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)
