def test_model_chemistry_consistency(self):
"""
Test that ErrorCancelingReaction objects properly check that all species use the same model chemistry
"""
# Take ethane as the target
ethane = ErrorCancelingSpecies(self.molecule1, (100.0, 'kJ/mol'), 'test_A')
methyl = ErrorCancelingSpecies(self.molecule2, (20.0, 'kcal/mol'), 'test_B', (21000.0, 'cal/mol'))
# This should throw an exception because the model chemistry is different
with self.assertRaises(ValueError):
ErrorCancelingReaction(ethane, {methyl: 2})
def test_error_canceling_reactions(self):
"""
Test that ErrorCancelingReaction object can be created and that hf298 can be calculated for the target
"""
# Take ethane as the target
ethane = ErrorCancelingSpecies(self.molecule1, (100.0, 'kJ/mol'), 'test')
methyl = ErrorCancelingSpecies(self.molecule2, (20.0, 'kcal/mol'), 'test', (21000.0, 'cal/mol'))
# This reaction is not an isodesmic reaction, but that does not matter for the unit test
rxn = ErrorCancelingReaction(ethane, {methyl: 2})
self.assertAlmostEqual(rxn.calculate_target_thermo().value_si, 2*21000.0*4.184-(2*20.0*4184-100.0*1000))
def test_error_canceling_species(self):
"""
Test that ErrorCancelingSpecies can be created properly
"""
error_canceling_species = ErrorCancelingSpecies(self.molecule1, (123.4, 'kcal/mol'), 'test', (100.0, 'kJ/mol'))
self.assertIsInstance(error_canceling_species, ErrorCancelingSpecies)
self.assertAlmostEqual(error_canceling_species.low_level_hf298.value_si, 123.4*4184)
# For target species the high level data is not given
target_species = ErrorCancelingSpecies(self.molecule2, (10.1, 'J/mol'), 'test')
self.assertIs(target_species.high_level_hf298, None)
def setUpClass(cls):
"""
A method called before each unit test in this class.
"""
# Give all species a low level Hf298 of 100 J/mol--this is not important for this test
hf = (100.0, 'J/mol')
cls.propene = ErrorCancelingSpecies(Molecule(smiles='CC=C'), hf, 'test')
cls.butane = ErrorCancelingSpecies(Molecule(smiles='CCCC'), hf, 'test')
cls.benzene = ErrorCancelingSpecies(Molecule(smiles='c1ccccc1'), hf, 'test')
cls.caffeine = ErrorCancelingSpecies(Molecule(smiles='CN1C=NC2=C1C(=O)N(C(=O)N2C)C'), hf, 'test')
cls.ethyne = ErrorCancelingSpecies(Molecule(smiles='C#C'), hf, 'test')
def to_error_canceling_spcs(self, level_of_theory, source=None):
"""
Extract calculated and reference data from a specified model chemistry and source and return as a new
ErrorCancelingSpecies object
Args:
level_of_theory ((Composite)LevelOfTheory): Level of theory to use as the low level data
source (str): Reference data source to take the high level data from
Raises:
KeyError: If ``level_of_theory`` is not available for this reference species
Returns:
ErrorCancelingSpecies
"""
if level_of_theory not in self.calculated_data:
raise KeyError(
f'Level of theory `{level_of_theory}` not available for species {self}'
)
molecule = Molecule().from_adjacency_list(
self.adjacency_list,
raise_atomtype_exception=False,
raise_charge_exception=False)
reference_enthalpy = self.get_reference_enthalpy(source=source)
low_level_h298 = self.calculated_data[level_of_theory].thermo_data.H298
return ErrorCancelingSpecies(molecule,
low_level_h298,
level_of_theory,
high_level_hf298=reference_enthalpy.h298,
source=reference_enthalpy.source)
def test_molecule_input_in_error_canceling_species(self):
"""
Test that an exception is raised if an rmgpy Molecule object is not passed to an ErrorCancelingSpecies
"""
with self.assertRaises(ValueError):
ErrorCancelingSpecies(self.species, (100.0, 'J/mol'),
LevelOfTheory('test'))
def setUpClass(cls):
try:
import pyomo as pyo
except ImportError:
pyo = None
cls.pyo = pyo
lot = LevelOfTheory('test')
cls.propene = ErrorCancelingSpecies(Molecule(smiles='CC=C'),
(100, 'kJ/mol'), lot,
(105, 'kJ/mol'))
cls.propane = ErrorCancelingSpecies(Molecule(smiles='CCC'),
(75, 'kJ/mol'), lot,
(80, 'kJ/mol'))
cls.butane = ErrorCancelingSpecies(Molecule(smiles='CCCC'),
(150, 'kJ/mol'), lot,
(145, 'kJ/mol'))
cls.butene = ErrorCancelingSpecies(Molecule(smiles='C=CCC'),
(175, 'kJ/mol'), lot,
(180, 'kJ/mol'))
cls.pentane = ErrorCancelingSpecies(Molecule(smiles='CCCCC'),
(200, 'kJ/mol'), lot,
(190, 'kJ/mol'))
cls.pentene = ErrorCancelingSpecies(Molecule(smiles='C=CCCC'),
(225, 'kJ/mol'), lot,
(220, 'kJ/mol'))
cls.hexane = ErrorCancelingSpecies(Molecule(smiles='CCCCCC'),
(250, 'kJ/mol'), lot,
(260, 'kJ/mol'))
cls.hexene = ErrorCancelingSpecies(Molecule(smiles='C=CCCCC'),
(275, 'kJ/mol'), lot,
(275, 'kJ/mol'))
cls.benzene = ErrorCancelingSpecies(Molecule(smiles='c1ccccc1'),
(-50, 'kJ/mol'), lot,
(-80, 'kJ/mol'))
cls.caffeine = ErrorCancelingSpecies(
Molecule(smiles='CN1C=NC2=C1C(=O)N(C(=O)N2C)C'), (300, 'kJ/mol'),
lot)
cls.ethyne = ErrorCancelingSpecies(Molecule(smiles='C#C'),
(200, 'kJ/mol'), lot)