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: Trung Dac Nguyen (ORNL)
------------------------------------------------------------------------- */

#include "pair_lj_sf_dipole_sf_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 "gpu_extra.h"

using namespace LAMMPS_NS;

// External functions from cuda library for atom decomposition

int dplsf_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
                   double **host_lj2, double **host_lj3, double **host_lj4,
                   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);
void dplsf_gpu_clear();
int ** dplsf_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 **host_mu,
                           double *boxlo, double *prd);
void dplsf_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, double **host_mu, const int nlocal,
                       double *boxlo, double *prd);
double dplsf_gpu_bytes();

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

PairLJSFDipoleSFGPU::PairLJSFDipoleSFGPU(LAMMPS *lmp) : PairLJSFDipoleSF(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
------------------------------------------------------------------------- */

PairLJSFDipoleSFGPU::~PairLJSFDipoleSFGPU()
{
  dplsf_gpu_clear();
}

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

void PairLJSFDipoleSFGPU::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 = dplsf_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, atom->mu, domain->boxlo,
                                     domain->prd);
  } else {
    inum = list->inum;
    ilist = list->ilist;
    numneigh = list->numneigh;
    firstneigh = list->firstneigh;
    dplsf_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->mu, 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 PairLJSFDipoleSFGPU::init_style()
{
  if (!atom->q_flag || !atom->mu_flag || !atom->torque_flag)
    error->all(FLERR,"Pair dipole/sf/gpu requires atom attributes q, mu, torque");

  if (force->newton_pair)
    error->all(FLERR,"Cannot use newton pair with dipole/sf/gpu pair style");

  if (strcmp(update->unit_style,"electron") == 0)
    error->all(FLERR,"Cannot (yet) use 'electron' units with dipoles");

  // Repeat cutsq calculation because done after call to init_style
  double maxcut = -1.0;
  double cut;
  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)) {
        cut = init_one(i,j);
        cut *= cut;
        if (cut > maxcut)
          maxcut = cut;
        cutsq[i][j] = cutsq[j][i] = cut;
      } else
        cutsq[i][j] = cutsq[j][i] = 0.0;
    }
  }
  double cell_size = sqrt(maxcut) + neighbor->skin;

  int maxspecial=0;
  if (atom->molecular)
    maxspecial=atom->maxspecial;
  int success = dplsf_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
                               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);
  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 PairLJSFDipoleSFGPU::memory_usage()
{
  double bytes = Pair::memory_usage();
  return bytes + dplsf_gpu_bytes();
}

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

void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
                                  int *ilist, int *numneigh,
                                  int **firstneigh)
{
  int i,j,ii,jj,jnum,itype,jtype;
  double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fx,fy,fz;
  double rsq,rinv,r2inv,r6inv,r3inv,r5inv;
  double forcecoulx,forcecouly,forcecoulz,crossx,crossy,crossz;
  double tixcoul,tiycoul,tizcoul,tjxcoul,tjycoul,tjzcoul;
  double fq,pdotp,pidotr,pjdotr,pre1,pre2,pre3,pre4;
  double forcelj,factor_coul,factor_lj;
  double presf,afac,bfac,pqfac,qpfac,forceljcut,forceljsf;
  double aforcecoulx,aforcecouly,aforcecoulz;
  double bforcecoulx,bforcecouly,bforcecoulz;
  double rcutlj2inv, rcutcoul2inv,rcutlj6inv;
  int *jlist;

  evdwl = ecoul = 0.0;
  ev_init(eflag,vflag);

  double **x = atom->x;
  double **f = atom->f;
  double *q = atom->q;
  double **mu = atom->mu;
  double **torque = atom->torque;
  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;
      jtype = type[j];

      if (rsq < cutsq[itype][jtype]) {
        r2inv = 1.0/rsq;
        rinv = sqrt(r2inv);

        // atom can have both a charge and dipole
        // i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole

        forcecoulx = forcecouly = forcecoulz = 0.0;
        tixcoul = tiycoul = tizcoul = 0.0;
        tjxcoul = tjycoul = tjzcoul = 0.0;

        if (rsq < cut_coulsq[itype][jtype]) {

          if (qtmp != 0.0 && q[j] != 0.0) {
            pre1 = qtmp*q[j]*rinv*(r2inv-1.0/cut_coulsq[itype][jtype]);

            forcecoulx += pre1*delx;
            forcecouly += pre1*dely;
            forcecoulz += pre1*delz;
          }

          if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
            r3inv = r2inv*rinv;
            r5inv = r3inv*r2inv;
            rcutcoul2inv=1.0/cut_coulsq[itype][jtype];

            pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
            pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
            pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;

            afac = 1.0 - rsq*rsq * rcutcoul2inv*rcutcoul2inv;
            pre1 = afac * ( pdotp - 3.0 * r2inv * pidotr * pjdotr );
            aforcecoulx = pre1*delx;
            aforcecouly = pre1*dely;
            aforcecoulz = pre1*delz;

