510 lines
15 KiB
C++
510 lines
15 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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/* ----------------------------------------------------------------------
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Contributing author: Christina Payne (Vanderbilt U)
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Stan Moore (Sandia) for dipole terms
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------------------------------------------------------------------------- */
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#include "fix_efield.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.h"
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#include "error.h"
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#include "force.h"
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#include "input.h"
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#include "memory.h"
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#include "modify.h"
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#include "pair.h"
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#include "region.h"
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#include "respa.h"
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#include "update.h"
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#include "variable.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), estr(nullptr),
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pstr(nullptr), idregion(nullptr), region(nullptr), efield(nullptr)
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{
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if (narg < 6) utils::missing_cmd_args(FLERR, std::string("fix ") + style, error);
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dynamic_group_allow = 1;
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vector_flag = 1;
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scalar_flag = 1;
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size_vector = 3;
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global_freq = 1;
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extvector = 1;
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extscalar = 1;
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respa_level_support = 1;
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ilevel_respa = 0;
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energy_global_flag = 1;
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virial_global_flag = virial_peratom_flag = 1;
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qe2f = force->qe2f;
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xstyle = ystyle = zstyle = estyle = pstyle = NONE;
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if (utils::strmatch(arg[3], "^v_")) {
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xstr = utils::strdup(arg[3] + 2);
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} else {
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ex = qe2f * utils::numeric(FLERR, arg[3], false, lmp);
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xstyle = CONSTANT;
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}
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if (utils::strmatch(arg[4], "^v_")) {
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ystr = utils::strdup(arg[4] + 2);
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} else {
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ey = qe2f * utils::numeric(FLERR, arg[4], false, lmp);
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ystyle = CONSTANT;
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}
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if (utils::strmatch(arg[5], "^v_")) {
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zstr = utils::strdup(arg[5] + 2);
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} else {
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ez = qe2f * utils::numeric(FLERR, arg[5], false, lmp);
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zstyle = CONSTANT;
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}
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// optional args
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int iarg = 6;
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while (iarg < narg) {
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if (strcmp(arg[iarg], "region") == 0) {
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if (iarg + 2 > narg)
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utils::missing_cmd_args(FLERR, std::string("fix ") + style + " region", error);
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region = domain->get_region_by_id(arg[iarg + 1]);
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if (!region) error->all(FLERR, "Region {} for fix efield does not exist", arg[iarg + 1]);
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idregion = utils::strdup(arg[iarg + 1]);
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iarg += 2;
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} else if (strcmp(arg[iarg], "energy") == 0) {
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if (iarg + 2 > narg)
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utils::missing_cmd_args(FLERR, std::string("fix ") + style + "energy", error);
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if (utils::strmatch(arg[iarg + 1], "^v_")) {
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estr = utils::strdup(arg[iarg + 1] + 2);
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} else
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error->all(FLERR, "Unsupported argument for fix {} energy command: {}", style, arg[iarg]);
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iarg += 2;
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} else if (strcmp(arg[iarg], "potential") == 0) {
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if (iarg + 2 > narg)
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utils::missing_cmd_args(FLERR, std::string("fix ") + style + "potential", error);
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if (utils::strmatch(arg[iarg + 1], "^v_")) {
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pstr = utils::strdup(arg[iarg + 1] + 2);
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} else
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error->all(FLERR, "Unsupported argument for fix {} energy command: {}", style, arg[iarg]);
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iarg += 2;
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} else {
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error->all(FLERR, "Unknown keyword for fix {} command: {}", style, arg[iarg]);
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}
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}
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if (estr && pstr)
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error->all(FLERR, "Must not use energy and potential keywords at the same time with fix efield");
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force_flag = 0;
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fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
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maxatom = atom->nmax;
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memory->create(efield, maxatom, 4, "efield:efield");
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maxatom_energy = 0;
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}
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/* ---------------------------------------------------------------------- */
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FixEfield::~FixEfield()
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{
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delete[] xstr;
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delete[] ystr;
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delete[] zstr;
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delete[] estr;
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delete[] pstr;
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delete[] idregion;
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memory->destroy(efield);
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}
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/* ---------------------------------------------------------------------- */
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int FixEfield::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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mask |= POST_FORCE_RESPA;
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mask |= MIN_POST_FORCE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixEfield::init()
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{
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qflag = muflag = 0;
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if (atom->q_flag) qflag = 1;
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if (atom->mu_flag && atom->torque_flag) muflag = 1;
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if (!qflag && !muflag) error->all(FLERR, "Fix {} requires atom attribute q or mu", style);
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// warn if TIP4P pair style is used with plain fix efield
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if ((strcmp(style, "efield") == 0) && (comm->me == 0)) {
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int itmp;
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if (force->pair && force->pair->extract("qdist", itmp))
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error->warning(FLERR, "Fix efield produces incorrect forces when applied to TIP4P atoms");
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}
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// check variables
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if (xstr) {
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xvar = input->variable->find(xstr);
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if (xvar < 0) error->all(FLERR, "Variable {} for x-field in fix {} does not exist", xstr, style);
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if (input->variable->equalstyle(xvar))
