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19e8c92a906e96200926345a13b591630c4c3823
lammps/src/MC/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 "update.h"
#include "modify.h"
#include "fix.h"
#include "comm.h"
#include "group.h"
#include "domain.h"
#include "random_park.h"
#include "force.h"
#include "pair.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
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 = 6;
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]);
ntype = atoi(arg[6]);
seed = atoi(arg[7]);
reservoir_temperature = atof(arg[8]);
chemical_potential = atof(arg[9]);
displace = atof(arg[10]);
if (ntype <= 0 || ntype > atom->ntypes)
error->all(FLERR,"Invalid atom type in fix GCMC command");
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");
// compute beta, lambda, sigma, and the zz factor
beta = 1.0/(force->boltz*reservoir_temperature);
double PI = 4.0*atan(1.0);
double gas_mass = atom->mass[ntype];
double lambda = sqrt(force->hplanck*force->hplanck/
(2.0*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));
// set defaults
molflag = 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);
// 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
nmove_attempts = 0.0;
nmove_successes = 0.0;
ndel_attempts = 0.0;
ndel_successes = 0.0;
ninsert_attempts = 0.0;
ninsert_successes = 0.0;
nmax = 0;
local_gas_list = NULL;
}
/* ---------------------------------------------------------------------- */
FixGCMC::~FixGCMC()
{
delete random_equal;
delete random_unequal;
memory->sfree(local_gas_list);
}
/* ---------------------------------------------------------------------- */
int FixGCMC::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixGCMC::init()
{
// check that no deletable atoms are in atom->firstgroup
// deleting such an atom would not leave firstgroup atoms first
int *type = atom->type;
if (atom->firstgroup >= 0) {
int *mask = atom->mask;
int nlocal = atom->nlocal;
int firstgroupbit = group->bitmask[atom->firstgroup];
int flag = 0;
for (int i = 0; i < nlocal; i++)
if ((type[i] == ntype) && (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");
}
// 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 nlocal = atom->nlocal;
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (type[i] == ntype)
if (molecule[i]) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && comm->me == 0)
error->warning(FLERR,"Fix GCMC may delete atom with non-zero molecule ID");
}
if (molflag && atom->molecule_flag == 0)
error->all(FLERR,"Fix GCMC molecule command requires atom attribute molecule");
if (molflag != 0) error->all(FLERR,"Fix GCMC molecule feature does not yet work");
if (force->pair->single_enable == 0)
error->all(FLERR,"Fix GCMC incompatible with given pair_style");
}
/* ----------------------------------------------------------------------
attempt particle 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;
if (domain->triclinic == 0) {
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;
} else {
xlo = domain->boxlo_bound[0];
xhi = domain->boxhi_bound[0];
ylo = domain->boxlo_bound[1];
yhi = domain->boxhi_bound[1];
zlo = domain->boxlo_bound[2];
zhi = domain->boxhi_bound[2];
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
volume = domain->xprd * domain->yprd * domain->zprd;
// grow local_gas_list array if necessary
if (atom->nlocal > nmax) {
memory->sfree(local_gas_list);
nmax = atom->nmax;
local_gas_list = (int *) memory->smalloc(nmax*sizeof(int),
"GCMC:local_gas_list");
}
int *type = atom->type;
ngas_local = 0;
for (int i = 0; i < atom->nlocal; i++)
if (type[i] == ntype)
local_gas_list[ngas_local++] = i;
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;
// perform ncycles MC cycles
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_move();
} else {
if (random_equal->uniform() < 0.5) attempt_deletion();
else attempt_insertion();
}
}
next_reneighbor = update->ntimestep + nevery;
}
/* ----------------------------------------------------------------------
choose particle randomly across all procs and attempt displacement
------------------------------------------------------------------------- */
void FixGCMC::attempt_move()
{
int i,iwhichglobal,iwhichlocal;
double rx,ry,rz;
double coord[3];
double **x = atom->x;
nmove_attempts += 1.0;
int success = 0;
iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
iwhichlocal = iwhichglobal - ngas_before;
i = local_gas_list[iwhichlocal];
double energy_before = energy(i,x[i]);
double rsq = 1.1;
while (rsq > 1.0) {
rx = 2*random_unequal->uniform() - 1.0;
ry = 2*random_unequal->uniform() - 1.0;
if (domain->dimension == 3) rz = 2*random_unequal->uniform() - 1.0;
