1155 lines
37 KiB
C++
1155 lines
37 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 authors: Carolyn Phillips (U Mich), reservoir energy tally
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Aidan Thompson (SNL) GJF formulation
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Charles Sievers & Niels Gronbech-Jensen (UC Davis)
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updated GJF formulation and included
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statistically correct 2GJ velocity
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------------------------------------------------------------------------- */
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#include "fix_langevin.h"
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#include "atom.h"
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#include "atom_vec_ellipsoid.h"
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#include "comm.h"
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#include "compute.h"
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#include "error.h"
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#include "force.h"
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#include "group.h"
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#include "input.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "modify.h"
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#include "random_mars.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 <cmath>
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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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enum { NOBIAS, BIAS };
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enum { CONSTANT, EQUAL, ATOM };
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static constexpr double SINERTIA = 0.4; // moment of inertia prefactor for sphere
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static constexpr double EINERTIA = 0.2; // moment of inertia prefactor for ellipsoid
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/* ---------------------------------------------------------------------- */
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FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg), gjfflag(0), gfactor1(nullptr), gfactor2(nullptr), ratio(nullptr),
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tstr(nullptr), flangevin(nullptr), tforce(nullptr), franprev(nullptr), lv(nullptr),
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id_temp(nullptr), random(nullptr)
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{
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if (narg < 7) error->all(FLERR, "Illegal fix langevin command");
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dynamic_group_allow = 1;
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scalar_flag = 1;
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global_freq = 1;
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extscalar = 1;
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ecouple_flag = 1;
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nevery = 1;
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if (utils::strmatch(arg[3], "^v_")) {
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tstr = utils::strdup(arg[3] + 2);
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} else {
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t_start = utils::numeric(FLERR, arg[3], false, lmp);
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t_target = t_start;
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tstyle = CONSTANT;
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}
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t_stop = utils::numeric(FLERR, arg[4], false, lmp);
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t_period = utils::numeric(FLERR, arg[5], false, lmp);
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seed = utils::inumeric(FLERR, arg[6], false, lmp);
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if (t_period <= 0.0) error->all(FLERR, "Fix langevin period must be > 0.0");
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if (seed <= 0) error->all(FLERR, "Illegal fix langevin command");
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// initialize Marsaglia RNG with processor-unique seed
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random = new RanMars(lmp, seed + comm->me);
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// allocate per-type arrays for force prefactors
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gfactor1 = new double[atom->ntypes + 1];
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gfactor2 = new double[atom->ntypes + 1];
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ratio = new double[atom->ntypes + 1];
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// optional args
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for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;
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ascale = 0.0;
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gjfflag = 0;
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nvalues = 0;
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oflag = 0;
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tallyflag = 0;
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zeroflag = 0;
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osflag = 0;
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int iarg = 7;
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while (iarg < narg) {
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if (strcmp(arg[iarg], "angmom") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal fix langevin command");
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if (strcmp(arg[iarg + 1], "no") == 0)
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ascale = 0.0;
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else
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ascale = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "gjf") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal fix langevin command");
