96 lines
3.1 KiB
C++
96 lines
3.1 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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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_oxdna.h"
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#include "atom.h"
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#include "comm.h"
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#include "error.h"
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#include "force.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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AtomVecOxdna::AtomVecOxdna(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 *) "id5p";
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fields_copy = (char *) "id5p";
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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 *) "id5p";
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fields_border_vel = (char *) "";
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fields_exchange = (char *) "id5p";
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fields_restart = (char *) "id5p";
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fields_create = (char *) "";
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fields_data_atom = (char *) "id type x";
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fields_data_vel = (char *) "id v";
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setup_fields();
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if(!force->newton_bond) error->warning(FLERR,"Write_data command requires newton on to preserve 3'->5' bond polarity");
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}
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/* ---------------------------------------------------------------------- */
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AtomVecOxdna::~AtomVecOxdna() {}
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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 AtomVecOxdna::grow_pointers()
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{
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id5p = atom->id5p;
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}
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/* ----------------------------------------------------------------------
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initialize atom quantity 5' partner
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------------------------------------------------------------------------- */
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void AtomVecOxdna::data_atom_post(int ilocal)
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{
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tagint *id5p = atom->id5p;
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id5p[ilocal] = -1;
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}
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/* ----------------------------------------------------------------------
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process bond information as per data file
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store 5' partner to inform 3'->5' bond directionality
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------------------------------------------------------------------------- */
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void AtomVecOxdna::data_bonds_post(int /*m*/, int /*num_bond*/, tagint atom1, tagint atom2,
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tagint id_offset)
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{
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int n;
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tagint *id5p = atom->id5p;
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if (id_offset) {
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atom1 += id_offset;
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atom2 += id_offset;
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}
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if ((n = atom->map(atom1)) >= 0) { id5p[n] = atom2; }
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}
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