pair_dpd_fdt.cpp

/* ----------------------------------------------------------------------
   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: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */

#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "update.h"
#include "fix.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "random_mars.h"
#include "memory.h"
#include "modify.h"
#include "pair_dpd_fdt.h"
#include "error.h"

using namespace LAMMPS_NS;

#define EPSILON 1.0e-10

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

PairDPDfdt::PairDPDfdt(LAMMPS *lmp) : Pair(lmp)
{
  random = NULL;
  splitFDT_flag = false;
}

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

PairDPDfdt::~PairDPDfdt()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(cutsq);

    memory->destroy(cut);
    memory->destroy(a0);
    memory->destroy(sigma);
  }


  if (random) delete random;
}

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

void PairDPDfdt::compute(int eflag, int vflag)
{
  int i,j,ii,jj,inum,jnum,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
  double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
  double rsq,r,rinv,dot,wd,wr,randnum,factor_dpd;
  int *ilist,*jlist,*numneigh,**firstneigh;
  double gamma_ij;

  evdwl = 0.0;
  if (eflag || vflag) ev_setup(eflag,vflag);
  else evflag = vflag_fdotr = 0;

  double **x = atom->x;
  double **v = atom->v;
  double **f = atom->f;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;
  double dtinvsqrt = 1.0/sqrt(update->dt);

  inum = list->inum;
  ilist = list->ilist;
  numneigh = list->numneigh;
  firstneigh = list->firstneigh;

  // loop over neighbors of my atoms

  if (splitFDT_flag) {
    for (ii = 0; 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_dpd = 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]) {
          r = sqrt(rsq);
          if (r < EPSILON) continue;     // r can be 0.0 in DPD systems
          rinv = 1.0/r;
          wr = 1.0 - r/cut[itype][jtype];
          wd = wr*wr;

          // conservative force = a0 * wr
          fpair = a0[itype][jtype]*wr;
          fpair *= factor_dpd*rinv;

          f[i][0] += delx*fpair;
          f[i][1] += dely*fpair;
          f[i][2] += delz*fpair;
          if (newton_pair || j < nlocal) {
            f[j][0] -= delx*fpair;
            f[j][1] -= dely*fpair;
            f[j][2] -= delz*fpair;
          }

          if (eflag) {
            // unshifted eng of conservative term:
            // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
            // eng shifted to 0.0 at cutoff
            evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd;
            evdwl *= factor_dpd;
          }

          if (evflag) ev_tally(i,j,nlocal,newton_pair,
                               evdwl,0.0,fpair,delx,dely,delz);
        }
      }
    }
  } else {
    for (ii = 0; ii < inum; ii++) {
      i = ilist[ii];
      xtmp = x[i][0];
      ytmp = x[i][1];
      ztmp = x[i][2];
      vxtmp = v[i][0];
      vytmp = v[i][1];
      vztmp = v[i][2];
      itype = type[i];
      jlist = firstneigh[i];
      jnum = numneigh[i];

      for (jj = 0; jj < jnum; jj++) {
        j = jlist[jj];
        factor_dpd = 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]) {
          r = sqrt(rsq);
          if (r < EPSILON) continue;     // r can be 0.0 in DPD systems
          rinv = 1.0/r;
          delvx = vxtmp - v[j][0];
          delvy = vytmp - v[j][1];
          delvz = vztmp - v[j][2];
          dot = delx*delvx + dely*delvy + delz*delvz;
          wr = 1.0 - r/cut[itype][jtype];
          wd = wr*wr;
          randnum = random->gaussian();
          gamma_ij = sigma[itype][jtype]*sigma[itype][jtype]
                     / (2.0*force->boltz*temperature);

          // conservative force = a0 * wd
          // drag force = -gamma * wd^2 * (delx dot delv) / r
          // random force = sigma * wd * rnd * dtinvsqrt;

          fpair = a0[itype][jtype]*wr;
          fpair -= gamma_ij*wd*dot*rinv;
          fpair += sigma[itype][jtype]*wr*randnum*dtinvsqrt;
          fpair *= factor_dpd*rinv;

          f[i][0] += delx*fpair;
          f[i][1] += dely*fpair;
          f[i][2] += delz*fpair;
          if (newton_pair || j < nlocal) {
            f[j][0] -= delx*fpair;
            f[j][1] -= dely*fpair;
            f[j][2] -= delz*fpair;
          }

          if (eflag) {
            // unshifted eng of conservative term:
            // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
            // eng shifted to 0.0 at cutoff
            evdwl = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd;
            evdwl *= factor_dpd;
          }

          if (evflag) ev_tally(i,j,nlocal,newton_pair,
                               evdwl,0.0,fpair,delx,dely,delz);
        }
      }
    }
  }
  if (vflag_fdotr) virial_fdotr_compute();
}

/* ----------------------------------------------------------------------
   allocate all arrays
------------------------------------------------------------------------- */

void PairDPDfdt::allocate()
{
  allocated = 1;
  int n = atom->ntypes;

  memory->create(setflag,n+1,n+1,"pair:setflag");
  for (int i = 1; i <= n; i++)
    for (int j = i; j <= n; j++)
      setflag[i][j] = 0;

  memory->create(cutsq,n+1,n+1,"pair:cutsq");

  memory->create(cut,n+1,n+1,"pair:cut");
  memory->create(a0,n+1,n+1,"pair:a0");
  memory->create(sigma,n+1,n+1,"pair:sigma");
}

