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

#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "pair_rgl.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "neighbor.h"
#include "error.h"
#include <iostream>

using namespace LAMMPS_NS;
using namespace std;

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

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

PairRGL::PairRGL(LAMMPS *lmp) : Pair(lmp) {
	nmax = 0;	
  phi = NULL;
}

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

PairRGL::~PairRGL()
{
		memory->sfree(phi);

  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(cutbsq);
    memory->destroy_2d_double_array(rr0);
    memory->destroy_2d_double_array(repsilon);
    memory->destroy_2d_double_array(rc);
    memory->destroy_2d_double_array(rp);
    memory->destroy_2d_double_array(rq);
  }
}

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

void PairRGL::compute(int eflag, int vflag)
{
  int i,j,k,numneigh,itype,jtype;
  double xtmp,ytmp,ztmp,delx,dely,delz;
  double rsq,r,dr,dexp,pexp,bexp,pforce,bforce,fforce,peng,beng,eng_bond;
  int *neighs;
  double **f;

 // grow energy array if necessary

  if (atom->nmax > nmax) {
		memory->sfree(phi);
		nmax = atom->nmax;
		phi = (double *)memory->smalloc(nmax*sizeof(double),"pair:phi");
	}

  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 = nlocal + atom->nghost;
  int newton_pair = force->newton_pair;

// zero out density

  if (newton_pair) {
    for (i = 0; i < nall; i++) phi[i] = 0.0;
  } else for (i = 0; i < nlocal; i++) phi[i] = 0.0;


// loop over neighbors of my atoms, calculating phi


  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];

      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 < cutbsq[itype][jtype]) {
				r = sqrt(rsq);
				phi[i] += exp(-2.0 * rq[itype][jtype] * (r / rr0[itype][jtype] - 1.0));
			} 
		}
	}

	 // loop over neighbors of my atoms, compute force 

  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];
		eng_bond = 0.0;

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

      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);
	pexp = exp(-rp[itype][jtype] * (r / rr0[itype][jtype] - 1.0));
	pforce = -repsilon[itype][jtype] * rp[itype][jtype] / rr0[itype][jtype] * pexp;
	bexp = exp(-2.0 * rq[itype][jtype] * (r / rr0[itype][jtype] - 1.0));
	bforce = rq[itype][jtype] * rc[itype][jtype] / rr0[itype][jtype] * (1.0 / sqrt(phi[i]) + 1.0 / sqrt(phi[j])) * bexp;  
	fforce = pforce + bforce;

	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) {
	  peng = 0.5 * repsilon[itype][jtype] * pexp;
		beng = rc[itype][jtype] * rc[itype][jtype] * bexp; 
	  if (newton_pair || j < nlocal) {
			eng_vdwl += peng;
			eng_bond += beng;
		}
	  else {
			eng_vdwl += 0.5 * peng;
			eng_bond += 0.5 * beng;
		}
	}
	
	if (vflag == 1) {
	  if (newton_pair == 0 && j >= nlocal) fforce *= 0.5;
	  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;
	}
      }
    }
	if (eflag) {
			eng_vdwl -= sqrt(eng_bond); 
		}
  } 

  if (vflag == 2) virial_compute();
}

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

void PairRGL::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");
  cutbsq = memory->create_2d_double_array(n+1,n+1,"pair:cutbsq");

  cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
  rr0 = memory->create_2d_double_array(n+1,n+1,"pair:rr0");
  repsilon = memory->create_2d_double_array(n+1,n+1,"pair:repsilon");
  rc = memory->create_2d_double_array(n+1,n+1,"pair:rc");
  rp = memory->create_2d_double_array(n+1,n+1,"pair:rp");
  rq = memory->create_2d_double_array(n+1,n+1,"pair:rq");
//  offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
}

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

void PairRGL::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 PairRGL::coeff(int narg, char **arg)
{
  if (narg < 8 || narg > 9) error->all("Incrrect 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 rr0_one = atof(arg[2]);
  double repsilon_one = atof(arg[3]);
  double rc_one = atof(arg[4]);
  double rp_one = atof(arg[6]);
  double rq_one = atof(arg[5]);
  double cutb_one = atof(arg[7]);

  double cut_one = cut_global;
 // if (narg == 9) cut_one = atof(arg[8]);

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    for (int j = MAX(jlo,i); j <= jhi; j++) {
      rr0[i][j] = rr0_one;
      repsilon[i][j] = repsilon_one;
      rc[i][j] = rc_one;
      rp[i][j] = rp_one;
      rq[i][j] = rq_one;
			cut[i][j] = cut_one;
			cutbsq[i][j] = cutb_one * cutb_one;
      setflag[i][j] = 1;
      count++;
    }
  }

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


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

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

/*  if (offset_flag) {
    double alpha_dr = -repsilon[i][j] * (cut[i][j] - rc[i][j]);
    offset[i][j] = rr0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
  } else offset[i][j] = 0.0;
*/
  rr0[j][i] = rr0[i][j];
  repsilon[j][i] = repsilon[i][j];
  rc[j][i] = rc[i][j];
  rp[j][i] = rp[i][j];
  rq[j][i] = rq[i][j];
	cutbsq[j][i] = cutbsq[i][j];
//  offset[j][i] = offset[i][j];

  return cut[i][j];
}

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

void PairRGL::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(&rr0[i][j],sizeof(double),1,fp);
	fwrite(&repsilon[i][j],sizeof(double),1,fp);
	fwrite(&rc[i][j],sizeof(double),1,fp);
	fwrite(&rp[i][j],sizeof(double),1,fp);
	fwrite(&rq[i][j],sizeof(double),1,fp);
	fwrite(&cut[i][j],sizeof(double),1,fp);
      }
    }
}

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

void PairRGL::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(&rr0[i][j],sizeof(double),1,fp);
	  fread(&repsilon[i][j],sizeof(double),1,fp);
	  fread(&rc[i][j],sizeof(double),1,fp);
	  fread(&rp[i][j],sizeof(double),1,fp);
	  fread(&rq[i][j],sizeof(double),1,fp);
	  fread(&cut[i][j],sizeof(double),1,fp);
	}
	MPI_Bcast(&rr0[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&repsilon[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&rc[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&rp[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&rq[i][j],1,MPI_DOUBLE,0,world);
	MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
      }
    }
}

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

void PairRGL::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 PairRGL::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);
}

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

void PairRGL::single(int i, int j, int itype, int jtype, double rsq,
		       double factor_coul, double factor_lj, int eflag,
		       One &one)
{
  double r,pexp,bexp,pforce,bforce,peng,beng;

	r = sqrt(rsq);
	pexp = exp(-rp[itype][jtype] * (r / rr0[itype][jtype] - 1.0));
	pforce = -repsilon[itype][jtype] * rp[itype][jtype] / rr0[itype][jtype] * pexp;
	bexp = exp(-2.0 * rq[itype][jtype] * (r / rr0[itype][jtype] - 1.0));
	bforce = rq[itype][jtype] * rc[itype][jtype] / rr0[itype][jtype] * (1.0 / sqrt(phi[i]) + 1.0 / sqrt(phi[j])) *  bexp;
  one.fforce = (pforce + bforce);
  
  if (eflag) {
    peng = 0.5 * repsilon[itype][jtype] * pexp;
		beng =0.0; 
    one.eng_vdwl = peng;
    one.eng_coul = 0.0;
  }
}