343 lines
12 KiB
C++
343 lines
12 KiB
C++
/* ----------------------------------------------------------------------
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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 authors: Trung Dac Nguyen (ORNL)
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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_table_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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#define LOOKUP 0
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#define LINEAR 1
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#define SPLINE 2
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#define BITMAP 3
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// External functions from cuda library for atom decomposition
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int table_gpu_init(const int ntypes, double **cutsq,
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double ***host_table_coeffs, double **host_table_data,
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double *special_lj, 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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int tabstyle, int ntables, int tablength);
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void table_gpu_clear();
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int ** table_gpu_compute_n(const int ago, const int inum, const int nall,
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double **host_x, int *host_type, double *sublo,
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double *subhi, int *tag, int **nspecial,
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int **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);
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void table_gpu_compute(const int ago, const int inum, const int nall,
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double **host_x, int *host_type, int *ilist, int *numj,
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int **firstneigh, const bool eflag, const bool vflag,
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const bool eatom, const bool vatom, int &host_start,
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const double cpu_time, bool &success);
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double table_gpu_bytes();
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp),
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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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PairTableGPU::~PairTableGPU()
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{
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table_gpu_clear();
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}
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/* ---------------------------------------------------------------------- */
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void PairTableGPU::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 = table_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);
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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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table_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);
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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 PairTableGPU::init_style()
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{
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if (force->newton_pair)
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error->all(FLERR,"Cannot use newton pair with table/gpu pair style");
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int ntypes = atom->ntypes;
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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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// pack tables and send them to device
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double ***table_coeffs = NULL;
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double **table_data = NULL;
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memory->create(table_coeffs, ntypes+1, ntypes+1, 6, "table:coeffs");
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Table *tb;
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = 1; j <= atom->ntypes; j++) {
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int n = tabindex[i][j];
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tb = &tables[n];
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table_coeffs[i][j][0] = n;
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table_coeffs[i][j][1] = tb->nshiftbits;
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table_coeffs[i][j][2] = tb->nmask;
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table_coeffs[i][j][3] = tb->innersq;
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table_coeffs[i][j][4] = tb->invdelta;
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table_coeffs[i][j][5] = tb->deltasq6;
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}
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if (tabstyle != BITMAP) {
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memory->create(table_data, ntables, 6*tablength, "table:data");
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for (int n = 0; n < ntables; n++) {
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tb = &tables[n];
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if (tabstyle == LOOKUP) {
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for (int k = 0; k<tablength-1; k++) {
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table_data[n][6*k+1] = tb->e[k];
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table_data[n][6*k+2] = tb->f[k];
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}
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} else if (tabstyle == LINEAR) {
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for (int k = 0; k<tablength; k++) {
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table_data[n][6*k+0] = tb->rsq[k];
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table_data[n][6*k+1] = tb->e[k];
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table_data[n][6*k+2] = tb->f[k];
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if (k<tablength-1) {
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table_data[n][6*k+3] = tb->de[k];
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table_data[n][6*k+4] = tb->df[k];
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}
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}
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} else if (tabstyle == SPLINE) {
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for (int k = 0; k<tablength; k++) {
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table_data[n][6*k+0] = tb->rsq[k];
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table_data[n][6*k+1] = tb->e[k];
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table_data[n][6*k+2] = tb->f[k];
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table_data[n][6*k+3] = tb->e2[k];
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table_data[n][6*k+4] = tb->f2[k];
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}
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}
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}
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} else {
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int ntable = 1 << tablength;
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memory->create(table_data, ntables, 6*ntable, "table:data");
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for (int n = 0; n < ntables; n++) {
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tb = &tables[n];
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for (int k = 0; k<ntable; k++) {
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table_data[n][6*k+0] = tb->rsq[k];
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table_data[n][6*k+1] = tb->e[k];
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table_data[n][6*k+2] = tb->f[k];
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table_data[n][6*k+3] = tb->de[k];
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table_data[n][6*k+4] = tb->df[k];
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table_data[n][6*k+5] = tb->drsq[k];
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}
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}
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}
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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 = table_gpu_init(atom->ntypes+1, cutsq, table_coeffs, table_data,
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force->special_lj, atom->nlocal,
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atom->nlocal+atom->nghost, 300, maxspecial,
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cell_size, gpu_mode, screen, tabstyle, ntables,
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tablength);
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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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memory->destroy(table_coeffs);
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memory->destroy(table_data);
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}
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/* ---------------------------------------------------------------------- */
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double PairTableGPU::memory_usage()
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{
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double bytes = Pair::memory_usage();
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return bytes + table_gpu_bytes();
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}
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/* ---------------------------------------------------------------------- */
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void PairTableGPU::cpu_compute(int start, int inum, int eflag, int vflag,
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int *ilist, int *numneigh, int **firstneigh) {
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int i,j,ii,jj,jnum,itype,jtype,itable;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,factor_lj,fraction,value,a,b;
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int *jlist;
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Table *tb;
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union_int_float_t rsq_lookup;
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int tlm1 = tablength - 1;
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double **x = atom->x;
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double **f = atom->f;
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int *type = atom->type;
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double *special_lj = force->special_lj;
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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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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_lj = special_lj[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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tb = &tables[tabindex[itype][jtype]];
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if (rsq < tb->innersq)
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error->one(FLERR,"Pair distance < table inner cutoff");
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if (tabstyle == LOOKUP) {
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itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
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if (itable >= tlm1)
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error->one(FLERR,"Pair distance > table outer cutoff");
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fpair = factor_lj * tb->f[itable];
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} else if (tabstyle == LINEAR) {
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itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
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if (itable >= tlm1)
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error->one(FLERR,"Pair distance > table outer cutoff");
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fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
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value = tb->f[itable] + fraction*tb->df[itable];
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fpair = factor_lj * value;
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} else if (tabstyle == SPLINE) {
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itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
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if (itable >= tlm1)
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error->one(FLERR,"Pair distance > table outer cutoff");
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b = (rsq - tb->rsq[itable]) * tb->invdelta;
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a = 1.0 - b;
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value = a * tb->f[itable] + b * tb->f[itable+1] +
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((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
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tb->deltasq6;
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fpair = factor_lj * value;
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} else {
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rsq_lookup.f = rsq;
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itable = rsq_lookup.i & tb->nmask;
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itable >>= tb->nshiftbits;
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fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
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value = tb->f[itable] + fraction*tb->df[itable];
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fpair = factor_lj * value;
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}
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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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if (tabstyle == LOOKUP)
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evdwl = tb->e[itable];
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else if (tabstyle == LINEAR || tabstyle == BITMAP)
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evdwl = tb->e[itable] + fraction*tb->de[itable];
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else
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evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
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((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
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tb->deltasq6;
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evdwl *= factor_lj;
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}
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if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
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}
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}
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}
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}
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