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ntopo_dihedral_template.cpp
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Mon, Nov 18, 13:10

ntopo_dihedral_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_dihedral_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
/* ---------------------------------------------------------------------- */
NTopoDihedralTemplate::NTopoDihedralTemplate(LAMMPS *lmp) :
NTopo(lmp)
{
allocate_dihedral();
}
/* ---------------------------------------------------------------------- */
void NTopoDihedralTemplate::build()
{
int i,m,atom1,atom2,atom3,atom4;
int imol,iatom;
tagint tagprev;
int *num_dihedral;
tagint **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
int **dihedral_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;
ndihedrallist = 0;
for (i = 0; i < nlocal; i++) {
if (molindex[i] < 0) continue;
imol = molindex[i];
iatom = molatom[i];
tagprev = tag[i] - iatom - 1;
num_dihedral = onemols[imol]->num_dihedral;
dihedral_atom1 = onemols[imol]->dihedral_atom1;
dihedral_atom2 = onemols[imol]->dihedral_atom2;
dihedral_atom3 = onemols[imol]->dihedral_atom3;
dihedral_atom4 = onemols[imol]->dihedral_atom4;
dihedral_type = onemols[imol]->dihedral_type;
for (m = 0; m < num_dihedral[iatom]; m++) {
atom1 = atom->map(dihedral_atom1[iatom][m]+tagprev);
atom2 = atom->map(dihedral_atom2[iatom][m]+tagprev);
atom3 = atom->map(dihedral_atom3[iatom][m]+tagprev);
atom4 = atom->map(dihedral_atom4[iatom][m]+tagprev);
if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
nmissing++;
if (lostbond == ERROR) {
char str[128];
sprintf(str,"Dihedral atoms "
TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT
" missing on proc %d at step " BIGINT_FORMAT,
dihedral_atom1[iatom][m]+tagprev,
dihedral_atom2[iatom][m]+tagprev,
dihedral_atom3[iatom][m]+tagprev,
dihedral_atom4[iatom][m]+tagprev,
me,update->ntimestep);
error->one(FLERR,str);
}
continue;
}
atom1 = domain->closest_image(i,atom1);
atom2 = domain->closest_image(i,atom2);
atom3 = domain->closest_image(i,atom3);
atom4 = domain->closest_image(i,atom4);
if (newton_bond ||
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += DELTA;
memory->grow(dihedrallist,maxdihedral,5,"neigh_topo:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
dihedrallist[ndihedrallist][2] = atom3;
dihedrallist[ndihedrallist][3] = atom4;
dihedrallist[ndihedrallist][4] = dihedral_type[iatom][m];
ndihedrallist++;
}
}
}
if (cluster_check) dihedral_check(ndihedrallist,dihedrallist);
if (lostbond == IGNORE) return;
int all;
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
if (all) {
char str[128];
sprintf(str,
"Dihedral atoms missing at step " BIGINT_FORMAT,update->ntimestep);
if (me == 0) error->warning(FLERR,str);
}
}

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