def anharmonicity_matrix(file_prefix): """ generate anharmonicity matrix DataFile """ name = autofile.data_types.name.anharmonicity_matrix(file_prefix) writer_ = autofile.data_types.swrite.anharmonicity_matrix reader_ = autofile.data_types.sread.anharmonicity_matrix return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def trajectory(file_prefix): """ generate trajectory DataFile """ name = autofile.data_types.name.trajectory(file_prefix) writer_ = autofile.data_types.swrite.trajectory reader_ = _not_implemented return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def anharmonic_frequencies(file_prefix): """ generate anharmonic_frequencies DataFile """ name = autofile.data_types.name.anharmonic_frequencies(file_prefix) writer_ = autofile.data_types.swrite.anharmonic_frequencies reader_ = autofile.data_types.sread.anharmonic_frequencies return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def lennard_jones_sigma(file_prefix): """ generate lennard_jones_sigma DataFile """ name = autofile.data_types.name.lennard_jones_sigma(file_prefix) writer_ = autofile.data_types.swrite.lennard_jones_sigma reader_ = autofile.data_types.sread.lennard_jones_sigma return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def transformation(file_prefix): """ generate transformation DataFile """ name = autofile.data_types.name.transformation(file_prefix) writer_ = autofile.data_types.swrite.transformation reader_ = autofile.data_types.sread.transformation return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def geometry(file_prefix): """ generate geometry DataFile """ name = autofile.data_types.name.geometry(file_prefix) writer_ = autofile.data_types.swrite.geometry reader_ = autofile.data_types.sread.geometry return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def energy(file_prefix): """ generate energy DataFile """ name = autofile.data_types.name.energy(file_prefix) writer_ = autofile.data_types.swrite.energy reader_ = autofile.data_types.sread.energy return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def hessian(file_prefix): """ generate hessian DataFile """ name = autofile.data_types.name.hessian(file_prefix) writer_ = autofile.data_types.swrite.hessian reader_ = autofile.data_types.sread.hessian return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def gradient(file_prefix): """ generate gradient DataFile """ name = autofile.data_types.name.gradient(file_prefix) writer_ = autofile.data_types.swrite.gradient reader_ = autofile.data_types.sread.gradient return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def torsions(file_prefix): """ generate torsions DataFile """ name = autofile.data_types.name.torsions(file_prefix) writer_ = autofile.data_types.swrite.torsions reader_ = autofile.data_types.sread.torsions return model.DataFile(name=name, writer_=writer_, reader_=reader_)
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] """ def writer_(locs): inf_dct = {key: map_(locs) for key, map_ in map_dct_.items()} inf_obj = autofile.info.object_(inf_dct) return autofile.data_types.swrite.information(inf_obj) def reader_(inf_str): inf_obj = autofile.data_types.sread.information(inf_str) inf_dct = dict(inf_obj) return list(map(inf_dct.__getitem__, loc_keys)) name = autofile.data_types.name.information(file_prefix) return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def information(file_prefix, function=None): """ information DataFile :param file_prefix: path to file :type file_prefix: str :param function: optional information-generator function, for checking the function signature against the information object :type function: callable :return: instance of DataFile class :rtype: Datafile """ 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.DataFile(name=name, writer_=writer_, reader_=reader_)
def vmatrix(file_prefix): """ generate vmatrix DataFile """ name = autofile.data_types.name.vmatrix(file_prefix) writer_ = autofile.data_types.swrite.vmatrix reader_ = autofile.data_types.sread.vmatrix return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def instability(file_prefix): """ Generate a data file for instabiliy """ name = autofile.data_types.name.instability(file_prefix) writer_ = autofile.data_types.swrite.instability reader_ = autofile.data_types.sread.instability return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def quartic_centrifugal_dist_consts(file_prefix): """ generate vibro_rot_alpha matrix DataFile """ name = ( autofile.data_types.name.quartic_centrifugal_dist_consts(file_prefix)) writer_ = autofile.data_types.swrite.quartic_centrifugal_dist_consts reader_ = autofile.data_types.sread.quartic_centrifugal_dist_consts return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def lennard_jones_elstruct(file_prefix): """ generate elec struct template file for the LJ params program :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.lennard_jones_elstruct(file_prefix) return model.DataFile(name=name)
def vrctst_flux(file_prefix): """ generate vrctst_flux DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.vrctst_flux(file_prefix) return model.DataFile(name=name)
def output_file(file_prefix): """ generate output file DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.output_file(file_prefix) return model.DataFile(name=name)
def harmonic_frequencies(file_prefix): """ generate harmonic_frequencies DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.harmonic_frequencies(file_prefix) writer_ = autofile.data_types.swrite.harmonic_frequencies reader_ = autofile.data_types.sread.harmonic_frequencies return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def anharmonicity_matrix(file_prefix): """ generate anharmonicity matrix DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.anharmonicity_matrix(file_prefix) writer_ = autofile.data_types.swrite.anharmonicity_matrix reader_ = autofile.data_types.sread.anharmonicity_matrix return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def vibro_rot_alpha_matrix(file_prefix): """ generate vibro_rot_alpha matrix DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.vibro_rot_alpha_matrix(file_prefix) writer_ = autofile.data_types.swrite.vibro_rot_alpha_matrix reader_ = autofile.data_types.sread.vibro_rot_alpha_matrix return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def lennard_jones_sigma(file_prefix): """ generate lennard_jones_sigma DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.lennard_jones_sigma(file_prefix) writer_ = autofile.data_types.swrite.lennard_jones_sigma reader_ = autofile.data_types.sread.lennard_jones_sigma return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def internal_symmetry_number(file_prefix): """ generate internal_symmetry_number DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.internal_symmetry_factor(file_prefix) writer_ = autofile.data_types.swrite.internal_symmetry_factor reader_ = autofile.data_types.sread.internal_symmetry_factor return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def dipole_moment(file_prefix): """ generate dipole_moment DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.dipole_moment(file_prefix) writer_ = autofile.data_types.swrite.dipole_moment reader_ = autofile.data_types.sread.dipole_moment return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def geometry(file_prefix): """ generate geometry DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.geometry(file_prefix) writer_ = autofile.data_types.swrite.geometry reader_ = autofile.data_types.sread.geometry return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def quartic_force_constants(file_prefix): """ generate quartic_force_constants DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = autofile.data_types.name.quartic_force_constants(file_prefix) writer_ = autofile.data_types.swrite.quartic_force_constants reader_ = autofile.data_types.sread.quartic_force_constants return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def quartic_centrifugal_dist_consts(file_prefix): """ generate vibro_rot_alpha matrix DataFile :param file_prefix: path to file :type file_prefix: str :return: instance of DataFile class :rtype: Datafile """ name = ( autofile.data_types.name.quartic_centrifugal_dist_consts(file_prefix)) writer_ = autofile.data_types.swrite.quartic_centrifugal_dist_consts reader_ = autofile.data_types.sread.quartic_centrifugal_dist_consts return model.DataFile(name=name, writer_=writer_, reader_=reader_)
def output_file(file_prefix): """ generate output file DataFile """ name = autofile.data_types.name.output_file(file_prefix) return model.DataFile(name=name)
def vrctst_flux(file_prefix): """ generate vrctst_flux DataFile """ name = autofile.data_types.name.vrctst_flux(file_prefix) return model.DataFile(name=name)