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

   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 "string.h"

#include "stdlib.h"

#include "compute_coord_atom.h"

#include "atom.h"

#include "modify.h"

#include "neighbor.h"

#include "force.h"

#include "pair.h"

#include "comm.h"

#include "memory.h"

#include "error.h"

using namespace LAMMPS_NS;

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

ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :

  Compute(lmp, narg, arg)

{

  if (narg != 4) error->all("Illegal compute centro/atom command");

  cutoff = atof(arg[3]);

  peratom_flag = 1;

  size_peratom = 0;

  neigh_full_once = 1;

  nmax = 0;

  coordination = NULL;

}

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

ComputeCoordAtom::~ComputeCoordAtom()

{

  memory->sfree(coordination);

}

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

void ComputeCoordAtom::init()

{

  if (force->pair == NULL || cutoff > force->pair->cutforce) 

    error->all("Compute coord/atom cutoff is longer than pairwise cutoff");

  int count = 0;

  for (int i = 0; i < modify->ncompute; i++)

    if (strcmp(modify->compute[i]->style,"coord/atom") == 0) count++;

  if (count > 1 && comm->me == 0)

    error->warning("More than one compute coord/atom defined");

}

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

void ComputeCoordAtom::compute_peratom()

{

  int j,k,jj,kk,n,numneigh;

  double xtmp,ytmp,ztmp,delx,dely,delz,rsq;

  int *neighs;

  // grow coordination array if necessary

  if (atom->nlocal > nmax) {

    memory->sfree(coordination);

    nmax = atom->nmax;

    coordination = (double *) 

      memory->smalloc(nmax*sizeof(double),"compute/coord/atom:coordination");

    scalar_atom = coordination;

  }

  // if needed, build a full neighbor list

  if (!neighbor->full_every) neighbor->build_full();

  // compute coordination number for each atom in group

  // use full neighbor list to count atoms less than cutoff

  double **x = atom->x;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  int nall = atom->nlocal + atom->nghost;

  double cutsq = cutoff*cutoff;

  for (int i = 0; i < nlocal; i++)

    if (mask[i] & groupbit) {

      xtmp = x[i][0];

      ytmp = x[i][1];

      ztmp = x[i][2];

      neighs = neighbor->firstneigh_full[i];

      numneigh = neighbor->numneigh_full[i];

      n = 0;

      for (k = 0; k < numneigh; k++) {

	j = neighs[k];

	if (j >= nall) j %= nall;

	delx = xtmp - x[j][0];

	dely = ytmp - x[j][1];

	delz = ztmp - x[j][2];

	rsq = delx*delx + dely*dely + delz*delz;

	if (rsq < cutsq) n++;

      }

      coordination[i] = n;

    }

}

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

   memory usage of local atom-based array

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

int ComputeCoordAtom::memory_usage()

{

  int bytes = nmax * sizeof(double);

  return bytes;

}

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

   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.

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

#ifndef COMPUTE_COORD_ATOM_H

#define COMPUTE_COORD_ATOM_H

#include "compute.h"

namespace LAMMPS_NS {

class ComputeCoordAtom : public Compute {

 public:

  ComputeCoordAtom(class LAMMPS *, int, char **);

  ~ComputeCoordAtom();

  void init();

  void compute_peratom();

  int memory_usage();

 private:

  int nmax;

  double cutoff;

  double *coordination;

};

}

#endif

#ifdef ComputeInclude

#include "compute_centro_atom.h"

#include "compute_coord_atom.h"

#include "compute_epair_atom.h"

#include "compute_etotal_atom.h"

#include "compute_ke_atom.h"

#ifdef ComputeClass

ComputeStyle(centro/atom,ComputeCentroAtom)

ComputeStyle(coord/atom,ComputeCoordAtom)

ComputeStyle(epair/atom,ComputeEpairAtom)

ComputeStyle(etotal/atom,ComputeEtotalAtom)

ComputeStyle(ke/atom,ComputeKEAtom)