def get_molecule(self):
from Molecule import molecule
try:
xyz_fn = self.get_xyz_filename()
except PyAdfError:
return self.job.mol
return molecule(xyz_fn)
def metarun(self):
dataSetJobResults = []
for p in self.pathNames:
filelist = glob.glob(os.path.join(p, '*.xyz'))
molecules = []
for f in filelist:
molecules.append(
molecule(os.path.join(p, f), inputformat='xyz'))
dataSetJob = adffdeanalysisjob(
molecules=molecules,
settings=self.settings,
adfsettings=self.adfsettings,
basis=self.basis,
core=self.core,
fde=self.fde,
adffdesettings=self.adffdesettings).run()
dataSetJobResults.append(dataSetJob)
dictTmp = []
for key, value1 in dataSetJobResults[0].iteritems():
value2 = dataSetJobResults[1][key]
dictTmp.append((key, self.add_lists(value1, value2)))
dictTmp = dict(dictTmp)
if len(dataSetJobResults) >= 3:
for i in range(2, len(dataSetJobResults)):
tmpAvrg = []
for key, value1 in dictTmp.iteritems():
value2 = dataSetJobResults[i][key]
tmpAvrg.append((key, self.add_lists(value1, value2)))
tmpAvrg = dict(tmpAvrg)
dictTmp.update(tmpAvrg)
tmpAvrg = dict(tmpAvrg)
else:
tmpAvrg = dictTmp
AvrgResults = []
number = len(dataSetJobResults)
for key, value in tmpAvrg.iteritems():
AvrgResults.append((key, self.divide_by_number(value, number)))
AvrgResults = dict(AvrgResults)
return AvrgResults, dataSetJobResults
def get_molecule(self):
"""
Return the molecular geometry after the ADF job.
This can be changes with respect to the input geometry
because it was optimized in the calculation.
@returns: The molecular geometry.
@rtype: L{molecule}
"""
nnuc = self.get_result_from_tape('Molecule', 'nAtoms')
atnums = self.get_result_from_tape('Molecule', 'AtomicNumbers')
xyz = self.get_result_from_tape('Molecule', 'Coords')
xyznuc = xyz.reshape(nnuc, 3)
m = molecule()
m.add_atoms(atnums, xyznuc, atomicunits=True)
return m