text: /* ----------------------------------------------------------------------
     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 <math.h>
  #include <stdio.h>
  #include <stdlib.h>
  #include "pair_colloid_gpu.h"
  #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 <string.h>
  #include "gpu_extra.h"
  
  using namespace LAMMPS_NS;
  
  // External functions from cuda library for atom decomposition
  
  int colloid_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
                       double **host_lj2, double **host_lj3, double **host_lj4,
                       double **offset, double *special_lj, double **host_a12,
                       double **host_a1, double **host_a2, double **host_d1,
                       double **host_d2, double **host_sigma3, double **host_sigma6,
                       int **host_form, const int nlocal,
                       const int nall, const int max_nbors, const int maxspecial,
                       const double cell_size, int &gpu_mode, FILE *screen);
  void colloid_gpu_clear();
  int ** colloid_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);
  void colloid_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 colloid_gpu_bytes();
  
  /* ---------------------------------------------------------------------- */
  
  PairColloidGPU::PairColloidGPU(LAMMPS *lmp) : PairColloid(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
  ------------------------------------------------------------------------- */
  
  PairColloidGPU::~PairColloidGPU()
  {
    colloid_gpu_clear();
  }
  
  /* ---------------------------------------------------------------------- */
  
  void PairColloidGPU::compute(int eflag, int vflag)
  {
    if (eflag || vflag) ev_setup(eflag,vflag);
    else evflag = vflag_fdotr = 0;
  
    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 = colloid_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);
    } else {
      inum = list->inum;
      ilist = list->ilist;
      numneigh = list->numneigh;
      firstneigh = list->firstneigh;
      colloid_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
                          ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
                          vflag_atom, host_start, cpu_time, success);
    }
    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 PairColloidGPU::init_style()
  {
    if (force->newton_pair)
      error->all(FLERR,"Cannot use newton pair with colloid/gpu pair style");
  
    // 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 **_form = NULL;
    int n=atom->ntypes;
    memory->create(_form,n+1,n+1,"colloid/gpu:_form");
    for (int i = 1; i <= n; i++) {
      for (int j = 1; j <= n; j++) {
        if (form[i][j] == SMALL_SMALL) _form[i][j] = 0;
        else if (form[i][j] == SMALL_LARGE) _form[i][j] = 1;
        else if (form[i][j] == LARGE_LARGE) _form[i][j] = 2;
      }
    }
    int maxspecial=0;
    if (atom->molecular)
      maxspecial=atom->maxspecial;
    int success = colloid_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
                                   offset, force->special_lj, a12, a1, a2,
                                   d1, d2, sigma3, sigma6, _form, atom->nlocal,
                                   atom->nlocal+atom->nghost, 300, maxspecial,
                                   cell_size, gpu_mode, screen);
    memory->destroy(_form);
    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 PairColloidGPU::memory_usage()
  {
    double bytes = Pair::memory_usage();
    return bytes + colloid_gpu_bytes();
  }
  
  /* ---------------------------------------------------------------------- */
  
  void PairColloidGPU::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 xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
    double r,rsq,r2inv,r6inv,forcelj,factor_lj;
    double c1,c2,fR,dUR,dUA;
    double K[9],h[4],g[4];
    int *jlist;
  
    double **x = atom->x;
    double **f = atom->f;
    int *type = atom->type;
    double *special_lj = force->special_lj;
  
    // loop over neighbors of my atoms
  
    for (ii = start; ii < inum; ii++) {
      i = ilist[ii];
      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)];
        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]) continue;
  
        switch (form[itype][jtype]) {
        case SMALL_SMALL:
          r2inv = 1.0/rsq;
          r6inv = r2inv*r2inv*r2inv;
          forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
          fpair = factor_lj*forcelj*r2inv;
          if (eflag)
            evdwl = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
              offset[itype][jtype];
          break;
  
        case SMALL_LARGE:
          c2 = a2[itype][jtype];
          K[1] = c2*c2;
          K[2] = rsq;
          K[0] = K[1] - rsq;
          K[4] = rsq*rsq;
          K[3] = K[1] - K[2];
          K[3] *= K[3]*K[3];
          K[6] = K[3]*K[3];
          fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
          fpair = 4.0/15.0*fR*factor_lj *
            (2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
            sigma6[itype][jtype]/K[6]-5.0) / K[0];
          if (eflag)
            evdwl = 2.0/9.0*fR *
              (1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
              sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
          if (rsq <= K[1])
            error->one(FLERR,"Overlapping small/large in pair colloid");
          break;
  
        case LARGE_LARGE:
          r = sqrt(rsq);
          c1 = a1[itype][jtype];
          c2 = a2[itype][jtype];
          K[0] = c1*c2;
          K[1] = c1+c2;
          K[2] = c1-c2;
          K[3] = K[1]+r;
          K[4] = K[1]-r;
          K[5] = K[2]+r;
          K[6] = K[2]-r;
          K[7] = 1.0/(K[3]*K[4]);
          K[8] = 1.0/(K[5]*K[6]);
          g[0] = pow(K[3],-7.0);
          g[1] = pow(K[4],-7.0);
          g[2] = pow(K[5],-7.0);
          g[3] = pow(K[6],-7.0);
          h[0] = ((K[3]+5.0*K[1])*K[3]+30.0*K[0])*g[0];
          h[1] = ((K[4]+5.0*K[1])*K[4]+30.0*K[0])*g[1];
          h[2] = ((K[5]+5.0*K[2])*K[5]-30.0*K[0])*g[2];
          h[3] = ((K[6]+5.0*K[2])*K[6]-30.0*K[0])*g[3];
          g[0] *= 42.0*K[0]/K[3]+6.0*K[1]+K[3];
          g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
          g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
          g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
  
          fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
          evdwl = fR * (h[0]-h[1]-h[2]+h[3]);
          dUR = evdwl/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
          dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
            (2.0*K[0]*K[8]-1.0)*K[8]);
          fpair = factor_lj * (dUR+dUA)/r;
          if (eflag)
            evdwl += a12[itype][jtype]/6.0 *
              (2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
          if (r <= K[1])
            error->one(FLERR,"Overlapping large/large in pair colloid");
          break;
        }
  
        if (eflag) evdwl *= factor_lj;
  
        f[i][0] += delx*fpair;
        f[i][1] += dely*fpair;
        f[i][2] += delz*fpair;
  
        if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
      }
    }
  }
  