341 lines
11 KiB
C++
341 lines
11 KiB
C++
/* ----------------------------------------------------------------------
|
|
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 MIN(a,b) ((a) < (b) ? (a) : (b))
|
|
#define MAX(a,b) ((a) > (b) ? (a) : (b))
|
|
|
|
#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_PAIR)
|
|
{
|
|
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_NEIGH) {
|
|
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("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("Pair style cg/cmm/coul/long requires atom attribute q");
|
|
if (force->newton_pair)
|
|
error->all("Cannot use newton pair with GPU cg/cmm 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("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_NEIGH) {
|
|
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);
|
|
}
|
|
}
|
|
}
|
|
}
|