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lammps/src/GPU/pair_eam_alloy_gpu.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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_alloy_gpu.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "gpu_extra.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "potential_file_reader.h"
#include "suffix.h"
#include "tokenizer.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int eam_alloy_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_alloy_gpu_clear();
int **eam_alloy_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_alloy_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_alloy_gpu_compute_force(int *ilist, const bool eflag, const bool vflag, const bool eatom,
const bool vatom);
double eam_alloy_gpu_bytes();
/* ---------------------------------------------------------------------- */
PairEAMAlloyGPU::PairEAMAlloyGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
{
one_coeff = 1;
respa_enable = 0;
reinitflag = 0;
cpu_time = 0.0;
suffix_flag |= Suffix::GPU;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ---------------------------------------------------------------------- */
PairEAMAlloyGPU::~PairEAMAlloyGPU()
{
eam_alloy_gpu_clear();
}
/* ---------------------------------------------------------------------- */
double PairEAMAlloyGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + eam_alloy_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairEAMAlloyGPU::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_alloy_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_alloy_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_alloy_gpu_compute_force(nullptr, eflag, vflag, eflag_atom, vflag_atom);
else
eam_alloy_gpu_compute_force(ilist, eflag, vflag, eflag_atom, vflag_atom);
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0) neighbor->build_topology();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairEAMAlloyGPU::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_alloy_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 PairEAMAlloyGPU::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 PairEAMAlloyGPU::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 PairEAMAlloyGPU::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++];
}
}
/* ----------------------------------------------------------------------
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, "Number of element to type mappings does not match number of atom types");
// read EAM setfl file
if (setfl) {
for (i = 0; i < setfl->nelements; i++) delete[] setfl->elements[i];
delete[] setfl->elements;
memory->destroy(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(FLERR, i, setfl->mass[map[i]]);
count++;
}
scale[i][j] = 1.0;
}
}
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;
// read potential file
if (comm->me == 0) {
PotentialFileReader reader(PairEAM::lmp, filename, "eam/alloy", unit_convert_flag);
// transparently convert units for supported conversions
int unit_convert = reader.get_unit_convert();
double conversion_factor = utils::get_conversion_factor(utils::ENERGY, unit_convert);
try {
reader.skip_line();
reader.skip_line();
reader.skip_line();
// extract element names from nelements line
ValueTokenizer values = reader.next_values(1);
file->nelements = values.next_int();
if ((int) values.count() != file->nelements + 1)
error->one(FLERR, "Incorrect element names in EAM potential file");
file->elements = new char *[file->nelements];
for (int i = 0; i < file->nelements; i++)
file->elements[i] = utils::strdup(values.next_string());
//
values = reader.next_values(5);
file->nrho = values.next_int();
file->drho = values.next_double();
file->nr = values.next_int();
file->dr = values.next_double();
file->cut = values.next_double();
if ((file->nrho <= 0) || (file->nr <= 0) || (file->dr <= 0.0))
error->one(FLERR, "Invalid EAM potential file");
memory->create(file->mass, file->nelements, "pair:mass");
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");
for (int i = 0; i < file->nelements; i++) {
values = reader.next_values(2);
values.next_int(); // ignore
file->mass[i] = values.next_double();
reader.next_dvector(&file->frho[i][1], file->nrho);
reader.next_dvector(&file->rhor[i][1], file->nr);
if (unit_convert) {
for (int j = 1; j < file->nrho; ++j) file->frho[i][j] *= conversion_factor;
}
}
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) {
reader.next_dvector(&file->z2r[i][j][1], file->nr);
if (unit_convert) {
for (int k = 1; k < file->nr; ++k) file->z2r[i][j][k] *= conversion_factor;
}
}
}
} catch (TokenizerException &e) {
error->one(FLERR, e.what());
}
}
// broadcast potential information
MPI_Bcast(&file->nelements, 1, MPI_INT, 0, world);
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);
// allocate memory on other procs
if (comm->me != 0) {
file->elements = new char *[file->nelements];
for (int i = 0; i < file->nelements; i++) file->elements[i] = nullptr;
memory->create(file->mass, file->nelements, "pair:mass");
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");
}
// broadcast file->elements string array
for (int i = 0; i < file->nelements; i++) {
int n;
if (comm->me == 0) n = strlen(file->elements[i]) + 1;
MPI_Bcast(&n, 1, MPI_INT, 0, world);
if (comm->me != 0) file->elements[i] = new char[n];
MPI_Bcast(file->elements[i], n, MPI_CHAR, 0, world);
}
// broadcast file->mass, frho, rhor
for (int i = 0; i < file->nelements; i++) {
MPI_Bcast(&file->mass[i], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&file->frho[i][1], file->nrho, MPI_DOUBLE, 0, world);
MPI_Bcast(&file->rhor[i][1], file->nr, MPI_DOUBLE, 0, world);
}
// broadcast file->z2r
for (int i = 0; i < file->nelements; i++) {
for (int j = 0; j <= i; j++) { MPI_Bcast(&file->z2r[i][j][1], file->nr, MPI_DOUBLE, 0, world); }
}
}
/* ----------------------------------------------------------------------
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;
rhomax = (nrho - 1) * drho;
// ------------------------------------------------------------------
// 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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