forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12148 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
8a9e1676eb
commit
b9531f508f
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@ -0,0 +1,247 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Trung Dac Nguyen
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "pair_coul_cut_gpu.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "integrate.h"
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#include "memory.h"
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#include "error.h"
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#include "neigh_request.h"
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#include "universe.h"
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#include "update.h"
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#include "domain.h"
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#include "string.h"
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#include "gpu_extra.h"
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using namespace LAMMPS_NS;
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// External functions from cuda library for atom decomposition
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int coul_gpu_init(const int ntypes, double **host_scale, double **cutsq,
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double *special_coul, const int nlocal,
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const int nall, const int max_nbors, const int maxspecial,
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const double cell_size, int &gpu_mode, FILE *screen,
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const double qqrd2e);
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void coul_gpu_reinit(const int ntypes, double **host_scale);
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void coul_gpu_clear();
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int ** coul_gpu_compute_n(const int ago, const int inum,
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const int nall, double **host_x, int *host_type,
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double *sublo, double *subhi, tagint *tag, int **nspecial,
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tagint **special, const bool eflag, const bool vflag,
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const bool eatom, const bool vatom, int &host_start,
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int **ilist, int **jnum, const double cpu_time,
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bool &success, double *host_q, double *boxlo,
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double *prd);
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void coul_gpu_compute(const int ago, const int inum,
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const int nall, double **host_x, int *host_type,
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int *ilist, int *numj, int **firstneigh,
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const bool eflag, const bool vflag, const bool eatom,
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const bool vatom, int &host_start, const double cpu_time,
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bool &success, double *host_q, const int nlocal,
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double *boxlo, double *prd);
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double coul_gpu_bytes();
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/* ---------------------------------------------------------------------- */
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PairCoulCutGPU::PairCoulCutGPU(LAMMPS *lmp) : PairCoulCut(lmp), gpu_mode(GPU_FORCE)
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{
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respa_enable = 0;
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cpu_time = 0.0;
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GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
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}
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/* ----------------------------------------------------------------------
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free all arrays
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------------------------------------------------------------------------- */
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PairCoulCutGPU::~PairCoulCutGPU()
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{
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coul_gpu_clear();
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}
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/* ---------------------------------------------------------------------- */
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void PairCoulCutGPU::compute(int eflag, int vflag)
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{
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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int nall = atom->nlocal + atom->nghost;
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int inum, host_start;
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bool success = true;
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int *ilist, *numneigh, **firstneigh;
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if (gpu_mode != GPU_FORCE) {
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inum = atom->nlocal;
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firstneigh = coul_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
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atom->type, domain->sublo, domain->subhi,
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atom->tag, atom->nspecial, atom->special,
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eflag, vflag, eflag_atom, vflag_atom,
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host_start, &ilist, &numneigh, cpu_time,
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success, atom->q, domain->boxlo,
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domain->prd);
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} else {
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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coul_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
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ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
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vflag_atom, host_start, cpu_time, success, atom->q,
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atom->nlocal, domain->boxlo, domain->prd);
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}
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if (!success)
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error->one(FLERR,"Insufficient memory on accelerator");
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if (host_start<inum) {
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cpu_time = MPI_Wtime();
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cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
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cpu_time = MPI_Wtime() - cpu_time;
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}
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairCoulCutGPU::init_style()
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{
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if (!atom->q_flag)
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error->all(FLERR,"Pair style coul/cut/gpu requires atom attribute q");
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if (force->newton_pair)
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error->all(FLERR,"Cannot use newton pair with coul/cut/gpu pair style");
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// Repeat cutsq calculation because done after call to init_style
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double maxcut = -1.0;
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double cut;
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for (int i = 1; i <= atom->ntypes; i++) {
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for (int j = i; j <= atom->ntypes; j++) {
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if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
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cut = init_one(i,j);
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cut *= cut;
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if (cut > maxcut)
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maxcut = cut;
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cutsq[i][j] = cutsq[j][i] = cut;
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} else
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cutsq[i][j] = cutsq[j][i] = 0.0;
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}
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}
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double cell_size = sqrt(maxcut) + neighbor->skin;
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int maxspecial=0;
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if (atom->molecular)
