/* ----------------------------------------------------------------------
   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_gauss.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))

#define EPSILON 1.0e-10

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

PairGauss::PairGauss(LAMMPS *lmp) :Pair(lmp)
{
  nextra = 1;
  pvector = new double[1];
}

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

PairGauss::~PairGauss()
{
  delete [] pvector;

  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(b);
    memory->destroy_2d_double_array(offset);
  }
}

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

void PairGauss::compute(int eflag, int vflag)
{   
  int i,j,ii,jj,inum,jnum,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
  double r,rsq,r2inv,r6inv,forcelj,rexp;
  int *ilist,*jlist,*numneigh,**firstneigh;
  
  evdwl = 0.0;
  if (eflag || vflag) ev_setup(eflag,vflag);
  else evflag = vflag_fdotr = 0;
  int occ = 0;

  double **x = atom->x;
  double **f = atom->f;
  int *type = atom->type;
  int nlocal = atom->nlocal;
  int nall = nlocal + atom->nghost;
  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];
	
      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];
      
      // define a Gaussian well to be occupied if
      // the site it interacts with is within the force maximum    
    
      if (eflag_global && rsq < 0.5/b[itype][jtype]) occ++;

      if (rsq < cutsq[itype][jtype]) {
	r2inv = 1.0/rsq;
	r = sqrt(rsq);
	forcelj = - 2.0*a[itype][jtype]*b[itype][jtype] * rsq * 
	  exp(-b[itype][jtype]*rsq); 
	fpair = 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)
	  evdwl = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) -
		    offset[itype][jtype]);

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

  if (eflag_global) pvector[0] = occ;
  if (vflag_fdotr) virial_compute();
}

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

void PairGauss::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 = 1; 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_gauss");
  a = memory->create_2d_double_array(n+1,n+1,"pair:a");
  b = memory->create_2d_double_array(n+1,n+1,"pair:b");
  offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");  
}

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

void PairGauss::settings(int narg, char **arg)
{ 
  if (narg != 1) error->all("Illegal pair_style command");
  
  cut_global = atof(arg[0]);

  // reset cutoffs that have been explicity 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 PairGauss::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 a_one = atof(arg[2]);
  double b_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++) {
      a[i][j] = a_one; 
      b[i][j] = b_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 PairGauss::init_one(int i, int j)
{
  if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
  
  if (offset_flag) offset[i][j] = a[i][j]*exp(-b[i][j]*cut[i][j]*cut[i][j]);
  else offset[i][j] = 0.0;
  
  a[j][i] = a[i][j];
  b[j][i] = b[i][j];
  offset[j][i] = offset[i][j];
  
  return cut[i][j]; 
}

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

void PairGauss::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(&b[i][j],sizeof(double),1,fp);
	fwrite(&cut[i][j],sizeof(double),1,fp);
      }
    }
}

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

void PairGauss::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(&b[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(&b[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
      }
    }
}

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

void PairGauss::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 PairGauss::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 PairGauss::single(int i, int j, int itype, int jtype, double rsq,
			 double factor_coul, double factor_lj,
			 double &fforce)
{
  double r2inv,r6inv,forcelj,philj,r;

  r = sqrt(rsq);
  
  r2inv = 1.0/rsq;
  philj = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) - offset[itype][jtype]);
  
  forcelj = -2.0*a[itype][jtype]*b[itype][jtype]*rsq*exp(-b[itype][jtype]*rsq);
  fforce = forcelj*r2inv;
  return philj;
}

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

void *PairGauss::extract(char *str, int &dim)
{
  dim = 2;
  if (strcmp(str,"a") == 0) return (void *) a;
  return NULL;
}