def test_optimization_pass_serialization(water, opti_input, opti_success):
opti_in = OptimizationInput(initial_molecule=water, **opti_input)
assert isinstance(opti_in.dict(), dict)
assert isinstance(opti_in.json(), str)
opti_out = Optimization(initial_molecule=water, **opti_input, **opti_success)
assert isinstance(opti_out.dict(), dict)
assert isinstance(opti_out.json(), str)
def _generate_optimization_input(mol, compute_spec, factory):
import ast
from qcelemental.models import OptimizationInput
# TODO: bug report in openff where `atom_map` is a string
if isinstance(mol.properties.get('atom_map'), str):
mol.properties['atom_map'] = ast.literal_eval(
mol.properties['atom_map'])
# This block will fail for OFF Toolkit 0.8.4, but succeed for 0.8.4rc1
try:
attributes = factory.create_cmiles_metadata(mol)
qcmol = mol.to_qcschema(extras=attributes)
# In OFFTK 0.8.4, the CMILES field is automatically populated by this method
except:
qcmol = mol.to_qcschema()
method = compute_spec['method']
basis = compute_spec['basis']
program = compute_spec['program']
# generate optimization inputs
input_data = OptimizationInput(keywords={
"coordsys": "dlc",
"enforce": 0,
"epsilon": 1e-05,
"reset": True,
"qccnv": False,
"molcnv": False,
"check": 0,
"trust": 0.1,
"tmax": 0.3,
"maxiter": 300,
"convergence_set": "gau",
"program": program
},
extras={},
protocols={},
input_specification={
"driver": "gradient",
"model": {
"method": method,
"basis": basis,
},
"keywords": {
"maxiter":
200,
"scf_properties": [
"dipole", "quadrupole",
"wiberg_lowdin_indices",
"mayer_indices"
]
},
},
initial_molecule=qcmol)
return input_data.dict()
def _args_from_optimizationrecord(opt, client):
from qcelemental.models import OptimizationInput
# generate optimization inputs
input_data = OptimizationInput(
keywords=opt.keywords,
extras={},
protocols={},
input_specification={
"driver": "gradient",
"model": {
"method": opt.qc_spec.method,
"basis": opt.qc_spec.basis,
},
"keywords":
client.query_keywords(opt.qc_spec.keywords)[0].values
},
initial_molecule=opt.get_initial_molecule())
return input_data.dict()
