def testOutputPath(self):
""" Check that the default path is set correctly. """
# Setup the calculator.
feff = FEFFPhotonMatterInteractor(parameters=self.__parameters)
self.__dirs_to_remove.append('pmi')
# Execute the code.
status = feff.backengine()
# Check that the pmi dir was created.
self.assertTrue(os.path.isdir('pmi'))
def testShapedConstructionPaths(self):
""" Testing the construction of the class with parameters. """
# Construct.
feff = FEFFPhotonMatterInteractor(
parameters=self.__parameters,
input_path=TestUtilities.generateTestFilePath('prop'),
output_path='absorption.h5')
# Check type.
self.assertIsInstance(feff, FEFFPhotonMatterInteractor)
# Get parameters and check.
parameters = feff.parameters
self.assertEqual(parameters.atoms, self.__atoms)
self.assertEqual(parameters.potentials, self.__potentials)
self.assertEqual(parameters.edge, self.__edge)
self.assertEqual(parameters.amplitude_reduction_factor,
self.__amplitude_reduction_factor)
self.assertEqual(parameters.effective_path_distance,
self.__effective_path_distance)
self.assertEqual(feff.output_path,
os.path.join(os.getcwd(), 'absorption.h5'))
def testBackengine(self):
""" Test the backengine execution. """
# Setup the calculator.
feff = FEFFPhotonMatterInteractor(parameters=self.__parameters)
self.__dirs_to_remove.append('pmi')
# Execute the code.
status = feff.backengine()
# Check success.
self.assertEqual(status, 0)
# Check directory content.
self.assertIn('atoms.dat', os.listdir(feff.working_directory))
self.assertIn('chi.dat', os.listdir(feff.working_directory))
self.assertIn('feff.bin', os.listdir(feff.working_directory))
self.assertIn('feff.inp', os.listdir(feff.working_directory))
self.assertIn('feff85L', os.listdir(feff.working_directory))
self.assertIn('fort.38', os.listdir(feff.working_directory))
self.assertIn('fort.39', os.listdir(feff.working_directory))
self.assertIn('fpf0.dat', os.listdir(feff.working_directory))
self.assertIn('geom.dat', os.listdir(feff.working_directory))
self.assertIn('global.dat', os.listdir(feff.working_directory))
self.assertIn('list.dat', os.listdir(feff.working_directory))
self.assertIn('log.dat', os.listdir(feff.working_directory))
self.assertIn('log1.dat', os.listdir(feff.working_directory))
self.assertIn('log2.dat', os.listdir(feff.working_directory))
self.assertIn('log4.dat', os.listdir(feff.working_directory))
self.assertIn('log5.dat', os.listdir(feff.working_directory))
self.assertIn('log6.dat', os.listdir(feff.working_directory))
self.assertIn('mod1.inp', os.listdir(feff.working_directory))
self.assertIn('mod2.inp', os.listdir(feff.working_directory))
self.assertIn('mod3.inp', os.listdir(feff.working_directory))
self.assertIn('mod4.inp', os.listdir(feff.working_directory))
self.assertIn('mod5.inp', os.listdir(feff.working_directory))
self.assertIn('mod6.inp', os.listdir(feff.working_directory))
self.assertIn('mpse.dat', os.listdir(feff.working_directory))
self.assertIn('paths.dat', os.listdir(feff.working_directory))
self.assertIn('phase.bin', os.listdir(feff.working_directory))
self.assertIn('pot.bin', os.listdir(feff.working_directory))
self.assertIn('s02.inp', os.listdir(feff.working_directory))
self.assertIn('xmu.dat', os.listdir(feff.working_directory))
self.assertIn('xsect.bin', os.listdir(feff.working_directory))
def testWorkingDirectorySetup(self):
""" Test the initialization of the working directory. """
