def test_get_number_of_atoms():
"""Test determining the number of atoms in a coordinates dictionary"""
assert common.get_number_of_atoms(None) is None
assert common.get_number_of_atoms(ch4_coords) == 5
assert common.get_number_of_atoms(n3h5_xyz) == 8
ch4_coords_in_dict = {'coordinates': ch4_coords}
assert common.get_number_of_atoms(ch4_coords_in_dict) == 5
def rotational_constants_validator(cls, value, values):
"""Species.rotational_constants validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
if value is None and common.get_number_of_atoms(values) > 1:
raise ValueError(f'No rotational constants specified{label}.')
if value is not None:
if common.get_number_of_atoms(values) == 1:
raise ValueError(f'Rotational constants were specified for a monoatomic species{label} ({value}).')
if 'coordinates' in values and 'coords' in values['coordinates']:
linear = is_linear(coordinates=np.array(values['coordinates']['coords']))
if len(value) != 1 and linear:
raise ValueError(f'More than one rotational constant was specified for a linear species{label} '
f'({value}).')
if len(value) != 3 and not linear:
raise ValueError(f'The number of rotational constants for a non-linear species{label} must be 3.\n'
f'Got {len(value)} rotational constants: {value}.')
return value
def statmech_treatment_validator(cls, value, values):
"""Species.statmech_treatment validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
allowed_values = ['RRHO', 'RRHO-1D', 'RRHO-1D-ND', 'RRHO-ND', 'RRHO-AD', 'RRAO']
if value is None and common.get_number_of_atoms(values) > 2:
raise ValueError(f'statmech_treatment was not given{label}. A statistical mechanics treatment '
f'(one of {allowed_values}) must be specified for polyatomic species.')
if value is not None and value not in allowed_values:
raise ValueError(f'The statmech_treatment {value} is not recognized.\n'
f'Allowed values are: {allowed_values}')
return value
def frequencies_validator(cls, value, values):
"""Species.frequencies validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
if value is None and common.get_number_of_atoms(values) > 1:
raise ValueError(f'Frequencies were not given{label}. Frequencies must be specified for polyatomic species.')
if value is not None:
if any(i == 0 for i in value):
raise ValueError(f'A frequency cannot be zero, got {value}{label}.')
if values['coordinates'] is not None and value is not None:
linear = is_linear(coordinates=np.array(values['coordinates']['coords']))
num_atoms = common.get_number_of_atoms(values)
if num_atoms is not None:
expected_num_freqs = 3 * num_atoms - (6 - int(linear)) # 3N-6 for non linear, 3N-5 for linear
if len(value) != expected_num_freqs:
linear_txt = 'linear' if linear else 'non-linear'
raise ValueError(f'Expected {expected_num_freqs} frequencies for a {linear_txt} molecule, '
f'got {len(value)} frequencies{label}.')
if 'is_ts' in values and values['is_ts'] and all(freq > 0 for freq in value):
raise ValueError(f'An imaginary frequency must be present for a TS species. '
f'Got all real frequencies{label}.')
return value
def hessian_validator(cls, value, values):
"""Species.hessian validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
num_atoms = common.get_number_of_atoms(values)
if num_atoms > 1:
if value is None:
raise ValueError(f'The Hessian was not given{label}. It must be given for polyatomic species.')
if len(value) != num_atoms * 3:
raise ValueError(f'The number of rows in the Hessian matrix ({len(value)}){label} is invalid, '
f'expected {num_atoms * 3} rows for {num_atoms} atoms.')
for i, row in enumerate(value):
if len(row) < i + 1:
raise ValueError(f'Row {i} of the Hesian matrix{label} has only {len(row)} elements, '
f'expected {i + 1} elements.')
return value
def scaled_projected_frequencies_validator(cls, value, values):
"""Species.scaled_projected_frequencies validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
if value is None and common.get_number_of_atoms(values) > 1:
raise ValueError(f'Scaled projected frequencies were not given{label}.'
f'Must be specified for polyatomic species.')
if value is not None:
if any(i == 0 for i in value):
raise ValueError(f'A frequency (scaled_projected_frequencies) cannot be zero, got {value}{label}.')
if 'frequencies' in values:
if len(value) > len(values['frequencies']):
raise ValueError(f"The scaled_projected_frequencies (length {len(value)}) cannot have more "
f"entries that the frequencies (length {len(values['frequencies'])}{label}.")
if value == values['frequencies']:
raise ValueError(f'The scaled_projected_frequencies are identical to the frequencies.\n'
f'Did you forget to scale?')
return value
def normal_displacement_modes_validator(cls, value, values):
"""Species.normal_displacement_modes validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
if 'frequencies' in values and values['frequencies'] is not None:
if value is None:
raise ValueError(f'Normal displacement modes were not given{label}.')
if len(value) != len(values['frequencies']):
raise ValueError(f"The number of normal displacement modes ({len(value)}) "
f"differs from the number of frequencies ({len(values['frequencies'])}){label}.")
num_atoms = common.get_number_of_atoms(values)
if num_atoms is not None:
for ndm in value:
if len(ndm) != num_atoms:
raise ValueError(f'The number of normal displacement modes per frequency must be equal '
f'to the number of atoms ({num_atoms}), got {len(ndm)}.')
for displacement in ndm:
if len(displacement) != 3:
raise ValueError(f'Each displacement (per frequency per atom) must be a list of length 3, '
f'got {len(displacement)}.')
return value
def freq_path_validator(cls, value, values):
"""Species.freq_path validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
if common.get_number_of_atoms(values) > 1 and value is None:
raise ValueError(f'The freq_path was not given{label}.')
return value