diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp
index d13135b8a..2deeb56c6 100644
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@@ -1,1303 +1,1310 @@
/* ----------------------------------------------------------------------
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: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_gcmc.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_hybrid.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "comm.h"
#include "group.h"
#include "domain.h"
#include "region.h"
#include "random_park.h"
#include "force.h"
#include "pair.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include <iostream>
using namespace std;
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 11) error->all(FLERR,"Illegal fix gcmc command");
vector_flag = 1;
size_vector = 8;
global_freq = 1;
extvector = 0;
restart_global = 1;
time_depend = 1;
// required args
nevery = atoi(arg[3]);
nexchanges = atoi(arg[4]);
nmcmoves = atoi(arg[5]);
ngcmc_type = atoi(arg[6]);
seed = atoi(arg[7]);
reservoir_temperature = atof(arg[8]);
chemical_potential = atof(arg[9]);
displace = atof(arg[10]);
if (nexchanges < 0) error->all(FLERR,"Illegal fix gcmc command");
if (nmcmoves < 0) error->all(FLERR,"Illegal fix gcmc command");
if (seed <= 0) error->all(FLERR,"Illegal fix gcmc command");
if (reservoir_temperature < 0.0)
error->all(FLERR,"Illegal fix gcmc command");
if (displace < 0.0) error->all(FLERR,"Illegal fix gcmc command");
// set defaults
molflag = 0;
max_rotation_angle = 10*MY_PI/180;
regionflag = 0;
iregion = -1;
region_volume = 0;
max_region_attempts = 1000;
rotation_group = 0;
rotation_groupbit = 0;
rotation_inversegroupbit = 0;
// read options from end of input line
options(narg-11,&arg[11]);
// random number generator, same for all procs
random_equal = new RanPark(lmp,seed);
// random number generator, not the same for all procs
random_unequal = new RanPark(lmp,seed);
// error checks on region and its extent being inside simulation box
region_xlo = region_xhi = region_ylo = region_yhi =
region_zlo = region_zhi = 0.0;
if (regionflag) {
if (domain->regions[iregion]->bboxflag == 0)
error->all(FLERR,"Fix gcmc region does not support a bounding box");
if (domain->regions[iregion]->dynamic_check())
error->all(FLERR,"Fix gcmc region cannot be dynamic");
region_xlo = domain->regions[iregion]->extent_xlo;
region_xhi = domain->regions[iregion]->extent_xhi;
region_ylo = domain->regions[iregion]->extent_ylo;
region_yhi = domain->regions[iregion]->extent_yhi;
region_zlo = domain->regions[iregion]->extent_zlo;
region_zhi = domain->regions[iregion]->extent_zhi;
if (region_xlo < domain->boxlo[0] || region_xhi > domain->boxhi[0] ||
region_ylo < domain->boxlo[1] || region_yhi > domain->boxhi[1] ||
region_zlo < domain->boxlo[2] || region_zhi > domain->boxhi[2])
error->all(FLERR,"Fix gcmc region extends outside simulation box");
// estimate region volume using MC trials
double coord[3];
int inside = 0;
int attempts = 10000000;
for (int i = 0; i < attempts; i++) {
coord[0] = region_xlo + random_equal->uniform() * (region_xhi-region_xlo);
coord[1] = region_ylo + random_equal->uniform() * (region_yhi-region_ylo);
coord[2] = region_zlo + random_equal->uniform() * (region_zhi-region_zlo);
if (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) != 0) inside++;
}
double max_region_volume = (region_xhi - region_xlo)*
(region_yhi - region_ylo)*(region_zhi - region_zlo);
region_volume = max_region_volume*static_cast<double> (inside)/
static_cast<double> (attempts);
}
// compute the number of MC cycles that occur nevery timesteps
ncycles = nexchanges + nmcmoves;
// set up reneighboring
force_reneighbor = 1;
next_reneighbor = update->ntimestep + 1;
// zero out counters
ntranslation_attempts = 0.0;
ntranslation_successes = 0.0;
nrotation_attempts = 0.0;
nrotation_successes = 0.0;
ndeletion_attempts = 0.0;
ndeletion_successes = 0.0;
ninsertion_attempts = 0.0;
ninsertion_successes = 0.0;
gcmc_nmax = 0;
local_gas_list = NULL;
model_atom = NULL;
}
/* ----------------------------------------------------------------------
parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixGCMC::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal fix gcmc command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"molecule") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
