From 5a1c8053a0b296fc35f68a7982dc35a51210eeb8 Mon Sep 17 00:00:00 2001 From: doublylinkedlist Date: Sat, 9 Sep 2023 02:59:15 -0500 Subject: [PATCH] Update cif2system.py --- mofa/simulation/cif2lammps/cif2system.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mofa/simulation/cif2lammps/cif2system.py b/mofa/simulation/cif2lammps/cif2system.py index 67b2ed16..3d97d409 100644 --- a/mofa/simulation/cif2lammps/cif2system.py +++ b/mofa/simulation/cif2lammps/cif2system.py @@ -204,7 +204,7 @@ def initialize_system(filename, charges=False, small_molecule_cutoff=5, read_pym for e, n, cc, fc, charge in zip(elems, names, ccoords, fcoords, charge_list): index += 1 G.add_node(index, element_symbol=e, mol_flag='1', index=index, force_field_type='', cartesian_position=cc, - fractional_position=fc, charge=charge, replication=np.array([0.0, 0.0, 0.0]), duplicated_version_of=None) + fractional_position=fc, charge=charge, replication=np.array([0.0, 0.0, 0.0]), duplicated_version_of=None, cif_label=n) index_key[n] = index for b in bonds: @@ -314,7 +314,7 @@ def initialize_system(filename, charges=False, small_molecule_cutoff=5, read_pym data['index'] = index SM = nx.relabel_nodes(SM, sm_remap) - return {'box': (A, B, C, alpha, beta, gamma), 'graph': framework, 'SM_graph': SM, 'max_ind': index, 'names': names} + return {'box': (A, B, C, alpha, beta, gamma), 'graph': framework, 'SM_graph': SM, 'max_ind': index} def duplicate_system(system, replications, small_molecule_cutoff=10):