261 lines
8.7 KiB
C++
261 lines
8.7 KiB
C++
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://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 "pair_born_gpu.h"
|
|
#include <cmath>
|
|
#include <cstdio>
|
|
|
|
#include <cstring>
|
|
#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 "gpu_extra.h"
|
|
#include "suffix.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
|
|
// External functions from cuda library for atom decomposition
|
|
|
|
int born_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
|
|
double **host_born1, double **host_born2, double **host_born3,
|
|
double **host_a, double **host_c, double **host_d,
|
|
double **host_sigma, 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 born_gpu_reinit(const int ntypes, double **host_rhoinv,
|
|
double **host_born1, double **host_born2,
|
|
double **host_born3, double **host_a, double **host_c,
|
|
double **host_d, double **offset);
|
|
void born_gpu_clear();
|
|
int ** born_gpu_compute_n(const int ago, const int inum_full, const int nall,
|
|
double **host_x, int *host_type, double *sublo,
|
|
double *subhi, tagint *tag, int **nspecial,
|
|
tagint **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 born_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 born_gpu_bytes();
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
PairBornGPU::PairBornGPU(LAMMPS *lmp) : PairBorn(lmp), gpu_mode(GPU_FORCE)
|
|
{
|
|
respa_enable = 0;
|
|
cpu_time = 0.0;
|
|
suffix_flag |= Suffix::GPU;
|
|
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
free all arrays
|
|
------------------------------------------------------------------------- */
|
|
|
|
PairBornGPU::~PairBornGPU()
|
|
{
|
|
born_gpu_clear();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairBornGPU::compute(int eflag, int vflag)
|
|
{
|
|
ev_init(eflag,vflag);
|
|
|
|
int nall = atom->nlocal + atom->nghost;
|
|
int inum, host_start;
|
|
|
|
bool success = true;
|
|
int *ilist, *numneigh, **firstneigh;
|
|
if (gpu_mode != GPU_FORCE) {
|
|
double sublo[3],subhi[3];
|
|
if (domain->triclinic == 0) {
|
|
sublo[0] = domain->sublo[0];
|
|
sublo[1] = domain->sublo[1];
|
|
sublo[2] = domain->sublo[2];
|
|
subhi[0] = domain->subhi[0];
|
|
subhi[1] = domain->subhi[1];
|
|
subhi[2] = domain->subhi[2];
|
|
} else {
|
|
domain->bbox(domain->sublo_lamda,domain->subhi_lamda,sublo,subhi);
|
|
}
|
|
inum = atom->nlocal;
|
|
firstneigh = born_gpu_compute_n(neighbor->ago, inum, nall,
|
|
atom->x, atom->type, sublo,
|
|
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;
|
|
born_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,"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 PairBornGPU::init_style()
|
|
{
|
|
if (force->newton_pair)
|
|
error->all(FLERR,"Cannot use newton pair with born/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 != Atom::ATOMIC)
|
|
maxspecial=atom->maxspecial;
|
|
int mnf = 5e-2 * neighbor->oneatom;
|
|
int success = born_gpu_init(atom->ntypes+1, cutsq, rhoinv,
|
|
born1, born2, born3, a, c, d, sigma,
|
|
offset, force->special_lj, atom->nlocal,
|
|
atom->nlocal+atom->nghost, mnf, maxspecial,
|
|
cell_size, gpu_mode, screen);
|
|
GPU_EXTRA::check_flag(success,error,world);
|
|
|
|
if (gpu_mode == GPU_FORCE) {
|
|
int irequest = neighbor->request(this,instance_me);
|
|
neighbor->requests[irequest]->half = 0;
|
|
neighbor->requests[irequest]->full = 1;
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairBornGPU::reinit()
|
|
{
|
|
Pair::reinit();
|
|
|
|
born_gpu_reinit(atom->ntypes+1, rhoinv, born1, born2, born3,
|
|
a, c, d, offset);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairBornGPU::memory_usage()
|
|
{
|
|
double bytes = Pair::memory_usage();
|
|
return bytes + born_gpu_bytes();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairBornGPU::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,forceborn,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((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
|
|
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv +
|
|
born3[itype][jtype]*r2inv*r6inv;
|
|
fpair = factor_lj*forceborn*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 +
|
|
d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
|
|
evdwl *= factor_lj;
|
|
}
|
|
|
|
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
|
|
}
|
|
}
|
|
}
|
|
}
|