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lammps/src/MC/fix_gcmc.cpp
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fix_gcmc.cpp
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/* ----------------------------------------------------------------------
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 "molecule.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "comm.h"
#include "compute.h"
#include "group.h"
#include "domain.h"
#include "region.h"
#include "random_park.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "math_extra.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "thermo.h"
#include "output.h"
#include "neighbor.h"
#include <iostream>
using namespace std;
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{ATOM,MOLECULE};
/* ---------------------------------------------------------------------- */
FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 11) error->all(FLERR,"Illegal fix gcmc command");
if (atom->molecular == 2)
error->all(FLERR,"Fix gcmc does not (yet) work with atom_style template");
dynamic_group_allow = 1;
vector_flag = 1;
size_vector = 8;
global_freq = 1;
extvector = 0;
restart_global = 1;
time_depend = 1;
// required args
nevery = force->inumeric(FLERR,arg[3]);
nexchanges = force->inumeric(FLERR,arg[4]);
nmcmoves = force->inumeric(FLERR,arg[5]);
ngcmc_type = force->inumeric(FLERR,arg[6]);
seed = force->inumeric(FLERR,arg[7]);
reservoir_temperature = force->numeric(FLERR,arg[8]);
chemical_potential = force->numeric(FLERR,arg[9]);
displace = force->numeric(FLERR,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");
// 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);
}
// error check and further setup for mode = MOLECULE
if (mode == MOLECULE) {
if (onemols[imol]->xflag == 0)
error->all(FLERR,"Fix gcmc molecule must have coordinates");
if (onemols[imol]->typeflag == 0)
error->all(FLERR,"Fix gcmc molecule must have atom types");
if (ngcmc_type+onemols[imol]->ntypes <= 0 || ngcmc_type+onemols[imol]->ntypes > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix gcmc mol command");
if (atom->molecular == 2 && onemols != atom->avec->onemols)
error->all(FLERR,"Fix gcmc molecule template ID must be same "
"as atom_style template ID");
onemols[imol]->check_attributes(0);
}
if (shakeflag && mode == ATOM)
error->all(FLERR,"Cannot use fix gcmc shake and not molecule");
// setup of coords and imageflags array
if (mode == ATOM) natoms_per_molecule = 1;
else natoms_per_molecule = onemols[imol]->natoms;
memory->create(coords,natoms_per_molecule,3,"gcmc:coords");
memory->create(imageflags,natoms_per_molecule,"gcmc:imageflags");
memory->create(atom_coord,natoms_per_molecule,3,"gcmc:atom_coord");
// 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;
}
/* ----------------------------------------------------------------------
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");
// defaults
mode = ATOM;
max_rotation_angle = 10*MY_PI/180;
regionflag = 0;
iregion = -1;
region_volume = 0;
max_region_attempts = 1000;
molecule_group = 0;
molecule_group_bit = 0;
molecule_group_inversebit = 0;
exclusion_group = 0;
exclusion_group_bit = 0;
pressure_flag = false;
pressure = 0.0;
fugacity_coeff = 1.0;
shakeflag = 0;
charge = 0.0;
charge_flag = false;
full_flag = false;
idshake = NULL;
ngroups = 0;
int ngroupsmax = 0;
groupstrings = NULL;
ngrouptypes = 0;
int ngrouptypesmax = 0;
grouptypestrings = NULL;
grouptypes = NULL;
grouptypebits = NULL;
energy_intra = 0.0;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"mol") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
imol = atom->find_molecule(arg[iarg+1]);
if (imol == -1)
error->all(FLERR,"Molecule template ID for fix gcmc does not exist");
if (atom->molecules[imol]->nset > 1 && comm->me == 0)
error->warning(FLERR,"Molecule template for "
"fix gcmc has multiple molecules");
mode = MOLECULE;
onemols = &atom->molecules[imol];
nmol = onemols[0]->nset;
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 = force->numeric(FLERR,arg[iarg+1]);
max_rotation_angle *= MY_PI/180;
iarg += 2;
} else if (strcmp(arg[iarg],"pressure") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
pressure = force->numeric(FLERR,arg[iarg+1]);
pressure_flag = true;
iarg += 2;
} else if (strcmp(arg[iarg],"fugacity_coeff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
fugacity_coeff = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"charge") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
