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pair_resquared_gpu.cpp
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Sat, Nov 9, 19:31

pair_resquared_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_resquared_gpu.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.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"
#include "gpu_extra.h"
// External functions from cuda library for atom decomposition
int re_gpu_init(const int ntypes, double **shape, double **well,
double **cutsq, double **sigma, double **epsilon,
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 int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void re_gpu_clear();
int ** re_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, double **host_quat);
int * re_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 **host_quat);
double re_gpu_bytes();
using namespace LAMMPS_NS;
enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
/* ---------------------------------------------------------------------- */
PairRESquaredGPU::PairRESquaredGPU(LAMMPS *lmp) : PairRESquared(lmp),
gpu_mode(GPU_FORCE)
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Pair resquared/gpu requires atom style ellipsoid");
quat_nmax = 0;
quat = NULL;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairRESquaredGPU::~PairRESquaredGPU()
{
re_gpu_clear();
cpu_time = 0.0;
memory->destroy(quat);
}
/* ---------------------------------------------------------------------- */
void PairRESquaredGPU::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 (nall > quat_nmax) {
quat_nmax = static_cast<int>(1.1 * nall);
memory->grow(quat, quat_nmax, 4, "pair:quat");
}
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
for (int i=0; i<nall; i++) {
int qi = ellipsoid[i];
if (qi > -1) {
quat[i][0] = bonus[qi].quat[0];
quat[i][1] = bonus[qi].quat[1];
quat[i][2] = bonus[qi].quat[2];
quat[i][3] = bonus[qi].quat[3];
}
}
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = re_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, quat);
} else {
inum = list->inum;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ilist = re_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
list->ilist, numneigh, firstneigh, eflag, vflag,
eflag_atom, vflag_atom, host_start,
cpu_time, success, quat);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
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 PairRESquaredGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with resquared/gpu pair style");
if (!atom->ellipsoid_flag)
error->all(FLERR,"Pair resquared/gpu requires atom style ellipsoid");
// per-type shape precalculations
// require that atom shapes are identical within each type
// if shape = 0 for point particle, set shape = 1 as required by Gay-Berne
for (int i = 1; i <= atom->ntypes; i++) {
if (!atom->shape_consistency(i,shape1[i][0],shape1[i][1],shape1[i][2]))
error->all(FLERR,"Pair resquared/gpu requires atoms with same type have same shape");
if (setwell[i]) {
shape2[i][0] = shape1[i][0]*shape1[i][0];
shape2[i][1] = shape1[i][1]*shape1[i][1];
shape2[i][2] = shape1[i][2]*shape1[i][2];
lshape[i] = shape1[i][0]*shape1[i][1]*shape1[i][2];
}
}
// 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 = re_gpu_init(atom->ntypes+1, shape1, well, cutsq, sigma,
epsilon, form, lj1, lj2, lj3, lj4, 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;
}
quat_nmax = static_cast<int>(1.1 * (atom->nlocal + atom->nghost));
memory->grow(quat, quat_nmax, 4, "pair:quat");
}
/* ---------------------------------------------------------------------- */
double PairRESquaredGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + memory->usage(quat,quat_nmax)+re_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairRESquaredGPU::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 evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
double fforce[3],ttor[3],rtor[3],r12[3];
int *jlist;
RE2Vars wi,wj;
double **x = atom->x;
double **f = atom->f;
double **tor = atom->torque;
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];
itype = type[i];
// not a LJ sphere
if (lshape[itype] != 0.0) precompute_i(i,wi);
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
// 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;
break;
case SPHERE_ELLIPSE:
precompute_i(j,wj);
one_eng = resquared_lj(j,i,wj,r12,rsq,fforce,rtor,false);
break;
case ELLIPSE_SPHERE:
one_eng = resquared_lj(i,j,wi,r12,rsq,fforce,ttor,true);
tor[i][0] += ttor[0]*factor_lj;
tor[i][1] += ttor[1]*factor_lj;
tor[i][2] += ttor[2]*factor_lj;
break;
default:
precompute_i(j,wj);
one_eng = resquared_analytic(i,j,wi,wj,r12,rsq,fforce,ttor,rtor);
tor[i][0] += ttor[0]*factor_lj;
tor[i][1] += ttor[1]*factor_lj;
tor[i][2] += ttor[2]*factor_lj;
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
f[i][0] += fforce[0];
f[i][1] += fforce[1];
f[i][2] += fforce[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]);
}
}
}
}

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