/* ----------------------------------------------------------------------
   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 "lmptype.h"
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_replica.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "neigh_list.h"
#include "comm.h"
#include "domain.h"
#include "lattice.h"
#include "region.h"
#include "group.h"
#include "memory.h"
#include "error.h"


using namespace LAMMPS_NS;

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

FixReplica::FixReplica(LAMMPS *lmp, int narg, char **arg) :
  Fix(lmp, narg, arg)
{
  if (narg < 5) error->all("Illegal fix replica command");

  nmax = 0;

  iregion = -1;
  idregion = NULL;

  int iarg = 3;
  while (iarg < narg) {
    if (strcmp(arg[iarg],"region") == 0) {
      if (iarg+2 > narg) error->all("Illegal fix replica command");
      iregion = domain->find_region(arg[iarg+1]);
      if (iregion == -1)
	error->all("Region ID for fix replica does not exist");
      int n = strlen(arg[iarg+1]) + 1;
      idregion = new char[n];
      strcpy(idregion,arg[iarg+1]);
      iarg += 2;
    } else error->all("Illegal fix replica command");
  }

  xlo = domain->regions[iregion]->extent_xlo;
  xhi = domain->regions[iregion]->extent_xhi;
  ylo = domain->regions[iregion]->extent_ylo;
  yhi = domain->regions[iregion]->extent_yhi;
  zlo = domain->regions[iregion]->extent_zlo;
  zhi = domain->regions[iregion]->extent_zhi;


}

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

FixReplica::~FixReplica()
{
  delete [] idregion;
}

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

int FixReplica::setmask()
{
  int mask = 0;
  mask |= POST_FORCE;
  return mask;
}

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

void FixReplica::init()
{
   if (iregion >= 0) {
		iregion = domain->find_region(idregion);
		if (iregion == -1) error->all("Region ID for fix replica does not exist");
  }
}

/* ---------------------------------------------------------------------- */
void FixReplica::post_force(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,factor_coul,eng;
  int *ilist,*jlist,*numneigh,**firstneigh;


  int irequest = neighbor->request((void *) this);
  neighbor->requests[irequest]->pair = 0;
  neighbor->requests[irequest]->fix = 1;
  neighbor->requests[irequest]->half = 0;
  neighbor->requests[irequest]->full = 1;

  if (force->pair == NULL)
    error->all("Delete_atoms requires a pair style be defined");

  NeighList *list = neighbor->lists[irequest];
  neighbor->build_one(irequest);

  double **x = atom->x;
  double **f = atom->f;
  int *type = atom->type;
  int *mask = atom->mask;
  int nlocal = atom->nlocal;
  double *special_lj = force->special_lj;
  double *special_coul = force->special_coul;
  int newton_pair = force->newton_pair;

  Pair *pair = force->pair;
  double **cutsq = force->pair->cutsq;

  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)];
	  factor_coul = special_coul[sbmask(j)];
      j &= NEIGHMASK;
	  if ( mask[i] & groupbit && domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]) && 
		  mask[j] & groupbit && domain->regions[iregion]->match(x[j][0],x[j][1],x[j][2]) ) {

			 delx = xtmp - x[j][0]  + (xhi-xlo);
			 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]) {
				eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
				f[i][0] += delx*fpair;
				f[i][1] += dely*fpair;
				f[i][2] += delz*fpair;
			}
	  }
    }
  }


}