def _run(self, molName):
self.molName = molName
logger.info("Molecule: {}".format(self.molName))
molFile = os.path.join(home("test-charge"), self.molName + ".mol2")
self.mol = Molecule(molFile)
self.new_mols = {}
self.extras = {}
self.new_mols["Gasteiger"] = fitGasteigerCharges(self.mol)
try:
self.new_mols["AM1-BCC"] = fitChargesWithAntechamber(self.mol,
type="bcc")
except:
pass
qm = Psi4()
qm.theory = "B3LYP"
qm.basis = "6-311++G**"
workDir = os.path.join("tmp", self.molName)
os.makedirs(workDir, exist_ok=True)
for factor in [-10, -5, -4, -3, -2, -1]:
logger.info("Factor: {}".format(factor))
key = "ESP b {}".format(factor)
np.random.seed(20181114) # Make ESP grid generation deterministic
self.new_mols[key], self.extras[key] = fitESPCharges(
self.mol, qm, workDir, restraint_factor=10**factor)
def setUp(self):
# For Slurm, the test directory has to be on a shared filesystem
self.testDir = os.getcwd()
self.qm = Psi4()
self.qm.queue = SlurmQueue()
self.qm.queue.partition = "normalGPU" # TODO use CPU partition when available
self.qm.queue.jobname = "Psi4_test"
super().setUp()
def _get_qm_calculator(args, queue):
from parameterize.qm import Psi4, Gaussian, FakeQM2
logger.info("=== QM configuration ===")
# Create a QM object
logger.info("Code: {}".format(args.code))
if args.code == "Psi4":
qm = Psi4()
elif args.code == "Gaussian":
qm = Gaussian()
else:
raise AssertionError()
# Override with a FakeQM object
if args.fake_qm:
qm = FakeQM2()
logger.warning("Using FakeQM")
# Configure the QM object
qm.theory = args.theory
logger.info("Theory: {}".format(qm.theory))
qm.basis = args.basis
logger.info("Basis sets: {}".format(qm.basis))
qm.solvent = args.environment
logger.info("Environment: {}".format(qm.solvent))
qm.queue = queue
qm.charge = args.charge
# Update B3LYP to B3LYP-D3
# TODO: this is silent and not documented stuff
if qm.theory == "B3LYP":
qm.correction = "D3"
logger.warning("The dispersion correction is set to {}".format(
qm.correction))
# Update basis sets
# TODO: this is silent and not documented stuff
if args.charge < 0 and qm.solvent == "vacuum":
if qm.basis == "6-31G*":
qm.basis = "6-31+G*"
if qm.basis == "6-311G**":
qm.basis = "6-311++G**"
if qm.basis == "cc-pVDZ":
qm.basis = "aug-cc-pVDZ"
logger.warning("Basis sets are changed to {}".format(qm.basis))
return qm
def setUp(self):
self.skipTest("No Slurm tests")
if "TRAVIS" in os.environ:
self.skipTest("No Psi4 Slurm tests on Travis")
# For Slurm, the test directory has to be on a shared filesystem
self.testDir = os.getcwd()
self.qm = Psi4()
self.qm.queue = SlurmQueue()
self.qm.queue.partition = "normalGPU" # TODO use CPU partition when available
self.qm.queue.jobname = "Psi4_test"
super().setUp()
def setUp(self):
self.qm = Psi4()
super().setUp()