async def test_exporter_inclusion(event_loop, exporter, options, tmp_path, dry_run):
mat1 = Material("Mat1", {79: 0.5, 47: 0.5}, 2.0)
mat2 = Material("Mat2", {29: 0.5, 30: 0.5}, 3.0)
options.sample = InclusionSample(mat1, mat2, 10e-6)
await exporter.export(options, tmp_path, dry_run=dry_run)
_test_export(tmp_path, 2, 2, dry_run)
def create_model_sample(data, density_start = None, density_end = None):
elements_data = get_elements_data(data)
colors = generate_colors(steps = len(data) - 1)
densities = generate_densities(elements_data, density_start, density_end)
material_start, material_end = generate_end_materials(elements_data, colors, density_start, density_end)
sample = VerticalLayerSample(material_start, material_end)
# Iterate through all regions
for i in range(1, len(data) - 1): # create the remaining regions (in the middle)
density = densities[i]
color = colors[i]
material = Material(
name = f'region_{i}',
composition = to_weight_fraction(dict(elements_data.iloc[i])),
density_kg_per_m3 = density,
color = color)
sample.add_layer(material, thickness_m = data[THICKNESS].iloc[i] / 1e6) # thickness is in micrometer
# creating dummy materials to match template
dummy_material = Material.from_formula('H', color = None, density_kg_per_m3 = MIN_DENSITY)
for i in range(TEMPLATE_NUM_REGIONS - len(data)):
sample.add_layer(dummy_material, thickness_m = MIN_THICKNESS)
return sample
def test_convert_geometry(self):
self.ops.geometry = [Substrate(Material.pure(29)),
Inclusion(Material.pure(29), Material.pure(30), 10e-6)]
opss = self.converter.convert(self.ops)
self.assertEqual(1, len(opss))
def testhorizontallayers5(self):
sample = HorizontalLayerSample(Material.pure(39))
sample.add_layer(Material.pure(40), 20e-9)
sample.add_layer(Material.pure(41), 20e-9)
sample.add_layer(Material.pure(42), 20e-9)
sample.add_layer(Material.pure(44), 20e-9)
self._run_and_test(sample)
def testconvert_parse(self):
handler = KRatioAnalysisHDF5Handler()
detector = self.create_basic_photondetector()
standard_materials = {29: Material.from_formula('CuZn'),
28: Material.from_formula('NiAl')}
analysis = KRatioAnalysis(detector, standard_materials)
analysis2 = self.convert_parse_hdf5handler(handler, analysis)
self.assertEqual(analysis2, analysis)
async def test_exporter_verticallayers_couple(
event_loop, exporter, options, tmp_path, dry_run
):
mat1 = Material("Mat1", {79: 0.5, 47: 0.5}, 2.0)
mat2 = Material("Mat2", {29: 0.5, 30: 0.5}, 3.0)
options.sample = VerticalLayerSample(mat1, mat2)
await exporter.export(options, tmp_path, dry_run=dry_run)
_test_export(tmp_path, 2, 2, dry_run)
def test__eq__(self):
m2 = Material('Pure Cu', {29: 1.0}, 8960.0)
self.assertEqual(m2, self.m)
m2 = Material('Pure Cu', {29: 1.0}, 8961.0)
self.assertNotEqual(m2, self.m)
m2 = Material('Pure Cu', {29: 0.5, 30: 0.5}, 8960.0)
self.assertNotEqual(m2, self.m)
def test_material_getparameters_validate(parameter_types, error_count):
material = Material("TiCrCu", {22: 0.2, 24: 0.2, 29: 0.6})
parameters = material.get_parameters(lambda options: material)
# Set parameter types
for parameter, parameter_type in zip(parameters, parameter_types):
parameter.type_ = parameter_type
errors = parameters[0].validate(None)
assert len(errors) == error_count
async def test_exporter_horizontallayers(
event_loop, exporter, options, tmp_path, dry_run
):
mat1 = Material("Mat1", {79: 0.5, 47: 0.5}, 2.0)
mat2 = Material("Mat2", {29: 0.5, 30: 0.5}, 3.0)
options.sample = HorizontalLayerSample(mat1)
options.sample.add_layer(mat2, 10e-9)
await exporter.export(options, tmp_path, dry_run=dry_run)
_test_export(tmp_path, 2, 2, dry_run)
def setUp(self):
unittest.TestCase.setUp(self)
