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lammps/src/GPU/pair_eam_gpu.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, 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 "pair_eam_gpu.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "suffix.h"
#include <cmath>
#define MAXLINE 1024
using namespace LAMMPS_NS;
// 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 **host_cutsq,
double rdr, double rdrho, double rhomax, 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, 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, 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;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
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)
{
ev_init(eflag, vflag);
// compute density on each atom on GPU
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int inum, host_start, inum_dev;
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 =
eam_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, 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, "Insufficient memory on accelerator");
// communicate derivative of embedding function
comm->forward_comm(this);
// compute forces on each atom on GPU
if (gpu_mode != GPU_FORCE)
eam_gpu_compute_force(nullptr, 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()
{
// 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 != Atom::ATOMIC) maxspecial = atom->maxspecial;
int fp_size;
int mnf = 5e-2 * neighbor->oneatom;
int success = eam_gpu_init(atom->ntypes + 1, cutforcesq, type2rhor, type2z2r, type2frho,
rhor_spline, z2r_spline, frho_spline, cutsq, rdr, rdrho, rhomax, nrhor,
nrho, nz2r, nfrho, nr, atom->nlocal, atom->nlocal + atom->nghost, mnf,
maxspecial, cell_size, gpu_mode, screen, fp_size);
GPU_EXTRA::check_flag(success, error, world);
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
fp_single = fp_size != sizeof(double);
embedstep = -1;
}
/* ---------------------------------------------------------------------- */
double PairEAMGPU::single(int i, int j, int itype, int jtype, double rsq, double /* factor_coul */,
double /* factor_lj */, double &fforce)
{
int m;
double r, p, rhoip, rhojp, z2, z2p, recip, phi, phip, psip;
double *coeff;
r = sqrt(rsq);
p = r * rdr + 1.0;
m = static_cast<int>(p);
m = MIN(m, nr - 1);
p -= m;
p = MIN(p, 1.0);
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rhoip = (coeff[0] * p + coeff[1]) * p + coeff[2];
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rhojp = (coeff[0] * p + coeff[1]) * p + coeff[2];
coeff = z2r_spline[type2z2r[itype][jtype]][m];
z2p = (coeff[0] * p + coeff[1]) * p + coeff[2];
z2 = ((coeff[3] * p + coeff[4]) * p + coeff[5]) * p + coeff[6];
double fp_i, fp_j;
if (!fp_single) {
fp_i = ((double *) fp_pinned)[i];
fp_j = ((double *) fp_pinned)[j];
} else {
fp_i = ((float *) fp_pinned)[i];
fp_j = ((float *) fp_pinned)[j];
}
recip = 1.0 / r;
phi = z2 * recip;
phip = z2p * recip - phi * recip;
psip = fp_i * rhojp + fp_j * rhoip + phip;
fforce = -psip * recip;
return phi;
}
/* ---------------------------------------------------------------------- */
int PairEAMGPU::pack_forward_comm(int n, int *list, double *buf, int /* pbc_flag */,
int * /* pbc */)
{
int i, j, m;
m = 0;
if (fp_single) {
auto fp_ptr = (float *) fp_pinned;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = static_cast<double>(fp_ptr[j]);
}
} else {
auto fp_ptr = (double *) fp_pinned;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = fp_ptr[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairEAMGPU::unpack_forward_comm(int n, int first, double *buf)
{
int i, m, last;
m = 0;
last = first + n;
if (fp_single) {
auto fp_ptr = (float *) fp_pinned;
for (i = first; i < last; i++) fp_ptr[i] = buf[m++];
} else {
auto fp_ptr = (double *) fp_pinned;
for (i = first; i < last; i++) fp_ptr[i] = buf[m++];
}
}
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