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if (strcmp(arg[iarg + 1], "no") == 0) {
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gjfflag = 0;
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osflag = 0;
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} else if (strcmp(arg[iarg + 1], "vfull") == 0) {
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gjfflag = 1;
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osflag = 1;
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} else if (strcmp(arg[iarg + 1], "vhalf") == 0) {
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gjfflag = 1;
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osflag = 0;
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} else
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error->all(FLERR, "Illegal fix langevin command");
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iarg += 2;
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} else if (strcmp(arg[iarg], "omega") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal fix langevin command");
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oflag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "scale") == 0) {
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if (iarg + 3 > narg) error->all(FLERR, "Illegal fix langevin command");
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int itype = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
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double scale = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
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if (itype <= 0 || itype > atom->ntypes) error->all(FLERR, "Illegal fix langevin command");
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ratio[itype] = scale;
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iarg += 3;
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} else if (strcmp(arg[iarg], "tally") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal fix langevin command");
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tallyflag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else if (strcmp(arg[iarg], "zero") == 0) {
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if (iarg + 2 > narg) error->all(FLERR, "Illegal fix langevin command");
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zeroflag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
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iarg += 2;
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} else
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error->all(FLERR, "Illegal fix langevin command");
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}
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// set temperature = nullptr, user can override via fix_modify if wants bias
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id_temp = nullptr;
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temperature = nullptr;
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energy = 0.0;
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// flangevin is unallocated until first call to setup()
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// compute_scalar checks for this and returns 0.0
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// if flangevin_allocated is not set
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flangevin = nullptr;
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flangevin_allocated = 0;
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franprev = nullptr;
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lv = nullptr;
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tforce = nullptr;
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maxatom1 = maxatom2 = 0;
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// setup atom-based array for franprev
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// register with Atom class
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// no need to set peratom_flag, b/c data is for internal use only
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if (gjfflag) {
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FixLangevin::grow_arrays(atom->nmax);
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atom->add_callback(Atom::GROW);
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// initialize franprev to zero
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++) {
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franprev[i][0] = 0.0;
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franprev[i][1] = 0.0;
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franprev[i][2] = 0.0;
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lv[i][0] = 0.0;
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lv[i][1] = 0.0;
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lv[i][2] = 0.0;
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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FixLangevin::~FixLangevin()
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{
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delete random;
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delete[] tstr;
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delete[] gfactor1;
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delete[] gfactor2;
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delete[] ratio;
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delete[] id_temp;
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memory->destroy(flangevin);
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memory->destroy(tforce);
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if (gjfflag) {
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memory->destroy(franprev);
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memory->destroy(lv);
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if (modify->get_fix_by_id(id)) atom->delete_callback(id, Atom::GROW);
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}
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}
