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lammps/src/GPU/pair_gayberne_gpu.cpp

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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: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_gayberne_gpu.h"
#include "lmptype.h"
#include "math_extra.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 "domain.h"
#include "update.h"
#include "string.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
// External functions from cuda library for atom decomposition
bool gb_gpu_init(const int ntypes, const double gamma, const double upsilon,
const double mu, double **shape, double **well, double **cutsq,
double **sigma, double **epsilon, double *host_lshape,
int **form, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset,
double *special_lj, const int nlocal, const int nall,
const int max_nbors, const double cell_size,
int &gpu_mode, FILE *screen);
void gb_gpu_clear();
int * gb_gpu_compute_n(const int timestep, const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *boxlo, double *boxhi, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, const double cpu_time, bool &success,
double **host_quat);
int * gb_gpu_compute(const int timestep, 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 **host_quat);
double gb_gpu_bytes();
using namespace LAMMPS_NS;
enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
/* ---------------------------------------------------------------------- */
PairGayBerneGPU::PairGayBerneGPU(LAMMPS *lmp) : PairGayBerne(lmp),
gpu_mode(GPU_PAIR)
{
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairGayBerneGPU::~PairGayBerneGPU()
{
gb_gpu_clear();
cpu_time = 0.0;
}
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::compute(int eflag, int vflag)
{
if (update->ntimestep > MAXSMALLINT)
error->all("Timestep too big for GPU pair style");
int ntimestep = update->ntimestep;
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;
if (gpu_mode == GPU_NEIGH) {
inum = atom->nlocal;
gpulist = gb_gpu_compute_n(ntimestep, neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo, domain->subhi,
eflag, vflag, eflag_atom, vflag_atom, host_start,
cpu_time, success, atom->quat);
} else {
inum = list->inum;
olist = gb_gpu_compute(ntimestep, neighbor->ago, inum, nall, atom->x,
atom->type, list->ilist, list->numneigh,
list->firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success,
atom->quat);
}
if (!success)
error->one("Out of memory on GPGPU");
if (host_start < inum) {
cpu_time = MPI_Wtime();
if (gpu_mode == GPU_NEIGH)
cpu_compute(gpulist,host_start,eflag,vflag);
else
cpu_compute(host_start,eflag,vflag);
cpu_time = MPI_Wtime() - cpu_time;
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairGayBerneGPU::init_style()
{
if (force->pair_match("gpu",0) == NULL)
error->all("Cannot use pair hybrid with multiple GPU pair styles");
if (!atom->quat_flag || !atom->torque_flag || !atom->avec->shape_type)
error->all("Pair gayberne requires atom attributes quat, torque, shape");
if (atom->radius_flag)
error->all("Pair gayberne cannot be used with atom attribute diameter");
// per-type shape precalculations
for (int i = 1; i <= atom->ntypes; i++) {
if (setwell[i]) {
double *one = atom->shape[i];
shape[i][0] = one[0]*one[0];
shape[i][1] = one[1]*one[1];
shape[i][2] = one[2]*one[2];
lshape[i] = (one[0]*one[1]+one[2]*one[2])*sqrt(one[0]*one[1]);
}
}
// 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;
bool init_ok = gb_gpu_init(atom->ntypes+1, gamma, upsilon, mu,
shape, well, cutsq, sigma, epsilon, lshape, form,
lj1, lj2, lj3, lj4, offset, force->special_lj,
atom->nlocal, atom->nlocal+atom->nghost, 300,
cell_size, gpu_mode, screen);
if (!init_ok)
error->one("Insufficient memory on accelerator (or no fix gpu).");
if (force->newton_pair)
error->all("Cannot use newton pair with GPU Gay-Berne pair style");
if (gpu_mode != GPU_NEIGH) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairGayBerneGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + gb_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::cpu_compute(int start, int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
double fforce[3],ttor[3],rtor[3],r12[3];
double a1[3][3],b1[3][3],g1[3][3],a2[3][3],b2[3][3],g2[3][3],temp[3][3];
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **f = atom->f;
double **quat = atom->quat;
double **tor = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
inum = list->inum;
ilist = olist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
itype = type[i];
if (form[itype][itype] == ELLIPSE_ELLIPSE) {
MathExtra::quat_to_mat_trans(quat[i],a1);
MathExtra::diag_times3(well[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,b1);
MathExtra::diag_times3(shape[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,g1);
}
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
// r12 = center to center vector
r12[0] = x[j][0]-x[i][0];
r12[1] = x[j][1]-x[i][1];
r12[2] = x[j][2]-x[i][2];
rsq = MathExtra::dot3(r12,r12);
jtype = type[j];
// compute if less than cutoff
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag) one_eng =
r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
case SPHERE_ELLIPSE:
MathExtra::quat_to_mat_trans(quat[j],a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
case ELLIPSE_SPHERE:
one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
default:
MathExtra::quat_to_mat_trans(quat[j],a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
fforce,ttor,rtor);
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
f[i][0] += fforce[0];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
tor[i][0] += ttor[0];
tor[i][1] += ttor[1];
tor[i][2] += ttor[2];
if (eflag) evdwl = factor_lj*one_eng;
if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
}
}
}
}
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::cpu_compute(int *nbors, int start, int eflag, int vflag)
{
int i,j,itype,jtype;
double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
double fforce[3],ttor[3],rtor[3],r12[3];
double a1[3][3],b1[3][3],g1[3][3],a2[3][3],b2[3][3],g2[3][3],temp[3][3];
double **x = atom->x;
double **f = atom->f;
double **quat = atom->quat;
double **tor = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int stride = nlocal-start;
double *special_lj = force->special_lj;
// loop over neighbors of my atoms
for (i = start; i < nlocal; i++) {
itype = type[i];
if (form[itype][itype] == ELLIPSE_ELLIPSE) {
MathExtra::quat_to_mat_trans(quat[i],a1);
MathExtra::diag_times3(well[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,b1);
MathExtra::diag_times3(shape[itype],a1,temp);
MathExtra::transpose_times3(a1,temp,g1);
}
int *nbor = nbors+i-start;
int jnum =* nbor;
nbor += stride;
int *nbor_end = nbor + stride * jnum;
for ( ; nbor < nbor_end; nbor += stride) {
j = *nbor;
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
// r12 = center to center vector
r12[0] = x[j][0]-x[i][0];
r12[1] = x[j][1]-x[i][1];
r12[2] = x[j][2]-x[i][2];
rsq = MathExtra::dot3(r12,r12);
jtype = type[j];
// compute if less than cutoff
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag) one_eng =
r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
case SPHERE_ELLIPSE:
MathExtra::quat_to_mat_trans(quat[j],a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
case ELLIPSE_SPHERE:
one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
default:
MathExtra::quat_to_mat_trans(quat[j],a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
fforce,ttor,rtor);
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
f[i][0] += fforce[0];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
tor[i][0] += ttor[0];
tor[i][1] += ttor[1];
tor[i][2] += ttor[2];
if (eflag) evdwl = factor_lj*one_eng;
if (j<start) {
if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],
fforce[2],-r12[0],-r12[1],-r12[2]);
} else {
if (j < nlocal) {
rtor[0] *= factor_lj;
rtor[1] *= factor_lj;
rtor[2] *= factor_lj;
f[j][0] -= fforce[0];
f[j][1] -= fforce[1];
f[j][2] -= fforce[2];
tor[j][0] += rtor[0];
tor[j][1] += rtor[1];
tor[j][2] += rtor[2];
}
if (evflag) ev_tally_xyz(i,j,nlocal,0,
evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
}
}
}
}
}
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