def GetSystem(self, doQCMM=True, log=logFile, nbModel=None, qcModel=None):
"""Get the system with the energy model defined."""
# . Basic setup.
molecule = MOLFile_ToSystem(
os.path.join(self.dataPath, self.fileName + ".mol"))
molecule.label = self.label
molecule.DefineMMModel(self.mmModel)
# . Set up the QC model.
if qcModel is not None:
molecule.electronicState = ElectronicState(
charge=self.qcCharge, multiplicity=self.multiplicity)
if doQCMM:
molecule.DefineQCModel(qcModel, qcSelection=self.qcSelection)
else:
molecule.DefineQCModel(qcModel)
# . Set up the NB model.
if (qcModel is None) or doQCMM:
if nbModel is None: molecule.DefineNBModel(self.nbModel)
else: molecule.DefineNBModel(nbModel)
# . Summary.
if LogFileActive(log):
molecule.Summary(log=log)
log.Paragraph("\nFormula = " + molecule.atoms.FormulaString() +
".")
# . Finish up.
return molecule
def GetSystem(self, log=logFile, maximumAtoms=None):
"""Get the system with the energy model defined."""
# . Get the QC model options.
convergerKeywords = getattr(self, "convergerKeywords", {})
qcModelArguments = getattr(self, "qcModelArguments", [])
qcModelClass = getattr(self, "qcModelClass", None)
qcModelKeywords = getattr(self, "qcModelKeywords", {})
# . Basic setup.
if self.fileFormat == "mol":
molecule = MOLFile_ToSystem(
os.path.join(self.dataPath, self.fileName + ".mol"))
elif self.fileFormat == "xyz":
molecule = XYZFile_ToSystem(
os.path.join(self.dataPath, self.fileName + ".xyz"))
molecule.electronicState = ElectronicState(
charge=getattr(self, "charge", 0),
multiplicity=getattr(self, "multiplicity", 1))
molecule.label = self.label
# . Only keep the molecule if it is not too large.
if (maximumAtoms is None) or ((maximumAtoms is not None) and
(len(molecule.atoms) <= maximumAtoms)):
# . Define the QC model.
if qcModelClass is not None:
converger = DIISSCFConverger(**convergerKeywords)
kwargs = dict(qcModelKeywords)
kwargs["converger"] = converger
qcModel = qcModelClass(*qcModelArguments, **kwargs)
molecule.DefineQCModel(qcModel, log=log)
# . Summary.
if LogFileActive(log):
molecule.Summary(log=log)
log.Paragraph("\nFormula = " + molecule.atoms.FormulaString() +
".")
# . Molecule rejected.
else:
molecule = None
# . Finish up.
return molecule
def runTest(self):
"""The test."""
# . Initialization.
dataPath = os.path.join(os.getenv("PDYNAMO_PMOLECULE"), "data", "mol")
log = self.GetLog()
translation = Vector3.Uninitialized()
# . Get the individual systems.
energies = []
molecules = []
for (i, label) in enumerate(_Molecules):
molecule = MOLFile_ToSystem(os.path.join(dataPath, label + ".mol"))
molecule.label = label
molecule.DefineMMModel(_mmModel)
molecule.DefineNBModel(_nbModel)
molecule.Summary(log=log)
molecule.coordinates3.TranslateToCenter()
molecule.configuration.Clear()
energies.append(molecule.Energy(log=log, doGradients=True))
molecules.append(molecule)
# . Data initialization.
observed = {}
referenceData = TestDataSet("Merge/Prune Energies")
# . Loop over the tests.
for (testIndex, (moleculeFrequencies,
moleculePruneIndices)) in enumerate(_Tests):
# . Heading.
if log is not None:
log.Heading("Merge/Prune Test {:d}".format(testIndex),
QBLANKLINE=True)
# . Initialization.
mergedEnergy = 0.0
prunedEnergy = 0.0
translation.Set(0.0)
# . Gather items.
index = 0
numberAtoms = 0
pruneIndices = []
toMerge = []
for (i, frequency) in enumerate(moleculeFrequencies):
molecule = molecules[i]
mergedEnergy += energies[i] * frequency
for f in range(frequency):
cloned = Clone(molecule)
translation[0] += _Displacement
cloned.coordinates3.Translate(translation)
toMerge.append(cloned)
if index in moleculePruneIndices:
pruneIndices.extend(
range(numberAtoms,
numberAtoms + len(cloned.atoms)))
prunedEnergy += energies[i]
index += 1
numberAtoms += len(cloned.atoms)
