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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7573 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-01-25 15:30:11 +00:00
parent 53f0f2130c
commit 6e48e4e6db
18 changed files with 2743 additions and 0 deletions
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36
src/GPU/Install.sh
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@ -17,6 +17,40 @@ if (test $1 = 1) then
sed -i -e '/^include.*gpu.*$/d' ../Makefile.package.settings
sed -i '4 i include ..\/..\/lib\/gpu\/Makefile.lammps' ../Makefile.package.settings
fi
if (test -e ../pair_yukawa.cpp) then
cp pair_yukawa_gpu.cpp ..
cp pair_yukawa_gpu.h ..
fi
if (test -e ../pair_table.cpp) then
cp pair_table_gpu.cpp ..
cp pair_table_gpu.h ..
fi
if (test -e ../pair_buck.cpp) then
cp pair_buck_gpu.cpp ..
cp pair_buck_gpu.h ..
fi
if (test -e ../pair_buck_coul_cut.cpp) then
cp pair_buck_coul_cut_gpu.cpp ..
cp pair_buck_coul_cut_gpu.h ..
fi
if (test -e ../pair_buck_coul_long.cpp) then
cp pair_buck_coul_long_gpu.cpp ..
cp pair_buck_coul_long_gpu.h ..
fi
if (test -e ../pair_eam.cpp) then
cp pair_eam_gpu.cpp ..
cp pair_eam_gpu.h ..
cp pair_eam_alloy_gpu.cpp ..
cp pair_eam_alloy_gpu.h ..
cp pair_eam_fs_gpu.cpp ..
cp pair_eam_fs_gpu.h ..
fi
if (test -e ../pair_gayberne.cpp) then
cp pair_gayberne_gpu.cpp ..
@ -93,6 +127,7 @@ elif (test $1 = 0) then
fi
rm -f ../pppm_gpu.cpp
rm -f ../pair_eam_gpu.cpp
rm -f ../pair_gayberne_gpu.cpp
rm -f ../pair_resquared_gpu.cpp
rm -f ../pair_lj_cut_gpu.cpp
@ -111,6 +146,7 @@ elif (test $1 = 0) then
rm -f ../fix_gpu.cpp
rm -f ../pppm_gpu.h
rm -f ../pair_eam_gpu.h
rm -f ../pair_gayberne_gpu.h
rm -f ../pair_resquared_gpu.h
rm -f ../pair_lj_cut_gpu.h

3
src/GPU/gpu_extra.h
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@ -45,6 +45,9 @@ namespace GPU_EXTRA {
else if (all_success == -7)
error->all(FLERR,
"Accelerator sharing is not currently supported on system");
else if (all_success == -8)
error->all(FLERR,
"GPU particle split must be set to 1 for this pair style.");
else
error->all(FLERR,"Unknown error in GPU library");
}

260
src/GPU/pair_buck_coul_cut_gpu.cpp Normal file
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@ -0,0 +1,260 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_buck_coul_cut_gpu.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "gpu_extra.h"
// External functions from cuda library for atom decomposition
int buckc_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
double **host_buck1, double **host_buck2, double **host_a,
double **host_c, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
int &gpu_mode, FILE *screen, double **host_cut_ljsq,
double **host_cut_coulsq, double *host_special_coul,
const double qqrd2e);
void buckc_gpu_clear();
int ** buckc_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
void buckc_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double buckc_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairBuckCoulCutGPU::PairBuckCoulCutGPU(LAMMPS *lmp) : PairBuckCoulCut(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairBuckCoulCutGPU::~PairBuckCoulCutGPU()
{
buckc_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulCutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = buckc_gpu_compute_n(neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success,
atom->q, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
buckc_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairBuckCoulCutGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,
"Cannot use newton pair with buck/coul/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = buckc_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul, force->qqrd2e);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairBuckCoulCutGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + buckc_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh,
int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,r2inv,r6inv,forcecoul,forcebuck,factor_coul,factor_lj;
double r,rexp;
int *jlist;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]/r;
else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
fpair = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * qtmp*q[j]/r;
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}

62
src/GPU/pair_buck_coul_cut_gpu.h Normal file
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@ -0,0 +1,62 @@
/* ----------------------------------------------------------------------
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(buck/coul/cut/gpu,PairBuckCoulCutGPU)
#else
#ifndef LMP_PAIR_BUCK_COUL_CUT_GPU_H
#define LMP_PAIR_BUCK_COUL_CUT_GPU_H
#include "pair_buck_coul_cut.h"
namespace LAMMPS_NS {
class PairBuckCoulCutGPU : public PairBuckCoulCut {
public:
PairBuckCoulCutGPU(LAMMPS *lmp);
~PairBuckCoulCutGPU();
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int);
void init_style();
double memory_usage();
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
int *gpulist;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Out of memory on GPGPU
UNDOCUMENTED
E: Cannot use newton pair with buck/coul/cut/gpu pair style
UNDOCUMENTED
E: Pair style buck/coul/cut/gpu requires atom attribute q
The atom style defined does not have this attribute.
