def build_input(
self,
input_model: AtomicInput,
config: "TaskConfig",
template: Optional[str] = None,
) -> Dict[str, Any]:
"""
Use the template files stored in QUBEKit to build a gaussian input file for the given driver.
"""
import os
from jinja2 import Template
template_file = get_data(os.path.join("templates", "gaussian.com"))
with open(template_file) as file:
template = Template(file.read())
template_data = {
"memory": int(config.memory),
"threads": config.ncores,
"driver": self.driver_conversion(driver=input_model.driver),
"title": "gaussian job",
}
molecule = input_model.molecule
spec = input_model.model
theory = self.functional_converter(method=spec.method)
template_data["theory"] = theory
template_data["basis"] = spec.basis
template_data["charge"] = int(molecule.molecular_charge)
template_data["multiplicity"] = molecule.molecular_multiplicity
template_data["scf_maxiter"] = input_model.extras.get("maxiter", 300)
# work around for extra cmdline args
template_data["cmdline_extra"] = input_model.keywords.get(
"cmdline_extra", [])
# work around for extra trailing input
template_data["add_input"] = input_model.keywords.get("add_input", [])
template_data.update(input_model.keywords)
# now we need to build the coords data
data = []
for i, symbol in enumerate(molecule.symbols):
# we must convert the atomic input back to angstroms
data.append(
(symbol, molecule.geometry[i] * constants.BOHR_TO_ANGS))
template_data["data"] = data
rendered_template = template.render(**template_data)
return {
"infiles": {
"gaussian.com": rendered_template
},
"scratch_directory": config.scratch_directory,
"input_result": input_model.copy(deep=True),
}
def atomic_input_to_job_input(atomic_input: AtomicInput) -> pb.JobInput:
"""Convert AtomicInput to JobInput"""
# Don't mutate original atomic_input object
ai_copy = atomic_input.copy(deep=True)
# Create Mol instance
mol_msg = pb.Mol()
mol_msg.atoms.extend(ai_copy.molecule.symbols)
mol_msg.xyz.extend(ai_copy.molecule.geometry.flatten())
mol_msg.units = pb.Mol.UnitType.BOHR # Molecule always in bohr
mol_msg.charge = int(ai_copy.molecule.molecular_charge)
mol_msg.multiplicity = ai_copy.molecule.molecular_multiplicity
mol_msg.closed = ai_copy.keywords.pop("closed_shell", True)
mol_msg.restricted = ai_copy.keywords.pop("restricted", True)
# Drop keyword terms already applied from Molecule object
ai_copy.keywords.pop("charge", None) # mol_msg.charge
ai_copy.keywords.pop("spinmult", None) # mol_msg.multiplicity
# Create JobInput message
ji = pb.JobInput(mol=mol_msg)
# Set driver
driver = ai_copy.driver.upper()
if driver not in SUPPORTED_DRIVERS:
# Only support QCEngine supported drivers; energy, gradient, hessian, properties
raise ValueError(
f"Driver '{driver}' not supported, please select from {SUPPORTED_DRIVERS}"
)
ji.run = pb.JobInput.RunType.Value(driver)
# Set Method
ji.method = pb.JobInput.MethodType.Value(ai_copy.model.method.upper())
# Set Basis
ji.basis = ai_copy.model.basis
# Get keywords that have specific protobuf fields
ji.return_bond_order = ai_copy.keywords.pop("bond_order", False)
# Request AO and MO information
if ai_copy.keywords.pop("mo_output", False):
ji.imd_orbital_type = pb.JobInput.ImdOrbitalType.WHOLE_C
# Set all other keywords under the "user_options" catch all
for key, value in ai_copy.keywords.items():
ji.user_options.extend([key, str(value)])
return ji