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/* ---------------------------------------------------------------------- */
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int FixLangevin::setmask()
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{
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int mask = 0;
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if (gjfflag) mask |= INITIAL_INTEGRATE;
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mask |= POST_FORCE;
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mask |= POST_FORCE_RESPA;
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if (tallyflag || gjfflag) mask |= END_OF_STEP;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixLangevin::init()
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{
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if (gjfflag) {
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if (t_period * 2 == update->dt)
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error->all(FLERR, "Fix langevin gjf cannot have t_period equal to dt/2");
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// warn if any integrate fix comes after this one
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int before = 1;
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int flag = 0;
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for (auto ifix : modify->get_fix_list()) {
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if (strcmp(id, ifix->id) == 0)
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before = 0;
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else if ((modify->get_fix_mask(ifix) && utils::strmatch(ifix->style, "^nve")) && before)
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flag = 1;
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}
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if (flag) error->all(FLERR, "Fix langevin gjf should come before fix nve");
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}
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if (oflag && !atom->omega_flag)
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error->all(FLERR, "Fix langevin omega requires atom attribute omega");
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if (oflag && !atom->radius_flag)
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error->all(FLERR, "Fix langevin omega requires atom attribute radius");
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if (ascale && !atom->ellipsoid_flag)
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error->all(FLERR, "Fix langevin angmom requires atom style ellipsoid");
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// check variable
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if (tstr) {
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tvar = input->variable->find(tstr);
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if (tvar < 0) error->all(FLERR, "Variable name {} for fix langevin does not exist", tstr);
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if (input->variable->equalstyle(tvar))
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tstyle = EQUAL;
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else if (input->variable->atomstyle(tvar))
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tstyle = ATOM;
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else
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error->all(FLERR, "Variable {} for fix langevin is invalid style", tstr);
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}
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// if oflag or ascale set, check that all group particles are finite-size
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if (oflag) {
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double *radius = atom->radius;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (radius[i] == 0.0) error->one(FLERR, "Fix langevin omega requires extended particles");
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}
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if (ascale) {
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avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
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if (!avec) error->all(FLERR, "Fix langevin angmom requires atom style ellipsoid");
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int *ellipsoid = atom->ellipsoid;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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if (ellipsoid[i] < 0) error->one(FLERR, "Fix langevin angmom requires extended particles");
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}
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// set force prefactors
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if (!atom->rmass) {
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for (int i = 1; i <= atom->ntypes; i++) {
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gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
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gfactor2[i] = sqrt(atom->mass[i]) / force->ftm2v;
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if (gjfflag)
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gfactor2[i] *= sqrt(2.0 * force->boltz / t_period / update->dt / force->mvv2e);
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else
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gfactor2[i] *= sqrt(24.0 * force->boltz / t_period / update->dt / force->mvv2e);
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gfactor1[i] *= 1.0 / ratio[i];
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gfactor2[i] *= 1.0 / sqrt(ratio[i]);
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}
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}
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if (temperature && temperature->tempbias)
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tbiasflag = BIAS;
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else
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tbiasflag = NOBIAS;