charge = force->numeric(FLERR,arg[iarg+1]);
charge_flag = true;
iarg += 2;
} else if (strcmp(arg[iarg],"shake") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
int n = strlen(arg[iarg+1]) + 1;
delete [] idshake;
idshake = new char[n];
strcpy(idshake,arg[iarg+1]);
shakeflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"full_energy") == 0) {
full_flag = true;
iarg += 1;
} else if (strcmp(arg[iarg],"group") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
if (ngroups >= ngroupsmax) {
ngroupsmax = ngroups+1;
groupstrings = (char **)
memory->srealloc(groupstrings,
ngroupsmax*sizeof(char *),
"fix_gcmc:groupstrings");
}
int n = strlen(arg[iarg+1]) + 1;
groupstrings[ngroups] = new char[n];
strcpy(groupstrings[ngroups],arg[iarg+1]);
ngroups++;
iarg += 2;
} else if (strcmp(arg[iarg],"grouptype") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix gcmc command");
if (ngrouptypes >= ngrouptypesmax) {
ngrouptypesmax = ngrouptypes+1;
grouptypes = (int*) memory->srealloc(grouptypes,ngrouptypesmax*sizeof(int),
"fix_gcmc:grouptypes");
grouptypestrings = (char**)
memory->srealloc(grouptypestrings,
ngrouptypesmax*sizeof(char *),
"fix_gcmc:grouptypestrings");
}
grouptypes[ngrouptypes] = atoi(arg[iarg+1]);
int n = strlen(arg[iarg+2]) + 1;
grouptypestrings[ngrouptypes] = new char[n];
strcpy(grouptypestrings[ngrouptypes],arg[iarg+2]);
ngrouptypes++;
iarg += 3;
} else if (strcmp(arg[iarg],"intra_energy") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
energy_intra = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix gcmc command");
}
}
/* ---------------------------------------------------------------------- */
FixGCMC::~FixGCMC()
{
if (regionflag) delete [] idregion;
delete random_equal;
delete random_unequal;
memory->destroy(local_gas_list);
memory->destroy(atom_coord);
memory->destroy(coords);
memory->destroy(imageflags);
delete [] idshake;
if (ngroups > 0) {
for (int igroup = 0; igroup < ngroups; igroup++)
delete [] groupstrings[igroup];
memory->sfree(groupstrings);
}
if (ngrouptypes > 0) {
memory->destroy(grouptypes);
memory->destroy(grouptypebits);
for (int igroup = 0; igroup < ngrouptypes; igroup++)
delete [] grouptypestrings[igroup];
memory->sfree(grouptypestrings);
}
}
/* ---------------------------------------------------------------------- */
int FixGCMC::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixGCMC::init()
{
// decide whether to switch to the full_energy option
if (!full_flag) {
if ((force->kspace) ||
(force->pair == NULL) ||
(force->pair->single_enable == 0) ||
(force->pair_match("hybrid",0)) ||
(force->pair_match("eam",0)) ||
(domain->triclinic == 1)) {
full_flag = true;
if (comm->me == 0)
error->warning(FLERR,"Fix gcmc using full_energy option");
}
}
if (full_flag) {
char *id_pe = (char *) "thermo_pe";
int ipe = modify->find_compute(id_pe);
c_pe = modify->compute[ipe];
}
int *type = atom->type;
if (mode == ATOM) {
if (ngcmc_type <= 0 || ngcmc_type > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix gcmc command");
}
// if mode == ATOM, warn if any deletable atom has a mol ID
if ((mode == ATOM) && atom->molecule_flag) {
tagint *molecule = atom->molecule;
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 mode == MOLECULE, check for unset mol IDs
if (mode == MOLECULE) {
tagint *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 (((mode == MOLECULE) && (atom->molecule_flag == 0)) ||
((mode == MOLECULE) && (!atom->tag_enable || !atom->map_style)))
error->all(FLERR,
"Fix gcmc molecule command requires that "
"atoms have molecule attributes");
// if shakeflag defined, check for SHAKE fix
// its molecule template must be same as this one
fixshake = NULL;
if (shakeflag) {
int ifix = modify->find_fix(idshake);
if (ifix < 0) error->all(FLERR,"Fix gcmc shake fix does not exist");
fixshake = modify->fix[ifix];
int tmp;
if (onemols != (Molecule **) fixshake->extract("onemol",tmp))
error->all(FLERR,"Fix gcmc and fix shake not using "
"same molecule template ID");
}
if (domain->dimension == 2)
error->all(FLERR,"Cannot use fix gcmc in a 2d simulation");
// create a new group for interaction exclusions
if (full_flag) {
char **group_arg = new char*[4];
// create unique group name for atoms to be excluded
int len = strlen(id) + 30;
group_arg[0] = new char[len];
sprintf(group_arg[0],"FixGCMC:gcmc_exclusion_group:%s",id);
group_arg[1] = (char *) "subtract";
group_arg[2] = (char *) "all";
group_arg[3] = (char *) "all";