if (strcmp(arg[iarg+1],"no") == 0) molflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) molflag = 1;
else error->all(FLERR,"Illegal fix gcmc command");
iarg += 2;
} else if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix gcmc does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
regionflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"maxangle") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
max_rotation_angle = atof(arg[iarg+1]);
max_rotation_angle *= MY_PI/180;
iarg += 2;
} else error->all(FLERR,"Illegal fix gcmc command");
}
}
/* ---------------------------------------------------------------------- */
FixGCMC::~FixGCMC()
{
delete random_equal;
delete random_unequal;
memory->destroy(local_gas_list);
memory->destroy(atom_coord);
memory->destroy(model_atom_buf);
delete model_atom;
}
/* ---------------------------------------------------------------------- */
int FixGCMC::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixGCMC::init()
{
int *type = atom->type;
if (molflag == 0) {
if (ngcmc_type <= 0 || ngcmc_type > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix gcmc command");
}
// if molflag not set, warn if any deletable atom has a mol ID
if (molflag == 0 && atom->molecule_flag) {
int *molecule = atom->molecule;
int *mask = atom->mask;
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if (type[i] == ngcmc_type)
if (molecule[i]) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->all(FLERR,
"Fix gcmc cannot exchange individual atoms belonging to a molecule");
}
// if molflag set, check for unset mol IDs
if (molflag == 1) {
int *molecule = atom->molecule;
int *mask = atom->mask;
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if (mask[i] == groupbit)
if (molecule[i] == 0) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->all(FLERR,
"All mol IDs should be set for fix gcmc group atoms");
}
if ((molflag && (atom->molecule_flag == 0)) ||
(molflag && ((!atom->tag_enable) || (!atom->map_style))))
error->all(FLERR,
"Fix gcmc molecule command requires that atoms have molecule attributes");
if (force->pair->single_enable == 0)
error->all(FLERR,"Fix gcmc incompatible with given pair_style");
if (domain->dimension == 2)
error->all(FLERR,"Cannot use fix gcmc in a 2d simulation");
if (domain->triclinic == 1)
error->all(FLERR,"Cannot use fix gcmc with a triclinic box");
// create a new group for rotation molecules
if (molflag) {
char **group_arg = new char*[3];
group_arg[0] = (char *) "rotation_gas_atoms";
group_arg[1] = (char *) "molecule";
char digits[12];
sprintf(digits,"%d",ngcmc_type);
group_arg[2] = digits;
group->assign(3,group_arg);
rotation_group = group->find(group_arg[0]);
if (rotation_group == -1)
error->all(FLERR,"Could not find fix gcmc rotation group ID");
rotation_groupbit = group->bitmask[rotation_group];
rotation_inversegroupbit = rotation_groupbit ^ ~0;
delete [] group_arg;
}
// get all of the needed molecule data if molflag,
// otherwise just get the gas mass
if (molflag) get_model_molecule();
else gas_mass = atom->mass[ngcmc_type];
if (gas_mass <= 0.0)
error->all(FLERR,"Illegal fix gcmc gas mass <= 0");
// check that no deletable atoms are in atom->firstgroup
// deleting such an atom would not leave firstgroup atoms first
if (atom->firstgroup >= 0) {
int *mask = atom->mask;
int firstgroupbit = group->bitmask[atom->firstgroup];
int flag = 0;
for (int i = 0; i < atom->nlocal; i++)
if ((mask[i] == groupbit) && (mask[i] && firstgroupbit)) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall)
error->all(FLERR,"Cannot do GCMC on atoms in atom_modify first group");
}
// compute beta, lambda, sigma, and the zz factor
beta = 1.0/(force->boltz*reservoir_temperature);
double lambda = sqrt(force->hplanck*force->hplanck/
(2.0*MY_PI*gas_mass*force->mvv2e*
force->boltz*reservoir_temperature));
sigma = sqrt(force->boltz*reservoir_temperature/gas_mass/force->mvv2e);
zz = exp(beta*chemical_potential)/(pow(lambda,3.0));
imagetmp = ((tagint) IMGMAX << IMG2BITS) |
((tagint) IMGMAX << IMGBITS) | IMGMAX;
}
/* ----------------------------------------------------------------------
