100 lines
3.4 KiB
C++
100 lines
3.4 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://lammps.sandia.gov/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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_all.h"
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#include "atom.h"
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#include "force.h"
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#include "domain.h"
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#include "update.h"
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#include "output.h"
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#include "thermo.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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NTopoImproperAll::NTopoImproperAll(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 NTopoImproperAll::build()
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{
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int i,m,atom1,atom2,atom3,atom4;
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int nlocal = atom->nlocal;
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int *num_improper = atom->num_improper;
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tagint **improper_atom1 = atom->improper_atom1;
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tagint **improper_atom2 = atom->improper_atom2;
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tagint **improper_atom3 = atom->improper_atom3;
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tagint **improper_atom4 = atom->improper_atom4;
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int **improper_type = atom->improper_type;
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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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for (m = 0; m < num_improper[i]; m++) {
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atom1 = atom->map(improper_atom1[i][m]);
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atom2 = atom->map(improper_atom2[i][m]);
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atom3 = atom->map(improper_atom3[i][m]);
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atom4 = atom->map(improper_atom4[i][m]);
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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,fmt::format("Improper atoms {} {} {} {} missing on "
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"proc {} at step {}",
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improper_atom1[i][m],improper_atom2[i][m],
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improper_atom3[i][m],improper_atom4[i][m],
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me,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 ||
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(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[i][m];
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nimproperlist++;
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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,fmt::format("Improper atoms missing at step {}",
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update->ntimestep));
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}
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