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lammps/src/ntopo_bond_template.cpp
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ntopo_bond_template.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 <mpi.h>
#include "ntopo_bond_template.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "domain.h"
#include "update.h"
#include "output.h"
#include "thermo.h"
#include "molecule.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 10000
/* ---------------------------------------------------------------------- */
NTopoBondTemplate::NTopoBondTemplate(LAMMPS *lmp) : NTopo(lmp)
{
allocate_bond();
}
/* ---------------------------------------------------------------------- */
void NTopoBondTemplate::build()
{
int i,m,atom1;
int imol,iatom;
tagint tagprev;
int *num_bond;
tagint **bond_atom;
int **bond_type;
Molecule **onemols = atom->avec->onemols;
tagint *tag = atom->tag;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
int lostbond = output->thermo->lostbond;
int nmissing = 0;
nbondlist = 0;
for (i = 0; i < nlocal; i++) {
if (molindex[i] < 0) continue;
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
num_bond = onemols[imol]->num_bond;
bond_atom = onemols[imol]->bond_atom;
bond_type = onemols[imol]->bond_type;
for (m = 0; m < num_bond[iatom]; m++) {
if (bond_type[iatom][m] <= 0) continue;
atom1 = atom->map(bond_atom[iatom][m]+tagprev);
if (atom1 == -1) {
nmissing++;
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Bond atoms " TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
tag[i],bond_atom[iatom][m]+tagprev,me,update->ntimestep);
error->one(FLERR,str);
}
continue;
}
atom1 = domain->closest_image(i,atom1);
if (newton_bond || i < atom1) {
if (nbondlist == maxbond) {
maxbond += DELTA;
memory->grow(bondlist,maxbond,3,"neigh_topo:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = atom1;
bondlist[nbondlist][2] = bond_type[iatom][m];
nbondlist++;
}
}
}
if (cluster_check) bond_check();
if (lostbond == IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
if (all) {
char str[128];
sprintf(str,
"Bond atoms missing at step " BIGINT_FORMAT,update->ntimestep);
if (me == 0) error->warning(FLERR,str);
}
}
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