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if (utils::strmatch(update->integrate_style, "^respa")) {
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nlevels_respa = (static_cast<Respa *>(update->integrate))->nlevels;
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if (gjfflag) error->all(FLERR, "Fix langevin gjf and run style respa are not compatible");
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}
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if (gjfflag) {
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gjfa = (1.0 - update->dt / 2.0 / t_period) / (1.0 + update->dt / 2.0 / t_period);
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gjfsib = sqrt(1.0 + update->dt / 2.0 / t_period);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixLangevin::setup(int vflag)
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{
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if (gjfflag) {
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double dtfm;
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double dt = update->dt;
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double **v = atom->v;
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double **f = atom->f;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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int *type = atom->type;
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if (rmass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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dtfm = force->ftm2v * 0.5 * dt / rmass[i];
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v[i][0] -= dtfm * f[i][0];
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v[i][1] -= dtfm * f[i][1];
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v[i][2] -= dtfm * f[i][2];
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if (tbiasflag) temperature->remove_bias(i, v[i]);
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v[i][0] /= gjfa * gjfsib * gjfsib;
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v[i][1] /= gjfa * gjfsib * gjfsib;
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v[i][2] /= gjfa * gjfsib * gjfsib;
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if (tbiasflag) temperature->restore_bias(i, v[i]);
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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dtfm = force->ftm2v * 0.5 * dt / mass[type[i]];
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v[i][0] -= dtfm * f[i][0];
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v[i][1] -= dtfm * f[i][1];
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v[i][2] -= dtfm * f[i][2];
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if (tbiasflag) temperature->remove_bias(i, v[i]);
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v[i][0] /= gjfa * gjfsib * gjfsib;
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v[i][1] /= gjfa * gjfsib * gjfsib;
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v[i][2] /= gjfa * gjfsib * gjfsib;
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if (tbiasflag) temperature->restore_bias(i, v[i]);
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}
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}
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}
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if (utils::strmatch(update->integrate_style, "^verlet"))
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post_force(vflag);
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else {
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auto respa = static_cast<Respa *>(update->integrate);
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respa->copy_flevel_f(nlevels_respa - 1);
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post_force_respa(vflag, nlevels_respa - 1, 0);
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respa->copy_f_flevel(nlevels_respa - 1);
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}
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if (gjfflag) {
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double dtfm;
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double dt = update->dt;
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double **f = atom->f;
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double **v = atom->v;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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int *type = atom->type;
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if (rmass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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dtfm = force->ftm2v * 0.5 * dt / rmass[i];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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lv[i][0] = v[i][0];
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lv[i][1] = v[i][1];
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lv[i][2] = v[i][2];
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}
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//
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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dtfm = force->ftm2v * 0.5 * dt / mass[type[i]];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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lv[i][0] = v[i][0];
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lv[i][1] = v[i][1];
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lv[i][2] = v[i][2];
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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 FixLangevin::initial_integrate(int /* vflag */)
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{
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double **v = atom->v;
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double **f = atom->f;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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f[i][0] /= gjfa;
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f[i][1] /= gjfa;
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f[i][2] /= gjfa;
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v[i][0] = lv[i][0];
