279 lines
10 KiB
C++
279 lines
10 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, 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: Mike Brown (SNL)
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------------------------------------------------------------------------- */
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#include "pair_lj_charmm_coul_charmm_gpu.h"
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#include "atom.h"
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#include "domain.h"
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#include "error.h"
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#include "force.h"
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#include "gpu_extra.h"
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#include "neigh_list.h"
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#include "neighbor.h"
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#include <cmath>
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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 crm_gpu_init(const int ntypes, double cut_bothsq, double **host_lj1, double **host_lj2,
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double **host_lj3, double **host_lj4, double *special_lj, const int nlocal,
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const int nall, const int max_nbors, const int maxspecial, const double cell_size,
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int &gpu_mode, FILE *screen, double host_cut_ljsq, double host_cut_coulsq,
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double *host_special_coul, const double qqrd2e, const double cut_lj_innersq,
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const double cut_coul_innersq, const double denom_lj, const double denom_coul,
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double **epsilon, double **sigma, const bool mix_arithmetic);
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void crm_gpu_clear();
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int **crm_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x,
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int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial,
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tagint **special, const bool eflag, const bool vflag, const bool eatom,
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const bool vatom, int &host_start, int **ilist, int **jnum,
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const double cpu_time, bool &success, double *host_q, double *boxlo,
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double *prd);
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void crm_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type,
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int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag,
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const bool eatom, const bool vatom, int &host_start, const double cpu_time,
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bool &success, double *host_q, const int nlocal, double *boxlo, double *prd);
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double crm_gpu_bytes();
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/* ---------------------------------------------------------------------- */
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PairLJCharmmCoulCharmmGPU::PairLJCharmmCoulCharmmGPU(LAMMPS *lmp) :
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PairLJCharmmCoulCharmm(lmp), gpu_mode(GPU_FORCE)
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{
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reinitflag = 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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PairLJCharmmCoulCharmmGPU::~PairLJCharmmCoulCharmmGPU()
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{
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crm_gpu_clear();
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCharmmCoulCharmmGPU::compute(int eflag, int vflag)
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{
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if (eflag || vflag)
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ev_setup(eflag, vflag);
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else
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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 = crm_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, domain->sublo,
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domain->subhi, atom->tag, atom->nspecial, atom->special, eflag,
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vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
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cpu_time, success, atom->q, domain->boxlo, 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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crm_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
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eflag, vflag, eflag_atom, 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) error->one(FLERR, "Insufficient memory on accelerator");
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if (host_start < inum) {
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cpu_time = platform::walltime();
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cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
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cpu_time = platform::walltime() - 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 PairLJCharmmCoulCharmmGPU::init_style()
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{
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if (!atom->q_flag)
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error->all(FLERR, "Pair style lj/charmm/coul/long/gpu requires atom attribute q");
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// Repeated cutsq calculation in init_one() is required for GPU package
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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)) init_one(i, j);
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}
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}
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cut_lj_innersq = cut_lj_inner * cut_lj_inner;
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cut_coul_innersq = cut_coul_inner * cut_coul_inner;
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cut_ljsq = cut_lj * cut_lj;
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cut_coulsq = cut_coul * cut_coul;
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cut_bothsq = MAX(cut_ljsq, cut_coulsq);
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denom_lj =
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(cut_ljsq - cut_lj_innersq) * (cut_ljsq - cut_lj_innersq) * (cut_ljsq - cut_lj_innersq);
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denom_lj = 1.0 / denom_lj;
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denom_coul = (cut_coulsq - cut_coul_innersq) * (cut_coulsq - cut_coul_innersq) *
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(cut_coulsq - cut_coul_innersq);
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denom_coul = 1.0 / denom_coul;
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double cell_size = sqrt(cut_bothsq) + neighbor->skin;
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int maxspecial = 0;
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if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
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bool arithmetic = true;
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for (int i = 1; i < atom->ntypes + 1; i++)
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for (int j = i + 1; j < atom->ntypes + 1; j++) {
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if (epsilon[i][j] != sqrt(epsilon[i][i] * epsilon[j][j])) arithmetic = false;
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if (sigma[i][j] != 0.5 * (sigma[i][i] + sigma[j][j])) arithmetic = false;
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}
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int mnf = 5e-2 * neighbor->oneatom;
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int success =
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crm_gpu_init(atom->ntypes + 1, cut_bothsq, lj1, lj2, lj3, lj4, force->special_lj,
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atom->nlocal, atom->nlocal + atom->nghost, mnf, maxspecial, cell_size, gpu_mode,
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screen, cut_ljsq, cut_coulsq, force->special_coul, force->qqrd2e, cut_lj_innersq,
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cut_coul_innersq, denom_lj, denom_coul, epsilon, sigma, arithmetic);
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GPU_EXTRA::check_flag(success, error, world);
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if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
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}
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/* ---------------------------------------------------------------------- */
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double PairLJCharmmCoulCharmmGPU::memory_usage()
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{
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double bytes = Pair::memory_usage();
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return bytes + crm_gpu_bytes();
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCharmmCoulCharmmGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
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int *ilist, int *numneigh, 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, evdwl, ecoul, fpair;
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double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj;
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double philj, switch1, switch2;
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int *jlist;
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evdwl = 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 *special_lj = force->special_lj;
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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_lj = special_lj[sbmask(j)];
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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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if (rsq < cut_bothsq) {
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r2inv = 1.0 / rsq;
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if (rsq < cut_coulsq) {
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forcecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv);
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if (rsq > cut_coul_innersq) {
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switch1 = (cut_coulsq - rsq) * (cut_coulsq - rsq) *
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(cut_coulsq + 2.0 * rsq - 3.0 * cut_coul_innersq) * denom_coul;
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forcecoul *= switch1;
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}
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} else
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forcecoul = 0.0;
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if (rsq < cut_ljsq) {
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r6inv = r2inv * r2inv * r2inv;
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jtype = type[j];
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forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
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if (rsq > cut_lj_innersq) {
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switch1 = (cut_ljsq - rsq) * (cut_ljsq - rsq) *
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(cut_ljsq + 2.0 * rsq - 3.0 * cut_lj_innersq) * denom_lj;
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switch2 = 12.0 * rsq * (cut_ljsq - rsq) * (rsq - cut_lj_innersq) * denom_lj;
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philj = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]);
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forcelj = forcelj * switch1 + philj * switch2;
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}
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} else
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forcelj = 0.0;
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fpair = (factor_coul * forcecoul + factor_lj * forcelj) * 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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if (rsq < cut_coulsq) {
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ecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv);
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if (rsq > cut_coul_innersq) {
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switch1 = (cut_coulsq - rsq) * (cut_coulsq - rsq) *
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(cut_coulsq + 2.0 * rsq - 3.0 * cut_coul_innersq) * denom_coul;
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ecoul *= switch1;
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}
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ecoul *= factor_coul;
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} else
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ecoul = 0.0;
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if (rsq < cut_ljsq) {
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evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]);
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if (rsq > cut_lj_innersq) {
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switch1 = (cut_ljsq - rsq) * (cut_ljsq - rsq) *
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(cut_ljsq + 2.0 * rsq - 3.0 * cut_lj_innersq) * denom_lj;
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evdwl *= switch1;
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}
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evdwl *= factor_lj;
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} else
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evdwl = 0.0;
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}
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if (evflag) ev_tally_full(i, evdwl, 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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