def testShapedConstruction(self):
""" Testing the construction of the class with parameters. """
feff_parameters = FEFFPhotonMatterInteractorParameters(
atoms=self.__atoms,
potentials=self.__potentials,
edge=self.__edge,
effective_path_distance=self.__effective_path_distance,
amplitude_reduction_factor=self.__amplitude_reduction_factor)
self.assertIsInstance(feff_parameters,
FEFFPhotonMatterInteractorParameters)
# Check attributes
self.assertEqual(
feff_parameters._FEFFPhotonMatterInteractorParameters__atoms,
self.__atoms)
self.assertEqual(
feff_parameters._FEFFPhotonMatterInteractorParameters__potentials,
self.__potentials)
self.assertEqual(
feff_parameters._FEFFPhotonMatterInteractorParameters__edge,
self.__edge)
self.assertEqual(
feff_parameters.
_FEFFPhotonMatterInteractorParameters__amplitude_reduction_factor,
self.__amplitude_reduction_factor)
self.assertEqual(
feff_parameters.
_FEFFPhotonMatterInteractorParameters__effective_path_distance,
self.__effective_path_distance)
def testSetters(self):
""" Test that setting parameters works correctly. """
# Construct the object.
feff_parameters = FEFFPhotonMatterInteractorParameters(
atoms=self.__atoms,
potentials=self.__potentials,
edge=self.__edge,
effective_path_distance=self.__effective_path_distance,
amplitude_reduction_factor=self.__amplitude_reduction_factor)
# Set new parameters.
feff_parameters.atoms = self.__atoms[:10]
feff_parameters.potentials = None
feff_parameters.edge = 'L2'
feff_parameters.amplitude_reduction_factor = 0.1
feff_parameters.effective_path_distance = 5.0
# Check attributes
self.assertEqual(
feff_parameters._FEFFPhotonMatterInteractorParameters__atoms,
self.__atoms[:10])
self.assertEqual(
feff_parameters._FEFFPhotonMatterInteractorParameters__potentials,
None)
self.assertEqual(
feff_parameters._FEFFPhotonMatterInteractorParameters__edge, 'L2')
self.assertEqual(
feff_parameters.
_FEFFPhotonMatterInteractorParameters__amplitude_reduction_factor,
0.1)
self.assertEqual(
feff_parameters.
_FEFFPhotonMatterInteractorParameters__effective_path_distance,
5.0)
def testFinalization(self):
""" That that the finalization flag is set correctly. """
feff_parameters = FEFFPhotonMatterInteractorParameters(
atoms=self.__atoms,
potentials=self.__potentials,
edge=self.__edge,
effective_path_distance=self.__effective_path_distance,
amplitude_reduction_factor=self.__amplitude_reduction_factor)
# Is finalized after construction.
self.assertTrue(feff_parameters.finalized)
# Change a parameter
feff_parameters.edge = 'L1'
self.assertFalse(feff_parameters.finalized)
# Finalize.
feff_parameters.finalize()
self.assertTrue(feff_parameters.finalized)
def testFinalize(self):
# Setup parameters.
feff_parameters = FEFFPhotonMatterInteractorParameters(
atoms=self.__atoms,
potentials=self.__potentials,
edge=self.__edge,
effective_path_distance=5.5,
amplitude_reduction_factor=1.0,
)
# Get potential list.
potential_list = feff_parameters._FEFFPhotonMatterInteractorParameters__potential_list
self.assertEqual(potential_list, [[0, 29, 'Cu'], [1, 29, 'Cu']])
def testQueries(self):
""" Test that all queries return the correct value. """
feff_parameters = FEFFPhotonMatterInteractorParameters(
atoms=self.__atoms,
potentials=self.__potentials,
edge=self.__edge,
effective_path_distance=self.__effective_path_distance,
amplitude_reduction_factor=self.__amplitude_reduction_factor)
# Check queries.
self.assertEqual(feff_parameters.atoms, self.__atoms)
self.assertEqual(feff_parameters.potentials, self.__potentials)
self.assertEqual(feff_parameters.edge, self.__edge)
self.assertEqual(feff_parameters.amplitude_reduction_factor,
self.__amplitude_reduction_factor)
self.assertEqual(feff_parameters.effective_path_distance,
self.__effective_path_distance)
def testSerialize(self):
""" Check that the serialize() method produces a valid feff.inp file."""