self.h = SubstrateXMLHandler()
self.obj = Substrate([Material.pure(29), Material.pure(30)], 1.1, 2.2)
etree.register_namespace('mc', 'http://pymontecarlo.sf.net')
source = BytesIO(b'<mc:substrate xmlns:mc="http://pymontecarlo.sf.net" rotation="2.2" tilt="1.1"><materials><mc:material _index="1" density="8960.0" name="Copper"><composition><element weightFraction="1.0" z="29" /></composition></mc:material><mc:material _index="2" density="7140.0" name="Zinc"><composition><element weightFraction="1.0" z="30" /></composition></mc:material></materials><body material="1,2" /></mc:substrate>')
self.element = etree.parse(source).getroot()
def testbuild(self):
b = LayeredSampleBuilderMock()
b.add_layer(Material.pure(29), 10)
b.add_layer(Material.pure(30), 20)
samples = b.build()
self.assertEqual(1, len(samples))
sample = samples[0]
self.assertEqual(2, len(sample.layers))
def testverticallayers10(self):
sample = VerticalLayerSample(Material.pure(39), Material.pure(40))
sample.add_layer(Material.pure(41), 20e-9)
sample.add_layer(Material.pure(42), 20e-9)
sample.add_layer(Material.pure(44), 20e-9)
sample.add_layer(Material.pure(45), 20e-9)
sample.add_layer(Material.pure(46), 20e-9)
sample.add_layer(Material.pure(47), 20e-9)
sample.add_layer(Material.pure(48), 20e-9)
sample.add_layer(Material.pure(49), 20e-9)
self._run_and_test(sample)
def test_layeredsamplebuilderbase_twomaterials(layeredbuilder):
layerbuilder = layeredbuilder.add_layer(Material.pure(29), 10)
layerbuilder.add_material(Material.pure(30))
samples = layeredbuilder.build()
assert len(layeredbuilder) == 2
assert len(samples) == 2
sample = samples[0]
assert len(sample.layers) == 1
assert sample.layers[0].thickness_m == pytest.approx(10.0, abs=1e-4)
def testset_color_set(self):
Material.set_color_set(['#00FF00', '#0000FF'])
m = Material.pure(13)
self.assertEqual('#00FF00', m.color)
m = Material.pure(14)
self.assertEqual('#0000FF', m.color)
m = Material.pure(15)
self.assertEqual('#00FF00', m.color)
def testbuild2(self):
b = LayeredSampleBuilderMock()
bl = b.add_layer(Material.pure(29), 10)
bl.add_material(Material.pure(30))
samples = b.build()
self.assertEqual(2, len(samples))
sample = samples[0]
self.assertEqual(1, len(sample.layers))
self.assertAlmostEqual(10, sample.layers[0].thickness_m, 4)
def test_layeredsamplebuilderbase(layeredbuilder):
layeredbuilder = LayeredSampleBuilderMock()
layeredbuilder.add_layer(Material.pure(29), 10)
layeredbuilder.add_layer(Material.pure(30), 20)
samples = layeredbuilder.build()
assert len(layeredbuilder) == 1
assert len(samples) == 1
sample = samples[0]
assert len(sample.layers) == 2
def test_material_pure_widget(qtbot, material_pure_widget):
button = material_pure_widget.wdg_periodic_table._group.button(13)
qtbot.mouseClick(button, QtCore.Qt.LeftButton)
button = material_pure_widget.wdg_periodic_table._group.button(29)
qtbot.mouseClick(button, QtCore.Qt.LeftButton)
materials = material_pure_widget.materials()
assert len(materials) == 2
assert Material.pure(13) in materials
assert Material.pure(29) in materials
def generate_end_materials(elements_data, colors, density_start = None, density_end = None):
material_start = Material(
name = 'substrate_start',
composition = to_weight_fraction(dict(elements_data.iloc[0])), # create the first region
density_kg_per_m3 = density_start,
color = colors[0] if colors else None)
material_end = Material(
name = 'substrate_end',
composition = to_weight_fraction(dict(elements_data.iloc[-1])), # create the last region
density_kg_per_m3 = density_end,
color = colors[-1] if colors else None)
return material_start, material_end
def setUp(self):
TestCase.setUp(self)
