class QChemInputGenerator(TemplateInputGenerator):
"""
"""
property_generators = [
PropertyGenerator(
filename = template_dir + "basic.mako",
property = [Energy, Gradient],
details = ComputationDetails(
method = (
# The "dotted keyword" syntax is on it's way out, since it's too confusing
Methods.HF, 'HF',
Methods.DFT, 'DFT'
),
required_details = [
'basis'
],
),
unsupported_details = {
'basis' : Basis.custom_basis,
'optimization' : True
}
),
PropertyGenerator(
filename = template_dir + "basic.mako",
property = [Energy, Hessian],
details = ComputationDetails(
method = (
# The "dotted keyword" syntax is on it's way out, since it's too confusing
Methods.HF, 'HF',
Methods.DFT, 'DFT'
),
required_details = [
'basis'
],
),
unsupported_details = {
'basis' : Basis.custom_basis,
'optimization' : True
}
),
PropertyGenerator(
filename = template_dir + "qcopt.mako",
property = [Energy],
details= ComputationDetails(
method = (
'HF', 'DFT'
),
optimization = ( True, ),
required_details = [
'basis'
]
),
unsupported_details = {
'basis' : Basis.custom_basis,
'optimization' : False
}
)
]
def get_property_for_molecule(self, molecule, property, details=None):
for p in self.properties_for_molecules[molecule]:
if MolecularProperty.is_same_property(property, p):
if ComputationDetails.is_compatible_details(details, p.details):
return p
props = self.properties[molecule]
for p in props:
pcopy = copy(p)
pcopy.molecule = molecule
self.properties_for_molecules[molecule].append(pcopy)
if MolecularProperty.is_same_property(property, p):
if ComputationDetails.is_compatible_details(details, p.details):
return pcopy
raise PropertyUnavailableError
def get_property_for_molecule(self, molecule, property, details=None):
for p in self.properties_for_molecules[molecule]:
if MolecularProperty.is_same_property(property, p):
if ComputationDetails.is_compatible_details(
details, p.details):
return p
props = self.properties[molecule]
for p in props:
pcopy = copy(p)
pcopy.molecule = molecule
self.properties_for_molecules[molecule].append(pcopy)
if MolecularProperty.is_same_property(property, p):
if ComputationDetails.is_compatible_details(
details, p.details):
return pcopy
raise PropertyUnavailableError
def _parse_file(self, file):
def _get_at_least_one(parent, tag, dispnum):
ret_val = parent.findall(tag)
if sanity_checking_enabled:
if len(ret_val) == 0:
raise InvalidLegacyXMLFileError(
"missing {} section "
"for displacement number {}".format(tag, dispnum))
return ret_val
def _get_exactly_one(parent, tag, dispnum):
ret_val = _get_at_least_one(parent, tag, dispnum)
if sanity_checking_enabled:
if len(ret_val) > 1:
raise InvalidLegacyXMLFileError(
"multiple {} sections "
"for displacement number {}".format(tag, dispnum))
return ret_val[0]
#========================================#
etr = ElementTree.parse(file)
for disp in etr.iter('displacement'):
disp_number = disp.get('number', '<unnumbered>')
# Get the molecule part
mol_sect = _get_exactly_one(disp, 'molecule', disp_number)
# Get the XYZ section
xyz_sect = _get_exactly_one(mol_sect, 'xyz', disp_number)
if 'units' in xyz_sect.keys():
unitstr = xyz_sect.get('units')
units = eval(unitstr.title(), globals())
else:
units = DistanceUnit.default
energy_el = _get_at_least_one(disp, 'energy', disp_number)
# for now just use the "molecular" energy
energy_el = [
e for e in energy_el if e.get('type', '') == 'molecular'
]
if len(energy_el) == 0:
raise InvalidLegacyXMLFileError(
"missing energy with type='molecular' "
"for displacement number {}".format(disp_number))
elif len(energy_el) > 1:
raise InvalidLegacyXMLFileError(
"multiple energy elements with type='molecular' "
"for displacement number {}".format(disp_number))
energy_el = energy_el[0]
if 'units' in energy_el.keys():
unitstr = energy_el.get('units')
energy_units = eval(unitstr.title(), globals())
else:
energy_units = Hartrees
energy_val = float(energy_el.get('value')) * energy_units
mol_stub = MoleculeStub(xyz_sect.text, units=units)
energy = Energy(mol_stub,
units=energy_units,
details=ComputationDetails(type='molecular'))
energy.value = energy_val
self.properties[mol_stub].append(energy)
def has_property_for_molecule(self, molecule, property, details=None, verbose=True):
if molecule in self.properties:
props = self.properties[molecule]
for p in props:
pcopy = copy(p)
pcopy.molecule = molecule
self.properties_for_molecules[molecule].append(pcopy)
if MolecularProperty.is_same_property(property, p):
if ComputationDetails.is_compatible_details(details, p.details):
return True
return False
def has_property_for_molecule(self,
molecule,
property,
details=None,
verbose=True):
if molecule in self.properties:
props = self.properties[molecule]
for p in props:
pcopy = copy(p)
pcopy.molecule = molecule
self.properties_for_molecules[molecule].append(pcopy)
if MolecularProperty.is_same_property(property, p):
if ComputationDetails.is_compatible_details(
details, p.details):
return True
return False