attempt Monte Carlo translations, rotations, insertions, and deletions
done before exchange, borders, reneighbor
so that ghost atoms and neighbor lists will be correct
------------------------------------------------------------------------- */
void FixGCMC::pre_exchange()
{
// just return if should not be called on this timestep
if (next_reneighbor != update->ntimestep) return;
xlo = domain->boxlo[0];
xhi = domain->boxhi[0];
ylo = domain->boxlo[1];
yhi = domain->boxhi[1];
zlo = domain->boxlo[2];
zhi = domain->boxhi[2];
sublo = domain->sublo;
subhi = domain->subhi;
if (regionflag) volume = region_volume;
else volume = domain->xprd * domain->yprd * domain->zprd;
update_gas_atoms_list();
if (molflag) {
for (int i = 0; i < ncycles; i++) {
int random_int_fraction =
static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (random_int_fraction <= nmcmoves) {
if (random_equal->uniform() < 0.5) attempt_molecule_translation();
else attempt_molecule_rotation();
} else {
if (random_equal->uniform() < 0.5) attempt_molecule_deletion();
else attempt_molecule_insertion();
}
}
} else {
for (int i = 0; i < ncycles; i++) {
int random_int_fraction =
static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (random_int_fraction <= nmcmoves) {
attempt_atomic_translation();
} else {
if (random_equal->uniform() < 0.5) attempt_atomic_deletion();
else attempt_atomic_insertion();
}
}
}
next_reneighbor = update->ntimestep + nevery;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_atomic_translation()
{
ntranslation_attempts += 1.0;
if (ngas == 0) return;
int i;
if (regionflag) i = pick_random_gas_atom_in_region();
else i = pick_random_gas_atom();
int success = 0;
if (i >= 0) {
double **x = atom->x;
double energy_before = energy(i,ngcmc_type,-1,x[i]);
double rsq = 1.1;
double rx,ry,rz;
rx = ry = rz = 0.0;
while (rsq > 1.0) {
rx = 2*random_unequal->uniform() - 1.0;
ry = 2*random_unequal->uniform() - 1.0;
rz = 2*random_unequal->uniform() - 1.0;
rsq = rx*rx + ry*ry + rz*rz;
}
double coord[3];
coord[0] = x[i][0] + displace*rx;
coord[1] = x[i][1] + displace*ry;
coord[2] = x[i][2] + displace*rz;
double energy_after = energy(i,ngcmc_type,-1,coord);
if (random_unequal->uniform() < exp(-beta*(energy_after - energy_before))) {
x[i][0] = coord[0];
x[i][1] = coord[1];
x[i][2] = coord[2];
success = 1;
}
}
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
if (success_all) {
+ atom->nghost = 0;
comm->borders();
update_gas_atoms_list();
ntranslation_successes += 1.0;
}
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_atomic_deletion()
{
ndeletion_attempts += 1.0;
if (ngas == 0) return;
int i;
if (regionflag) i = pick_random_gas_atom_in_region();
else i = pick_random_gas_atom();
int success = 0;
if (i >= 0) {
double deletion_energy = energy(i,ngcmc_type,-1,atom->x[i]);
if (random_unequal->uniform() < ngas*exp(beta*deletion_energy)/(zz*volume)) {
atom->avec->copy(atom->nlocal-1,i,1);
atom->nlocal--;
success = 1;
}
}
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
if (success_all) {
if (atom->tag_enable) {
atom->natoms--;
if (atom->map_style) atom->map_init();
}
+ atom->nghost = 0;
comm->borders();
update_gas_atoms_list();
ndeletion_successes += 1.0;
}
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_atomic_insertion()
{
ninsertion_attempts += 1.0;
double coord[3];
if (regionflag) {
int region_attempt = 0;
coord[0] = region_xlo + random_equal->uniform() * (region_xhi-region_xlo);
coord[1] = region_ylo + random_equal->uniform() * (region_yhi-region_ylo);
coord[2] = region_zlo + random_equal->uniform() * (region_zhi-region_zlo);
while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0) {
coord[0] = region_xlo + random_equal->uniform() * (region_xhi-region_xlo);
coord[1] = region_ylo + random_equal->uniform() * (region_yhi-region_ylo);
coord[2] = region_zlo + random_equal->uniform() * (region_zhi-region_zlo);
region_attempt++;
if (region_attempt >= max_region_attempts) return;
}
} else {
coord[0] = xlo + random_equal->uniform() * (xhi-xlo);
coord[1] = ylo + random_equal->uniform() * (yhi-ylo);
coord[2] = zlo + random_equal->uniform() * (zhi-zlo);
}
int proc_flag = 0;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) proc_flag = 1;
int success = 0;
if (proc_flag) {
