHostType>();
+ atomKK->k_dihedral_atom1.sync<LMPHostType>();
+ atomKK->k_dihedral_atom2.sync<LMPHostType>();
+ atomKK->k_dihedral_atom3.sync<LMPHostType>();
+ atomKK->k_dihedral_atom4.sync<LMPHostType>();
+ }
+ if (mask && IMPROPER_MASK) {
+ atomKK->k_num_improper.sync<LMPHostType>();
+ atomKK->k_improper_type.sync<LMPHostType>();
+ atomKK->k_improper_atom1.sync<LMPHostType>();
+ atomKK->k_improper_atom2.sync<LMPHostType>();
+ atomKK->k_improper_atom3.sync<LMPHostType>();
+ atomKK->k_improper_atom3.sync<LMPHostType>();
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecMolecularKokkos::modified(ExecutionSpace space, unsigned int mask)
+{
+ if (space == Device) {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPDeviceType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPDeviceType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPDeviceType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPDeviceType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPDeviceType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPDeviceType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPDeviceType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.modify<LMPDeviceType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.modify<LMPDeviceType>();
+ atomKK->k_special.modify<LMPDeviceType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.modify<LMPDeviceType>();
+ atomKK->k_bond_type.modify<LMPDeviceType>();
+ atomKK->k_bond_atom.modify<LMPDeviceType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.modify<LMPDeviceType>();
+ atomKK->k_angle_type.modify<LMPDeviceType>();
+ atomKK->k_angle_atom1.modify<LMPDeviceType>();
+ atomKK->k_angle_atom2.modify<LMPDeviceType>();
+ atomKK->k_angle_atom3.modify<LMPDeviceType>();
+ }
+ if (mask && DIHEDRAL_MASK) {
+ atomKK->k_num_dihedral.modify<LMPDeviceType>();
+ atomKK->k_dihedral_type.modify<LMPDeviceType>();
+ atomKK->k_dihedral_atom1.modify<LMPDeviceType>();
+ atomKK->k_dihedral_atom2.modify<LMPDeviceType>();
+ atomKK->k_dihedral_atom3.modify<LMPDeviceType>();
+ atomKK->k_dihedral_atom4.modify<LMPDeviceType>();
+ }
+ if (mask && IMPROPER_MASK) {
+ atomKK->k_num_improper.modify<LMPDeviceType>();
+ atomKK->k_improper_type.modify<LMPDeviceType>();
+ atomKK->k_improper_atom1.modify<LMPDeviceType>();
+ atomKK->k_improper_atom2.modify<LMPDeviceType>();
+ atomKK->k_improper_atom3.modify<LMPDeviceType>();
+ atomKK->k_improper_atom3.modify<LMPDeviceType>();
+ }
+ } else {
+ if (mask & X_MASK) atomKK->k_x.modify<LMPHostType>();
+ if (mask & V_MASK) atomKK->k_v.modify<LMPHostType>();
+ if (mask & F_MASK) atomKK->k_f.modify<LMPHostType>();
+ if (mask & TAG_MASK) atomKK->k_tag.modify<LMPHostType>();
+ if (mask & TYPE_MASK) atomKK->k_type.modify<LMPHostType>();
+ if (mask & MASK_MASK) atomKK->k_mask.modify<LMPHostType>();
+ if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPHostType>();
+ if (mask && MOLECULE_MASK) atomKK->k_molecule.modify<LMPHostType>();
+ if (mask && SPECIAL_MASK) {
+ atomKK->k_nspecial.modify<LMPHostType>();
+ atomKK->k_special.modify<LMPHostType>();
+ }
+ if (mask && BOND_MASK) {
+ atomKK->k_num_bond.modify<LMPHostType>();
+ atomKK->k_bond_type.modify<LMPHostType>();
+ atomKK->k_bond_atom.modify<LMPHostType>();
+ }
+ if (mask && ANGLE_MASK) {
+ atomKK->k_num_angle.modify<LMPHostType>();
+ atomKK->k_angle_type.modify<LMPHostType>();
+ atomKK->k_angle_atom1.modify<LMPHostType>();
+ atomKK->k_angle_atom2.modify<LMPHostType>();
+ atomKK->k_angle_atom3.modify<LMPHostType>();
+ }
+ if (mask && DIHEDRAL_MASK) {
+ atomKK->k_num_dihedral.modify<LMPHostType>();
+ atomKK->k_dihedral_type.modify<LMPHostType>();
+ atomKK->k_dihedral_atom1.modify<LMPHostType>();
+ atomKK->k_dihedral_atom2.modify<LMPHostType>();
+ atomKK->k_dihedral_atom3.modify<LMPHostType>();
+ atomKK->k_dihedral_atom4.modify<LMPHostType>();
+ }
+ if (mask && IMPROPER_MASK) {
+ atomKK->k_num_improper.modify<LMPHostType>();
+ atomKK->k_improper_type.modify<LMPHostType>();
+ atomKK->k_improper_atom1.modify<LMPHostType>();
+ atomKK->k_improper_atom2.modify<LMPHostType>();
+ atomKK->k_improper_atom3.modify<LMPHostType>();
+ atomKK->k_improper_atom3.modify<LMPHostType>();
+ }
+ }
+}
diff --git a/src/KOKKOS/atom_vec_molecular_kokkos.h b/src/KOKKOS/atom_vec_molecular_kokkos.h
new file mode 100644
index 0000000000..24093beefd
--- /dev/null
+++ b/src/KOKKOS/atom_vec_molecular_kokkos.h
@@ -0,0 +1,178 @@
+/* ----------------------------------------------------------------------
+ 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 ATOM_CLASS
+
+AtomStyle(molecular/kk,AtomVecMolecularKokkos)
+
+#else
+
+#ifndef LMP_ATOM_VEC_MOLECULAR_KOKKOS_H
+#define LMP_ATOM_VEC_MOLECULAR_KOKKOS_H
+
+#include "atom_vec_kokkos.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecMolecularKokkos : public AtomVecKokkos {
+ public:
+ AtomVecMolecularKokkos(class LAMMPS *);
+ virtual ~AtomVecMolecularKokkos() {}
+ void grow(int);
+ void copy(int, int, int);
+ int pack_comm(int, int *, double *, int, int *);
+ int pack_comm_vel(int, int *, double *, int, int *);
+ void unpack_comm(int, int, double *);
+ void unpack_comm_vel(int, int, double *);
+ int pack_reverse(int, int, double *);
+ void unpack_reverse(int, int *, double *);
+ int pack_border(int, int *, double *, int, int *);
+ int pack_border_vel(int, int *, double *, int, int *);
+ int pack_border_hybrid(int, int *, double *);
+ void unpack_border(int, int, double *);
+ void unpack_border_vel(int, int, double *);
+ int unpack_border_hybrid(int, int, double *);
+ int pack_exchange(int, double *);
+ int unpack_exchange(double *);
+ int size_restart();
+ int pack_restart(int, double *);
+ int unpack_restart(double *);
+ void create_atom(int, double *);
+ void data_atom(double *, tagint, char **);
+ int data_atom_hybrid(int, char **);
+ void pack_data(double **);
+ int pack_data_hybrid(int, double *);
+ void write_data(FILE *, int, double **);
+ int write_data_hybrid(FILE *, double *);
+ bigint memory_usage();
+
+ void grow_reset();
+ int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist,
+ const int & iswap,
+ const DAT::tdual_xfloat_2d &buf,
+ const int &pbc_flag, const int pbc[]);
+ void unpack_comm_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf);
+ int pack_comm_self(const int &n, const DAT::tdual_int_2d &list,
+ const int & iswap, const int nfirst,
+ const int &pbc_flag, const int pbc[]);
+ int 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);
+ void unpack_border_kokkos(const int &n, const int &nfirst,
+ const DAT::tdual_xfloat_2d &buf,
+ ExecutionSpace space);
+ int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
+ DAT::tdual_int_1d k_sendlist,
+ DAT::tdual_int_1d k_copylist,
+ ExecutionSpace space, int dim,
+ X_FLOAT lo, X_FLOAT hi);
+ int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
+ int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
+ ExecutionSpace space);
+
+ void sync(ExecutionSpace space, unsigned int mask);
+ void modified(ExecutionSpace space, unsigned int mask);
+
+ protected:
+
+ tagint *tag;
+ int *type,*mask;
+ imageint *image;
+ double **x,**v,**f;
+
+ tagint *molecule;
+ int **nspecial;
+ tagint **special;
+ int *num_bond;
+ int **bond_type;
+ tagint **bond_atom;
+
+ int *num_angle;
+ int **angle_type;
+ tagint **angle_atom1,**angle_atom2,**angle_atom3;
+
+ int *num_dihedral;
+ int **dihedral_type;
+ tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
+ int *num_improper;
+ int **improper_type;
+ tagint **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
+
+ DAT::t_tagint_1d d_tag;
+ DAT::t_int_1d d_type, d_mask;
+ HAT::t_tagint_1d h_tag;
+ HAT::t_int_1d h_type, h_mask;
+
+ DAT::t_imageint_1d d_image;
+ HAT::t_imageint_1d h_image;
+
+ DAT::t_x_array d_x;
+ DAT::t_v_array d_v;
+ DAT::t_f_array d_f;
+ HAT::t_x_array h_x;
+ HAT::t_v_array h_v;
+ HAT::t_f_array h_f;
+
+ DAT::t_tagint_1d d_molecule;
+ DAT::t_int_2d d_nspecial;
+ DAT::t_tagint_2d d_special;
+ DAT::t_int_1d d_num_bond;
+ DAT::t_int_2d d_bond_type;
+ DAT::t_tagint_2d d_bond_atom;
+
+ HAT::t_tagint_1d h_molecule;
+ HAT::t_int_2d h_nspecial;
+ HAT::t_tagint_2d h_special;
+ HAT::t_int_1d h_num_bond;
+ HAT::t_int_2d h_bond_type;
+ HAT::t_tagint_2d h_bond_atom;
+
+ DAT::t_int_1d d_num_angle;
+ DAT::t_int_2d d_angle_type;
+ DAT::t_tagint_2d d_angle_atom1,d_angle_atom2,d_angle_atom3;
+
+ HAT::t_int_1d h_num_angle;
+ HAT::t_int_2d h_angle_type;
+ HAT::t_tagint_2d h_angle_atom1,h_angle_atom2,h_angle_atom3;
+
+ DAT::t_int_1d d_num_dihedral;
+ DAT::t_int_2d d_dihedral_type;
+ DAT::t_tagint_2d d_dihedral_atom1,d_dihedral_atom2,
+ d_dihedral_atom3,d_dihedral_atom4;
+ DAT::t_int_1d d_num_improper;
+ DAT::t_int_2d d_improper_type;
+ DAT::t_tagint_2d d_improper_atom1,d_improper_atom2,
+ d_improper_atom3,d_improper_atom4;
+
+ HAT::t_int_1d h_num_dihedral;
+ HAT::t_int_2d h_dihedral_type;
+ HAT::t_tagint_2d h_dihedral_atom1,h_dihedral_atom2,
+ h_dihedral_atom3,h_dihedral_atom4;
+ HAT::t_int_1d h_num_improper;
+ HAT::t_int_2d h_improper_type;
+ HAT::t_tagint_2d h_improper_atom1,h_improper_atom2,
+ h_improper_atom3,h_improper_atom4;
+
+ HAT::tdual_int_1d k_count;
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp
index 5211d11a02..1319503c1e 100644
--- a/src/KOKKOS/comm_kokkos.cpp
+++ b/src/KOKKOS/comm_kokkos.cpp
@@ -21,6 +21,13 @@
#include "atom_masks.h"
#include "error.h"
#include "memory.h"
+#include "force.h"
+#include "pair.h"
+#include "fix.h"
+#include "compute.h"
+#include "dump.h"
+#include "output.h"
+#include "modify.h"
using namespace LAMMPS_NS;
@@ -43,15 +50,19 @@ CommKokkos::CommKokkos(LAMMPS *lmp) : CommBrick(lmp)
// initialize comm buffers & exchange memory
- maxsend = BUFMIN;
- k_buf_send = ArrayTypes<LMPDeviceType>::
- tdual_xfloat_2d("comm:k_buf_send",(maxsend+BUFEXTRA+5)/6,6);
- buf_send = k_buf_send.view<LMPHostType>().ptr_on_device();
+ // maxsend = BUFMIN;
+ // k_buf_send = ArrayTypes<LMPDeviceType>::
+ // tdual_xfloat_2d("comm:k_buf_send",(maxsend+BUFEXTRA+5)/6,6);
+ // buf_send = k_buf_send.view<LMPHostType>().ptr_on_device();
+ maxsend = 0;
+ buf_send = NULL;
- maxrecv = BUFMIN;
- k_buf_recv = ArrayTypes<LMPDeviceType>::
- tdual_xfloat_2d("comm:k_buf_recv",(maxrecv+5)/6,6);
- buf_recv = k_buf_recv.view<LMPHostType>().ptr_on_device();
+ // maxrecv = BUFMIN;
+ // k_buf_recv = ArrayTypes<LMPDeviceType>::
+ // tdual_xfloat_2d("comm:k_buf_recv",(maxrecv+5)/6,6);
+ // buf_recv = k_buf_recv.view<LMPHostType>().ptr_on_device();
+ maxrecv = 0;
+ buf_recv = NULL;
k_exchange_sendlist = ArrayTypes<LMPDeviceType>::
tdual_int_1d("comm:k_exchange_sendlist",100);
@@ -89,6 +100,34 @@ void CommKokkos::init()
forward_comm_on_host = lmp->kokkos->forward_comm_on_host;
CommBrick::init();
+
+ int check_forward = 0;
+ int check_reverse = 0;
+ if (force->pair)
+ check_forward += force->pair->comm_forward;
+ if (force->pair)
+ check_reverse += force->pair->comm_reverse;
+
+ for (int i = 0; i < modify->nfix; i++) {
+ check_forward += modify->fix[i]->comm_forward;
+ check_reverse += modify->fix[i]->comm_reverse;
+ }
+
+ for (int i = 0; i < modify->ncompute; i++) {
+ check_forward += modify->compute[i]->comm_forward;
+ check_reverse += modify->compute[i]->comm_reverse;
+ }
+
+ for (int i = 0; i < output->ndump; i++) {
+ check_forward += output->dump[i]->comm_forward;
+ check_reverse += output->dump[i]->comm_reverse;
+ }
+
+ if (force->newton == 0) check_reverse = 0;
+ if (force->pair) check_reverse += force->pair->comm_reverse_off;
+
+ if(check_reverse || check_forward)
+ forward_comm_classic = true;
}
/* ----------------------------------------------------------------------
@@ -98,8 +137,7 @@ void CommKokkos::init()
void CommKokkos::forward_comm(int dummy)
{
-
- if (!forward_comm_classic) {
+ if (!forward_comm_classic) {
if (forward_comm_on_host) forward_comm_device<LMPHostType>(dummy);
else forward_comm_device<LMPDeviceType>(dummy);
return;
@@ -205,6 +243,68 @@ void CommKokkos::forward_comm_device(int dummy)
}
}
}
+void CommKokkos::reverse_comm()
+{
+ k_sendlist.sync<LMPHostType>();
+ if (comm_f_only)
+ atomKK->sync(Host,F_MASK);
+ else
+ atomKK->sync(Host,ALL_MASK);
+ CommBrick::reverse_comm();
+ if (comm_f_only)
+ atomKK->modified(Host,F_MASK);
+ else
+ atomKK->modified(Host,ALL_MASK);
+ atomKK->sync(Device,ALL_MASK);
+}
+
+void CommKokkos::forward_comm_fix(Fix *fix)
+{
+ k_sendlist.sync<LMPHostType>();
+ CommBrick::forward_comm_fix(fix);
+}
+
+void CommKokkos::reverse_comm_fix(Fix *fix)
+{
+ k_sendlist.sync<LMPHostType>();
+ CommBrick::reverse_comm_fix(fix);
+}
+
+void CommKokkos::forward_comm_compute(Compute *compute)
+{
+ k_sendlist.sync<LMPHostType>();
+ CommBrick::forward_comm_compute(compute);
+}
+
+void CommKokkos::reverse_comm_compute(Compute *compute)
+{
+ k_sendlist.sync<LMPHostType>();
+ CommBrick::reverse_comm_compute(compute);
+}
+
+void CommKokkos::forward_comm_pair(Pair *pair)
+{
+ k_sendlist.sync<LMPHostType>();
+ CommBrick::forward_comm_pair(pair);
+}
+
+void CommKokkos::reverse_comm_pair(Pair *pair)
+{
+ k_sendlist.sync<LMPHostType>();
+ CommBrick::reverse_comm_pair(pair);
+}
+
+void CommKokkos::forward_comm_dump(Dump *dump)
+{
+ k_sendlist.sync<LMPHostType>();
+ CommBrick::forward_comm_dump(dump);
+}
+
+void CommKokkos::reverse_comm_dump(Dump *dump)
+{
+ k_sendlist.sync<LMPHostType>();
+ CommBrick::reverse_comm_dump(dump);
+}
/* ----------------------------------------------------------------------
exchange: move atoms to correct processors
@@ -219,6 +319,16 @@ void CommKokkos::forward_comm_device(int dummy)
void CommKokkos::exchange()
{
+ if(atom->nextra_grow + atom->nextra_border) {
+ if(!exchange_comm_classic) {
+ static int print = 1;
+ if(print) {
+ error->warning(FLERR,"Kokkos communication does not currently support fixes sending data. Switching to classic communication.");
+ print = 0;
+ }
+ exchange_comm_classic = true;
+ }
+ }
if (!exchange_comm_classic) {
if (exchange_comm_on_host) exchange_device<LMPHostType>();
else exchange_device<LMPDeviceType>();
@@ -463,10 +573,12 @@ void CommKokkos::borders()
}
atomKK->sync(Host,ALL_MASK);
+
k_sendlist.modify<LMPHostType>();
atomKK->modified(Host,ALL_MASK);
-
CommBrick::borders();
+ k_sendlist.modify<LMPHostType>();
+ atomKK->modified(Host,ALL_MASK);
}
/* ---------------------------------------------------------------------- */
@@ -496,7 +608,7 @@ struct BuildBorderListFunctor {
KOKKOS_INLINE_FUNCTION
- void operator() (DeviceType dev) const {
+ void operator() (typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const {
const int chunk = ((nlast - nfirst + dev.league_size() - 1 ) /
dev.league_size());
const int teamstart = chunk*dev.league_rank() + nfirst;
@@ -517,7 +629,7 @@ struct BuildBorderListFunctor {
}
}
- size_t shmem_size() const { return 1000u;}
+ size_t shmem_size(const int team_size) const { (void) team_size; return 1000u;}
};
/* ---------------------------------------------------------------------- */
@@ -591,16 +703,19 @@ void CommKokkos::borders_device() {
total_send.template modify<DeviceType>();
total_send.template sync<LMPDeviceType>();
}
+
BuildBorderListFunctor<DeviceType> f(atomKK->k_x,k_sendlist,
total_send,nfirst,nlast,dim,lo,hi,iswap,maxsendlist[iswap]);
- Kokkos::ParallelWorkRequest config((nlast-nfirst+127)/128,128);
+ Kokkos::TeamPolicy<DeviceType> config((nlast-nfirst+127)/128,128);
Kokkos::parallel_for(config,f);
DeviceType::fence();
+
total_send.template modify<DeviceType>();
total_send.template sync<LMPHostType>();
if(total_send.h_view(0) >= maxsendlist[iswap]) {
grow_list(iswap,total_send.h_view(0));
+ k_sendlist.modify<DeviceType>();
total_send.h_view(0) = 0;
if(exec_space == Device) {
total_send.template modify<LMPHostType>();
@@ -608,7 +723,7 @@ void CommKokkos::borders_device() {
}
BuildBorderListFunctor<DeviceType> f(atomKK->k_x,k_sendlist,
total_send,nfirst,nlast,dim,lo,hi,iswap,maxsendlist[iswap]);
- Kokkos::ParallelWorkRequest config((nlast-nfirst+127)/128,128);
+ Kokkos::TeamPolicy<DeviceType> config((nlast-nfirst+127)/128,128);
Kokkos::parallel_for(config,f);
DeviceType::fence();
total_send.template modify<DeviceType>();
@@ -742,6 +857,25 @@ void CommKokkos::borders_device() {
atomKK->modified(exec_space,ALL_MASK);
DeviceType::fence();
}
+/* ----------------------------------------------------------------------
+ realloc the size of the send buffer as needed with BUFFACTOR and bufextra
+ if flag = 1, realloc
+ if flag = 0, don't need to realloc with copy, just free/malloc
+------------------------------------------------------------------------- */
+
+void CommKokkos::grow_send(int n, int flag)
+{
+ grow_send_kokkos(n,flag,Host);
+}
+
+/* ----------------------------------------------------------------------
+ free/malloc the size of the recv buffer as needed with BUFFACTOR
+------------------------------------------------------------------------- */
+
+void CommKokkos::grow_recv(int n)
+{
+ grow_recv_kokkos(n,Host);
+}
/* ----------------------------------------------------------------------
realloc the size of the send buffer as needed with BUFFACTOR & BUFEXTRA
diff --git a/src/KOKKOS/comm_kokkos.h b/src/KOKKOS/comm_kokkos.h
index 46d3552d2d..539156af09 100644
--- a/src/KOKKOS/comm_kokkos.h
+++ b/src/KOKKOS/comm_kokkos.h
@@ -33,9 +33,19 @@ class CommKokkos : public CommBrick {
void init();
void forward_comm(int dummy = 0); // forward comm of atom coords
+ void reverse_comm(); // reverse comm of atom coords
void exchange(); // move atoms to new procs
void borders(); // setup list of atoms to comm
+ void forward_comm_pair(class Pair *); // forward comm from a Pair
+ void reverse_comm_pair(class Pair *); // reverse comm from a Pair
+ void forward_comm_fix(class Fix *); // forward comm from a Fix
+ void reverse_comm_fix(class Fix *); // reverse comm from a Fix
+ void forward_comm_compute(class Compute *); // forward from a Compute
+ void reverse_comm_compute(class Compute *); // reverse from a Compute
+ void forward_comm_dump(class Dump *); // forward comm from a Dump
+ void reverse_comm_dump(class Dump *); // reverse comm from a Dump
+
template<class DeviceType> void forward_comm_device(int dummy);
template<class DeviceType> void exchange_device();
template<class DeviceType> void borders_device();
@@ -48,6 +58,8 @@ class CommKokkos : public CommBrick {
//double *buf_send; // send buffer for all comm
//double *buf_recv; // recv buffer for all comm
+ void grow_send(int, int);
+ void grow_recv(int);
void grow_send_kokkos(int, int, ExecutionSpace space = Host);
void grow_recv_kokkos(int, ExecutionSpace space = Host);
void grow_list(int, int);
diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp
new file mode 100644
index 0000000000..cd34d3a964
--- /dev/null
+++ b/src/KOKKOS/fix_langevin_kokkos.cpp
@@ -0,0 +1,810 @@
+/* ----------------------------------------------------------------------
+ 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 "stdio.h"
+#include "string.h"
+#include "fix_langevin_kokkos.h"
+#include "atom_masks.h"
+#include "atom_kokkos.h"
+#include "force.h"
+#include "update.h"
+#include "respa.h"
+#include "error.h"
+#include "memory.h"
+#include "group.h"
+#include "random_mars.h"
+#include "compute.h"
+#include "comm.h"
+#include "modify.h"
+#include "input.h"
+#include "variable.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+enum{NOBIAS,BIAS};
+enum{CONSTANT,EQUAL,ATOM};
+#define SINERTIA 0.4 // moment of inertia prefactor for sphere
+#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+FixLangevinKokkos<DeviceType>::FixLangevinKokkos(LAMMPS *lmp, int narg, char **arg) :
+ FixLangevin(lmp, narg, arg),rand_pool(seed + comm->me)
+{
+ atomKK = (AtomKokkos *) atom;
+ int ntypes = atomKK->ntypes;
+
+ // allocate per-type arrays for force prefactors
+ memory->create_kokkos(k_gfactor1,gfactor1,ntypes+1,"langevin:gfactor1");
+ memory->create_kokkos(k_gfactor2,gfactor2,ntypes+1,"langevin:gfactor2");
+ memory->create_kokkos(k_ratio,ratio,ntypes+1,"langevin:ratio");
+ d_gfactor1 = k_gfactor1.template view<DeviceType>();
+ h_gfactor1 = k_gfactor1.template view<LMPHostType>();
+ d_gfactor2 = k_gfactor2.template view<DeviceType>();
+ h_gfactor2 = k_gfactor2.template view<LMPHostType>();
+ d_ratio = k_ratio.template view<DeviceType>();
+ h_ratio = k_ratio.template view<LMPHostType>();
+
+ // optional args
+ for (int i = 1; i <= ntypes; i++) ratio[i] = 1.0;
+ k_ratio.template modify<LMPHostType>();
+
+ if(gjfflag){
+ nvalues = 3;
+ grow_arrays(atomKK->nmax);
+ atom->add_callback(0);
+ // initialize franprev to zero
+ for (int i = 0; i < atomKK->nlocal; i++) {
+ franprev[i][0] = 0.0;
+ franprev[i][1] = 0.0;
+ franprev[i][2] = 0.0;
+ }
+ k_franprev.template modify<LMPHostType>();
+ }
+ if(zeroflag){
+ k_fsumall = tdual_double_1d_3n("langevin:fsumall");
+ h_fsumall = k_fsumall.template view<LMPHostType>();
+ d_fsumall = k_fsumall.template view<DeviceType>();
+ }
+
+ execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+ datamask_read = V_MASK | F_MASK | MASK_MASK | RMASS_MASK | TYPE_MASK;
+ datamask_modify = F_MASK;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+FixLangevinKokkos<DeviceType>::~FixLangevinKokkos()
+{
+ memory->destroy_kokkos(k_gfactor1,gfactor1);
+ memory->destroy_kokkos(k_gfactor2,gfactor2);
+ memory->destroy_kokkos(k_ratio,ratio);
+ memory->destroy_kokkos(k_flangevin,flangevin);
