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)
