def gradient(file_prefix): """ generate gradient DataFile """ name = autofile.data_types.name.gradient(file_prefix) writer_ = autofile.data_types.swrite.gradient_array reader_ = autofile.data_types.sread.gradient_array return model.JSONObject(writer_=writer_, reader_=reader_, name=name)
def information(file_prefix, function=None, json_prefix=(None, None)): """ information JSONObject :param file_prefix: path to file :type file_prefix: str :param json_prefix: top level keys ex: ('energy', ['gaussian', 'b3lyp', 'cc-pvdz', 'RR']) :type json_prefix: tuple :param function: optional information-generator function, for checking the function signature against the information object :type function: callable :return: instance of JSONObject class :rtype: JSONObject """ def writer_(inf_obj): if function is not None: assert autofile.info.matches_function_signature(inf_obj, function) inf_str = autofile.data_types.swrite.information(inf_obj) return inf_str def reader_(inf_str): inf_obj = autofile.data_types.sread.information(inf_str) if function is not None: assert autofile.info.matches_function_signature(inf_obj, function) return inf_obj name = autofile.data_types.name.information(file_prefix) return model.JSONObject(name=name, json_prefix=json_prefix, writer_=writer_, reader_=reader_)
def input_file(file_prefix, json_prefix=(None, None)): """ generate input entry in json file :param file_prefix: path to file :type file_prefix: str :param json_prefix: top level keys ex: ('energy', ['gaussian', 'b3lyp', 'cc-pvdz', 'RR']) :type json_prefix: tuple :return: instance of JSONObject class :rtype: JSONObject """ name = autofile.data_types.name.input_file(file_prefix) return model.JSONObject(name=name, json_prefix=json_prefix)
def lennard_jones_sigma(file_prefix): """ generate lennard_jones_sigma JSONObject :param file_prefix: path to file :type file_prefix: str :param json_prefix: top level keys ex: ('energy', ['gaussian', 'b3lyp', 'cc-pvdz', 'RR']) :type json_prefix: tuple :return: instance of JSONObject class :rtype: JSONObject """ name = autofile.data_types.name.lennard_jones_sigma(file_prefix) return model.JSONObject(name=name)
def vibro_rot_alpha_matrix(file_prefix): """ generate vibro_rot_alpha matrix JSONObject :param file_prefix: path to file :type file_prefix: str :param json_prefix: top level keys ex: ('energy', ['gaussian', 'b3lyp', 'cc-pvdz', 'RR']) :type json_prefix: tuple :return: instance of JSONObject class :rtype: JSONObject """ name = autofile.data_types.name.vibro_rot_alpha_matrix(file_prefix) return model.JSONObject(name=name)
def anharmonic_frequencies(file_prefix): """ generate anharmonic_frequencies JSONObject :param file_prefix: path to file :type file_prefix: str :param json_prefix: top level keys ex: ('energy', ['gaussian', 'b3lyp', 'cc-pvdz', 'RR']) :type json_prefix: tuple :return: instance of JSONObject class :rtype: JSONObject """ name = autofile.data_types.name.anharmonic_frequencies(file_prefix) return model.JSONObject(name=name)
def gradient(file_prefix): """ generate gradient JSONObject :param file_prefix: path to file :type file_prefix: str :param json_prefix: top level keys ex: ('energy', ['gaussian', 'b3lyp', 'cc-pvdz', 'RR']) :type json_prefix: tuple :return: instance of JSONObject class :rtype: JSONObject """ name = autofile.data_types.name.gradient(file_prefix) writer_ = autofile.data_types.swrite.gradient_array reader_ = autofile.data_types.sread.gradient_array return model.JSONObject(writer_=writer_, reader_=reader_, name=name)
def locator(file_prefix, map_dct_, loc_keys): """ locator DataFile Specifiers are stored in information files according to `map_dct_` and read back out according to `loc_keys_`. The file may contain auxiliary information (such as SMILES along with InChI), but for the read to work it must contain each locator value. :param map_dct_: Maps on the locator list to the values stored in the information file, by key. :type map_dct_: dict[key: callable] :param loc_keys: Keys to the original locator values. :type loc_keys: tuple[str] """ name = autofile.data_types.name.information(file_prefix) return model.JSONObject(name=name)
def information(file_prefix, function=None, json_prefix=(None, None)): """ information DataFile :param function: optional information-generator function, for checking the function signature against the information object :type function: callable """ def writer_(inf_obj): if function is not None: assert autofile.info.matches_function_signature(inf_obj, function) inf_str = autofile.data_types.swrite.information(inf_obj) return inf_str def reader_(inf_str): inf_obj = autofile.data_types.sread.information(inf_str) if function is not None: assert autofile.info.matches_function_signature(inf_obj, function) return inf_obj name = autofile.data_types.name.information(file_prefix) return model.JSONObject(name=name, json_prefix=json_prefix, writer_=writer_, reader_=reader_)
def trajectory(file_prefix): """ generate trajectory DataFile """ name = autofile.data_types.name.trajectory(file_prefix) return model.JSONObject(name=name)
def harmonic_frequencies(file_prefix): """ generate harmonic_frequencies DataFile """ name = autofile.data_types.name.harmonic_frequencies(file_prefix) return model.JSONObject(name=name)
def hessian(file_prefix): """ generate hessian DataFile """ name = autofile.data_types.name.hessian(file_prefix) return model.JSONObject(name=name)
def anharmonic_zpve(file_prefix): """ generate anharmonic_zpve DataFile """ name = autofile.data_types.name.anharmonic_zpve(file_prefix) return model.JSONObject(name=name)
def input_file(file_prefix, json_prefix=(None, None)): """ generate input entry in json file """ name = autofile.data_types.name.input_file(file_prefix) return model.JSONObject(name=name, json_prefix=json_prefix)
def lennard_jones_sigma(file_prefix): """ generate lennard_jones_sigma DataFile """ name = autofile.data_types.name.lennard_jones_sigma(file_prefix) return model.JSONObject(name=name)
def geometry(file_prefix): """ generate geometry entry in json file """ name = autofile.data_types.name.geometry(file_prefix) return model.JSONObject(name=name)
def graph(file_prefix): """ generate graph DataFile """ name = autofile.data_types.name.graph(file_prefix) return model.JSONObject(name=name)
def transformation(file_prefix): """ generate transformation DataFile """ name = autofile.data_types.name.transformation(file_prefix) return model.JSONObject(name=name)
def anharmonicity_matrix(file_prefix): """ generate anharmonicity matrix DataFile """ name = autofile.data_types.name.anharmonicity_matrix(file_prefix) return model.JSONObject(name=name)
def vmatrix(file_prefix): """ generate vmatrix DataFile """ name = autofile.data_types.name.vmatrix(file_prefix) return model.JSONObject(name=name)
def output_file(file_prefix): """ generate output entry in json file """ name = autofile.data_types.name.output_file(file_prefix) return model.JSONObject(name=name)
def quartic_centrifugal_dist_consts(file_prefix): """ generate vibro_rot_alpha matrix DataFile """ name = ( autofile.data_types.name.quartic_centrifugal_dist_consts(file_prefix)) return model.JSONObject(name=name)
def vibro_rot_alpha_matrix(file_prefix): """ generate vibro_rot_alpha matrix DataFile """ name = autofile.data_types.name.vibro_rot_alpha_matrix(file_prefix) return model.JSONObject(name=name)