def perturb(self, entry, unperturb=False):
"""
Perturb E0 of `entry` which could be either a :class:TransitionState or a :class:Configuration
In the latter case, only the first species in the Configuration.species list is perturbed.
The perturbation is done by addition of the energy amount in self.perturbation.
If unperturb is `False`, the perturbation is addition of the energy amount in self.perturbation.
If unperturb is `False`, this is done by subtracting.
"""
perturbation = self.perturbation.value_si
if unperturb:
perturbation *= -1
if isinstance(entry, TransitionState):
entry.conformer.E0 = quantity.Energy(entry.conformer.E0.value_si + perturbation, 'J/mol')
elif isinstance(entry, Configuration):
entry.species[0].conformer.E0 = quantity.Energy(entry.species[0].conformer.E0.value_si + perturbation,
'J/mol')
def test_Kelvin(self):
"""
Test the creation of an energy quantity with units of K (not really an energy!).
"""
q = quantity.Energy(10.0, "K")
self.assertAlmostEqual(q.value, 10 * 8.314472, delta=1e-6)
self.assertEqual(q.units, "J/mol")
def test_kcalpermol(self):
"""
Test the creation of an energy quantity with units of kcal/mol.
"""
q = quantity.Energy(1.0, "kcal/mol")
self.assertAlmostEqual(q.value, 1.0, 6)
self.assertAlmostEqual(q.value_si, 4184., delta=1e-6)
self.assertEqual(q.units, "kcal/mol")
def test_joule_per_mol(self):
"""
Test the creation of an energy quantity with units of J/mol.
"""
q = quantity.Energy(1.0, "J/mol")
self.assertAlmostEqual(q.value, 1.0, 6)
self.assertAlmostEqual(q.value_si, 1.0, delta=1e-6)
self.assertEqual(q.units, "J/mol")
def test_kcal(self):
"""
Test the creation of an energy quantity with units of kcal.
"""
try:
q = quantity.Energy(1.0, "kcal")
self.fail('Allowed invalid unit type "kcal".')
except quantity.QuantityError:
pass
def test_joule(self):
"""
Test the creation of an energy quantity with units of J.
"""
try:
quantity.Energy(1.0, "J")
self.fail('Allowed invalid unit type "J".')
except quantity.QuantityError:
pass
def maximum_grain_size(self, value):
self._maximum_grain_size = quantity.Energy(value)
def maximumGrainSize(self, value):
self._maximumGrainSize = quantity.Energy(value)