catkit.hub.ase_tools package

Submodules

catkit.hub.ase_tools.gas_phase_references module

catkit.hub.ase_tools.gas_phase_references.construct_reference_system(symbols, candidates=['H2', 'H2O', 'NH3', 'CH4', 'CO', 'SH2', 'HCl', 'N2', 'O2'])[source]

Take a list of symbols and construct gas phase references system, when possible avoiding O2. Candidates can be rearranged, where earlier candidates get higher preference than later candidates

assume symbols sorted by atomic number

catkit.hub.ase_tools.gas_phase_references.get_atomic_stoichiometry(references)[source]

Given a list of references (tuples of (symbol, molecule)) return stoichiometry matrix that connects atomic symbols to its molecular references.

catkit.hub.ase_tools.gas_phase_references.get_stoichiometry_factors(adsorbates, references)[source]

Take a list of adsorabtes and a corresponding reference system and return a list of dictionaries encoding the stoichiometry factors converting between adsorbates and reference molecules.

catkit.hub.ase_tools.gas_phase_references.molecules2symbols(molecules, add_hydrogen=True)[source]

Take a list of molecules and return just a list of atomic symbols, possibly adding hydrogen

Module contents

catkit.hub.ase_tools.check_in_ase(filename, ase_db, energy=None)[source]

Check if entry is allready in ASE db

catkit.hub.ase_tools.check_traj(filename, strict=True, verbose=True)[source]
catkit.hub.ase_tools.clear_prefactor(molecule)[source]
catkit.hub.ase_tools.clear_state(name)[source]
catkit.hub.ase_tools.debug_assert(expression, message, debug=False)[source]
catkit.hub.ase_tools.get_atomic_numbers(filename)[source]
catkit.hub.ase_tools.get_atoms(molecule)[source]
catkit.hub.ase_tools.get_bulk_composition(filename)[source]
catkit.hub.ase_tools.get_chemical_formula(filename, mode='metal')[source]
catkit.hub.ase_tools.get_energies(filenames)[source]
catkit.hub.ase_tools.get_energy(filename)[source]
catkit.hub.ase_tools.get_energy_diff(filename, filename_ref)[source]
catkit.hub.ase_tools.get_formula_from_numbers(numbers)[source]
catkit.hub.ase_tools.get_layers(atoms)[source]
catkit.hub.ase_tools.get_n_layers(filename)[source]
catkit.hub.ase_tools.get_number_of_atoms(filename)[source]
catkit.hub.ase_tools.get_numbers_from_formula(formula)[source]
catkit.hub.ase_tools.get_pbc(filename)[source]
catkit.hub.ase_tools.get_reaction_atoms(reaction)[source]
catkit.hub.ase_tools.get_reaction_energy(traj_files, reaction, reaction_atoms, states, prefactors, prefactors_TS, energy_corrections)[source]
catkit.hub.ase_tools.get_reaction_from_folder(folder_name)[source]
catkit.hub.ase_tools.get_reference(filename)[source]
catkit.hub.ase_tools.get_state(name)[source]
catkit.hub.ase_tools.get_surface_composition(filename)[source]
catkit.hub.ase_tools.get_traj_str(filename)[source]
catkit.hub.ase_tools.read_ase(filename)[source]
catkit.hub.ase_tools.tag_atoms(atoms, types=None)[source]
catkit.hub.ase_tools.update_ase(db_file, identity, **key_value_pairs)[source]

Connect to ASE db

catkit.hub.ase_tools.write_ase(filename, db_file, user=None, data=None, **key_value_pairs)[source]

Connect to ASE db