self.g1 = VerticalLayers(Material.pure(29), Material.pure(30))
self.g1.add_layer(Material.pure(31), 500.0)
self.g2 = VerticalLayers(Material.pure(29), Material.pure(30))
self.g2.add_layer(Material.pure(29), 100.0)
self.g2.add_layer(Material.pure(32), 200.0)
self.g3 = VerticalLayers(Material.pure(29), Material.pure(30))
self.g3.add_layer(Material.pure(31), 500.0)
self.g3.depth_m = 400.0
def testexport_multilayers2(self):
# Options
mat1 = Material('Mat1', {79: 0.5, 47: 0.5}, 2.0)
mat2 = Material('Mat2', {29: 0.5, 30: 0.5}, 3.0)
mat3 = Material('Mat3', {13: 0.5, 14: 0.5}, 4.0)
sample = HorizontalLayerSample()
sample.add_layer(mat1, 15e-9)
sample.add_layer(mat2, 25e-9)
sample.add_layer(mat3, 55e-9)
self.options.sample = sample
# Export
self.e.export(self.options, self.tmpdir)
# Test
filepaths = glob.glob(os.path.join(self.tmpdir, '*.sim'))
self.assertEqual(1, len(filepaths))
casfile = File()
casfile.readFromFilepath(filepaths[0])
simdata = casfile.getOptionSimulationData()
regionops = simdata.getRegionOptions()
self.assertEqual(3, regionops.getNumberRegions())
region = regionops.getRegion(0)
elements = list(map(operator.attrgetter('Z'), region.getElements()))
self.assertAlmostEqual(mat1.density_kg_per_m3 / 1000.0, region.Rho, 4)
self.assertEqual('Mat1', region.Name)
self.assertEqual(2, len(elements))
self.assertTrue(79 in elements)
self.assertTrue(47 in elements)
region = regionops.getRegion(1)
elements = list(map(operator.attrgetter('Z'), region.getElements()))
self.assertAlmostEqual(mat2.density_kg_per_m3 / 1000.0, region.Rho, 4)
self.assertEqual('Mat2', region.Name)
self.assertEqual(2, len(elements))
self.assertTrue(29 in elements)
self.assertTrue(30 in elements)
region = regionops.getRegion(2)
elements = list(map(operator.attrgetter('Z'), region.getElements()))
self.assertAlmostEqual(mat3.density_kg_per_m3 / 1000.0, region.Rho, 4)
self.assertEqual('Mat3', region.Name)
self.assertEqual(2, len(elements))
self.assertTrue(13 in elements)
self.assertTrue(14 in elements)
def test_material_getparameters_parametertype(parameter_types,
expected_composition):
material = Material("TiCrCu", {22: 0.2, 24: 0.2, 29: 0.6})
parameters = material.get_parameters(lambda options: material)
# Set parameter types
for parameter, parameter_type in zip(parameters, parameter_types):
parameter.type_ = parameter_type
# Set titanium concentration
parameters[0].set_value(None, 0.5)
# Test
for z, expected_wf in expected_composition.items():
assert material.composition[z] == pytest.approx(expected_wf, abs=1e-6)
def create_homogeneous_sample(data, density_start = None, density_end = None):
'''
Function to create a list of substrate samples for Xray signal reference
input: dataframe of atomic fractions at various positions
output: list[Substrate]
'''
elements_data = get_elements_data(data)
colors = generate_colors(steps = len(data) - 1)
densities = generate_densities(elements_data, density_start, density_end)
# 1. Creating materials at both ends
material_start, material_end = generate_end_materials(elements_data, colors, density_start, density_end)
materials = [material_start, material_end]
# 2. Iterate through all regions, create the material representations
for i in range(1, len(data) - 1):
density = densities[i]
color = colors[i]
material = Material(
name = f'region_{i}',
composition = to_weight_fraction(dict(elements_data.iloc[i])),
density_kg_per_m3 = density,
color = color)
materials.append(material)
# 3. Creating substrate sample from the materials
substrate_list = [SubstrateSample(mat) for mat in materials]
return substrate_list
def __init__(self, tilt, rotation):
_Geometry.__init__(self, tilt, rotation)
mat = Material.pure(29)
