237 lines
8.5 KiB
C++
237 lines
8.5 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_dielectric.h"
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#include "atom.h"
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#include "citeme.h"
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#include <cmath>
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using namespace LAMMPS_NS;
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static const char cite_user_dielectric_package[] =
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"DIELECTRIC package:\n\n"
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"@Article{TrungCPC19,\n"
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" author = {Trung Dac Nguyen, Honghao Li, Debarshee Bagchi,"
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" Francisco J. Solis, Monica Olvera de la Cruz,\n"
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" title = {Incorporating surface polarization effects into large-scale"
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" coarse-grained Molecular Dynamics simulation},\n"
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" journal = {Comp.~Phys.~Comm.},\n"
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" year = 2019,\n"
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" volume = 241,\n"
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" pages = {80--91}\n"
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"}\n\n";
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/* ---------------------------------------------------------------------- */
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AtomVecDielectric::AtomVecDielectric(LAMMPS *lmp) : AtomVec(lmp)
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{
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if (lmp->citeme) lmp->citeme->add(cite_user_dielectric_package);
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molecular = Atom::MOLECULAR;
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bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 1;
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mass_type = PER_TYPE;
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atom->molecule_flag = atom->q_flag = atom->mu_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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// clang-format off
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fields_grow = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
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"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
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"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
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"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special",
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"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
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fields_copy = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle", "angle_type",
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"angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type", "dihedral_atom1",
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"dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper", "improper_type",
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"improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4", "nspecial", "special",
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"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
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fields_comm = {"q", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
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fields_border = {"q", "molecule", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
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fields_border_vel = {"q", "molecule", "mu", "area", "ed", "em", "epsilon", "curvature",
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"q_unscaled"};
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fields_exchange = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
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"angle_type", "angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type",
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"dihedral_atom1", "dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper",
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"improper_type", "improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4",
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"nspecial", "special", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
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fields_restart = {"q", "molecule", "num_bond", "bond_type", "bond_atom", "num_angle",
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"angle_type", "angle_atom1", "angle_atom2", "angle_atom3", "num_dihedral", "dihedral_type",
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"dihedral_atom1", "dihedral_atom2", "dihedral_atom3", "dihedral_atom4", "num_improper",
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"improper_type", "improper_atom1", "improper_atom2", "improper_atom3", "improper_atom4",
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"mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
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fields_create = {"q", "molecule", "num_bond", "num_angle", "num_dihedral", "num_improper",
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"nspecial", "mu", "area", "ed", "em", "epsilon", "curvature", "q_unscaled"};
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fields_data_atom = { "id", "molecule", "type", "q", "x", "mu3", "area", "ed", "em", "epsilon",
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"curvature"};
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fields_data_vel = {"id v"};
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// clang-format on
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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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}
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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 AtomVecDielectric::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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num_angle = atom->num_angle;
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angle_type = atom->angle_type;
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num_dihedral = atom->num_dihedral;
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dihedral_type = atom->dihedral_type;
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num_improper = atom->num_improper;
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improper_type = atom->improper_type;
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nspecial = atom->nspecial;
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mu = atom->mu;
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area = atom->area;
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ed = atom->ed;
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em = atom->em;
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epsilon = atom->epsilon;
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curvature = atom->curvature;
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q_unscaled = atom->q_unscaled;
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}
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/* ----------------------------------------------------------------------
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initialize non-zero atom quantities
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------------------------------------------------------------------------- */
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void AtomVecDielectric::create_atom_post(int ilocal)
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{
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area[ilocal] = 1.0;
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em[ilocal] = 1.0;
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epsilon[ilocal] = 1.0;
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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 AtomVecDielectric::data_atom_post(int ilocal)
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{
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num_bond[ilocal] = 0;
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num_angle[ilocal] = 0;
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num_dihedral[ilocal] = 0;
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num_improper[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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double *q = atom->q;
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q_unscaled[ilocal] = q[ilocal];
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q[ilocal] /= epsilon[ilocal];
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double *mu_one = mu[ilocal];
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mu_one[3] = sqrt(mu_one[0] * mu_one[0] + mu_one[1] * mu_one[1] + mu_one[2] * mu_one[2]);
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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 AtomVecDielectric::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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assign an index to named atom property and return index
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return -1 if name is unknown to this atom style
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------------------------------------------------------------------------- */
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int AtomVecDielectric::property_atom(const std::string &name)
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{
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if (name == "area") return 0;
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if (name == "ed") return 1;
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if (name == "em") return 2;
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if (name == "epsilon") return 3;
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if (name == "curvature") return 4;
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if (name == "q_unscaled") return 5;
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return -1;
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}
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/* ----------------------------------------------------------------------
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pack per-atom data into buf for ComputePropertyAtom
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index maps to data specific to this atom style
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------------------------------------------------------------------------- */
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void AtomVecDielectric::pack_property_atom(int index, double *buf, int nvalues, int groupbit)
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{
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int n = 0;
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if (index == 0) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit)
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buf[n] = area[i];
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else
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buf[n] = 0.0;
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n += nvalues;
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}
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} else if (index == 1) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit)
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buf[n] = ed[i];
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else
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buf[n] = 0.0;
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n += nvalues;
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}
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} else if (index == 2) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit)
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buf[n] = em[i];
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else
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buf[n] = 0.0;
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n += nvalues;
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}
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} else if (index == 3) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit)
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buf[n] = epsilon[i];
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else
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buf[n] = 0.0;
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n += nvalues;
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}
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} else if (index == 4) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit)
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buf[n] = curvature[i];
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else
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buf[n] = 0.0;
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n += nvalues;
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}
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} else if (index == 5) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit)
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buf[n] = q_unscaled[i];
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else
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buf[n] = 0.0;
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n += nvalues;
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}
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}
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}
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