double insertion_energy = energy(-1,ngcmc_type,-1,coord);
if (random_unequal->uniform() <
zz*volume*exp(-beta*insertion_energy)/(ngas+1)) {
atom->avec->create_atom(ngcmc_type,coord);
int m = atom->nlocal - 1;
atom->mask[m] = 1 | groupbit;
atom->v[m][0] = random_unequal->gaussian()*sigma;
atom->v[m][1] = random_unequal->gaussian()*sigma;
atom->v[m][2] = random_unequal->gaussian()*sigma;
int nfix = modify->nfix;
Fix **fix = modify->fix;
for (int j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(m);
success = 1;
}
}
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
if (success_all) {
if (atom->tag_enable) {
atom->natoms++;
atom->tag_extend();
if (atom->map_style) atom->map_init();
}
+ atom->nghost = 0;
comm->borders();
update_gas_atoms_list();
ninsertion_successes += 1.0;
}
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_molecule_translation()
{
ntranslation_attempts += 1.0;
if (ngas == 0) return;
int translation_molecule;
if (regionflag) translation_molecule = pick_random_gas_molecule_in_region();
else translation_molecule = pick_random_gas_molecule();
if (translation_molecule == -1) return;
double energy_before_sum = molecule_energy(translation_molecule);
double **x = atom->x;
double rx,ry,rz;
double com_displace[3],coord[3];
double rsq = 1.1;
while (rsq > 1.0) {
rx = 2*random_equal->uniform() - 1.0;
ry = 2*random_equal->uniform() - 1.0;
rz = 2*random_equal->uniform() - 1.0;
rsq = rx*rx + ry*ry + rz*rz;
}
com_displace[0] = displace*rx;
com_displace[1] = displace*ry;
com_displace[2] = displace*rz;
double energy_after = 0.0;
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == translation_molecule) {
coord[0] = x[i][0] + com_displace[0];
coord[1] = x[i][1] + com_displace[1];
coord[2] = x[i][2] + com_displace[2];
energy_after += energy(i,atom->type[i],translation_molecule,coord);
}
}
double energy_after_sum = 0.0;
MPI_Allreduce(&energy_after,&energy_after_sum,1,MPI_DOUBLE,MPI_SUM,world);
if (random_equal->uniform() < exp(-beta*(energy_after_sum - energy_before_sum))) {
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == translation_molecule) {
x[i][0] += com_displace[0];
x[i][1] += com_displace[1];
x[i][2] += com_displace[2];
}
}
+ atom->nghost = 0;
comm->borders();
update_gas_atoms_list();
ntranslation_successes += 1.0;
}
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_molecule_rotation()
{
nrotation_attempts += 1.0;
if (ngas == 0) return;
int rotation_molecule;
if (regionflag) rotation_molecule = pick_random_gas_molecule_in_region();
else rotation_molecule = pick_random_gas_molecule();
if (rotation_molecule == -1) return;
double energy_before_sum = molecule_energy(rotation_molecule);
int nlocal = atom->nlocal;
int *mask = atom->mask;
for (int i = 0; i < nlocal; i++) {
if (atom->molecule[i] == rotation_molecule) {
mask[i] |= rotation_groupbit;
} else {
mask[i] &= rotation_inversegroupbit;
}
}
double com[3];
com[0] = com[1] = com[2] = 0.0;
group->xcm(rotation_group,gas_mass,com);
double rot[9];
get_rotation_matrix(max_rotation_angle,&rot[0]);
double **x = atom->x;
tagint *image = atom->image;
double energy_after = 0.0;
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & rotation_groupbit) {
double xtmp[3];
domain->unmap(x[i],image[i],xtmp);
xtmp[0] -= com[0];
xtmp[1] -= com[1];
xtmp[2] -= com[2];
atom_coord[n][0] = rot[0]*xtmp[0] + rot[1]*xtmp[1] + rot[2]*xtmp[2] + com[0];
atom_coord[n][1] = rot[3]*xtmp[0] + rot[4]*xtmp[1] + rot[5]*xtmp[2] + com[1];
atom_coord[n][2] = rot[6]*xtmp[0] + rot[7]*xtmp[1] + rot[8]*xtmp[2] + com[2];
xtmp[0] = atom_coord[n][0];
xtmp[1] = atom_coord[n][1];
xtmp[2] = atom_coord[n][2];
domain->remap(xtmp);
energy_after += energy(i,atom->type[i],rotation_molecule,xtmp);
n++;
}
}
double energy_after_sum = 0.0;
MPI_Allreduce(&energy_after,&energy_after_sum,1,MPI_DOUBLE,MPI_SUM,world);
if (random_equal->uniform() < exp(-beta*(energy_after_sum - energy_before_sum))) {
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & rotation_groupbit) {
image[i] = imagetmp;
x[i][0] = atom_coord[n][0];
x[i][1] = atom_coord[n][1];
x[i][2] = atom_coord[n][2];
domain->remap(x[i],image[i]);
n++;
}
}
+ atom->nghost = 0;
comm->borders();
update_gas_atoms_list();
nrotation_successes += 1.0;
}
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_molecule_deletion()