group->assign(4,group_arg);
exclusion_group = group->find(group_arg[0]);
if (exclusion_group == -1)
error->all(FLERR,"Could not find fix gcmc exclusion group ID");
exclusion_group_bit = group->bitmask[exclusion_group];
// neighbor list exclusion setup
// turn off interactions between group all and the exclusion group
int narg = 4;
char **arg = new char*[narg];;
arg[0] = (char *) "exclude";
arg[1] = (char *) "group";
arg[2] = group_arg[0];
arg[3] = (char *) "all";
neighbor->modify_params(narg,arg);
delete [] group_arg[0];
delete [] group_arg;
delete [] arg;
}
// create a new group for temporary use with selected molecules
if (mode == MOLECULE) {
char **group_arg = new char*[3];
// create unique group name for atoms to be rotated
int len = strlen(id) + 30;
group_arg[0] = new char[len];
sprintf(group_arg[0],"FixGCMC:rotation_gas_atoms:%s",id);
group_arg[1] = (char *) "molecule";
char digits[12];
sprintf(digits,"%d",ngcmc_type);
group_arg[2] = digits;
group->assign(3,group_arg);
molecule_group = group->find(group_arg[0]);
if (molecule_group == -1)
error->all(FLERR,"Could not find fix gcmc rotation group ID");
molecule_group_bit = group->bitmask[molecule_group];
molecule_group_inversebit = molecule_group_bit ^ ~0;
delete [] group_arg[0];
delete [] group_arg;
}
// get all of the needed molecule data if mode == MOLECULE,
// otherwise just get the gas mass
if (mode == MOLECULE) {
onemols[imol]->compute_mass();
onemols[imol]->compute_com();
gas_mass = onemols[imol]->masstotal;
for (int i = 0; i < onemols[imol]->natoms; i++) {
onemols[imol]->x[i][0] -= onemols[imol]->com[0];
onemols[imol]->x[i][1] -= onemols[imol]->com[1];
onemols[imol]->x[i][2] -= onemols[imol]->com[2];
}
} 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));
if (pressure_flag) zz = pressure*fugacity_coeff*beta/force->nktv2p;
imagetmp = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
// construct group bitmask for all new atoms
// aggregated over all group keywords
groupbitall = 1 | groupbit;
for (int igroup = 0; igroup < ngroups; igroup++) {
int jgroup = group->find(groupstrings[igroup]);
if (jgroup == -1)
error->all(FLERR,"Could not find specified fix gcmc group ID");
groupbitall |= group->bitmask[jgroup];
}
// construct group type bitmasks
// not aggregated over all group keywords
if (ngrouptypes > 0) {
memory->create(grouptypebits,ngrouptypes,"fix_gcmc:grouptypebits");
for (int igroup = 0; igroup < ngrouptypes; igroup++) {
int jgroup = group->find(grouptypestrings[igroup]);
if (jgroup == -1)
error->all(FLERR,"Could not find specified fix gcmc group ID");
grouptypebits[igroup] = group->bitmask[jgroup];
}
}
}
/* ----------------------------------------------------------------------
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;
domain->pbc();
comm->exchange();
atom->nghost = 0;
comm->borders();
update_gas_atoms_list();
if (full_flag) {
energy_stored = energy_full();
if (mode == MOLECULE) {
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_full();
else attempt_molecule_rotation_full();
} else {
if (random_equal->uniform() < 0.5) attempt_molecule_deletion_full();
else attempt_molecule_insertion_full();
}
}
} 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_full();
} else {
if (random_equal->uniform() < 0.5) attempt_atomic_deletion_full();
else attempt_atomic_insertion_full();
}
}
}
domain->pbc();
comm->exchange();
atom->nghost = 0;
comm->borders();
} else {
if (mode == MOLECULE) {
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 = 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;
double coord[3];
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;
}
coord[0] = x[i][0] + displace*rx;
coord[1] = x[i][1] + displace*ry;
coord[2] = x[i][2] + displace*rz;
if (regionflag) {
while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0) {
rsq = 1.1;
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;
}
coord[0] = x[i][0] + displace*rx;
coord[1] = x[i][1] + displace*ry;
coord[2] = x[i][2] + displace*rz;
}
}
if (!domain->inside_nonperiodic(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
double energy_after = energy(i,ngcmc_type,-1,coord);
if (random_unequal->uniform() <
exp(beta*(energy_before - energy_after))) {
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) {
domain->pbc();
comm->exchange();
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 = 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) {
atom->natoms--;
if (atom->tag_enable) {
