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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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176
src/MC/fix_gcmc.cpp
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@ -5,7 +5,7 @@
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
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.
@ -53,7 +53,7 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
time_depend = 1;
// required args
nevery = atoi(arg[3]);
nexchanges = atoi(arg[4]);
nmcmoves = atoi(arg[5]);
@ -63,22 +63,22 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
chemical_potential = atof(arg[9]);
displace = atof(arg[10]);
if (ntype <= 0 || ntype > atom->ntypes)
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");
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 gas_mass = atom->mass[ntype];
double lambda = sqrt(force->hplanck*force->hplanck/
(2.0*MY_PI*gas_mass*force->mvv2e*
force->boltz*reservoir_temperature));
(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));
@ -97,23 +97,23 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
// 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;
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;
@ -146,7 +146,7 @@ void FixGCMC::init()
// 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;
@ -177,17 +177,17 @@ void FixGCMC::init()
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");
"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)
"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");
}
@ -200,7 +200,7 @@ void FixGCMC::init()
void FixGCMC::pre_exchange()
{
// just return if should not be called on this timestep
if (next_reneighbor != update->ntimestep) return;
if (domain->triclinic == 0) {
@ -221,34 +221,34 @@ void FixGCMC::pre_exchange()
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");
"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;
int random_int_fraction =
static_cast<int>(random_equal->uniform()*ncycles) + 1;
if (random_int_fraction <= nmcmoves) {
attempt_move();
} else {
@ -256,26 +256,26 @@ void FixGCMC::pre_exchange()
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) &&
if ((iwhichglobal >= ngas_before) &&
(iwhichglobal < ngas_before + ngas_local)) {
iwhichlocal = iwhichglobal - ngas_before;
i = local_gas_list[iwhichlocal];
@ -293,19 +293,19 @@ void FixGCMC::attempt_move()
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][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();
nmove_successes += 1.0;
comm->borders();
}
}
@ -314,7 +314,7 @@ void FixGCMC::attempt_move()
------------------------------------------------------------------------- */
void FixGCMC::attempt_deletion()
{
{
ndel_attempts += 1.0;
if (ngas == 0) return;
@ -325,32 +325,32 @@ void FixGCMC::attempt_deletion()
// 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) &&
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)) {
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;
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--;
if (iwhichglobal < ngas_before) ngas_before--;
comm->borders();
if (atom->tag_enable) {
atom->tag_extend();
@ -367,13 +367,13 @@ void FixGCMC::attempt_deletion()
------------------------------------------------------------------------- */
void FixGCMC::attempt_insertion()
{
{
int flag,success;
double coord[3],lamda[3];
double *newcoord;
double *newcoord;
ninsert_attempts += 1.0;
// choose random position for new atom within box
coord[0] = xlo + random_equal->uniform() * (xhi-xlo);
@ -384,7 +384,7 @@ void FixGCMC::attempt_insertion()
// 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;
@ -394,21 +394,21 @@ void FixGCMC::attempt_insertion()
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);
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++)
@ -416,20 +416,20 @@ void FixGCMC::attempt_insertion()
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 = (int *)
memory->srealloc(local_gas_list,nmax*sizeof(int),
"GCMC:local_gas_list");
}
local_gas_list[ngas_local] = atom->nlocal;
ngas_local++;
success = 1;
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;
@ -443,15 +443,15 @@ void FixGCMC::attempt_insertion()
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 FixGCMC::energy(int i, double *coord)
{
double delx,dely,delz,rsq;
@ -464,7 +464,7 @@ double FixGCMC::energy(int i, double *coord)
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++) {
@ -477,15 +477,15 @@ double FixGCMC::energy(int i, double *coord)
int jtype = type[j];
if (rsq < cutsq[ntype][jtype])
total_energy +=
pair->single(i,j,ntype,jtype,rsq,factor_coul,factor_lj,fpair);
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
parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixGCMC::options(int narg, char **arg)
@ -530,7 +530,7 @@ double FixGCMC::memory_usage()
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixGCMC::write_restart(FILE *fp)
@ -549,7 +549,7 @@ void FixGCMC::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixGCMC::restart(char *buf)
@ -559,9 +559,9 @@ void FixGCMC::restart(char *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++]);
}