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xstyle = EQUAL;
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else if (input->variable->atomstyle(xvar))
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xstyle = ATOM;
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else
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error->all(FLERR, "Variable {} for x-field in fix {} is invalid style", xstr, style);
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}
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if (ystr) {
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yvar = input->variable->find(ystr);
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if (yvar < 0) error->all(FLERR, "Variable {} for y-field in fix {} does not exist", ystr, style);
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if (input->variable->equalstyle(yvar))
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ystyle = EQUAL;
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else if (input->variable->atomstyle(yvar))
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ystyle = ATOM;
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else
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error->all(FLERR, "Variable {} for y-field in fix {} is invalid style", ystr, style);
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}
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if (zstr) {
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zvar = input->variable->find(zstr);
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if (zvar < 0) error->all(FLERR, "Variable {} for z-field in fix {} does not exist", zstr, style);
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if (input->variable->equalstyle(zvar))
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zstyle = EQUAL;
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else if (input->variable->atomstyle(zvar))
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zstyle = ATOM;
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else
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error->all(FLERR, "Variable {} for z-field in fix {} is invalid style", zstr, style);
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}
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if (estr) {
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evar = input->variable->find(estr);
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if (evar < 0) error->all(FLERR, "Variable {} for energy in fix {} does not exist", estr, style);
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if (input->variable->atomstyle(evar))
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estyle = ATOM;
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else
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error->all(FLERR, "Variable {} for energy in fix {} must be atom-style", estr, style);
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}
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if (pstr) {
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pvar = input->variable->find(pstr);
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if (pvar < 0) error->all(FLERR, "Variable {} for potential in fix {} does not exist", pstr, style);
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if (input->variable->atomstyle(pvar))
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pstyle = ATOM;
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else
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error->all(FLERR, "Variable {} for potential in fix {} must be atom-style", pstr, style);
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}
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// set index and check validity of region
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if (idregion) {
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region = domain->get_region_by_id(idregion);
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if (!region) error->all(FLERR, "Region {} for fix {} does not exist", idregion, style);
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}
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if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
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varflag = ATOM;
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else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
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varflag = EQUAL;
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else
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varflag = CONSTANT;
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if (muflag && varflag == ATOM)
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error->all(FLERR, "Fix {} with dipoles cannot use atom-style variables", style);
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if (muflag && update->whichflag == 2 && comm->me == 0)
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error->warning(FLERR, "The minimizer does not re-orient dipoles when using fix {}", style);
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if (varflag == CONSTANT && estyle != NONE)
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error->all(FLERR, "Cannot use variable energy with constant efield in fix {}", style);
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if (varflag == CONSTANT && pstyle != NONE)
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error->all(FLERR, "Cannot use variable potential with constant efield in fix {}", style);
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if ((varflag == EQUAL || varflag == ATOM) && update->whichflag == 2 && estyle == NONE && pstyle == NONE)
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error->all(FLERR, "Must use variable energy or potential with fix {} during minimization", style);
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if (utils::strmatch(update->integrate_style, "^respa")) {
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ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels - 1;
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if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixEfield::setup(int vflag)
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{
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if (utils::strmatch(update->integrate_style, "^respa")) {
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auto respa = dynamic_cast<Respa *>(update->integrate);
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respa->copy_flevel_f(ilevel_respa);
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post_force_respa(vflag, ilevel_respa, 0);
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respa->copy_f_flevel(ilevel_respa);
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} else {
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post_force(vflag);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixEfield::min_setup(int vflag)
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{
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post_force(vflag);
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}
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/* ----------------------------------------------------------------------
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apply F = qE
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------------------------------------------------------------------------- */
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void FixEfield::post_force(int vflag)
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{
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double **f = atom->f;
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double *q = atom->q;
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int *mask = atom->mask;
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imageint *image = atom->image;
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int nlocal = atom->nlocal;
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// virial setup
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v_init(vflag);
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// reallocate efield array if necessary
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if ((varflag == ATOM) && (atom->nmax > maxatom)) {
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maxatom = atom->nmax;
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memory->destroy(efield);
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memory->create(efield, maxatom, 4, "efield:efield");
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}
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// update region if necessary
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if (region) region->prematch();
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// fsum[0] = "potential energy" for added force
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// fsum[123] = extra force added to atoms
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fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
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force_flag = 0;
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double **x = atom->x;
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double fx, fy, fz;
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double v[6], unwrap[3];
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;
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// constant efield
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if (varflag == CONSTANT) {
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// charge interactions
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// force = qE, potential energy = F dot x in unwrapped coords
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if (qflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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fx = q[i] * ex;
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fy = q[i] * ey;
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fz = q[i] * ez;
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f[i][0] += fx;
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f[i][1] += fy;
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f[i][2] += fz;