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v[i][1] = lv[i][1];
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v[i][2] = lv[i][2];
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}
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}
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/* ---------------------------------------------------------------------- */
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// clang-format off
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void FixLangevin::post_force(int /*vflag*/)
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{
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double *rmass = atom->rmass;
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// enumerate all 2^6 possibilities for template parameters
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// this avoids testing them inside inner loop:
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// TSTYLEATOM, GJF, TALLY, BIAS, RMASS, ZERO
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if (tstyle == ATOM)
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if (gjfflag)
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if (tallyflag || osflag)
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if (tbiasflag == BIAS)
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if (rmass)
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if (zeroflag) post_force_templated<1,1,1,1,1,1>();
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else post_force_templated<1,1,1,1,1,0>();
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else
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if (zeroflag) post_force_templated<1,1,1,1,0,1>();
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else post_force_templated<1,1,1,1,0,0>();
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else
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if (rmass)
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if (zeroflag) post_force_templated<1,1,1,0,1,1>();
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else post_force_templated<1,1,1,0,1,0>();
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else
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if (zeroflag) post_force_templated<1,1,1,0,0,1>();
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else post_force_templated<1,1,1,0,0,0>();
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else
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if (tbiasflag == BIAS)
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if (rmass)
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if (zeroflag) post_force_templated<1,1,0,1,1,1>();
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else post_force_templated<1,1,0,1,1,0>();
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else
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if (zeroflag) post_force_templated<1,1,0,1,0,1>();
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else post_force_templated<1,1,0,1,0,0>();
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else
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if (rmass)
|
|
if (zeroflag) post_force_templated<1,1,0,0,1,1>();
|
|
else post_force_templated<1,1,0,0,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<1,1,0,0,0,1>();
|
|
else post_force_templated<1,1,0,0,0,0>();
|
|
else
|
|
if (tallyflag || osflag)
|
|
if (tbiasflag == BIAS)
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<1,0,1,1,1,1>();
|
|
else post_force_templated<1,0,1,1,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<1,0,1,1,0,1>();
|
|
else post_force_templated<1,0,1,1,0,0>();
|
|
else
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<1,0,1,0,1,1>();
|
|
else post_force_templated<1,0,1,0,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<1,0,1,0,0,1>();
|
|
else post_force_templated<1,0,1,0,0,0>();
|
|
else
|
|
if (tbiasflag == BIAS)
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<1,0,0,1,1,1>();
|
|
else post_force_templated<1,0,0,1,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<1,0,0,1,0,1>();
|
|
else post_force_templated<1,0,0,1,0,0>();
|
|
else
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<1,0,0,0,1,1>();
|
|
else post_force_templated<1,0,0,0,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<1,0,0,0,0,1>();
|
|
else post_force_templated<1,0,0,0,0,0>();
|
|
else
|
|
if (gjfflag)
|
|
if (tallyflag || osflag)
|
|
if (tbiasflag == BIAS)
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<0,1,1,1,1,1>();
|
|
else post_force_templated<0,1,1,1,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<0,1,1,1,0,1>();
|
|
else post_force_templated<0,1,1,1,0,0>();
|
|
else
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<0,1,1,0,1,1>();
|
|
else post_force_templated<0,1,1,0,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<0,1,1,0,0,1>();
|
|
else post_force_templated<0,1,1,0,0,0>();
|
|
else
|
|
if (tbiasflag == BIAS)
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<0,1,0,1,1,1>();
|
|
else post_force_templated<0,1,0,1,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<0,1,0,1,0,1>();
|
|
else post_force_templated<0,1,0,1,0,0>();
|
|
else
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<0,1,0,0,1,1>();
|
|
else post_force_templated<0,1,0,0,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<0,1,0,0,0,1>();
|
|
else post_force_templated<0,1,0,0,0,0>();
|
|
else
|
|
if (tallyflag || osflag)
|
|
if (tbiasflag == BIAS)
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<0,0,1,1,1,1>();
|
|
else post_force_templated<0,0,1,1,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<0,0,1,1,0,1>();
|
|
else post_force_templated<0,0,1,1,0,0>();
|
|
else
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<0,0,1,0,1,1>();
|
|
else post_force_templated<0,0,1,0,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<0,0,1,0,0,1>();
|
|
else post_force_templated<0,0,1,0,0,0>();
|
|
else
|
|
if (tbiasflag == BIAS)
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<0,0,0,1,1,1>();
|
|
else post_force_templated<0,0,0,1,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<0,0,0,1,0,1>();
|
|
else post_force_templated<0,0,0,1,0,0>();
