git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7573 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
343
src/GPU/pair_table_gpu.cpp
Normal file
343
src/GPU/pair_table_gpu.cpp
Normal file
@ -0,0 +1,343 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
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 authors: Trung Dac Nguyen (ORNL)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "lmptype.h"
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "pair_table_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"
|
||||
|
||||
#define LOOKUP 0
|
||||
#define LINEAR 1
|
||||
#define SPLINE 2
|
||||
#define BITMAP 3
|
||||
|
||||
// External functions from cuda library for atom decomposition
|
||||
|
||||
int table_gpu_init(const int ntypes, double **cutsq,
|
||||
double ***host_table_coeffs, double **host_table_data,
|
||||
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,
|
||||
int tabstyle, int ntables, int tablength);
|
||||
void table_gpu_clear();
|
||||
int ** table_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);
|
||||
void table_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 table_gpu_bytes();
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp),
|
||||
gpu_mode(GPU_FORCE)
|
||||
{
|
||||
respa_enable = 0;
|
||||
cpu_time = 0.0;
|
||||
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
free all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
PairTableGPU::~PairTableGPU()
|
||||
{
|
||||
table_gpu_clear();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTableGPU::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 = table_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);
|
||||
} else {
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
table_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
|
||||
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
|
||||
vflag_atom, host_start, cpu_time, success);
|
||||
}
|
||||
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 PairTableGPU::init_style()
|
||||
{
|
||||
if (force->newton_pair)
|
||||
error->all(FLERR,"Cannot use newton pair with table/gpu pair style");
|
||||
|
||||
int ntypes = atom->ntypes;
|
||||
|
||||
// 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;
|
||||
|
||||
// pack tables and send them to device
|
||||
double ***table_coeffs = NULL;
|
||||
double **table_data = NULL;
|
||||
memory->create(table_coeffs, ntypes+1, ntypes+1, 6, "table:coeffs");
|
||||
|
||||
Table *tb;
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = 1; j <= atom->ntypes; j++) {
|
||||
int n = tabindex[i][j];
|
||||
tb = &tables[n];
|
||||
table_coeffs[i][j][0] = n;
|
||||
table_coeffs[i][j][1] = tb->nshiftbits;
|
||||
table_coeffs[i][j][2] = tb->nmask;
|
||||
table_coeffs[i][j][3] = tb->innersq;
|
||||
table_coeffs[i][j][4] = tb->invdelta;
|
||||
table_coeffs[i][j][5] = tb->deltasq6;
|
||||
}
|
||||
|
||||
if (tabstyle != BITMAP) {
|
||||
memory->create(table_data, ntables, 6*tablength, "table:data");
|
||||
for (int n = 0; n < ntables; n++) {
|
||||
tb = &tables[n];
|
||||
if (tabstyle == LOOKUP) {
|
||||
for (int k = 0; k<tablength-1; k++) {
|
||||
table_data[n][6*k+1] = tb->e[k];
|
||||
table_data[n][6*k+2] = tb->f[k];
|
||||
}
|
||||
} else if (tabstyle == LINEAR) {
|
||||
for (int k = 0; k<tablength; k++) {
|
||||
table_data[n][6*k+0] = tb->rsq[k];
|
||||
table_data[n][6*k+1] = tb->e[k];
|
||||
table_data[n][6*k+2] = tb->f[k];
|
||||
if (k<tablength-1) {
|
||||
table_data[n][6*k+3] = tb->de[k];
|
||||
table_data[n][6*k+4] = tb->df[k];
|
||||
}
|
||||
}
|
||||
} else if (tabstyle == SPLINE) {
|
||||
for (int k = 0; k<tablength; k++) {
|
||||
table_data[n][6*k+0] = tb->rsq[k];
|
||||
table_data[n][6*k+1] = tb->e[k];
|
||||
table_data[n][6*k+2] = tb->f[k];
|
||||
table_data[n][6*k+3] = tb->e2[k];
|
||||
table_data[n][6*k+4] = tb->f2[k];
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
int ntable = 1 << tablength;
|
||||
memory->create(table_data, ntables, 6*ntable, "table:data");
|
||||
|
||||
for (int n = 0; n < ntables; n++) {
|
||||
tb = &tables[n];
|
||||
for (int k = 0; k<ntable; k++) {
|
||||
table_data[n][6*k+0] = tb->rsq[k];
|
||||
table_data[n][6*k+1] = tb->e[k];
|
||||
table_data[n][6*k+2] = tb->f[k];
|
||||
table_data[n][6*k+3] = tb->de[k];
|
||||
table_data[n][6*k+4] = tb->df[k];
|
||||
table_data[n][6*k+5] = tb->drsq[k];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
int maxspecial=0;
|
||||
if (atom->molecular)
|
||||
maxspecial=atom->maxspecial;
|
||||
int success = table_gpu_init(atom->ntypes+1, cutsq, table_coeffs, table_data,
|
||||
force->special_lj, atom->nlocal,
|
||||
atom->nlocal+atom->nghost, 300, maxspecial,
|
||||
cell_size, gpu_mode, screen, tabstyle, ntables,
|
||||
tablength);
|
||||
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;
|
||||
}
|
||||
|
||||
memory->destroy(table_coeffs);
|
||||
memory->destroy(table_data);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairTableGPU::memory_usage()
|
||||
{
|
||||
double bytes = Pair::memory_usage();
|
||||
return bytes + table_gpu_bytes();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTableGPU::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 xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,factor_lj,fraction,value,a,b;
|
||||
int *jlist;
|
||||
Table *tb;
|
||||
|
||||
union_int_float_t rsq_lookup;
|
||||
int tlm1 = tablength - 1;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
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];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = 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];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
tb = &tables[tabindex[itype][jtype]];
|
||||
if (rsq < tb->innersq)
|
||||
error->one(FLERR,"Pair distance < table inner cutoff");
|
||||
|
||||
if (tabstyle == LOOKUP) {
|
||||
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
|
||||
if (itable >= tlm1)
|
||||
error->one(FLERR,"Pair distance > table outer cutoff");
|
||||
fpair = factor_lj * tb->f[itable];
|
||||
} else if (tabstyle == LINEAR) {
|
||||
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
|
||||
if (itable >= tlm1)
|
||||
error->one(FLERR,"Pair distance > table outer cutoff");
|
||||
fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
|
||||
value = tb->f[itable] + fraction*tb->df[itable];
|
||||
fpair = factor_lj * value;
|
||||
} else if (tabstyle == SPLINE) {
|
||||
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
|
||||
if (itable >= tlm1)
|
||||
error->one(FLERR,"Pair distance > table outer cutoff");
|
||||
b = (rsq - tb->rsq[itable]) * tb->invdelta;
|
||||
a = 1.0 - b;
|
||||
value = a * tb->f[itable] + b * tb->f[itable+1] +
|
||||
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
|
||||
tb->deltasq6;
|
||||
fpair = factor_lj * value;
|
||||
} else {
|
||||
rsq_lookup.f = rsq;
|
||||
itable = rsq_lookup.i & tb->nmask;
|
||||
itable >>= tb->nshiftbits;
|
||||
fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
|
||||
value = tb->f[itable] + fraction*tb->df[itable];
|
||||
fpair = factor_lj * value;
|
||||
}
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
|
||||
if (eflag) {
|
||||
if (tabstyle == LOOKUP)
|
||||
evdwl = tb->e[itable];
|
||||
else if (tabstyle == LINEAR || tabstyle == BITMAP)
|
||||
evdwl = tb->e[itable] + fraction*tb->de[itable];
|
||||
else
|
||||
evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
|
||||
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
|
||||
tb->deltasq6;
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user