*/

291
src/GPU/pair_buck_coul_long_gpu.cpp Normal file
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@ -0,0 +1,291 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_buck_coul_long_gpu.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "kspace.h"
#include "gpu_extra.h"
#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
// External functions from cuda library for atom decomposition
int buckcl_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
double **host_buck1, double **host_buck2, double **host_a,
double **host_c, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
int &gpu_mode, FILE *screen, double **host_cut_ljsq,
double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald);
void buckcl_gpu_clear();
int** buckcl_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
void buckcl_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double buckcl_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairBuckCoulLongGPU::PairBuckCoulLongGPU(LAMMPS *lmp) :
PairBuckCoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairBuckCoulLongGPU::~PairBuckCoulLongGPU()
{
buckcl_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = buckcl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
buckcl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairBuckCoulLongGPU::init_style()
{
if (!atom->q_flag)
error->all(FLERR,
"Pair style buck/coul/long/gpu requires atom attribute q");
if (force->newton_pair)
error->all(FLERR,
"Cannot use newton pair with buck/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
cut_coulsq = cut_coul * cut_coul;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = buckcl_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul, force->qqrd2e,
g_ewald);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairBuckCoulLongGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + buckcl_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulLongGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double r,rexp,r2inv,r6inv,forcecoul,forcebuck,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
int *jlist;
double rsq;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
fpair = (forcecoul + factor_lj*forcebuck) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}

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src/GPU/pair_buck_coul_long_gpu.h Normal file
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/* ----------------------------------------------------------------------
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(buck/coul/long/gpu,PairBuckCoulLongGPU)
#else
#ifndef LMP_PAIR_BUCK_COUL_LONG_GPU_H
#define LMP_PAIR_BUCK_COUL_LONG_GPU_H
#include "pair_buck_coul_long.h"
namespace LAMMPS_NS {
class PairBuckCoulLongGPU : public PairBuckCoulLong {
public:
PairBuckCoulLongGPU(LAMMPS *lmp);
~PairBuckCoulLongGPU();
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int);
void init_style();
double memory_usage();
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
int *gpulist;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Out of memory on GPGPU
UNDOCUMENTED
E: Cannot use newton pair with buck/coul/long/gpu pair style
UNDOCUMENTED
E: Pair style buck/coul/long/gpu requires atom attribute q
The atom style defined does not have this attribute.