|
|
else
|
|
if (rmass)
|
|
if (zeroflag) post_force_templated<0,0,0,0,1,1>();
|
|
else post_force_templated<0,0,0,0,1,0>();
|
|
else
|
|
if (zeroflag) post_force_templated<0,0,0,0,0,1>();
|
|
else post_force_templated<0,0,0,0,0,0>();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixLangevin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
|
|
{
|
|
if (ilevel == nlevels_respa-1) post_force(vflag);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
modify forces using one of the many Langevin styles
|
|
------------------------------------------------------------------------- */
|
|
|
|
template<int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY, int Tp_BIAS, int Tp_RMASS, int Tp_ZERO>
|
|
void FixLangevin::post_force_templated()
|
|
{
|
|
double gamma1,gamma2;
|
|
|
|
double **v = atom->v;
|
|
double **f = atom->f;
|
|
double *rmass = atom->rmass;
|
|
int *type = atom->type;
|
|
int *mask = atom->mask;
|
|
int nlocal = atom->nlocal;
|
|
|
|
// apply damping and thermostat to atoms in group
|
|
|
|
// for Tp_TSTYLEATOM:
|
|
// use per-atom per-coord target temperature
|
|
// for Tp_GJF:
|
|
// use Gronbech-Jensen/Farago algorithm
|
|
// else use regular algorithm
|
|
// for Tp_TALLY:
|
|
// store drag plus random forces in flangevin[nlocal][3]
|
|
// for Tp_BIAS:
|
|
// calculate temperature since some computes require temp
|
|
// computed on current nlocal atoms to remove bias
|
|
// test v = 0 since some computes mask non-participating atoms via v = 0
|
|
// and added force has extra term not multiplied by v = 0
|
|
// for Tp_RMASS:
|
|
// use per-atom masses
|
|
// else use per-type masses
|
|
// for Tp_ZERO:
|
|
// sum random force over all atoms in group
|
|
// subtract sum/count from each atom in group
|
|
|
|
double fdrag[3],fran[3],fsum[3],fsumall[3];
|
|
bigint count;
|
|
double fswap;
|
|
|
|
double boltz = force->boltz;
|
|
double dt = update->dt;
|
|
double mvv2e = force->mvv2e;
|
|
double ftm2v = force->ftm2v;
|
|
|
|
compute_target();
|
|
|
|
if (Tp_ZERO) {
|
|
fsum[0] = fsum[1] = fsum[2] = 0.0;
|
|
count = group->count(igroup);
|
|
if (count == 0)
|
|
error->all(FLERR,"Cannot zero Langevin force of 0 atoms");
|
|
}
|
|
|
|
// reallocate flangevin if necessary
|
|
|
|
if (Tp_TALLY) {
|
|
if (atom->nmax > maxatom1) {
|
|
memory->destroy(flangevin);
|
|
maxatom1 = atom->nmax;
|
|
memory->create(flangevin,maxatom1,3,"langevin:flangevin");
|
|
}
|
|
flangevin_allocated = 1;
|
|
}
|
|
|
|
if (Tp_BIAS) temperature->compute_scalar();
|
|
|
|
for (int i = 0; i < nlocal; i++) {
|
|
if (mask[i] & groupbit) {
|
|
if (Tp_TSTYLEATOM) tsqrt = sqrt(tforce[i]);
|
|
if (Tp_RMASS) {
|
|
gamma1 = -rmass[i] / t_period / ftm2v;
|
|
if (Tp_GJF)
|
|
gamma2 = sqrt(rmass[i]) * sqrt(2.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
|
else
|
|
gamma2 = sqrt(rmass[i]) * sqrt(24.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
|
gamma1 *= 1.0/ratio[type[i]];
|
|
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
|
} else {
|
|
gamma1 = gfactor1[type[i]];
|
|
gamma2 = gfactor2[type[i]] * tsqrt;
|
|
}
|
|
|
|
if (Tp_GJF) {
|
|
fran[0] = gamma2*random->gaussian();
|
|
fran[1] = gamma2*random->gaussian();
|
|
fran[2] = gamma2*random->gaussian();
|
|
} else {
|
|
fran[0] = gamma2*(random->uniform()-0.5);
|
|
fran[1] = gamma2*(random->uniform()-0.5);
|
|
fran[2] = gamma2*(random->uniform()-0.5);
|
|
}
|
|
|
|
if (Tp_BIAS) {
|
|
temperature->remove_bias(i,v[i]);
|
|
fdrag[0] = gamma1*v[i][0];
|
|
fdrag[1] = gamma1*v[i][1];
|
|
fdrag[2] = gamma1*v[i][2];
|
|
if (v[i][0] == 0.0) fran[0] = 0.0;
|
|
if (v[i][1] == 0.0) fran[1] = 0.0;
|
|
if (v[i][2] == 0.0) fran[2] = 0.0;
|
|
temperature->restore_bias(i,v[i]);
|
|
} else {
|
|
fdrag[0] = gamma1*v[i][0];
|
|
fdrag[1] = gamma1*v[i][1];
|
|
fdrag[2] = gamma1*v[i][2];
|
|
}
|
|
|
|
if (Tp_GJF) {
|
|
if (Tp_BIAS)
|
|
temperature->remove_bias(i,v[i]);
|
|
lv[i][0] = gjfsib*v[i][0];
|
|
lv[i][1] = gjfsib*v[i][1];
|
|
lv[i][2] = gjfsib*v[i][2];
|
|
if (Tp_BIAS)
|
|
temperature->restore_bias(i,v[i]);
|
|
if (Tp_BIAS)
|
|
temperature->restore_bias(i,lv[i]);
|
|
|
|
fswap = 0.5*(fran[0]+franprev[i][0]);
|
|
franprev[i][0] = fran[0];
|
|
fran[0] = fswap;
|
|
fswap = 0.5*(fran[1]+franprev[i][1]);
|
|
franprev[i][1] = fran[1];
|
|
fran[1] = fswap;
|
|
fswap = 0.5*(fran[2]+franprev[i][2]);
|
|
franprev[i][2] = fran[2];
|
|
fran[2] = fswap;
|
|
|
|
fdrag[0] *= gjfa;
|
|
fdrag[1] *= gjfa;
|
|
fdrag[2] *= gjfa;
|
|
fran[0] *= gjfa;
|
|
fran[1] *= gjfa;
|
|
fran[2] *= gjfa;
|
|
f[i][0] *= gjfa;
|
|
f[i][1] *= gjfa;
|
|
f[i][2] *= gjfa;
|
|
}
|
|
|
|
f[i][0] += fdrag[0] + fran[0];
|
|
f[i][1] += fdrag[1] + fran[1];
|
|
f[i][2] += fdrag[2] + fran[2];
|
|
|
|
if (Tp_ZERO) {
|
|
fsum[0] += fran[0];
|
|
fsum[1] += fran[1];
|
|
fsum[2] += fran[2];
|
|
}
|
|
|
|
if (Tp_TALLY) {
|
|
if (Tp_GJF) {
|
|
fdrag[0] = gamma1*lv[i][0]/gjfsib/gjfsib;
|
|
fdrag[1] = gamma1*lv[i][1]/gjfsib/gjfsib;
|
|
fdrag[2] = gamma1*lv[i][2]/gjfsib/gjfsib;
|
|
fswap = (2*fran[0]/gjfa - franprev[i][0])/gjfsib;
|
|
fran[0] = fswap;
|
|
fswap = (2*fran[1]/gjfa - franprev[i][1])/gjfsib;
|
|
fran[1] = fswap;
|
|
fswap = (2*fran[2]/gjfa - franprev[i][2])/gjfsib;
|
|
fran[2] = fswap;
|
|
}
|
|
flangevin[i][0] = fdrag[0] + fran[0];
|
|
flangevin[i][1] = fdrag[1] + fran[1];
|
|
flangevin[i][2] = fdrag[2] + fran[2];
|
|
|
|
}
|
|
}
|
|
}
|
|
|
|
// set total force to zero
|
|
|
|
if (Tp_ZERO) {
|
|
MPI_Allreduce(fsum,fsumall,3,MPI_DOUBLE,MPI_SUM,world);
|
|
fsumall[0] /= count;
|
|
fsumall[1] /= count;
|
|
fsumall[2] /= count;
|
|
for (int i = 0; i < nlocal; i++) {
|
|
if (mask[i] & groupbit) {
|
|
f[i][0] -= fsumall[0];
|
|
f[i][1] -= fsumall[1];
|
|
f[i][2] -= fsumall[2];
|
|
if (Tp_TALLY) {
|
|
flangevin[i][0] -= fsumall[0];
|
|
flangevin[i][1] -= fsumall[1];
|
|
flangevin[i][2] -= fsumall[2];
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
// thermostat omega and angmom
|
|
|
|
if (oflag) omega_thermostat();
|
|
if (ascale) angmom_thermostat();
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set current t_target and t_sqrt
|
|
------------------------------------------------------------------------- */
|
|
|
|
void FixLangevin::compute_target()
|
|
{
|
|
