lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

/* ----------------------------------------------------------------------
   Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */

#include "pair_lj_charmm_coul_long_gpu.h"
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "integrate.h"
#include "memory.h"
#include "error.h"
#include "neigh_request.h"
#include "universe.h"
#include "update.h"
#include "domain.h"
#include "kspace.h"
#include "gpu_extra.h"

#define EWALD_F   1.12837917
#define EWALD_P   0.3275911
#define A1        0.254829592
#define A2       -0.284496736
#define A3        1.421413741
#define A4       -1.453152027
#define A5        1.061405429

using namespace LAMMPS_NS;

// External functions from cuda library for atom decomposition

int crml_gpu_init(const int ntypes, double cut_bothsq, double **host_lj1,
                  double **host_lj2, double **host_lj3, double **host_lj4,
                  double **offset, double *special_lj, const int nlocal,
                  const int nall, const int max_nbors, const int maxspecial,
                  const double cell_size, int &gpu_mode, FILE *screen,
                  double host_cut_ljsq, double host_cut_coulsq,
                  double *host_special_coul, const double qqrd2e,
                  const double g_ewald, const double cut_lj_innersq,
                  const double denom_lj, double **epsilon, double **sigma,
                  const bool mix_arithmetic);
void crml_gpu_clear();
int ** crml_gpu_compute_n(const int ago, const int inum,
                          const int nall, double **host_x, int *host_type,
                          double *sublo, double *subhi, tagint *tag,
                          int **nspecial, tagint **special, const bool eflag,
                          const bool vflag, const bool eatom, const bool vatom,
                          int &host_start, int **ilist, int **jnum,
                          const double cpu_time, bool &success, double *host_q,
                          double *boxlo, double *prd);
void crml_gpu_compute(const int ago, const int inum, const int nall,
                      double **host_x, int *host_type, int *ilist, int *numj,
                      int **firstneigh, const bool eflag, const bool vflag,
                      const bool eatom, const bool vatom, int &host_start,
                      const double cpu_time, bool &success, double *host_q,
                      const int nlocal, double *boxlo, double *prd);
double crml_gpu_bytes();

/* ---------------------------------------------------------------------- */

PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
  PairLJCharmmCoulLong(lmp), gpu_mode(GPU_FORCE)
{
  respa_enable = 0;
  reinitflag = 0;
  cpu_time = 0.0;
  GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}

/* ----------------------------------------------------------------------
   free all arrays
------------------------------------------------------------------------- */

PairLJCharmmCoulLongGPU::~PairLJCharmmCoulLongGPU()
{
  crml_gpu_clear();
}

/* ---------------------------------------------------------------------- */

void PairLJCharmmCoulLongGPU::compute(int eflag, int vflag)
{
  ev_init(eflag,vflag);

  int nall = atom->nlocal + atom->nghost;
  int inum, host_start;

  bool success = true;
  int *ilist, *numneigh, **firstneigh;
  if (gpu_mode != GPU_FORCE) {
    inum = atom->nlocal;
    firstneigh = crml_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
                                    atom->type, domain->sublo, domain->subhi,
                                    atom->tag, atom->nspecial, atom->special,
                                    eflag, vflag, eflag_atom, vflag_atom,
                                    host_start, &ilist, &numneigh, cpu_time,
                                    success, atom->q, domain->boxlo,
                                    domain->prd);
  } else {
    inum = list->inum;
    ilist = list->ilist;
    numneigh = list->numneigh;
    firstneigh = list->firstneigh;
    crml_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
                     ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
                     vflag_atom, host_start, cpu_time, success, atom->q,
                     atom->nlocal, domain->boxlo, domain->prd);
  }
  if (!success)
    error->one(FLERR,"Insufficient memory on accelerator");

  if (host_start<inum) {
    cpu_time = MPI_Wtime();
    cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
    cpu_time = MPI_Wtime() - cpu_time;
  }
}

/* ----------------------------------------------------------------------
   init specific to this pair style
------------------------------------------------------------------------- */

void PairLJCharmmCoulLongGPU::init_style()
{
  cut_respa = NULL;

  if (!atom->q_flag)
    error->all(FLERR,"Pair style lj/charmm/coul/long/gpu requires atom attribute q");
  if (force->newton_pair)
    error->all(FLERR,"Cannot use newton pair with lj/charmm/coul/long/gpu pair style");

  // Repeat cutsq calculation because done after call to init_style

  for (int i = 1; i <= atom->ntypes; i++) {
    for (int j = i; j <= atom->ntypes; j++) {
      if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0))
        init_one(i,j);
    }
  }

  cut_lj_innersq = cut_lj_inner * cut_lj_inner;
  cut_ljsq = cut_lj * cut_lj;
  cut_coulsq = cut_coul * cut_coul;
  cut_bothsq = MAX(cut_ljsq,cut_coulsq);

  denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
    (cut_ljsq-cut_lj_innersq);

  double cell_size = sqrt(cut_bothsq) + neighbor->skin;

  // insure use of KSpace long-range solver, set g_ewald

  if (force->kspace == NULL)
    error->all(FLERR,"Pair style requires a KSpace style");
  g_ewald = force->kspace->g_ewald;