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_buck_gpu.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "gpu_extra.h"
// External functions from cuda library for atom decomposition
int buck_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
double **host_buck1, double **host_buck2,
double **host_a, double **host_c,
double **offset, double *special_lj, const int inum,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void buck_gpu_clear();
int ** buck_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success);
void buck_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double buck_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairBuckGPU::PairBuckGPU(LAMMPS *lmp) : PairBuck(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairBuckGPU::~PairBuckGPU()
{
buck_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairBuckGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = buck_gpu_compute_n(neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
buck_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairBuckGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with buck/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = buck_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairBuckGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + buck_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcebuck,factor_lj;
double r,rexp;
int *jlist;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
double *special_lj = force->special_lj;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
fpair = factor_lj*forcebuck*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}

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/* ----------------------------------------------------------------------
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(buck/gpu,PairBuckGPU)
#else
#ifndef LMP_PAIR_BUCK_GPU_H
#define LMP_PAIR_BUCK_GPU_H
#include "pair_buck.h"
namespace LAMMPS_NS {
class PairBuckGPU : public PairBuck {
public:
PairBuckGPU(LAMMPS *lmp);
~PairBuckGPU();
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int);
void init_style();
double memory_usage();
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
int *gpulist;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Out of memory on GPGPU
UNDOCUMENTED
E: Cannot use newton pair with buck/gpu pair style
UNDOCUMENTED
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
------------------------------------------------------------------------- */
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_eam_alloy_gpu.h"
#include "atom.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairEAMAlloyGPU::PairEAMAlloyGPU(LAMMPS *lmp) : PairEAMGPU(lmp)
{
one_coeff = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
read DYNAMO setfl file
------------------------------------------------------------------------- */
void PairEAMAlloyGPU::coeff(int narg, char **arg)
{
int i,j;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read EAM setfl file
if (setfl) {
for (i = 0; i < setfl->nelements; i++) delete [] setfl->elements[i];
delete [] setfl->elements;
delete [] setfl->mass;
memory->destroy(setfl->frho);
memory->destroy(setfl->rhor);
memory->destroy(setfl->z2r);
delete setfl;
}
setfl = new Setfl();
read_file(arg[2]);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < setfl->nelements; j++)
if (strcmp(arg[i],setfl->elements[j]) == 0) break;
if (j < setfl->nelements) map[i-2] = j;
else error->all(FLERR,"No matching element in EAM potential file");
}
// clear setflag since coeff() called once with I,J = * *
int n = atom->ntypes;
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
// set mass of atom type if i = j
int count = 0;
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
count++;
}
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
read a multi-element DYNAMO setfl file
------------------------------------------------------------------------- */
void PairEAMAlloyGPU::read_file(char *filename)
{
Setfl *file = setfl;
// open potential file
int me = comm->me;
FILE *fptr;
char line[MAXLINE];
if (me == 0) {
fptr = fopen(filename,"r");
if (fptr == NULL) {
char str[128];
sprintf(str,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
// read and broadcast header
// extract element names from nelements line
int n;
if (me == 0) {
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
sscanf(line,"%d",&file->nelements);
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
file->elements = new char*[file->nelements];
for (int i = 0; i < file->nelements; i++) {
n = strlen(words[i]) + 1;
file->elements[i] = new char[n];
strcpy(file->elements[i],words[i]);
}
delete [] words;
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->nr,1,MPI_INT,0,world);
MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
file->mass = new double[file->nelements];
memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
"pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg",&tmp,&file->mass[i]);
}
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
