Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F92485585
pair_resquared_gpu.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Nov 20, 17:23
Size
9 KB
Mime Type
text/x-c
Expires
Fri, Nov 22, 17:23 (1 d, 21 h)
Engine
blob
Format
Raw Data
Handle
22442716
Attached To
rLAMMPS lammps
pair_resquared_gpu.cpp
View Options
/* ----------------------------------------------------------------------
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_resquared_gpu.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.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 "domain.h"
#include "update.h"
#include "string.h"
#include "gpu_extra.h"
// External functions from cuda library for atom decomposition
int re_gpu_init(const int ntypes, double **shape, double **well,
double **cutsq, double **sigma, double **epsilon,
int **form, 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);
void re_gpu_clear();
int ** re_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_quat);
int * re_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_quat);
double re_gpu_bytes();
using namespace LAMMPS_NS;
enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
/* ---------------------------------------------------------------------- */
PairRESquaredGPU::PairRESquaredGPU(LAMMPS *lmp) : PairRESquared(lmp),
gpu_mode(GPU_FORCE)
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Pair gayberne requires atom style ellipsoid");
quat_nmax = 0;
quat = NULL;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
PairRESquaredGPU::~PairRESquaredGPU()
{
re_gpu_clear();
cpu_time = 0.0;
memory->destroy(quat);
}
/* ---------------------------------------------------------------------- */
void PairRESquaredGPU::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 (nall > quat_nmax) {
quat_nmax = static_cast<int>(1.1 * nall);
memory->grow(quat, quat_nmax, 4, "pair:quat");
}
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
for (int i=0; i<nall; i++) {
int qi = ellipsoid[i];
if (qi > -1) {
quat[i][0] = bonus[qi].quat[0];
quat[i][1] = bonus[qi].quat[1];
quat[i][2] = bonus[qi].quat[2];
quat[i][3] = bonus[qi].quat[3];
}
}
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = re_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, quat);
} else {
inum = list->inum;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ilist = re_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
list->ilist, numneigh, firstneigh, eflag, vflag,
eflag_atom, vflag_atom, host_start,
cpu_time, success, quat);
}
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 PairRESquaredGPU::init_style()
{
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with resquared/gpu pair style");
if (!atom->ellipsoid_flag)
error->all(FLERR,"Pair resquared/gpu requires atom style ellipsoid");
// per-type shape precalculations
// require that atom shapes are identical within each type
// if shape = 0 for point particle, set shape = 1 as required by Gay-Berne
for (int i = 1; i <= atom->ntypes; i++) {
if (!atom->shape_consistency(i,shape1[i][0],shape1[i][1],shape1[i][2]))
error->all(FLERR,"Pair resquared/gpu requires atoms with same type have same shape");
if (setwell[i]) {
shape2[i][0] = shape1[i][0]*shape1[i][0];
shape2[i][1] = shape1[i][1]*shape1[i][1];
shape2[i][2] = shape1[i][2]*shape1[i][2];
lshape[i] = shape1[i][0]*shape1[i][1]*shape1[i][2];
}
}
// 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 = re_gpu_init(atom->ntypes+1, shape1, well, cutsq, sigma,
epsilon, form, lj1, lj2, lj3, lj4, offset,
force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
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;
}
quat_nmax = static_cast<int>(1.1 * (atom->nlocal + atom->nghost));
memory->grow(quat, quat_nmax, 4, "pair:quat");
}
/* ---------------------------------------------------------------------- */
double PairRESquaredGPU::memory_usage()
{
double bytes = Pair::memory_usage();
return bytes + memory->usage(quat,quat_nmax)+re_gpu_bytes();
}
/* ---------------------------------------------------------------------- */
void PairRESquaredGPU::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 evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
double fforce[3],ttor[3],rtor[3],r12[3];
int *jlist;
RE2Vars wi,wj;
double **x = atom->x;
double **f = atom->f;
double **tor = atom->torque;
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];
itype = type[i];
// not a LJ sphere
if (lshape[itype] != 0.0) precompute_i(i,wi);
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
// r12 = center to center vector
r12[0] = x[j][0]-x[i][0];
r12[1] = x[j][1]-x[i][1];
r12[2] = x[j][2]-x[i][2];
rsq = MathExtra::dot3(r12,r12);
jtype = type[j];
// compute if less than cutoff
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag) one_eng =
r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
break;
case SPHERE_ELLIPSE:
precompute_i(j,wj);
one_eng = resquared_lj(j,i,wj,r12,rsq,fforce,rtor,false);
break;
case ELLIPSE_SPHERE:
one_eng = resquared_lj(i,j,wi,r12,rsq,fforce,ttor,true);
tor[i][0] += ttor[0]*factor_lj;
tor[i][1] += ttor[1]*factor_lj;
tor[i][2] += ttor[2]*factor_lj;
break;
default:
precompute_i(j,wj);
one_eng = resquared_analytic(i,j,wi,wj,r12,rsq,fforce,ttor,rtor);
tor[i][0] += ttor[0]*factor_lj;
tor[i][1] += ttor[1]*factor_lj;
tor[i][2] += ttor[2]*factor_lj;
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
f[i][0] += fforce[0];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
if (eflag) evdwl = factor_lj*one_eng;
if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],
fforce[2],-r12[0],-r12[1],-r12[2]);
}
}
}
}
Event Timeline
Log In to Comment