+ if(gjfflag) memory->destroy_kokkos(k_franprev,franprev);
+ memory->destroy_kokkos(k_tforce,tforce);
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void FixLangevinKokkos<DeviceType>::init()
+{
+ FixLangevin::init();
+ if(oflag)
+ error->all(FLERR,"Fix langevin omega is not yet implemented with kokkos");
+ if(ascale)
+ error->all(FLERR,"Fix langevin angmom is not yet implemented with kokkos");
+
+ // prefactors are modified in the init
+ k_gfactor1.template modify<LMPHostType>();
+ k_gfactor2.template modify<LMPHostType>();
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void FixLangevinKokkos<DeviceType>::grow_arrays(int nmax)
+{
+ memory->grow_kokkos(k_franprev,franprev,nmax,3,"langevin:franprev");
+ d_franprev = k_franprev.template view<DeviceType>();
+ h_franprev = k_franprev.template view<LMPHostType>();
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void FixLangevinKokkos<DeviceType>::post_force(int vflag)
+{
+ // sync the device views which might have been modified on host
+ atomKK->sync(execution_space,datamask_read);
+ rmass = atomKK->rmass;
+ f = atomKK->k_f.template view<DeviceType>();
+ v = atomKK->k_v.template view<DeviceType>();
+ type = atomKK->k_type.template view<DeviceType>();
+ mask = atomKK->k_mask.template view<DeviceType>();
+
+ k_gfactor1.template sync<DeviceType>();
+ k_gfactor2.template sync<DeviceType>();
+ k_ratio.template sync<DeviceType>();
+ if(gjfflag) k_franprev.template sync<DeviceType>();
+
+ boltz = force->boltz;
+ dt = update->dt;
+ mvv2e = force->mvv2e;
+ ftm2v = force->ftm2v;
+ fran_prop_const = sqrt(24.0*boltz/t_period/dt/mvv2e);
+
+ compute_target(); // modifies tforce vector, hence sync here
+ k_tforce.template sync<DeviceType>();
+
+ double fsum[3],fsumall[3];
+ bigint count;
+ int nlocal = atomKK->nlocal;
+
+ if (zeroflag) {
+ fsum[0] = fsum[1] = fsum[2] = 0.0;
+ count = group->count(igroup);
+ if (count == 0)
+ error->all(FLERR,"Cannot zero Langevin force of 0 atoms");
+ }
+
+ // reallocate flangevin if necessary
+ if (tallyflag) {
+ if (nlocal > maxatom1) {
+ memory->destroy_kokkos(k_flangevin,flangevin);
+ maxatom1 = atomKK->nmax;
+ memory->create_kokkos(k_flangevin,flangevin,maxatom1,3,"langevin:flangevin");
+ d_flangevin = k_flangevin.template view<DeviceType>();
+ h_flangevin = k_flangevin.template view<LMPHostType>();
+ }
+ }
+
+ // account for bias velocity
+ if(tbiasflag == BIAS){
+ temperature->compute_scalar();
+ temperature->remove_bias_all(); // modifies velocities
+ // if temeprature compute is kokkosized host-devcie comm won't be needed
+ atomKK->modified(Host,V_MASK);
+ atomKK->sync(execution_space,V_MASK);
+ }
+
+ // compute langevin force in parallel on the device
+ FSUM s_fsum;
+ if (tstyle == ATOM)
+ if (gjfflag)
+ if (tallyflag)
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,1,1,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else{
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,1,1,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,1,1,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,1,1,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,1,0,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,1,0,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,1,0,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else{
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,1,0,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,0,1,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,0,1,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,0,1,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,0,1,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,0,0,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,0,0,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,0,0,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,1,0,0,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (tallyflag)
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,1,1,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,1,1,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,1,1,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,1,1,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,1,0,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,1,0,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,1,0,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,1,0,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,0,1,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,0,1,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,0,1,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,0,1,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,0,0,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,0,0,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,0,0,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,1,0,0,0,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (gjfflag)
+ if (tallyflag)
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,1,1,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,1,1,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,1,1,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,1,1,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,1,0,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,1,0,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,1,0,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,1,0,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,0,1,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,0,1,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,0,1,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,0,1,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,0,0,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,0,0,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,0,0,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,1,0,0,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (tallyflag)
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,1,1,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,1,1,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,1,1,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,1,1,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,1,0,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,1,0,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,1,0,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,1,0,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (tbiasflag == BIAS)
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,0,1,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,0,1,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,0,1,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,0,1,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (rmass)
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,0,0,1,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,0,0,1,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+ else
+ if (zeroflag) {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,0,0,0,1> post_functor(this);
+ Kokkos::parallel_reduce(nlocal,post_functor,s_fsum);
+ }
+ else {
+ FixLangevinKokkosPostForceFunctor<DeviceType,0,0,0,0,0,0> post_functor(this);
+ Kokkos::parallel_for(nlocal,post_functor);
+ }
+
+ DeviceType::fence();
+
+ if(tbiasflag == BIAS){
+ temperature->restore_bias_all(); // modifies velocities
+ atomKK->modified(Host,V_MASK);
+ }
+
+ // set modify flags for the views modified in post_force functor
+ if (gjfflag) k_franprev.template modify<DeviceType>();
+ if (tallyflag) k_flangevin.template modify<DeviceType>();
+
+ // set total force to zero
+ if (zeroflag) {
+ fsum[0] = s_fsum.fx; fsum[1] = s_fsum.fy; fsum[2] = s_fsum.fz;
+ MPI_Allreduce(fsum,fsumall,3,MPI_DOUBLE,MPI_SUM,world);
+ h_fsumall(0) = fsumall[0]/count;
+ h_fsumall(1) = fsumall[1]/count;
+ h_fsumall(2) = fsumall[2]/count;
+ k_fsumall.template modify<LMPHostType>();
+ k_fsumall.template sync<DeviceType>();
+ // set total force zero in parallel on the device
+ FixLangevinKokkosZeroForceFunctor<DeviceType> zero_functor(this);
+ Kokkos::parallel_for(nlocal,zero_functor);
+ DeviceType::fence();
+ }
+ // f is modified by both post_force and zero_force functors
+ atomKK->modified(execution_space,datamask_modify);
+
+ // thermostat omega and angmom
+ // if (oflag) omega_thermostat();
+ // if (ascale) angmom_thermostat();
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+template<int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
+ int Tp_BIAS, int Tp_RMASS, int Tp_ZERO>
+KOKKOS_INLINE_FUNCTION
+FSUM FixLangevinKokkos<DeviceType>::post_force_item(int i) const
+{
+ FSUM fsum;
+ double fdrag[3],fran[3];
+ double gamma1,gamma2;
+ double fswap;
+ double tsqrt_t = tsqrt;
+
+ if (mask[i] & groupbit) {
+ rand_type rand_gen = rand_pool.get_state();
+ if(Tp_TSTYLEATOM) tsqrt_t = sqrt(d_tforce[i]);
+ if(Tp_RMASS){
+ gamma1 = -rmass[i] / t_period / ftm2v;
+ gamma2 = sqrt(rmass[i]) * fran_prop_const / ftm2v;
+ gamma1 *= 1.0/d_ratio[type[i]];
+ gamma2 *= 1.0/sqrt(d_ratio[type[i]]) * tsqrt_t;
+ } else {
+ gamma1 = d_gfactor1[type[i]];
+ gamma2 = d_gfactor2[type[i]] * tsqrt_t;
+ }
+
+ fran[0] = gamma2 * (rand_gen.drand() - 0.5); //(random->uniform()-0.5);
+ fran[1] = gamma2 * (rand_gen.drand() - 0.5); //(random->uniform()-0.5);
+ fran[2] = gamma2 * (rand_gen.drand() - 0.5); //(random->uniform()-0.5);
+
+ if(Tp_BIAS){
+ fdrag[0] = gamma1*v(i,0);
+ fdrag[1] = gamma1*v(i,1);
+ fdrag[2] = gamma1*v(i,2);
+ if (v(i,0) == 0.0) fran[0] = 0.0;
+ if (v(i,1) == 0.0) fran[1] = 0.0;
+ if (v(i,2) == 0.0) fran[2] = 0.0;
+ }else{
+ fdrag[0] = gamma1*v(i,0);
+ fdrag[1] = gamma1*v(i,1);
+ fdrag[2] = gamma1*v(i,2);
+ }
+
+ if (Tp_GJF) {
+ fswap = 0.5*(fran[0]+d_franprev(i,0));
+ d_franprev(i,0) = fran[0];
+ fran[0] = fswap;
+ fswap = 0.5*(fran[1]+d_franprev(i,1));
+ d_franprev(i,1) = fran[1];
+ fran[1] = fswap;
+ fswap = 0.5*(fran[2]+d_franprev(i,2));
+ d_franprev(i,2) = fran[2];
+ fran[2] = fswap;
+
+ fdrag[0] *= gjffac;
+ fdrag[1] *= gjffac;
+ fdrag[2] *= gjffac;
+ fran[0] *= gjffac;
+ fran[1] *= gjffac;
+ fran[2] *= gjffac;
+ f(i,0) *= gjffac;
+ f(i,1) *= gjffac;
+ f(i,2) *= gjffac;
+ }
+
+ f(i,0) += fdrag[0] + fran[0];
+ f(i,1) += fdrag[1] + fran[1];
+ f(i,2) += fdrag[2] + fran[2];
+
+ if (Tp_TALLY) {
+ d_flangevin(i,0) = fdrag[0] + fran[0];
+ d_flangevin(i,1) = fdrag[1] + fran[1];
+ d_flangevin(i,2) = fdrag[2] + fran[2];
+ }
+
+ if (Tp_ZERO) {
+ fsum.fx = fran[0];
+ fsum.fy = fran[1];
+ fsum.fz = fran[2];
+ }
+ rand_pool.free_state(rand_gen);
+ }
+
+ return fsum;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+void FixLangevinKokkos<DeviceType>::zero_force_item(int i) const
+{
+ if (mask[i] & groupbit) {
+ f(i,0) -= d_fsumall[0];
+ f(i,1) -= d_fsumall[1];
+ f(i,2) -= d_fsumall[2];
+ }
+
+}
+
+/* ----------------------------------------------------------------------
+ set current t_target and t_sqrt
+ ------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void FixLangevinKokkos<DeviceType>::compute_target()
+{
+ atomKK->sync(Host, MASK_MASK);
+ mask = atomKK->k_mask.template view<DeviceType>();
+ int nlocal = atomKK->nlocal;
+
+ double delta = update->ntimestep - update->beginstep;
+ if (delta != 0.0) delta /= update->endstep - update->beginstep;
+
+ // if variable temp, evaluate variable, wrap with clear/add
+ // reallocate tforce array if necessary
+
+ if (tstyle == CONSTANT) {
+ t_target = t_start + delta * (t_stop-t_start);
+ tsqrt = sqrt(t_target);
+ } else {
+ modify->clearstep_compute();
+ if (tstyle == EQUAL) {
+ t_target = input->variable->compute_equal(tvar);
+ if (t_target < 0.0)
+ error->one(FLERR,"Fix langevin variable returned negative temperature");
+ tsqrt = sqrt(t_target);
+ } else {
+ if (nlocal > maxatom2) {
+ maxatom2 = atom->nmax;
+ memory->destroy_kokkos(k_tforce,tforce);
+ memory->create_kokkos(k_tforce,tforce,maxatom2,"langevin:tforce");
+ d_tforce = k_tforce.template view<DeviceType>();
+ h_tforce = k_tforce.template view<LMPHostType>();
+ }
+ input->variable->compute_atom(tvar,igroup,tforce,1,0); // tforce is modified on host
+ k_tforce.template modify<LMPHostType>();
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit)
+ if (h_tforce[i] < 0.0)
+ error->one(FLERR,
+ "Fix langevin variable returned negative temperature");
+ }
+ modify->addstep_compute(update->ntimestep + 1);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void FixLangevinKokkos<DeviceType>::reset_dt()
+{
+ if (atomKK->mass) {
+ for (int i = 1; i <= atomKK->ntypes; i++) {
+ h_gfactor2[i] = sqrt(atomKK->mass[i]) *
+ sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
+ force->ftm2v;
+ h_gfactor2[i] *= 1.0/sqrt(h_ratio[i]);
+ }
+ k_gfactor2.template modify<LMPHostType>();
+ }
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+double FixLangevinKokkos<DeviceType>::compute_scalar()
+{
+ if (!tallyflag || flangevin == NULL) return 0.0;
+
+ v = atomKK->k_v.template view<DeviceType>();
+ mask = atomKK->k_mask.template view<DeviceType>();
+
+ // capture the very first energy transfer to thermal reservoir
+
+ if (update->ntimestep == update->beginstep) {
+ energy_onestep = 0.0;
+ atomKK->sync(execution_space,V_MASK | MASK_MASK);
+ int nlocal = atomKK->nlocal;
+ k_flangevin.template sync<DeviceType>();
+ FixLangevinKokkosTallyEnergyFunctor<DeviceType> scalar_functor(this);
+ Kokkos::parallel_reduce(nlocal,scalar_functor,energy_onestep);
+ DeviceType::fence();
+ energy = 0.5*energy_onestep*update->dt;
+ }
+
+ // convert midstep energy back to previous fullstep energy
+ double energy_me = energy - 0.5*energy_onestep*update->dt;
+ double energy_all;
+ MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
+ return -energy_all;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+KOKKOS_INLINE_FUNCTION
+double FixLangevinKokkos<DeviceType>::compute_energy_item(int i) const
+{
+ double energy;
+ if (mask[i] & groupbit)
+ energy = d_flangevin(i,0)*v(i,0) + d_flangevin(i,1)*v(i,1) +
+ d_flangevin(i,2)*v(i,2);
+ return energy;
+}
+
+/* ----------------------------------------------------------------------
+ tally energy transfer to thermal reservoir
+ ------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void FixLangevinKokkos<DeviceType>::end_of_step()
+{
+ if (!tallyflag) return;
+
+ v = atomKK->k_v.template view<DeviceType>();
+ mask = atomKK->k_mask.template view<DeviceType>();
+
+ atomKK->sync(execution_space,V_MASK | MASK_MASK);
+ int nlocal = atomKK->nlocal;
+
+ energy_onestep = 0.0;
+
+ k_flangevin.template sync<DeviceType>();
+ FixLangevinKokkosTallyEnergyFunctor<DeviceType> tally_functor(this);
+ Kokkos::parallel_reduce(nlocal,tally_functor,energy_onestep);
+ DeviceType::fence();
+
+ energy += energy_onestep*update->dt;
+}
+
+/* ----------------------------------------------------------------------
+ copy values within local atom-based array
+ ------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void FixLangevinKokkos<DeviceType>::copy_arrays(int i, int j, int delflag)
+{
+ for (int m = 0; m < nvalues; m++)
+ h_franprev(j,m) = h_franprev(i,m);
+
+ k_franprev.template modify<LMPHostType>();
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void FixLangevinKokkos<DeviceType>::cleanup_copy()
+{
+ random = NULL;
+ tstr = NULL;
+ gfactor1 = NULL;
+ gfactor2 = NULL;
+ ratio = NULL;
+ id_temp = NULL;
+ flangevin = NULL;
+ tforce = NULL;
+ gjfflag = 0;
+ franprev = NULL;
+ id = style = NULL;
+ vatom = NULL;
+}
+
+template class FixLangevinKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class FixLangevinKokkos<LMPHostType>;
+#endif
diff --git a/src/KOKKOS/fix_langevin_kokkos.h b/src/KOKKOS/fix_langevin_kokkos.h
new file mode 100644
index 0000000000..48a7d5ec57
--- /dev/null
+++ b/src/KOKKOS/fix_langevin_kokkos.h
@@ -0,0 +1,266 @@
+/* ----------------------------------------------------------------------
+ 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(langevin/kk,FixLangevinKokkos<LMPDeviceType>)
+FixStyle(langevin/kk/device,FixLangevinKokkos<LMPDeviceType>)
+FixStyle(langevin/kk/host,FixLangevinKokkos<LMPHostType>)
+
+#else
+
+#ifndef LMP_FIX_LANGEVIN_KOKKOS_H
+#define LMP_FIX_LANGEVIN_KOKKOS_H
+
+#include "fix_langevin.h"
+#include "kokkos_type.h"
+#include "Kokkos_Random.hpp"
+#include "comm_kokkos.h"
+
+namespace LAMMPS_NS {
+
+ struct s_FSUM {
+ double fx, fy, fz;
+ KOKKOS_INLINE_FUNCTION
+ s_FSUM() {
+ fx = fy = fz = 0.0;
+ }
+ KOKKOS_INLINE_FUNCTION
+ s_FSUM& operator+=(const s_FSUM &rhs){
+ fx += rhs.fx;
+ fy += rhs.fy;
+ fz += rhs.fz;
+ return *this;
+ }
+ };
+ typedef s_FSUM FSUM;
+
+ template<class DeviceType>
+ class FixLangevinKokkos;
+
+ template<class DeviceType,int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
+ int Tp_BIAS, int Tp_RMASS, int Tp_ZERO>
+ class FixLangevinKokkosPostForceFunctor;
+
+ template<class DeviceType> class FixLangevinKokkosZeroForceFunctor;
+
+ template<class DeviceType> class FixLangevinKokkosTallyEnergyFunctor;
+
+ template<class DeviceType>
+ class FixLangevinKokkos : public FixLangevin {
+ public:
+ FixLangevinKokkos(class LAMMPS *, int, char **);
+ ~FixLangevinKokkos();
+
+ void cleanup_copy();
+ void init();
+ void post_force(int);
+ void reset_dt();
+ void grow_arrays(int);
+ void copy_arrays(int i, int j, int delflag);
+ double compute_scalar();
+ void end_of_step();
+
+ template<int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
+ int Tp_BIAS, int Tp_RMASS, int Tp_ZERO>
+ KOKKOS_INLINE_FUNCTION
+ FSUM post_force_item(int) const;
+
+ KOKKOS_INLINE_FUNCTION
+ void zero_force_item(int) const;
+
+ KOKKOS_INLINE_FUNCTION
+ double compute_energy_item(int) const;
+
+ private:
+ class CommKokkos *commKK;
+ class AtomKokkos *atomKK;
+ double *rmass;
+ typename ArrayTypes<DeviceType>::tdual_double_2d k_franprev;
+ typename ArrayTypes<DeviceType>::t_double_2d d_franprev;
+ HAT::t_double_2d h_franprev;
+
+ typename ArrayTypes<DeviceType>::tdual_double_2d k_flangevin;
+ typename ArrayTypes<DeviceType>::t_double_2d d_flangevin;
+ HAT::t_double_2d h_flangevin;
+
+ typename ArrayTypes<DeviceType>::tdual_double_1d k_tforce;
+ typename ArrayTypes<DeviceType>::t_double_1d d_tforce;
+ HAT::t_double_1d h_tforce;
+
+ typename ArrayTypes<DeviceType>::t_v_array v;
+ typename ArrayTypes<DeviceType>::t_f_array f;
+ typename ArrayTypes<DeviceType>::t_int_1d type;
+ typename ArrayTypes<DeviceType>::t_int_1d mask;
+
+ typename ArrayTypes<DeviceType>::tdual_double_1d k_gfactor1, k_gfactor2, k_ratio;
+ typename ArrayTypes<DeviceType>::t_double_1d d_gfactor1, d_gfactor2, d_ratio;
+ HAT::t_double_1d h_gfactor1, h_gfactor2, h_ratio;
+
+ typedef Kokkos::DualView<double[3], DeviceType>
+ tdual_double_1d_3n;
+ tdual_double_1d_3n k_fsumall;
+ typename tdual_double_1d_3n::t_dev d_fsumall;
+ typename tdual_double_1d_3n::t_host h_fsumall;
+
+ double boltz,dt,mvv2e,ftm2v,fran_prop_const;
+
+ void compute_target();
+
+ Kokkos::Random_XorShift64_Pool<DeviceType> rand_pool;
+ typedef typename Kokkos::Random_XorShift64_Pool<DeviceType>::generator_type rand_type;
+
+ };
+
+ template <class DeviceType,int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
+ int Tp_BIAS, int Tp_RMASS, int Tp_ZERO>
+ struct FixLangevinKokkosPostForceFunctor {
+
+ typedef DeviceType device_type;
+ typedef FSUM value_type;
+ FixLangevinKokkos<DeviceType> c;
+
+ FixLangevinKokkosPostForceFunctor(FixLangevinKokkos<DeviceType>* c_ptr):
+ c(*c_ptr) {}
+ ~FixLangevinKokkosPostForceFunctor(){c.cleanup_copy();}
+
+ KOKKOS_INLINE_FUNCTION
+ void operator()(const int i) const {
+ c.template post_force_item<Tp_TSTYLEATOM,Tp_GJF, Tp_TALLY,
+ Tp_BIAS,Tp_RMASS,Tp_ZERO>(i);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator()(const int i, value_type &fsum) const {
+
+ fsum += c.template post_force_item<Tp_TSTYLEATOM,Tp_GJF, Tp_TALLY,
+ Tp_BIAS,Tp_RMASS,Tp_ZERO>(i);
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ static void init(volatile value_type &update) {
+ update.fx = 0.0;
+ update.fy = 0.0;
+ update.fz = 0.0;
+ }
+ KOKKOS_INLINE_FUNCTION
+ static void join(volatile value_type &update,
+ const volatile value_type &source) {
+ update.fx += source.fx;
+ update.fy += source.fy;
+ update.fz += source.fz;
+ }
+
+ };
+
+ template <class DeviceType>
+ struct FixLangevinKokkosZeroForceFunctor {
+ typedef DeviceType device_type ;
+ FixLangevinKokkos<DeviceType> c;
+
+ FixLangevinKokkosZeroForceFunctor(FixLangevinKokkos<DeviceType>* c_ptr):
+ c(*c_ptr) {c.cleanup_copy();}
+
+ KOKKOS_INLINE_FUNCTION
+ void operator()(const int i) const {
+ c.zero_force_item(i);
+ }
+ };
+
+ template<class DeviceType>
+ struct FixLangevinKokkosTallyEnergyFunctor {
+ typedef DeviceType device_type ;
+ FixLangevinKokkos<DeviceType> c;
+ typedef double value_type;
+ FixLangevinKokkosTallyEnergyFunctor(FixLangevinKokkos<DeviceType>* c_ptr):
+ c(*c_ptr) {c.cleanup_copy();}
+
+ KOKKOS_INLINE_FUNCTION
+ void operator()(const int i, value_type &energy) const {
+ energy += c.compute_energy_item(i);
+ }
+ KOKKOS_INLINE_FUNCTION
+ static void init(volatile value_type &update) {
+ update = 0.0;
+ }
+ KOKKOS_INLINE_FUNCTION
+ static void join(volatile value_type &update,
+ const volatile value_type &source) {
+ update += source;
+ }
+ };
+}
+
+#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: Fix langevin period must be > 0.0
+
+ The time window for temperature relaxation must be > 0
+
+ E: Fix langevin omega requires atom style sphere
+
+ Self-explanatory.
