From 8e179220ec17d655423eb138140cf0a2dca988b3 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 17 Dec 2013 00:22:16 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11115 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/MC/fix_gcmc.cpp | 42 ++++++++++++++++++++++++++++-------------- 1 file changed, 28 insertions(+), 14 deletions(-) diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index baee0c7912..c6cfff6d2f 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -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)