233 lines
8.0 KiB
C++
233 lines
8.0 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://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 "atom_vec_full.h"
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#include "atom.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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AtomVecFull::AtomVecFull(LAMMPS *lmp) : AtomVec(lmp)
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{
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molecular = 1;
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bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 1;
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mass_type = 1;
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atom->molecule_flag = atom->q_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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"q molecule num_bond bond_type bond_atom "
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"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
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"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
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"dihedral_atom3 dihedral_atom4 "
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"num_improper improper_type improper_atom1 improper_atom2 "
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"improper_atom3 improper_atom4 "
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"nspecial special";
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fields_copy = (char *)
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"q molecule num_bond bond_type bond_atom "
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"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
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"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
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"dihedral_atom3 dihedral_atom4 "
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"num_improper improper_type improper_atom1 improper_atom2 "
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"improper_atom3 improper_atom4 "
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"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 *) "q molecule";
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fields_border_vel = (char *) "q molecule";
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fields_exchange = (char *)
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"q molecule num_bond bond_type bond_atom "
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"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
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"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
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"dihedral_atom3 dihedral_atom4 "
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"num_improper improper_type improper_atom1 improper_atom2 "
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"improper_atom3 improper_atom4 "
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"nspecial special";
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fields_restart = (char *)
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"q molecule num_bond bond_type bond_atom "
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"num_angle angle_type angle_atom1 angle_atom2 angle_atom3 "
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"num_dihedral dihedral_type dihedral_atom1 dihedral_atom2 "
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"dihedral_atom3 dihedral_atom4 "
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"num_improper improper_type improper_atom1 improper_atom2 "
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"improper_atom3 improper_atom4";
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fields_create = (char *)
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"q molecule num_bond num_angle num_dihedral num_improper nspecial";
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fields_data_atom = (char *) "id molecule type q x";
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fields_data_vel = (char *) "id v";
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setup_fields();
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bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
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bond_negative = angle_negative = dihedral_negative = improper_negative = NULL;
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}
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/* ---------------------------------------------------------------------- */
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AtomVecFull::~AtomVecFull()
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{
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delete [] bond_negative;
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delete [] angle_negative;
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delete [] dihedral_negative;
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delete [] improper_negative;
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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 AtomVecFull::pack_restart_pre(int ilocal)
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{
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// insure negative vectors are 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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if (angle_per_atom < atom->angle_per_atom) {
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delete [] angle_negative;
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angle_per_atom = atom->angle_per_atom;
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angle_negative = new int[angle_per_atom];
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}
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if (dihedral_per_atom < atom->dihedral_per_atom) {
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delete [] dihedral_negative;
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dihedral_per_atom = atom->dihedral_per_atom;
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dihedral_negative = new int[dihedral_per_atom];
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}
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if (improper_per_atom < atom->improper_per_atom) {
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delete [] improper_negative;
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improper_per_atom = atom->improper_per_atom;
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improper_negative = new int[improper_per_atom];
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}
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// flip any negative types to positive and flag which ones
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int *num_bond = atom->num_bond;
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int **bond_type = atom->bond_type;
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int *num_angle = atom->num_angle;
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int **angle_type = atom->angle_type;
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int *num_dihedral = atom->num_dihedral;
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int **dihedral_type = atom->dihedral_type;
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int *num_improper = atom->num_improper;
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int **improper_type = atom->improper_type;
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int 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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int any_angle_negative = 0;
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for (int m = 0; m < num_angle[ilocal]; m++) {
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if (angle_type[ilocal][m] < 0) {
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angle_negative[m] = 1;
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angle_type[ilocal][m] = -angle_type[ilocal][m];
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any_angle_negative = 1;
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} else angle_negative[m] = 0;
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}
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int any_dihedral_negative = 0;
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for (int m = 0; m < num_dihedral[ilocal]; m++) {
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if (dihedral_type[ilocal][m] < 0) {
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dihedral_negative[m] = 1;
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dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
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any_dihedral_negative = 1;
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} else dihedral_negative[m] = 0;
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}
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int any_improper_negative = 0;
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for (int m = 0; m < num_improper[ilocal]; m++) {
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if (improper_type[ilocal][m] < 0) {
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improper_negative[m] = 1;
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improper_type[ilocal][m] = -improper_type[ilocal][m];
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any_improper_negative = 1;
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} else improper_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 AtomVecFull::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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int *num_bond = atom->num_bond;
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int **bond_type = atom->bond_type;
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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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if (any_angle_negative) {
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int *num_angle = atom->num_angle;
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int **angle_type = atom->angle_type;
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for (int m = 0; m < num_angle[ilocal]; m++)
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if (angle_negative[m]) angle_type[ilocal][m] = -angle_type[ilocal][m];
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}
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if (any_dihedral_negative) {
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int *num_dihedral = atom->num_dihedral;
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int **dihedral_type = atom->dihedral_type;
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for (int m = 0; m < num_dihedral[ilocal]; m++)
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if (dihedral_negative[m])
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dihedral_type[ilocal][m] = -dihedral_type[ilocal][m];
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}
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if (any_improper_negative) {
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int *num_improper = atom->num_improper;
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int **improper_type = atom->improper_type;
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for (int m = 0; m < num_improper[ilocal]; m++)
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if (improper_negative[m])
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improper_type[ilocal][m] = -improper_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 AtomVecFull::unpack_restart_init(int ilocal)
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{
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atom->nspecial[ilocal][0] = 0;
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atom->nspecial[ilocal][1] = 0;
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atom->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 AtomVecFull::data_atom_post(int ilocal)
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{
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atom->num_bond[ilocal] = 0;
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atom->num_angle[ilocal] = 0;
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atom->num_dihedral[ilocal] = 0;
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atom->num_improper[ilocal] = 0;
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atom->nspecial[ilocal][0] = 0;
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atom->nspecial[ilocal][1] = 0;
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atom->nspecial[ilocal][2] = 0;
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}
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