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);
}
if (!domain->inside_nonperiodic(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
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;
// add to groups
// optionally add to type-based groups
atom->mask[m] = groupbitall;
for (int igroup = 0; igroup < ngrouptypes; igroup++) {
if (ngcmc_type == grouptypes[igroup])
atom->mask[m] |= grouptypebits[igroup];
}
atom->v[m][0] = random_unequal->gaussian()*sigma;
atom->v[m][1] = random_unequal->gaussian()*sigma;
atom->v[m][2] = random_unequal->gaussian()*sigma;
modify->create_attribute(m);
success = 1;
}
}
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
if (success_all) {
atom->natoms++;
if (atom->tag_enable) {
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;
tagint 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;
int nlocal = atom->nlocal;
if (regionflag) {
int *mask = atom->mask;
for (int i = 0; i < nlocal; i++) {
if (atom->molecule[i] == translation_molecule) {
mask[i] |= molecule_group_bit;
} else {
mask[i] &= molecule_group_inversebit;
}
}
double com[3];
com[0] = com[1] = com[2] = 0.0;
group->xcm(molecule_group,gas_mass,com);
coord[0] = com[0] + displace*rx;
coord[1] = com[1] + displace*ry;
coord[2] = com[2] + displace*rz;
while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0) {
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;
}
coord[0] = com[0] + displace*rx;
coord[1] = com[1] + displace*ry;
coord[2] = com[2] + displace*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 < 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];
if (!domain->inside_nonperiodic(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
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_before_sum - energy_after_sum))) {
for (int i = 0; i < 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];
}
}
domain->pbc();
comm->exchange();
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;
tagint 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] |= molecule_group_bit;
} else {
mask[i] &= molecule_group_inversebit;
}
}
double com[3];
com[0] = com[1] = com[2] = 0.0;
group->xcm(molecule_group,gas_mass,com);
double r[3],rotmat[3][3],quat[4];
r[0] = random_equal->uniform() - 0.5;
r[1] = random_equal->uniform() - 0.5;
r[2] = random_equal->uniform() - 0.5;
double theta = random_equal->uniform() * max_rotation_angle;
MathExtra::norm3(r);
MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat);
double **x = atom->x;
imageint *image = atom->image;
double energy_after = 0.0;
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & molecule_group_bit) {
double xtmp[3];
domain->unmap(x[i],image[i],xtmp);
xtmp[0] -= com[0];
xtmp[1] -= com[1];
xtmp[2] -= com[2];
MathExtra::matvec(rotmat,xtmp,atom_coord[n]);
atom_coord[n][0] += com[0];
atom_coord[n][1] += com[1];
atom_coord[n][2] += com[2];
xtmp[0] = atom_coord[n][0];
xtmp[1] = atom_coord[n][1];
xtmp[2] = atom_coord[n][2];
domain->remap(xtmp);
if (!domain->inside_nonperiodic(xtmp))
error->one(FLERR,"Fix gcmc put atom outside box");
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_before_sum - energy_after_sum))) {
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & molecule_group_bit) {
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++;
}
}
domain->pbc();
comm->exchange();
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;
tagint 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*natoms_per_molecule)) {
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;
if (atom->map_style) 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 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 r[3],rotmat[3][3],quat[4];
r[0] = random_equal->uniform() - 0.5;
r[1] = random_equal->uniform() - 0.5;
r[2] = random_equal->uniform() - 0.5;
double theta = random_equal->uniform() * MY_2PI;
MathExtra::norm3(r);
MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat);
double insertion_energy = 0.0;
bool procflag[natoms_per_molecule];
for (int i = 0; i < natoms_per_molecule; i++) {
MathExtra::matvec(rotmat,onemols[imol]->x[i],atom_coord[i]);
atom_coord[i][0] += com_coord[0];
atom_coord[i][1] += com_coord[1];
atom_coord[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);
if (!domain->inside_nonperiodic(xtmp))
error->one(FLERR,"Fix gcmc put atom outside box");
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,onemols[imol]->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*natoms_per_molecule*
