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pair_yukawa_colloid_gpu.cpp
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Thu, May 23, 14:57

pair_yukawa_colloid_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: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "pair_yukawa_colloid_gpu.h"
#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 <string.h>
#include "gpu_extra.h"
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;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairYukawaColloidGPU::~PairYukawaColloidGPU()
{
ykcolloid_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairYukawaColloidGPU::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 (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ykcolloid_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, 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 (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 PairYukawaColloidGPU::init_style()
{
if (!atom->sphere_flag)
error->all(FLERR,"Pair yukawa/colloid/gpu requires atom style sphere");
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with yukawa/colloid/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)
maxspecial=atom->maxspecial;
int success = ykcolloid_gpu_init(atom->ntypes+1, cutsq, a,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, kappa);
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;
}
}
/* ---------------------------------------------------------------------- */
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);
}
}
}
}

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