+
+ E: Fix langevin angmom requires atom style ellipsoid
+
+ Self-explanatory.
+
+ E: Variable name for fix langevin does not exist
+
+ Self-explanatory.
+
+ E: Variable for fix langevin is invalid style
+
+ It must be an equal-style variable.
+
+ E: Fix langevin omega requires extended particles
+
+ One of the particles has radius 0.0.
+
+ E: Fix langevin angmom requires extended particles
+
+ This fix option cannot be used with point paritlces.
+
+ E: Cannot zero Langevin force of 0 atoms
+
+ The group has zero atoms, so you cannot request its force
+ be zeroed.
+
+ E: Fix langevin variable returned negative temperature
+
+ Self-explanatory.
+
+ E: Could not find fix_modify temperature ID
+
+ The compute ID for computing temperature does not exist.
+
+ E: Fix_modify temperature ID does not compute temperature
+
+ The compute ID assigned to the fix must compute temperature.
+
+ W: Group for fix_modify temp != fix group
+
+ The fix_modify command is specifying a temperature computation that
+ computes a temperature on a different group of atoms than the fix
+ itself operates on. This is probably not what you want to do.
+
+*/
diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp
index 3076dca4fa..6f7f1e6300 100644
--- a/src/KOKKOS/fix_nve_kokkos.cpp
+++ b/src/KOKKOS/fix_nve_kokkos.cpp
@@ -172,6 +172,6 @@ void FixNVEKokkos<DeviceType>::cleanup_copy()
}
template class FixNVEKokkos<LMPDeviceType>;
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
template class FixNVEKokkos<LMPHostType>;
#endif
diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp
index b73e25dbc6..5ddd1bac60 100644
--- a/src/KOKKOS/kokkos.cpp
+++ b/src/KOKKOS/kokkos.cpp
@@ -23,8 +23,6 @@
using namespace LAMMPS_NS;
-enum{FULL,HALFTHREAD,HALF};
-
/* ---------------------------------------------------------------------- */
KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
@@ -49,13 +47,13 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
strcmp(arg[iarg],"gpus") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Invalid Kokkos command-line args");
int ngpu = atoi(arg[iarg+1]);
- iarg += 2;
int skip_gpu = 9999;
if (iarg+2 < narg && isdigit(arg[iarg+2][0])) {
skip_gpu = atoi(arg[iarg+2]);
iarg++;
}
+ iarg += 2;
char *str;
if (str = getenv("SLURM_LOCALID")) {
@@ -89,7 +87,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
// initialize Kokkos
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
Kokkos::Cuda::host_mirror_device_type::initialize(num_threads,numa);
Kokkos::Cuda::SelectDevice select_device(device);
Kokkos::Cuda::initialize(select_device);
@@ -112,7 +110,7 @@ KokkosLMP::~KokkosLMP()
{
// finalize Kokkos
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
Kokkos::Cuda::finalize();
Kokkos::Cuda::host_mirror_device_type::finalize();
#else
diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h
index d115ed0bb9..4d62ec747d 100644
--- a/src/KOKKOS/kokkos_type.h
+++ b/src/KOKKOS/kokkos_type.h
@@ -14,71 +14,43 @@
#ifndef LMP_LMPTYPE_KOKKOS_H
#define LMP_LMPTYPE_KOKKOS_H
-#include <Kokkos_View.hpp>
-#include <Kokkos_Macros.hpp>
-#include <Kokkos_Atomic.hpp>
+#include <Kokkos_Core.hpp>
#include <Kokkos_DualView.hpp>
#include <impl/Kokkos_Timer.hpp>
#include <Kokkos_Vectorization.hpp>
#define MAX_TYPES_STACKPARAMS 12
#define NeighClusterSize 8
-// set LMPHostype and LMPDeviceType
-#ifndef DEVICE
-#define DEVICE 1
+#ifndef __CUDACC__
+ struct double2 {
+ double x, y;
+ };
+ struct float2 {
+ float x, y;
+ };
+ struct double4 {
+ double x, y, z, w;
+ };
+ struct float4 {
+ float x, y, z, w;
+ };
#endif
-#if DEVICE==1
- #ifdef KOKKOS_HAVE_OPENMP
- #include "Kokkos_OpenMP.hpp"
- typedef Kokkos::OpenMP LMPDeviceType;
- typedef Kokkos::OpenMP LMPHostType;
- #else
- #include "Kokkos_Threads.hpp"
- typedef Kokkos::Threads LMPDeviceType;
- typedef Kokkos::Threads LMPHostType;
- #endif
- #ifndef __CUDACC__
- struct double2 {
- double x, y;
- };
- struct float2 {
- float x, y;
- };
- struct double4 {
- double x, y, z, w;
- };
- struct float4 {
- float x, y, z, w;
- };
- #endif
-#else
- #include "cuda.h"
- #include "cuda_runtime.h"
- #include "Kokkos_Cuda.hpp"
- #include "Kokkos_Threads.hpp"
- typedef Kokkos::Cuda LMPDeviceType;
- typedef Kokkos::Cuda::host_mirror_device_type LMPHostType;
-#endif
+// set LMPHostype and LMPDeviceType from Kokkos Default Types
+typedef Kokkos::DefaultExecutionSpace LMPDeviceType;
+typedef Kokkos::DefaultExecutionSpace::host_mirror_device_type LMPHostType;
// set ExecutionSpace stuct with variable "space"
template<class Device>
struct ExecutionSpaceFromDevice;
-#ifdef KOKKOS_HAVE_OPENMP
-template<>
-struct ExecutionSpaceFromDevice<Kokkos::OpenMP> {
- static const LAMMPS_NS::ExecutionSpace space = LAMMPS_NS::Host;
-};
-#else
template<>
-struct ExecutionSpaceFromDevice<Kokkos::Threads> {
+struct ExecutionSpaceFromDevice<LMPHostType> {
static const LAMMPS_NS::ExecutionSpace space = LAMMPS_NS::Host;
};
-#endif
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
template<>
struct ExecutionSpaceFromDevice<Kokkos::Cuda> {
static const LAMMPS_NS::ExecutionSpace space = LAMMPS_NS::Device;
@@ -142,16 +114,27 @@ struct s_EV_FLOAT {
}
KOKKOS_INLINE_FUNCTION
- s_EV_FLOAT& operator+=(const s_EV_FLOAT &rhs) {
- evdwl += rhs.evdwl;
- ecoul += rhs.ecoul;
- v[0] += rhs.v[0];
- v[1] += rhs.v[1];
- v[2] += rhs.v[2];
- v[3] += rhs.v[3];
- v[4] += rhs.v[4];
- v[5] += rhs.v[5];
- return *this;
+ void operator+=(const s_EV_FLOAT &rhs) {
+ evdwl += rhs.evdwl;
+ ecoul += rhs.ecoul;
+ v[0] += rhs.v[0];
+ v[1] += rhs.v[1];
+ v[2] += rhs.v[2];
+ v[3] += rhs.v[3];
+ v[4] += rhs.v[4];
+ v[5] += rhs.v[5];
+ }
+
+ KOKKOS_INLINE_FUNCTION
+ void operator+=(const volatile s_EV_FLOAT &rhs) volatile {
+ evdwl += rhs.evdwl;
+ ecoul += rhs.ecoul;
+ v[0] += rhs.v[0];
+ v[1] += rhs.v[1];
+ v[2] += rhs.v[2];
+ v[3] += rhs.v[3];
+ v[4] += rhs.v[4];
+ v[5] += rhs.v[5];
}
};
typedef struct s_EV_FLOAT EV_FLOAT;
@@ -240,7 +223,7 @@ typedef tdual_int_2d::t_dev_const_um t_int_2d_const_um;
typedef tdual_int_2d::t_dev_const_randomread t_int_2d_randomread;
typedef Kokkos::
- DualView<LAMMPS_NS::tagint*, LMPDeviceType::array_layout, LMPDeviceType>
+ DualView<LAMMPS_NS::tagint*, LMPDeviceType::array_layout, LMPDeviceType>
tdual_tagint_1d;
typedef tdual_tagint_1d::t_dev t_tagint_1d;
typedef tdual_tagint_1d::t_dev_const t_tagint_1d_const;
@@ -249,7 +232,16 @@ typedef tdual_tagint_1d::t_dev_const_um t_tagint_1d_const_um;
typedef tdual_tagint_1d::t_dev_const_randomread t_tagint_1d_randomread;
typedef Kokkos::
- DualView<LAMMPS_NS::imageint*, LMPDeviceType::array_layout, LMPDeviceType>
+ DualView<LAMMPS_NS::tagint**, LMPDeviceType::array_layout, LMPDeviceType>
+ tdual_tagint_2d;
+typedef tdual_tagint_2d::t_dev t_tagint_2d;
+typedef tdual_tagint_2d::t_dev_const t_tagint_2d_const;
+typedef tdual_tagint_2d::t_dev_um t_tagint_2d_um;
+typedef tdual_tagint_2d::t_dev_const_um t_tagint_2d_const_um;
+typedef tdual_tagint_2d::t_dev_const_randomread t_tagint_2d_randomread;
+
+typedef Kokkos::
+ DualView<LAMMPS_NS::imageint*, LMPDeviceType::array_layout, LMPDeviceType>
tdual_imageint_1d;
typedef tdual_imageint_1d::t_dev t_imageint_1d;
typedef tdual_imageint_1d::t_dev_const t_imageint_1d_const;
@@ -257,6 +249,22 @@ typedef tdual_imageint_1d::t_dev_um t_imageint_1d_um;
typedef tdual_imageint_1d::t_dev_const_um t_imageint_1d_const_um;
typedef tdual_imageint_1d::t_dev_const_randomread t_imageint_1d_randomread;
+typedef Kokkos::
+ DualView<double*, Kokkos::LayoutRight, LMPDeviceType> tdual_double_1d;
+typedef tdual_double_1d::t_dev t_double_1d;
+typedef tdual_double_1d::t_dev_const t_double_1d_const;
+typedef tdual_double_1d::t_dev_um t_double_1d_um;
+typedef tdual_double_1d::t_dev_const_um t_double_1d_const_um;
+typedef tdual_double_1d::t_dev_const_randomread t_double_1d_randomread;
+
+typedef Kokkos::
+ DualView<double**, Kokkos::LayoutRight, LMPDeviceType> tdual_double_2d;
+typedef tdual_double_2d::t_dev t_double_2d;
+typedef tdual_double_2d::t_dev_const t_double_2d_const;
+typedef tdual_double_2d::t_dev_um t_double_2d_um;
+typedef tdual_double_2d::t_dev_const_um t_double_2d_const_um;
+typedef tdual_double_2d::t_dev_const_randomread t_double_2d_randomread;
+
// 1d float array n
typedef Kokkos::DualView<LMP_FLOAT*, LMPDeviceType::array_layout, LMPDeviceType> tdual_float_1d;
@@ -406,7 +414,7 @@ typedef tdual_neighbors_2d::t_dev_const_randomread t_neighbors_2d_randomread;
};
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
template <>
struct ArrayTypes<LMPHostType> {
@@ -446,13 +454,40 @@ typedef tdual_tagint_1d::t_host_um t_tagint_1d_um;
typedef tdual_tagint_1d::t_host_const_um t_tagint_1d_const_um;
typedef tdual_tagint_1d::t_host_const_randomread t_tagint_1d_randomread;
-typedef Kokkos::DualView<LAMMPS_NS::imageint*, LMPDeviceType::array_layout, LMPDeviceType> tdual_imageint_1d;
+typedef Kokkos::
+ DualView<LAMMPS_NS::tagint**, LMPDeviceType::array_layout, LMPDeviceType>
+ tdual_tagint_2d;
+typedef tdual_tagint_2d::t_host t_tagint_2d;
+typedef tdual_tagint_2d::t_host_const t_tagint_2d_const;
+typedef tdual_tagint_2d::t_host_um t_tagint_2d_um;
+typedef tdual_tagint_2d::t_host_const_um t_tagint_2d_const_um;
+typedef tdual_tagint_2d::t_host_const_randomread t_tagint_2d_randomread;
+
+typedef Kokkos::
+ DualView<LAMMPS_NS::imageint*, LMPDeviceType::array_layout, LMPDeviceType>
+ tdual_imageint_1d;
typedef tdual_imageint_1d::t_host t_imageint_1d;
typedef tdual_imageint_1d::t_host_const t_imageint_1d_const;
typedef tdual_imageint_1d::t_host_um t_imageint_1d_um;
typedef tdual_imageint_1d::t_host_const_um t_imageint_1d_const_um;
typedef tdual_imageint_1d::t_host_const_randomread t_imageint_1d_randomread;
+typedef Kokkos::
+ DualView<double*, Kokkos::LayoutRight, LMPDeviceType> tdual_double_1d;
+typedef tdual_double_1d::t_host t_double_1d;
+typedef tdual_double_1d::t_host_const t_double_1d_const;
+typedef tdual_double_1d::t_host_um t_double_1d_um;
+typedef tdual_double_1d::t_host_const_um t_double_1d_const_um;
+typedef tdual_double_1d::t_host_const_randomread t_double_1d_randomread;
+
+typedef Kokkos::
+ DualView<double**, Kokkos::LayoutRight, LMPDeviceType> tdual_double_2d;
+typedef tdual_double_2d::t_host t_double_2d;
+typedef tdual_double_2d::t_host_const t_double_2d_const;
+typedef tdual_double_2d::t_host_um t_double_2d_um;
+typedef tdual_double_2d::t_host_const_um t_double_2d_const_um;
+typedef tdual_double_2d::t_host_const_randomread t_double_2d_randomread;
+
//1d float array n
typedef Kokkos::DualView<LMP_FLOAT*, LMPDeviceType::array_layout, LMPDeviceType> tdual_float_1d;
typedef tdual_float_1d::t_host t_float_1d;
diff --git a/src/KOKKOS/neigh_full_kokkos.h b/src/KOKKOS/neigh_full_kokkos.h
index 9112e5049a..effc1cf622 100644
--- a/src/KOKKOS/neigh_full_kokkos.h
+++ b/src/KOKKOS/neigh_full_kokkos.h
@@ -13,6 +13,7 @@
#include "atom_kokkos.h"
#include "atom_masks.h"
+#include "domain_kokkos.h"
using namespace LAMMPS_NS;
@@ -24,7 +25,7 @@ void NeighborKokkos::full_bin_kokkos(NeighListKokkos<DeviceType> *list)
const int nall = includegroup?atom->nfirst:atom->nlocal;
list->grow(nall);
- NeighborKokkosExecute<DeviceType>
+ NeighborKokkosExecute<DeviceType>
data(*list,
k_cutneighsq.view<DeviceType>(),
k_bincount.view<DeviceType>(),
@@ -33,14 +34,46 @@ void NeighborKokkos::full_bin_kokkos(NeighListKokkos<DeviceType> *list)
atomKK->k_type.view<DeviceType>(),
atomKK->k_mask.view<DeviceType>(),
atomKK->k_molecule.view<DeviceType>(),
+ atomKK->k_tag.view<DeviceType>(),
+ atomKK->k_special.view<DeviceType>(),
+ atomKK->k_nspecial.view<DeviceType>(),
+ atomKK->molecular,
nbinx,nbiny,nbinz,mbinx,mbiny,mbinz,mbinxlo,mbinylo,mbinzlo,
bininvx,bininvy,bininvz,
- bboxhi,bboxlo);
+ exclude, nex_type,maxex_type,
+ k_ex1_type.view<DeviceType>(),
+ k_ex2_type.view<DeviceType>(),
+ k_ex_type.view<DeviceType>(),
+ nex_group,maxex_group,
+ k_ex1_group.view<DeviceType>(),
+ k_ex2_group.view<DeviceType>(),
+ k_ex1_bit.view<DeviceType>(),
+ k_ex2_bit.view<DeviceType>(),
+ nex_mol, maxex_mol,
+ k_ex_mol_group.view<DeviceType>(),
+ k_ex_mol_bit.view<DeviceType>(),
+ bboxhi,bboxlo,
+ domain->xperiodic,domain->yperiodic,domain->zperiodic,
+ domain->xprd_half,domain->yprd_half,domain->zprd_half);
k_cutneighsq.sync<DeviceType>();
- atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK);
+ k_ex1_type.sync<DeviceType>();
+ k_ex2_type.sync<DeviceType>();
+ k_ex_type.sync<DeviceType>();
+ k_ex1_group.sync<DeviceType>();
+ k_ex2_group.sync<DeviceType>();
+ k_ex1_bit.sync<DeviceType>();
+ k_ex2_bit.sync<DeviceType>();
+ k_ex_mol_group.sync<DeviceType>();
+ k_ex_mol_bit.sync<DeviceType>();
+ atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
Kokkos::deep_copy(list->d_stencil,list->h_stencil);
+ data.special_flag[0] = special_flag[0];
+ data.special_flag[1] = special_flag[1];
+ data.special_flag[2] = special_flag[2];
+ data.special_flag[3] = special_flag[3];
+
while(data.h_resize() > 0) {
data.h_resize() = 0;
deep_copy(data.resize, data.h_resize);
@@ -78,24 +111,24 @@ void NeighborKokkos::full_bin_kokkos(NeighListKokkos<DeviceType> *list)
Kokkos::deep_copy(data.resize, data.h_resize);
Kokkos::deep_copy(data.new_maxneighs, data.h_new_maxneighs);
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
#define BINS_PER_BLOCK 2
const int factor = atoms_per_bin<64?2:1;
- Kokkos::ParallelWorkRequest config((mbins+factor-1)/factor,atoms_per_bin*factor);
+ Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,atoms_per_bin*factor);
#else
const int factor = 1;
#endif
if(newton_pair) {
NeighborKokkosBuildFunctor<DeviceType,HALF_NEIGH,1> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
Kokkos::parallel_for(config, f);
#else
Kokkos::parallel_for(nall, f);
#endif
} else {
NeighborKokkosBuildFunctor<DeviceType,HALF_NEIGH,0> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
Kokkos::parallel_for(config, f);
#else
Kokkos::parallel_for(nall, f);
@@ -134,6 +167,62 @@ void NeighborKokkosExecute<Device>::binatomsItem(const int &i) const
}
}
+/* ---------------------------------------------------------------------- */
+template<class Device>
+KOKKOS_INLINE_FUNCTION
+int NeighborKokkosExecute<Device>::find_special(const int &i, const int &j) const
+{
+ const int n1 = nspecial(i,0);
+ const int n2 = nspecial(i,1);
+ const int n3 = nspecial(i,2);
+
+ for (int k = 0; k < n3; k++) {
+ if (special(i,k) == tag(j)) {
+ if (k < n1) {
+ if (special_flag[1] == 0) return -1;
+ else if (special_flag[1] == 1) return 0;
+ else return 1;
+ } else if (k < n2) {
+ if (special_flag[2] == 0) return -1;
+ else if (special_flag[2] == 1) return 0;
+ else return 2;
+ } else {
+ if (special_flag[3] == 0) return -1;
+ else if (special_flag[3] == 1) return 0;
+ else return 3;
+ }
+ }
+ }
+ return 0;
+};
+
+/* ---------------------------------------------------------------------- */
+
+template<class Device>
+KOKKOS_INLINE_FUNCTION
+int NeighborKokkosExecute<Device>::exclusion(const int &i,const int &j,
+ const int &itype,const int &jtype) const
+{
+ int m;
+
+ if (nex_type && ex_type(itype,jtype)) return 1;
+
+ if (nex_group) {
+ for (m = 0; m < nex_group; m++) {
+ if (mask(i) & ex1_bit(m) && mask(j) & ex2_bit(m)) return 1;
+ if (mask(i) & ex2_bit(m) && mask(j) & ex1_bit(m)) return 1;
+ }
+ }
+
+ if (nex_mol) {
+ for (m = 0; m < nex_mol; m++)
+ if (mask(i) & ex_mol_bit(m) && mask(j) & ex_mol_bit(m) &&
+ molecule(i) == molecule(j)) return 1;
+ }
+
+ return 0;
+}
+
/* ---------------------------------------------------------------------- */
template<class Device> template<int HalfNeigh,int GhostNewton>
@@ -142,7 +231,10 @@ void NeighborKokkosExecute<Device>::
{
/* if necessary, goto next page and add pages */
int n = 0;
-
+ int which = 0;
+ int moltemplate;
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
// get subview of neighbors of i
const AtomNeighbors neighbors_i = neigh_list.get_neighbors(i);
@@ -161,52 +253,81 @@ void NeighborKokkosExecute<Device>::
if(HalfNeigh)
for(int m = 0; m < c_bincount(ibin); m++) {
const int j = c_bins(ibin,m);
- // printf("%i %i %i\n",i,ibin,m,c_bincount(ibin),j);
const int jtype = type(j);
+
//for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using HalfNeighborlists
if((j == i) || (HalfNeigh && !GhostNewton && (j < i)) ||
(HalfNeigh && GhostNewton && ((j < i) || ((j >= nlocal) &&
((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) ||
(x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp)))))
) continue;
- //if(Exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
-
+ if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - x(j, 0);
const X_FLOAT dely = ytmp - x(j, 1);
const X_FLOAT delz = ztmp - x(j, 2);
const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq <= cutneighsq(itype,jtype)) {
- if(n<neigh_list.maxneighs) neighbors_i(n) = j;
- n++;
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(i,j);
+ /* else if (imol >= 0) */
+ /* which = find_special(onemols[imol]->special[iatom], */
+ /* onemols[imol]->nspecial[iatom], */
+ /* tag[j]-tagprev); */
+ /* else which = 0; */
+ if (which == 0){
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }else if (minimum_image_check(delx,dely,delz)){
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }
+ else if (which > 0) {
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
+ }
+ } else {
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }
}
}
for(int k = 0; k < nstencil; k++) {
const int jbin = ibin + stencil[k];
// get subview of jbin
- if(!GhostNewton&&HalfNeigh&&(ibin==jbin)) continue;
+ if(HalfNeigh&&(ibin==jbin)) continue;
//const ArrayTypes<Device>::t_int_1d_const_um =Kokkos::subview<t_int_1d_const_um>(bins,jbin,ALL);
for(int m = 0; m < c_bincount(jbin); m++) {
const int j = c_bins(jbin,m);
- //if(i==0)
- //printf("%i %i %i %i %i %i %i\n",i,jbin,m,c_bincount(jbin),j,k,stencil[k]);
const int jtype = type(j);
if(HalfNeigh && !GhostNewton && (j < i)) continue;
if(!HalfNeigh && j==i) continue;
- //if(Exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+ if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - x(j, 0);
const X_FLOAT dely = ytmp - x(j, 1);
const X_FLOAT delz = ztmp - x(j, 2);
const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
- //if(i==0)
- //printf("%i %i %lf %lf NEIGHS\n",i,j,rsq,cutneighsq(itype,jtype));
if(rsq <= cutneighsq(itype,jtype)) {
- if(n<neigh_list.maxneighs) neighbors_i(n) = j;
- n++;
+ if (molecular) {
+ if (!moltemplate)
+ which = find_special(i,j);
+ /* else if (imol >= 0) */
+ /* which = find_special(onemols[imol]->special[iatom], */
+ /* onemols[imol]->nspecial[iatom], */
+ /* tag[j]-tagprev); */
+ /* else which = 0; */
+ if (which == 0){
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }else if (minimum_image_check(delx,dely,delz)){
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }
+ else if (which > 0) {
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
+ }
+ } else {
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }
}
}
@@ -222,23 +343,23 @@ void NeighborKokkosExecute<Device>::
neigh_list.d_ilist(i) = i;
}
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
extern __shared__ X_FLOAT sharedmem[];
/* ---------------------------------------------------------------------- */
-template<class DeviceType> template<int HalfNeigh>
+template<class DeviceType> template<int HalfNeigh,int GhostNewton>
__device__ inline
-void NeighborKokkosExecute<DeviceType>::build_ItemCuda(DeviceType dev) const
+void NeighborKokkosExecute<DeviceType>::build_ItemCuda(typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const
{
/* loop over atoms in i's bin,
*/
const int atoms_per_bin = c_bins.dimension_1();
- const int BINS_PER_TEAM = blockDim.x/atoms_per_bin;
- const int MY_BIN = threadIdx.x/atoms_per_bin;
- const int MY_II = threadIdx.x%atoms_per_bin;
+ const int BINS_PER_TEAM = dev.team_size()/atoms_per_bin<1?1:dev.team_size()/atoms_per_bin;
+ const int TEAMS_PER_BIN = atoms_per_bin/dev.team_size()<1?1:atoms_per_bin/dev.team_size();
+ const int MY_BIN = dev.team_rank()/atoms_per_bin;
- const int ibin = (blockIdx.x)*BINS_PER_TEAM+MY_BIN;
+ const int ibin = dev.league_rank()*BINS_PER_TEAM+MY_BIN;
if(ibin >=c_bincount.dimension_0()) return;
X_FLOAT* other_x = sharedmem;