exp(-beta*insertion_energy_sum)/(ngas + natoms_per_molecule)) {
tagint maxmol = 0;
for (int i = 0; i < atom->nlocal; i++) maxmol = MAX(maxmol,atom->molecule[i]);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol_all++;
if (maxmol_all >= MAXTAGINT)
error->all(FLERR,"Fix gcmc ran out of available molecule IDs");
tagint maxtag = 0;
for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag,atom->tag[i]);
tagint maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
int nlocalprev = atom->nlocal;
double vnew[3];
vnew[0] = random_unequal->gaussian()*sigma;
vnew[1] = random_unequal->gaussian()*sigma;
vnew[2] = random_unequal->gaussian()*sigma;
for (int i = 0; i < natoms_per_molecule; i++) {
if (procflag[i]) {
atom->avec->create_atom(ngcmc_type+onemols[imol]->type[i],atom_coord[i]);
int m = atom->nlocal - 1;
// add to groups
// optionally add to type-based groups
atom->mask[m] = groupbitall;
for (int igroup = 0; igroup < ngrouptypes; igroup++) {
if (ngcmc_type == grouptypes[igroup])
atom->mask[m] |= grouptypebits[igroup];
}
atom->image[m] = imagetmp;
domain->remap(atom->x[m],atom->image[m]);
atom->molecule[m] = maxmol_all;
if (maxtag_all+i+1 >= MAXTAGINT)
error->all(FLERR,"Fix gcmc ran out of available atom IDs");
atom->tag[m] = maxtag_all + i + 1;
atom->v[m][0] = vnew[0];
atom->v[m][1] = vnew[1];
atom->v[m][2] = vnew[2];
atom->add_molecule_atom(onemols[imol],i,m,maxtag_all);
modify->create_attribute(m);
}
}
if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
atom->nbonds += onemols[imol]->nbonds;
atom->nangles += onemols[imol]->nangles;
atom->ndihedrals += onemols[imol]->ndihedrals;
atom->nimpropers += onemols[imol]->nimpropers;
if (atom->map_style) 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, tagint imolecule, double *coord)
{
double delx,dely,delz,rsq;
double **x = atom->x;
int *type = atom->type;
tagint *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 (mode == MOLECULE)
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;
}
/* ----------------------------------------------------------------------
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(tagint 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;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_atomic_translation_full()
{
ntranslation_attempts += 1.0;
if (ngas == 0) return;
double energy_before = energy_stored;
int i = pick_random_gas_atom();
double **x = atom->x;
double xtmp[3];
xtmp[0] = xtmp[1] = xtmp[2] = 0.0;
tagint tmptag = -1;
if (i >= 0) {
double rsq = 1.1;
double rx,ry,rz;
rx = ry = rz = 0.0;
double coord[3];
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;
}
coord[0] = x[i][0] + displace*rx;
coord[1] = x[i][1] + displace*ry;
coord[2] = x[i][2] + displace*rz;
if (regionflag) {
while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0) {
rsq = 1.1;
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;
}
coord[0] = x[i][0] + displace*rx;
coord[1] = x[i][1] + displace*ry;
coord[2] = x[i][2] + displace*rz;
}
}
if (!domain->inside(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
xtmp[0] = x[i][0];
xtmp[1] = x[i][1];
xtmp[2] = x[i][2];
x[i][0] = coord[0];
x[i][1] = coord[1];
x[i][2] = coord[2];
tmptag = atom->tag[i];
}
double energy_after = energy_full();
if (random_equal->uniform() <
exp(beta*(energy_before - energy_after))) {
energy_stored = energy_after;
ntranslation_successes += 1.0;
} else {
tagint tmptag_all;
MPI_Allreduce(&tmptag,&tmptag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
double xtmp_all[3];
MPI_Allreduce(&xtmp,&xtmp_all,3,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < atom->nlocal; i++) {
if (tmptag_all == atom->tag[i]) {
x[i][0] = xtmp_all[0];
x[i][1] = xtmp_all[1];
x[i][2] = xtmp_all[2];
}
}
energy_stored = energy_before;
}
update_gas_atoms_list();
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_atomic_deletion_full()
{
double q_tmp;
const int q_flag = atom->q_flag;
ndeletion_attempts += 1.0;
if (ngas == 0) return;
double energy_before = energy_stored;
const int i = pick_random_gas_atom();
int tmpmask;
if (i >= 0) {
tmpmask = atom->mask[i];
atom->mask[i] = exclusion_group_bit;
if (q_flag) {
q_tmp = atom->q[i];
atom->q[i] = 0.0;
}
}
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
if (random_equal->uniform() <
ngas*exp(beta*(energy_before - energy_after))/(zz*volume)) {
if (i >= 0) {
atom->avec->copy(atom->nlocal-1,i,1);
atom->nlocal--;
}
atom->natoms--;
if (atom->map_style) atom->map_init();
