225 lines
7.9 KiB
C++
225 lines
7.9 KiB
C++
/* ----------------------------------------------------------------------
|
|
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 author: Trung Dac Nguyen (ORNL)
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "pair_yukawa_colloid_gpu.h"
|
|
|
|
#include "atom.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>
|
|
|
|
using namespace LAMMPS_NS;
|
|
|
|
// External functions from cuda library for atom decomposition
|
|
|
|
int ykcolloid_gpu_init(const int ntypes, double **cutsq, double **host_a, double **host_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,
|
|
const double kappa);
|
|
void ykcolloid_gpu_clear();
|
|
int **ykcolloid_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, double *host_rad);
|
|
void ykcolloid_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 *host_rad);
|
|
double ykcolloid_gpu_bytes();
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
PairYukawaColloidGPU::PairYukawaColloidGPU(LAMMPS *lmp) :
|
|
PairYukawaColloid(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);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
free all arrays
|
|
------------------------------------------------------------------------- */
|
|
|
|
PairYukawaColloidGPU::~PairYukawaColloidGPU()
|
|
{
|
|
ykcolloid_gpu_clear();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairYukawaColloidGPU::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 = ykcolloid_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, atom->radius);
|
|
} else {
|
|
inum = list->inum;
|
|
ilist = list->ilist;
|
|
numneigh = list->numneigh;
|
|
firstneigh = list->firstneigh;
|
|
ykcolloid_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh,
|
|
firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time,
|
|
success, atom->radius);
|
|
}
|
|
if (!success) error->one(FLERR, "Insufficient memory on accelerator");
|
|
|
|
if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
|
|
neighbor->build_topology();
|
|
if (host_start < inum) {
|
|
cpu_time = platform::walltime();
|
|
cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
|
|
cpu_time = platform::walltime() - cpu_time;
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
init specific to this pair style
|
|
------------------------------------------------------------------------- */
|
|
|
|
void PairYukawaColloidGPU::init_style()
|
|
{
|
|
if (!atom->radius_flag) error->all(FLERR, "Pair style yukawa/colloid/gpu requires atom attribute radius");
|
|
|
|
// 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 = ykcolloid_gpu_init(atom->ntypes + 1, cutsq, a, offset, force->special_lj,
|
|
atom->nlocal, atom->nlocal + atom->nghost, mnf, maxspecial,
|
|
cell_size, gpu_mode, screen, kappa);
|
|
GPU_EXTRA::check_flag(success, error, world);
|
|
|
|
if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double PairYukawaColloidGPU::memory_usage()
|
|
{
|
|
double bytes = Pair::memory_usage();
|
|
return bytes + ykcolloid_gpu_bytes();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void PairYukawaColloidGPU::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, radi, radj;
|
|
double r, rsq, rinv, screening, forceyukawa, factor;
|
|
int *jlist;
|
|
|
|
double **x = atom->x;
|
|
double **f = atom->f;
|
|
int *type = atom->type;
|
|
double *radius = atom->radius;
|
|
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];
|
|
radi = radius[i];
|
|
jlist = firstneigh[i];
|
|
jnum = numneigh[i];
|
|
|
|
for (jj = 0; jj < jnum; jj++) {
|
|
j = jlist[jj];
|
|
factor = 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];
|
|
radj = radius[j];
|
|
|
|
if (rsq < cutsq[itype][jtype]) {
|
|
r = sqrt(rsq);
|
|
rinv = 1.0 / r;
|
|
screening = exp(-kappa * (r - (radi + radj)));
|
|
forceyukawa = a[itype][jtype] * screening;
|
|
|
|
fpair = factor * forceyukawa * rinv;
|
|
|
|
f[i][0] += delx * fpair;
|
|
f[i][1] += dely * fpair;
|
|
f[i][2] += delz * fpair;
|
|
|
|
if (eflag) {
|
|
evdwl = a[itype][jtype] / kappa * screening - offset[itype][jtype];
|
|
evdwl *= factor;
|
|
}
|
|
|
|
if (evflag) ev_tally_full(i, evdwl, 0.0, fpair, delx, dely, delz);
|
|
}
|
|
}
|
|
}
|
|
}
|