self.bodies = [_Body(self, mat),
_Body(self, VACUUM),
_Body(self, mat)]
def testexport_spectrum(self):
# Create options
mat = Material({
79: 0.5,
47: 0.5
},
'Mat1',
absorption_energy_eV={ELECTRON: 123.0})
ops = Options()
ops.beam.energy_eV = 1234
ops.beam.diameter_m = 25e-9
ops.geometry.body.material = mat
ops.limits.add(ShowersLimit(5678))
ops.detectors['spectrum'] = \
PhotonSpectrumDetector((radians(30), radians(40)), (0, radians(360.0)),
500, (0, 1234))
# Export to WinX-Ray options
wxrops = self.e.export_wxroptions(ops)
# Test
self.assertTrue(wxrops.isXrayCompute())
self.assertTrue(wxrops.isXrayComputeCharacteristic())
self.assertAlmostEqual(35.0, wxrops.getTOA_deg(), 4)
self.assertAlmostEqual(55, wxrops.getAngleThetaDetector_deg(), 4)
self.assertAlmostEqual(180.0, wxrops.getAnglePhiDetector_deg(), 4)
self.assertEqual(EvPerChannel.TYPE_5, wxrops.getTypeEVChannel())
self.assertEqual(246, wxrops.getNumberChannel())
def pure(cls, z, absorption_energy_eV=None, elastic_scattering=(0.0, 0.0),
cutoff_energy_inelastic_eV=50.0, cutoff_energy_bremsstrahlung_eV=50.0,
interaction_forcings=None, maximum_step_length_m=1e20):
mat = _Material.pure(z, absorption_energy_eV)
return cls(mat.composition, mat.name, mat.density_kg_m3, mat.absorption_energy_eV,
elastic_scattering, cutoff_energy_inelastic_eV, cutoff_energy_bremsstrahlung_eV,
interaction_forcings, maximum_step_length_m)
def estimated_builder(builder):
program_mock_added = False
if not builder.programs:
builder.add_program(ProgramMock())
program_mock_added = True
beam_mock_added = False
if not builder.beams:
builder.add_beam(PencilBeam(10e3))
beam_mock_added = True
sample_mock_added = False
if not builder.samples:
builder.add_sample(SubstrateSample(Material.pure(26)))
sample_mock_added = True
try:
yield builder
finally:
if program_mock_added:
builder.programs.clear()
if beam_mock_added:
builder.beams.clear()
if sample_mock_added:
builder.samples.clear()
def simulation():
program = ProgramMock()
beam = GaussianBeam(15e3, 10e-9)
sample = SubstrateSample(Material.pure(29))
detector = PhotonDetector("xray", math.radians(40.0))
analyses = [PhotonIntensityAnalysis(detector)]
tags = ["basic", "test"]
options = Options(program, beam, sample, analyses, tags)
results = []
analysis = PhotonIntensityAnalysis(detector)
builder = EmittedPhotonIntensityResultBuilder(analysis)
builder.add_intensity((29, "Ka1"), 1.0, 0.1)
builder.add_intensity((29, "Ka2"), 2.0, 0.2)
builder.add_intensity((29, "Kb1"), 4.0, 0.5)
builder.add_intensity((29, "Kb3"), 5.0, 0.7)
builder.add_intensity((29, "Kb5I"), 1.0, 0.1)
builder.add_intensity((29, "Kb5II"), 0.5, 0.1)
builder.add_intensity((29, "Ll"), 3.0, 0.1)
results.append(builder.build())
analysis = KRatioAnalysis(detector)
builder = KRatioResultBuilder(analysis)
builder.add_kratio((29, "Ka1"), 1.0, 1.0)
builder.add_kratio((29, "Ka2"), 2.0, 1.0)
builder.add_kratio((29, "Kb1"), 0.5, 1.0)
builder.add_kratio((29, "Kb3"), 1.5, 1.0)
builder.add_kratio((29, "Kb5I"), 1.0, 1.0)
builder.add_kratio((29, "Kb5II"), 0.5, 1.0)
builder.add_kratio((29, "Ll"), 2.0, 1.0)
results.append(builder.build())
return Simulation(options, results)
def test_substratesample_getparameters(sample):
parameters = sample.get_parameters(lambda options: sample)
assert len(parameters) == 1
sample.material = Material.from_formula("CaSiO3")
parameters = sample.get_parameters(lambda options: sample)
assert len(parameters) == 4
def test_lazylowestenergyxrayline(options, z, beam_energy_eV,
minimum_energy_eV, expected):
options.beam.energy_eV = beam_energy_eV
options.sample.material = Material.pure(z)
assert LazyLowestEnergyXrayLine(minimum_energy_eV).apply(
None, options) == expected