# Requirements:
# - By default, setup tmp dir, copy executable and write serialize parameters
# - User may specify working directory ### TODO
# - If feff.inp already exists: backup and overwrite. ### TODO
# - enhancement: initialize parameters from given feff.inp ### TODO
# Test default behavior.
self.__dirs_to_remove.append('pmi')
feff = FEFFPhotonMatterInteractor(parameters=self.__parameters)
# Setup working directory.
feff._setupWorkingDirectory()
# Assert it is created.
self.assertTrue(os.path.isdir(feff.working_directory))
def testShapedConstruction(self):
""" Testing the construction of the class with parameters. """
# Construct.
self.__dirs_to_remove.append( 'pmi' )
feff = FEFFPhotonMatterInteractor(parameters=self.__parameters)
# Check type.
self.assertIsInstance( feff, FEFFPhotonMatterInteractor )
# Get parameters and check.
parameters = feff.parameters
self.assertEqual( parameters.atoms, self.__atoms)
self.assertEqual( parameters.potentials, self.__potentials)
self.assertEqual( parameters.edge, self.__edge)
self.assertEqual( parameters.amplitude_reduction_factor, self.__amplitude_reduction_factor)
self.assertEqual( parameters.effective_path_distance, self.__effective_path_distance)
def testSaveH5(self):
# Setup the calculator.
feff = FEFFPhotonMatterInteractor(parameters=self.__parameters,
output_path='feff.h5')
self.__files_to_remove.append(feff.output_path)
# Execute the code.
status = feff.backengine()
# Save.
feff.saveH5()
# Check content of newly generated file.
expected_sets = [
'data/snp_0000001/r',
#'data/snp_0000001/xyz',
#'data/snp_0000001/Z',
#'data/snp_0000001/T',
'data/snp_0000001/E',
'data/snp_0000001/DeltaE',
'data/snp_0000001/k',
'data/snp_0000001/mu',
'data/snp_0000001/mu0',
'data/snp_0000001/chi',
'data/snp_0000001/ampl',
'data/snp_0000001/phase',
'data/snp_0000001/potential_index',
'params/amplitude_reduction_factor',
'params/edge',
'params/effective_path_distance',
#'history/parent',
#'misc/polarization_tensor',
#'misc/evec',
#'misc/xivec',
#'misc/spvec',
#'misc/nabs',
#'misc/iphabs',
#'misc/cf_average_data',
#'misc/ipol',
#'misc/ispin',
#'misc/le2',
#'misc/elpty',
#'misc/angks',
'info/contact',
'info/data_description',
'info/interface_version',
'info/credits',
'info/package_version',
]
with h5py.File(feff.output_path, 'r') as h5:
for st in expected_sets:
self.assertIsInstance(h5[st], h5py.Dataset)
# Check attributes
self.assertEqual(h5['data/snp_0000001/r'].attrs['unit'],
'Angstrom')
self.assertEqual(h5['data/snp_0000001/E'].attrs['unit'], 'eV')
self.assertEqual(h5['data/snp_0000001/DeltaE'].attrs['unit'], 'eV')
self.assertEqual(h5['data/snp_0000001/k'].attrs['unit'], '1')
self.assertEqual(h5['data/snp_0000001/mu'].attrs['unit'],
'1/Angstrom')
self.assertEqual(h5['data/snp_0000001/mu0'].attrs['unit'],
'1/Angstrom')
self.assertEqual(h5['data/snp_0000001/chi'].attrs['unit'], '1')
self.assertEqual(h5['data/snp_0000001/ampl'].attrs['unit'], '1')
self.assertEqual(h5['data/snp_0000001/phase'].attrs['unit'], 'rad')
self.assertEqual(
h5['data/snp_0000001/potential_index'].attrs['unit'], '1')
self.assertEqual(
h5['params/amplitude_reduction_factor'].attrs['unit'], '1')
self.assertEqual(h5['params/edge'].attrs['unit'], '')
self.assertEqual(
h5['params/effective_path_distance'].attrs['unit'], 'Angstrom')
h5.close()