def testTokenizerOptimizationInfo(self): # fold>>
data = FileSnippets.optimizationInfo() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.OptimizationInfoToken)
def testTokenizerResponseHeader(self): # fold>>
data = FileSnippets.responseHeader() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.ResponseHeaderToken)
def testTokenizerCartesianCoordinates(self): # fold>>
data = FileSnippets.cartesianCoordinates() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.CartesianCoordinatesToken)
def testTokenizerTotalMass(self): # fold>>
data = FileSnippets.totalMass() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.TotalMassToken)
def testTokenizerMomentsOfInertia(self): # fold>>
data = FileSnippets.momentsOfInertia() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.MomentsOfInertiaToken)
def parse(self, output_filename): # fold>>
logging.debug("Output filename : " + output_filename)
token_list = Dalton20.tokenizeOutFile(output_filename)
result = {}
result["input_molecule"] = None
result["run_data"] = None
result["molecules"] = []
result["triples"] = []
result["run_data"] = []
cartesian_coordinates_token = tokenfilters.getCartesianCoordinatesToken(
token_list)
atom_basis_set_token = tokenfilters.getAtomsAndBasisSetsToken(
token_list)
final_geometry_token = tokenfilters.getFinalGeometryToken(token_list)
if atom_basis_set_token is not None and final_geometry_token is not None:
final_geometry, triples = self._parseGeometryOptimization(
final_geometry_token, atom_basis_set_token)
result["molecules"].append(final_geometry)
result["triples"].extend(triples)
return result
def testTokenizerHOMOLUMOSeparation(self): # fold>>
data = FileSnippets.HomoLumoSeparation() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.HOMOLUMOSeparationToken)
def testTokenizerSevereError(self): # fold>>
data = FileSnippets.severeError() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.SevereErrorToken)
def testTokenizerDipoleMoment(self): # fold>>
data = FileSnippets.dipoleMoment() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.DipoleMomentToken)
def testTokenizerFinalGeometry(self): # fold>>
data = FileSnippets.finalGeometry() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.FinalGeometryToken)
def testTokenizerAtomsAndBasisSetsTable(self): # fold>>
data = FileSnippets.atomsAndBasisSetsTable() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__, Tokens.AtomsAndBasisSetsToken)
def testTokenizerGeometryConvergenceNumIterations(self): # fold>>
data = FileSnippets.geometryConvergenceNumIterations() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__,
Tokens.GeometryConvergenceNumIterationsToken)
def testTokenizerSecondHyperpolarizability(self): # fold>>
data = FileSnippets.secondHyperpolarizability() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__,
Tokens.SecondHyperpolarizabilityToken)
def testTokenizerFirstHyperpolarizabilityComponent(self): # fold>>
data = FileSnippets.firstHyperpolarizability() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__,
Tokens.FirstHyperpolarizabilityComponentToken)
def testTokenizerEndOfOptimizationHeader(self): # fold>>
data = FileSnippets.endOfOptimizationHeader() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__,
Tokens.EndOfOptimizationHeaderToken)
def testTokenizerNormalModesEigenvalues(self): # fold>>
data = FileSnippets.normalModesEigenvalues() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 1)
self.assertEqual(tokens[0].__class__,
Tokens.NormalModesEigenvaluesToken)
def testTokenizer(self): # fold>>
data = FileSnippets.fileHeader() + "\n" + FileSnippets.centerOfMass(
) + "\n" + FileSnippets.isotopicMasses(
) + "\n" + FileSnippets.totalMass(
) + "\n" + FileSnippets.momentsOfInertia() + "\n"
writeToTestFile(data)
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(len(tokens), 5)
self.assertEqual(tokens[0].__class__, Tokens.FileHeaderToken)
self.assertEqual(tokens[1].__class__, Tokens.CenterOfMassToken)
self.assertEqual(tokens[2].__class__, Tokens.IsotopicMassesToken)
self.assertEqual(tokens[3].__class__, Tokens.TotalMassToken)
self.assertEqual(tokens[4].__class__, Tokens.MomentsOfInertiaToken)
def main(argv): # fold>>
options = _getOptions(argv)
token_list = Dalton20.tokenizeOutFile(options.dalton_out_filename)
error_tokens = _getErrorTokens(token_list)
if options.verbose:
for token in error_tokens:
print "Error: " + token.reason()
if len(error_tokens) != 0:
sys.exit(1)
sys.exit(0)
def main(argv):
if len(argv) < 2:
_usage()
sys.exit(1)
dalton_out_filename = argv[1]
token_list = Dalton20.tokenizeOutFile(dalton_out_filename)
tokens = filter(lambda x: x.__class__ == Tokens.DipoleMomentToken,