# Setup parameters.
feff_parameters = FEFFPhotonMatterInteractorParameters(
atoms=self.__atoms,
potentials=self.__potentials,
edge=self.__edge,
effective_path_distance=5.5,
amplitude_reduction_factor=1.0,
)
# Setup a stream to write to.
stream = StringIO.StringIO()
feff_parameters._serialize(stream=stream)
# Compare to reference.
reference_inp = """EDGE K
S02 1.000000
CONTROL 1 1 1 1 1 1
PRINT 0 0 0 0 0 0
RPATH 5.500000
EXAFS
POTENTIALS
0 29 Cu
1 29 Cu
ATOMS
0.00000 0.00000 0.00000 0
0.00000 1.80500 -1.80500 1
-1.80500 -1.80500 0.00000 1
1.80500 0.00000 -1.80500 1
0.00000 -1.80500 1.80500 1
1.80500 1.80500 0.00000 1
0.00000 -1.80500 -1.80500 1
-1.80500 1.80500 0.00000 1
0.00000 1.80500 1.80500 1
-1.80500 0.00000 -1.80500 1
-1.80500 0.00000 1.80500 1
1.80500 0.00000 1.80500 1
1.80500 -1.80500 0.00000 1
0.00000 -3.61000 0.00000 1
0.00000 0.00000 -3.61000 1
0.00000 0.00000 3.61000 1
-3.61000 0.00000 0.00000 1
3.61000 0.00000 0.00000 1
0.00000 3.61000 0.00000 1
-1.80500 3.61000 1.80500 1
1.80500 3.61000 1.80500 1
-1.80500 -3.61000 -1.80500 1
-1.80500 3.61000 -1.80500 1
1.80500 3.61000 -1.80500 1
-1.80500 -3.61000 1.80500 1
-3.61000 1.80500 -1.80500 1
1.80500 -3.61000 1.80500 1
3.61000 1.80500 -1.80500 1
-3.61000 1.80500 1.80500 1
-3.61000 -1.80500 -1.80500 1
3.61000 -1.80500 1.80500 1
1.80500 -3.61000 -1.80500 1
-3.61000 -1.80500 1.80500 1
3.61000 1.80500 1.80500 1
-1.80500 -1.80500 3.61000 1
-1.80500 -1.80500 -3.61000 1
1.80500 1.80500 -3.61000 1
1.80500 -1.80500 -3.61000 1
1.80500 -1.80500 3.61000 1
-1.80500 1.80500 -3.61000 1
-1.80500 1.80500 3.61000 1
1.80500 1.80500 3.61000 1
3.61000 -1.80500 -1.80500 1
3.61000 -3.61000 0.00000 1
3.61000 0.00000 -3.61000 1
3.61000 0.00000 3.61000 1
-3.61000 3.61000 0.00000 1
0.00000 3.61000 3.61000 1
-3.61000 0.00000 3.61000 1
-3.61000 -3.61000 0.00000 1
0.00000 -3.61000 3.61000 1
-3.61000 0.00000 -3.61000 1
3.61000 3.61000 0.00000 1
0.00000 -3.61000 -3.61000 1
0.00000 3.61000 -3.61000 1
0.00000 -5.41500 1.80500 1
1.80500 -5.41500 0.00000 1
0.00000 -5.41500 -1.80500 1
-1.80500 0.00000 5.41500 1
-5.41500 0.00000 -1.80500 1
5.41500 -1.80500 0.00000 1
-1.80500 5.41500 0.00000 1
5.41500 0.00000 -1.80500 1
-5.41500 -1.80500 0.00000 1
1.80500 5.41500 0.00000 1
5.41500 1.80500 0.00000 1
0.00000 5.41500 -1.80500 1
0.00000 -1.80500 -5.41500 1
0.00000 5.41500 1.80500 1
1.80500 0.00000 5.41500 1
0.00000 1.80500 5.41500 1
5.41500 0.00000 1.80500 1
1.80500 0.00000 -5.41500 1
0.00000 1.80500 -5.41500 1
0.00000 -1.80500 5.41500 1
-5.41500 0.00000 1.80500 1
-5.41500 1.80500 0.00000 1
-1.80500 0.00000 -5.41500 1
-1.80500 -5.41500 0.00000 1
END"""
comp = stream.getvalue()
self.assertEqual(comp, reference_inp)
def setUp(self):
""" Setting up a test. """
self.__files_to_remove = []
self.__dirs_to_remove = []
self.__atoms = (
[[0.00000, 0.00000, 0.00000], 'Cu', 0],
[[0.00000, 1.80500, -1.80500], 'Cu', 1],
[[-1.80500, -1.80500, 0.00000], 'Cu', 1],
[[1.80500, 0.00000, -1.80500], 'Cu', 1],
[[0.00000, -1.80500, 1.80500], 'Cu', 1],
[[1.80500, 1.80500, 0.00000], 'Cu', 1],
[[0.00000, -1.80500, -1.80500], 'Cu', 1],
[[-1.80500, 1.80500, 0.00000], 'Cu', 1],
[[0.00000, 1.80500, 1.80500], 'Cu', 1],
[[-1.80500, 0.00000, -1.80500], 'Cu', 1],
