Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/MC/fix_tfmc.cpp
76acb8caf15fefficient_neuronet

Last Change
Raw File

fix_tfmc.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Kristof Bal (University of Antwerp, Belgium)
------------------------------------------------------------------------- */
#include "fix_tfmc.h"
#include <mpi.h>
#include <string.h>
#include <math.h>
#include <float.h>
#include "atom.h"
#include "force.h"
#include "update.h"
#include "group.h"
#include "random_mars.h"
#include "comm.h"
#include "domain.h"
#include "memory.h"
#include "modify.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixTFMC::FixTFMC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
xd(NULL), rotflag(0)
{
if (narg < 6) error->all(FLERR,"Illegal fix tfmc command");
// although we are not doing MD, we would like to use tfMC as an MD "drop in"
time_integrate = 1;
d_max = force->numeric(FLERR,arg[3]);
T_set = force->numeric(FLERR,arg[4]);
seed = force->inumeric(FLERR,arg[5]);
if (d_max <= 0) error->all(FLERR,"Fix tfmc displacement length must be > 0");
if (T_set <= 0) error->all(FLERR,"Fix tfmc temperature must be > 0");
if (seed <= 0) error->all(FLERR,"Illegal fix tfmc random seed");
// additional keywords
comflag = 0;
rotflag = 0;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"com") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix tfmc command");
comflag = 1;
xflag = force->inumeric(FLERR,arg[iarg+1]);
yflag = force->inumeric(FLERR,arg[iarg+2]);
zflag = force->inumeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"rot") == 0) {
if (iarg+1 > narg) error->all(FLERR,"Illegal fix tfmc command");
rotflag = 1;
iarg += 1;
} else error->all(FLERR,"Illegal fix tfmc command");
}
// error checks
if (comflag)
if (xflag < 0 || xflag > 1 || yflag < 0 || yflag > 1 ||
zflag < 0 || zflag > 1)
error->all(FLERR,"Illegal fix tfmc command");
if (xflag + yflag + zflag == 0)
comflag = 0;
if (rotflag) {
xd = NULL;
nmax = -1;
}
random_num = new RanMars(lmp,seed + comm->me);
}
/* ---------------------------------------------------------------------- */
FixTFMC::~FixTFMC()
{
delete random_num;
if (rotflag) {
memory->destroy(xd);
xd = NULL;
nmax = -1;
}
}
/* ---------------------------------------------------------------------- */
int FixTFMC::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTFMC::init()
{
// shake cannot be handled because it requires velocities
// (and real MD in general)
int has_shake = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"shake") == 0) ++has_shake;
if (has_shake > 0)
error->all(FLERR,"Fix tfmc is not compatible with fix shake");
// obtain lowest mass in the system
// We do this here, in init(), rather than in initial_integrate().
// This might seem somewhat odd: after all, another atom could be added with a
// mass smaller than mass_min (in the case of a per-particle mass), so mass_min
// should change during the run. However, this would imply that the overall
// meaning of the input Delta is not very well-defined, because its meaning
// can change during the run. So we'll assume all particle types (in terms of
// possible masses) are defined before the run starts
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double mass_min_local = DBL_MAX;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (mass_min_local > rmass[i]) mass_min_local = rmass[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (mass_min_local > mass[type[i]]) mass_min_local = mass[type[i]];
}
}
MPI_Allreduce(&mass_min_local,&mass_min,1,MPI_DOUBLE,MPI_MIN,world);
}
/* ---------------------------------------------------------------------- */
void FixTFMC::initial_integrate(int vflag)
{
double boltz = force->boltz;
double **x = atom->x;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
double massone;
double masstotal;
double xcm_d[3], xcm_dall[3];
double d_i, xi;
double gamma, gamma_exp, gamma_expi;
double P_acc, P_ran;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// in case we wish to track (and zero) the com movement
if (comflag) {
xcm_d[0] = 0.0;
xcm_d[1] = 0.0;
xcm_d[2] = 0.0;
}
// displacement vector, needed to calculate (and zero) rotation
if (rotflag && nmax < nlocal) {
nmax = nlocal + 1;
memory->destroy(xd);
memory->create(xd,nmax,3,"tfmc:xd");
}
// generate displacements for each atom
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
d_i = d_max * pow(mass_min/massone, 0.25);
for (int j = 0; j < 3; j++) {
P_acc = 0.0;
P_ran = 1.0;
gamma = f[i][j] * d_i / (2.0*boltz*T_set);
gamma_exp = exp(gamma);
gamma_expi = 1.0/gamma_exp;
// generate displacements according to the tfMC distribution
while (P_acc < P_ran) {
xi = 2.0*random_num->uniform() - 1.0;
P_ran = random_num->uniform();
if (xi < 0) {
P_acc = exp(2.0*xi*gamma) * gamma_exp - gamma_expi;
P_acc = P_acc / (gamma_exp - gamma_expi);
} else if (xi > 0) {
P_acc = gamma_exp - exp(2.0*xi*gamma) * gamma_expi;
P_acc = P_acc / (gamma_exp - gamma_expi);
} else {
P_acc = 1.0;
}
}
// displace
x[i][j] += xi * d_i;
if (comflag) xcm_d[j] += xi * d_i * massone;
if (rotflag) xd[i][j] = xi * d_i;
}
}
}
// if post factum zeroing of linear or rotational motion
if (comflag || rotflag) masstotal = group->mass(igroup);
// zero com motion
if (comflag == 1 && group->count(igroup) != 0) {
MPI_Allreduce(xcm_d,xcm_dall,3,MPI_DOUBLE,MPI_SUM,world);
if (masstotal > 0.0) {
xcm_dall[0] /= masstotal;
xcm_dall[1] /= masstotal;
xcm_dall[2] /= masstotal;
} else xcm_dall[0] = xcm_dall[1] = xcm_dall[2] = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (xflag) x[i][0] -= xcm_dall[0];
if (yflag) x[i][1] -= xcm_dall[1];
if (zflag) x[i][2] -= xcm_dall[2];
}
}
}
// zero rotation
if (rotflag == 1 && group->count(igroup) != 0) {
double dx, dy, dz;
double unwrap[3];
double cm[3], angmom[3], inertia[3][3], omega[3];
tagint *image = atom->image;
group->xcm(igroup,masstotal,cm);
// to zero rotations, we can employ the same principles the
// velocity command uses to zero the angular momentum. of course,
// there is no (conserved) momentum in MC, but we can substitute
// "velocities" by a displacement vector and proceed from there.
// this of course requires "forking" group->angmom(), which is
// what we do here.
double p[3];
p[0] = p[1] = p[2] = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - cm[0];
dy = unwrap[1] - cm[1];
dz = unwrap[2] - cm[2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
p[0] += massone * (dy*xd[i][2] - dz*xd[i][1]);
p[1] += massone * (dz*xd[i][0] - dx*xd[i][2]);
p[2] += massone * (dx*xd[i][1] - dy*xd[i][0]);
}
}
MPI_Allreduce(p,angmom,3,MPI_DOUBLE,MPI_SUM,world);
// end "angmom" calculation
group->inertia(igroup,cm,inertia);
group->omega(angmom,inertia,omega);
// now, get rid of the rotation
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - cm[0];
dy = unwrap[1] - cm[1];
dz = unwrap[2] - cm[2];
x[i][0] -= omega[1]*dz - omega[2]*dy;
x[i][1] -= omega[2]*dx - omega[0]*dz;
x[i][2] -= omega[0]*dy - omega[1]*dx;
}
}
}
}
c4science · Help