if (me == 0) grab(fptr,file->nr,&file->rhor[i][1]);
MPI_Bcast(&file->rhor[i][1],file->nr,MPI_DOUBLE,0,world);
}
for (i = 0; i < file->nelements; i++)
for (j = 0; j <= i; j++) {
if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
// close the potential file
if (me == 0) fclose(fptr);
}
/* ----------------------------------------------------------------------
copy read-in setfl potential to standard array format
------------------------------------------------------------------------- */
void PairEAMAlloyGPU::file2array()
{
int i,j,m,n;
int ntypes = atom->ntypes;
// set function params directly from setfl file
nrho = setfl->nrho;
nr = setfl->nr;
drho = setfl->drho;
dr = setfl->dr;
// ------------------------------------------------------------------
// setup frho arrays
// ------------------------------------------------------------------
// allocate frho arrays
// nfrho = # of setfl elements + 1 for zero array
nfrho = setfl->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
// copy each element's frho to global frho
for (i = 0; i < setfl->nelements; i++)
for (m = 1; m <= nrho; m++) frho[i][m] = setfl->frho[i][m];
// add extra frho of zeroes for non-EAM types to point to (pair hybrid)
// this is necessary b/c fp is still computed for non-EAM atoms
for (m = 1; m <= nrho; m++) frho[nfrho-1][m] = 0.0;
// type2frho[i] = which frho array (0 to nfrho-1) each atom type maps to
// if atom type doesn't point to element (non-EAM atom in pair hybrid)
// then map it to last frho array of zeroes
for (i = 1; i <= ntypes; i++)
if (map[i] >= 0) type2frho[i] = map[i];
else type2frho[i] = nfrho-1;
// ------------------------------------------------------------------
// setup rhor arrays
// ------------------------------------------------------------------
// allocate rhor arrays
// nrhor = # of setfl elements
nrhor = setfl->nelements;
memory->destroy(rhor);
memory->create(rhor,nrhor,nr+1,"pair:rhor");
// copy each element's rhor to global rhor
for (i = 0; i < setfl->nelements; i++)
for (m = 1; m <= nr; m++) rhor[i][m] = setfl->rhor[i][m];
// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
// for setfl files, I,J mapping only depends on I
// OK if map = -1 (non-EAM atom in pair hybrid) b/c type2rhor not used
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
type2rhor[i][j] = map[i];
// ------------------------------------------------------------------
// setup z2r arrays
// ------------------------------------------------------------------
// allocate z2r arrays
// nz2r = N*(N+1)/2 where N = # of setfl elements
nz2r = setfl->nelements * (setfl->nelements+1) / 2;
memory->destroy(z2r);
memory->create(z2r,nz2r,nr+1,"pair:z2r");
// copy each element pair z2r to global z2r, only for I >= J
n = 0;
for (i = 0; i < setfl->nelements; i++)
for (j = 0; j <= i; j++) {
for (m = 1; m <= nr; m++) z2r[n][m] = setfl->z2r[i][j][m];
n++;
}
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
// set of z2r arrays only fill lower triangular Nelement matrix
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
// swap indices when irow < icol to stay lower triangular
// if map = -1 (non-EAM atom in pair hybrid):
// type2z2r is not used by non-opt
// but set type2z2r to 0 since accessed by opt
int irow,icol;
for (i = 1; i <= ntypes; i++) {
for (j = 1; j <= ntypes; j++) {
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
type2z2r[i][j] = 0;
continue;
}
if (irow < icol) {
irow = map[j];
icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
n += icol;
type2z2r[i][j] = n;
}
}
}

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/* ----------------------------------------------------------------------
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(eam/alloy/gpu,PairEAMAlloyGPU)
#else
#ifndef LMP_PAIR_EAM_ALLOY_GPU_H
#define LMP_PAIR_EAM_ALLOY_GPU_H
#include "pair_eam_gpu.h"
namespace LAMMPS_NS {
class PairEAMAlloyGPU : public PairEAMGPU {
public:
PairEAMAlloyGPU(class LAMMPS *);
virtual ~PairEAMAlloyGPU() {}
void coeff(int, char **);
protected:
void read_file(char *);
void file2array();
};
}
#endif
#endif

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
------------------------------------------------------------------------- */
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_eam_fs_gpu.h"
#include "atom.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairEAMFSGPU::PairEAMFSGPU(LAMMPS *lmp) : PairEAMGPU(lmp)
{
one_coeff = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
read EAM Finnis-Sinclair file
------------------------------------------------------------------------- */
void PairEAMFSGPU::coeff(int narg, char **arg)
{
int i,j;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read EAM Finnis-Sinclair file
if (fs) {
for (i = 0; i < fs->nelements; i++) delete [] fs->elements[i];
delete [] fs->elements;
delete [] fs->mass;
memory->destroy(fs->frho);
memory->destroy(fs->rhor);
memory->destroy(fs->z2r);
delete fs;
}
fs = new Fs();
read_file(arg[2]);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < fs->nelements; j++)
