115 lines
3.6 KiB
C++
115 lines
3.6 KiB
C++
// clang-format off
|
|
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://www.lammps.org/, 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 "ntopo_angle_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
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
NTopoAngleTemplate::NTopoAngleTemplate(LAMMPS *lmp) : NTopo(lmp)
|
|
{
|
|
allocate_angle();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void NTopoAngleTemplate::build()
|
|
{
|
|
int i,m,atom1,atom2,atom3;
|
|
int imol,iatom;
|
|
tagint tagprev;
|
|
int *num_angle;
|
|
tagint **angle_atom1,**angle_atom2,**angle_atom3;
|
|
int **angle_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;
|
|
nanglelist = 0;
|
|
|
|
for (i = 0; i < nlocal; i++) {
|
|
if (molindex[i] < 0) continue;
|
|
imol = molindex[i];
|
|
iatom = molatom[i];
|
|
tagprev = tag[i] - iatom - 1;
|
|
num_angle = onemols[imol]->num_angle;
|
|
angle_atom1 = onemols[imol]->angle_atom1;
|
|
angle_atom2 = onemols[imol]->angle_atom2;
|
|
angle_atom3 = onemols[imol]->angle_atom3;
|
|
angle_type = onemols[imol]->angle_type;
|
|
|
|
for (m = 0; m < num_angle[iatom]; m++) {
|
|
if (angle_type[iatom][m] <= 0) continue;
|
|
atom1 = atom->map(angle_atom1[iatom][m]+tagprev);
|
|
atom2 = atom->map(angle_atom2[iatom][m]+tagprev);
|
|
atom3 = atom->map(angle_atom3[iatom][m]+tagprev);
|
|
if (atom1 == -1 || atom2 == -1 || atom3 == -1) {
|
|
nmissing++;
|
|
if (lostbond == Thermo::ERROR)
|
|
error->one(FLERR,"Angle atoms {} {} {} missing on "
|
|
"proc {} at step {}",
|
|
angle_atom1[iatom][m]+tagprev,
|
|
angle_atom2[iatom][m]+tagprev,
|
|
angle_atom3[iatom][m]+tagprev,
|
|
me,update->ntimestep);
|
|
continue;
|
|
}
|
|
atom1 = domain->closest_image(i,atom1);
|
|
atom2 = domain->closest_image(i,atom2);
|
|
atom3 = domain->closest_image(i,atom3);
|
|
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
|
|
if (nanglelist == maxangle) {
|
|
maxangle += DELTA;
|
|
memory->grow(anglelist,maxangle,4,"neigh_topo:anglelist");
|
|
}
|
|
anglelist[nanglelist][0] = atom1;
|
|
anglelist[nanglelist][1] = atom2;
|
|
anglelist[nanglelist][2] = atom3;
|
|
anglelist[nanglelist][3] = angle_type[iatom][m];
|
|
nanglelist++;
|
|
}
|
|
}
|
|
}
|
|
|
|
if (cluster_check) angle_check();
|
|
if (lostbond == Thermo::IGNORE) return;
|
|
|
|
int all;
|
|
MPI_Allreduce(&nmissing,&all,1,MPI_INT,MPI_SUM,world);
|
|
if (all && (me == 0))
|
|
error->warning(FLERR,"Angle atoms missing at step {}",update->ntimestep);
|
|
}
|