def CalcCompoundDescriptorsForComposition(self,
compos='',
composList=None,
propDict={}):
""" calculates all simple descriptors for a given composition
**Arguments**
- compos: a string representation of the composition
- composList: a *composVect*
- propDict: a dictionary containing the properties of the composition
as a whole (e.g. structural variables, etc.)
The client must provide either _compos_ or _composList_. If both are
provided, _composList_ takes priority.
**Returns**
the list of descriptor values
**Notes**
- when _compos_ is provided, this uses _chemutils.SplitComposition_
to split the composition into its individual pieces
"""
if composList is None:
composList = chemutils.SplitComposition(compos)
res = []
for cl in self.compoundList:
val = Parser.CalcSingleCompoundDescriptor(composList, cl[1:],
self.atomDict, propDict)
res.append(val)
return res
def CalcDescriptorsForComposition(self, composVect, propDict):
""" calculates all descriptors for a given composition
**Arguments**
- compos: a string representation of the composition
- propDict: a dictionary containing the properties of the composition
as a whole (e.g. structural variables, etc.). These are used to
generate Compound Descriptors
**Returns**
the list of all descriptor values
**Notes**
- this uses _chemutils.SplitComposition_
to split the composition into its individual pieces
"""
composList = chemutils.SplitComposition(composVect[0])
try:
r1 = self.CalcSimpleDescriptorsForComposition(
composList=composList)
except KeyError:
res = []
else:
r2 = self.CalcCompoundDescriptorsForComposition(
composList=composList, propDict=propDict)
res = r1 + r2
return tuple(res)
def test_chemutils(self):
self.assertEqual(chemutils.SplitComposition('Fe'), [('Fe', 1)])
self.assertEqual(chemutils.SplitComposition('Fe3Al'), [('Fe', 3.0),
('Al', 1)])
self.assertEqual(chemutils.SplitComposition('Fe99PdAl'), [('Fe', 99.0),
('Pd', 1),
('Al', 1)])
self.assertEqual(chemutils.SplitComposition('TiNiSiSO12P'),
[('Ti', 1), ('Ni', 1), ('Si', 1), ('S', 1),
('O', 12.0), ('P', 1)])
temp = [
'[Xe] 4f^12 6s^2', '[Xe] 4f^14 5d^6 6s^2', '[Xe] 4f^14 5d^10 6s^2',
'[Xe] 4f^14 5d^10 6s^2 6p^1', '[Xe] 5d^10'
]
for entry, expected in zip(temp, (14, 8, 2, 3, 10)):
self.assertEqual(
chemutils.ConfigToNumElectrons(entry,
ignoreFullD=True,
ignoreFullF=True), expected)
for entry, expected in zip(temp, (14, 8, 12, 13, 10)):
self.assertEqual(
chemutils.ConfigToNumElectrons(entry,
ignoreFullD=False,
ignoreFullF=True), expected)
for entry, expected in zip(temp, (14, 22, 16, 17, 10)):
self.assertEqual(
chemutils.ConfigToNumElectrons(entry,
ignoreFullD=True,
ignoreFullF=False), expected)
for entry, expected in zip(temp, (14, 22, 26, 27, 10)):
self.assertEqual(
chemutils.ConfigToNumElectrons(entry,
ignoreFullD=False,
ignoreFullF=False), expected)
def CalcSimpleDescriptorsForComposition(self, compos='', composList=None):
""" calculates all simple descriptors for a given composition
**Arguments**
- compos: a string representation of the composition
- composList: a *composVect*
The client must provide either _compos_ or _composList_. If both are
provided, _composList_ takes priority.
**Returns**
the list of descriptor values
**Notes**
- when _compos_ is provided, this uses _chemutils.SplitComposition_
to split the composition into its individual pieces
- if problems are encountered because of either an unknown descriptor or
atom type, a _KeyError_ will be raised.
"""
if composList is None:
composList = chemutils.SplitComposition(compos)
try:
res = []
for i in xrange(len(self.simpleList)):
descName, targets = self.simpleList[i]
for target in targets:
try:
method = getattr(self, target)
except AttributeError:
print('Method %s does not exist' % (target))
else:
res.append(method(descName, composList))
except KeyError as msg:
print('composition %s caused problems' % composList)
raise KeyError(msg)
return res