ndeletion_successes += 1.0;
energy_stored = energy_after;
} else {
if (i >= 0) {
atom->mask[i] = tmpmask;
if (q_flag) atom->q[i] = q_tmp;
}
if (force->kspace) force->kspace->qsum_qsq();
energy_stored = energy_before;
}
update_gas_atoms_list();
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_atomic_insertion_full()
{
ninsertion_attempts += 1.0;
double energy_before = energy_stored;
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);
}
if (!domain->inside(coord))
error->one(FLERR,"Fix gcmc put atom outside box");
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;
atom->avec->create_atom(ngcmc_type,coord);
int m = atom->nlocal - 1;
// add to groups
// optionally add to type-based groups
atom->mask[m] = groupbitall;
for (int igroup = 0; igroup < ngrouptypes; igroup++) {
if (ngcmc_type == grouptypes[igroup])
atom->mask[m] |= grouptypebits[igroup];
}
atom->v[m][0] = random_unequal->gaussian()*sigma;
atom->v[m][1] = random_unequal->gaussian()*sigma;
atom->v[m][2] = random_unequal->gaussian()*sigma;
if (charge_flag) atom->q[m] = charge;
modify->create_attribute(m);
}
atom->natoms++;
if (atom->tag_enable) {
atom->tag_extend();
if (atom->map_style) atom->map_init();
}
atom->nghost = 0;
comm->borders();
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
if (random_equal->uniform() <
zz*volume*exp(beta*(energy_before - energy_after))/(ngas+1)) {
ninsertion_successes += 1.0;
energy_stored = energy_after;
} else {
atom->natoms--;
if (proc_flag) atom->nlocal--;
if (force->kspace) force->kspace->qsum_qsq();
energy_stored = energy_before;
}
update_gas_atoms_list();
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_molecule_translation_full()
{
ntranslation_attempts += 1.0;
if (ngas == 0) return;
tagint translation_molecule = pick_random_gas_molecule();
if (translation_molecule == -1) return;
double energy_before = energy_stored;
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;
int nlocal = atom->nlocal;
if (regionflag) {
int *mask = atom->mask;
for (int i = 0; i < nlocal; i++) {
if (atom->molecule[i] == translation_molecule) {
mask[i] |= molecule_group_bit;
} else {
mask[i] &= molecule_group_inversebit;
}
}
double com[3];
com[0] = com[1] = com[2] = 0.0;
group->xcm(molecule_group,gas_mass,com);
coord[0] = com[0] + displace*rx;
coord[1] = com[1] + displace*ry;
coord[2] = com[2] + displace*rz;
while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0) {
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;
}
coord[0] = com[0] + displace*rx;
coord[1] = com[1] + displace*ry;
coord[2] = com[2] + displace*rz;
}
com_displace[0] = displace*rx;
com_displace[1] = displace*ry;
com_displace[2] = displace*rz;
}
for (int i = 0; i < 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];
if (!domain->inside(x[i]))
error->one(FLERR,"Fix gcmc put atom outside box");
}
}
double energy_after = energy_full();
if (random_equal->uniform() <
exp(beta*(energy_before - energy_after))) {
ntranslation_successes += 1.0;
energy_stored = energy_after;
} else {
energy_stored = energy_before;
for (int i = 0; i < 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];
}
}
}
update_gas_atoms_list();
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_molecule_rotation_full()
{
nrotation_attempts += 1.0;
if (ngas == 0) return;
tagint rotation_molecule = pick_random_gas_molecule();
if (rotation_molecule == -1) return;
double energy_before = energy_stored;
int nlocal = atom->nlocal;
int *mask = atom->mask;
for (int i = 0; i < nlocal; i++) {
if (atom->molecule[i] == rotation_molecule) {
mask[i] |= molecule_group_bit;
} else {
mask[i] &= molecule_group_inversebit;
}
}
double com[3];
com[0] = com[1] = com[2] = 0.0;
group->xcm(molecule_group,gas_mass,com);
double r[3],rotmat[3][3],quat[4];
r[0] = random_equal->uniform() - 0.5;
r[1] = random_equal->uniform() - 0.5;
r[2] = random_equal->uniform() - 0.5;
double theta = random_equal->uniform() * max_rotation_angle;
MathExtra::norm3(r);
MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat);
double **x = atom->x;
imageint *image = atom->image;
imageint image_orig[natoms_per_molecule];
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & molecule_group_bit) {
atom_coord[n][0] = x[i][0];
atom_coord[n][1] = x[i][1];
atom_coord[n][2] = x[i][2];
image_orig[n] = image[i];
double xtmp[3];
domain->unmap(x[i],image[i],xtmp);
xtmp[0] -= com[0];
xtmp[1] -= com[1];
xtmp[2] -= com[2];
MathExtra::matvec(rotmat,xtmp,x[i]);
x[i][0] += com[0];
x[i][1] += com[1];
