def _get_properties(self):
"""
Loads all properties to object's attributes.
"""
self._ab_initio_program = self.getProperty("AbInitioProgram").value
self._vibrational_or_phonon_data_file = self.getProperty(
"VibrationalOrPhononFile").value
self._experimental_file = self.getProperty("ExperimentalFile").value
self._temperature = self.getProperty("TemperatureInKelvin").value
self._bin_width = self.getProperty("BinWidthInWavenumber").value
self._scale = self.getProperty("Scale").value
self._sample_form = self.getProperty("SampleForm").value
instrument_name = self.getProperty("Instrument").value
if instrument_name in AbinsModules.AbinsConstants.ALL_INSTRUMENTS:
self._instrument_name = instrument_name
instrument_producer = AbinsModules.InstrumentProducer()
self._instrument = instrument_producer.produce_instrument(
name=self._instrument_name)
else:
raise ValueError("Unknown instrument %s" % instrument_name)
self._atoms = self.getProperty("Atoms").value
self._sum_contributions = self.getProperty("SumContributions").value
# conversion from str to int
self._num_quantum_order_events = int(
self.getProperty("QuantumOrderEventsNumber").value)
self._scale_by_cross_section = self.getPropertyValue(
'ScaleByCrossSection')
self._out_ws_name = self.getPropertyValue('OutputWorkspace')
self._calc_partial = (len(self._atoms) > 0)
# user defined interval is exclusive with respect to
# AbinsModules.AbinsParameters.min_wavenumber
# AbinsModules.AbinsParameters.max_wavenumber
# with bin width AbinsModules.AbinsParameters.bin_width
step = self._bin_width
start = AbinsModules.AbinsParameters.min_wavenumber + step / 2.0
stop = AbinsModules.AbinsParameters.max_wavenumber + step / 2.0
self._bins = np.arange(start=start,
stop=stop,
step=step,
dtype=AbinsModules.AbinsConstants.FLOAT_TYPE)
class AbinsCalculateSPowderTest(unittest.TestCase):
"""
Test of CalculateS for the Powder scenario.
"""
_temperature = 10 # 10 K, temperature for the benchmark
_sample_form = "Powder"
_instrument = AbinsModules.InstrumentProducer().produce_instrument("TOSCA")
_order_event = AbinsModules.AbinsConstants.FUNDAMENTALS
_si2 = "Si2-sc_CalculateSPowder"
def setUp(self):
AbinsModules.AbinsParameters.atoms_threads = 1
def tearDown(self):
AbinsModules.AbinsTestHelpers.remove_output_files(list_of_names=["CalculateSPowder"])
# test input
def test_wrong_input(self):
full_path_filename = AbinsModules.AbinsTestHelpers.find_file(filename=self._si2 + ".phonon")
castep_reader = AbinsModules.LoadCASTEP(input_ab_initio_filename=full_path_filename)
good_data = castep_reader.read_vibrational_or_phonon_data()
# wrong filename
with self.assertRaises(ValueError):
AbinsModules.CalculateS.init(filename=1, temperature=self._temperature, sample_form=self._sample_form,
abins_data=good_data, instrument=self._instrument,
quantum_order_num=self._order_event)
# wrong temperature
with self.assertRaises(ValueError):
AbinsModules.CalculateS.init(filename=full_path_filename, temperature=-1, sample_form=self._sample_form,
abins_data=good_data, instrument=self._instrument,
quantum_order_num=self._order_event)
# wrong sample
with self.assertRaises(ValueError):
AbinsModules.CalculateS.init(filename=full_path_filename, temperature=self._temperature,
sample_form="SOLID", abins_data=good_data, instrument=self._instrument,
quantum_order_num=self._order_event)
# wrong abins data: content of abins data instead of object abins_data
with self.assertRaises(ValueError):
AbinsModules.CalculateS.init(filename=full_path_filename, temperature=self._temperature,
sample_form=self._sample_form, abins_data=good_data.extract(),
instrument=self._instrument, quantum_order_num=self._order_event)
# wrong instrument
with self.assertRaises(ValueError):
# noinspection PyUnusedLocal
AbinsModules.CalculateS.init(filename=full_path_filename, temperature=self._temperature,
sample_form=self._sample_form, abins_data=good_data.extract(),
instrument=self._instrument, quantum_order_num=self._order_event)
# main test
def test_good_case(self):
self._good_case(name=self._si2)
# helper functions
def _good_case(self, name=None):
# calculation of powder data
good_data = self._get_good_data(filename=name)
good_tester = AbinsModules.CalculateS.init(
filename=AbinsModules.AbinsTestHelpers.find_file(filename=name + ".phonon"), temperature=self._temperature,
sample_form=self._sample_form, abins_data=good_data["DFT"], instrument=self._instrument,
quantum_order_num=self._order_event)
calculated_data = good_tester.get_formatted_data()
self._check_data(good_data=good_data["S"], data=calculated_data.extract())
# check if loading powder data is correct
new_tester = AbinsModules.CalculateS.init(
filename=AbinsModules.AbinsTestHelpers.find_file(filename=name + ".phonon"), temperature=self._temperature,
sample_form=self._sample_form, abins_data=good_data["DFT"], instrument=self._instrument,
quantum_order_num=self._order_event)
loaded_data = new_tester.load_formatted_data()
self._check_data(good_data=good_data["S"], data=loaded_data.extract())
def _get_good_data(self, filename=None):
castep_reader = AbinsModules.LoadCASTEP(
input_ab_initio_filename=AbinsModules.AbinsTestHelpers.find_file(filename=filename + ".phonon"))
s_data = self._prepare_data(filename=AbinsModules.AbinsTestHelpers.find_file(filename=filename + "_S.txt"))
return {"DFT": castep_reader.read_vibrational_or_phonon_data(), "S": s_data}
# noinspection PyMethodMayBeStatic
def _prepare_data(self, filename=None):
"""Reads a correct values from ASCII file."""
with open(filename) as data_file:
# noinspection PyPep8
correct_data = json.loads(data_file.read().replace("\\n", " ").
replace("array", "").
replace("([", "[").
replace("])", "]").
replace("'", '"').
replace("0. ", "0.0"))
temp = np.asarray(correct_data["frequencies"])
correct_data["frequencies"] = temp
# we need to - 1 because one entry is "frequencies"
for el in range(len(correct_data) - 1):
temp = np.asarray(correct_data["atom_%s" % el]["s"]["order_%s" % AbinsModules.AbinsConstants.FUNDAMENTALS])
correct_data["atom_%s" % el]["s"]["order_%s" % AbinsModules.AbinsConstants.FUNDAMENTALS] = temp
return correct_data
def _check_data(self, good_data=None, data=None):
good_temp = good_data["frequencies"]
data_temp = data["frequencies"]
self.assertEqual(True, np.allclose(good_temp, data_temp))
# we need to - 1 because one entry is "frequencies"
for el in range(len(good_data) - 1):
good_temp = good_data["atom_%s" % el]["s"]["order_%s" % AbinsModules.AbinsConstants.FUNDAMENTALS]
data_temp = data["atom_%s" % el]["s"]["order_%s" % AbinsModules.AbinsConstants.FUNDAMENTALS]
self.assertEqual(True, np.allclose(good_temp, data_temp))