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domain->unmap(x[i], image[i], unwrap);
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fsum[0] -= fx * unwrap[0] + fy * unwrap[1] + fz * unwrap[2];
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fsum[1] += fx;
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fsum[2] += fy;
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fsum[3] += fz;
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if (evflag) {
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v[0] = fx * unwrap[0];
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v[1] = fy * unwrap[1];
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v[2] = fz * unwrap[2];
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v[3] = fx * unwrap[1];
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v[4] = fx * unwrap[2];
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v[5] = fy * unwrap[2];
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v_tally(i, v);
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}
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}
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}
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// dipole interactions
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// no force, torque = mu cross E, potential energy = -mu dot E
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if (muflag) {
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double **mu = atom->mu;
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double **t = atom->torque;
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double tx, ty, tz;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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tx = ez * mu[i][1] - ey * mu[i][2];
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ty = ex * mu[i][2] - ez * mu[i][0];
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tz = ey * mu[i][0] - ex * mu[i][1];
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t[i][0] += tx;
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t[i][1] += ty;
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t[i][2] += tz;
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fsum[0] -= mu[i][0] * ex + mu[i][1] * ey + mu[i][2] * ez;
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}
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}
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// variable efield, wrap with clear/add
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// potential energy = evar if defined, else 0.0
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} else {
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update_efield_variables();
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// charge interactions
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// force = qE
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if (qflag) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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if (xstyle == ATOM) {
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fx = qe2f * q[i] * efield[i][0];
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} else {
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fx = q[i] * ex;
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}
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f[i][0] += fx;
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fsum[1] += fx;
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if (ystyle == ATOM) {
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fy = qe2f * q[i] * efield[i][1];
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} else {
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fy = q[i] * ey;
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}
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f[i][1] += fy;
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fsum[2] += fy;
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if (zstyle == ATOM) {
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fz = qe2f * q[i] * efield[i][2];
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} else {
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fz = q[i] * ez;
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}
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f[i][2] += fz;
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fsum[3] += fz;
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if (pstyle == ATOM) fsum[0] += qe2f * q[i] * efield[i][3];
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else if (estyle == ATOM) fsum[0] += efield[i][3];
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}
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}
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// dipole interactions
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// no force, torque = mu cross E
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if (muflag) {
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double **mu = atom->mu;
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double **t = atom->torque;
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double tx, ty, tz;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0], x[i][1], x[i][2])) continue;
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tx = ez * mu[i][1] - ey * mu[i][2];
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ty = ex * mu[i][2] - ez * mu[i][0];
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tz = ey * mu[i][0] - ex * mu[i][1];
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t[i][0] += tx;
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t[i][1] += ty;
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t[i][2] += tz;
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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixEfield::post_force_respa(int vflag, int ilevel, int /*iloop*/)
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{
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if (ilevel == ilevel_respa) post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixEfield::min_post_force(int vflag)
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{
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post_force(vflag);
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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double FixEfield::memory_usage()
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{
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double bytes = 0.0;
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if (varflag == ATOM) bytes = atom->nmax * 4 * sizeof(double);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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return energy added by fix
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------------------------------------------------------------------------- */
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double FixEfield::compute_scalar()
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{
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if (force_flag == 0) {
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MPI_Allreduce(fsum, fsum_all, 4, MPI_DOUBLE, MPI_SUM, world);
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force_flag = 1;
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}
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return fsum_all[0];
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}
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/* ----------------------------------------------------------------------
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return total extra force due to fix
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------------------------------------------------------------------------- */
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double FixEfield::compute_vector(int n)
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{
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if (force_flag == 0) {
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MPI_Allreduce(fsum, fsum_all, 4, MPI_DOUBLE, MPI_SUM, world);
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force_flag = 1;
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}
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return fsum_all[n + 1];
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}
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/* ----------------------------------------------------------------------
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update efield variables without doing anything else
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called by fix_qeq_reaxff
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------------------------------------------------------------------------- */
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void FixEfield::update_efield_variables()
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{
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modify->clearstep_compute();
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if (xstyle == EQUAL) {
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ex = qe2f * input->variable->compute_equal(xvar);
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} else if (xstyle == ATOM) {
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input->variable->compute_atom(xvar, igroup, &efield[0][0], 4, 0);
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}
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if (ystyle == EQUAL) {
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ey = qe2f * input->variable->compute_equal(yvar);
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} else if (ystyle == ATOM) {
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input->variable->compute_atom(yvar, igroup, &efield[0][1], 4, 0);
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}
|
|
if (zstyle == EQUAL) {
|
|
ez = qe2f * input->variable->compute_equal(zvar);
|
|
} else if (zstyle == ATOM) {
|
|
input->variable->compute_atom(zvar, igroup, &efield[0][2], 4, 0);
|
|
}
|
|
if (pstyle == ATOM) input->variable->compute_atom(pvar, igroup, &efield[0][3], 4, 0);
|
|
else if (estyle == ATOM) input->variable->compute_atom(evar, igroup, &efield[0][3], 4, 0);
|
|
|
|
modify->addstep_compute(update->ntimestep + 1);
|
|
}
|