lammps/src/pair_soft.cpp

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   www.cs.sandia.gov/~sjplimp/lammps.html
   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories

   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.
------------------------------------------------------------------------- */

#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_soft.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "neighbor.h"
#include "error.h"

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

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

PairSoft::PairSoft()
{
  PI = 4.0*atan(1.0);
}

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

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

    memory->destroy_2d_double_array(prestart);
    memory->destroy_2d_double_array(prestop);
    memory->destroy_2d_double_array(prefactor);
    memory->destroy_2d_double_array(cut);
  }
}

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

void PairSoft::compute(int eflag, int vflag)
{
  int i,j,k,numneigh,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz;
  double r,rsq,arg,fforce,factor_lj,philj;
  int *neighs;
  double **f;

  // set current prefactor
  // for minimization, set to prestop
  // for dynamics, ramp from prestart to prestop
  // for 0-step dynamics, set to prestart

  double delta = update->ntimestep - update->beginstep;
  if (update->whichflag == 1) delta = 1.0;
  else if (update->nsteps) delta /= update->endstep - update->beginstep;
  else delta = 0.0;
  int ntypes = atom->ntypes;
  for (i = 1; i <= ntypes; i++)
    for (j = 1; j <= ntypes; j++)
      prefactor[i][j] = prestart[i][j] + 
	delta * (prestop[i][j] - prestart[i][j]);

  eng_vdwl = 0.0;
  if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;

  if (vflag == 2) f = update->f_pair;
  else f = atom->f;
  double **x = atom->x;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  int nall = atom->nlocal + atom->nghost;
  double *special_lj = force->special_lj;
  int newton_pair = force->newton_pair;

  // loop over neighbors of my atoms

  for (i = 0; i < nlocal; i++) {
    xtmp = x[i][0];
    ytmp = x[i][1];
    ztmp = x[i][2];
    itype = type[i];
    neighs = neighbor->firstneigh[i];
    numneigh = neighbor->numneigh[i];

    for (k = 0; k < numneigh; k++) {
      j = neighs[k];

      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]) {
	r = sqrt(rsq);
	arg = PI*r/cut[itype][jtype];
	if (r == 0.0) fforce = 0.0;
	else fforce = factor_lj * prefactor[itype][jtype] * 
	       sin(arg) * PI/cut[itype][jtype]/r;

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

	if (eflag) {
	  philj = prefactor[itype][jtype] * (1.0+cos(arg));
	  if (newton_pair || j < nlocal) eng_vdwl += factor_lj*philj;
	  else eng_vdwl += 0.5*factor_lj*philj;
	}

	if (vflag == 1) {
	  if (newton_pair || j < nlocal) {
	    virial[0] += delx*delx*fforce;
	    virial[1] += dely*dely*fforce;
	    virial[2] += delz*delz*fforce;
	    virial[3] += delx*dely*fforce;
	    virial[4] += delx*delz*fforce;
	    virial[5] += dely*delz*fforce;
	  } else {
	    virial[0] += 0.5*delx*delx*fforce;
	    virial[1] += 0.5*dely*dely*fforce;
	    virial[2] += 0.5*delz*delz*fforce;
	    virial[3] += 0.5*delx*dely*fforce;
	    virial[4] += 0.5*delx*delz*fforce;
	    virial[5] += 0.5*dely*delz*fforce;
	  }
	}
      }
    }
  }
  if (vflag == 2) virial_compute();
}

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

void PairSoft::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");

  prestart = memory->create_2d_double_array(n+1,n+1,"pair:prestart");
  prestop = memory->create_2d_double_array(n+1,n+1,"pair:prestop");
  prefactor = memory->create_2d_double_array(n+1,n+1,"pair:prefactor");
  cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");

  // init prestart and prestop to 0.0
  // since pair_hybrid can use all types even if pair_soft sub-class
  //   never sets them

  for (int i = 1; i <= n; i++)
    for (int j = i; j <= n; j++) {
      prestart[i][j] = 0.0;
      prestop[i][j] = 0.0;
    }
}

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

void PairSoft::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 PairSoft::coeff(int narg, char **arg)
{
  if (narg < 4 || narg > 5) 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 prestart_one = atof(arg[2]);
  double prestop_one = atof(arg[3]);

  double cut_one = cut_global;
  if (narg == 5) cut_one = atof(arg[4]);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo,i); j <= jhi; j++) {
      prestart[i][j] = prestart_one;
      prestop[i][j] = prestop_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 PairSoft::init_one(int i, int j)
{
  // always mix prefactors geometrically

  if (setflag[i][j] == 0) {
    prestart[i][j] = sqrt(prestart[i][i]*prestart[j][j]);
    prestop[i][j] = sqrt(prestop[i][i]*prestop[j][j]);
    cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
  }

  prestart[j][i] = prestart[i][j];
  prestop[j][i] = prestop[i][j];
  cut[j][i] = cut[i][j];

  return cut[i][j];
}

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

void PairSoft::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(&prestart[i][j],sizeof(double),1,fp);
	fwrite(&prestop[i][j],sizeof(double),1,fp);
	fwrite(&cut[i][j],sizeof(double),1,fp);
      }
    }
}

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

void PairSoft::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(&prestart[i][j],sizeof(double),1,fp);
	  fread(&prestop[i][j],sizeof(double),1,fp);
	  fread(&cut[i][j],sizeof(double),1,fp);
	}
	MPI_Bcast(&prestart[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&prestop[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
      }
    }
}

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

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

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

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

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

void PairSoft::single(int i, int j, int itype, int jtype, double rsq,
		      double factor_coul, double factor_lj, int eflag,
		      One &one)
{
  double r,arg,philj;

  r = sqrt(rsq);
  arg = PI*r/cut[itype][jtype];
  one.fforce = factor_lj * prefactor[itype][jtype] * 
    sin(arg) * PI/cut[itype][jtype]/r;
  
  if (eflag) {
    philj = prefactor[itype][jtype] * (1.0+cos(arg));
    one.eng_vdwl = factor_lj*philj;
    one.eng_coul = 0.0;
  }
}