if (strcmp(arg[i],fs->elements[j]) == 0) break;
if (j < fs->nelements) map[i-2] = j;
else error->all(FLERR,"No matching element in EAM potential file");
}
// clear setflag since coeff() called once with I,J = * *
int n = atom->ntypes;
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
// set mass of atom type if i = j
int count = 0;
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,fs->mass[map[i]]);
count++;
}
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
read a multi-element DYNAMO setfl file
------------------------------------------------------------------------- */
void PairEAMFSGPU::read_file(char *filename)
{
Fs *file = fs;
// open potential file
int me = comm->me;
FILE *fptr;
char line[MAXLINE];
if (me == 0) {
fptr = fopen(filename,"r");
if (fptr == NULL) {
char str[128];
sprintf(str,"Cannot open EAM potential file %s",filename);
error->one(FLERR,str);
}
}
// read and broadcast header
// extract element names from nelements line
int n;
if (me == 0) {
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
fgets(line,MAXLINE,fptr);
n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
sscanf(line,"%d",&file->nelements);
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
file->elements = new char*[file->nelements];
for (int i = 0; i < file->nelements; i++) {
n = strlen(words[i]) + 1;
file->elements[i] = new char[n];
strcpy(file->elements[i],words[i]);
}
delete [] words;
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->nr,1,MPI_INT,0,world);
MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
file->mass = new double[file->nelements];
memory->create(file->frho,file->nelements,file->nrho+1,
"pair:frho");
memory->create(file->rhor,file->nelements,file->nelements,
file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,
file->nr+1,"pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg",&tmp,&file->mass[i]);
}
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
if (me == 0) grab(fptr,file->nrho,&file->frho[i][1]);
MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
for (j = 0; j < file->nelements; j++) {
if (me == 0) grab(fptr,file->nr,&file->rhor[i][j][1]);
MPI_Bcast(&file->rhor[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
}
for (i = 0; i < file->nelements; i++)
for (j = 0; j <= i; j++) {
if (me == 0) grab(fptr,file->nr,&file->z2r[i][j][1]);
MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
// close the potential file
if (me == 0) fclose(fptr);
}
/* ----------------------------------------------------------------------
copy read-in setfl potential to standard array format
------------------------------------------------------------------------- */
void PairEAMFSGPU::file2array()
{
int i,j,m,n;
int ntypes = atom->ntypes;
// set function params directly from fs file
nrho = fs->nrho;
nr = fs->nr;
drho = fs->drho;
dr = fs->dr;
// ------------------------------------------------------------------
// setup frho arrays
// ------------------------------------------------------------------
// allocate frho arrays
// nfrho = # of fs elements + 1 for zero array
nfrho = fs->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
// copy each element's frho to global frho
for (i = 0; i < fs->nelements; i++)
for (m = 1; m <= nrho; m++) frho[i][m] = fs->frho[i][m];
// add extra frho of zeroes for non-EAM types to point to (pair hybrid)
// this is necessary b/c fp is still computed for non-EAM atoms
for (m = 1; m <= nrho; m++) frho[nfrho-1][m] = 0.0;
// type2frho[i] = which frho array (0 to nfrho-1) each atom type maps to
// if atom type doesn't point to element (non-EAM atom in pair hybrid)
// then map it to last frho array of zeroes
for (i = 1; i <= ntypes; i++)
if (map[i] >= 0) type2frho[i] = map[i];
else type2frho[i] = nfrho-1;
// ------------------------------------------------------------------
// setup rhor arrays
// ------------------------------------------------------------------
// allocate rhor arrays
// nrhor = square of # of fs elements
nrhor = fs->nelements * fs->nelements;
memory->destroy(rhor);
memory->create(rhor,nrhor,nr+1,"pair:rhor");
// copy each element pair rhor to global rhor
n = 0;
for (i = 0; i < fs->nelements; i++)
for (j = 0; j < fs->nelements; j++) {
for (m = 1; m <= nr; m++) rhor[n][m] = fs->rhor[i][j][m];
n++;
}
// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
// for fs files, there is a full NxN set of rhor arrays
// OK if map = -1 (non-EAM atom in pair hybrid) b/c type2rhor not used
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
type2rhor[i][j] = map[i] * fs->nelements + map[j];
// ------------------------------------------------------------------
// setup z2r arrays
// ------------------------------------------------------------------
// allocate z2r arrays
// nz2r = N*(N+1)/2 where N = # of fs elements
nz2r = fs->nelements * (fs->nelements+1) / 2;
memory->destroy(z2r);
memory->create(z2r,nz2r,nr+1,"pair:z2r");
// copy each element pair z2r to global z2r, only for I >= J
n = 0;
for (i = 0; i < fs->nelements; i++)
for (j = 0; j <= i; j++) {
for (m = 1; m <= nr; m++) z2r[n][m] = fs->z2r[i][j][m];
