115 lines
3.6 KiB
C++
115 lines
3.6 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 "atom_vec_tdpd.h"
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#include "atom.h"
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#include "error.h"
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#include "update.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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AtomVecTDPD::AtomVecTDPD(LAMMPS *lmp) : AtomVec(lmp)
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{
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molecular = Atom::ATOMIC;
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mass_type = PER_TYPE;
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forceclearflag = 1;
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atom->tdpd_flag = 1;
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atom->vest_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 = {"cc", "cc_flux", "vest"};
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fields_copy = {"cc", "vest"};
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fields_comm = {"cc", "vest"};
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fields_comm_vel = {"cc", "vest"};
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fields_reverse = {"cc_flux"};
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fields_border = {"cc", "vest"};
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fields_border_vel = {"cc", "vest"};
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fields_exchange = {"cc", "vest"};
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fields_restart = {"cc", "vest"};
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fields_create = {"cc", "vest"};
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fields_data_atom = {"id", "type", "x", "cc"};
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fields_data_vel = {"id", "v"};
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}
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/* ----------------------------------------------------------------------
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process additional args
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single arg = number of cc_species
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------------------------------------------------------------------------- */
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void AtomVecTDPD::process_args(int narg, char **arg)
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{
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if (narg < 1) error->all(FLERR, "Invalid atom_style tdpd command");
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atom->cc_species = utils::inumeric(FLERR, arg[0], false, lmp);
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cc_species = atom->cc_species;
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atom->add_peratom_change_columns("cc", cc_species);
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atom->add_peratom_change_columns("cc_flux", cc_species);
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// delay setting up of fields until now
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setup_fields();
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecTDPD::init()
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{
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AtomVec::init();
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if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Atom style tdpd requires lj units");
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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 AtomVecTDPD::grow_pointers()
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{
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cc_flux = atom->cc_flux;
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vest = atom->vest;
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}
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/* ----------------------------------------------------------------------
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clear extra forces starting at atom N
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nbytes = # of bytes to clear for a per-atom vector
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------------------------------------------------------------------------- */
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void AtomVecTDPD::force_clear(int n, size_t nbytes)
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{
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memset(&cc_flux[n][0], 0, cc_species * nbytes);
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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 AtomVecTDPD::data_atom_post(int ilocal)
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{
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atom->vest[ilocal][0] = 0.0;
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atom->vest[ilocal][1] = 0.0;
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atom->vest[ilocal][2] = 0.0;
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}
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