114 lines
3.9 KiB
C++
114 lines
3.9 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "ntopo_improper_template.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "domain.h"
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#include "error.h"
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#include "force.h"
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#include "memory.h"
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#include "molecule.h"
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#include "output.h"
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#include "thermo.h"
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#include "update.h"
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using namespace LAMMPS_NS;
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static constexpr int DELTA = 10000;
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/* ---------------------------------------------------------------------- */
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NTopoImproperTemplate::NTopoImproperTemplate(LAMMPS *lmp) : NTopo(lmp)
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{
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allocate_improper();
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}
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/* ---------------------------------------------------------------------- */
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void NTopoImproperTemplate::build()
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{
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int i, m, atom1, atom2, atom3, atom4;
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int imol, iatom;
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tagint tagprev;
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int *num_improper;
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tagint **improper_atom1, **improper_atom2, **improper_atom3, **improper_atom4;
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int **improper_type;
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Molecule **onemols = atom->avec->onemols;
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tagint *tag = atom->tag;
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int *molindex = atom->molindex;
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int *molatom = atom->molatom;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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int lostbond = output->thermo->lostbond;
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int nmissing = 0;
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nimproperlist = 0;
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for (i = 0; i < nlocal; i++) {
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if (molindex[i] < 0) continue;
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imol = molindex[i];
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iatom = molatom[i];
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tagprev = tag[i] - iatom - 1;
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num_improper = onemols[imol]->num_improper;
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improper_atom1 = onemols[imol]->improper_atom1;
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improper_atom2 = onemols[imol]->improper_atom2;
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improper_atom3 = onemols[imol]->improper_atom3;
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improper_atom4 = onemols[imol]->improper_atom4;
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improper_type = onemols[imol]->improper_type;
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for (m = 0; m < num_improper[iatom]; m++) {
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atom1 = atom->map(improper_atom1[iatom][m] + tagprev);
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atom2 = atom->map(improper_atom2[iatom][m] + tagprev);
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atom3 = atom->map(improper_atom3[iatom][m] + tagprev);
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atom4 = atom->map(improper_atom4[iatom][m] + tagprev);
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if (atom1 == -1 || atom2 == -1 || atom3 == -1 || atom4 == -1) {
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nmissing++;
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if (lostbond == Thermo::ERROR)
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error->one(FLERR, "Improper atoms {} {} {} {} missing on proc {} at step {}",
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improper_atom1[iatom][m] + tagprev, improper_atom2[iatom][m] + tagprev,
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improper_atom3[iatom][m] + tagprev, improper_atom4[iatom][m] + tagprev, me,
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update->ntimestep);
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continue;
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}
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atom1 = domain->closest_image(i, atom1);
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atom2 = domain->closest_image(i, atom2);
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atom3 = domain->closest_image(i, atom3);
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atom4 = domain->closest_image(i, atom4);
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if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
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if (nimproperlist == maximproper) {
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maximproper += DELTA;
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memory->grow(improperlist, maximproper, 5, "neigh_topo:improperlist");
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}
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improperlist[nimproperlist][0] = atom1;
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improperlist[nimproperlist][1] = atom2;
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improperlist[nimproperlist][2] = atom3;
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improperlist[nimproperlist][3] = atom4;
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improperlist[nimproperlist][4] = improper_type[iatom][m];
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nimproperlist++;
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}
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}
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}
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if (cluster_check) dihedral_check(nimproperlist, improperlist);
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if (lostbond == Thermo::IGNORE) return;
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int all;
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MPI_Allreduce(&nmissing, &all, 1, MPI_INT, MPI_SUM, world);
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if (all && (me == 0))
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error->warning(FLERR, "Improper atoms missing at step {}", update->ntimestep);
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}
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