[[-1.80500, 0.00000, 1.80500], 'Cu', 1],
[[1.80500, 0.00000, 1.80500], 'Cu', 1],
[[1.80500, -1.80500, 0.00000], 'Cu', 1],
[[0.00000, -3.61000, 0.00000], 'Cu', 1],
[[0.00000, 0.00000, -3.61000], 'Cu', 1],
[[0.00000, 0.00000, 3.61000], 'Cu', 1],
[[-3.61000, 0.00000, 0.00000], 'Cu', 1],
[[3.61000, 0.00000, 0.00000], 'Cu', 1],
[[0.00000, 3.61000, 0.00000], 'Cu', 1],
[[-1.80500, 3.61000, 1.80500], 'Cu', 1],
[[1.80500, 3.61000, 1.80500], 'Cu', 1],
[[-1.80500, -3.61000, -1.80500], 'Cu', 1],
[[-1.80500, 3.61000, -1.80500], 'Cu', 1],
[[1.80500, 3.61000, -1.80500], 'Cu', 1],
[[-1.80500, -3.61000, 1.80500], 'Cu', 1],
[[-3.61000, 1.80500, -1.80500], 'Cu', 1],
[[1.80500, -3.61000, 1.80500], 'Cu', 1],
[[3.61000, 1.80500, -1.80500], 'Cu', 1],
[[-3.61000, 1.80500, 1.80500], 'Cu', 1],
[[-3.61000, -1.80500, -1.80500], 'Cu', 1],
[[3.61000, -1.80500, 1.80500], 'Cu', 1],
[[1.80500, -3.61000, -1.80500], 'Cu', 1],
[[-3.61000, -1.80500, 1.80500], 'Cu', 1],
[[3.61000, 1.80500, 1.80500], 'Cu', 1],
[[-1.80500, -1.80500, 3.61000], 'Cu', 1],
[[-1.80500, -1.80500, -3.61000], 'Cu', 1],
[[1.80500, 1.80500, -3.61000], 'Cu', 1],
[[1.80500, -1.80500, -3.61000], 'Cu', 1],
[[1.80500, -1.80500, 3.61000], 'Cu', 1],
[[-1.80500, 1.80500, -3.61000], 'Cu', 1],
[[-1.80500, 1.80500, 3.61000], 'Cu', 1],
[[1.80500, 1.80500, 3.61000], 'Cu', 1],
[[3.61000, -1.80500, -1.80500], 'Cu', 1],
[[3.61000, -3.61000, 0.00000], 'Cu', 1],
[[3.61000, 0.00000, -3.61000], 'Cu', 1],
[[3.61000, 0.00000, 3.61000], 'Cu', 1],
[[-3.61000, 3.61000, 0.00000], 'Cu', 1],
[[0.00000, 3.61000, 3.61000], 'Cu', 1],
[[-3.61000, 0.00000, 3.61000], 'Cu', 1],
[[-3.61000, -3.61000, 0.00000], 'Cu', 1],
[[0.00000, -3.61000, 3.61000], 'Cu', 1],
[[-3.61000, 0.00000, -3.61000], 'Cu', 1],
[[3.61000, 3.61000, 0.00000], 'Cu', 1],
[[0.00000, -3.61000, -3.61000], 'Cu', 1],
[[0.00000, 3.61000, -3.61000], 'Cu', 1],
[[0.00000, -5.41500, 1.80500], 'Cu', 1],
[[1.80500, -5.41500, 0.00000], 'Cu', 1],
[[0.00000, -5.41500, -1.80500], 'Cu', 1],
[[-1.80500, 0.00000, 5.41500], 'Cu', 1],
[[-5.41500, 0.00000, -1.80500], 'Cu', 1],
[[5.41500, -1.80500, 0.00000], 'Cu', 1],
[[-1.80500, 5.41500, 0.00000], 'Cu', 1],
[[5.41500, 0.00000, -1.80500], 'Cu', 1],
[[-5.41500, -1.80500, 0.00000], 'Cu', 1],
[[1.80500, 5.41500, 0.00000], 'Cu', 1],
[[5.41500, 1.80500, 0.00000], 'Cu', 1],
[[0.00000, 5.41500, -1.80500], 'Cu', 1],
[[0.00000, -1.80500, -5.41500], 'Cu', 1],
[[0.00000, 5.41500, 1.80500], 'Cu', 1],
[[1.80500, 0.00000, 5.41500], 'Cu', 1],
[[0.00000, 1.80500, 5.41500], 'Cu', 1],
[[5.41500, 0.00000, 1.80500], 'Cu', 1],
[[1.80500, 0.00000, -5.41500], 'Cu', 1],
[[0.00000, 1.80500, -5.41500], 'Cu', 1],
[[0.00000, -1.80500, 5.41500], 'Cu', 1],
[[-5.41500, 0.00000, 1.80500], 'Cu', 1],
[[-5.41500, 1.80500, 0.00000], 'Cu', 1],
[[-1.80500, 0.00000, -5.41500], 'Cu', 1],
[[-1.80500, -5.41500, 0.00000], 'Cu', 1],
)
self.__potentials = None
self.__edge = 'K'
self.__amplitude_reduction_factor = 0.9
self.__effective_path_distance = 5.5
self.__parameters = FEFFPhotonMatterInteractorParameters(
atoms=self.__atoms,
potentials=self.__potentials,
edge=self.__edge,
amplitude_reduction_factor=self.__amplitude_reduction_factor,
effective_path_distance=self.__effective_path_distance,
)