git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/fix_langevin.cpp
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196
src/fix_langevin.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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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 "mpi.h"
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#include "math.h"
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#include "string.h"
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#include "stdlib.h"
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#include "fix_langevin.h"
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "domain.h"
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#include "region.h"
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#include "respa.h"
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#include "comm.h"
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#include "random_mars.h"
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#include "error.h"
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/* ---------------------------------------------------------------------- */
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FixLangevin::FixLangevin(int narg, char **arg) : Fix(narg, arg)
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{
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if (narg < 7) error->all("Illegal fix langevin command");
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t_start = atof(arg[3]);
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t_stop = atof(arg[4]);
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t_period = atof(arg[5]);
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int seed = atoi(arg[6]);
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if (t_period <= 0.0) error->all("Fix langevin period must be > 0.0");
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if (seed <= 0 || seed > 900000000)
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error->all("Illegal fix langevin command");
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// initialize Marsaglia RNG with processor-unique seed
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random = new RanMars(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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flagx = flagy = flagz = 1;
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for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;
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iregion = -1;
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int iarg = 7;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"axes") == 0) {
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if (iarg+4 > narg) error->all("Illegal fix langevin command");
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flagx = atoi(arg[iarg+1]);
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flagy = atoi(arg[iarg+2]);
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flagz = atoi(arg[iarg+3]);
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iarg += 4;
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} else if (strcmp(arg[iarg],"scale") == 0) {
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if (iarg+3 > narg) error->all("Illegal fix langevin command");
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int itype = atoi(arg[iarg+1]);
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double scale = atof(arg[iarg+2]);
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if (itype <= 0 || itype > atom->ntypes)
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error->all("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],"region") == 0) {
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for (iregion = 0; iregion < domain->nregion; iregion++)
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if (strcmp(arg[iarg+1],domain->regions[iregion]->id) == 0) break;
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if (iregion == domain->nregion)
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error->all("Fix langevin region ID does not exist");
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iarg += 2;
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} else error->all("Illegal fix langevin command");
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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 [] gfactor1;
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delete [] gfactor2;
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delete [] ratio;
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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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mask |= POST_FORCE;
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mask |= POST_FORCE_RESPA;
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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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// set force prefactors
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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]) *
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sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / force->ftm2v;
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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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if (strcmp(update->integrate_style,"respa") == 0)
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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}
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/* ---------------------------------------------------------------------- */
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void FixLangevin::setup()
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{
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if (strcmp(update->integrate_style,"verlet") == 0)
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post_force(1);
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else {
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((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
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post_force_respa(1,nlevels_respa-1,0);
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((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixLangevin::post_force(int vflag)
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{
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double delta = update->ntimestep - update->beginstep;
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delta /= update->endstep - update->beginstep;
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double t_target = t_start + delta * (t_stop-t_start);
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double tsqrt = sqrt(t_target);
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double gamma1,gamma2;
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// apply damping and thermostat to all atoms in fix group
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if (iregion == -1) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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gamma1 = gfactor1[type[i]];
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gamma2 = gfactor2[type[i]] * tsqrt;
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if (flagx) f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
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if (flagy) f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
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if (flagz) f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
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}
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}
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// apply damping and thermostat to all atoms in fix group and in region
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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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domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
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gamma1 = gfactor1[type[i]];
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gamma2 = gfactor2[type[i]] * tsqrt;
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if (flagx) f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
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if (flagy) f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
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if (flagz) f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
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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::post_force_respa(int vflag, int ilevel, int iloop)
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{
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if (ilevel == nlevels_respa-1) post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixLangevin::reset_target(double t_new)
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{
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t_start = t_stop = t_new;
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}
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