139 lines
4.4 KiB
C++
139 lines
4.4 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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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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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 "atom_vec_bond.h"
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#include "atom.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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AtomVecBond::AtomVecBond(LAMMPS *lmp) : AtomVec(lmp)
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{
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molecular = Atom::MOLECULAR;
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bonds_allow = 1;
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mass_type = PER_TYPE;
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atom->molecule_flag = 1;
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// strings with peratom variables to include in each AtomVec method
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// strings cannot contain fields in corresponding AtomVec default strings
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// order of fields in a string does not matter
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// except: fields_data_atom & fields_data_vel must match data file
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fields_grow = (char *)
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"molecule num_bond bond_type bond_atom nspecial special";
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fields_copy = (char *)
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"molecule num_bond bond_type bond_atom nspecial special";
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fields_comm = (char *) "";
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fields_comm_vel = (char *) "";
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fields_reverse = (char *) "";
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fields_border = (char *) "molecule";
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fields_border_vel = (char *) "molecule";
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fields_exchange = (char *)
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"molecule num_bond bond_type bond_atom nspecial special";
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fields_restart = (char *) "molecule num_bond bond_type bond_atom";
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fields_create = (char *) "molecule num_bond nspecial";
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fields_data_atom = (char *) "id molecule type x";
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fields_data_vel = (char *) "id v";
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setup_fields();
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bond_per_atom = 0;
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bond_negative = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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AtomVecBond::~AtomVecBond()
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{
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delete [] bond_negative;
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}
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/* ----------------------------------------------------------------------
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set local copies of all grow ptrs used by this class, except defaults
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needed in replicate when 2 atom classes exist and it calls pack_restart()
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------------------------------------------------------------------------- */
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void AtomVecBond::grow_pointers()
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{
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num_bond = atom->num_bond;
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bond_type = atom->bond_type;
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nspecial = atom->nspecial;
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}
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/* ----------------------------------------------------------------------
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modify values for AtomVec::pack_restart() to pack
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------------------------------------------------------------------------- */
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void AtomVecBond::pack_restart_pre(int ilocal)
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{
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// insure bond_negative vector is needed length
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if (bond_per_atom < atom->bond_per_atom) {
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delete [] bond_negative;
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bond_per_atom = atom->bond_per_atom;
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bond_negative = new int[bond_per_atom];
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}
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// flip any negative types to positive and flag which ones
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any_bond_negative = 0;
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for (int m = 0; m < num_bond[ilocal]; m++) {
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if (bond_type[ilocal][m] < 0) {
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bond_negative[m] = 1;
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bond_type[ilocal][m] = -bond_type[ilocal][m];
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any_bond_negative = 1;
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} else bond_negative[m] = 0;
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}
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}
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/* ----------------------------------------------------------------------
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unmodify values packed by AtomVec::pack_restart()
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------------------------------------------------------------------------- */
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void AtomVecBond::pack_restart_post(int ilocal)
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{
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// restore the flagged types to their negative values
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if (any_bond_negative) {
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for (int m = 0; m < num_bond[ilocal]; m++)
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if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];
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}
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}
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/* ----------------------------------------------------------------------
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initialize other atom quantities after AtomVec::unpack_restart()
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------------------------------------------------------------------------- */
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void AtomVecBond::unpack_restart_init(int ilocal)
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{
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nspecial[ilocal][0] = 0;
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nspecial[ilocal][1] = 0;
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nspecial[ilocal][2] = 0;
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}
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/* ----------------------------------------------------------------------
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modify what AtomVec::data_atom() just unpacked
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or initialize other atom quantities
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------------------------------------------------------------------------- */
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void AtomVecBond::data_atom_post(int ilocal)
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{
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num_bond[ilocal] = 0;
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nspecial[ilocal][0] = 0;
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nspecial[ilocal][1] = 0;
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nspecial[ilocal][2] = 0;
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}
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