Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F90938668
fix_tfmc.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Wed, Nov 6, 05:21
Size
8 KB
Mime Type
text/x-c
Expires
Fri, Nov 8, 05:21 (2 d)
Engine
blob
Format
Raw Data
Handle
22163539
Attached To
rLAMMPS lammps
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;
}
}
}
}
Event Timeline
Log In to Comment