def testvalidate_analysis_kratio(self):
detector = PhotonDetector('det', 1.1, 2.2)
analysis = KRatioAnalysis(detector)
analysis.add_standard_material(13, Material.pure(13))
analysis2 = self.v.validate_analysis(analysis, self.options)
self.assertEqual(analysis2, analysis)
self.assertIsNot(analysis2, analysis)
def testcalculate_composition(self):
# Wildcard
composition = Material.calculate_composition({29: 0.7, 30: '?'})
self.assertIn(29, composition)
self.assertAlmostEqual(0.7, composition[29], 4)
self.assertIn(30, composition)
self.assertAlmostEqual(0.3, composition[30], 4)
# Multiple wildcards
composition = Material.calculate_composition({29: '?', 30: '?'})
self.assertIn(29, composition)
self.assertAlmostEqual(0.5, composition[29], 4)
self.assertIn(30, composition)
self.assertAlmostEqual(0.5, composition[30], 4)
def testvalidate_material_exception(self):
material = Material(' ', {120: 0.5}, -1.0, 'blah')
self.assertRaises(ValidationError, self.v.validate_material, material,
self.options)
errors = set()
self.v._validate_material(material, self.options, errors)
self.assertEqual(5, len(errors))
def get_standard_material(self, z):
if z in self.standard_materials:
return self.standard_materials[z]
if z in self.DEFAULT_NONPURE_STANDARD_MATERIALS:
return self.DEFAULT_NONPURE_STANDARD_MATERIALS[z]
return Material.pure(z)
def options():
program = Casino2Program(number_trajectories=50)
beam = GaussianBeam(15e3, 10e-9)
sample = SubstrateSample(Material.pure(29))
detector = PhotonDetector("xray", math.radians(40.0))
analyses = [PhotonIntensityAnalysis(detector)]
tags = ["basic", "test"]
return Options(program, beam, sample, analyses, tags)
def materials(self):
try:
formula = self.field_formula.formula()
density_kg_per_m3 = self.field_density.density_kg_per_m3()
color = self.field_color.color()
return (Material.from_formula(formula, density_kg_per_m3, color), )
except:
return ()
def options():
program = PenepmaProgram(number_trajectories=100)
program.exporter.dump_interval_s = 2
beam = CylindricalBeam(15e3, 10e-9)
sample = SubstrateSample(Material.pure(29))
detector = PhotonDetector("xray", math.radians(40.0))
analyses = [PhotonIntensityAnalysis(detector)]
tags = ["basic", "test"]
return Options(program, beam, sample, analyses, tags)
def setUp(self):
unittest.TestCase.setUp(self)
self.h = SphereXMLHandler()
self.obj = Sphere(Material.pure(29), 123.456, 1.1, 2.2)
etree.register_namespace('mc', 'http://pymontecarlo.sf.net')
source = BytesIO(b'<mc:sphere xmlns:mc="http://pymontecarlo.sf.net" rotation="2.2" tilt="1.1"><materials><mc:material _index="1" density="8960.0" name="Copper"><composition><element weightFraction="1.0" z="29" /></composition></mc:material></materials><body diameter="123.456" material="1" /></mc:sphere>')
self.element = etree.parse(source).getroot()
def setUp(self):
unittest.TestCase.setUp(self)
self.ops = Options()
self.ops.beam = PencilBeam(15e3)
self.ops.geometry = Substrate(Material.pure(29))
self.ops.detectors['det1'] = TimeDetector()
self.ops.limits.add(ShowersLimit(5678))
self.ops.models.add(ELASTIC_CROSS_SECTION.rutherford)
self.ops.models.add(MASS_ABSORPTION_COEFFICIENT.henke1993)
self.converter = MockConverter()
def setUp(self):
unittest.TestCase.setUp(self)
self.h = HorizontalLayersXMLHandler()
self.obj1 = HorizontalLayers(Material.pure(29), None, 1.1, 2.2)
self.obj1.add_layer(Material.pure(30), 123.456)
self.obj1.add_layer(Material.pure(31), 456.789)
self.obj2 = HorizontalLayers()
self.obj2.add_layer(Material.pure(30), 123.456)
self.obj2.add_layer(VACUUM, 50.0)
self.obj2.add_layer(Material.pure(31), 456.789)
etree.register_namespace('mc', 'http://pymontecarlo.sf.net')