{
ndeletion_attempts += 1.0;
if (ngas == 0) return;
int deletion_molecule;
if (regionflag) deletion_molecule = pick_random_gas_molecule_in_region();
else deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;
double deletion_energy_sum = molecule_energy(deletion_molecule);
if (random_equal->uniform() < ngas*exp(beta*deletion_energy_sum)/(zz*volume)) {
int i = 0;
while (i < atom->nlocal) {
if (atom->molecule[i] == deletion_molecule) {
atom->avec->copy(atom->nlocal-1,i,1);
atom->nlocal--;
} else i++;
}
atom->natoms -= natoms_per_molecule;
atom->map_init();
+ atom->nghost = 0;
comm->borders();
update_gas_atoms_list();
ndeletion_successes += 1.0;
}
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_molecule_insertion()
{
ninsertion_attempts += 1.0;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double com_coord[3];
if (regionflag) {
int region_attempt = 0;
com_coord[0] = region_xlo + random_equal->uniform() * (region_xhi-region_xlo);
com_coord[1] = region_ylo + random_equal->uniform() * (region_yhi-region_ylo);
com_coord[2] = region_zlo + random_equal->uniform() * (region_zhi-region_zlo);
while (domain->regions[iregion]->match(com_coord[0],com_coord[1],com_coord[2]) == 0) {
com_coord[0] = region_xlo + random_equal->uniform() * (region_xhi-region_xlo);
com_coord[1] = region_ylo + random_equal->uniform() * (region_yhi-region_ylo);
com_coord[2] = region_zlo + random_equal->uniform() * (region_zhi-region_zlo);
region_attempt++;
if (region_attempt >= max_region_attempts) return;
}
} else {
com_coord[0] = xlo + random_equal->uniform() * (xhi-xlo);
com_coord[1] = ylo + random_equal->uniform() * (yhi-ylo);
com_coord[2] = zlo + random_equal->uniform() * (zhi-zlo);
}
double rot[9];
get_rotation_matrix(MY_2PI,&rot[0]);
double **model_x = model_atom->x;
double insertion_energy = 0.0;
bool procflag[natoms_per_molecule];
for (int i = 0; i < natoms_per_molecule; i++) {
atom_coord[i][0] = rot[0]*model_x[i][0] + rot[1]*model_x[i][1] + rot[2]*model_x[i][2] + com_coord[0];
atom_coord[i][1] = rot[3]*model_x[i][0] + rot[4]*model_x[i][1] + rot[5]*model_x[i][2] + com_coord[1];
atom_coord[i][2] = rot[6]*model_x[i][0] + rot[7]*model_x[i][1] + rot[8]*model_x[i][2] + com_coord[2];
double xtmp[3];
xtmp[0] = atom_coord[i][0];
xtmp[1] = atom_coord[i][1];
xtmp[2] = atom_coord[i][2];
domain->remap(xtmp);
procflag[i] = false;
if (xtmp[0] >= sublo[0] && xtmp[0] < subhi[0] &&
xtmp[1] >= sublo[1] && xtmp[1] < subhi[1] &&
xtmp[2] >= sublo[2] && xtmp[2] < subhi[2]) {
procflag[i] = true;
insertion_energy += energy(-1,model_atom->type[i],-1,xtmp);
}
}
double insertion_energy_sum = 0.0;
MPI_Allreduce(&insertion_energy,&insertion_energy_sum,1,MPI_DOUBLE,MPI_SUM,world);
if (random_equal->uniform() < zz*volume*exp(-beta*insertion_energy_sum)/(ngas+1)) {
maxmol++;
if (maxmol >= MAXSMALLINT)
error->all(FLERR,"Fix gcmc ran out of available molecule IDs");
int maxtag = 0;
for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag,atom->tag[i]);
int maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
int atom_offset = maxtag_all;
int k = 0;
double **x = atom->x;
double **v = atom->v;
tagint *image = atom->image;
int *molecule = atom->molecule;
int *tag = atom->tag;
for (int i = 0; i < natoms_per_molecule; i++) {
k += atom->avec->unpack_restart(&model_atom_buf[k]);
if (procflag[i]) {
int m = atom->nlocal - 1;
image[m] = imagetmp;
x[m][0] = atom_coord[i][0];
x[m][1] = atom_coord[i][1];
x[m][2] = atom_coord[i][2];
domain->remap(x[m],image[m]);
atom->molecule[m] = maxmol;
tag[m] += atom_offset;
v[m][0] = random_unequal->gaussian()*sigma;
v[m][1] = random_unequal->gaussian()*sigma;
v[m][2] = random_unequal->gaussian()*sigma;
if (atom->avec->bonds_allow)
for (int j = 0; j < atom->num_bond[m]; j++)
atom->bond_atom[m][j] += atom_offset;
if (atom->avec->angles_allow)
for (int j = 0; j < atom->num_angle[m]; j++) {
atom->angle_atom1[m][j] += atom_offset;
atom->angle_atom2[m][j] += atom_offset;
atom->angle_atom3[m][j] += atom_offset;
}
if (atom->avec->dihedrals_allow)
for (int j = 0; j < atom->num_dihedral[m]; j++) {
atom->dihedral_atom1[m][j] += atom_offset;
atom->dihedral_atom2[m][j] += atom_offset;
atom->dihedral_atom3[m][j] += atom_offset;
atom->dihedral_atom4[m][j] += atom_offset;