x[i][2] += com[2];
image[i] = imagetmp;
domain->remap(x[i],image[i]);
if (!domain->inside(x[i]))
error->one(FLERR,"Fix gcmc put atom outside box");
n++;
}
}
double energy_after = energy_full();
if (random_equal->uniform() <
exp(beta*(energy_before - energy_after))) {
nrotation_successes += 1.0;
energy_stored = energy_after;
} else {
energy_stored = energy_before;
int n = 0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & molecule_group_bit) {
x[i][0] = atom_coord[n][0];
x[i][1] = atom_coord[n][1];
x[i][2] = atom_coord[n][2];
image[i] = image_orig[n];
n++;
}
}
}
update_gas_atoms_list();
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_molecule_deletion_full()
{
ndeletion_attempts += 1.0;
if (ngas == 0) return;
tagint deletion_molecule = pick_random_gas_molecule();
if (deletion_molecule == -1) return;
double energy_before = energy_stored;
int m = 0;
double q_tmp[natoms_per_molecule];
int tmpmask[atom->nlocal];
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == deletion_molecule) {
tmpmask[i] = atom->mask[i];
atom->mask[i] = exclusion_group_bit;
if (atom->q_flag) {
q_tmp[m] = atom->q[i];
m++;
atom->q[i] = 0.0;
}
toggle_intramolecular(i);
}
}
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
// energy_before corrected by energy_intra
double deltaphi = ngas*exp(beta*((energy_before - energy_intra) - energy_after))/(zz*volume*natoms_per_molecule);
if (random_equal->uniform() < deltaphi) {
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;
if (atom->map_style) atom->map_init();
ndeletion_successes += 1.0;
energy_stored = energy_after;
} else {
energy_stored = energy_before;
int m = 0;
for (int i = 0; i < atom->nlocal; i++) {
if (atom->molecule[i] == deletion_molecule) {
atom->mask[i] = tmpmask[i];
toggle_intramolecular(i);
if (atom->q_flag) {
atom->q[i] = q_tmp[m];
m++;
}
}
}
if (force->kspace) force->kspace->qsum_qsq();
}
update_gas_atoms_list();
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::attempt_molecule_insertion_full()
{
ninsertion_attempts += 1.0;
double energy_before = energy_stored;
tagint maxmol = 0;
for (int i = 0; i < atom->nlocal; i++) maxmol = MAX(maxmol,atom->molecule[i]);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
maxmol_all++;
if (maxmol_all >= MAXTAGINT)
error->all(FLERR,"Fix gcmc ran out of available molecule IDs");
int insertion_molecule = maxmol_all;
tagint maxtag = 0;
for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag,atom->tag[i]);
tagint maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
int nlocalprev = atom->nlocal;
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 r[3],rotmat[3][3],quat[4];
r[0] = random_equal->uniform() - 0.5;
r[1] = random_equal->uniform() - 0.5;
r[2] = random_equal->uniform() - 0.5;
double theta = random_equal->uniform() * MY_2PI;
MathExtra::norm3(r);
MathExtra::axisangle_to_quat(r,theta,quat);
MathExtra::quat_to_mat(quat,rotmat);
double vnew[3];
vnew[0] = random_unequal->gaussian()*sigma;
vnew[1] = random_unequal->gaussian()*sigma;
vnew[2] = random_unequal->gaussian()*sigma;
for (int i = 0; i < natoms_per_molecule; i++) {
double xtmp[3];
MathExtra::matvec(rotmat,onemols[imol]->x[i],xtmp);
xtmp[0] += com_coord[0];
xtmp[1] += com_coord[1];
xtmp[2] += com_coord[2];
domain->remap(xtmp);
if (!domain->inside(xtmp))
error->one(FLERR,"Fix gcmc put atom outside box");
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]) {
atom->avec->create_atom(ngcmc_type+onemols[imol]->type[i],xtmp);
int m = atom->nlocal - 1;
// add to groups
// optionally add to type-based groups
atom->mask[m] = groupbitall;
for (int igroup = 0; igroup < ngrouptypes; igroup++) {
if (ngcmc_type == grouptypes[igroup])
atom->mask[m] |= grouptypebits[igroup];
}
atom->image[m] = imagetmp;
domain->remap(atom->x[m],atom->image[m]);
atom->molecule[m] = insertion_molecule;
if (maxtag_all+i+1 >= MAXTAGINT)
error->all(FLERR,"Fix gcmc ran out of available atom IDs");
atom->tag[m] = maxtag_all + i + 1;
atom->v[m][0] = vnew[0];
atom->v[m][1] = vnew[1];
atom->v[m][2] = vnew[2];
atom->add_molecule_atom(onemols[imol],i,m,maxtag_all);
modify->create_attribute(m);
}
}
if (shakeflag)
fixshake->set_molecule(nlocalprev,maxtag_all,imol,com_coord,vnew,quat);
atom->natoms += natoms_per_molecule;
if (atom->natoms < 0 || atom->natoms > MAXBIGINT)
error->all(FLERR,"Too many total atoms");
atom->nbonds += onemols[imol]->nbonds;
atom->nangles += onemols[imol]->nangles;
atom->ndihedrals += onemols[imol]->ndihedrals;
