340 lines
12 KiB
C++
340 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 author: Trung Dac Nguyen (Northwestern)
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------------------------------------------------------------------------- */
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#include <cmath>
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#include <cstdio>
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#include <cstdlib>
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#include <cstring>
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#include "pair_born_coul_long_cs_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 "math_const.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 "kspace.h"
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#include "gpu_extra.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define EWALD_F 1.12837917
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#define EWALD_P 9.95473818e-1
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#define B0 -0.1335096380159268
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#define B1 -2.57839507e-1
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#define B2 -1.37203639e-1
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#define B3 -8.88822059e-3
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#define B4 -5.80844129e-3
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#define B5 1.14652755e-1
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#define EPSILON 1.0e-20
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#define EPS_EWALD 1.0e-6
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#define EPS_EWALD_SQR 1.0e-12
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// External functions from cuda library for atom decomposition
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int bornclcs_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
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double **host_born1, double **host_born2,
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double **host_born3, double **host_a,
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double **host_c, double **host_d,
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double **sigma, double **offset, double *special_lj,
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const int inum, const int nall, const int max_nbors,
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const int maxspecial, const double cell_size,
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int &gpu_mode, FILE *screen, double **host_cut_ljsq,
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double host_cut_coulsq, double *host_special_coul,
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const double qqrd2e, const double g_ewald);
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void bornclcs_gpu_clear();
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int** bornclcs_gpu_compute_n(const int ago, const int inum_full, const int nall,
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double **host_x, int *host_type, double *sublo,
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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 bornclcs_gpu_compute(const int ago, const int inum_full, 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 bornclcs_gpu_bytes();
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/* ---------------------------------------------------------------------- */
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PairBornCoulLongCSGPU::PairBornCoulLongCSGPU(LAMMPS *lmp) :
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PairBornCoulLongCS(lmp), gpu_mode(GPU_FORCE)
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{
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respa_enable = 0;
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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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PairBornCoulLongCSGPU::~PairBornCoulLongCSGPU()
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{
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bornclcs_gpu_clear();
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}
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/* ---------------------------------------------------------------------- */
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void PairBornCoulLongCSGPU::compute(int eflag, int vflag)
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{
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ev_init(eflag,vflag);
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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 = bornclcs_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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bornclcs_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 PairBornCoulLongCSGPU::init_style()
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{
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if (!atom->q_flag)
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error->all(FLERR,
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"Pair style born/coul/long/cs/gpu requires atom attribute q");
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if (force->newton_pair)
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error->all(FLERR,
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"Cannot use newton pair with born/coul/long/cs/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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cut_coulsq = cut_coul * cut_coul;
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// insure use of KSpace long-range solver, set g_ewald
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if (force->kspace == NULL)
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error->all(FLERR,"Pair style requires a KSpace style");
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g_ewald = force->kspace->g_ewald;
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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 = bornclcs_gpu_init(atom->ntypes+1, cutsq, rhoinv,
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born1, born2, born3, a, c, d, sigma,
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offset, force->special_lj, atom->nlocal,
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atom->nlocal+atom->nghost, 300, maxspecial,
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cell_size, gpu_mode, screen, cut_ljsq,
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cut_coulsq, force->special_coul,
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force->qqrd2e, g_ewald);
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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 PairBornCoulLongCSGPU::memory_usage()
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{
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double bytes = Pair::memory_usage();
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return bytes + bornclcs_gpu_bytes();
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}
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/* ---------------------------------------------------------------------- */
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void PairBornCoulLongCSGPU::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,itable,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
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double fraction,table;
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double r,rsq,rexp,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
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double grij,expm2,prefactor,t,erfc,u;
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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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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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if (rsq < cut_coulsq) {
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rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
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r2inv = 1.0/rsq;
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if (!ncoultablebits || rsq <= tabinnersq) {
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r = sqrt(rsq);
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prefactor = qqrd2e * qtmp*q[j];
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if (factor_coul < 1.0) {
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// When bonded parts are being calculated a minimal distance (EPS_EWALD)
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// has to be added to the prefactor and erfc in order to make the
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// used approximation functions for the Ewald correction valid
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grij = g_ewald * (r+EPS_EWALD);
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expm2 = exp(-grij*grij);
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t = 1.0 / (1.0 + EWALD_P*grij);
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u = 1.0 - t;
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erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
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prefactor /= (r+EPS_EWALD);
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forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - (1.0-factor_coul));
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// Additionally r2inv needs to be accordingly modified since the later
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// scaling of the overall force shall be consistent
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r2inv = 1.0/(rsq + EPS_EWALD_SQR);
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} else {
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grij = g_ewald * r;
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expm2 = exp(-grij*grij);
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t = 1.0 / (1.0 + EWALD_P*grij);
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u = 1.0 - t;
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erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
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prefactor /= r;
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forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
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}
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} else {
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union_int_float_t rsq_lookup;
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rsq_lookup.f = rsq;
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itable = rsq_lookup.i & ncoulmask;
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itable >>= ncoulshiftbits;
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fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
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table = ftable[itable] + fraction*dftable[itable];
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forcecoul = qtmp*q[j] * table;
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if (factor_coul < 1.0) {
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table = ctable[itable] + fraction*dctable[itable];
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prefactor = qtmp*q[j] * table;
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forcecoul -= (1.0-factor_coul)*prefactor;
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}
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}
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forcecoul *= r2inv;
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} else forcecoul = 0;
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r2inv = 1.0/rsq;
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r = sqrt(rsq);
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if (rsq < cut_ljsq[itype][jtype]) {
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r6inv = r2inv*r2inv*r2inv;
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rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
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forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
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+ born3[itype][jtype]*r2inv*r6inv;
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} else forceborn = 0.0;
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fpair = forcecoul + factor_lj*forceborn * 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 = prefactor*erfc;
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if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
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} else ecoul = 0.0;
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if (rsq < cut_ljsq[itype][jtype]) {
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evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
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+ d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
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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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