(1f6a1f4a) · Commits · 郑智淋 / lammps

src/MC/fix_gcmc.cpp

+32 −3

Original line number	Diff line number	Diff line
		@@ -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() < zzvolumenatoms_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
		------------------------------------------------------------------------- */

src/MC/fix_gcmc.h

+2 −1

Original line number	Diff line number	Diff line
		@@ -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.

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