@@ -248,6 +369,8 @@ void NeighborKokkosExecute<DeviceType>::build_ItemCuda(DeviceType dev) const
int bincount_current = c_bincount[ibin];
+ for(int kk = 0; kk < TEAMS_PER_BIN; kk++) {
+ const int MY_II = dev.team_rank()%atoms_per_bin+kk*dev.team_size();
const int i = MY_II < bincount_current ? c_bins(ibin, MY_II) : -1;
/* if necessary, goto next page and add pages */
@@ -278,17 +401,45 @@ void NeighborKokkosExecute<DeviceType>::build_ItemCuda(DeviceType dev) const
#pragma unroll 4
for(int m = 0; m < bincount_current; m++) {
int j = other_id[m];
+ const int jtype = other_x[m + 3 * atoms_per_bin];
//for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists
- //if(j==i) continue;
- if((j == i) || (HalfNeigh && (j < i))) continue;
-
+ if((j == i) ||
+ (HalfNeigh && !GhostNewton && (j < i)) ||
+ (HalfNeigh && GhostNewton &&
+ ((j < i) ||
+ ((j >= nlocal) && ((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) ||
+ (x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp)))))
+ ) continue;
+ if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - other_x[m];
const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
- const int jtype = other_x[m + 3 * atoms_per_bin];
const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
- if((rsq <= cutneighsq(itype,jtype)) && (n < neigh_list.maxneighs)) neighbors_i(n++) = j;
+
+ if(rsq <= cutneighsq(itype,jtype)) {
+ if (molecular) {
+ int which = 0;
+ if (!moltemplate)
+ which = find_special(i,j);
+ /* else if (imol >= 0) */
+ /* which = find_special(onemols[imol]->special[iatom], */
+ /* onemols[imol]->nspecial[iatom], */
+ /* tag[j]-tagprev); */
+ /* else which = 0; */
+ if (which == 0){
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }else if (minimum_image_check(delx,dely,delz)){
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }
+ else if (which > 0) {
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
+ }
+ } else {
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }
+ }
+
}
}
__syncthreads();
@@ -319,15 +470,41 @@ void NeighborKokkosExecute<DeviceType>::build_ItemCuda(DeviceType dev) const
#pragma unroll 8
for(int m = 0; m < bincount_current; m++) {
const int j = other_id[m];
+ const int jtype = other_x[m + 3 * atoms_per_bin];
- if(HalfNeigh && (j < i)) continue;
+ //if(HalfNeigh && (j < i)) continue;
+ if(HalfNeigh && !GhostNewton && (j < i)) continue;
+ if(!HalfNeigh && j==i) continue;
+ if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - other_x[m];
const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
- const int jtype = other_x[m + 3 * atoms_per_bin];
const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
- if((rsq <= cutneighsq(itype,jtype)) && (n < neigh_list.maxneighs)) neighbors_i(n++) = j;
+
+ if(rsq <= cutneighsq(itype,jtype)) {
+ if (molecular) {
+ int which = 0;
+ if (!moltemplate)
+ which = find_special(i,j);
+ /* else if (imol >= 0) */
+ /* which = find_special(onemols[imol]->special[iatom], */
+ /* onemols[imol]->nspecial[iatom], */
+ /* tag[j]-tagprev); */
+ /* else which = 0; */
+ if (which == 0){
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }else if (minimum_image_check(delx,dely,delz)){
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }
+ else if (which > 0) {
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
+ }
+ } else {
+ if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
+ }
+ }
+
}
}
__syncthreads();
@@ -343,6 +520,7 @@ void NeighborKokkosExecute<DeviceType>::build_ItemCuda(DeviceType dev) const
if(n >= new_maxneighs()) new_maxneighs() = n;
}
+ }
}
#endif
@@ -361,12 +539,45 @@ void NeighborKokkos::full_bin_cluster_kokkos(NeighListKokkos<DeviceType> *list)
atomKK->k_type.view<DeviceType>(),
atomKK->k_mask.view<DeviceType>(),
atomKK->k_molecule.view<DeviceType>(),
+ atomKK->k_tag.view<DeviceType>(),
+ atomKK->k_special.view<DeviceType>(),
+ atomKK->k_nspecial.view<DeviceType>(),
+ atomKK->molecular,
nbinx,nbiny,nbinz,mbinx,mbiny,mbinz,mbinxlo,mbinylo,mbinzlo,
bininvx,bininvy,bininvz,
- bboxhi,bboxlo);
+ exclude, nex_type,maxex_type,
+ k_ex1_type.view<DeviceType>(),
+ k_ex2_type.view<DeviceType>(),
+ k_ex_type.view<DeviceType>(),
+ nex_group,maxex_group,
+ k_ex1_group.view<DeviceType>(),
+ k_ex2_group.view<DeviceType>(),
+ k_ex1_bit.view<DeviceType>(),
+ k_ex2_bit.view<DeviceType>(),
+ nex_mol, maxex_mol,
+ k_ex_mol_group.view<DeviceType>(),
+ k_ex_mol_bit.view<DeviceType>(),
+ bboxhi,bboxlo,
+ domain->xperiodic,domain->yperiodic,domain->zperiodic,
+ domain->xprd_half,domain->yprd_half,domain->zprd_half);
k_cutneighsq.sync<DeviceType>();
- atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK);
+ k_ex1_type.sync<DeviceType>();
+ k_ex2_type.sync<DeviceType>();
+ k_ex_type.sync<DeviceType>();
+ k_ex1_group.sync<DeviceType>();
+ k_ex2_group.sync<DeviceType>();
+ k_ex1_bit.sync<DeviceType>();
+ k_ex2_bit.sync<DeviceType>();
+ k_ex_mol_group.sync<DeviceType>();
+ k_ex_mol_bit.sync<DeviceType>();
+
+ data.special_flag[0] = special_flag[0];
+ data.special_flag[1] = special_flag[1];
+ data.special_flag[2] = special_flag[2];
+ data.special_flag[3] = special_flag[3];
+
+ atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
Kokkos::deep_copy(list->d_stencil,list->h_stencil);
DeviceType::fence();
@@ -407,24 +618,24 @@ void NeighborKokkos::full_bin_cluster_kokkos(NeighListKokkos<DeviceType> *list)
Kokkos::deep_copy(data.resize, data.h_resize);
Kokkos::deep_copy(data.new_maxneighs, data.h_new_maxneighs);
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
#define BINS_PER_BLOCK 2
const int factor = atoms_per_bin<64?2:1;
- Kokkos::ParallelWorkRequest config((mbins+factor-1)/factor,atoms_per_bin*factor);
+ Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,atoms_per_bin*factor);
#else
const int factor = 1;
#endif
if(newton_pair) {
NeighborClusterKokkosBuildFunctor<DeviceType,NeighClusterSize> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
-//#if DEVICE==2
+//#ifdef KOKKOS_HAVE_CUDA
// Kokkos::parallel_for(config, f);
//#else
Kokkos::parallel_for(nall, f);
//#endif
} else {
NeighborClusterKokkosBuildFunctor<DeviceType,NeighClusterSize> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
-//#if DEVICE==2
+//#ifdef KOKKOS_HAVE_CUDA
// Kokkos::parallel_for(config, f);
//#else
Kokkos::parallel_for(nall, f);
diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp
index dbb0aa5727..2730c15a2b 100644
--- a/src/KOKKOS/neigh_list_kokkos.cpp
+++ b/src/KOKKOS/neigh_list_kokkos.cpp
@@ -113,6 +113,6 @@ void NeighListKokkos<Device>::stencil_allocate(int smax, int style)
}
template class NeighListKokkos<LMPDeviceType>;
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
template class NeighListKokkos<LMPHostType>;
#endif
diff --git a/src/KOKKOS/neigh_list_kokkos.h b/src/KOKKOS/neigh_list_kokkos.h
index fd4ac3acc9..fa0eaba76a 100644
--- a/src/KOKKOS/neigh_list_kokkos.h
+++ b/src/KOKKOS/neigh_list_kokkos.h
@@ -20,7 +20,7 @@
namespace LAMMPS_NS {
-enum{FULL,HALFTHREAD,HALF,N2,FULLCLUSTER};
+enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u,FULLCLUSTER=16u};
class AtomNeighbors
{
diff --git a/src/KOKKOS/neighbor_kokkos.cpp b/src/KOKKOS/neighbor_kokkos.cpp
index adea823976..133ac7cea0 100644
--- a/src/KOKKOS/neighbor_kokkos.cpp
+++ b/src/KOKKOS/neighbor_kokkos.cpp
@@ -51,6 +51,16 @@ NeighborKokkos::~NeighborKokkos()
delete [] pair_build_device;
delete [] pair_build_host;
+
+ memory->destroy_kokkos(k_ex1_type,ex1_type);
+ memory->destroy_kokkos(k_ex2_type,ex2_type);
+ memory->destroy_kokkos(k_ex1_group,ex1_group);
+ memory->destroy_kokkos(k_ex2_group,ex2_group);
+ memory->destroy_kokkos(k_ex_mol_group,ex_mol_group);
+ memory->destroy_kokkos(k_ex1_bit,ex1_bit);
+ memory->destroy_kokkos(k_ex2_bit,ex2_bit);
+ memory->destroy_kokkos(k_ex_mol_bit,ex_mol_bit);
+
}
/* ---------------------------------------------------------------------- */
@@ -72,7 +82,7 @@ void NeighborKokkos::init_cutneighsq_kokkos(int n)
/* ---------------------------------------------------------------------- */
int NeighborKokkos::init_lists_kokkos()
-{
+{
int i;
for (i = 0; i < nlist_host; i++) delete lists_host[i];
@@ -211,6 +221,32 @@ void NeighborKokkos::init_list_grow_kokkos(int i)
/* ---------------------------------------------------------------------- */
+void NeighborKokkos::init_ex_type_kokkos(int n)
+{
+ memory->create_kokkos(k_ex_type,ex_type,n+1,n+1,"neigh:ex_type");
+ k_ex_type.modify<LMPHostType>();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NeighborKokkos::init_ex_bit_kokkos()
+{
+ memory->create_kokkos(k_ex1_bit, ex1_bit, nex_group, "neigh:ex1_bit");
+ k_ex1_bit.modify<LMPHostType>();
+ memory->create_kokkos(k_ex2_bit, ex2_bit, nex_group, "neigh:ex2_bit");
+ k_ex2_bit.modify<LMPHostType>();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void NeighborKokkos::init_ex_mol_bit_kokkos()
+{
+ memory->create_kokkos(k_ex_mol_bit, ex_mol_bit, nex_mol, "neigh:ex_mol_bit");
+ k_ex_mol_bit.modify<LMPHostType>();
+}
+
+/* ---------------------------------------------------------------------- */
+
void NeighborKokkos::choose_build(int index, NeighRequest *rq)
{
if (rq->kokkos_host != 0) {
@@ -264,6 +300,29 @@ void NeighborKokkos::setup_bins_kokkos(int i)
}
}
+/* ---------------------------------------------------------------------- */
+
+void NeighborKokkos::modify_ex_type_grow_kokkos(){
+ memory->grow_kokkos(k_ex1_type,ex1_type,maxex_type,"neigh:ex1_type");
+ k_ex1_type.modify<LMPHostType>();
+ memory->grow_kokkos(k_ex2_type,ex2_type,maxex_type,"neigh:ex2_type");
+ k_ex2_type.modify<LMPHostType>();
+}
+
+/* ---------------------------------------------------------------------- */
+void NeighborKokkos::modify_ex_group_grow_kokkos(){
+ memory->grow_kokkos(k_ex1_group,ex1_group,maxex_group,"neigh:ex1_group");
+ k_ex1_group.modify<LMPHostType>();
+ memory->grow_kokkos(k_ex2_group,ex2_group,maxex_group,"neigh:ex2_group");
+ k_ex2_group.modify<LMPHostType>();
+}
+
+/* ---------------------------------------------------------------------- */
+void NeighborKokkos::modify_mol_group_grow_kokkos(){
+ memory->grow_kokkos(k_ex_mol_group,ex_mol_group,maxex_mol,"neigh:ex_mol_group");
+ k_ex_mol_group.modify<LMPHostType>();
+}
+
// include to trigger instantiation of templated functions
#include "neigh_full_kokkos.h"
diff --git a/src/KOKKOS/neighbor_kokkos.h b/src/KOKKOS/neighbor_kokkos.h
index 9abbd00738..3736f1405b 100644
--- a/src/KOKKOS/neighbor_kokkos.h
+++ b/src/KOKKOS/neighbor_kokkos.h
@@ -17,6 +17,7 @@
#include "neighbor.h"
#include "neigh_list_kokkos.h"
#include "kokkos_type.h"
+#include <math.h>
namespace LAMMPS_NS {
@@ -33,8 +34,15 @@ class NeighborKokkosExecute
typename AT::t_int_2d bins;
typename AT::t_int_2d_const c_bins;
const typename AT::t_x_array_randomread x;
- const typename AT::t_int_1d_const type,mask;
- const typename AT::t_tagint_1d_const molecule;
+ const typename AT::t_int_1d_const type,mask,molecule;
+
+ const typename AT::t_tagint_1d_const tag;
+ const typename AT::t_tagint_2d_const special;
+ const typename AT::t_int_2d_const nspecial;
+ const int molecular;
+ int moltemplate;
+
+ int special_flag[4];
const int nbinx,nbiny,nbinz;
const int mbinx,mbiny,mbinz;
@@ -44,38 +52,88 @@ class NeighborKokkosExecute
const int nlocal;
+ const int exclude;
+
+ const int nex_type;
+ const int maxex_type;
+ const typename AT::t_int_1d_const ex1_type,ex2_type;
+ const typename AT::t_int_2d_const ex_type;
+
+ const int nex_group;
+ const int maxex_group;
+ const typename AT::t_int_1d_const ex1_group,ex2_group;
+ const typename AT::t_int_1d_const ex1_bit,ex2_bit;
+
+ const int nex_mol;
+ const int maxex_mol;
+ const typename AT::t_int_1d_const ex_mol_group;
+ const typename AT::t_int_1d_const ex_mol_bit;
+
typename AT::t_int_scalar resize;
typename AT::t_int_scalar new_maxneighs;
typename ArrayTypes<LMPHostType>::t_int_scalar h_resize;
typename ArrayTypes<LMPHostType>::t_int_scalar h_new_maxneighs;
+ const int xperiodic, yperiodic, zperiodic;
+ const int xprd_half, yprd_half, zprd_half;
+
NeighborKokkosExecute(
- const NeighListKokkos<Device> &_neigh_list,
- const typename AT::t_xfloat_2d_randomread &_cutneighsq,
- const typename AT::t_int_1d &_bincount,
- const typename AT::t_int_2d &_bins,
- const int _nlocal,
- const typename AT::t_x_array_randomread &_x,
- const typename AT::t_int_1d_const &_type,
- const typename AT::t_int_1d_const &_mask,
- const typename AT::t_tagint_1d_const &_molecule,
- const int & _nbinx,const int & _nbiny,const int & _nbinz,
- const int & _mbinx,const int & _mbiny,const int & _mbinz,
- const int & _mbinxlo,const int & _mbinylo,const int & _mbinzlo,
- const X_FLOAT &_bininvx,const X_FLOAT &_bininvy,const X_FLOAT &_bininvz,
- const X_FLOAT *_bboxhi, const X_FLOAT* _bboxlo):
+ const NeighListKokkos<Device> &_neigh_list,
+ const typename AT::t_xfloat_2d_randomread &_cutneighsq,
+ const typename AT::t_int_1d &_bincount,
+ const typename AT::t_int_2d &_bins,
+ const int _nlocal,
+ const typename AT::t_x_array_randomread &_x,
+ const typename AT::t_int_1d_const &_type,
+ const typename AT::t_int_1d_const &_mask,
+ const typename AT::t_int_1d_const &_molecule,
+ const typename AT::t_tagint_1d_const &_tag,
+ const typename AT::t_tagint_2d_const &_special,
+ const typename AT::t_int_2d_const &_nspecial,
+ const int &_molecular,
+ const int & _nbinx,const int & _nbiny,const int & _nbinz,
+ const int & _mbinx,const int & _mbiny,const int & _mbinz,
+ const int & _mbinxlo,const int & _mbinylo,const int & _mbinzlo,
+ const X_FLOAT &_bininvx,const X_FLOAT &_bininvy,const X_FLOAT &_bininvz,
+ const int & _exclude,const int & _nex_type,const int & _maxex_type,
+ const typename AT::t_int_1d_const & _ex1_type,
+ const typename AT::t_int_1d_const & _ex2_type,
+ const typename AT::t_int_2d_const & _ex_type,
+ const int & _nex_group,const int & _maxex_group,
+ const typename AT::t_int_1d_const & _ex1_group,
+ const typename AT::t_int_1d_const & _ex2_group,
+ const typename AT::t_int_1d_const & _ex1_bit,
+ const typename AT::t_int_1d_const & _ex2_bit,
+ const int & _nex_mol,const int & _maxex_mol,
+ const typename AT::t_int_1d_const & _ex_mol_group,
+ const typename AT::t_int_1d_const & _ex_mol_bit,
+ const X_FLOAT *_bboxhi, const X_FLOAT* _bboxlo,
+ const int & _xperiodic, const int & _yperiodic, const int & _zperiodic,
+ const int & _xprd_half, const int & _yprd_half, const int & _zprd_half):
neigh_list(_neigh_list), cutneighsq(_cutneighsq),
bincount(_bincount),c_bincount(_bincount),bins(_bins),c_bins(_bins),
nlocal(_nlocal),
x(_x),type(_type),mask(_mask),molecule(_molecule),
+ tag(_tag),special(_special),nspecial(_nspecial),molecular(_molecular),
nbinx(_nbinx),nbiny(_nbiny),nbinz(_nbinz),
mbinx(_mbinx),mbiny(_mbiny),mbinz(_mbinz),
mbinxlo(_mbinxlo),mbinylo(_mbinylo),mbinzlo(_mbinzlo),
- bininvx(_bininvx),bininvy(_bininvy),bininvz(_bininvz) {
+ bininvx(_bininvx),bininvy(_bininvy),bininvz(_bininvz),
+ exclude(_exclude),nex_type(_nex_type),maxex_type(_maxex_type),
+ ex1_type(_ex1_type),ex2_type(_ex2_type),ex_type(_ex_type),
+ nex_group(_nex_group),maxex_group(_maxex_group),
+ ex1_group(_ex1_group),ex2_group(_ex2_group),
+ ex1_bit(_ex1_bit),ex2_bit(_ex2_bit),nex_mol(_nex_mol),maxex_mol(_maxex_mol),
+ ex_mol_group(_ex_mol_group),ex_mol_bit(_ex_mol_bit),
+ xperiodic(_xperiodic),yperiodic(_yperiodic),zperiodic(_zperiodic),
+ xprd_half(_xprd_half),yprd_half(_yprd_half),zprd_half(_zprd_half){
+
+ if (molecular == 2) moltemplate = 1;
+ else moltemplate = 0;
bboxlo[0] = _bboxlo[0]; bboxlo[1] = _bboxlo[1]; bboxlo[2] = _bboxlo[2];
bboxhi[0] = _bboxhi[0]; bboxhi[1] = _bboxhi[1]; bboxhi[2] = _bboxhi[2];
-
+
resize = typename AT::t_int_scalar("NeighborKokkosFunctor::resize");
#ifndef KOKKOS_USE_UVM
h_resize = Kokkos::create_mirror_view(resize);
@@ -103,10 +161,10 @@ class NeighborKokkosExecute
KOKKOS_FUNCTION
void build_cluster_Item(const int &i) const;
-#if DEVICE==2
- template<int HalfNeigh>
+#ifdef KOKKOS_HAVE_CUDA
+ template<int HalfNeigh, int GhostNewton>
__device__ inline
- void build_ItemCuda(Device dev) const;
+ void build_ItemCuda(typename Kokkos::TeamPolicy<Device>::member_type dev) const;
#endif
KOKKOS_INLINE_FUNCTION
@@ -143,6 +201,21 @@ class NeighborKokkosExecute
return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
}
+
+ KOKKOS_INLINE_FUNCTION
+ int exclusion(const int &i,const int &j, const int &itype,const int &jtype) const;
+
+ KOKKOS_INLINE_FUNCTION
+ int find_special(const int &i, const int &j) const;
+
+ KOKKOS_INLINE_FUNCTION
+ int minimum_image_check(double dx, double dy, double dz) const {
+ if (xperiodic && fabs(dx) > xprd_half) return 1;
+ if (yperiodic && fabs(dy) > yprd_half) return 1;
+ if (zperiodic && fabs(dz) > zprd_half) return 1;
+ return 0;
+ }
+
};
template<class Device>
@@ -175,12 +248,12 @@ struct NeighborKokkosBuildFunctor {
void operator() (const int & i) const {
c.template build_Item<HALF_NEIGH,GHOST_NEWTON>(i);
}
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
KOKKOS_INLINE_FUNCTION
- void operator() (Device dev) const {
- c.template build_ItemCuda<HALF_NEIGH>(dev);
+ void operator() (typename Kokkos::TeamPolicy<Device>::member_type dev) const {
+ c.template build_ItemCuda<HALF_NEIGH,GHOST_NEWTON>(dev);
}
- size_t shmem_size() const { return sharedsize; }
+ size_t shmem_size(const int team_size) const { (void) team_size; return sharedsize; }
#endif
};
@@ -220,15 +293,28 @@ class NeighborKokkos : public Neighbor {
DAT::tdual_int_1d k_bincount;
DAT::tdual_int_2d k_bins;
+ DAT::tdual_int_1d k_ex1_type,k_ex2_type;
+ DAT::tdual_int_2d k_ex_type;
+ DAT::tdual_int_1d k_ex1_group,k_ex2_group;
+ DAT::tdual_int_1d k_ex1_bit,k_ex2_bit;
+ DAT::tdual_int_1d k_ex_mol_group;
+ DAT::tdual_int_1d k_ex_mol_bit;
+
void init_cutneighsq_kokkos(int);
int init_lists_kokkos();
void init_list_flags1_kokkos(int);
void init_list_flags2_kokkos(int);
void init_list_grow_kokkos(int);
+ void init_ex_type_kokkos(int);
+ void init_ex_bit_kokkos();
+ void init_ex_mol_bit_kokkos();
void choose_build(int, NeighRequest *);
void build_kokkos(int);
void setup_bins_kokkos(int);
-
+ void modify_ex_type_grow_kokkos();
+ void modify_ex_group_grow_kokkos();
+ void modify_mol_group_grow_kokkos();
+
typedef void (NeighborKokkos::*PairPtrHost)
(class NeighListKokkos<LMPHostType> *);
PairPtrHost *pair_build_host;
diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp
new file mode 100644
index 0000000000..494df9267f
--- /dev/null
+++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp
@@ -0,0 +1,266 @@
+/* ----------------------------------------------------------------------
+ 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 "stdio.h"
+#include "stdlib.h"
+#include "string.h"
+#include "pair_coul_cut_kokkos.h"
+#include "kokkos.h"
+#include "atom_kokkos.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define KOKKOS_CUDA_MAX_THREADS 256
+#define KOKKOS_CUDA_MIN_BLOCKS 8
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairCoulCutKokkos<DeviceType>::PairCoulCutKokkos(LAMMPS *lmp) : PairCoulCut(lmp)
+{
+ atomKK = (AtomKokkos *) atom;
+ execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+ datamask_read = X_MASK | F_MASK | TYPE_MASK | Q_MASK | ENERGY_MASK | VIRIAL_MASK;
+ datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
+ cutsq = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairCoulCutKokkos<DeviceType>::~PairCoulCutKokkos()
+{
+ if (allocated)
+ memory->destroy_kokkos(k_cutsq, cutsq);
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairCoulCutKokkos<DeviceType>::cleanup_copy() {
+ // WHY needed: this prevents parent copy from deallocating any arrays
+ allocated = 0;
+ cutsq = NULL;
+ eatom = NULL;
+ vatom = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairCoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
+{
+ eflag = eflag_in;
+ vflag = vflag_in;
+
+
+ if (neighflag == FULL || neighflag == FULLCLUSTER) no_virial_fdotr_compute = 1;
+
+ double ecoul = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ atomKK->sync(execution_space,datamask_read);
+ k_cutsq.template sync<DeviceType>();
+ k_cut_ljsq.template sync<DeviceType>();
+ k_cut_coulsq.template sync<DeviceType>();
+ k_params.template sync<DeviceType>();
+ if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
+ else atomKK->modified(execution_space,F_MASK);
+
+ x = atomKK->k_x.view<DeviceType>();