  // setup force tables

  if (ncoultablebits) init_tables(cut_coul,cut_respa);

  int maxspecial=0;
  if (atom->molecular)
    maxspecial=atom->maxspecial;

  bool arithmetic = true;
  for (int i = 1; i < atom->ntypes + 1; i++)
    for (int j = i + 1; j < atom->ntypes + 1; j++) {
      if (epsilon[i][j] != sqrt(epsilon[i][i] * epsilon[j][j]))
        arithmetic = false;
      if (sigma[i][j] != 0.5 * (sigma[i][i] + sigma[j][j]))
        arithmetic = false;
    }

  int success = crml_gpu_init(atom->ntypes+1, cut_bothsq, lj1, lj2, lj3, lj4,
                              offset, force->special_lj, atom->nlocal,
                              atom->nlocal+atom->nghost, 300, maxspecial,
                              cell_size, gpu_mode, screen, cut_ljsq,
                              cut_coulsq, force->special_coul, force->qqrd2e,
                              g_ewald, cut_lj_innersq,denom_lj,epsilon,sigma,
                              arithmetic);
  GPU_EXTRA::check_flag(success,error,world);

  if (gpu_mode == GPU_FORCE) {
    int irequest = neighbor->request(this,instance_me);
    neighbor->requests[irequest]->half = 0;
    neighbor->requests[irequest]->full = 1;
  }
}

/* ---------------------------------------------------------------------- */

double PairLJCharmmCoulLongGPU::memory_usage()
{
  double bytes = Pair::memory_usage();
  return bytes + crml_gpu_bytes();
}

/* ---------------------------------------------------------------------- */

void PairLJCharmmCoulLongGPU::cpu_compute(int start, int inum, int eflag,
                                          int /* vflag */, int *ilist,
                                          int *numneigh, int **firstneigh)
{
  int i,j,ii,jj,jnum,itype,jtype,itable;
  double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
  double fraction,table;
  double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
  double grij,expm2,prefactor,t,erfc;
  double philj,switch1,switch2;
  int *jlist;
  double rsq;

  evdwl = ecoul = 0.0;

  double **x = atom->x;
  double **f = atom->f;
  double *q = atom->q;
  int *type = atom->type;
  double *special_coul = force->special_coul;
  double *special_lj = force->special_lj;
  double qqrd2e = force->qqrd2e;

  // loop over neighbors of my atoms

  for (ii = start; ii < inum; ii++) {
    i = ilist[ii];
    qtmp = q[i];
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    itype = type[i];
    jlist = firstneigh[i];
    jnum = numneigh[i];

    for (jj = 0; jj < jnum; jj++) {
      j = jlist[jj];
      factor_lj = special_lj[sbmask(j)];
      factor_coul = special_coul[sbmask(j)];
      j &= NEIGHMASK;

      delx = xtmp - x[j][0];
      dely = ytmp - x[j][1];
      delz = ztmp - x[j][2];
      rsq = delx*delx + dely*dely + delz*delz;

      if (rsq < cut_bothsq) {
        r2inv = 1.0/rsq;

        if (rsq < cut_coulsq) {
          if (!ncoultablebits || rsq <= tabinnersq) {
            r = sqrt(rsq);
            grij = g_ewald * r;
            expm2 = exp(-grij*grij);
            t = 1.0 / (1.0 + EWALD_P*grij);
            erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
            prefactor = qqrd2e * qtmp*q[j]/r;
            forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
            if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
          } else {
            union_int_float_t rsq_lookup;
            rsq_lookup.f = rsq;
            itable = rsq_lookup.i & ncoulmask;
            itable >>= ncoulshiftbits;
            fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
            table = ftable[itable] + fraction*dftable[itable];
            forcecoul = qtmp*q[j] * table;
            if (factor_coul < 1.0) {
              table = ctable[itable] + fraction*dctable[itable];
              prefactor = qtmp*q[j] * table;
              forcecoul -= (1.0-factor_coul)*prefactor;
            }
          }
        } else forcecoul = 0.0;

        if (rsq < cut_ljsq) {
          r6inv = r2inv*r2inv*r2inv;
          jtype = type[j];
          forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
          if (rsq > cut_lj_innersq) {
            switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
              (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
            switch2 = 12.0*rsq * (cut_ljsq-rsq) *
              (rsq-cut_lj_innersq) / denom_lj;
            philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
            forcelj = forcelj*switch1 + philj*switch2;
          }
        } else forcelj = 0.0;

        fpair = (forcecoul + factor_lj*forcelj) * r2inv;

        f[i][0] += delx*fpair;
        f[i][1] += dely*fpair;
        f[i][2] += delz*fpair;

        if (eflag) {
          if (rsq < cut_coulsq) {
            if (!ncoultablebits || rsq <= tabinnersq)
              ecoul = prefactor*erfc;
            else {
              table = etable[itable] + fraction*detable[itable];
              ecoul = qtmp*q[j] * table;
            }
            if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
          } else ecoul = 0.0;

          if (rsq < cut_ljsq) {
            evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
            if (rsq > cut_lj_innersq) {
              switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
                (cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
              evdwl *= switch1;
            }
            evdwl *= factor_lj;
          } else evdwl = 0.0;
        }

        if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
      }
    }
  }
}