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maxspecial=atom->maxspecial;
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int success = coul_gpu_init(atom->ntypes+1, scale, cutsq,
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force->special_coul, atom->nlocal,
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atom->nlocal+atom->nghost, 300, maxspecial,
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cell_size, gpu_mode, screen, force->qqrd2e);
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GPU_EXTRA::check_flag(success,error,world);
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if (gpu_mode == GPU_FORCE) {
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int irequest = neighbor->request(this);
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairCoulCutGPU::reinit()
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{
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Pair::reinit();
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coul_gpu_reinit(atom->ntypes+1, scale);
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}
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/* ---------------------------------------------------------------------- */
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double PairCoulCutGPU::memory_usage()
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{
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double bytes = Pair::memory_usage();
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return bytes + coul_gpu_bytes();
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}
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/* ---------------------------------------------------------------------- */
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void PairCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
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int *ilist, int *numneigh,
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int **firstneigh)
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{
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int i,j,ii,jj,jnum,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
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double rsq,r2inv,forcecoul,factor_coul;
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int *jlist;
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ecoul = 0.0;
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double **x = atom->x;
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double **f = atom->f;
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double *q = atom->q;
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int *type = atom->type;
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double *special_coul = force->special_coul;
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double qqrd2e = force->qqrd2e;
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// loop over neighbors of my atoms
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for (ii = start; ii < inum; ii++) {
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i = ilist[ii];
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qtmp = q[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_coul = special_coul[sbmask(j)];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r2inv = 1.0/rsq;
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forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
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fpair = factor_coul*forcecoul * r2inv;
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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if (eflag) {
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ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
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}
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if (evflag) ev_tally_full(i,0.0,ecoul,fpair,delx,dely,delz);
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}
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}
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}
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}
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@ -0,0 +1,63 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(coul/cut/gpu,PairCoulCutGPU)
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#else
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#ifndef LMP_PAIR_COUL_CUT_GPU_H
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#define LMP_PAIR_COUL_CUT_GPU_H
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#include "pair_coul_cut.h"
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namespace LAMMPS_NS {
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class PairCoulCutGPU : public PairCoulCut {
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public:
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PairCoulCutGPU(LAMMPS *lmp);
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~PairCoulCutGPU();
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void cpu_compute(int, int, int, int, int *, int *, int **);
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void compute(int, int);
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void init_style();
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void reinit();
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double memory_usage();
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enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
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private:
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int gpu_mode;
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double cpu_time;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Insufficient memory on accelerator
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There is insufficient memory on one of the devices specified for the gpu
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package
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E: Pair style lj/cut/coul/cut/gpu requires atom attribute q
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The atom style defined does not have this attribute.
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E: Cannot use newton pair with lj/cut/coul/cut/gpu pair style
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Self-explanatory.
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*/
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@ -0,0 +1,256 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
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certain rights in this software. This software is distributed under
|
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Trung Dac Nguyen (ndtrung@umich.edu)
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------------------------------------------------------------------------- */
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#include "lmptype.h"
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#include "math.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "pair_coul_debye_gpu.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "integrate.h"
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#include "memory.h"
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#include "error.h"
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#include "neigh_request.h"
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#include "universe.h"
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#include "update.h"
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#include "domain.h"
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#include "string.h"
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#include "gpu_extra.h"
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using namespace LAMMPS_NS;
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// External functions from cuda library for atom decomposition
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int cdebye_gpu_init(const int ntypes, double **host_scale, double **cutsq,
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double *special_coul, const int nlocal, const int nall,
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const int max_nbors, const int maxspecial,
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const double cell_size, int &gpu_mode, FILE *screen,
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const double qqrd2e, const double kappa);
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void cdebye_gpu_reinit(const int ntypes, double **host_scale);
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void cdebye_gpu_clear();
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int ** cdebye_gpu_compute_n(const int ago, const int inum, const int nall,
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double **host_x, int *host_type,
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double *sublo, double *subhi, tagint *tag, int **nspecial,
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tagint **special, const bool eflag, const bool vflag,
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const bool eatom, const bool vatom, int &host_start,
