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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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194
src/GPU/pair_table_gpu.cpp
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@ -2,12 +2,12 @@
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
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.
------------------------------------------------------------------------- */
@ -42,37 +42,37 @@
// 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);
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 **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)
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);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -90,28 +90,28 @@ 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);
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);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -129,11 +129,11 @@ void PairTableGPU::compute(int eflag, int vflag)
void PairTableGPU::init_style()
{
if (force->newton_pair)
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;
@ -150,12 +150,12 @@ void PairTableGPU::init_style()
}
}
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++) {
@ -168,7 +168,7 @@ void PairTableGPU::init_style()
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++) {
@ -196,7 +196,7 @@ void PairTableGPU::init_style()
table_data[n][6*k+3] = tb->e2[k];
table_data[n][6*k+4] = tb->f2[k];
}
}
}
}
} else {
int ntable = 1 << tablength;
@ -212,17 +212,17 @@ void PairTableGPU::init_style()
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);
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) {
@ -230,7 +230,7 @@ void PairTableGPU::init_style()
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
memory->destroy(table_coeffs);
memory->destroy(table_data);
}
@ -245,17 +245,17 @@ double PairTableGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairTableGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
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;
@ -284,58 +284,58 @@ void PairTableGPU::cpu_compute(int start, int inum, int eflag, int vflag,
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 = &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;
}
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;
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 (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);
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}