}
if (atom->avec->impropers_allow)
for (int j = 0; j < atom->num_improper[m]; j++) {
atom->improper_atom1[m][j] += atom_offset;
atom->improper_atom2[m][j] += atom_offset;
atom->improper_atom3[m][j] += atom_offset;
atom->improper_atom4[m][j] += atom_offset;
}
int nfix = modify->nfix;
Fix **fix = modify->fix;
for (int j = 0; j < nfix; j++)
if (fix[j]->create_attribute) fix[j]->set_arrays(m);
} else atom->nlocal--;
}
atom->natoms += natoms_per_molecule;
atom->map_init();
+ atom->nghost = 0;
comm->borders();
update_gas_atoms_list();
ninsertion_successes += 1.0;
}
}
/* ----------------------------------------------------------------------
compute particle's interaction energy with the rest of the system
------------------------------------------------------------------------- */
double FixGCMC::energy(int i, int itype, int imolecule, double *coord)
{
double delx,dely,delz,rsq;
double **x = atom->x;
int *type = atom->type;
int *molecule = atom->molecule;
int nall = atom->nlocal + atom->nghost;
pair = force->pair;
cutsq = force->pair->cutsq;
double fpair = 0.0;
double factor_coul = 1.0;
double factor_lj = 1.0;
double total_energy = 0.0;
for (int j = 0; j < nall; j++) {
if (i == j) continue;
if (molflag)
if (imolecule == molecule[j]) continue;
delx = coord[0] - x[j][0];
dely = coord[1] - x[j][1];
delz = coord[2] - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
int jtype = type[j];
if (rsq < cutsq[itype][jtype])
total_energy +=
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
}
return total_energy;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
int FixGCMC::pick_random_gas_atom()
{
int i = -1;
int iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
int iwhichlocal = iwhichglobal - ngas_before;
i = local_gas_list[iwhichlocal];
}
return i;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
int FixGCMC::pick_random_gas_atom_in_region()
{
int i = -1;
int i_own_candidate = 0;
int i_own_candidate_all = 0;
int region_attempt = 0;
double **x = atom->x;
while (!i_own_candidate_all) {
int iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
i_own_candidate = 1;
int iwhichlocal = iwhichglobal - ngas_before;
i = local_gas_list[iwhichlocal];
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]) == 0)
i_own_candidate = 0;
}
MPI_Allreduce(&i_own_candidate,&i_own_candidate_all,1,MPI_INT,MPI_MAX,world);
region_attempt++;
if (region_attempt >= max_region_attempts) return -1;
}
return i;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
int FixGCMC::pick_random_gas_molecule()
{
int iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
int gas_molecule_id = 0;
if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
int iwhichlocal = iwhichglobal - ngas_before;
int i = local_gas_list[iwhichlocal];
gas_molecule_id = atom->molecule[i];
}
int gas_molecule_id_all = 0;
MPI_Allreduce(&gas_molecule_id,&gas_molecule_id_all,1,MPI_INT,MPI_MAX,world);
return gas_molecule_id_all;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
int FixGCMC::pick_random_gas_molecule_in_region()
{
int region_attempt = 0;
int gas_molecule_id = 0;
int gas_molecule_id_all = 0;
double **x = atom->x;
while (!gas_molecule_id_all) {
int iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
int iwhichlocal = iwhichglobal - ngas_before;
int i = local_gas_list[iwhichlocal];
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]) != 0) {
gas_molecule_id = atom->molecule[i];
}
}
gas_molecule_id_all = 0;
MPI_Allreduce(&gas_molecule_id,&gas_molecule_id_all,1,MPI_INT,MPI_MAX,world);
region_attempt++;
if (region_attempt >= max_region_attempts) return -1;
}
return gas_molecule_id_all;
}
/* ----------------------------------------------------------------------
compute the energy of the given gas molecule in its current position
sum across all procs that own atoms of the given molecule
------------------------------------------------------------------------- */
double FixGCMC::molecule_energy(int gas_molecule_id)
{
double mol_energy = 0.0;
for (int i = 0; i < atom->nlocal; i++)
if (atom->molecule[i] == gas_molecule_id) {
mol_energy += energy(i,atom->type[i],gas_molecule_id,atom->x[i]);
}
double mol_energy_sum = 0.0;
MPI_Allreduce(&mol_energy,&mol_energy_sum,1,MPI_DOUBLE,MPI_SUM,world);
