305 lines
11 KiB
C++
305 lines
11 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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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 "neigh_request.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,
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double **host_lj2, double **host_lj3, double **host_lj4,
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double *special_lj, 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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double host_cut_ljsq, double host_cut_coulsq,
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double *host_special_coul, const double qqrd2e,
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const double cut_lj_innersq, const double cut_coul_innersq,
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const double denom_lj, const double denom_coul,
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double **epsilon, double **sigma,
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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,
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const int nall, double **host_x, int *host_type,
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double *sublo, double *subhi, tagint *tag,
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int **nspecial, tagint **special, const bool eflag,
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const bool vflag, const bool eatom,
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const bool vatom, int &host_start, int **ilist,
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int **jnum, const double cpu_time, bool &success,
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double *host_q, double *boxlo, double *prd);
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void crm_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, double *host_q,
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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) 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 = crm_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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crm_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 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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/*
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if (force->newton_pair)
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error->all(FLERR, "Pair style lj/charmm/coul/long/gpu requires newton pair off");
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*/
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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))
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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 = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
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(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)
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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]))
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arithmetic = false;
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if (sigma[i][j] != 0.5 * (sigma[i][i] + sigma[j][j]))
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arithmetic = false;
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}
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int mnf = 5e-2 * neighbor->oneatom;
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int success = crm_gpu_init(atom->ntypes+1, cut_bothsq, lj1, lj2, lj3, lj4,
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force->special_lj, atom->nlocal,
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atom->nlocal+atom->nghost, mnf, maxspecial,
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cell_size, gpu_mode, screen, cut_ljsq,
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cut_coulsq, force->special_coul, force->qqrd2e,
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cut_lj_innersq,cut_coul_innersq,denom_lj,
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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) {
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int irequest = neighbor->request(this,instance_me);
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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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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,
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int /* vflag */, int *ilist,
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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 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) *
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(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 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) *
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denom_coul;
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ecoul *= switch1;
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}
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ecoul *= factor_coul;
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} else 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 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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