atom->nimpropers += onemols[imol]->nimpropers;
if (atom->map_style) atom->map_init();
atom->nghost = 0;
comm->borders();
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
// energy_after corrected by energy_intra
double deltaphi = zz*volume*natoms_per_molecule*
exp(beta*(energy_before - (energy_after - energy_intra)))/(ngas + natoms_per_molecule);
if (random_equal->uniform() < deltaphi) {
ninsertion_successes += 1.0;
energy_stored = energy_after;
} else {
atom->nbonds -= onemols[imol]->nbonds;
atom->nangles -= onemols[imol]->nangles;
atom->ndihedrals -= onemols[imol]->ndihedrals;
atom->nimpropers -= onemols[imol]->nimpropers;
atom->natoms -= natoms_per_molecule;
energy_stored = energy_before;
int i = 0;
while (i < atom->nlocal) {
if (atom->molecule[i] == insertion_molecule) {
atom->avec->copy(atom->nlocal-1,i,1);
atom->nlocal--;
} else i++;
}
if (force->kspace) force->kspace->qsum_qsq();
}
update_gas_atoms_list();
}
/* ----------------------------------------------------------------------
compute system potential energy
------------------------------------------------------------------------- */
double FixGCMC::energy_full()
{
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
comm->exchange();
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
if (modify->n_pre_neighbor) modify->pre_neighbor();
neighbor->build();
int eflag = 1;
int vflag = 0;
if (modify->n_pre_force) modify->pre_force(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
if (force->dihedral) force->dihedral->compute(eflag,vflag);
if (force->improper) force->improper->compute(eflag,vflag);
}
if (force->kspace) force->kspace->compute(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
update->eflag_global = update->ntimestep;
double total_energy = c_pe->compute_scalar();
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;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
tagint FixGCMC::pick_random_gas_molecule()
{
int iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
tagint 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];
}
tagint gas_molecule_id_all = 0;
MPI_Allreduce(&gas_molecule_id,&gas_molecule_id_all,1,
MPI_LMP_TAGINT,MPI_MAX,world);
return gas_molecule_id_all;
}
/* ----------------------------------------------------------------------
------------------------------------------------------------------------- */
void FixGCMC::toggle_intramolecular(int i)
{
if (atom->avec->bonds_allow)
for (int m = 0; m < atom->num_bond[i]; m++)
atom->bond_type[i][m] = -atom->bond_type[i][m];
if (atom->avec->angles_allow)
for (int m = 0; m < atom->num_angle[i]; m++)
atom->angle_type[i][m] = -atom->angle_type[i][m];
if (atom->avec->dihedrals_allow)
for (int m = 0; m < atom->num_dihedral[i]; m++)
atom->dihedral_type[i][m] = -atom->dihedral_type[i][m];
if (atom->avec->impropers_allow)
for (int m = 0; m < atom->num_improper[i]; m++)
atom->improper_type[i][m] = -atom->improper_type[i][m];
}
/* ----------------------------------------------------------------------
update the list of gas atoms
------------------------------------------------------------------------- */
void FixGCMC::update_gas_atoms_list()
{
int nlocal = atom->nlocal;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
double **x = atom->x;
if (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;
if (regionflag) {
if (mode == MOLECULE) {
tagint maxmol = 0;
for (int i = 0; i < nlocal; i++) maxmol = MAX(maxmol,molecule[i]);
tagint maxmol_all;
MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
double comx[maxmol_all];
double comy[maxmol_all];
double comz[maxmol_all];
for (int imolecule = 0; imolecule < maxmol_all; imolecule++) {
for (int i = 0; i < nlocal; i++) {
if (molecule[i] == imolecule) {
mask[i] |= molecule_group_bit;
} else {
mask[i] &= molecule_group_inversebit;
}
}
double com[3];
com[0] = com[1] = com[2] = 0.0;
group->xcm(molecule_group,gas_mass,com);
comx[imolecule] = com[0];
comy[imolecule] = com[1];
comz[imolecule] = com[2];
}
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (domain->regions[iregion]->match(comx[molecule[i]],
comy[molecule[i]],comz[molecule[i]]) == 1) {
local_gas_list[ngas_local] = i;
ngas_local++;
}
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]) == 1) {
local_gas_list[ngas_local] = i;
ngas_local++;
}
}
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (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++]);
}
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