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int **ilist, int **jnum, const double cpu_time,
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bool &success, double *host_q, double *boxlo,
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double *prd);
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void cdebye_gpu_compute(const int ago, const int inum, const int nall,
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double **host_x, int *host_type,
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int *ilist, int *numj, int **firstneigh,
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const bool eflag, const bool vflag, const bool eatom,
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const bool vatom, int &host_start, const double cpu_time,
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bool &success, double *host_q, const int nlocal,
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double *boxlo, double *prd);
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double cdebye_gpu_bytes();
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/* ---------------------------------------------------------------------- */
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PairCoulDebyeGPU::PairCoulDebyeGPU(LAMMPS *lmp) :
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PairCoulDebye(lmp), gpu_mode(GPU_FORCE)
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{
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respa_enable = 0;
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cpu_time = 0.0;
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GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
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}
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/* ----------------------------------------------------------------------
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free all arrays
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------------------------------------------------------------------------- */
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PairCoulDebyeGPU::~PairCoulDebyeGPU()
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{
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cdebye_gpu_clear();
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}
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/* ---------------------------------------------------------------------- */
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void PairCoulDebyeGPU::compute(int eflag, int vflag)
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{
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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int nall = atom->nlocal + atom->nghost;
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int inum, host_start;
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bool success = true;
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int *ilist, *numneigh, **firstneigh;
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if (gpu_mode != GPU_FORCE) {
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inum = atom->nlocal;
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firstneigh = cdebye_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
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atom->type, domain->sublo, domain->subhi,
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atom->tag, atom->nspecial, atom->special,
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eflag, vflag, eflag_atom, vflag_atom,
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host_start, &ilist, &numneigh, cpu_time,
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success, atom->q, domain->boxlo,
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domain->prd);
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} else {
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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cdebye_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
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ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
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vflag_atom, host_start, cpu_time, success, atom->q,
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atom->nlocal, domain->boxlo, domain->prd);
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}
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if (!success)
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error->one(FLERR,"Insufficient memory on accelerator");
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if (host_start<inum) {
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cpu_time = MPI_Wtime();
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cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
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cpu_time = MPI_Wtime() - cpu_time;
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}
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
|
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void PairCoulDebyeGPU::init_style()
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{
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if (!atom->q_flag)
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error->all(FLERR,"Pair style coul/debye/gpu requires atom attribute q");
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|
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if (force->newton_pair)
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error->all(FLERR,"Cannot use newton pair with coul/debye/gpu pair style");
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|
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// Repeat cutsq calculation because done after call to init_style
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double maxcut = -1.0;
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double cut;
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for (int i = 1; i <= atom->ntypes; i++) {
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for (int j = i; j <= atom->ntypes; j++) {
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if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
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cut = init_one(i,j);
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cut *= cut;
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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 = cdebye_gpu_init(atom->ntypes+1, scale, cutsq,
|
||||
force->special_coul, atom->nlocal,
|
||||
atom->nlocal+atom->nghost, 300, maxspecial,
|
||||
cell_size, gpu_mode, screen,
|
||||
force->qqrd2e, kappa);
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulDebyeGPU::reinit()
|
||||
{
|
||||
Pair::reinit();
|
||||
|
||||
cdebye_gpu_reinit(atom->ntypes+1, scale);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairCoulDebyeGPU::memory_usage()
|
||||
{
|
||||
double bytes = Pair::memory_usage();
|
||||
return bytes + cdebye_gpu_bytes();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulDebyeGPU::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 qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
|
||||
double rsq,r2inv,forcecoul,factor_coul;
|
||||
double r,rinv,screening;
|
||||
int *jlist;
|
||||
|
||||
ecoul = 0.0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
double *special_coul = force->special_coul;
|
||||
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_coul = special_coul[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]) {
|
||||
r2inv = 1.0/rsq;
|
||||
r = sqrt(rsq);
|
||||
rinv = 1.0/r;
|
||||
screening = exp(-kappa*r);
|
||||
forcecoul = qqrd2e * scale[itype][jtype] *
|
||||
qtmp*q[j] * screening * (kappa + rinv);
|
||||
fpair = factor_coul*forcecoul * r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
|
||||
if (eflag) {
|
||||
ecoul = factor_coul * qqrd2e * scale[itype][jtype] *
|
||||
qtmp*q[j] * rinv * screening;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally_full(i,0.0,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,63 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(coul/debye/gpu,PairCoulDebyeGPU)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_COUL_DEBYE_GPU_H
|
||||
#define LMP_PAIR_COUL_DEBYE_GPU_H
|
||||
|
||||
#include "pair_coul_debye.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairCoulDebyeGPU : public PairCoulDebye {
|
||||
public:
|
||||
PairCoulDebyeGPU(LAMMPS *lmp);
|
||||
~PairCoulDebyeGPU();
|
||||
void cpu_compute(int, int, int, int, int *, int *, int **);
|
||||
void compute(int, int);
|
||||
void init_style();
|
||||
void reinit();
|
||||
double memory_usage();
|
||||
|
||||
enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
|
||||
|
||||
private:
|
||||
int gpu_mode;
|
||||
double cpu_time;
|
||||
};
|
||||
|
||||
}
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Insufficient memory on accelerator
|
||||
|
||||
There is insufficient memory on one of the devices specified for the gpu
|
||||
package
|
||||
|
||||
E: Pair style lj/cut/coul/debye/gpu requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
E: Cannot use newton pair with lj/cut/coul/debye/gpu pair style
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue