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pair_cg_cmm_coul_long_gpu.cpp
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Fri, Jul 12, 08:07

pair_cg_cmm_coul_long_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: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_cg_cmm_coul_long_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 "kspace.h"
#include "gpu_extra.h"
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
// External functions from cuda library for atom decomposition
int cmml_gpu_init(const int ntypes, double **cutsq, int **cg_type,
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald);
void cmml_gpu_clear();
int ** cmml_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **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_q, double *boxlo,
double *prd);
void cmml_gpu_compute(const int ago, const int inum, 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_q,
const int nlocal, double *boxlo, double *prd);
double cmml_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairCGCMMCoulLongGPU::PairCGCMMCoulLongGPU(LAMMPS *lmp) : PairCGCMMCoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairCGCMMCoulLongGPU::~PairCGCMMCoulLongGPU()
{
cmml_gpu_clear();
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulLongGPU::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 = cmml_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->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
cmml_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->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Out of memory on GPGPU");
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 PairCGCMMCoulLongGPU::init_style()
{
cut_respa = NULL;
if (!atom->q_flag)
error->all(FLERR,"Pair style cg/cmm/coul/long/gpu requires atom attribute q");
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with cg/cmm/coul/long/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;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables
if (ncoultablebits) init_tables();
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = cmml_gpu_init(atom->ntypes+1, cutsq, cg_type, lj1, lj2, lj3,
lj4, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq_global, force->special_coul,
force->qqrd2e, g_ewald);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
/* ---------------------------------------------------------------------- */
double PairCGCMMCoulLongGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + cmml_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairCGCMMCoulLongGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double fraction,table;
double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
int *jlist;
double rsq;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
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)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
const int jtype = type[j];
double evdwl = 0.0;
double ecoul = 0.0;
double fpair = 0.0;
if (rsq < cutsq[itype][jtype]) {
const double r2inv = 1.0/rsq;
const int cgt=cg_type[itype][jtype];
double forcelj = 0.0;
double forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
forcelj=factor_lj;
if (eflag) evdwl=factor_lj;
if (cgt == CG_LJ12_4) {
const double r4inv=r2inv*r2inv;
forcelj *= r4inv*(lj1[itype][jtype]*r4inv*r4inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r4inv*(lj3[itype][jtype]*r4inv*r4inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else if (cgt == CG_LJ9_6) {
const double r3inv = r2inv*sqrt(r2inv);
const double r6inv = r3inv*r3inv;
forcelj *= r6inv*(lj1[itype][jtype]*r3inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r3inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else {
const double r6inv = r2inv*r2inv*r2inv;
forcelj *= r6inv*(lj1[itype][jtype]*r6inv
- lj2[itype][jtype]);
if (eflag) {
evdwl *= r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
}
}
if (rsq < cut_coulsq_global) {
if (!ncoultablebits || rsq <= tabinnersq) {
const double r = sqrt(rsq);
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
const double t = 1.0 / (1.0 + EWALD_P*grij);
const double erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
const double prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (eflag) ecoul = prefactor*erfc;
if (factor_coul < 1.0) {
forcecoul -= (1.0-factor_coul)*prefactor;
if (eflag) ecoul -= (1.0-factor_coul)*prefactor;
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
int itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
const double fraction = (rsq_lookup.f - rtable[itable]) *
drtable[itable];
const double table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (eflag) {
const double table2 = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table2;
}
if (factor_coul < 1.0) {
const double table2 = ctable[itable] + fraction*dctable[itable];
const double prefactor = qtmp*q[j] * table2;
forcecoul -= (1.0-factor_coul)*prefactor;
if (eflag) ecoul -= (1.0-factor_coul)*prefactor;
}
}
}
fpair = (forcecoul + forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
}

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