source = BytesIO(b'<mc:horizontalLayers xmlns:mc="http://pymontecarlo.sf.net" rotation="2.2" tilt="1.1"><materials><mc:material _index="1" density="7140.0" name="Zinc"><composition><element weightFraction="1.0" z="30" /></composition></mc:material><mc:material _index="2" density="5910.0" name="Gallium"><composition><element weightFraction="1.0" z="31" /></composition></mc:material><mc:material _index="3" density="8960.0" name="Copper"><composition><element weightFraction="1.0" z="29" /></composition></mc:material></materials><substrate material="3" /><layers><layer material="1" thickness="123.456" /><layer material="2" thickness="456.789" /></layers></mc:horizontalLayers>')
self.element1 = etree.parse(source).getroot()
etree.register_namespace('mc', 'http://pymontecarlo.sf.net')
source = BytesIO(b'<mc:horizontalLayers xmlns:mc="http://pymontecarlo.sf.net" rotation="0.0" tilt="0.0"><materials><mc:material _index="1" density="7140.0" name="Zinc"><composition><element weightFraction="1.0" z="30" /></composition></mc:material><mc:material _index="2" density="5910.0" name="Gallium"><composition><element weightFraction="1.0" z="31" /></composition></mc:material></materials><layers><layer material="1" thickness="123.456" /><layer material="0" thickness="50.0" /><layer material="2" thickness="456.789" /></layers></mc:horizontalLayers>')
self.element2 = etree.parse(source).getroot()
def setUp(self):
TestCase.setUp(self)
self.outputdir = tempfile.mkdtemp()
self.workdir = tempfile.mkdtemp()
ops = Options('test')
ops.beam.energy_keV = 10
ops.geometry.body.material = Material.pure(29)
ops.detectors['fraction'] = ElectronFractionDetector()
ops.limits.add(ShowersLimit(1))
self.ops = Converter().convert(ops)[0]
self.worker = Worker(program)
def setUp(self):
TestCase.setUp(self)
self.g1 = HorizontalLayers(Material.pure(29))
self.g2 = HorizontalLayers(None) # No substrate
self.g3 = HorizontalLayers(Material.pure(29)) # Empty layer
self.g1.add_layer(Material.pure(30), 123.456)
self.g1.add_layer(Material.pure(31), 456.789)
self.g2.add_layer(Material.pure(30), 123.456)
self.g2.add_layer(Material.pure(31), 456.789)
self.g3.add_layer(Material.pure(30), 123.456)
self.g3.add_layer(Material.pure(31), 456.789)
self.g3.add_layer(VACUUM, 456.123)
def testcomposition_from_formula(self):
weightFractionAl = 0.21358626371988801
weightFractionNa = 0.27298103136883051
weightFractionB = 0.51343270491128157
comp = Material.composition_from_formula('Al2Na3B12')
self.assertAlmostEqual(weightFractionAl, comp[13], 4)
self.assertAlmostEqual(weightFractionNa, comp[11], 4)
self.assertAlmostEqual(weightFractionB, comp[5], 4)
comp = Material.composition_from_formula('Al 2 Na 3 B 12')
self.assertAlmostEqual(weightFractionAl, comp[13], 4)
self.assertAlmostEqual(weightFractionNa, comp[11], 4)
self.assertAlmostEqual(weightFractionB, comp[5], 4)
comp = Material.composition_from_formula('Al2 Na3 B12')
self.assertAlmostEqual(weightFractionAl, comp[13], 4)
self.assertAlmostEqual(weightFractionNa, comp[11], 4)
self.assertAlmostEqual(weightFractionB, comp[5], 4)
self.assertRaises(ValueError, Material.composition_from_formula, 'Aq2 Na3 B12')
comp = Material.composition_from_formula('Al2')
self.assertAlmostEqual(1.0, comp[13], 4)
def testpure(self):
m = Material.pure(29)
self.assertEqual('Copper', str(m))
self.assertIn(29, m.composition)
self.assertAlmostEqual(1.0, m.composition[29], 4)
self.assertIn(29, self.m.composition_atomic)
self.assertAlmostEqual(1.0, self.m.composition_atomic[29], 4)
self.assertAlmostEqual(8.96, m.density_kg_m3 / 1000.0, 4)
self.assertAlmostEqual(8.96, m.density_g_cm3, 4)
self.assertAlmostEqual(50, m.absorption_energy_eV[ELECTRON], 4)