+ c_x = atomKK->k_x.view<DeviceType>();
+ f = atomKK->k_f.view<DeviceType>();
+ q = atomKK->k_q.view<DeviceType>();
+ type = atomKK->k_type.view<DeviceType>();
+ nlocal = atom->nlocal;
+ nall = atom->nlocal + atom->nghost;
+ newton_pair = force->newton_pair;
+ special_lj[0] = force->special_lj[0];
+ special_lj[1] = force->special_lj[1];
+ special_lj[2] = force->special_lj[2];
+ special_lj[3] = force->special_lj[3];
+ special_coul[0] = force->special_coul[0];
+ special_coul[1] = force->special_coul[1];
+ special_coul[2] = force->special_coul[2];
+ special_coul[3] = force->special_coul[3];
+ qqrd2e = force->qqrd2e;
+
+ // loop over neighbors of my atoms
+
+ EV_FLOAT ev = pair_compute<PairCoulCutKokkos<DeviceType>,void >
+ (this,(NeighListKokkos<DeviceType>*)list);
+
+ DeviceType::fence();
+
+ if (eflag) eng_coul += ev.ecoul;
+ if (vflag_global) {
+ virial[0] += ev.v[0];
+ virial[1] += ev.v[1];
+ virial[2] += ev.v[2];
+ virial[3] += ev.v[3];
+ virial[4] += ev.v[4];
+ virial[5] += ev.v[5];
+ }
+
+ if (vflag_fdotr) pair_virial_fdotr_compute(this);
+}
+
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairCoulCutKokkos<DeviceType>::
+compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j, const int& itype,
+ const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const {
+ const F_FLOAT r2inv = 1.0/rsq;
+ const F_FLOAT rinv = sqrt(r2inv);
+ F_FLOAT forcecoul;
+
+ forcecoul = qqrd2e*(STACKPARAMS?m_params[itype][jtype].scale:params(itype,jtype).scale)*
+ qtmp *q(j) *rinv;
+
+ return factor_coul*forcecoul*r2inv;
+}
+
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairCoulCutKokkos<DeviceType>::
+compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j, const int& itype,
+ const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const {
+ const F_FLOAT r2inv = 1.0/rsq;
+ const F_FLOAT rinv = sqrt(r2inv);
+
+ return factor_coul*qqrd2e * (STACKPARAMS?m_params[itype][jtype].scale:params(itype,jtype).scale)
+ * qtmp *q(j)*rinv;
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairCoulCutKokkos<DeviceType>::allocate()
+{
+ PairCoulCut::allocate();
+
+ int n = atom->ntypes;
+ memory->destroy(cutsq);
+ memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
+ d_cutsq = k_cutsq.template view<DeviceType>();
+
+ k_cut_ljsq = typename ArrayTypes<DeviceType>::tdual_ffloat_2d("pair:cut_ljsq",n+1,n+1);
+ d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
+ k_cut_coulsq = typename ArrayTypes<DeviceType>::tdual_ffloat_2d("pair:cut_coulsq",n+1,n+1);
+ d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
+
+ k_params = Kokkos::DualView<params_coul**,Kokkos::LayoutRight,DeviceType>("PairCoulCut::params",n+1,n+1);
+ params = k_params.d_view;
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairCoulCutKokkos<DeviceType>::settings(int narg, char **arg)
+{
+ // \todo check what should be the limit on narg
+ if (narg > 2) error->all(FLERR,"Illegal pair_style command");
+
+ PairCoulCut::settings(1,arg);
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairCoulCutKokkos<DeviceType>::init_style()
+{
+ PairCoulCut::init_style();
+
+ // irequest = neigh request made by parent class
+
+ neighflag = lmp->kokkos->neighflag;
+ int irequest = neighbor->nrequest - 1;
+
+ neighbor->requests[irequest]->
+ kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+ !Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+ neighbor->requests[irequest]->
+ kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+
+ if (neighflag == FULL) {
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full_cluster = 0;
+ } else if (neighflag == HALF || neighflag == HALFTHREAD) {
+ neighbor->requests[irequest]->full = 0;
+ neighbor->requests[irequest]->half = 1;
+ neighbor->requests[irequest]->full_cluster = 0;
+ } else {
+ error->all(FLERR,"Cannot use chosen neighbor list style with coul/cut/kk");
+ }
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+double PairCoulCutKokkos<DeviceType>::init_one(int i, int j)
+{
+ double cutone = PairCoulCut::init_one(i,j);
+
+ k_params.h_view(i,j).scale = scale[i][j];
+ k_params.h_view(i,j).cutsq = cutone*cutone;
+ k_params.h_view(j,i) = k_params.h_view(i,j);
+
+ if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
+ m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
+ m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
+ m_cut_ljsq[j][i] = m_cut_ljsq[i][j] = cutone*cutone;
+ m_cut_coulsq[j][i] = m_cut_coulsq[i][j] = cutone*cutone;
+ }
+ k_cutsq.h_view(i,j) = cutone*cutone;
+ k_cutsq.template modify<LMPHostType>();
+ k_cut_ljsq.h_view(i,j) = cutone*cutone;
+ k_cut_ljsq.template modify<LMPHostType>();
+ k_cut_coulsq.h_view(i,j) = cutone*cutone;
+ k_cut_coulsq.template modify<LMPHostType>();
+ k_params.template modify<LMPHostType>();
+
+ return cutone;
+}
+
+
+
+template class PairCoulCutKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class PairCoulCutKokkos<LMPHostType>;
+#endif
diff --git a/src/KOKKOS/pair_coul_cut_kokkos.h b/src/KOKKOS/pair_coul_cut_kokkos.h
new file mode 100644
index 0000000000..96e4ca0f63
--- /dev/null
+++ b/src/KOKKOS/pair_coul_cut_kokkos.h
@@ -0,0 +1,137 @@
+/* ----------------------------------------------------------------------
+ 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 PAIR_CLASS
+
+PairStyle(coul/cut/kk,PairCoulCutKokkos<LMPDeviceType>)
+PairStyle(coul/cut/kk/device,PairCoulCutKokkos<LMPDeviceType>)
+PairStyle(coul/cut/kk/host,PairCoulCutKokkos<LMPHostType>)
+
+#else
+
+#ifndef LMP_PAIR_COUL_CUT_KOKKOS_H
+#define LMP_PAIR_COUL_CUT_KOKKOS_H
+
+#include "pair_kokkos.h"
+#include "pair_coul_cut.h"
+#include "neigh_list_kokkos.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class PairCoulCutKokkos : public PairCoulCut {
+ public:
+ enum {EnabledNeighFlags=FULL&HALFTHREAD&HALF};
+ enum {COUL_FLAG=1};
+ typedef DeviceType device_type;
+ PairCoulCutKokkos(class LAMMPS *);
+ ~PairCoulCutKokkos();
+
+ void compute(int, int);
+
+ void settings(int, char **);
+ void init_style();
+ double init_one(int, int);
+
+ struct params_coul{
+ params_coul(){cutsq=0,scale=0;};
+ params_coul(int i){cutsq=0,scale=0;};
+ F_FLOAT cutsq, scale;
+ };
+
+ protected:
+ void cleanup_copy();
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const {
+ return 0.0;
+ }
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const;
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const{
+ return 0;
+ }
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const;
+
+ Kokkos::DualView<params_coul**,Kokkos::LayoutRight,DeviceType> k_params;
+ typename Kokkos::DualView<params_coul**,
+ Kokkos::LayoutRight,DeviceType>::t_dev_const params;
+ // hardwired to space for 15 atom types
+ params_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+
+ F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ F_FLOAT m_cut_ljsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ F_FLOAT m_cut_coulsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ typename ArrayTypes<DeviceType>::t_x_array_randomread x;
+ typename ArrayTypes<DeviceType>::t_x_array c_x;
+ typename ArrayTypes<DeviceType>::t_f_array f;
+ typename ArrayTypes<DeviceType>::t_float_1d_randomread q;
+ typename ArrayTypes<DeviceType>::t_int_1d_randomread type;
+ typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
+ typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+
+ int newton_pair;
+
+ typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
+ typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
+ typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_ljsq;
+ typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_ljsq;
+ typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
+ typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
+
+ class AtomKokkos *atomKK;
+ int neighflag;
+ int nlocal,nall,eflag,vflag;
+
+ double special_coul[4];
+ double special_lj[4];
+ double qqrd2e;
+
+ void allocate();
+ friend class PairComputeFunctor<PairCoulCutKokkos,FULL,true>;
+ friend class PairComputeFunctor<PairCoulCutKokkos,HALF,true>;
+ friend class PairComputeFunctor<PairCoulCutKokkos,HALFTHREAD,true>;
+ friend class PairComputeFunctor<PairCoulCutKokkos,N2,true>;
+ friend class PairComputeFunctor<PairCoulCutKokkos,FULLCLUSTER,true >;
+ friend class PairComputeFunctor<PairCoulCutKokkos,FULL,false>;
+ friend class PairComputeFunctor<PairCoulCutKokkos,HALF,false>;
+ friend class PairComputeFunctor<PairCoulCutKokkos,HALFTHREAD,false>;
+ friend class PairComputeFunctor<PairCoulCutKokkos,N2,false>;
+ friend class PairComputeFunctor<PairCoulCutKokkos,FULLCLUSTER,false >;
+ friend EV_FLOAT pair_compute<PairCoulCutKokkos,void>(PairCoulCutKokkos*,
+ NeighListKokkos<DeviceType>*);
+ friend void pair_virial_fdotr_compute<PairCoulCutKokkos>(PairCoulCutKokkos*);
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/pair_kokkos.h b/src/KOKKOS/pair_kokkos.h
index de67e7df0b..2204399a39 100644
--- a/src/KOKKOS/pair_kokkos.h
+++ b/src/KOKKOS/pair_kokkos.h
@@ -25,27 +25,72 @@
namespace LAMMPS_NS {
+template<int Table>
+struct CoulLongTable {
+ enum {DoTable = Table};
+};
+
+// Tags for doing coulomb calculations or not
+// They facilitate function overloading, since
+// partial template specialization of member functions is not allowed
+struct CoulTag {};
+struct NoCoulTag {};
+
+template<int FLAG>
+struct DoCoul {
+ typedef NoCoulTag type;
+};
+
+template<>
+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};
+};
+
+//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 ;
+
+ // Reduction type, contains evdwl, ecoul and virial[6]
typedef EV_FLOAT value_type;
+ // The copy of the pair style
PairStyle c;
+
+ // 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;
NeighListKokkos<device_type> list;
PairComputeFunctor(PairStyle* c_ptr,
NeighListKokkos<device_type>* list_ptr):
- c(*c_ptr),list(*list_ptr) {};
+ c(*c_ptr),f(c.f),list(*list_ptr) {};
+
+ // Call cleanup_copy which sets allocations NULL which are destructed by the PairStyle
~PairComputeFunctor() {c.cleanup_copy();list.clean_copy();};
KOKKOS_INLINE_FUNCTION int sbmask(const int& j) const {
return j >> SBBITS & 3;
}
+ // 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 {
+ const NeighListKokkos<device_type> &list, const NoCoulTag&) const {
EV_FLOAT ev;
const int i = list.d_ilist[ii];
const X_FLOAT xtmp = c.x(i,0);
@@ -77,25 +122,17 @@ struct PairComputeFunctor {
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
- if ((NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < c.nlocal)) {
- Kokkos::atomic_fetch_add(&c.f(j,0),-delx*fpair);
- Kokkos::atomic_fetch_add(&c.f(j,1),-dely*fpair);
- Kokkos::atomic_fetch_add(&c.f(j,2),-delz*fpair);
- }
- if ((NEIGHFLAG==HALF) && (NEWTON_PAIR || j < c.nlocal)) {
- c.f(j,0) -= delx*fpair;
- c.f(j,1) -= dely*fpair;
- c.f(j,2) -= 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;
}
if (EVFLAG) {
if (c.eflag) {
ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<c.nlocal)))?1.0:0.5)*
factor_lj * c.template compute_evdwl<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
- if (c.COUL_FLAG)
- ev.ecoul += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<c.nlocal)))?1.0:0.5)*
- factor_lj * c.template compute_ecoul<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
}
if (c.vflag_either) ev_tally(ev,i,j,fpair,delx,dely,delz);
@@ -103,16 +140,84 @@ struct PairComputeFunctor {
}
}
- if (NEIGHFLAG == HALFTHREAD) {
- Kokkos::atomic_fetch_add(&c.f(i,0),fxtmp);
- Kokkos::atomic_fetch_add(&c.f(i,1),fytmp);
- Kokkos::atomic_fetch_add(&c.f(i,2),fztmp);
- } else {
- c.f(i,0) += fxtmp;
- c.f(i,1) += fytmp;
- c.f(i,2) += fztmp;
+
+ f(i,0) += fxtmp;
+ f(i,1) += fytmp;
+ f(i,2) += fztmp;
+
+ return ev;
+ }
+
+ // Loop over neighbors of one atom with 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 CoulTag& ) const {
+ EV_FLOAT ev;
+ const int i = list.d_ilist[ii];
+ const X_FLOAT xtmp = c.x(i,0);
+ const X_FLOAT ytmp = c.x(i,1);
+ const X_FLOAT ztmp = c.x(i,2);
+ const int itype = c.type(i);
+ const F_FLOAT qtmp = c.q(i);
+
+ const AtomNeighborsConst neighbors_i = list.get_neighbors_const(i);
+ const int jnum = list.d_numneigh[i];
+
+ F_FLOAT fxtmp = 0.0;
+ F_FLOAT fytmp = 0.0;
+ F_FLOAT fztmp = 0.0;
+
+ for (int jj = 0; jj < jnum; jj++) {
+ int j = neighbors_i(jj);
+ const F_FLOAT factor_lj = c.special_lj[sbmask(j)];
+ const F_FLOAT factor_coul = c.special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+ const X_FLOAT delx = xtmp - c.x(j,0);
+ const X_FLOAT dely = ytmp - c.x(j,1);
+ const X_FLOAT delz = ztmp - c.x(j,2);
+ const int jtype = c.type(j);
+ const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
+
+ if(rsq < (STACKPARAMS?c.m_cutsq[itype][jtype]:c.d_cutsq(itype,jtype))) {
+
+ F_FLOAT fpair = F_FLOAT();
+
+ if(rsq < (STACKPARAMS?c.m_cut_ljsq[itype][jtype]:c.d_cut_ljsq(itype,jtype)))
+ fpair+=factor_lj*c.template compute_fpair<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
+ if(rsq < (STACKPARAMS?c.m_cut_coulsq[itype][jtype]:c.d_cut_coulsq(itype,jtype)))
+ fpair+=c.template compute_fcoul<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype,factor_coul,qtmp);
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ 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;
+ }
+
+ if (EVFLAG) {
+ if (c.eflag) {
+ if(rsq < (STACKPARAMS?c.m_cut_ljsq[itype][jtype]:c.d_cut_ljsq(itype,jtype)))
+ ev.evdwl += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<c.nlocal)))?1.0:0.5)*
+ factor_lj * c.template compute_evdwl<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
+ if(rsq < (STACKPARAMS?c.m_cut_coulsq[itype][jtype]:c.d_cut_coulsq(itype,jtype)))
+ ev.ecoul += (((NEIGHFLAG==HALF || NEIGHFLAG==HALFTHREAD)&&(NEWTON_PAIR||(j<c.nlocal)))?1.0:0.5)*
+ c.template compute_ecoul<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype,factor_coul,qtmp);
+ }
+
+ if (c.vflag_either) ev_tally(ev,i,j,fpair,delx,dely,delz);
+ }
+ }
}
+ f(i,0) += fxtmp;
+ f(i,1) += fytmp;
+ f(i,2) += fztmp;
+
return ev;
}
@@ -142,7 +247,7 @@ struct PairComputeFunctor {
const E_FLOAT v5 = dely*delz*fpair;
if (c.vflag_global) {
- if (NEIGHFLAG) {
+ if (NEIGHFLAG!=FULL) {
if (NEWTON_PAIR) {
ev.v[0] += v0;
ev.v[1] += v1;
@@ -202,43 +307,17 @@ struct PairComputeFunctor {
KOKKOS_INLINE_FUNCTION
void operator()(const int i) const {
- if (c.newton_pair) compute_item<0,1>(i,list);
- else compute_item<0,0>(i,list);
+ if (c.newton_pair) compute_item<0,1>(i,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
+ else compute_item<0,0>(i,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
}
KOKKOS_INLINE_FUNCTION
void operator()(const int i, value_type &energy_virial) const {
if (c.newton_pair)
- energy_virial += compute_item<1,1>(i,list);
+ energy_virial += compute_item<1,1>(i,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
else
- energy_virial += compute_item<1,0>(i,list);
- }
-
- KOKKOS_INLINE_FUNCTION
- static void init(volatile value_type &update) {
- update.evdwl = 0;
- update.ecoul = 0;
- update.v[0] = 0;
- update.v[1] = 0;
- update.v[2] = 0;
- update.v[3] = 0;
- update.v[4] = 0;
- update.v[5] = 0;
+ energy_virial += compute_item<1,0>(i,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
}
- KOKKOS_INLINE_FUNCTION
- static void join(volatile value_type &update,
- const volatile value_type &source) {
- update.evdwl += source.evdwl;
- update.ecoul += source.ecoul;
- update.v[0] += source.v[0];
- update.v[1] += source.v[1];
- update.v[2] += source.v[2];
- update.v[3] += source.v[3];
- update.v[4] += source.v[4];
- update.v[5] += source.v[5];
- }
-
-
};
template <class PairStyle, bool STACKPARAMS, class Specialisation>
@@ -261,8 +340,8 @@ struct PairComputeFunctor<PairStyle,FULLCLUSTER,STACKPARAMS,Specialisation> {
template<int EVFLAG, int NEWTON_PAIR>
KOKKOS_FUNCTION
- EV_FLOAT compute_item(const device_type& dev,
- const NeighListKokkos<device_type> &list) const {
+ 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 = vectorization::global_thread_rank(dev);
@@ -302,9 +381,6 @@ struct PairComputeFunctor<PairStyle,FULLCLUSTER,STACKPARAMS,Specialisation> {
if (c.eflag) {
ev.evdwl += 0.5*
factor_lj * c.template compute_evdwl<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
- if (c.COUL_FLAG)
- ev.ecoul += 0.5*
- factor_lj * c.template compute_ecoul<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
}
if (c.vflag_either) ev_tally(ev,i,j,fpair,delx,dely,delz);
@@ -373,44 +449,18 @@ struct PairComputeFunctor<PairStyle,FULLCLUSTER,STACKPARAMS,Specialisation> {
}
KOKKOS_INLINE_FUNCTION
- void operator()(const device_type& dev) const {
- if (c.newton_pair) compute_item<0,1>(dev,list);
- else compute_item<0,0>(dev,list);
+ void operator()(const typename Kokkos::TeamPolicy<device_type>::member_type& dev) const {
+ if (c.newton_pair) compute_item<0,1>(dev,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
+ else compute_item<0,0>(dev,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
}
KOKKOS_INLINE_FUNCTION
- void operator()(const device_type& dev, value_type &energy_virial) const {
+ void operator()(const typename Kokkos::TeamPolicy<device_type>::member_type& dev, value_type &energy_virial) const {
if (c.newton_pair)
- energy_virial += compute_item<1,1>(dev,list);
+ energy_virial += compute_item<1,1>(dev,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
else
- energy_virial += compute_item<1,0>(dev,list);
- }
-
- KOKKOS_INLINE_FUNCTION
- static void init(volatile value_type &update) {
- update.evdwl = 0;
- update.ecoul = 0;
- update.v[0] = 0;
- update.v[1] = 0;
- update.v[2] = 0;
- update.v[3] = 0;
- update.v[4] = 0;
- update.v[5] = 0;
- }
- KOKKOS_INLINE_FUNCTION
- static void join(volatile value_type &update,
- const volatile value_type &source) {
- update.evdwl += source.evdwl;
- update.ecoul += source.ecoul;
- update.v[0] += source.v[0];
- update.v[1] += source.v[1];
- update.v[2] += source.v[2];
- update.v[3] += source.v[3];
- update.v[4] += source.v[4];
- update.v[5] += source.v[5];
+ energy_virial += compute_item<1,0>(dev,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
}
-
-
};
template <class PairStyle, bool STACKPARAMS, class Specialisation>
@@ -433,7 +483,8 @@ struct PairComputeFunctor<PairStyle,N2,STACKPARAMS,Specialisation> {
template<int EVFLAG, int NEWTON_PAIR>
KOKKOS_FUNCTION
EV_FLOAT compute_item(const int& ii,
- const NeighListKokkos<device_type> &list) const {
+ const NeighListKokkos<device_type> &list, const NoCoulTag&) const {
+ (void) list;
EV_FLOAT ev;
const int i = ii;//list.d_ilist[ii];
const X_FLOAT xtmp = c.x(i,0);
@@ -470,9 +521,6 @@ struct PairComputeFunctor<PairStyle,N2,STACKPARAMS,Specialisation> {
if (c.eflag) {
ev.evdwl += 0.5*
factor_lj * c.template compute_evdwl<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
- if (c.COUL_FLAG)
- ev.ecoul += 0.5*
- factor_lj * c.template compute_ecoul<STACKPARAMS,Specialisation>(rsq,i,j,itype,jtype);
}
if (c.vflag_either) ev_tally(ev,i,j,fpair,delx,dely,delz);
@@ -535,116 +583,156 @@ struct PairComputeFunctor<PairStyle,N2,STACKPARAMS,Specialisation> {
KOKKOS_INLINE_FUNCTION
void operator()(const int i) const {
- compute_item<0,0>(i,list);
+ compute_item<0,0>(i,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
}
KOKKOS_INLINE_FUNCTION
void operator()(const int i, value_type &energy_virial) const {
- energy_virial += compute_item<1,0>(i,list);
+ energy_virial += compute_item<1,0>(i,list,typename DoCoul<PairStyle::COUL_FLAG>::type());
}
+};
- KOKKOS_INLINE_FUNCTION
- static void init(volatile value_type &update) {
- update.evdwl = 0;
- update.ecoul = 0;
- update.v[0] = 0;
- update.v[1] = 0;
- update.v[2] = 0;
- update.v[3] = 0;
- update.v[4] = 0;
- update.v[5] = 0;
- }
- KOKKOS_INLINE_FUNCTION
- static void join(volatile value_type &update,
- const volatile value_type &source) {
- update.evdwl += source.evdwl;
- update.ecoul += source.ecoul;
- update.v[0] += source.v[0];
- update.v[1] += source.v[1];
- update.v[2] += source.v[2];
- update.v[3] += source.v[3];
- update.v[4] += source.v[4];
- update.v[5] += source.v[5];
- }
+// Filter out Neighflags which are not supported for PairStyle
+// The enable_if clause will invalidate the last parameter of the function, so that
+// a match is only achieved, if PairStyle supports the specific neighborlist variant.
