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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Kristof Bal (University of Antwerp, Belgium)
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------------------------------------------------------------------------- */
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#include "fix_tfmc.h"
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#include "mpi.h"
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#include "string.h"
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#include "math.h"
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#include "float.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 "group.h"
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#include "random_mars.h"
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#include "comm.h"
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#include "domain.h"
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#include "memory.h"
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#include "modify.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixTFMC::FixTFMC(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 6) error->all(FLERR,"Illegal fix tfmc command");
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// although we are not doing MD, we would like to use tfMC as an MD "drop in"
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time_integrate = 1;
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d_max = force->numeric(FLERR,arg[3]);
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T_set = force->numeric(FLERR,arg[4]);
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seed = force->inumeric(FLERR,arg[5]);
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if (d_max <= 0) error->all(FLERR,"Fix tfmc displacement length must be > 0");
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if (T_set <= 0) error->all(FLERR,"Fix tfmc temperature must be > 0");
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if (seed <= 0) error->all(FLERR,"Illegal fix tfmc random seed");
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// additional keywords
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comflag = 0;
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rotflag = 0;
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int iarg = 6;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"com") == 0) {
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if (iarg+4 > narg) error->all(FLERR,"Illegal fix tfmc command");
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comflag = 1;
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xflag = force->inumeric(FLERR,arg[iarg+1]);
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yflag = force->inumeric(FLERR,arg[iarg+2]);
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zflag = force->inumeric(FLERR,arg[iarg+3]);
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iarg += 4;
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} else if (strcmp(arg[iarg],"rot") == 0) {
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if (iarg+1 > narg) error->all(FLERR,"Illegal fix tfmc command");
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rotflag = 1;
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iarg += 1;
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} else error->all(FLERR,"Illegal fix tfmc command");
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}
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// error checks
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if (comflag)
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if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
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zflag < 0 || zflag > 1)
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error->all(FLERR,"Illegal fix tfmc command");
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if (xflag + yflag + zflag == 0)
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comflag = 0;
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if (rotflag) {
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xd = NULL;
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nmax = -1;
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}
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random_num = new RanMars(lmp,seed + comm->me);
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}
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/* ---------------------------------------------------------------------- */
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FixTFMC::~FixTFMC()
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{
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delete random_num;
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if (rotflag) {
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memory->destroy(xd);
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xd = NULL;
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nmax = -1;
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}
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}
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/* ---------------------------------------------------------------------- */
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int FixTFMC::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixTFMC::init()
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{
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// shake cannot be handled because it requires velocities
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// (and real MD in general)
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int has_shake = 0;
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for (int i = 0; i < modify->nfix; i++)
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if (strcmp(modify->fix[i]->style,"shake") == 0) ++has_shake;
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if (has_shake > 0)
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error->all(FLERR,"Fix tfmc is not compatible with fix shake");
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// obtain lowest mass in the system
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// We do this here, in init(), rather than in initial_integrate().
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// This might seem somewhat odd: after all, another atom could be added with a
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// mass smaller than mass_min (in the case of a per-particle mass), so mass_min
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// should change during the run. However, this would imply that the overall
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// meaning of the input Delta is not very well-defined, because its meaning
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// can change during the run. So we'll assume all particle types (in terms of
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// possible masses) are defined before the run starts
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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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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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double mass_min_local = DBL_MAX;
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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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if (mass_min_local > rmass[i]) mass_min_local = rmass[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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if (mass_min_local > mass[type[i]]) mass_min_local = mass[type[i]];
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}
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}
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MPI_Allreduce(&mass_min_local,&mass_min,1,MPI_DOUBLE,MPI_MIN,world);
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}
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/* ---------------------------------------------------------------------- */
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void FixTFMC::initial_integrate(int vflag)
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{
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double boltz = force->boltz;
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double **x = atom->x;
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double **f = atom->f;
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double *rmass = atom->rmass;
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double *mass = atom->mass;
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double massone;
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double masstotal;
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double xcm_d[3], xcm_dall[3];
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double d_i, xi;
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double gamma, gamma_exp, gamma_expi;
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double P_acc, P_ran;
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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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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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// in case we wish to track (and zero) the com movement
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if (comflag) {
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xcm_d[0] = 0.0;
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xcm_d[1] = 0.0;
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xcm_d[2] = 0.0;
