def test_unique_confs_none():
conf1 = Conformer()
conf1.energy = 0.1
# Conformer with energy just below the threshold
conf2 = Conformer()
conf2.energy = 0.1 + (0.9 / Constants.ha2kJmol)
unique_confs = get_unique_confs(conformers=[conf1, conf2],
energy_threshold_kj=1)
assert len(unique_confs) == 1
# If the energy is above the threshold there should be two unique
# conformers
conf2.energy += 0.2 / Constants.ha2kJmol
unique_confs = get_unique_confs(conformers=[conf1, conf2],
energy_threshold_kj=1)
assert len(unique_confs) == 2
def find_lowest_energy_conformer(self, lmethod=None, hmethod=None):
"""
For a molecule object find the lowest conformer in energy and set the
molecule.atoms and molecule.energy
Arguments:
lmethod (autode.wrappers.ElectronicStructureMethod):
hmethod (autode.wrappers.ElectronicStructureMethod):
"""
logger.info('Finding lowest energy conformer')
if self.n_atoms <= 2:
logger.warning('Cannot have conformers of a species with 2 atoms '
'or fewer')
return None
if lmethod is None:
logger.info('Getting the default low level method')
lmethod = get_lmethod()
methods.add('Low energy conformers located with the')
self._generate_conformers()
# For all generated conformers optimise with the low level of theory
method_string = f'and optimised using {lmethod.name}'
if hmethod is not None:
method_string += f' then with {hmethod.name}'
methods.add(f'{method_string}.')
for conformer in self.conformers:
conformer.optimise(lmethod)
# Strip conformers that are similar based on an energy criteria or
# don't have an energy
self.conformers = get_unique_confs(conformers=self.conformers)
if hmethod is not None:
# Re-evaluate the energy of all the conformers with the higher
# level of theory
for conformer in self.conformers:
if Config.hmethod_sp_conformers:
assert hmethod.keywords.low_sp is not None
conformer.single_point(hmethod)
else:
# Otherwise run a full optimisation
conformer.optimise(hmethod)
self._set_lowest_energy_conformer()
logger.info(f'Lowest energy conformer found. E = {self.energy}')
return None
def test_unique_confs():
conf1 = Conformer()
conf2 = Conformer()
conf3 = Conformer()
# Set two energies the same and leave one as none..
conf1.energy = 1
conf2.energy = 1
unique_confs = get_unique_confs(conformers=[conf1, conf2, conf3])
assert len(unique_confs) == 1
assert type(unique_confs[0]) is Conformer
assert unique_confs[0].energy == 1
def find_lowest_energy_conformer(self, lmethod=None, hmethod=None):
"""
For a molecule object find the lowest conformer in energy and set the
molecule.atoms and molecule.energy
Arguments:
lmethod (autode.wrappers.ElectronicStructureMethod):
hmethod (autode.wrappers.ElectronicStructureMethod):
"""
logger.info('Finding lowest energy conformer')
if self.n_atoms <= 2:
logger.warning('Cannot have conformers of a species with 2 atoms '
'or fewer')
return None
if lmethod is None:
logger.info('Getting the default low level method')
lmethod = get_lmethod()
try:
self._generate_conformers()
except NotImplementedError:
logger.error('Could not generate conformers. generate_conformers()'
' not implemented')
return None
# For all generated conformers optimise with the low level of theory
for conformer in self.conformers:
conformer.optimise(lmethod)
# Strip conformers that are similar based on an energy criteria or
# don't have an energy
self.conformers = get_unique_confs(conformers=self.conformers)
if hmethod is not None:
# Re-optimise all the conformers with the higher level of theory
# to get more accurate energies
for conformer in self.conformers:
conformer.optimise(hmethod)
self._set_lowest_energy_conformer()
logger.info(f'Lowest energy conformer found. E = {self.energy}')
return None
