lammps/src/pair_born.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: Sai Jayaraman (Sandia)
------------------------------------------------------------------------- */

#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_born.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))

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

PairBorn::PairBorn(LAMMPS *lmp) : Pair(lmp) {}

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

PairBorn::~PairBorn()
{
  if (allocated) {
    memory->destroy_2d_int_array(setflag);
    memory->destroy_2d_double_array(cutsq);

    memory->destroy_2d_double_array(cut);
    memory->destroy_2d_double_array(a);
    memory->destroy_2d_double_array(rho);
    memory->destroy_2d_double_array(sigma);
    memory->destroy_2d_double_array(c);
    memory->destroy_2d_double_array(d);
    memory->destroy_2d_double_array(rhoinv);
    memory->destroy_2d_double_array(born1);
    memory->destroy_2d_double_array(born2);
    memory->destroy_2d_double_array(born3);
    memory->destroy_2d_double_array(offset);
  }
}

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

void PairBorn::compute(int eflag, int vflag)
{
  int i,j,ii,jj,inum,jnum,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
  double rsq,r2inv,r6inv,forceborn,factor_lj;
  double r,rexp;
  int *ilist,*jlist,*numneigh,**firstneigh;

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

  double **x = atom->x;
  double **f = atom->f;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  int nall = nlocal + atom->nghost;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;

  inum = list->inum;
  ilist = list->ilist;
  numneigh = list->numneigh;
  firstneigh = list->firstneigh;
  
  // loop over neighbors of my atoms

  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];

      if (j < nall) factor_lj = 1.0;
      else {
	factor_lj = special_lj[j/nall];
	j %= nall;
      }

      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;
	r6inv = r2inv*r2inv*r2inv;
	r = sqrt(rsq);
	rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
	forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
	  + born3[itype][jtype]*r2inv*r6inv;
	fpair = factor_lj*forceborn*r2inv;

	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) {
	  evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv 
	    + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
	  evdwl *= factor_lj;
	}

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

  if (vflag_fdotr) virial_compute();
}

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

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

  setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
  for (int i = 1; i <= n; i++)
    for (int j = i; j <= n; j++)
      setflag[i][j] = 0;

  cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");

  cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
  a = memory->create_2d_double_array(n+1,n+1,"pair:a");
  rho = memory->create_2d_double_array(n+1,n+1,"pair:rho");
  sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");
  c = memory->create_2d_double_array(n+1,n+1,"pair:c");
  d = memory->create_2d_double_array(n+1,n+1,"pair:d");
  rhoinv = memory->create_2d_double_array(n+1,n+1,"pair:rhoinv");
  born1 = memory->create_2d_double_array(n+1,n+1,"pair:born1");
  born2 = memory->create_2d_double_array(n+1,n+1,"pair:born2");
  born3 = memory->create_2d_double_array(n+1,n+1,"pair:born3");
  offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
}

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

void PairBorn::settings(int narg, char **arg)
{
  if (narg != 1) error->all("Illegal pair_style command");

  cut_global = atof(arg[0]);

  // 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 PairBorn::coeff(int narg, char **arg)
{
  if (narg < 7 || narg > 8) error->all("Incorrect args for pair coefficients");
  if (!allocated) allocate();

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

  double a_one = force->numeric(arg[2]);
  double rho_one = force->numeric(arg[3]);
  double sigma_one = force->numeric(arg[4]);
  if (rho_one <= 0) error->all("Incorrect args for pair coefficients");
  double c_one = force->numeric(arg[5]);
  double d_one = force->numeric(arg[6]);

  double cut_one = cut_global;
  if (narg == 8) cut_one = force->numeric(arg[7]);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo,i); j <= jhi; j++) {
      a[i][j] = a_one;
      rho[i][j] = rho_one;
      sigma[i][j] = sigma_one;
      c[i][j] = c_one;
      d[i][j] = d_one;
      cut[i][j] = cut_one;
      setflag[i][j] = 1;
      count++;
    }
  }

