96 lines
3.3 KiB
C++
96 lines
3.3 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_dihedral_partial.h"
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#include "atom.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 "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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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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NTopoDihedralPartial::NTopoDihedralPartial(LAMMPS *lmp) : NTopo(lmp)
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{
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allocate_dihedral();
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}
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/* ---------------------------------------------------------------------- */
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void NTopoDihedralPartial::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_dihedral = atom->num_dihedral;
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tagint **dihedral_atom1 = atom->dihedral_atom1;
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tagint **dihedral_atom2 = atom->dihedral_atom2;
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tagint **dihedral_atom3 = atom->dihedral_atom3;
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tagint **dihedral_atom4 = atom->dihedral_atom4;
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int **dihedral_type = atom->dihedral_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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ndihedrallist = 0;
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for (i = 0; i < nlocal; i++)
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for (m = 0; m < num_dihedral[i]; m++) {
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if (dihedral_type[i][m] <= 0) continue;
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atom1 = atom->map(dihedral_atom1[i][m]);
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atom2 = atom->map(dihedral_atom2[i][m]);
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atom3 = atom->map(dihedral_atom3[i][m]);
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atom4 = atom->map(dihedral_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, "Dihedral atoms {} {} {} {} missing on proc {} at step {}",
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dihedral_atom1[i][m], dihedral_atom2[i][m], dihedral_atom3[i][m],
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dihedral_atom4[i][m], 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 || (i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
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if (ndihedrallist == maxdihedral) {
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maxdihedral += DELTA;
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memory->grow(dihedrallist, maxdihedral, 5, "neigh_topo:dihedrallist");
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}
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dihedrallist[ndihedrallist][0] = atom1;
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dihedrallist[ndihedrallist][1] = atom2;
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dihedrallist[ndihedrallist][2] = atom3;
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dihedrallist[ndihedrallist][3] = atom4;
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dihedrallist[ndihedrallist][4] = dihedral_type[i][m];
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ndihedrallist++;
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}
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}
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if (cluster_check) dihedral_check(ndihedrallist, dihedrallist);
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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, "Dihedral atoms missing at step {}", update->ntimestep);
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}
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