return mol_energy_sum;
}
/* ----------------------------------------------------------------------
compute a 3x3 rotation matrix using 3 random Euler angles,
each with a random maximum value supplied by the caller
------------------------------------------------------------------------- */
void FixGCMC::get_rotation_matrix(double max_angle, double *rot)
{
double angle_x = max_angle*random_equal->uniform();
double angle_y = max_angle*random_equal->uniform();
double angle_z = max_angle*random_equal->uniform();
double a = cos(angle_x);
double b = sin(angle_x);
double c = cos(angle_y);
double d = sin(angle_y);
double e = cos(angle_z);
double f = sin(angle_z);
double ad = a*d;
double bd = b*d;
rot[0] = c*e;
rot[1] = -c*f;
rot[2] = -d;
rot[3] = -bd*e + a*f;
rot[4] = bd*f + a*e;
rot[5] = -b*c;
rot[6] = ad*e + b*f;
rot[7] = -ad*f + b*e;
rot[8] = a*c;
}
/* ----------------------------------------------------------------------
when using the molecule capability, populate model atom arrays from
the model molecule provided by the user that will then be used to build
inserted molecules
------------------------------------------------------------------------- */
void FixGCMC::get_model_molecule()
{
// find out how many atoms are in the model molecule
// just loop through all of the atoms I own, then sum up across procs
int model_molecule_number = ngcmc_type;
int natoms_per_molecule_local = 0;
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == model_molecule_number) {
natoms_per_molecule_local++;
}
}
natoms_per_molecule = 0;
MPI_Allreduce(&natoms_per_molecule_local,&natoms_per_molecule,1,MPI_INT,MPI_MAX,world);
if (natoms_per_molecule == 0)
error->all(FLERR,"Fix gcmc could not find any atoms in the user-supplied template molecule");
memory->create(atom_coord,natoms_per_molecule,3,"fixGCMC:atom_coord");
// maxmol = largest molecule tag across all existing atoms
maxmol = 0;
if (atom->molecular) {
for (int i = 0; i < atom->nlocal; i++) maxmol = MAX(atom->molecule[i],maxmol);
int maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_INT,MPI_MAX,world);
maxmol = maxmol_all;
}
// communication buffer for model atom's info
// max_size = largest buffer needed by any proc
// must do before new Atom class created,
// since size_restart() uses atom->nlocal
int max_size;
int buf_send_size = atom->avec->size_restart();
MPI_Allreduce(&buf_send_size,&max_size,1,MPI_INT,MPI_MAX,world);
double *buf;
memory->create(buf,max_size,"fixGCMC:buf");
// create storage space for the model molecule's atoms
// create a new atom object called atom to store the data
// old_atom = original atom class
// atom = new model atom class
// if old_atom style was hybrid, pass sub-style names to create_avec
Atom *old_atom = atom;
atom = new Atom(lmp);
atom->settings(old_atom);
int nstyles = 0;
char **keywords = NULL;
if (strcmp(old_atom->atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) old_atom->avec;
nstyles = avec_hybrid->nstyles;
keywords = avec_hybrid->keywords;
}
atom->create_avec(old_atom->atom_style,nstyles,keywords);
// assign atom and topology counts in model atom class from old_atom
atom->ntypes = old_atom->ntypes;
atom->nbondtypes = old_atom->nbondtypes;
atom->nangletypes = old_atom->nangletypes;
atom->ndihedraltypes = old_atom->ndihedraltypes;
atom->nimpropertypes = old_atom->nimpropertypes;
atom->bond_per_atom = old_atom->bond_per_atom;
atom->angle_per_atom = old_atom->angle_per_atom;
atom->dihedral_per_atom = old_atom->dihedral_per_atom;
atom->improper_per_atom = old_atom->improper_per_atom;
atom->extra_bond_per_atom = old_atom->extra_bond_per_atom;
atom->allocate_type_arrays();
atom->avec->grow(natoms_per_molecule);
// copy type arrays to model atom class
if (atom->mass) {
for (int itype = 1; itype <= atom->ntypes; itype++) {
atom->mass_setflag[itype] = old_atom->mass_setflag[itype];
if (atom->mass_setflag[itype]) atom->mass[itype] = old_atom->mass[itype];
}
}
// loop over all procs
// if this iteration of loop is me:
// pack my atom data into buf
// bcast it to all other procs
AtomVec *old_avec = old_atom->avec;
AtomVec *model_avec = atom->avec;
int model_buf_size = 0;
for (int iproc = 0; iproc < comm->nprocs; iproc++) {
int nbuf_iproc = 0;
if (comm->me == iproc) {