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

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

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

  rhoinv[i][j] = 1.0/rho[i][j];
  born1[i][j] = a[i][j]/rho[i][j];
  born2[i][j] = 6.0*c[i][j];
  born3[i][j] = 8.0*d[i][j]; 
     
  if (offset_flag) {
    double rexp = exp((sigma[i][j]-cut[i][j])*rhoinv[i][j]);
    offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut[i][j],6.0) +
      d[i][j]/pow(cut[i][j],8.0);
  } else offset[i][j] = 0.0;

  a[j][i] = a[i][j];
  c[j][i] = c[i][j];
  d[j][i] = d[i][j];
  rhoinv[j][i] = rhoinv[i][j];
  sigma[j][i] = sigma[i][j];
  born1[j][i] = born1[i][j];
  born2[j][i] = born2[i][j];
  born3[j][i] = born3[i][j];
  offset[j][i] = offset[i][j];

  // compute I,J contribution to long-range tail correction 
  // count total # of atoms of type I and J via Allreduce 

  if (tail_flag) { 
     int *type = atom->type; 
     int nlocal = atom->nlocal; 

     double count[2],all[2]; 
     count[0] = count[1] = 0.0; 
     for (int k = 0; k < nlocal; k++) { 
       if (type[k] == i) count[0] += 1.0; 
       if (type[k] == j) count[1] += 1.0; 
     } 
     MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);

     double PI = 4.0*atan(1.0);
     double rho1 = rho[i][j];
     double rho2 = rho1*rho1;
     double rho3 = rho2*rho1;
     double rc = cut[i][j];
     double rc2 = rc*rc;
     double rc3 = rc2*rc;
     double rc5 = rc3*rc2;
     etail_ij = 2.0*PI*all[0]*all[1] * 
       (a[i][j]*exp((sigma[i][j]-rc)/rho1)*rho1* 
	(rc2 + 2.0*rho1*rc + 2.0*rho2) - 
	c[i][j]/(3.0*rc3) + d[i][j]/(5.0*rc5));
     ptail_ij = (-1/3.0)*2.0*PI*all[0]*all[1] * 
       (-a[i][j]*exp((sigma[i][j]-rc)/rho1) * 
	(rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) + 
	2.0*c[i][j]/rc3 - 8.0*d[i][j]/(5.0*rc5)); 
   } 

   return cut[i][j];
}

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

void PairBorn::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(&a[i][j],sizeof(double),1,fp);
	fwrite(&rho[i][j],sizeof(double),1,fp);
	fwrite(&sigma[i][j],sizeof(double),1,fp);
	fwrite(&c[i][j],sizeof(double),1,fp);
        fwrite(&d[i][j],sizeof(double),1,fp);
	fwrite(&cut[i][j],sizeof(double),1,fp);
      }
    }
}

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

void PairBorn::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(&a[i][j],sizeof(double),1,fp);
	  fread(&rho[i][j],sizeof(double),1,fp);
	  fread(&sigma[i][j],sizeof(double),1,fp);
	  fread(&c[i][j],sizeof(double),1,fp);
          fread(&d[i][j],sizeof(double),1,fp);
	  fread(&cut[i][j],sizeof(double),1,fp);
	}
	MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&rho[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
        MPI_Bcast(&d[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
      }
    }
}

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

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

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

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

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

double PairBorn::single(int i, int j, int itype, int jtype,
			double rsq, double factor_coul, double factor_lj,
			double &fforce)
{
  double r2inv,r6inv,r,rexp,forceborn,phiborn;

  r2inv = 1.0/rsq;
  r6inv = r2inv*r2inv*r2inv;
  r = sqrt(rsq);
  rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
  forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv +
    born3[itype][jtype]*r2inv*r6inv;
  fforce = factor_lj*forceborn*r2inv;
  
  phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
    d[itype][jtype]*r2inv*r6inv - offset[itype][jtype];
  return factor_lj*phiborn;
}