+// This uses the fact that failure to match template parameters is not an error.
+// By having the enable_if with a ! and without it, exactly one of the two versions of the functions
+// pair_compute_neighlist and pair_compute_fullcluster will match - either the dummy version
+// or the real one further below.
+template<class PairStyle, unsigned NEIGHFLAG, class Specialisation>
+EV_FLOAT pair_compute_neighlist (PairStyle* fpair, typename Kokkos::Impl::enable_if<!(NEIGHFLAG&PairStyle::EnabledNeighFlags), NeighListKokkos<typename PairStyle::device_type>*>::type list) {
+ EV_FLOAT ev;
+ (void) fpair;
+ (void) list;
+ printf("ERROR: calling pair_compute with invalid neighbor list style: requested %i available %i",NEIGHFLAG,PairStyle::EnabledNeighFlags);
+ return ev;
+}
+template<class PairStyle, class Specialisation>
+EV_FLOAT pair_compute_fullcluster (PairStyle* fpair, typename Kokkos::Impl::enable_if<!(FULLCLUSTER&PairStyle::EnabledNeighFlags), NeighListKokkos<typename PairStyle::device_type>*>::type list) {
+ EV_FLOAT ev;
+ (void) fpair;
+ (void) list;
+ printf("ERROR: calling pair_compute with invalid neighbor list style: requested %i available %i",FULLCLUSTER,PairStyle::EnabledNeighFlags);
+ return ev;
+}
-};
+// Submit ParallelFor for NEIGHFLAG=HALF,HALFTHREAD,FULL,N2
+template<class PairStyle, unsigned NEIGHFLAG, class Specialisation>
+EV_FLOAT pair_compute_neighlist (PairStyle* fpair, typename Kokkos::Impl::enable_if<NEIGHFLAG&PairStyle::EnabledNeighFlags, NeighListKokkos<typename PairStyle::device_type>*>::type list) {
+ EV_FLOAT ev;
+ if(fpair->atom->ntypes > MAX_TYPES_STACKPARAMS) {
+ 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);
+ } 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);
+ }
+ return ev;
+}
+// Submit ParallelFor for NEIGHFLAG=FULLCLUSTER
template<class PairStyle, class Specialisation>
-EV_FLOAT pair_compute (PairStyle* fpair, NeighListKokkos<typename PairStyle::device_type>* list) {
+EV_FLOAT pair_compute_fullcluster (PairStyle* fpair, typename Kokkos::Impl::enable_if<FULLCLUSTER&PairStyle::EnabledNeighFlags, NeighListKokkos<typename PairStyle::device_type>*>::type list) {
EV_FLOAT ev;
if(fpair->atom->ntypes > MAX_TYPES_STACKPARAMS) {
- if (fpair->neighflag == FULL) {
- PairComputeFunctor<PairStyle,FULL,false,Specialisation >
- ff(fpair, list);
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
- else Kokkos::parallel_for(list->inum,ff);
- } else if (fpair->neighflag == HALFTHREAD) {
- PairComputeFunctor<PairStyle,HALFTHREAD,false,Specialisation >
- ff(fpair, list);
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
- else Kokkos::parallel_for(list->inum,ff);
- } else if (fpair->neighflag == HALF) {
- PairComputeFunctor<PairStyle,HALF,false,Specialisation >
- ff(fpair, list);
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
- else Kokkos::parallel_for(list->inum,ff);
- } else if (fpair->neighflag == N2) {
- PairComputeFunctor<PairStyle,N2,false,Specialisation >
- ff(fpair, list);
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(fpair->nlocal,ff,ev);
- else Kokkos::parallel_for(fpair->nlocal,ff);
- } else if (fpair->neighflag == FULLCLUSTER) {
- typedef PairComputeFunctor<PairStyle,FULLCLUSTER,false,Specialisation >
- f_type;
- f_type ff(fpair, list);
- #ifdef KOKKOS_HAVE_CUDA
- const int teamsize = Kokkos::Impl::is_same<typename f_type::device_type, Kokkos::Cuda>::value ? 256 : 1;
- #else
- const int teamsize = 1;
- #endif
- const int nteams = (list->inum*f_type::vectorization::increment+teamsize-1)/teamsize;
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(Kokkos::ParallelWorkRequest(nteams,teamsize),ff,ev);
- else Kokkos::parallel_for(Kokkos::ParallelWorkRequest(nteams,teamsize),ff);
- }
+ typedef PairComputeFunctor<PairStyle,FULLCLUSTER,false,Specialisation >
+ f_type;
+ f_type ff(fpair, list);
+ #ifdef KOKKOS_HAVE_CUDA
+ const int teamsize = Kokkos::Impl::is_same<typename f_type::device_type, Kokkos::Cuda>::value ? 256 : 1;
+ #else
+ const int teamsize = 1;
+ #endif
+ const int nteams = (list->inum*f_type::vectorization::increment+teamsize-1)/teamsize;
+ Kokkos::TeamPolicy<typename f_type::device_type> config(nteams,teamsize);
+ if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(config,ff,ev);
+ else Kokkos::parallel_for(config,ff);
} else {
- if (fpair->neighflag == FULL) {
- PairComputeFunctor<PairStyle,FULL,true,Specialisation >
- ff(fpair, list);
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
- else Kokkos::parallel_for(list->inum,ff);
- } else if (fpair->neighflag == HALFTHREAD) {
- PairComputeFunctor<PairStyle,HALFTHREAD,true,Specialisation >
- ff(fpair, list);
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
- else Kokkos::parallel_for(list->inum,ff);
- } else if (fpair->neighflag == HALF) {
- PairComputeFunctor<PairStyle,HALF,true,Specialisation >
- ff(fpair, list);
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(list->inum,ff,ev);
- else Kokkos::parallel_for(list->inum,ff);
- } else if (fpair->neighflag == N2) {
- PairComputeFunctor<PairStyle,N2,true,Specialisation >
- ff(fpair, list);
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(fpair->nlocal,ff,ev);
- else Kokkos::parallel_for(fpair->nlocal,ff);
- } else if (fpair->neighflag == FULLCLUSTER) {
- typedef PairComputeFunctor<PairStyle,FULLCLUSTER,true,Specialisation >
- f_type;
- f_type ff(fpair, list);
- #ifdef KOKKOS_HAVE_CUDA
- const int teamsize = Kokkos::Impl::is_same<typename f_type::device_type, Kokkos::Cuda>::value ? 256 : 1;
- #else
- const int teamsize = 1;
- #endif
- const int nteams = (list->inum*f_type::vectorization::increment+teamsize-1)/teamsize;
- if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(Kokkos::ParallelWorkRequest(nteams,teamsize),ff,ev);
- else Kokkos::parallel_for(Kokkos::ParallelWorkRequest(nteams,teamsize),ff);
- }
+ typedef PairComputeFunctor<PairStyle,FULLCLUSTER,true,Specialisation >
+ f_type;
+ f_type ff(fpair, list);
+ #ifdef KOKKOS_HAVE_CUDA
+ const int teamsize = Kokkos::Impl::is_same<typename f_type::device_type, Kokkos::Cuda>::value ? 256 : 1;
+ #else
+ const int teamsize = 1;
+ #endif
+ const int nteams = (list->inum*f_type::vectorization::increment+teamsize-1)/teamsize;
+ Kokkos::TeamPolicy<typename f_type::device_type> config(nteams,teamsize);
+ if (fpair->eflag || fpair->vflag) Kokkos::parallel_reduce(config,ff,ev);
+ else Kokkos::parallel_for(config,ff);
}
return ev;
}
+
+template<class PairStyle, class Specialisation>
+EV_FLOAT pair_compute (PairStyle* fpair, NeighListKokkos<typename PairStyle::device_type>* list) {
+ EV_FLOAT ev;
+ if (fpair->neighflag == FULL) {
+ ev = pair_compute_neighlist<PairStyle,FULL,Specialisation> (fpair,list);
+ } else if (fpair->neighflag == HALFTHREAD) {
+ ev = pair_compute_neighlist<PairStyle,HALFTHREAD,Specialisation> (fpair,list);
+ } else if (fpair->neighflag == HALF) {
+ ev = pair_compute_neighlist<PairStyle,HALF,Specialisation> (fpair,list);
+ } else if (fpair->neighflag == N2) {
+ ev = pair_compute_neighlist<PairStyle,N2,Specialisation> (fpair,list);
+ } else if (fpair->neighflag == FULLCLUSTER) {
+ ev = pair_compute_fullcluster<PairStyle,Specialisation> (fpair,list);
+ }
+ return ev;
+}
+
+template<class DeviceType>
+struct PairVirialFDotRCompute {
+ typedef ArrayTypes<DeviceType> AT;
+ typedef EV_FLOAT value_type;
+ typename AT::t_x_array_const x;
+ typename AT::t_f_array_const f;
+ const int offset;
+
+ PairVirialFDotRCompute( typename AT::t_x_array_const x_,
+ typename AT::t_f_array_const f_,
+ const int offset_):x(x_),f(f_),offset(offset_) {}
+
+ KOKKOS_INLINE_FUNCTION
+ void operator()(const int j, value_type &energy_virial) const {
+ const int i = j + offset;
+ energy_virial.v[0] += f(i,0)*x(i,0);
+ energy_virial.v[1] += f(i,1)*x(i,1);
+ energy_virial.v[2] += f(i,2)*x(i,2);
+ energy_virial.v[3] += f(i,1)*x(i,0);
+ energy_virial.v[4] += f(i,2)*x(i,0);
+ energy_virial.v[5] += f(i,2)*x(i,1);
+ }
+};
+
+template<class PairStyle>
+void pair_virial_fdotr_compute(PairStyle* fpair) {
+ EV_FLOAT virial;
+ if (fpair->neighbor->includegroup == 0) {
+ int nall = fpair->atom->nlocal + fpair->atom->nghost;
+ Kokkos::parallel_reduce(nall,PairVirialFDotRCompute<typename PairStyle::device_type>(fpair->x,fpair->f,0),virial);
+ } else {
+ Kokkos::parallel_reduce(fpair->atom->nfirst,PairVirialFDotRCompute<typename PairStyle::device_type>(fpair->x,fpair->f,0),virial);
+ EV_FLOAT virial_ghost;
+ Kokkos::parallel_reduce(fpair->atom->nghost,PairVirialFDotRCompute<typename PairStyle::device_type>(fpair->x,fpair->f,fpair->atom->nlocal),virial_ghost);
+ virial+=virial_ghost;
+ }
+ fpair->vflag_fdotr = 0;
+ fpair->virial[0] = virial.v[0];
+ fpair->virial[1] = virial.v[1];
+ fpair->virial[2] = virial.v[2];
+ fpair->virial[3] = virial.v[3];
+ fpair->virial[4] = virial.v[4];
+ fpair->virial[5] = virial.v[5];
+}
+
+
+
+
}
#endif
diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
new file mode 100644
index 0000000000..97fa91a453
--- /dev/null
+++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
@@ -0,0 +1,347 @@
+/* ----------------------------------------------------------------------
+ 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 "stdio.h"
+#include "stdlib.h"
+#include "string.h"
+#include "pair_lj_cut_coul_cut_kokkos.h"
+#include "kokkos.h"
+#include "atom_kokkos.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define KOKKOS_CUDA_MAX_THREADS 256
+#define KOKKOS_CUDA_MIN_BLOCKS 8
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairLJCutCoulCutKokkos<DeviceType>::PairLJCutCoulCutKokkos(LAMMPS *lmp):PairLJCutCoulCut(lmp)
+{
+ respa_enable = 0;
+
+ atomKK = (AtomKokkos *) atom;
+ execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+ datamask_read = X_MASK | F_MASK | TYPE_MASK | Q_MASK | ENERGY_MASK | VIRIAL_MASK;
+ datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
+ cutsq = NULL;
+ cut_ljsq = NULL;
+ cut_coulsq = NULL;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairLJCutCoulCutKokkos<DeviceType>::~PairLJCutCoulCutKokkos()
+{
+ if (allocated){
+ memory->destroy_kokkos(k_cutsq, cutsq);
+ memory->destroy_kokkos(k_cut_ljsq, cut_ljsq);
+ memory->destroy_kokkos(k_cut_coulsq, cut_coulsq);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulCutKokkos<DeviceType>::cleanup_copy() {
+ // WHY needed: this prevents parent copy from deallocating any arrays
+ allocated = 0;
+ cutsq = NULL;
+ cut_ljsq = NULL;
+ cut_coulsq = NULL;
+ eatom = NULL;
+ vatom = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
+{
+ eflag = eflag_in;
+ vflag = vflag_in;
+
+ if (neighflag == FULL || neighflag == FULLCLUSTER) no_virial_fdotr_compute = 1;
+
+ double evdwl = 0.0;
+ double ecoul = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ atomKK->sync(execution_space,datamask_read);
+ k_cutsq.template sync<DeviceType>();
+ k_cut_ljsq.template sync<DeviceType>();
+ k_cut_coulsq.template sync<DeviceType>();
+ k_params.template sync<DeviceType>();
+ if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
+ else atomKK->modified(execution_space,F_MASK);
+
+ x = atomKK->k_x.view<DeviceType>();
+ c_x = atomKK->k_x.view<DeviceType>();
+ f = atomKK->k_f.view<DeviceType>();
+ q = atomKK->k_q.view<DeviceType>();
+ type = atomKK->k_type.view<DeviceType>();
+ nlocal = atom->nlocal;
+ nall = atom->nlocal + atom->nghost;
+ special_lj[0] = force->special_lj[0];
+ special_lj[1] = force->special_lj[1];
+ special_lj[2] = force->special_lj[2];
+ special_lj[3] = force->special_lj[3];
+ special_coul[0] = force->special_coul[0];
+ special_coul[1] = force->special_coul[1];
+ special_coul[2] = force->special_coul[2];
+ special_coul[3] = force->special_coul[3];
+ qqrd2e = force->qqrd2e;
+ newton_pair = force->newton_pair;
+
+ // loop over neighbors of my atoms
+
+ EV_FLOAT ev = pair_compute<PairLJCutCoulCutKokkos<DeviceType>,void >
+ (this,(NeighListKokkos<DeviceType>*)list);
+
+ DeviceType::fence();
+
+ if (eflag) {
+ eng_vdwl += ev.evdwl;
+ eng_coul += ev.ecoul;
+ }
+ if (vflag_global) {
+ virial[0] += ev.v[0];
+ virial[1] += ev.v[1];
+ virial[2] += ev.v[2];
+ virial[3] += ev.v[3];
+ virial[4] += ev.v[4];
+ virial[5] += ev.v[5];
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+ compute LJ 12-6 pair force between atoms i and j
+ ---------------------------------------------------------------------- */
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairLJCutCoulCutKokkos<DeviceType>::
+compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const {
+ const F_FLOAT r2inv = 1.0/rsq;
+ const F_FLOAT r6inv = r2inv*r2inv*r2inv;
+ F_FLOAT forcelj;
+
+ forcelj = r6inv *
+ ((STACKPARAMS?m_params[itype][jtype].lj1:params(itype,jtype).lj1)*r6inv -
+ (STACKPARAMS?m_params[itype][jtype].lj2:params(itype,jtype).lj2));
+
+ return forcelj*r2inv;
+}
+
+/* ----------------------------------------------------------------------
+ compute coulomb pair force between atoms i and j
+ ---------------------------------------------------------------------- */
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairLJCutCoulCutKokkos<DeviceType>::
+compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const {
+ const F_FLOAT r2inv = 1.0/rsq;
+ const F_FLOAT rinv = sqrt(r2inv);
+ F_FLOAT forcecoul;
+
+ forcecoul = qqrd2e*qtmp*q(j) *rinv;
+
+ return factor_coul*forcecoul*r2inv;
+}
+
+/* ----------------------------------------------------------------------
+ compute LJ 12-6 pair potential energy between atoms i and j
+ ---------------------------------------------------------------------- */
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairLJCutCoulCutKokkos<DeviceType>::
+compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const {
+ const F_FLOAT r2inv = 1.0/rsq;
+ const F_FLOAT r6inv = r2inv*r2inv*r2inv;
+
+ return r6inv*
+ ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv
+ - (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4))
+ - (STACKPARAMS?m_params[itype][jtype].offset:params(itype,jtype).offset);
+
+}
+
+/* ----------------------------------------------------------------------
+ compute coulomb pair potential energy between atoms i and j
+ ---------------------------------------------------------------------- */
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairLJCutCoulCutKokkos<DeviceType>::
+compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const {
+ const F_FLOAT r2inv = 1.0/rsq;
+ const F_FLOAT rinv = sqrt(r2inv);
+
+ return factor_coul*qqrd2e*qtmp*q(j)*rinv;
+
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulCutKokkos<DeviceType>::allocate()
+{
+ PairLJCutCoulCut::allocate();
+
+ int n = atom->ntypes;
+ memory->destroy(cutsq);
+ memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
+ d_cutsq = k_cutsq.template view<DeviceType>();
+ memory->destroy(cut_ljsq);
+ memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
+ d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
+ memory->destroy(cut_coulsq);
+ memory->create_kokkos(k_cut_coulsq,cut_coulsq,n+1,n+1,"pair:cut_coulsq");
+ d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
+ k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJCutCoulCut::params",n+1,n+1);
+ params = k_params.d_view;
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulCutKokkos<DeviceType>::settings(int narg, char **arg)
+{
+ if (narg > 2) error->all(FLERR,"Illegal pair_style command");
+
+ PairLJCutCoulCut::settings(1,arg);
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulCutKokkos<DeviceType>::init_style()
+{
+ PairLJCutCoulCut::init_style();
+
+ // error if rRESPA with inner levels
+
+ if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
+ int respa = 0;
+ if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+ if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+ if (respa)
+ error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
+ }
+
+ // irequest = neigh request made by parent class
+
+ neighflag = lmp->kokkos->neighflag;
+ int irequest = neighbor->nrequest - 1;
+
+ neighbor->requests[irequest]->
+ kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+ !Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+ neighbor->requests[irequest]->
+ kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+
+ if (neighflag == FULL) {
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full_cluster = 0;
+ } else if (neighflag == HALF || neighflag == HALFTHREAD) {
+ neighbor->requests[irequest]->full = 0;
+ neighbor->requests[irequest]->half = 1;
+ neighbor->requests[irequest]->full_cluster = 0;
+ } else if (neighflag == N2) {
+ neighbor->requests[irequest]->full = 0;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full_cluster = 0;
+ } else if (neighflag == FULLCLUSTER) {
+ neighbor->requests[irequest]->full_cluster = 1;
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->half = 0;
+ } else {
+ error->all(FLERR,"Cannot use chosen neighbor list style with lj/cut/coul/cut/kk");
+ }
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+double PairLJCutCoulCutKokkos<DeviceType>::init_one(int i, int j)
+{
+ double cutone = PairLJCutCoulCut::init_one(i,j);
+ double cut_ljsqm = cut_ljsq[i][j];
+ double cut_coulsqm = cut_coulsq[i][j];
+
+ k_params.h_view(i,j).lj1 = lj1[i][j];
+ k_params.h_view(i,j).lj2 = lj2[i][j];
+ k_params.h_view(i,j).lj3 = lj3[i][j];
+ k_params.h_view(i,j).lj4 = lj4[i][j];
+ k_params.h_view(i,j).offset = offset[i][j];
+ k_params.h_view(i,j).cut_ljsq = cut_ljsqm;
+ k_params.h_view(i,j).cut_coulsq = cut_coulsqm;
+
+ k_params.h_view(j,i) = k_params.h_view(i,j);
+ if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
+ m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
+ m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
+ m_cut_ljsq[j][i] = m_cut_ljsq[i][j] = cut_ljsqm;
+ m_cut_coulsq[j][i] = m_cut_coulsq[i][j] = cut_coulsqm;
+ }
+ k_cutsq.h_view(i,j) = cutone*cutone;
+ k_cutsq.template modify<LMPHostType>();
+ k_cut_ljsq.h_view(i,j) = cut_ljsqm;
+ k_cut_ljsq.template modify<LMPHostType>();
+ k_cut_coulsq.h_view(i,j) = cut_coulsqm;
+ k_cut_coulsq.template modify<LMPHostType>();
+ k_params.template modify<LMPHostType>();
+
+ return cutone;
+}
+
+
+
+template class PairLJCutCoulCutKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class PairLJCutCoulCutKokkos<LMPHostType>;
+#endif
diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h
new file mode 100644
index 0000000000..cc91a5989a
--- /dev/null
+++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h
@@ -0,0 +1,131 @@
+/* ----------------------------------------------------------------------
+ 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 PAIR_CLASS
+
+PairStyle(lj/cut/coul/cut/kk,PairLJCutCoulCutKokkos<LMPDeviceType>)
+PairStyle(lj/cut/coul/cut/kk/device,PairLJCutCoulCutKokkos<LMPDeviceType>)
+PairStyle(lj/cut/coul/cut/kk/host,PairLJCutCoulCutKokkos<LMPHostType>)
+
+#else
+
+#ifndef LMP_PAIR_LJ_CUT_COUL_CUT_KOKKOS_H
+#define LMP_PAIR_LJ_CUT_COUL_CUT_KOKKOS_H
+
+#include "pair_kokkos.h"
+#include "pair_lj_cut_coul_cut.h"
+#include "neigh_list_kokkos.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class PairLJCutCoulCutKokkos : public PairLJCutCoulCut {
+ public:
+ enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
+ enum {COUL_FLAG=1};
+ typedef DeviceType device_type;
+ PairLJCutCoulCutKokkos(class LAMMPS *);
+ ~PairLJCutCoulCutKokkos();
+
+ void compute(int, int);
+
+ void settings(int, char **);
+ void init_style();
+ double init_one(int, int);
+
+ struct params_lj_coul{
+ params_lj_coul(){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
+ params_lj_coul(int i){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
+ F_FLOAT cut_ljsq,cut_coulsq,lj1,lj2,lj3,lj4,offset;
+ };
+
+ protected:
+ void cleanup_copy();
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const;
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const;
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const;
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const;
+
+ Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
+ typename Kokkos::DualView<params_lj_coul**,
+ Kokkos::LayoutRight,DeviceType>::t_dev_const params;
+ // hardwired to space for 15 atom types
+ params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+
+ F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ F_FLOAT m_cut_ljsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ F_FLOAT m_cut_coulsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ typename ArrayTypes<DeviceType>::t_x_array_randomread x;
+ typename ArrayTypes<DeviceType>::t_x_array c_x;
+ typename ArrayTypes<DeviceType>::t_f_array f;
+ typename ArrayTypes<DeviceType>::t_int_1d_randomread type;
+ typename ArrayTypes<DeviceType>::t_float_1d_randomread q;
+ typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
+ typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+
+ int newton_pair;
+
+ typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
+ typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
+ typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_ljsq;
+ typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_ljsq;
+ typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
+ typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
+
+ class AtomKokkos *atomKK;
+ int neighflag;
+ int nlocal,nall,eflag,vflag;
+
+ double special_coul[4];
+ double special_lj[4];
+ double qqrd2e;
+
+ void allocate();
+ friend class PairComputeFunctor<PairLJCutCoulCutKokkos,FULL,true>;
+ friend class PairComputeFunctor<PairLJCutCoulCutKokkos,HALF,true>;
+ friend class PairComputeFunctor<PairLJCutCoulCutKokkos,HALFTHREAD,true>;
+ friend class PairComputeFunctor<PairLJCutCoulCutKokkos,FULL,false>;
+ friend class PairComputeFunctor<PairLJCutCoulCutKokkos,HALF,false>;
+ friend class PairComputeFunctor<PairLJCutCoulCutKokkos,HALFTHREAD,false>;
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutCoulCutKokkos,FULL,void>(PairLJCutCoulCutKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutCoulCutKokkos,HALF,void>(PairLJCutCoulCutKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutCoulCutKokkos,HALFTHREAD,void>(PairLJCutCoulCutKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute<PairLJCutCoulCutKokkos,void>(PairLJCutCoulCutKokkos*,
+ NeighListKokkos<DeviceType>*);
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
new file mode 100644
index 0000000000..5c4b834bee
--- /dev/null
+++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.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.