int *mask = atom->mask;
|
|
int nlocal = atom->nlocal;
|
|
|
|
double delta = update->ntimestep - update->beginstep;
|
|
if (delta != 0.0) delta /= update->endstep - update->beginstep;
|
|
|
|
// if variable temp, evaluate variable, wrap with clear/add
|
|
// reallocate tforce array if necessary
|
|
|
|
if (tstyle == CONSTANT) {
|
|
t_target = t_start + delta * (t_stop-t_start);
|
|
tsqrt = sqrt(t_target);
|
|
} else {
|
|
modify->clearstep_compute();
|
|
if (tstyle == EQUAL) {
|
|
t_target = input->variable->compute_equal(tvar);
|
|
if (t_target < 0.0)
|
|
error->one(FLERR, "Fix langevin variable returned negative temperature");
|
|
tsqrt = sqrt(t_target);
|
|
} else {
|
|
if (atom->nmax > maxatom2) {
|
|
maxatom2 = atom->nmax;
|
|
memory->destroy(tforce);
|
|
memory->create(tforce,maxatom2,"langevin:tforce");
|
|
}
|
|
input->variable->compute_atom(tvar,igroup,tforce,1,0);
|
|
for (int i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit)
|
|
if (tforce[i] < 0.0)
|
|
error->one(FLERR, "Fix langevin variable returned negative temperature");
|
|
}
|
|
modify->addstep_compute(update->ntimestep + 1);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
thermostat rotational dof via omega
|
|
------------------------------------------------------------------------- */
|
|
|
|
void FixLangevin::omega_thermostat()
|
|
{
|
|
double gamma1,gamma2;
|
|
|
|
double boltz = force->boltz;
|
|
double dt = update->dt;
|
|
double mvv2e = force->mvv2e;
|
|
double ftm2v = force->ftm2v;
|
|
|
|
double **torque = atom->torque;
|
|
double **omega = atom->omega;
|
|
double *radius = atom->radius;
|
|
double *rmass = atom->rmass;
|
|
int *mask = atom->mask;
|
|
int *type = atom->type;
|
|
int nlocal = atom->nlocal;
|
|
|
|
// rescale gamma1/gamma2 by 10/3 & sqrt(10/3) for spherical particles
|
|
// does not affect rotational thermosatting
|
|
// gives correct rotational diffusivity behavior
|
|
|
|
double tendivthree = 10.0/3.0;
|
|
double tran[3];
|
|
double inertiaone;
|
|
|
|
for (int i = 0; i < nlocal; i++) {
|
|
if ((mask[i] & groupbit) && (radius[i] > 0.0)) {
|
|
inertiaone = SINERTIA*radius[i]*radius[i]*rmass[i];
|
|
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
|
gamma1 = -tendivthree*inertiaone / t_period / ftm2v;
|
|
gamma2 = sqrt(inertiaone) * sqrt(80.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
|
gamma1 *= 1.0/ratio[type[i]];
|
|
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
|
tran[0] = gamma2*(random->uniform()-0.5);
|
|
tran[1] = gamma2*(random->uniform()-0.5);
|
|
tran[2] = gamma2*(random->uniform()-0.5);
|
|
torque[i][0] += gamma1*omega[i][0] + tran[0];
|
|
torque[i][1] += gamma1*omega[i][1] + tran[1];
|
|
torque[i][2] += gamma1*omega[i][2] + tran[2];
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
thermostat rotational dof via angmom
|
|
------------------------------------------------------------------------- */
|
|
|
|
void FixLangevin::angmom_thermostat()
|
|
{
|
|
double gamma1,gamma2;
|
|
|
|
double boltz = force->boltz;
|
|
double dt = update->dt;
|
|
double mvv2e = force->mvv2e;
|
|
double ftm2v = force->ftm2v;
|
|
|
|
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
|
double **torque = atom->torque;
|
|
double **angmom = atom->angmom;
|
|
double *rmass = atom->rmass;
|
|
int *ellipsoid = atom->ellipsoid;
|
|
int *mask = atom->mask;
|
|
int *type = atom->type;
|
|
int nlocal = atom->nlocal;
|
|
|
|
// rescale gamma1/gamma2 by ascale for aspherical particles
|
|
// does not affect rotational thermosatting
|
|
// gives correct rotational diffusivity behavior if (nearly) spherical
|
|
// any value will be incorrect for rotational diffusivity if aspherical
|
|
|
|
double inertia[3],omega[3],tran[3];
|
|
double *shape,*quat;
|
|
|
|
for (int i = 0; i < nlocal; i++) {
|
|
if (mask[i] & groupbit) {
|
|
shape = bonus[ellipsoid[i]].shape;
|
|
inertia[0] = EINERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
|
|
inertia[1] = EINERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
|
|
inertia[2] = EINERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
|
|
quat = bonus[ellipsoid[i]].quat;
|
|
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
|
|
|
|
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
|
|
gamma1 = -ascale / t_period / ftm2v;
|
|
gamma2 = sqrt(ascale*24.0*boltz/t_period/dt/mvv2e) / ftm2v;
|
|
gamma1 *= 1.0/ratio[type[i]];
|
|
gamma2 *= 1.0/sqrt(ratio[type[i]]) * tsqrt;
|
|
tran[0] = sqrt(inertia[0])*gamma2*(random->uniform()-0.5);
|
|
tran[1] = sqrt(inertia[1])*gamma2*(random->uniform()-0.5);
|
|
tran[2] = sqrt(inertia[2])*gamma2*(random->uniform()-0.5);
|
|
torque[i][0] += inertia[0]*gamma1*omega[0] + tran[0];
|
|
torque[i][1] += inertia[1]*gamma1*omega[1] + tran[1];
|
|
torque[i][2] += inertia[2]*gamma1*omega[2] + tran[2];
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
tally energy transfer to thermal reservoir
|
|
------------------------------------------------------------------------- */
|
|
|
|
void FixLangevin::end_of_step()
|
|
{
|
|
double **v = atom->v;
|
|
int *mask = atom->mask;
|
|
int nlocal = atom->nlocal;
|
|
double dtfm;
|
|
double dt = update->dt;
|
|
double *mass = atom->mass;
|
|
double *rmass = atom->rmass;
|
|
double **f = atom->f;
|
|
int *type = atom->type;
|
|
|
|
energy_onestep = 0.0;
|
|
|
|
if (tallyflag) {
|
|
if (gjfflag) {
|
|
for (int i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit) {
|
|
if (tbiasflag)
|
|
temperature->remove_bias(i, lv[i]);
|
|
energy_onestep += flangevin[i][0]*lv[i][0] + flangevin[i][1]*lv[i][1] +
|
|
flangevin[i][2]*lv[i][2];
|
|
if (tbiasflag)
|
|
temperature->restore_bias(i, lv[i]);
|
|
}
|
|
}
|
|
else
|
|
for (int i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit)
|
|
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
|
|
flangevin[i][2]*v[i][2];
|
|
}
|
|
|
|
if (gjfflag) {
|
|
double tmp[3];
|
|
for (int i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit) {
|
|
tmp[0] = v[i][0];
|
|
tmp[1] = v[i][1];
|
|
tmp[2] = v[i][2];
|
|
if (!osflag) {
|
|
v[i][0] = lv[i][0];
|
|
v[i][1] = lv[i][1];
|
|
v[i][2] = lv[i][2];
|
|
} else {
|
|
if (atom->rmass) {
|
|
dtfm = force->ftm2v * 0.5 * dt / rmass[i];
|
|
} else {
|
|
