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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11115 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-12-17 00:22:16 +00:00
parent a9f063d9d9
commit 8e179220ec
1 changed files with 28 additions and 14 deletions
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42
src/MC/fix_gcmc.cpp
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@ -132,7 +132,8 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
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++;
if (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) != 0)
inside++;
}
double max_region_volume = (region_xhi - region_xlo)*
@ -440,7 +441,8 @@ void FixGCMC::attempt_atomic_translation()
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))) {
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];
@ -475,7 +477,8 @@ void FixGCMC::attempt_atomic_deletion()
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)) {
if (random_unequal->uniform() <
ngas*exp(beta*deletion_energy)/(zz*volume)) {
atom->avec->copy(atom->nlocal-1,i,1);
atom->nlocal--;
success = 1;
@ -606,7 +609,8 @@ void FixGCMC::attempt_molecule_translation()
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))) {
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];
@ -665,9 +669,12 @@ void FixGCMC::attempt_molecule_rotation()
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];
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];
@ -680,7 +687,8 @@ void FixGCMC::attempt_molecule_rotation()
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))) {
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) {
@ -715,7 +723,8 @@ void FixGCMC::attempt_molecule_deletion()
double deletion_energy_sum = molecule_energy(deletion_molecule);
if (random_equal->uniform() < ngas*exp(beta*deletion_energy_sum)/(zz*volume*natoms_per_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) {
@ -1015,10 +1024,12 @@ void FixGCMC::get_model_molecule()
}
natoms_per_molecule = 0;
MPI_Allreduce(&natoms_per_molecule_local,&natoms_per_molecule,1,MPI_INT,MPI_SUM,world);
MPI_Allreduce(&natoms_per_molecule_local,&natoms_per_molecule,1,
MPI_INT,MPI_SUM,world);
if (natoms_per_molecule == 0)
error->all(FLERR,"Fix gcmc could not find any atoms in the user-supplied template molecule");
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");
@ -1026,7 +1037,8 @@ void FixGCMC::get_model_molecule()
maxmol = 0;
if (atom->molecular) {
for (int i = 0; i < atom->nlocal; i++) maxmol = MAX(atom->molecule[i],maxmol);
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;
@ -1081,7 +1093,8 @@ void FixGCMC::get_model_molecule()
atom->nextra_grow = old_atom->nextra_grow;
if (atom->nextra_grow) {
memory->grow(atom->extra_grow,old_atom->nextra_grow_max,"fixGCMC:extra_grow");
memory->grow(atom->extra_grow,old_atom->nextra_grow_max,
"fixGCMC:extra_grow");
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
atom->extra_grow[iextra] = old_atom->extra_grow[iextra];
}
@ -1130,7 +1143,8 @@ void FixGCMC::get_model_molecule()
memory->destroy(buf);
// make sure that the number of model atoms is equal to the number of atoms per gas molecule
// 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)