n++;
}
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
// set of z2r arrays only fill lower triangular Nelement matrix
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
// swap indices when irow < icol to stay lower triangular
// if map = -1 (non-EAM atom in pair hybrid):
// type2z2r is not used by non-opt
// but set type2z2r to 0 since accessed by opt
int irow,icol;
for (i = 1; i <= ntypes; i++) {
for (j = 1; j <= ntypes; j++) {
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
type2z2r[i][j] = 0;
continue;
}
if (irow < icol) {
irow = map[j];
icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
n += icol;
type2z2r[i][j] = n;
}
}
}

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/* ----------------------------------------------------------------------
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(eam/fs/gpu,PairEAMFSGPU)
#else
#ifndef LMP_PAIR_EAM_FS_GPU_H
#define LMP_PAIR_EAM_FS_GPU_H
#include "pair_eam_gpu.h"
namespace LAMMPS_NS {
class PairEAMFSGPU : public PairEAMGPU {
public:
PairEAMFSGPU(class LAMMPS *);
virtual ~PairEAMFSGPU() {}
void coeff(int, char **);
protected:
void read_file(char *);
void file2array();
};
}
#endif
#endif

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Trung Dac Nguyen (ORNL), W. Michael Brown (ORNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_eam_gpu.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "gpu_extra.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
// External functions from cuda library for atom decomposition
int eam_gpu_init(const int ntypes, double host_cutforcesq,
int **host_type2rhor, int **host_type2z2r,
int *host_type2frho, double ***host_rhor_spline,
double ***host_z2r_spline, double ***host_frho_spline,
double rdr, double rdrho, int nrhor, int nrho, int nz2r,
int nfrho, int nr, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
int &fp_size);
void eam_gpu_clear();
int** eam_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial, int **special,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, int **ilist,
int **jnum, const double cpu_time, bool &success,
int &inum, void **fp_ptr);
void eam_gpu_compute(const int ago, const int inum_full, const int nlocal,
const int nall,double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, void **fp_ptr);
void eam_gpu_compute_force(int *ilist, const bool eflag, const bool vflag,
const bool eatom, const bool vatom);
double eam_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairEAMGPU::PairEAMGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairEAMGPU::~PairEAMGPU()
{
eam_gpu_clear();
}
/* ---------------------------------------------------------------------- */
double PairEAMGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + eam_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairEAMGPU::compute(int eflag, int vflag)
{
int i,j,ii,jj,m,jnum,itype,jtype;
double evdwl,*coeff;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
// compute density on each atom on GPU
int nall = atom->nlocal + atom->nghost;
int inum, host_start, inum_dev;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = eam_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, inum_dev, &fp_pinned);
} else { // gpu_mode == GPU_FORCE
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
eam_gpu_compute(neighbor->ago, inum, nlocal, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, &fp_pinned);
}
if (!success)
error->one(FLERR,"Out of memory on GPGPU");
// communicate derivative of embedding function
comm->forward_comm_pair(this);
// compute forces on each atom on GPU
if (gpu_mode != GPU_FORCE)
eam_gpu_compute_force(NULL, eflag, vflag, eflag_atom, vflag_atom);
else
eam_gpu_compute_force(ilist, eflag, vflag, eflag_atom, vflag_atom);
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairEAMGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with eam/gpu pair style");
if (!allocated) error->all(FLERR,"Not allocate memory eam/gpu pair style");
// convert read-in file(s) to arrays and spline them
file2array();
array2spline();
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int fp_size;
int success = eam_gpu_init(atom->ntypes+1, cutforcesq, type2rhor, type2z2r,
type2frho, rhor_spline, z2r_spline, frho_spline,
rdr, rdrho, nrhor, nrho, nz2r, nfrho, nr,
atom->nlocal, atom->nlocal+atom->nghost, 300,
maxspecial, cell_size, gpu_mode, screen, fp_size);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
if (fp_size == sizeof(double))
fp_single = false;
else
fp_single = true;
}
/* ---------------------------------------------------------------------- */
int PairEAMGPU::pack_comm(int n, int *list, double *buf, int pbc_flag,
int *pbc)
{
int i,j,m;
m = 0;
if (fp_single) {
float *fp_ptr = (float *)fp_pinned;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = static_cast<double>(fp_ptr[j]);
}
} else {
double *fp_ptr = (double *)fp_pinned;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = fp_ptr[j];
}
}
return 1;
}
/* ---------------------------------------------------------------------- */
