Added pair_style lj/cubic

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

   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: Aidan Thompson (SNL)

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

#include "math.h"

#include "stdio.h"

#include "stdlib.h"

#include "string.h"

#include "pair_lj_cubic.h"

#include "atom.h"

#include "comm.h"

#include "force.h"

#include "neighbor.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))

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

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

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

PairLJCubic::~PairLJCubic()

{

  if (allocated) {

    memory->destroy(setflag);

    memory->destroy(cutsq);

    memory->destroy(cut);

    memory->destroy(cut_inner);

    memory->destroy(cut_inner_sq);

    memory->destroy(epsilon);

    memory->destroy(sigma);

    memory->destroy(lj1);

    memory->destroy(lj2);

    memory->destroy(lj3);

    memory->destroy(lj4);

  }

}

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

void PairLJCubic::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,forcelj,factor_lj;

  double r,t,rmin;

  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;

  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];

      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]) {

	r2inv = 1.0/rsq;

        if (rsq <= cut_inner_sq[itype][jtype]) {

	  r6inv = r2inv*r2inv*r2inv;

	  forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);

	} else {

	  r = sqrt(rsq); 

	  rmin = sigma[itype][jtype]*rt6two;

	  t = (r - cut_inner[itype][jtype])/rmin;

	  forcelj = epsilon[itype][jtype]*(-dphids + a3*t*t/2.0)*r/rmin;

        }

	fpair = factor_lj*forcelj*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) {

          if (rsq <= cut_inner_sq[itype][jtype])

	    evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); 

	  else

	    evdwl = epsilon[itype][jtype]*

	      (phis + dphids*t - a3*t*t*t/6.0);

	  evdwl *= factor_lj;

	  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 PairLJCubic::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(cut_inner,n+1,n+1,"pair:cut_inner");

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

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

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

  memory->create(lj1,n+1,n+1,"pair:lj1");

  memory->create(lj2,n+1,n+1,"pair:lj2");

  memory->create(lj3,n+1,n+1,"pair:lj3");

  memory->create(lj4,n+1,n+1,"pair:lj4");

}

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

   global settings

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

void PairLJCubic::settings(int narg, char **arg)

{

  if (narg != 0) error->all("Illegal pair_style command");

  // 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] = 0.0;

  }

}

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

   set coeffs for one or more type pairs

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

void PairLJCubic::coeff(int narg, char **arg)

{

  if (narg != 4)

    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 epsilon_one = force->numeric(arg[2]);

  double sigma_one = force->numeric(arg[3]);

  double rmin = sigma_one*rt6two;

  int count = 0;

  for (int i = ilo; i <= ihi; i++) {

    for (int j = MAX(jlo,i); j <= jhi; j++) {

      epsilon[i][j] = epsilon_one;

      sigma[i][j] = sigma_one;

      cut_inner[i][j] = rmin*s;

      cut[i][j] = rmin*sm;

      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 PairLJCubic::init_one(int i, int j)

{

  if (setflag[i][j] == 0) {

    epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],

			       sigma[i][i],sigma[j][j]);

    sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);

    cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);

    cut[i][j] = mix_distance(cut[i][i],cut[j][j]);

  }

  cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j];

  lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);

  lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);

  lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);

  lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);

  cut_inner[j][i] = cut_inner[i][j];

  cut_inner_sq[j][i] = cut_inner_sq[i][j];

  lj1[j][i] = lj1[i][j];

  lj2[j][i] = lj2[i][j];

  lj3[j][i] = lj3[i][j];

  lj4[j][i] = lj4[i][j];

  return cut[i][j];

}

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

  proc 0 writes to restart file

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

void PairLJCubic::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(&epsilon[i][j],sizeof(double),1,fp);

	fwrite(&sigma[i][j],sizeof(double),1,fp);

	fwrite(&cut_inner[i][j],sizeof(double),1,fp);

	fwrite(&cut[i][j],sizeof(double),1,fp);

      }

    }

}

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

  proc 0 reads from restart file, bcasts

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

void PairLJCubic::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(&epsilon[i][j],sizeof(double),1,fp);

	  fread(&sigma[i][j],sizeof(double),1,fp);

	  fread(&cut_inner[i][j],sizeof(double),1,fp);

	  fread(&cut[i][j],sizeof(double),1,fp);

	}

	MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);

	MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);

	MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);

	MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);

      }

    }

}

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

  proc 0 writes to restart file

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

void PairLJCubic::write_restart_settings(FILE *fp)

{

  fwrite(&mix_flag,sizeof(int),1,fp);

}

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

  proc 0 reads from restart file, bcasts

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

void PairLJCubic::read_restart_settings(FILE *fp)

{

  int me = comm->me;

  if (me == 0) {

    fread(&mix_flag,sizeof(int),1,fp);

  }

  MPI_Bcast(&mix_flag,1,MPI_INT,0,world);

}

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

double PairLJCubic::single(int i, int j, int itype, int jtype,

			     double rsq,

			     double factor_coul, double factor_lj,

			     double &fforce)

{

  double r2inv,r6inv,forcelj,philj;

  double r,t;

  double rmin;

  r2inv = 1.0/rsq;

  if (rsq <= cut_inner_sq[itype][jtype]) {

    r6inv = r2inv*r2inv*r2inv;

    forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);

  } else {

    r = sqrt(rsq); 

    rmin = sigma[itype][jtype]*rt6two;

    t = (r - cut_inner[itype][jtype])/rmin;

    forcelj = epsilon[itype][jtype]*(-dphids + a3*t*t/2.0)*r/rmin;

  }

  fforce = factor_lj*forcelj*r2inv;

  if (rsq <= cut_inner_sq[itype][jtype])

    philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);

  else

    philj = epsilon[itype][jtype]*

      (phis + dphids*t - a3*t*t*t/6.0);

  return factor_lj*philj;

}

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

   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.

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

#ifdef PAIR_CLASS

PairStyle(lj/cubic,PairLJCubic)

#else

#ifndef LMP_PAIR_LJ_CUBIC_H

#define LMP_PAIR_LJ_CUBIC_H

#include "pair.h"

namespace LAMMPS_NS {

class PairLJCubic : public Pair {

 public:

  PairLJCubic(class LAMMPS *);

  virtual ~PairLJCubic();

  virtual void compute(int, int);

  virtual void settings(int, char **);

  void coeff(int, char **);

  double init_one(int, int);

  void write_restart(FILE *);

  void read_restart(FILE *);

  virtual void write_restart_settings(FILE *);

  virtual void read_restart_settings(FILE *);

  virtual double single(int, int, int, int, double, double, double, double &);

 protected:

  double **cut,**cut_inner,**cut_inner_sq;

  double **epsilon,**sigma;

  double **lj1,**lj2,**lj3,**lj4;

  // LJ quantities scaled by epsilon and rmin = sigma*2^1/6

  static const double rt6two = 1.1224621;  // 2^1/6

  static const double s = 1.1086834;       // inflection point = (13/7)^1/6

  static const double phis = -0.7869823;   // energy at s

  static const double dphids = 2.6899009;  // gradient at s

  static const double a3 = 27.93357;       // cubic coefficient

  static const double sm = 1.5475375;      // cubic cutoff = s*67/48

  void allocate();

};

}

#endif

#endif