else rz = 0.0;
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;
double energy_after = energy(i,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) {
nmove_successes += 1.0;
comm->borders();
}
}
/* ----------------------------------------------------------------------
attempt particle deletion
------------------------------------------------------------------------- */
void FixGCMC::attempt_deletion()
{
ndel_attempts += 1.0;
if (ngas == 0) return;
int i,iwhichglobal,iwhichlocal;
AtomVec *avec = atom->avec;
// choose particle randomly across all procs and delete it
// keep ngas, ngas_local, ngas_before, and local_gas_list current
// after each deletion
int success = 0;
iwhichglobal = static_cast<int> (ngas*random_equal->uniform());
if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
iwhichlocal = iwhichglobal - ngas_before;
i = local_gas_list[iwhichlocal];
double deletion_energy = energy(i,atom->x[i]);
if (random_unequal->uniform() <
ngas*exp(beta*deletion_energy)/(zz*volume)) {
avec->copy(atom->nlocal-1,i,1);
atom->nlocal--;
local_gas_list[iwhichlocal] = local_gas_list[ngas_local-1];
ngas_local--;
success = 1;
}
}
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
if (success_all) {
ngas--;
ndel_successes += 1.0;
atom->natoms--;
if (iwhichglobal < ngas_before) ngas_before--;
comm->borders();
if (atom->tag_enable) {
atom->tag_extend();
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
}
}
}
/* ----------------------------------------------------------------------
attempt particle insertion
------------------------------------------------------------------------- */
void FixGCMC::attempt_insertion()
{
int flag,success;
double coord[3],lamda[3];
double *newcoord;
ninsert_attempts += 1.0;
// choose random position for new atom within box
coord[0] = xlo + random_equal->uniform() * (xhi-xlo);
coord[1] = ylo + random_equal->uniform() * (yhi-ylo);
coord[2] = zlo + random_equal->uniform() * (zhi-zlo);
// check if new atom is in my sub-box or above it if I'm highest proc
// if so, add to my list via create_atom()
// initialize info about the atoms
// set group mask to "all" plus fix group
if (domain->triclinic) {
domain->x2lamda(coord,lamda);
newcoord = lamda;
} else newcoord = coord;
flag = 0;
if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
success = 0;
if (flag) {
int nall = atom->nlocal + atom->nghost;
double insertion_energy = energy(nall,coord);
if (random_unequal->uniform() <
zz*volume*exp(-beta*insertion_energy)/(ngas+1)) {
atom->avec->create_atom(ntype,coord);
int m = atom->nlocal - 1;
atom->type[m] = ntype;
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);
if (atom->nlocal > nmax) {
nmax = atom->nmax;
local_gas_list = (int *)
memory->srealloc(local_gas_list,nmax*sizeof(int),
"GCMC:local_gas_list");
}
local_gas_list[ngas_local] = atom->nlocal;
ngas_local++;
success = 1;
}
}
int success_all = 0;
MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
if (success_all) {
ngas++;
ninsert_successes += 1.0;
MPI_Scan(&ngas_local,&ngas_before,1,MPI_INT,MPI_SUM,world);
ngas_before -= ngas_local;
comm->borders();
if (atom->tag_enable) {
atom->natoms++;
atom->tag_extend();
if (atom->map_style) {
atom->map_init();
atom->map_set();
}
}
}
}
/* ----------------------------------------------------------------------
compute particle's interaction energy with the rest of the system
------------------------------------------------------------------------- */
double FixGCMC::energy(int i, double *coord)
{
double delx,dely,delz,rsq;
double **x = atom->x;
int *type = atom->type;
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;
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[ntype][jtype])
total_energy +=
pair->single(i,j,ntype,jtype,rsq,factor_coul,factor_lj,fpair);
}
return total_energy;
}
/* ----------------------------------------------------------------------
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 evaporate command");
iarg += 2;
} else error->all(FLERR,"Illegal fix GCMC command");
}
}
/* ----------------------------------------------------------------------
return acceptance ratios
------------------------------------------------------------------------- */
double FixGCMC::compute_vector(int n)
{
if (n == 0) return nmove_attempts;
if (n == 1) return nmove_successes;
if (n == 2) return ndel_attempts;
if (n == 3) return ndel_successes;
if (n == 4) return ninsert_attempts;
if (n == 5) return ninsert_successes;
return 0.0;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixGCMC::memory_usage()
{
double bytes = 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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