/* ----------------------------------------------------------------------
   global settings
------------------------------------------------------------------------- */

void PairDPDfdt::settings(int narg, char **arg)
{
  // process keywords
  if (narg != 3) error->all(FLERR,"Illegal pair_style command");

  temperature = force->numeric(FLERR,arg[0]);
  cut_global = force->numeric(FLERR,arg[1]);
  seed = force->inumeric(FLERR,arg[2]);

  // initialize Marsaglia RNG with processor-unique seed

  if (seed <= 0) error->all(FLERR,"Illegal pair_style command");
  delete random;
  random = new RanMars(lmp,seed + comm->me);

  // reset cutoffs that have been explicitly set

  if (allocated) {
    int i,j;
    for (i = 1; i <= atom->ntypes; i++)
      for (j = i+1; j <= atom->ntypes; j++)
        if (setflag[i][j]) cut[i][j] = cut_global;
  }
}

/* ----------------------------------------------------------------------
   set coeffs for one or more type pairs
------------------------------------------------------------------------- */

void PairDPDfdt::coeff(int narg, char **arg)
{
  if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients");
  if (!allocated) allocate();

  int ilo,ihi,jlo,jhi;
  force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
  force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);

  double a0_one = force->numeric(FLERR,arg[2]);
  double sigma_one = force->numeric(FLERR,arg[3]);
  double cut_one = cut_global;

  if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo,i); j <= jhi; j++) {
      a0[i][j] = a0_one;
      sigma[i][j] = sigma_one;
      cut[i][j] = cut_one;
      setflag[i][j] = 1;
      count++;
    }
  }

  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}

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

void PairDPDfdt::init_style()
{
  if (comm->ghost_velocity == 0)
    error->all(FLERR,"Pair dpd/fdt requires ghost atoms store velocity");

  // if newton off, forces between atoms ij will be double computed
  // using different random numbers

  if (force->newton_pair == 0 && comm->me == 0) error->warning(FLERR,
      "Pair dpd/fdt requires newton pair on");

  splitFDT_flag = false;
  int irequest = neighbor->request(this,instance_me);
  for (int i = 0; i < modify->nfix; i++)
    if (strcmp(modify->fix[i]->style,"shardlow") == 0){
      splitFDT_flag = true;
    }
}

/* ----------------------------------------------------------------------
   init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */

double PairDPDfdt::init_one(int i, int j)
{
  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

  cut[j][i] = cut[i][j];
  a0[j][i] = a0[i][j];
  sigma[j][i] = sigma[i][j];

  return cut[i][j];
}

/* ----------------------------------------------------------------------
   proc 0 writes to restart file
------------------------------------------------------------------------- */

void PairDPDfdt::write_restart(FILE *fp)
{
  write_restart_settings(fp);

  int i,j;
  for (i = 1; i <= atom->ntypes; i++)
    for (j = i; j <= atom->ntypes; j++) {
      fwrite(&setflag[i][j],sizeof(int),1,fp);
      if (setflag[i][j]) {
        fwrite(&a0[i][j],sizeof(double),1,fp);
        fwrite(&sigma[i][j],sizeof(double),1,fp);
        fwrite(&cut[i][j],sizeof(double),1,fp);
      }
    }
}

/* ----------------------------------------------------------------------
   proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */

void PairDPDfdt::read_restart(FILE *fp)
{
  read_restart_settings(fp);

  allocate();

  int i,j;
  int me = comm->me;
  for (i = 1; i <= atom->ntypes; i++)
    for (j = i; j <= atom->ntypes; j++) {
      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
      if (setflag[i][j]) {
        if (me == 0) {
          fread(&a0[i][j],sizeof(double),1,fp);
          fread(&sigma[i][j],sizeof(double),1,fp);
          fread(&cut[i][j],sizeof(double),1,fp);
        }
        MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
      }
    }
}

/* ----------------------------------------------------------------------
   proc 0 writes to restart file
------------------------------------------------------------------------- */

void PairDPDfdt::write_restart_settings(FILE *fp)
{
  fwrite(&temperature,sizeof(double),1,fp);
  fwrite(&cut_global,sizeof(double),1,fp);
  fwrite(&seed,sizeof(int),1,fp);
  fwrite(&mix_flag,sizeof(int),1,fp);
}

/* ----------------------------------------------------------------------
   proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */

void PairDPDfdt::read_restart_settings(FILE *fp)
{
  if (comm->me == 0) {
    fread(&temperature,sizeof(double),1,fp);
    fread(&cut_global,sizeof(double),1,fp);
    fread(&seed,sizeof(int),1,fp);
    fread(&mix_flag,sizeof(int),1,fp);
  }
  MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
  MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
  MPI_Bcast(&seed,1,MPI_INT,0,world);
  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);

  // initialize Marsaglia RNG with processor-unique seed
  // same seed that pair_style command initially specified

  if (random) delete random;
  random = new RanMars(lmp,seed + comm->me);
}

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

double PairDPDfdt::single(int i, int j, int itype, int jtype, double rsq,
                       double factor_coul, double factor_dpd, double &fforce)
{
  double r,rinv,wr,wd,phi;

  r = sqrt(rsq);
  if (r < EPSILON) {
    fforce = 0.0;
    return 0.0;
  }

  rinv = 1.0/r;
  wr = 1.0 - r/cut[itype][jtype];
  wd = wr*wr;
  fforce = a0[itype][jtype]*wr * factor_dpd*rinv;

  phi = 0.5*a0[itype][jtype]*cut[itype][jtype] * wd;
  return factor_dpd*phi;
}