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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13298 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
pscrozi
2015-03-25 19:00:59 +00:00
parent 4d2f68754f
commit 1f6a1f4ad4
2 changed files with 34 additions and 4 deletions
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35
src/MC/fix_gcmc.cpp
View File

@ -1288,6 +1288,7 @@ void FixGCMC::attempt_atomic_deletion_full()
atom->q[i] = 0.0;
}
}
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
if (random_equal->uniform() <
@ -1305,6 +1306,7 @@ void FixGCMC::attempt_atomic_deletion_full()
atom->mask[i] = tmpmask;
if (atom->q_flag) atom->q[i] = q_tmp;
}
if (force->kspace) force->kspace->qsum_qsq();
energy_stored = energy_before;
}
update_gas_atoms_list();
@ -1360,7 +1362,7 @@ void FixGCMC::attempt_atomic_insertion_full()
}
atom->nghost = 0;
comm->borders();
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
if (random_equal->uniform() <
@ -1371,6 +1373,7 @@ void FixGCMC::attempt_atomic_insertion_full()
} else {
atom->natoms--;
if (proc_flag) atom->nlocal--;
if (force->kspace) force->kspace->qsum_qsq();
energy_stored = energy_before;
}
update_gas_atoms_list();
@ -1575,10 +1578,10 @@ void FixGCMC::attempt_molecule_deletion_full()
m++;
atom->q[i] = 0.0;
}
toggle_intramolecular(i);
}
}
if (force->kspace) force->kspace->qsum_qsq();
double energy_after = energy_full();
if (random_equal->uniform() <
@ -1600,12 +1603,14 @@ void FixGCMC::attempt_molecule_deletion_full()
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();
}
@ -1720,6 +1725,7 @@ void FixGCMC::attempt_molecule_insertion_full()
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*natoms_per_molecule*
@ -1744,6 +1750,7 @@ void FixGCMC::attempt_molecule_insertion_full()
atom->nlocal--;
} else i++;
}
if (force->kspace) force->kspace->qsum_qsq();
}
update_gas_atoms_list();
}
@ -1823,6 +1830,28 @@ tagint FixGCMC::pick_random_gas_molecule()
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
------------------------------------------------------------------------- */

3
src/MC/fix_gcmc.h
View File

@ -50,6 +50,7 @@ class FixGCMC : public Fix {
double energy_full();
int pick_random_gas_atom();
tagint pick_random_gas_molecule();
void toggle_intramolecular(int);
double molecule_energy(tagint);
void update_gas_atoms_list();
double compute_vector(int);
@ -245,7 +246,7 @@ E: Illegal fix gcmc gas mass <= 0
The computed mass of the designated gas molecule or atom type was less
than or equal to zero.
E: Cannot do GCMC on atoms in atom_modify first group
E: Cannot do gcmc on atoms in atom_modify first group
This is a restriction due to the way atoms are organized in a list to
enable the atom_modify first command.