blues.runjanpa

blues.runjanpa.get_bond_orders(wiberg_file)

Extracts the Wiberg-Mayer bond orders from generated file.

Parameters

wiberg_file (str) – Name of file containing Wiberg-Mayer bond orders generated from JANPA execution.

Returns

• elements (list) – List of atoms in system in the same order as input file.

• bond_orders (np.ndarray) – Wiberg-Mayer bond orders calculated in JANPA.

blues.runjanpa.parse_atom_list(raw_atom_list)

Converts single string to list of elemental symbols.

Parameters

raw_atom_list (str) –

Returns

atom_list

Return type

list

blues.runjanpa.parse_bond_orders(raw_bond_orders)

Converts a list of string to a matrix of bond orders.

Parameters

raw_bond_orders (list of str) –

Returns

bond_orders

Return type

np.ndarray

blues.runjanpa.run_janpa(molden_file, wiberg_file='wiberg.dat', delete_wiberg_file=False)

Runs JANPA with specified input file.

Parameters

molden_file (str) – Name of MOLDEN file automatically generated from NWChem run.

Returns

• elements (list) – List of atoms in system in the same order as input file.

• bond_orders (np.ndarray) – Wiberg-Mayer bond orders calculated in JANPA.