# . Merging.
merged = toMerge[0].Merge(toMerge[1:])
merged.Summary(log=log)
eMerged = merged.Energy(log=log)
# . Pruning.
pruned = merged.Prune(Selection.FromIterable(pruneIndices))
pruned.Summary(log=log)
ePruned = pruned.Energy(log=log)
# . Get the observed and reference data.
for (tag, eObserved,
eReference) in (("Merged Energy {:d}".format(testIndex),
eMerged, mergedEnergy),
("Pruned Energy {:d}".format(testIndex),
ePruned, prunedEnergy)):
observed[tag] = eObserved
referenceData.AddDatum(
TestReal(
tag,
eReference,
referenceData,
absoluteErrorTolerance=_EnergyAbsoluteErrorTolerance,
toleranceFormat="{:.3f}",
valueFormat="{:.3f}"))
# . Finish up.
if log is not None: log.Separator()
# . Check for success/failure.
if len(observed) > 0:
results = referenceData.VerifyAgainst(observed)
results.Summary(log=log, fullSummary=self.fullVerificationSummary)
isOK = results.WasSuccessful()
else:
isOK = True
# . Success/failure.
self.assertTrue(isOK)
def runTest(self):
"""The test."""
# . Initialization.
isOK = True
log = self.GetLog()
molPath = os.path.join(os.getenv("PDYNAMO_PMOLECULE"), "data", "mol")
# . Options.
converger = DIISSCFConverger(densityTolerance=1.0e-6,
maximumSCFCycles=500)
qcModel = QCModelMNDO("am1",
converger=converger,
isSpinRestricted=False)
singlet = ElectronicState(charge=1, multiplicity=1)
triplet = ElectronicState(charge=1, multiplicity=3)
# . Optimizer.
optimizer = QuasiNewtonMinimizer(logFrequency=1,
maximumIterations=500,
rmsGradientTolerance=0.05)
optimizer.Summary(log=log)
# . Set up the system.
system = MOLFile_ToSystem(os.path.join(molPath, "phenylCation.mol"))
system.electronicState = singlet
system.label = "Phenyl Cation"
system.DefineQCModel(qcModel)
system.Summary(log=log)
# . Check both methods.
numberNotConverged = 0
results = {}
for method in ("GP", "PF"):
# . Reset coordinates.
system.coordinates3 = MOLFile_ToCoordinates3(
os.path.join(molPath, "phenylCation.mol"))
system.configuration.Clear()
# . Set up the objective function.
seamOF = SEAMObjectiveFunction.FromSystem(system,
singlet,
triplet,
method=method)
#seamOF.RemoveRotationTranslation ( )
# . Minimize.
#seamOF.TestGradients ( delta = 1.0e-05 ) # . Works with 1.0e-10 density tolerance.
cpu = CPUTime()
report = optimizer.Iterate(seamOF, log=log)
report["CPU Time"] = cpu.CurrentAsString()
# . Final energies.
(f1, f2) = seamOF.Energies(doGradients=True, log=log)
report["Energy 1"] = f1
report["Energy 2"] = f2
results[method] = report
if not report.get("Converged", False): numberNotConverged += 1
# . Print out a summary of the results.
if LogFileActive(log):
table = log.GetTable(columns=[10, 20, 20, 10, 10, 20])
table.Start()
table.Title("Surface Crossing Optimizations")
table.Heading("Method")
table.Heading("State Energies", columnSpan=2)
table.Heading("Converged")
table.Heading("Calls")
table.Heading("Time")
for method in ("GP", "PF"):
report = results[method]
table.Entry(method, alignment="left")
table.Entry("{:20.1f}".format(report["Energy 1"]))
table.Entry("{:20.1f}".format(report["Energy 2"]))
table.Entry("{!r}".format(report.get("Converged", False)))
table.Entry("{:d}".format(report["Function Calls"]))
table.Entry(report["CPU Time"])
table.Stop()
# . Finish up.
self.assertTrue(numberNotConverged == 0)