/* ----------------------------------------------------------------------
   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.
   ------------------------------------------------------------------------- */
/*
 *  dump_neighbors.cpp
 *  lammps-3Jun05
 *
 *  Created by Craig Maloney on 9/29/05.
 *  Copyright 2005 __MyCompanyName__. All rights reserved.
 *
 */

#include "string.h"
#include "dump_neighbors.h"
#include "atom.h"
#include "domain.h"
#include "update.h"
#include "error.h"
#include "modify.h"
#include "neighbor.h"

using namespace std;

/* ---------------------------------------------------------------------- */
// Similar to DumpBond
DumpNeighbors::DumpNeighbors(int narg, char **arg) : Dump(narg, arg) 
{
  if (narg != 5) error->all("Illegal dump neighbors command");
	
  size_one = 4;
	
  char *str = "%d %d %d %d %d";
  int n = strlen(str) + 1;
  format_default = new char[n];
  strcpy(format_default,str);

  // one-time file open
  
  if (multifile == 0) openfile();

}

DumpNeighbors::~DumpNeighbors(){
}


/* ---------------------------------------------------------------------- */
// Identical to DumpBond
void DumpNeighbors::init()
{
  delete [] format;
  char *str;
  if (format_user) str = format_user;
  else str = format_default;
	
  int n = strlen(str) + 2;
  format = new char[n];
  strcpy(format,str);
  strcat(format,"\n");
}

/* ---------------------------------------------------------------------- */
// Identical to DumpBond
void DumpNeighbors::write_header(int ndump)
{
  fprintf(fp,"ITEM: TIMESTEP\n");
  fprintf(fp,"%d\n",update->ntimestep);
  fprintf(fp,"ITEM: NUMBER OF PAIRS\n");
  fprintf(fp,"%d\n",ndump);
  fprintf(fp,"ITEM: PAIRS\n");
}

/* ---------------------------------------------------------------------- */
int DumpNeighbors::count()
{
  int c=0;
    
  int *tag = atom->tag;
  int *mask = atom->mask;
  int *type = atom->type;
  int nlocal = atom->nlocal;

  int nall = atom->nlocal + atom->nghost;
	
  int i,j,k;
	
  for (i = 0; i < nlocal; i++) {
    if (!(mask[i] & groupbit)) continue;
    int numneigh = neighbor->numneigh[i];
    int *neighs = neighbor->firstneigh[i];
        
    for (k = 0; k < numneigh; k++) {
      j = neighs[k];
      if (j >= nall) j = j % nall;
      if (!(mask[j]&groupbit)) continue;
      c++;
    }
  }
  return c;
}

/* ---------------------------------------------------------------------- */
int DumpNeighbors::pack()
{
  // cem
  // We need to discuss the 1nn bonds... not the static (molecular) 
  // bonds stored in atom_bond.
  //cem
	
  int *tag = atom->tag;
  int *mask = atom->mask;
  int *type = atom->type;
  int nlocal = atom->nlocal;
	
  int i,j,k;
	
  int nall = atom->nlocal + atom->nghost;
    
  int m = 0;
  for (i = 0; i < nlocal; i++) {
    if (!(mask[i] & groupbit)) continue;
    int numneigh = neighbor->numneigh[i];
    int *neighs = neighbor->firstneigh[i];

    for (k = 0; k < numneigh; k++) {
      j = neighs[k];
      if (j >= nall) j = j % nall;
      if (!(mask[j]&groupbit)) continue;
      buf[m++] = tag[i]; 
      buf[m++] = tag[j];
      buf[m++] = type[i];
      buf[m++] = type[j];
    }
  }
  return m;
}

/* ---------------------------------------------------------------------- */
// Identical to DumpBond
void DumpNeighbors::write_data(int n, double *buf)
{
  int m = 0;
  for (int i = 0; i < n; i++) {
    index++;
    fprintf(fp,format,
	    index, 
	    static_cast<int> (buf[m]),
	    static_cast<int> (buf[m+1]), 
	    static_cast<int> (buf[m+2]),
	    static_cast<int> (buf[m+3]));
    m += size_one;
  }
}