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lammps/src/MOLECULE/dump_bond.cpp
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dump_bond.cpp
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/* ----------------------------------------------------------------------
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);
// one-time file open
if (multifile == 0) openfile();
}
/* ---------------------------------------------------------------------- */
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");
}
/* ---------------------------------------------------------------------- */
void DumpBond::write_header(int ndump)
{
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;
}
}
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