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdio.h"
+#include "stdlib.h"
+#include "string.h"
+#include "pair_lj_cut_coul_long_kokkos.h"
+#include "kokkos.h"
+#include "atom_kokkos.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define KOKKOS_CUDA_MAX_THREADS 256
+#define KOKKOS_CUDA_MIN_BLOCKS 8
+
+
+#define EWALD_F 1.12837917
+#define EWALD_P 0.3275911
+#define A1 0.254829592
+#define A2 -0.284496736
+#define A3 1.421413741
+#define A4 -1.453152027
+#define A5 1.061405429
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairLJCutCoulLongKokkos<DeviceType>::PairLJCutCoulLongKokkos(LAMMPS *lmp):PairLJCutCoulLong(lmp)
+{
+ respa_enable = 0;
+
+ atomKK = (AtomKokkos *) atom;
+ execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+ datamask_read = X_MASK | F_MASK | TYPE_MASK | Q_MASK | ENERGY_MASK | VIRIAL_MASK;
+ datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
+ cutsq = NULL;
+ cut_ljsq = NULL;
+ cut_coulsq = NULL;
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairLJCutCoulLongKokkos<DeviceType>::~PairLJCutCoulLongKokkos()
+{
+ if (allocated){
+ memory->destroy_kokkos(k_cutsq, cutsq);
+ memory->destroy_kokkos(k_cut_ljsq, cut_ljsq);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulLongKokkos<DeviceType>::cleanup_copy() {
+ // WHY needed: this prevents parent copy from deallocating any arrays
+ allocated = 0;
+ cutsq = NULL;
+ cut_ljsq = NULL;
+ eatom = NULL;
+ vatom = NULL;
+ ftable = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulLongKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
+{
+ eflag = eflag_in;
+ vflag = vflag_in;
+
+ if (neighflag == FULL || neighflag == FULLCLUSTER) no_virial_fdotr_compute = 1;
+
+ double evdwl = 0.0;
+ double ecoul = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ atomKK->sync(execution_space,datamask_read);
+ k_cutsq.template sync<DeviceType>();
+ k_cut_ljsq.template sync<DeviceType>();
+ k_cut_coulsq.template sync<DeviceType>();
+ k_params.template sync<DeviceType>();
+ if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
+ else atomKK->modified(execution_space,F_MASK);
+
+ x = atomKK->k_x.view<DeviceType>();
+ c_x = atomKK->k_x.view<DeviceType>();
+ f = atomKK->k_f.view<DeviceType>();
+ q = atomKK->k_q.view<DeviceType>();
+ type = atomKK->k_type.view<DeviceType>();
+ nlocal = atom->nlocal;
+ nall = atom->nlocal + atom->nghost;
+ special_lj[0] = force->special_lj[0];
+ special_lj[1] = force->special_lj[1];
+ special_lj[2] = force->special_lj[2];
+ special_lj[3] = force->special_lj[3];
+ special_coul[0] = force->special_coul[0];
+ special_coul[1] = force->special_coul[1];
+ special_coul[2] = force->special_coul[2];
+ special_coul[3] = force->special_coul[3];
+ qqrd2e = force->qqrd2e;
+ newton_pair = force->newton_pair;
+
+ // loop over neighbors of my atoms
+
+ EV_FLOAT ev;
+ if(ncoultablebits)
+ ev = pair_compute<PairLJCutCoulLongKokkos<DeviceType>,CoulLongTable<1> >
+ (this,(NeighListKokkos<DeviceType>*)list);
+ else
+ ev = pair_compute<PairLJCutCoulLongKokkos<DeviceType>,CoulLongTable<0> >
+ (this,(NeighListKokkos<DeviceType>*)list);
+
+
+ DeviceType::fence();
+
+ if (eflag) {
+ eng_vdwl += ev.evdwl;
+ eng_coul += ev.ecoul;
+ }
+ if (vflag_global) {
+ virial[0] += ev.v[0];
+ virial[1] += ev.v[1];
+ virial[2] += ev.v[2];
+ virial[3] += ev.v[3];
+ virial[4] += ev.v[4];
+ virial[5] += ev.v[5];
+ }
+
+ if (vflag_fdotr) pair_virial_fdotr_compute(this);
+}
+
+/* ----------------------------------------------------------------------
+ compute LJ 12-6 pair force between atoms i and j
+ ---------------------------------------------------------------------- */
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairLJCutCoulLongKokkos<DeviceType>::
+compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const {
+ const F_FLOAT r2inv = 1.0/rsq;
+ const F_FLOAT r6inv = r2inv*r2inv*r2inv;
+ F_FLOAT forcelj;
+
+ forcelj = r6inv *
+ ((STACKPARAMS?m_params[itype][jtype].lj1:params(itype,jtype).lj1)*r6inv -
+ (STACKPARAMS?m_params[itype][jtype].lj2:params(itype,jtype).lj2));
+
+ return forcelj*r2inv;
+}
+
+/* ----------------------------------------------------------------------
+ compute coulomb pair force between atoms i and j
+ ---------------------------------------------------------------------- */
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairLJCutCoulLongKokkos<DeviceType>::
+compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const {
+ if(Specialisation::DoTable && rsq > tabinnersq) {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits;
+ const F_FLOAT fraction = (rsq_lookup.f - d_rtable[itable]) * d_drtable[itable];
+ const F_FLOAT table = d_ftable[itable] + fraction*d_dftable[itable];
+ F_FLOAT forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ const F_FLOAT table = d_ctable[itable] + fraction*d_dctable[itable];
+ const F_FLOAT prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ return forcecoul/rsq;
+ } else {
+ const F_FLOAT r = sqrt(rsq);
+ const F_FLOAT grij = g_ewald * r;
+ const F_FLOAT expm2 = exp(-grij*grij);
+ const F_FLOAT t = 1.0 / (1.0 + EWALD_P*grij);
+ const F_FLOAT rinv = 1.0/r;
+ const F_FLOAT erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ const F_FLOAT prefactor = qqrd2e * qtmp*q[j]*rinv;
+ F_FLOAT forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+
+ return forcecoul*rinv*rinv;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ compute LJ 12-6 pair potential energy between atoms i and j
+ ---------------------------------------------------------------------- */
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairLJCutCoulLongKokkos<DeviceType>::
+compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const {
+ const F_FLOAT r2inv = 1.0/rsq;
+ const F_FLOAT r6inv = r2inv*r2inv*r2inv;
+
+ return r6inv*
+ ((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv
+ - (STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4))
+ - (STACKPARAMS?m_params[itype][jtype].offset:params(itype,jtype).offset);
+
+}
+
+/* ----------------------------------------------------------------------
+ compute coulomb pair potential energy between atoms i and j
+ ---------------------------------------------------------------------- */
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairLJCutCoulLongKokkos<DeviceType>::
+compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const {
+ if(Specialisation::DoTable) {
+ union_int_float_t rsq_lookup;
+ rsq_lookup.f = rsq;
+ const int itable = (rsq_lookup.i & ncoulmask) >> ncoulshiftbits;
+ const F_FLOAT fraction = (rsq_lookup.f - d_rtable[itable]) * d_drtable[itable];
+ const F_FLOAT table = d_etable[itable] + fraction*d_detable[itable];
+ F_FLOAT ecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ const F_FLOAT table = d_ctable[itable] + fraction*d_dctable[itable];
+ const F_FLOAT prefactor = qtmp*q[j] * table;
+ ecoul -= (1.0-factor_coul)*prefactor;
+ }
+ return ecoul;
+ } else {
+ const F_FLOAT r = sqrt(rsq);
+ const F_FLOAT grij = g_ewald * r;
+ const F_FLOAT expm2 = exp(-grij*grij);
+ const F_FLOAT t = 1.0 / (1.0 + EWALD_P*grij);
+ const F_FLOAT erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ const F_FLOAT prefactor = qqrd2e * qtmp*q[j]/r;
+ F_FLOAT ecoul = prefactor * erfc;
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ return ecoul;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulLongKokkos<DeviceType>::allocate()
+{
+ PairLJCutCoulLong::allocate();
+
+ int n = atom->ntypes;
+ memory->destroy(cutsq);
+ memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
+ d_cutsq = k_cutsq.template view<DeviceType>();
+ memory->destroy(cut_ljsq);
+ memory->create_kokkos(k_cut_ljsq,cut_ljsq,n+1,n+1,"pair:cut_ljsq");
+ d_cut_ljsq = k_cut_ljsq.template view<DeviceType>();
+
+ memory->create_kokkos(k_cut_coulsq,n+1,n+1,"pair:cut_coulsq");
+ d_cut_coulsq = k_cut_coulsq.template view<DeviceType>();
+ k_params = Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType>("PairLJCutCoulLong::params",n+1,n+1);
+ params = k_params.d_view;
+}
+
+template<class DeviceType>
+void PairLJCutCoulLongKokkos<DeviceType>::init_tables(double cut_coul, double *cut_respa)
+{
+ Pair::init_tables(cut_coul,cut_respa);
+
+ typedef typename ArrayTypes<DeviceType>::t_ffloat_1d table_type;
+ typedef typename ArrayTypes<LMPHostType>::t_ffloat_1d host_table_type;
+
+ int ntable = 1;
+ for (int i = 0; i < ncoultablebits; i++) ntable *= 2;
+
+
+ // Copy rtable and drtable
+ {
+ host_table_type h_table("HostTable",ntable);
+ table_type d_table("DeviceTable",ntable);
+ for(int i = 0; i < ntable; i++) {
+ h_table(i) = rtable[i];
+ }
+ Kokkos::deep_copy(d_table,h_table);
+ d_rtable = d_table;
+ }
+
+ {
+ host_table_type h_table("HostTable",ntable);
+ table_type d_table("DeviceTable",ntable);
+ for(int i = 0; i < ntable; i++) {
+ h_table(i) = drtable[i];
+ }
+ Kokkos::deep_copy(d_table,h_table);
+ d_drtable = d_table;
+ }
+
+ {
+ host_table_type h_table("HostTable",ntable);
+ table_type d_table("DeviceTable",ntable);
+
+ // Copy ftable and dftable
+ for(int i = 0; i < ntable; i++) {
+ h_table(i) = ftable[i];
+ }
+ Kokkos::deep_copy(d_table,h_table);
+ d_ftable = d_table;
+ }
+
+ {
+ host_table_type h_table("HostTable",ntable);
+ table_type d_table("DeviceTable",ntable);
+
+ for(int i = 0; i < ntable; i++) {
+ h_table(i) = dftable[i];
+ }
+ Kokkos::deep_copy(d_table,h_table);
+ d_dftable = d_table;
+ }
+
+ {
+ host_table_type h_table("HostTable",ntable);
+ table_type d_table("DeviceTable",ntable);
+
+ // Copy ctable and dctable
+ for(int i = 0; i < ntable; i++) {
+ h_table(i) = ctable[i];
+ }
+ Kokkos::deep_copy(d_table,h_table);
+ d_ctable = d_table;
+ }
+
+ {
+ host_table_type h_table("HostTable",ntable);
+ table_type d_table("DeviceTable",ntable);
+
+ for(int i = 0; i < ntable; i++) {
+ h_table(i) = dctable[i];
+ }
+ Kokkos::deep_copy(d_table,h_table);
+ d_dctable = d_table;
+ }
+
+ {
+ host_table_type h_table("HostTable",ntable);
+ table_type d_table("DeviceTable",ntable);
+
+ // Copy etable and detable
+ for(int i = 0; i < ntable; i++) {
+ h_table(i) = etable[i];
+ }
+ Kokkos::deep_copy(d_table,h_table);
+ d_etable = d_table;
+ }
+
+ {
+ host_table_type h_table("HostTable",ntable);
+ table_type d_table("DeviceTable",ntable);
+
+ for(int i = 0; i < ntable; i++) {
+ h_table(i) = detable[i];
+ }
+ Kokkos::deep_copy(d_table,h_table);
+ d_detable = d_table;
+ }
+}
+
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulLongKokkos<DeviceType>::settings(int narg, char **arg)
+{
+ if (narg > 2) error->all(FLERR,"Illegal pair_style command");
+
+ PairLJCutCoulLong::settings(narg,arg);
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairLJCutCoulLongKokkos<DeviceType>::init_style()
+{
+ PairLJCutCoulLong::init_style();
+
+ // error if rRESPA with inner levels
+
+ if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
+ int respa = 0;
+ if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+ if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+ if (respa)
+ error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
+ }
+
+ // irequest = neigh request made by parent class
+
+ neighflag = lmp->kokkos->neighflag;
+ int irequest = neighbor->nrequest - 1;
+
+ neighbor->requests[irequest]->
+ kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+ !Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+ neighbor->requests[irequest]->
+ kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+
+ if (neighflag == FULL) {
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full_cluster = 0;
+ } else if (neighflag == HALF || neighflag == HALFTHREAD) {
+ neighbor->requests[irequest]->full = 0;
+ neighbor->requests[irequest]->half = 1;
+ neighbor->requests[irequest]->full_cluster = 0;
+ } else {
+ error->all(FLERR,"Cannot use chosen neighbor list style with lj/cut/coul/long/kk");
+ }
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+double PairLJCutCoulLongKokkos<DeviceType>::init_one(int i, int j)
+{
+ double cutone = PairLJCutCoulLong::init_one(i,j);
+ double cut_ljsqm = cut_ljsq[i][j];
+ double cut_coulsqm = cut_coulsq;
+
+ k_params.h_view(i,j).lj1 = lj1[i][j];
+ k_params.h_view(i,j).lj2 = lj2[i][j];
+ k_params.h_view(i,j).lj3 = lj3[i][j];
+ k_params.h_view(i,j).lj4 = lj4[i][j];
+ k_params.h_view(i,j).offset = offset[i][j];
+ k_params.h_view(i,j).cut_ljsq = cut_ljsqm;
+ k_params.h_view(i,j).cut_coulsq = cut_coulsqm;
+
+ k_params.h_view(j,i) = k_params.h_view(i,j);
+ if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
+ m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
+ m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
+ m_cut_ljsq[j][i] = m_cut_ljsq[i][j] = cut_ljsqm;
+ m_cut_coulsq[j][i] = m_cut_coulsq[i][j] = cut_coulsqm;
+ }
+
+ k_cutsq.h_view(i,j) = cutone*cutone;
+ k_cutsq.template modify<LMPHostType>();
+ k_cut_ljsq.h_view(i,j) = cut_ljsqm;
+ k_cut_ljsq.template modify<LMPHostType>();
+ k_cut_coulsq.h_view(i,j) = cut_coulsqm;
+ k_cut_coulsq.template modify<LMPHostType>();
+ k_params.template modify<LMPHostType>();
+
+ return cutone;
+}
+
+
+
+template class PairLJCutCoulLongKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class PairLJCutCoulLongKokkos<LMPHostType>;
+#endif
diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h
new file mode 100644
index 0000000000..d6512174f1
--- /dev/null
+++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.h
@@ -0,0 +1,147 @@
+/* ----------------------------------------------------------------------
+ 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 PAIR_CLASS
+
+PairStyle(lj/cut/coul/long/kk,PairLJCutCoulLongKokkos<LMPDeviceType>)
+PairStyle(lj/cut/coul/long/kk/device,PairLJCutCoulLongKokkos<LMPDeviceType>)
+PairStyle(lj/cut/coul/long/kk/host,PairLJCutCoulLongKokkos<LMPHostType>)
+
+#else
+
+#ifndef LMP_PAIR_LJ_CUT_COUL_LONG_KOKKOS_H
+#define LMP_PAIR_LJ_CUT_COUL_LONG_KOKKOS_H
+
+#include "pair_kokkos.h"
+#include "pair_lj_cut_coul_long.h"
+#include "neigh_list_kokkos.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class PairLJCutCoulLongKokkos : public PairLJCutCoulLong {
+ public:
+ enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
+ enum {COUL_FLAG=1};
+ typedef DeviceType device_type;
+ PairLJCutCoulLongKokkos(class LAMMPS *);
+ ~PairLJCutCoulLongKokkos();
+
+ void compute(int, int);
+
+ void settings(int, char **);
+ void init_tables(double cut_coul, double *cut_respa);
+ void init_style();
+ double init_one(int, int);
+
+ struct params_lj_coul{
+ params_lj_coul(){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
+ params_lj_coul(int i){cut_ljsq=0;cut_coulsq=0;lj1=0;lj2=0;lj3=0;lj4=0;offset=0;};
+ F_FLOAT cut_ljsq,cut_coulsq,lj1,lj2,lj3,lj4,offset;
+ };
+
+ protected:
+ void cleanup_copy();
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const;
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_fcoul(const F_FLOAT& rsq, const int& i, const int&j, const int& itype,
+ const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const;
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype) const;
+
+ template<bool STACKPARAMS, class Specialisation>
+ KOKKOS_INLINE_FUNCTION
+ F_FLOAT compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
+ const int& itype, const int& jtype, const F_FLOAT& factor_coul, const F_FLOAT& qtmp) const;
+
+ Kokkos::DualView<params_lj_coul**,Kokkos::LayoutRight,DeviceType> k_params;
+ typename Kokkos::DualView<params_lj_coul**,
+ Kokkos::LayoutRight,DeviceType>::t_dev_const params;
+ // hardwired to space for 15 atom types
+ params_lj_coul m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+
+ F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ F_FLOAT m_cut_ljsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ F_FLOAT m_cut_coulsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+ typename ArrayTypes<DeviceType>::t_x_array_randomread x;
+ typename ArrayTypes<DeviceType>::t_x_array c_x;
+ typename ArrayTypes<DeviceType>::t_f_array f;
+ typename ArrayTypes<DeviceType>::t_int_1d_randomread type;
+ typename ArrayTypes<DeviceType>::t_float_1d_randomread q;
+ typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
+ typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+
+ int newton_pair;
+
+ typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
+ typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
+ typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_ljsq;
+ typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_ljsq;
+ typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cut_coulsq;
+ typename ArrayTypes<DeviceType>::t_ffloat_2d d_cut_coulsq;
+
+ typename ArrayTypes<DeviceType>::t_ffloat_1d_randomread
+ d_rtable, d_drtable, d_ftable, d_dftable,
+ d_ctable, d_dctable, d_etable, d_detable;
+ class AtomKokkos *atomKK;
+ int neighflag;
+ int nlocal,nall,eflag,vflag;
+
+ double special_coul[4];
+ double special_lj[4];
+ double qqrd2e;
+
+ void allocate();
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,FULL,true,CoulLongTable<1> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,HALF,true,CoulLongTable<1> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,HALFTHREAD,true,CoulLongTable<1> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,FULL,false,CoulLongTable<1> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,HALF,false,CoulLongTable<1> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,HALFTHREAD,false,CoulLongTable<1> >;
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutCoulLongKokkos,FULL,CoulLongTable<1> >(PairLJCutCoulLongKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutCoulLongKokkos,HALF,CoulLongTable<1> >(PairLJCutCoulLongKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutCoulLongKokkos,HALFTHREAD,CoulLongTable<1> >(PairLJCutCoulLongKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute<PairLJCutCoulLongKokkos,CoulLongTable<1> >(PairLJCutCoulLongKokkos*,
+ NeighListKokkos<DeviceType>*);
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,FULL,true,CoulLongTable<0> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,HALF,true,CoulLongTable<0> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,HALFTHREAD,true,CoulLongTable<0> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,FULL,false,CoulLongTable<0> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,HALF,false,CoulLongTable<0> >;
+ friend class PairComputeFunctor<PairLJCutCoulLongKokkos,HALFTHREAD,false,CoulLongTable<0> >;
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutCoulLongKokkos,FULL,CoulLongTable<0> >(PairLJCutCoulLongKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutCoulLongKokkos,HALF,CoulLongTable<0> >(PairLJCutCoulLongKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutCoulLongKokkos,HALFTHREAD,CoulLongTable<0> >(PairLJCutCoulLongKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute<PairLJCutCoulLongKokkos,CoulLongTable<0> >(PairLJCutCoulLongKokkos*,
+ NeighListKokkos<DeviceType>*);
+ friend void pair_virial_fdotr_compute<PairLJCutCoulLongKokkos>(PairLJCutCoulLongKokkos*);
+
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+*/
diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp
index 94576a36c7..c69fbe89f5 100644
--- a/src/KOKKOS/pair_lj_cut_kokkos.cpp
+++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp
@@ -99,18 +99,18 @@ void PairLJCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
c_x = atomKK->k_x.view<DeviceType>();
f = atomKK->k_f.view<DeviceType>();
type = atomKK->k_type.view<DeviceType>();
+ tag = atomKK->k_tag.view<DeviceType>();
nlocal = atom->nlocal;
nall = atom->nlocal + atom->nghost;
+ newton_pair = force->newton_pair;
special_lj[0] = force->special_lj[0];
special_lj[1] = force->special_lj[1];
special_lj[2] = force->special_lj[2];
special_lj[3] = force->special_lj[3];
- newton_pair = force->newton_pair;
// loop over neighbors of my atoms
EV_FLOAT ev = pair_compute<PairLJCutKokkos<DeviceType>,void >(this,(NeighListKokkos<DeviceType>*)list);
-
DeviceType::fence();
if (eflag) eng_vdwl += ev.evdwl;
@@ -123,7 +123,7 @@ void PairLJCutKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