for (int i = 0; i < old_atom->nlocal; i++) {
if (old_atom->molecule[i] == model_molecule_number) {
nbuf_iproc += old_avec->pack_restart(i,&buf[nbuf_iproc]);
}
}
}
MPI_Bcast(&nbuf_iproc,1,MPI_INT,iproc,world);
MPI_Bcast(buf,nbuf_iproc,MPI_DOUBLE,iproc,world);
model_buf_size += nbuf_iproc;
int m = 0;
while (m < nbuf_iproc)
m += model_avec->unpack_restart(&buf[m]);
}
// free communication buffer
memory->destroy(buf);
// make sure that the number of model atoms is equal to the number of atoms per gas molecule
int nlocal = atom->nlocal;
if (nlocal != natoms_per_molecule)
error->all(FLERR,"Fix gcmc incorrect number of atoms per molecule");
// compute the model molecule's mass and center-of-mass
// then recenter model molecule on the origin
double com[3];
gas_mass = group->mass(0);
group->xcm(0,gas_mass,com);
double **x = atom->x;
for (int i = 0; i < nlocal; i++) {
domain->unmap(x[i],atom->image[i]);
x[i][0] -= com[0];
x[i][1] -= com[1];
x[i][2] -= com[2];
}
int mintag = atom->tag[0];
for (int i = 0; i < atom->nlocal; i++) mintag = MIN(mintag,atom->tag[i]);
int atom_offset = mintag - 1;
for (int i = 0; i < nlocal; i++) {
atom->mask[i] = 1 | groupbit;
atom->tag[i] -= atom_offset;
if (atom->avec->bonds_allow)
for (int j = 0; j < atom->num_bond[i]; j++)
atom->bond_atom[i][j] -= atom_offset;
if (atom->avec->angles_allow)
for (int j = 0; j < atom->num_angle[i]; j++) {
atom->angle_atom1[i][j] -= atom_offset;
atom->angle_atom2[i][j] -= atom_offset;
atom->angle_atom3[i][j] -= atom_offset;
}
if (atom->avec->dihedrals_allow)
for (int j = 0; j < atom->num_dihedral[i]; j++) {
atom->dihedral_atom1[i][j] -= atom_offset;
atom->dihedral_atom2[i][j] -= atom_offset;
atom->dihedral_atom3[i][j] -= atom_offset;
atom->dihedral_atom4[i][j] -= atom_offset;
}
if (atom->avec->impropers_allow)
for (int j = 0; j < atom->num_improper[i]; j++) {
atom->improper_atom1[i][j] -= atom_offset;
atom->improper_atom2[i][j] -= atom_offset;
atom->improper_atom3[i][j] -= atom_offset;
atom->improper_atom4[i][j] -= atom_offset;
}
}
// pack model atoms into a buffer for use during molecule insertions
memory->create(model_atom_buf,model_buf_size,"fixGCMC:model_atom_buf");
int n = 0;
for (int i = 0; i < nlocal; i++)
n += model_avec->pack_restart(i,&model_atom_buf[n]);
// move atom to model_atom and restore old_atom class pointer back to atom
model_atom = atom;
atom = old_atom;
}
/* ----------------------------------------------------------------------
update the list of gas atoms
------------------------------------------------------------------------- */
void FixGCMC::update_gas_atoms_list()
{
if (atom->nlocal > gcmc_nmax) {
memory->sfree(local_gas_list);
gcmc_nmax = atom->nmax;
local_gas_list = (int *) memory->smalloc(gcmc_nmax*sizeof(int),
"GCMC:local_gas_list");
}
ngas_local = 0;
for (int i = 0; i < atom->nlocal; i++) {
if (atom->mask[i] & groupbit) {
local_gas_list[ngas_local] = i;
ngas_local++;
}
}
MPI_Allreduce(&ngas_local,&ngas,1,MPI_INT,MPI_SUM,world);
MPI_Scan(&ngas_local,&ngas_before,1,MPI_INT,MPI_SUM,world);
ngas_before -= ngas_local;
}
/* ----------------------------------------------------------------------
return acceptance ratios
------------------------------------------------------------------------- */
double FixGCMC::compute_vector(int n)
{
if (n == 0) return ntranslation_attempts;
if (n == 1) return ntranslation_successes;
if (n == 2) return ninsertion_attempts;
if (n == 3) return ninsertion_successes;
if (n == 4) return ndeletion_attempts;
if (n == 5) return ndeletion_successes;
if (n == 6) return nrotation_attempts;
if (n == 7) return nrotation_successes;
return 0.0;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixGCMC::memory_usage()
{
double bytes = gcmc_nmax * sizeof(int);
return bytes;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixGCMC::write_restart(FILE *fp)
{
int n = 0;
double list[4];
list[n++] = random_equal->state();
list[n++] = random_unequal->state();
list[n++] = next_reneighbor;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixGCMC::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
seed = static_cast<int> (list[n++]);
random_equal->reset(seed);
seed = static_cast<int> (list[n++]);
random_unequal->reset(seed);
next_reneighbor = static_cast<int> (list[n++]);
}