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}
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// displacement vector, needed to calculate (and zero) rotation
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if (rotflag && nmax < nlocal) {
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nmax = nlocal + 1;
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memory->destroy(xd);
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memory->create(xd,nmax,3,"tfmc:xd");
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}
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// generate displacements for each atom
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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d_i = d_max * pow(mass_min/massone, 0.25);
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for (int j = 0; j < 3; j++) {
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P_acc = 0.0;
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P_ran = 1.0;
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gamma = f[i][j] * d_i / (2.0*boltz*T_set);
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gamma_exp = exp(gamma);
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gamma_expi = 1.0/gamma_exp;
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// generate displacements according to the tfMC distribution
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while (P_acc < P_ran) {
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xi = 2.0*random_num->uniform() - 1.0;
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P_ran = random_num->uniform();
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if (xi < 0) {
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P_acc = exp(2.0*xi*gamma) * gamma_exp - gamma_expi;
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P_acc = P_acc / (gamma_exp - gamma_expi);
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} else if (xi > 0) {
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P_acc = gamma_exp - exp(2.0*xi*gamma) * gamma_expi;
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P_acc = P_acc / (gamma_exp - gamma_expi);
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} else {
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P_acc = 1.0;
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}
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}
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// displace
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x[i][j] += xi * d_i;
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if (comflag) xcm_d[j] += xi * d_i * massone;
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if (rotflag) xd[i][j] = xi * d_i;
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}
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}
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}
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// if post factum zeroing of linear or rotational motion
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if (comflag || rotflag) masstotal = group->mass(igroup);
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// zero com motion
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if (comflag == 1 && group->count(igroup) != 0) {
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MPI_Allreduce(xcm_d,xcm_dall,3,MPI_DOUBLE,MPI_SUM,world);
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xcm_dall[0] /= masstotal;
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xcm_dall[1] /= masstotal;
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xcm_dall[2] /= masstotal;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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if (xflag) x[i][0] -= xcm_dall[0];
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if (yflag) x[i][1] -= xcm_dall[1];
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if (zflag) x[i][2] -= xcm_dall[2];
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}
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}
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}
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// zero rotation
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if (rotflag == 1 && group->count(igroup) != 0) {
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double dx, dy, dz;
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double unwrap[3];
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double cm[3], angmom[3], inertia[3][3], omega[3];
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tagint *image = atom->image;
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group->xcm(igroup,masstotal,cm);
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// to zero rotations, we can employ the same principles the
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// velocity command uses to zero the angular momentum. of course,
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// there is no (conserved) momentum in MC, but we can substitute
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// "velocities" by a displacement vector and proceed from there.
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// this of course requires "forking" group->angmom(), which is
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// what we do here.
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double p[3];
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p[0] = p[1] = p[2] = 0.0;
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - cm[0];
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dy = unwrap[1] - cm[1];
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dz = unwrap[2] - cm[2];
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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p[0] += massone * (dy*xd[i][2] - dz*xd[i][1]);
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p[1] += massone * (dz*xd[i][0] - dx*xd[i][2]);
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p[2] += massone * (dx*xd[i][1] - dy*xd[i][0]);
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}
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}
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MPI_Allreduce(p,angmom,3,MPI_DOUBLE,MPI_SUM,world);
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// end "angmom" calculation
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group->inertia(igroup,cm,inertia);
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group->omega(angmom,inertia,omega);
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// now, get rid of the rotation
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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domain->unmap(x[i],image[i],unwrap);
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dx = unwrap[0] - cm[0];
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dy = unwrap[1] - cm[1];
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dz = unwrap[2] - cm[2];
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x[i][0] -= omega[1]*dz - omega[2]*dy;
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x[i][1] -= omega[2]*dx - omega[0]*dz;
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x[i][2] -= omega[0]*dy - omega[1]*dx;
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}
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}
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}
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}
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@ -0,0 +1,72 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef FIX_CLASS
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FixStyle(tfmc,FixTFMC)
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#else
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#ifndef LMP_FIX_TFMC_H
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#define LMP_FIX_TFMC_H
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixTFMC : public Fix {
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public:
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FixTFMC(class LAMMPS *, int, char **);
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~FixTFMC();
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int setmask();
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void init();
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void initial_integrate(int);
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private:
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double d_max;
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double T_set;
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double mass_min;
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double **xd;
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int mass_require;
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int seed;
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int comflag, rotflag, xflag, yflag, zflag;
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int nmax;
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class RanMars *random_num;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: fix tfmc displacement length must be > 0
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Self-explanatory. You can only enter strictly positive displacement lengths.
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E: Fix tfmc temperature must be > 0"
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Self-explanatory.
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E: Illegal fix tfmc random seed
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Seeds can only be nonzero positive integers.
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*/
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