virial[5] += ev.v[5];
}
- if (vflag_fdotr) virial_fdotr_compute();
+ if (vflag_fdotr) pair_virial_fdotr_compute(this);
}
template<class DeviceType>
@@ -131,12 +131,15 @@ template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairLJCutKokkos<DeviceType>::
compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
+ (void) i;
+ (void) j;
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT r6inv = r2inv*r2inv*r2inv;
const F_FLOAT forcelj = r6inv *
((STACKPARAMS?m_params[itype][jtype].lj1:params(itype,jtype).lj1)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj2:params(itype,jtype).lj2));
+
return forcelj*r2inv;
}
@@ -145,8 +148,11 @@ template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairLJCutKokkos<DeviceType>::
compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
+ (void) i;
+ (void) j;
const F_FLOAT r2inv = 1.0/rsq;
const F_FLOAT r6inv = r2inv*r2inv*r2inv;
+
return r6inv*((STACKPARAMS?m_params[itype][jtype].lj3:params(itype,jtype).lj3)*r6inv -
(STACKPARAMS?m_params[itype][jtype].lj4:params(itype,jtype).lj4)) -
(STACKPARAMS?m_params[itype][jtype].offset:params(itype,jtype).offset);
@@ -262,6 +268,6 @@ double PairLJCutKokkos<DeviceType>::init_one(int i, int j)
template class PairLJCutKokkos<LMPDeviceType>;
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
template class PairLJCutKokkos<LMPHostType>;
#endif
diff --git a/src/KOKKOS/pair_lj_cut_kokkos.h b/src/KOKKOS/pair_lj_cut_kokkos.h
index 5c3c002af5..0ba40b4d54 100644
--- a/src/KOKKOS/pair_lj_cut_kokkos.h
+++ b/src/KOKKOS/pair_lj_cut_kokkos.h
@@ -31,6 +31,7 @@ namespace LAMMPS_NS {
template<class DeviceType>
class PairLJCutKokkos : public PairLJCut {
public:
+ enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2|FULLCLUSTER};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
PairLJCutKokkos(class LAMMPS *);
@@ -76,9 +77,10 @@ class PairLJCutKokkos : public PairLJCut {
typename ArrayTypes<DeviceType>::t_int_1d_randomread type;
typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
- //typename ArrayTypes<DeviceType>::t_ffloat_1d special_lj;
+ typename ArrayTypes<DeviceType>::t_tagint_1d tag;
int newton_pair;
+ double special_lj[4];
typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
@@ -98,8 +100,13 @@ class PairLJCutKokkos : public PairLJCut {
friend class PairComputeFunctor<PairLJCutKokkos,HALFTHREAD,false>;
friend class PairComputeFunctor<PairLJCutKokkos,N2,false>;
friend class PairComputeFunctor<PairLJCutKokkos,FULLCLUSTER,false >;
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutKokkos,FULL,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutKokkos,HALF,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutKokkos,HALFTHREAD,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_neighlist<PairLJCutKokkos,N2,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
+ friend EV_FLOAT pair_compute_fullcluster<PairLJCutKokkos,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
friend EV_FLOAT pair_compute<PairLJCutKokkos,void>(PairLJCutKokkos*,NeighListKokkos<DeviceType>*);
-
+ friend void pair_virial_fdotr_compute<PairLJCutKokkos>(PairLJCutKokkos*);
};
}
diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp
index cc8072991a..b4cc32adf5 100644
--- a/src/KOKKOS/pair_table_kokkos.cpp
+++ b/src/KOKKOS/pair_table_kokkos.cpp
@@ -153,8 +153,9 @@ void PairTableKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
const int teamsize = 1;
#endif
const int nteams = (list->inum*f_type::vectorization::increment+teamsize-1)/teamsize;
- if (eflag || vflag) Kokkos::parallel_reduce(Kokkos::ParallelWorkRequest(nteams,teamsize),f,ev);
- else Kokkos::parallel_for(Kokkos::ParallelWorkRequest(nteams,teamsize),f);
+ Kokkos::TeamPolicy<DeviceType> config(nteams,teamsize);
+ if (eflag || vflag) Kokkos::parallel_reduce(config,f,ev);
+ else Kokkos::parallel_for(config,f);
}
} else {
if (neighflag == FULL) {
@@ -187,8 +188,9 @@ void PairTableKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
const int teamsize = 1;
#endif
const int nteams = (list->inum*f_type::vectorization::increment+teamsize-1)/teamsize;
- if (eflag || vflag) Kokkos::parallel_reduce(Kokkos::ParallelWorkRequest(nteams,teamsize),f,ev);
- else Kokkos::parallel_for(Kokkos::ParallelWorkRequest(nteams,teamsize),f);
+ Kokkos::TeamPolicy<DeviceType> config(nteams,teamsize);
+ if (eflag || vflag) Kokkos::parallel_reduce(config,f,ev);
+ else Kokkos::parallel_for(config,f);
}
}
DeviceType::fence();
@@ -203,7 +205,7 @@ void PairTableKokkos<DeviceType>::compute_style(int eflag_in, int vflag_in)
virial[5] += ev.v[5];
}
- if (vflag_fdotr) virial_fdotr_compute();
+ if (vflag_fdotr) pair_virial_fdotr_compute(this);
}
template<class DeviceType>
@@ -211,6 +213,8 @@ template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairTableKokkos<DeviceType>::
compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
+ (void) i;
+ (void) j;
union_int_float_t rsq_lookup;
double fpair;
const int tidx = d_table_const.tabindex(itype,jtype);
@@ -254,6 +258,8 @@ template<bool STACKPARAMS, class Specialisation>
KOKKOS_INLINE_FUNCTION
F_FLOAT PairTableKokkos<DeviceType>::
compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
+ (void) i;
+ (void) j;
double evdwl;
union_int_float_t rsq_lookup;
const int tidx = d_table_const.tabindex(itype,jtype);
@@ -292,128 +298,6 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, c
return evdwl;
}
-/*
-template<class DeviceType>
-template<int EVFLAG, int NEIGHFLAG, int NEWTON_PAIR,int TABSTYLE>
-KOKKOS_FUNCTION
-EV_FLOAT PairTableKokkos<DeviceType>::
-compute_item(const int &ii, const NeighListKokkos<DeviceType> &list) const
-{
- EV_FLOAT ev;
- const int tlm1 = tablength - 1;
- union_int_float_t rsq_lookup;
- const int i = list.d_ilist[ii];
- const X_FLOAT xtmp = x(i,0);
- const X_FLOAT ytmp = x(i,1);
- const X_FLOAT ztmp = x(i,2);
- const int itype = type(i);
-
- const AtomNeighborsConst neighbors_i = list.get_neighbors_const(i);
- const int jnum = list.d_numneigh[i];
-
- F_FLOAT fxtmp = 0.0;
- F_FLOAT fytmp = 0.0;
- F_FLOAT fztmp = 0.0;
-
- for (int jj = 0; jj < jnum; jj++) {
- int j = neighbors_i(jj);
- const F_FLOAT factor_lj = 1.0; //special_lj[sbmask(j)];
- j &= NEIGHMASK;
- const X_FLOAT delx = xtmp - x(j,0);
- const X_FLOAT dely = ytmp - x(j,1);
- const X_FLOAT delz = ztmp - x(j,2);
- const int jtype = type(j);
- const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq < d_table_const.cutsq(itype,jtype)) {
- double fpair;
- const int tidx = d_table_const.tabindex(itype,jtype);
- //const Table* const tb = &tables[tabindex[itype][jtype]];
-
- //if (rsq < d_table_const.innersq(tidx))
- // error->one(FLERR,"Pair distance < table inner cutoff");
-
- if (TABSTYLE == LOOKUP) {
- const int itable = static_cast<int> ((rsq - d_table_const.innersq(tidx)) * d_table_const.invdelta(tidx));
- //if (itable >= tlm1)
- // error->one(FLERR,"Pair distance > table outer cutoff");
- fpair = factor_lj * d_table_const.f(tidx,itable);
- if (EVFLAG)
- ev.evdwl = d_table_const.e(tidx,itable);
- } else if (TABSTYLE == LINEAR) {
- const int itable = static_cast<int> ((rsq - d_table_const.innersq(tidx)) * d_table_const.invdelta(tidx));
- //if (itable >= tlm1)
- // error->one(FLERR,"Pair distance > table outer cutoff");
- const double fraction = (rsq - d_table_const.rsq(tidx,itable)) * d_table_const.invdelta(tidx);
- const double value = d_table_const.f(tidx,itable) + fraction*d_table_const.df(tidx,itable);
- fpair = factor_lj * value;
- if (EVFLAG)
- ev.evdwl = d_table_const.e(tidx,itable) + fraction*d_table_const.de(tidx,itable);
- } else if (TABSTYLE == SPLINE) {
- const int itable = static_cast<int> ((rsq - d_table_const.innersq(tidx)) * d_table_const.invdelta(tidx));
- //if (itable >= tlm1)
- // error->one(FLERR,"Pair distance > table outer cutoff");
- const double b = (rsq - d_table_const.rsq(tidx,itable)) * d_table_const.invdelta(tidx);
- const double a = 1.0 - b;
- const double value = a * d_table_const.f(tidx,itable) + b * d_table_const.f(tidx,itable+1) +
- ((a*a*a-a)*d_table_const.f2(tidx,itable) + (b*b*b-b)*d_table_const.f2(tidx,itable+1)) *
- d_table_const.deltasq6(tidx);
- fpair = factor_lj * value;
- if (EVFLAG)
- ev.evdwl = a * d_table_const.e(tidx,itable) + b * d_table_const.e(tidx,itable+1) +
- ((a*a*a-a)*d_table_const.e2(tidx,itable) + (b*b*b-b)*d_table_const.e2(tidx,itable+1)) *
- d_table_const.deltasq6(tidx);
- } else {
- rsq_lookup.f = rsq;
- int itable = rsq_lookup.i & d_table_const.nmask(tidx);
- itable >>= d_table_const.nshiftbits(tidx);
- const double fraction = (rsq_lookup.f - d_table_const.rsq(tidx,itable)) * d_table_const.drsq(tidx,itable);
- const double value = d_table_const.f(tidx,itable) + fraction*d_table_const.df(tidx,itable);
- fpair = factor_lj * value;
- if (EVFLAG)
- ev.evdwl = d_table_const.e(tidx,itable) + fraction*d_table_const.de(tidx,itable);
- }
-
- fxtmp += delx*fpair;
- fytmp += dely*fpair;
- fztmp += delz*fpair;
- if ((NEIGHFLAG==HALFTHREAD) && (NEWTON_PAIR || j < nlocal)) {
- Kokkos::atomic_fetch_add(&f(j,0),-delx*fpair);
- Kokkos::atomic_fetch_add(&f(j,1),-dely*fpair);
- Kokkos::atomic_fetch_add(&f(j,2),-delz*fpair);
- }
-
- if ((NEIGHFLAG==HALF) && (NEWTON_PAIR || j < nlocal)) {
- f(j,0) -= delx*fpair;
- f(j,1) -= dely*fpair;
- f(j,2) -= delz*fpair;
- }
-
- if(EVFLAG) {
- if (eflag) {
- ev.evdwl *= factor_lj;
- }
-
- if (evflag) ev_tally<NEIGHFLAG>(ev,i,j
-,fpair,delx,dely,delz);
- }
- }
- }
-
- if (NEIGHFLAG == HALFTHREAD) {
- Kokkos::atomic_fetch_add(&f(i,0),fxtmp);
- Kokkos::atomic_fetch_add(&f(i,1),fytmp);
- Kokkos::atomic_fetch_add(&f(i,2),fztmp);
- } else {
- f(i,0) += fxtmp;
- f(i,1) += fytmp;
- f(i,2) += fztmp;
- }
-
- return ev;
-}
-*/
-
template<class DeviceType>
void PairTableKokkos<DeviceType>::create_kokkos_tables()
{
@@ -880,7 +764,6 @@ void PairTableKokkos<DeviceType>::param_extract(Table *tb, char *line)
word = strtok(NULL," \t\n\r\f");
tb->fphi = atof(word);
} else {
- printf("WORD: %s\n",word);
error->one(FLERR,"Invalid keyword in pair table parameters");
}
word = strtok(NULL," \t\n\r\f");
@@ -1494,7 +1377,7 @@ void PairTableKokkos<DeviceType>::cleanup_copy() {
}
template class PairTableKokkos<LMPDeviceType>;
-#if DEVICE==2
+#ifdef KOKKOS_HAVE_CUDA
template class PairTableKokkos<LMPHostType>;
#endif
diff --git a/src/KOKKOS/pair_table_kokkos.h b/src/KOKKOS/pair_table_kokkos.h
index 317703c895..10c7c6db7b 100644
--- a/src/KOKKOS/pair_table_kokkos.h
+++ b/src/KOKKOS/pair_table_kokkos.h
@@ -41,6 +41,7 @@ template<class DeviceType>
class PairTableKokkos : public Pair {
public:
+ enum {EnabledNeighFlags=FULL&HALFTHREAD&HALF&N2&FULLCLUSTER};
enum {COUL_FLAG=0};
typedef DeviceType device_type;
@@ -208,67 +209,10 @@ class PairTableKokkos : public Pair {
friend class PairComputeFunctor<PairTableKokkos,HALFTHREAD,false,S_TableCompute<DeviceType,BITMAP> >;
friend class PairComputeFunctor<PairTableKokkos,N2,false,S_TableCompute<DeviceType,BITMAP> >;
friend class PairComputeFunctor<PairTableKokkos,FULLCLUSTER,false,S_TableCompute<DeviceType,BITMAP> >;
-/*template<int FULL_NEIGH>
- KOKKOS_INLINE_FUNCTION
- void ev_tally(EV_FLOAT &ev, const int &i, const int &j,
- const F_FLOAT &fpair, const F_FLOAT &delx,
- const F_FLOAT &dely, const F_FLOAT &delz) const;
-*/
-};
-/*
-template <class DeviceType, int NEIGHFLAG, int TABSTYLE>
-struct PairTableComputeFunctor {
- typedef DeviceType device_type ;
- typedef EV_FLOAT value_type;
-
- PairTableKokkos<DeviceType> c;
- NeighListKokkos<DeviceType> list;
-
- PairTableComputeFunctor(PairTableKokkos<DeviceType>* c_ptr,
- NeighListKokkos<DeviceType>* list_ptr):
- c(*c_ptr),list(*list_ptr) {};
- ~PairTableComputeFunctor() {c.cleanup_copy();list.clean_copy();};
-
- KOKKOS_INLINE_FUNCTION
- void operator()(const int i) const {
- if (c.newton_pair) c.template compute_item<0,NEIGHFLAG,1,TABSTYLE>(i,list);
- else c.template compute_item<0,NEIGHFLAG,0,TABSTYLE>(i,list);
- }
- KOKKOS_INLINE_FUNCTION
- void operator()(const int i, value_type &energy_virial) const {
- if (c.newton_pair)
- energy_virial += c.template compute_item<1,NEIGHFLAG,1,TABSTYLE>(i,list);
- else
- energy_virial += c.template compute_item<1,NEIGHFLAG,0,TABSTYLE>(i,list);
- }
-
- KOKKOS_INLINE_FUNCTION
- static void init(volatile value_type &update) {
- update.evdwl = 0;
- update.ecoul = 0;
- update.v[0] = 0;
- update.v[1] = 0;
- update.v[2] = 0;
- update.v[3] = 0;
- update.v[4] = 0;
- update.v[5] = 0;
- }
- KOKKOS_INLINE_FUNCTION
- static void join(volatile value_type &update,
- const volatile value_type &source) {
- update.evdwl += source.evdwl;
- update.ecoul += source.ecoul;
- update.v[0] += source.v[0];
- update.v[1] += source.v[1];
- update.v[2] += source.v[2];
- update.v[3] += source.v[3];
- update.v[4] += source.v[4];
- update.v[5] += source.v[5];
- }
+ friend void pair_virial_fdotr_compute<PairTableKokkos>(PairTableKokkos*);
};
-*/
diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp
index 5f5d1542bd..1e7475dc49 100644
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@@ -53,6 +53,7 @@ VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) :
void VerletKokkos::setup()
{
+
if (comm->me == 0 && screen) fprintf(screen,"Setting up run ...\n");
update->setupflag = 1;
@@ -65,19 +66,24 @@ void VerletKokkos::setup()
atomKK->setup();
modify->setup_pre_exchange();
// debug
- atomKK->sync(Host,ALL_MASK);
- atomKK->modified(Host,ALL_MASK);
+ atomKK->sync(Host,ALL_MASK);
+ atomKK->modified(Host,ALL_MASK);
if (triclinic) domain->x2lamda(atomKK->nlocal);
domain->pbc();
atomKK->sync(Host,ALL_MASK);
+
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
+
comm->exchange();
+
if (atomKK->sortfreq > 0) atomKK->sort();
+
comm->borders();
+
if (triclinic) domain->lamda2x(atomKK->nlocal+atomKK->nghost);
atomKK->sync(Host,ALL_MASK);
@@ -97,20 +103,47 @@ void VerletKokkos::setup()
force_clear();
modify->setup_pre_force(vflag);
- if (pair_compute_flag) force->pair->compute(eflag,vflag);
+ if (pair_compute_flag) {
+ atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
+ atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
+ force->pair->compute(eflag,vflag);
+ timer->stamp(TIME_PAIR);
+ }
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
+
if (atomKK->molecular) {
- if (force->bond) force->bond->compute(eflag,vflag);
- if (force->angle) force->angle->compute(eflag,vflag);
- if (force->dihedral) force->dihedral->compute(eflag,vflag);
- if (force->improper) force->improper->compute(eflag,vflag);
+ if (force->bond) {
+ atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
+ atomKK->modified(force->bond->execution_space,force->bond->datamask_modify);
+ force->bond->compute(eflag,vflag);
+ }
+ if (force->angle) {
+ atomKK->sync(force->angle->execution_space,force->angle->datamask_read);
+ atomKK->modified(force->angle->execution_space,force->angle->datamask_modify);
+ force->angle->compute(eflag,vflag);
+ }
+ if (force->dihedral) {
+ atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read);
+ atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify);
+ force->dihedral->compute(eflag,vflag);
+ }
+ if (force->improper) {
+ atomKK->sync(force->improper->execution_space,force->improper->datamask_read);
+ atomKK->modified(force->improper->execution_space,force->improper->datamask_modify);
+ force->improper->compute(eflag,vflag);
+ }
+ timer->stamp(TIME_BOND);
}
- if (force->kspace) {
+ if(force->kspace) {
force->kspace->setup();
- if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
- else force->kspace->compute_dummy(eflag,vflag);
+ if (kspace_compute_flag) {
+ atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read);
+ atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify);
+ force->kspace->compute(eflag,vflag);
+ timer->stamp(TIME_KSPACE);
+ } else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
@@ -172,20 +205,47 @@ void VerletKokkos::setup_minimal(int flag)
force_clear();
modify->setup_pre_force(vflag);
- if (pair_compute_flag) force->pair->compute(eflag,vflag);
+ if (pair_compute_flag) {
+ atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
+ atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
+ force->pair->compute(eflag,vflag);
+ timer->stamp(TIME_PAIR);
+ }
else if (force->pair) force->pair->compute_dummy(eflag,vflag);
+
if (atomKK->molecular) {
- if (force->bond) force->bond->compute(eflag,vflag);
- if (force->angle) force->angle->compute(eflag,vflag);
- if (force->dihedral) force->dihedral->compute(eflag,vflag);
- if (force->improper) force->improper->compute(eflag,vflag);
+ if (force->bond) {
+ atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
+ atomKK->modified(force->bond->execution_space,force->bond->datamask_modify);
+ force->bond->compute(eflag,vflag);
+ }
+ if (force->angle) {
+ atomKK->sync(force->angle->execution_space,force->angle->datamask_read);
+ atomKK->modified(force->angle->execution_space,force->angle->datamask_modify);
+ force->angle->compute(eflag,vflag);
+ }
+ if (force->dihedral) {
+ atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read);
+ atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify);
+ force->dihedral->compute(eflag,vflag);
+ }
+ if (force->improper) {
+ atomKK->sync(force->improper->execution_space,force->improper->datamask_read);
+ atomKK->modified(force->improper->execution_space,force->improper->datamask_modify);
+ force->improper->compute(eflag,vflag);
+ }
+ timer->stamp(TIME_BOND);
}
- if (force->kspace) {
+ if(force->kspace) {
force->kspace->setup();
- if (kspace_compute_flag) force->kspace->compute(eflag,vflag);
- else force->kspace->compute_dummy(eflag,vflag);
+ if (kspace_compute_flag) {
+ atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read);
+ atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify);
+ force->kspace->compute(eflag,vflag);
+ timer->stamp(TIME_KSPACE);
+ } else force->kspace->compute_dummy(eflag,vflag);
}
if (force->newton) comm->reverse_comm();
@@ -291,31 +351,47 @@ void VerletKokkos::run(int n)
timer->stamp();
if (pair_compute_flag) {
+ atomKK->sync(force->pair->execution_space,force->pair->datamask_read);
+ atomKK->modified(force->pair->execution_space,force->pair->datamask_modify);
force->pair->compute(eflag,vflag);
timer->stamp(TIME_PAIR);
}
if (atomKK->molecular) {
- if (force->bond) force->bond->compute(eflag,vflag);
- if (force->angle) force->angle->compute(eflag,vflag);
- if (force->dihedral) force->dihedral->compute(eflag,vflag);
- if (force->improper) force->improper->compute(eflag,vflag);
+ if (force->bond) {
+ atomKK->sync(force->bond->execution_space,force->bond->datamask_read);
+ atomKK->modified(force->bond->execution_space,force->bond->datamask_modify);
+ force->bond->compute(eflag,vflag);
+ }
+ if (force->angle) {
+ atomKK->sync(force->angle->execution_space,force->angle->datamask_read);
+ atomKK->modified(force->angle->execution_space,force->angle->datamask_modify);
+ force->angle->compute(eflag,vflag);
+ }
+ if (force->dihedral) {
+ atomKK->sync(force->dihedral->execution_space,force->dihedral->datamask_read);
+ atomKK->modified(force->dihedral->execution_space,force->dihedral->datamask_modify);
+ force->dihedral->compute(eflag,vflag);
+ }
+ if (force->improper) {
+ atomKK->sync(force->improper->execution_space,force->improper->datamask_read);
+ atomKK->modified(force->improper->execution_space,force->improper->datamask_modify);
+ force->improper->compute(eflag,vflag);
+ }
timer->stamp(TIME_BOND);
}
if (kspace_compute_flag) {
+ atomKK->sync(force->kspace->execution_space,force->kspace->datamask_read);
+ atomKK->modified(force->kspace->execution_space,force->kspace->datamask_modify);
force->kspace->compute(eflag,vflag);
timer->stamp(TIME_KSPACE);
}
// reverse communication of forces
- if (force->newton) {
- atomKK->sync(Host,F_MASK);
- comm->reverse_comm();
- atomKK->modified(Host,F_MASK);
- timer->stamp(TIME_COMM);
- }
+ if (force->newton) comm->reverse_comm();
+ timer->stamp(TIME_COMM);
// force modifications, final time integration, diagnostics
--
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