cp dihedral_hybrid.cpp ..

  cp dihedral_multi_harmonic.cpp ..

  cp dihedral_opls.cpp ..

  cp dump_bond.cpp ..

  cp fix_bond_break.cpp ..

  cp fix_bond_create.cpp ..

  cp fix_bond_swap.cpp ..

  cp dihedral_hybrid.h ..

  cp dihedral_multi_harmonic.h ..

  cp dihedral_opls.h ..

  cp dump_bond.h ..

  cp fix_bond_break.h ..

  cp fix_bond_create.h ..

  cp fix_bond_swap.h ..

  rm ../dihedral_hybrid.cpp

  rm ../dihedral_multi_harmonic.cpp

  rm ../dihedral_opls.cpp

  rm ../dump_bond.cpp

  rm ../fix_bond_break.cpp

  rm ../fix_bond_create.cpp

  rm ../fix_bond_swap.cpp

  rm ../dihedral_hybrid.h

  rm ../dihedral_multi_harmonic.h

  rm ../dihedral_opls.h

  rm ../dump_bond.h

  rm ../fix_bond_break.h

  rm ../fix_bond_create.h

  rm ../fix_bond_swap.h

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

   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 "dump_bond.h"

#include "atom.h"

#include "domain.h"

#include "update.h"

#include "error.h"

using namespace LAMMPS_NS;

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

DumpBond::DumpBond(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)

{

  if (narg != 5) error->all("Illegal dump bond command");

  if (atom->molecular == 0)

    error->all("Cannot use dump bond with non-molecular system");

  size_one = 3;

  char *str = (char *) "%d %d %d %d";

  int n = strlen(str) + 1;

  format_default = new char[n];

  strcpy(format_default,str);

}

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

void DumpBond::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");

  // open single file, one time only

  if (multifile == 0) openfile();

}

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

void DumpBond::write_header(int ndump)

{

  if (me == 0) {

    fprintf(fp,"ITEM: TIMESTEP\n");

    fprintf(fp,"%d\n",update->ntimestep);

    fprintf(fp,"ITEM: NUMBER OF BONDS\n");

    fprintf(fp,"%d\n",ndump);

    fprintf(fp,"ITEM: BONDS\n");

  }

}

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

int DumpBond::count()

{

  index = 0;

  int *num_bond = atom->num_bond;

  int **bond_type = atom->bond_type;

  int **bond_atom = atom->bond_atom;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  int i,j,k;

  int m = 0;

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

    if (!(mask[i] & groupbit)) continue;

    for (j = 0; j < num_bond[i]; j++) {

      k = atom->map(bond_atom[i][j]);

      if (k >= 0 && !(mask[k] & groupbit)) continue;

      if (bond_type[i][j] == 0) continue;

      m++;

    }

  }

  return m;

}

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

int DumpBond::pack()

{

  int *num_bond = atom->num_bond;

  int **bond_type = atom->bond_type;

  int **bond_atom = atom->bond_atom;

  int *tag = atom->tag;

  int *mask = atom->mask;

  int nlocal = atom->nlocal;

  int i,j,k,type,iatom;

  int m = 0;

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

    if (!(mask[i] & groupbit)) continue;

    for (j = 0; j < num_bond[i]; j++) {

      iatom = bond_atom[i][j];

      k = atom->map(iatom);

      if (k >= 0 && !(mask[k] & groupbit)) continue;

      type = bond_type[i][j];

      if (type == 0) continue;

      buf[m++] = type;

      buf[m++] = tag[i];

      buf[m++] = iatom;

    }

  }

  return m;

}

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

void DumpBond::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]));

    m += size_one;

  }

}

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

   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 DUMP_BOND_H

#define DUMP_BOND_H

#include "dump.h"

namespace LAMMPS_NS {

class DumpBond : public Dump {

 public:

  DumpBond(LAMMPS *, int, char **);

  void init();

 private:

  int index;            // counter for bond output

  void write_header(int);

  int count();

  int pack();

  void write_data(int, double *);

};

}

#endif

DihedralStyle(opls,DihedralOPLS)

#endif

#ifdef DumpInclude

#include "dump_bond.h"

#endif

#ifdef DumpClass

DumpStyle(bond,DumpBond)

#endif

#ifdef FixInclude

#include "fix_bond_break.h"

#include "fix_bond_create.h"