dtfm = force->ftm2v * 0.5 * dt / mass[type[i]];
|
|
}
|
|
v[i][0] = 0.5 * gjfsib*gjfsib*(v[i][0] + dtfm * f[i][0] / gjfa) +
|
|
dtfm * 0.5 * (gjfsib * flangevin[i][0] - franprev[i][0]) +
|
|
(gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][0];
|
|
v[i][1] = 0.5 * gjfsib*gjfsib*(v[i][1] + dtfm * f[i][1] / gjfa) +
|
|
dtfm * 0.5 * (gjfsib * flangevin[i][1] - franprev[i][1]) +
|
|
(gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][1];
|
|
v[i][2] = 0.5 * gjfsib*gjfsib*(v[i][2] + dtfm * f[i][2] / gjfa) +
|
|
dtfm * 0.5 * (gjfsib * flangevin[i][2] - franprev[i][2]) +
|
|
(gjfsib * gjfa * 0.5 + dt * 0.25 / t_period / gjfsib) * lv[i][2];
|
|
}
|
|
lv[i][0] = tmp[0];
|
|
lv[i][1] = tmp[1];
|
|
lv[i][2] = tmp[2];
|
|
}
|
|
}
|
|
|
|
energy += energy_onestep*update->dt;
|
|
}
|
|
|
|
// clang-format on
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixLangevin::reset_target(double t_new)
|
|
{
|
|
t_target = t_start = t_stop = t_new;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void FixLangevin::reset_dt()
|
|
{
|
|
if (atom->mass) {
|
|
for (int i = 1; i <= atom->ntypes; i++) {
|
|
gfactor2[i] = sqrt(atom->mass[i]) / force->ftm2v;
|
|
if (gjfflag)
|
|
gfactor2[i] *= sqrt(2.0 * force->boltz / t_period / update->dt / force->mvv2e);
|
|
else
|
|
gfactor2[i] *= sqrt(24.0 * force->boltz / t_period / update->dt / force->mvv2e);
|
|
gfactor2[i] *= 1.0 / sqrt(ratio[i]);
|
|
}
|
|
}
|
|
if (gjfflag) {
|
|
gjfa = (1.0 - update->dt / 2.0 / t_period) / (1.0 + update->dt / 2.0 / t_period);
|
|
gjfsib = sqrt(1.0 + update->dt / 2.0 / t_period);
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int FixLangevin::modify_param(int narg, char **arg)
|
|
{
|
|
if (strcmp(arg[0], "temp") == 0) {
|
|
if (narg < 2) utils::missing_cmd_args(FLERR, "fix_modify", error);
|
|
delete[] id_temp;
|
|
id_temp = utils::strdup(arg[1]);
|
|
temperature = modify->get_compute_by_id(id_temp);
|
|
if (!temperature)
|
|
error->all(FLERR, "Could not find fix_modify temperature compute ID: {}", id_temp);
|
|
|
|
if (temperature->tempflag == 0)
|
|
error->all(FLERR, "Fix_modify temperature compute {} does not compute temperature", id_temp);
|
|
if (temperature->igroup != igroup && comm->me == 0)
|
|
error->warning(FLERR, "Group for fix_modify temp != fix group: {} vs {}",
|
|
group->names[igroup], group->names[temperature->igroup]);
|
|
return 2;
|
|
}
|
|
return 0;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double FixLangevin::compute_scalar()
|
|
{
|
|
if (!tallyflag || !flangevin_allocated) return 0.0;
|
|
|
|
// capture the very first energy transfer to thermal reservoir
|
|
|
|
double **v = atom->v;
|
|
int *mask = atom->mask;
|
|
int nlocal = atom->nlocal;
|
|
|
|
if (update->ntimestep == update->beginstep) {
|
|
energy_onestep = 0.0;
|
|
if (!gjfflag) {
|
|
for (int i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit)
|
|
energy_onestep +=
|
|
flangevin[i][0] * v[i][0] + flangevin[i][1] * v[i][1] + flangevin[i][2] * v[i][2];
|
|
energy = 0.5 * energy_onestep * update->dt;
|
|
} else {
|
|
for (int i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit) {
|
|
if (tbiasflag) temperature->remove_bias(i, lv[i]);
|
|
energy_onestep +=
|
|
flangevin[i][0] * lv[i][0] + flangevin[i][1] * lv[i][1] + flangevin[i][2] * lv[i][2];
|
|
if (tbiasflag) temperature->restore_bias(i, lv[i]);
|
|
}
|
|
energy = -0.5 * energy_onestep * update->dt;
|
|
}
|
|
}
|
|
|
|
// convert midstep energy back to previous fullstep energy
|
|
|
|
double energy_me = energy - 0.5 * energy_onestep * update->dt;
|
|
|
|
double energy_all;
|
|
MPI_Allreduce(&energy_me, &energy_all, 1, MPI_DOUBLE, MPI_SUM, world);
|
|
return -energy_all;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
extract thermostat properties
|
|
------------------------------------------------------------------------- */
|
|
|
|
void *FixLangevin::extract(const char *str, int &dim)
|
|
{
|
|
dim = 0;
|
|
if (strcmp(str, "t_target") == 0) { return &t_target; }
|
|
return nullptr;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
memory usage of tally array
|
|
------------------------------------------------------------------------- */
|
|
|
|
double FixLangevin::memory_usage()
|
|
{
|
|
double bytes = 0.0;
|
|
if (gjfflag) bytes += (double) atom->nmax * 6 * sizeof(double);
|
|
if (tallyflag || osflag) bytes += (double) atom->nmax * 3 * sizeof(double);
|
|
if (tforce) bytes += (double) atom->nmax * sizeof(double);
|
|
return bytes;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
allocate atom-based array for franprev
|
|
------------------------------------------------------------------------- */
|
|
|
|
void FixLangevin::grow_arrays(int nmax)
|
|
{
|
|
memory->grow(franprev, nmax, 3, "fix_langevin:franprev");
|
|
memory->grow(lv, nmax, 3, "fix_langevin:lv");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
copy values within local atom-based array
|
|
------------------------------------------------------------------------- */
|
|
|
|
void FixLangevin::copy_arrays(int i, int j, int /*delflag*/)
|
|
{
|
|
franprev[j][0] = franprev[i][0];
|
|
franprev[j][1] = franprev[i][1];
|
|
franprev[j][2] = franprev[i][2];
|
|
lv[j][0] = lv[i][0];
|
|
lv[j][1] = lv[i][1];
|
|
lv[j][2] = lv[i][2];
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack values in local atom-based array for exchange with another proc
|
|
------------------------------------------------------------------------- */
|
|
|
|
int FixLangevin::pack_exchange(int i, double *buf)
|
|
{
|
|
int n = 0;
|
|
buf[n++] = franprev[i][0];
|
|
buf[n++] = franprev[i][1];
|
|
buf[n++] = franprev[i][2];
|
|
buf[n++] = lv[i][0];
|
|
buf[n++] = lv[i][1];
|
|
buf[n++] = lv[i][2];
|
|
return n;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack values in local atom-based array from exchange with another proc
|
|
------------------------------------------------------------------------- */
|
|
|
|
int FixLangevin::unpack_exchange(int nlocal, double *buf)
|
|
{
|
|
int n = 0;
|
|
franprev[nlocal][0] = buf[n++];
|
|
franprev[nlocal][1] = buf[n++];
|
|
franprev[nlocal][2] = buf[n++];
|
|
lv[nlocal][0] = buf[n++];
|
|
lv[nlocal][1] = buf[n++];
|
|
lv[nlocal][2] = buf[n++];
|
|
return n;
|
|
}
|