diff --git a/parser/parser-dl_poly/dlPolyParser.py b/parser/parser-dl_poly/dlPolyParser.py index c8caeb2f6b6e1b19c504c06f10639244b9fa5a41..ed8e9b4307e51bba5609dd515fac555620641b11 100644 --- a/parser/parser-dl_poly/dlPolyParser.py +++ b/parser/parser-dl_poly/dlPolyParser.py @@ -140,9 +140,9 @@ def parse(output_file_name): push(jbe, mol, 'molecule_type_name') push(jbe, mol, 'number_of_atoms_in_molecule', lambda s: s.As(int)) - push_array(jbe, mol, 'atom_in_molecule_name') #TODO - push_array(jbe, mol, 'atom_in_molecule_charge') # TODO - push_array_values(jbe, np.asarray(atom_gid_list), 'atom_in_molecule_to_atom_type_ref') #TODO + push_array(jbe, mol, 'atom_in_molecule_name') + push_array(jbe, mol, 'atom_in_molecule_charge') + push_array_values(jbe, np.asarray(atom_gid_list), 'atom_in_molecule_to_atom_type_ref') # Global molecule type map molecule_to_molecule_type = [] for mol in top.molecules: @@ -151,7 +151,7 @@ def parse(output_file_name): n_this_mol = mol['number_of_molecules'].As(int) for i in range(n_this_mol): molecule_to_molecule_type.append(type_gid_this_mol) - push_array_values(jbe, np.asarray(molecule_to_molecule_type), 'molecule_to_molecule_type_map') #TODO + push_array_values(jbe, np.asarray(molecule_to_molecule_type), 'molecule_to_molecule_type_map') # Global atom map atoms_to_molidx_atomidx = [] @@ -165,7 +165,7 @@ def parse(output_file_name): atoms_to_molidx_atomidx.append(molidx_atomidx) atomidx += 1 molidx += 1 - push_array_values(jbe, np.asarray(atoms_to_molidx_atomidx), 'atom_to_molecule') #TODO + push_array_values(jbe, np.asarray(atoms_to_molidx_atomidx), 'atom_to_molecule') # SAMPLING-METHOD SECTION with open_section(jbe, 'section_sampling_method'):