self.assertAlmostEqual(50, m.absorption_energy_eV[PHOTON], 4)
def test_convert_geometry_substrate(self):
# Base options
ops = Options(name="Test")
mat = Material.pure(29, absorption_energy_eV={POSITRON: 63.4})
ops.geometry = Substrate(mat)
ops.limits.add(TimeLimit(100))
# Convert
self.converter._convert_geometry(ops)
# Test
self.assertEqual('Copper', str(ops.geometry.body.material))
for material in ops.geometry.get_materials():
self.assertAlmostEqual(0.1, material.elastic_scattering[0], 4)
self.assertAlmostEqual(0.2, material.elastic_scattering[1], 4)
self.assertAlmostEqual(51.2, material.cutoff_energy_inelastic_eV, 4)
self.assertAlmostEqual(53.4, material.cutoff_energy_bremsstrahlung_eV, 4)
self.assertAlmostEqual(63.4, material.absorption_energy_eV[POSITRON], 4)
self.assertAlmostEqual(1e20, material.maximum_step_length_m, 4)
def setUp(self):
unittest.TestCase.setUp(self)
self.h = VerticalLayersXMLHandler()
self.obj1 = VerticalLayers(Material.pure(29), Material.pure(30), None,
tilt_rad=1.1, rotation_rad=2.2)
self.obj1.add_layer(Material.pure(31), 500.0)
self.obj2 = VerticalLayers(Material.pure(29), Material.pure(30))
self.obj2.add_layer(Material.pure(31), 500.0)
self.obj2.depth_m = 400.0
etree.register_namespace('mc', 'http://pymontecarlo.sf.net')
source = BytesIO(b'<mc:verticalLayers xmlns:mc="http://pymontecarlo.sf.net" depth="inf" rotation="2.2" tilt="1.1"><materials><mc:material _index="1" density="5910.0" name="Gallium"><composition><element weightFraction="1.0" z="31" /></composition></mc:material><mc:material _index="2" density="8960.0" name="Copper"><composition><element weightFraction="1.0" z="29" /></composition></mc:material><mc:material _index="3" density="7140.0" name="Zinc"><composition><element weightFraction="1.0" z="30" /></composition></mc:material></materials><leftSubstrate material="2" /><rightSubstrate material="3" /><layers><layer material="1" thickness="500.0" /></layers></mc:verticalLayers>')
self.element1 = etree.parse(source).getroot()
etree.register_namespace('mc', 'http://pymontecarlo.sf.net')
source = BytesIO(b'<mc:verticalLayers xmlns:mc="http://pymontecarlo.sf.net" depth="400.0" rotation="0.0" tilt="0.0"><materials><mc:material _index="1" density="8960.0" name="Copper"><composition><element weightFraction="1.0" z="29" /></composition></mc:material><mc:material _index="2" density="5910.0" name="Gallium"><composition><element weightFraction="1.0" z="31" /></composition></mc:material><mc:material _index="3" density="7140.0" name="Zinc"><composition><element weightFraction="1.0" z="30" /></composition></mc:material></materials><leftSubstrate material="1" /><rightSubstrate material="3" /><layers><layer material="2" thickness="500.0" /></layers></mc:verticalLayers>')
self.element2 = etree.parse(source).getroot()
def setUp(self):
TestCase.setUp(self)
self.g = Inclusion(Material.pure(29), Material.pure(30), 123.456)
def testmaterial(self):
self.g.body.material = [Material.pure(14), Material.pure(15)]
self.assertEqual(2, len(self.g.body.material))
def setUp(self):
TestCase.setUp(self)
self.g = Substrate(Material.pure(29))
def setUp(self):
TestCase.setUp(self)
self.g = Sphere(Material.pure(29), 123.456)
def testexpand(self):
self.assertEqual(1, len(expand(self.g1)))
self.g1.add_layer(Material.pure(79), [1.0, 2.0])
self.assertEqual(2, len(expand(self.g1)))
def __init__(self, composition, name=None, density_kg_m3=None, absorption_energy_eV=None,
elastic_scattering=(0.0, 0.0),
cutoff_energy_inelastic_eV=50.0, cutoff_energy_bremsstrahlung_eV=50.0,
interaction_forcings=None, maximum_step_length_m=1e15, *args, **kwargs):
"""
Creates a new material.