void PairEAMGPU::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
if (fp_single) {
float *fp_ptr = (float *)fp_pinned;
for (i = first; i < last; i++) fp_ptr[i] = buf[m++];
} else {
double *fp_ptr = (double *)fp_pinned;
for (i = first; i < last; i++) fp_ptr[i] = buf[m++];
}
}

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/* ----------------------------------------------------------------------
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(eam/gpu,PairEAMGPU)
#else
#ifndef LMP_PAIR_EAM_GPU_H
#define LMP_PAIR_EAM_GPU_H
#include "stdio.h"
#include "pair_eam.h"
namespace LAMMPS_NS {
class PairEAMGPU : public PairEAM {
public:
PairEAMGPU(class LAMMPS *);
virtual ~PairEAMGPU();
void compute(int, int);
void init_style();
double memory_usage();
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
protected:
int gpu_mode;
double cpu_time;
int *gpulist;
void *fp_pinned;
bool fp_single;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Out of memory on GPGPU
UNDOCUMENTED
E: Cannot use newton pair with eam/gpu pair style
UNDOCUMENTED
E: Not allocate memory eam/gpu pair style
UNDOCUMENTED
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_table_gpu.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "gpu_extra.h"
#define LOOKUP 0
#define LINEAR 1
#define SPLINE 2
#define BITMAP 3
// External functions from cuda library for atom decomposition
int table_gpu_init(const int ntypes, double **cutsq,
double ***host_table_coeffs, double **host_table_data,
double *special_lj, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
int tabstyle, int ntables, int tablength);
void table_gpu_clear();
int ** table_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success);
void table_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double table_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairTableGPU::~PairTableGPU()
{
table_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairTableGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = table_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
table_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairTableGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with table/gpu pair style");
int ntypes = atom->ntypes;
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
// pack tables and send them to device
double ***table_coeffs = NULL;
double **table_data = NULL;
memory->create(table_coeffs, ntypes+1, ntypes+1, 6, "table:coeffs");
Table *tb;
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++) {
int n = tabindex[i][j];
tb = &tables[n];
table_coeffs[i][j][0] = n;
table_coeffs[i][j][1] = tb->nshiftbits;
table_coeffs[i][j][2] = tb->nmask;
table_coeffs[i][j][3] = tb->innersq;
table_coeffs[i][j][4] = tb->invdelta;
table_coeffs[i][j][5] = tb->deltasq6;
}
if (tabstyle != BITMAP) {
memory->create(table_data, ntables, 6*tablength, "table:data");
for (int n = 0; n < ntables; n++) {
tb = &tables[n];
if (tabstyle == LOOKUP) {
for (int k = 0; k<tablength-1; k++) {
table_data[n][6*k+1] = tb->e[k];
table_data[n][6*k+2] = tb->f[k];
}
} else if (tabstyle == LINEAR) {
for (int k = 0; k<tablength; k++) {
table_data[n][6*k+0] = tb->rsq[k];
table_data[n][6*k+1] = tb->e[k];
table_data[n][6*k+2] = tb->f[k];
if (k<tablength-1) {
table_data[n][6*k+3] = tb->de[k];
table_data[n][6*k+4] = tb->df[k];
}
}
} else if (tabstyle == SPLINE) {
for (int k = 0; k<tablength; k++) {
table_data[n][6*k+0] = tb->rsq[k];
table_data[n][6*k+1] = tb->e[k];
table_data[n][6*k+2] = tb->f[k];
table_data[n][6*k+3] = tb->e2[k];
table_data[n][6*k+4] = tb->f2[k];
}
}
}
} else {
int ntable = 1 << tablength;
memory->create(table_data, ntables, 6*ntable, "table:data");
for (int n = 0; n < ntables; n++) {
tb = &tables[n];
for (int k = 0; k<ntable; k++) {
table_data[n][6*k+0] = tb->rsq[k];
table_data[n][6*k+1] = tb->e[k];
table_data[n][6*k+2] = tb->f[k];
table_data[n][6*k+3] = tb->de[k];
table_data[n][6*k+4] = tb->df[k];
table_data[n][6*k+5] = tb->drsq[k];
}
}
}
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = table_gpu_init(atom->ntypes+1, cutsq, table_coeffs, table_data,
force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, tabstyle, ntables,
tablength);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
memory->destroy(table_coeffs);
memory->destroy(table_data);
}
/* ---------------------------------------------------------------------- */
double PairTableGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + table_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairTableGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype,itable;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,factor_lj,fraction,value,a,b;
int *jlist;
Table *tb;
union_int_float_t rsq_lookup;
int tlm1 = tablength - 1;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
double *special_lj = force->special_lj;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
tb = &tables[tabindex[itype][jtype]];
if (rsq < tb->innersq)
error->one(FLERR,"Pair distance < table inner cutoff");