token_list)
if len(tokens) == 0:
raise Exception("Sorry. Could not find dipole token")
# take the last one, at the end of a geometry optimization, we have two of them
print tokens[-1].dipole().value()
def main(filename):
tokens = Dalton20.tokenizeOutFile(filename)
try:
bond_length_token = filter(
lambda x: x.__class__ == Tokens.BondLengthsToken, tokens)[-1]
except:
print "Sorry, looks like there are no bond length entries in the file"
sys.exit(1)
atom_list = bond_length_token.atomList()
print "# %s" % (filename, )
for entry in atom_list:
if entry[0][0][0] == "C" and entry[1][0][0] == "C":
print "%s %s %s %s %s" % (entry[0][0], entry[0][1], entry[1][0],
entry[1][1], entry[2].asUnit(
Units.angstrom).value())
def main(argv):
if len(argv) < 2:
_usage()
sys.exit(1)
dalton_out_filename = argv[1]
token_list = Dalton20.tokenizeOutFile(dalton_out_filename)
tokens = filter(
lambda x: x.__class__ == Tokens.SecondHyperpolarizabilityToken,
token_list)
if len(tokens) == 0:
raise Exception("Sorry. Could not find gamma component tokens")
print "# bfreq|cfreq|dfreq|components|value|equal to"
for t in tokens:
printToken(t)
def main(dalton_out, cml_out):
tokenlist = Dalton20.tokenizeOutFile(dalton_out)
atom_basis_set_token = getAtomsAndBasisSetsToken(tokenlist)
geometry_token = getFinalGeometry(tokenlist)
datalist = atom_basis_set_token.atomDataList()
final_geometry = geometry_token.atomList()
doc = minidom.parseString(
"<cml xmlns=\"http://www.xml-cml.org/schema\" xmlns:sb=\"http://forthescience.org/NS/mycml\"/>"
)
namespace = "http://www.xml-cml.org/schema"
molecule = doc.createElementNS(namespace, "molecule")
doc.documentElement.appendChild(molecule)
name = doc.createElementNS(namespace, "name")
molecule.appendChild(name)
text = doc.createTextNode(os.path.splitext(dalton_out)[0])
name.appendChild(text)
atomarray = doc.createElementNS(namespace, "atomArray")
molecule.appendChild(atomarray)
for id, atom_entry in enumerate(final_geometry):
label, group, coords = atom_entry
atomic_number = labelToAtomicNumber(label, datalist)
atom = doc.createElementNS(namespace, "atom")
atom.setAttribute("id", "a" + str(id + 1))
atom.setAttribute("x3", str(coords.asUnit(Units.bohr).value()[0]))
atom.setAttribute("y3", str(coords.asUnit(Units.bohr).value()[1]))
atom.setAttribute("z3", str(coords.asUnit(Units.bohr).value()[2]))
atom.setAttributeNS("http://forthescience.org/NS/mycml",
"sb:atomicNumber", str(atomic_number))
label_node = doc.createElementNS(namespace, "label")
label_node.setAttribute("value", label)
atom.appendChild(label_node)
atomarray.appendChild(atom)
output = file(cml_out, "w")
output.write(doc.toprettyxml())
def main(argv):
if len(argv) < 2:
_usage()
sys.exit(1)
dalton_out_filename = argv[1]
token_list = Dalton20.tokenizeOutFile(dalton_out_filename)
tokens = filter(lambda x: x.__class__ == Tokens.LinearResponseToken,
token_list)
if len(tokens) == 0:
raise Exception("Sorry. Could not find linear response tokens")
print "# afreq|bfreq|components|value"
for t in tokens:
print "%7.6f|%7.6f|%s|%.8f|" % (t.AFreq().value(), t.BFreq().value(),
formatComponents(
t.components()), t.alpha().value())
def __init__(self, dalton_out_filename): # fold>>
token_list = Dalton20.tokenizeOutFile(dalton_out_filename)
atom_basis_set_token = self._getAtomsAndBasisSetsToken(token_list)
geometry_token = self._getFinalGeometryToken(token_list)
symmetry_token = self._getSymmetryToken(token_list)
mol = Molecule()
mol.symmetry_generators = symmetry_token.generators()
mol.basis_set = atom_basis_set_token.basisSet()
for label, symmetry, coords in geometry_token.atomList():
element = _labelToElement(label,
atom_basis_set_token.atomDataList())
mol.elements_list.append(element)
mol.labels_list.append(label)
mol.symmetries_list.append(symmetry)
mol.coordinates_list.append(coords)
self._molecule = mol
def main(argv):
if len(argv) < 2:
_usage()
sys.exit(1)
dalton_out_filename = argv[1]
token_list = Dalton20.tokenizeOutFile(dalton_out_filename)
tokens = filter(
lambda x: x.__class__ == Tokens.FirstHyperpolarizabilityComponentToken,
token_list)
if len(tokens) == 0:
raise Exception("Sorry. Could not find beta component tokens")
print "# bfreq|cfreq|components|value|equal to"
for t in tokens:
if t.beta() is not None:
print "%7.6f|%7.6f|%s|%.8f|" % (t.BFreq().value(), t.CFreq().value(
), formatComponents(t.components()), t.beta().value())
else:
print "%7.6f|%7.6f|%s||%s" % (t.BFreq().value(), t.CFreq().value(),
formatComponents(t.components()),
formatComponents(t.refersTo()))
def testTokenizerEmptyFile(self): # fold>>
writeToTestFile("")
tokens = Dalton20.tokenizeOutFile(testFilePath())
self.assertEqual(tokens, [])