:arg name: name of the material
:type name: :class:`str`
:arg composition: composition in weight fraction.
The composition is specified by a list of tuples.
The first element of each tuple can either be the atomic number or
the symbol of the element.
It will automatically be converted to the atomic number.
The second is the weight fraction between ]0.0, 1.0] or ``?``
indicating that the weight fraction is unknown and shall be
automatically calculated to make the total weight fraction equal
to 1.0.
:type composition: :class:`list`
:arg density_kg_m3: material's density in kg/m3.
If the density is ``None`` or less than 0 (default), it will be
automatically calculated based on the density of the elements and
their weight fraction.
:type density_kg_m3: :class:`float`
:arg elastic_scattering: elastic scattering coefficients.
They can either be specified as a :class:`tuple`: ``(C1, C2)`` or
as a single :class:`float` value, where ``C1=C2``.
The value of C1 or C2 must be between 0.0 and 0.2 inclusively.
:type elastic_scattering: :class:`tuple` or :class:`float`
:arg cutoff_energy_inelastic_eV: cutoff energy for inelastic collisions
(in eV).
:arg cutoff_energy_bremsstrahlung_eV: cutoff energy for Bremsstrahlung
emission (in eV).
:arg interaction_forcings: interaction forcing(s)
:arg maximum_step_length_m: maximum length of an electron trajectory
"""
_Material.__init__(self, composition, name, density_kg_m3, absorption_energy_eV)
elastic_scattering = ElasticScattering(*elastic_scattering)
if elastic_scattering.c1 < 0.0 or elastic_scattering.c1 > 0.2:
raise ValueError('C1 must be between [0.0, 0.2]')
if elastic_scattering.c2 < 0.0 or elastic_scattering.c2 > 0.2:
raise ValueError('C2 must be between [0.0, 0.2]')
self._elastic_scattering = elastic_scattering
if cutoff_energy_inelastic_eV < 0.0:
raise ValueError('Cutoff energy for inelastic collisions must be greater or equal to 0.0')
self._cutoff_energy_inelastic_eV = cutoff_energy_inelastic_eV
if cutoff_energy_inelastic_eV < 0.0:
raise ValueError('Cutoff energy for Bremsstrahlung emission must be greater or equal to 0.0')
self._cutoff_energy_bremsstrahlung_eV = cutoff_energy_bremsstrahlung_eV
if interaction_forcings is None:
interaction_forcings = set()
self._interaction_forcings = frozenset(interaction_forcings)
if maximum_step_length_m < 0.0:
raise ValueError("Length must be greater than 0.0")
if maximum_step_length_m > 1e20:
warnings.warn('Maximum step length set to maximum value: 1e20')
maximum_step_length_m = 1e20
self._maximum_step_length_m = maximum_step_length_m
def testphoton_range(self):
material = Material.pure(29)
transition = Transition(29, siegbahn='Ka1')
self.assertAlmostEqual(8.4064e-7, photon_range(20e3, material, transition), 10)