if (tabstyle == LOOKUP) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
fpair = factor_lj * tb->f[itable];
} else if (tabstyle == LINEAR) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
value = tb->f[itable] + fraction*tb->df[itable];
fpair = factor_lj * value;
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
b = (rsq - tb->rsq[itable]) * tb->invdelta;
a = 1.0 - b;
value = a * tb->f[itable] + b * tb->f[itable+1] +
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
fpair = factor_lj * value;
} else {
rsq_lookup.f = rsq;
itable = rsq_lookup.i & tb->nmask;
itable >>= tb->nshiftbits;
fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
value = tb->f[itable] + fraction*tb->df[itable];
fpair = factor_lj * value;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (tabstyle == LOOKUP)
evdwl = tb->e[itable];
else if (tabstyle == LINEAR || tabstyle == BITMAP)
evdwl = tb->e[itable] + fraction*tb->de[itable];
else
evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
tb->deltasq6;
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}

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/* ----------------------------------------------------------------------
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(table/gpu,PairTableGPU)
#else
#ifndef LMP_PAIR_TABLE_GPU_H
#define LMP_PAIR_TABLE_GPU_H
#include "pair_table.h"
namespace LAMMPS_NS {
class PairTableGPU : public PairTable {
public:
PairTableGPU(LAMMPS *lmp);
~PairTableGPU();
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int);
void init_style();
double memory_usage();
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
int *gpulist;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Out of memory on GPGPU
UNDOCUMENTED
E: Cannot use newton pair with table/gpu pair style
UNDOCUMENTED
E: Pair distance > table outer cutoff
Two atoms are further apart than the pairwise table allows.
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_yukawa_gpu.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "string.h"
#include "gpu_extra.h"
// External functions from cuda library for atom decomposition
int yukawa_gpu_init(const int ntypes, double **cutsq, double kappa,
double **host_a, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
int &gpu_mode, FILE *screen);
void yukawa_gpu_clear();
int ** yukawa_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success);
void yukawa_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double yukawa_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairYukawaGPU::PairYukawaGPU(LAMMPS *lmp) : PairYukawa(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairYukawaGPU::~PairYukawaGPU()
{
yukawa_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairYukawaGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = yukawa_gpu_compute_n(neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
yukawa_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Out of memory on GPGPU");
if (host_start<inum) {
cpu_time = MPI_Wtime();
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairYukawaGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with yukawa/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
for (int i = 1; i <= atom->ntypes; i++) {
for (int j = i; j <= atom->ntypes; j++) {
if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
cut = init_one(i,j);
cut *= cut;
if (cut > maxcut)
maxcut = cut;
cutsq[i][j] = cutsq[j][i] = cut;
} else
cutsq[i][j] = cutsq[j][i] = 0.0;
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = yukawa_gpu_init(atom->ntypes+1, cutsq, kappa, a,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairYukawaGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + yukawa_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairYukawaGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r,rinv,screening,forceyukawa,factor;
int *jlist;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
double *special_lj = force->special_lj;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*r);
forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
fpair = factor*forceyukawa * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = a[itype][jtype] * screening * rinv - offset[itype][jtype];
evdwl *= factor;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}

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/* ----------------------------------------------------------------------
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(yukawa/gpu,PairYukawaGPU)
#else
#ifndef LMP_PAIR_YUKAWA_GPU_H
#define LMP_PAIR_YUKAWA_GPU_H
#include "pair_yukawa.h"
namespace LAMMPS_NS {
class PairYukawaGPU : public PairYukawa {
public:
PairYukawaGPU(LAMMPS *lmp);
~PairYukawaGPU();
void cpu_compute(int, int, int, int, int *, int *, int **);
void compute(int, int);
void init_style();
double memory_usage();
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
private:
int gpu_mode;
double cpu_time;
int *gpulist;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Out of memory on GPGPU
UNDOCUMENTED
E: Cannot use newton pair with yukawa/gpu pair style
UNDOCUMENTED
*/