            bfac = 1.0 - 4.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv) +
              3.0*rsq*rsq*rcutcoul2inv*rcutcoul2inv;
            presf = 2.0 * r2inv * pidotr * pjdotr;
            bforcecoulx = bfac * (pjdotr*mu[i][0]+pidotr*mu[j][0]-presf*delx);
            bforcecouly = bfac * (pjdotr*mu[i][1]+pidotr*mu[j][1]-presf*dely);
            bforcecoulz = bfac * (pjdotr*mu[i][2]+pidotr*mu[j][2]-presf*delz);

            forcecoulx += 3.0 * r5inv * ( aforcecoulx + bforcecoulx );
            forcecouly += 3.0 * r5inv * ( aforcecouly + bforcecouly );
            forcecoulz += 3.0 * r5inv * ( aforcecoulz + bforcecoulz );

            pre2 = 3.0 * bfac * r5inv * pjdotr;
            pre3 = 3.0 * bfac * r5inv * pidotr;
            pre4 = -bfac * r3inv;

            crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
            crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
            crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);

            tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
            tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
            tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
            tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
            tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
            tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
          }

          if (mu[i][3] > 0.0 && q[j] != 0.0) {
            r3inv = r2inv*rinv;
            r5inv = r3inv*r2inv;
            pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
            rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
            pre1 = 3.0 * q[j] * r5inv * pidotr * (1-rsq*rcutcoul2inv);
            pqfac = 1.0 - 3.0*rsq*rcutcoul2inv +
              2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
            pre2 = q[j] * r3inv * pqfac;

            forcecoulx += pre2*mu[i][0] - pre1*delx;
            forcecouly += pre2*mu[i][1] - pre1*dely;
            forcecoulz += pre2*mu[i][2] - pre1*delz;
            tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
            tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
            tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
          }

          if (mu[j][3] > 0.0 && qtmp != 0.0) {
            r3inv = r2inv*rinv;
            r5inv = r3inv*r2inv;
            pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
            rcutcoul2inv=1.0/cut_coulsq[itype][jtype];
            pre1 = 3.0 * qtmp * r5inv * pjdotr * (1-rsq*rcutcoul2inv);
            qpfac = 1.0 - 3.0*rsq*rcutcoul2inv +
              2.0*rsq*sqrt(rsq)*rcutcoul2inv*sqrt(rcutcoul2inv);
            pre2 = qtmp * r3inv * qpfac;

            forcecoulx += pre1*delx - pre2*mu[j][0];
            forcecouly += pre1*dely - pre2*mu[j][1];
            forcecoulz += pre1*delz - pre2*mu[j][2];
            tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
            tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
            tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
          }
        }

        // LJ interaction

        if (rsq < cut_ljsq[itype][jtype]) {
          r6inv = r2inv*r2inv*r2inv;
          forceljcut = r6inv*(lj1[itype][jtype]*r6inv-lj2[itype][jtype])*r2inv;

          rcutlj2inv = 1.0 / cut_ljsq[itype][jtype];
          rcutlj6inv = rcutlj2inv * rcutlj2inv * rcutlj2inv;
          forceljsf = (lj1[itype][jtype]*rcutlj6inv - lj2[itype][jtype]) *
          rcutlj6inv * rcutlj2inv;

          forcelj = factor_lj * (forceljcut - forceljsf);
        } else forcelj = 0.0;

        // total force

        fq = factor_coul*qqrd2e;
        fx = fq*forcecoulx + delx*forcelj;
        fy = fq*forcecouly + dely*forcelj;
        fz = fq*forcecoulz + delz*forcelj;

        // force & torque accumulation

        f[i][0] += fx;
        f[i][1] += fy;
        f[i][2] += fz;
        torque[i][0] += fq*tixcoul;
        torque[i][1] += fq*tiycoul;
        torque[i][2] += fq*tizcoul;

        if (eflag) {
          if (rsq < cut_coulsq[itype][jtype]) {
            ecoul = qtmp*q[j]*rinv*
              pow((1.0-sqrt(rsq)/sqrt(cut_coulsq[itype][jtype])),2);
            if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
              ecoul += bfac * (r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr);
            if (mu[i][3] > 0.0 && q[j] != 0.0)
              ecoul += -q[j]*r3inv * pqfac * pidotr;
            if (mu[j][3] > 0.0 && qtmp != 0.0)
              ecoul += qtmp*r3inv * qpfac * pjdotr;
            ecoul *= factor_coul*qqrd2e;
          } else ecoul = 0.0;

          if (rsq < cut_ljsq[itype][jtype]) {
            evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) +
              rcutlj6inv*(6*lj3[itype][jtype]*rcutlj6inv-3*lj4[itype][jtype])*
              rsq*rcutlj2inv +
              rcutlj6inv*(-7*lj3[itype][jtype]*rcutlj6inv+4*lj4[itype][jtype]);
            evdwl *= factor_lj;
          } else evdwl = 0.0;
        }

        if (evflag) ev_tally_xyz_full(i,evdwl,ecoul,
                                      fx,fy,fz,delx,dely,delz);
      }
    }
  }
}