def testexport_multilayers1(self):
# Create options
mat1 = Material({79: 0.5, 47: 0.5}, "Mat1", absorption_energy_eV={ELECTRON: 123.0})
mat2 = Material({29: 0.5, 30: 0.5}, "Mat2", absorption_energy_eV={ELECTRON: 89.0})
mat3 = Material({13: 0.5, 14: 0.5}, "Mat3", absorption_energy_eV={ELECTRON: 89.0})
ops = Options()
ops.beam.energy_eV = 1234
ops.beam.diameter_m = 25e-9
ops.beam.origin_m = (100e-9, 0, 1)
ops.geometry = HorizontalLayers(mat1)
ops.geometry.add_layer(mat2, 25e-9)
ops.geometry.add_layer(mat3, 55e-9)
ops.limits.add(ShowersLimit(5678))
# Export to CAS
casfile = self.e.export_cas(ops)
# Test
simdata = casfile.getOptionSimulationData()
simops = simdata.getSimulationOptions()
regionops = simdata.getRegionOptions()
self.assertAlmostEqual(1.234, simops.getIncidentEnergy_keV(0), 4)
self.assertAlmostEqual(34.93392125, simops.Beam_Diameter, 4) # FWHM
self.assertAlmostEqual(100.0, simops._positionStart_nm, 4)
self.assertEqual(3, regionops.getNumberRegions())
region = regionops.getRegion(0)
elements = list(map(attrgetter("Z"), region.getElements()))
self.assertAlmostEqual(mat2.density_kg_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(1)
elements = list(map(attrgetter("Z"), region.getElements()))
self.assertAlmostEqual(mat3.density_kg_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)
region = regionops.getRegion(2)
elements = list(map(attrgetter("Z"), region.getElements()))
self.assertAlmostEqual(mat1.density_kg_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)
self.assertAlmostEqual(0.089, simops.Eminimum, 3)
self.assertEqual(5678, simops.getNumberElectrons())
self.assertFalse(simops.FEmissionRX)
def testexport_inclusion(self):
# Create
mat1 = PenelopeMaterial({79: 0.5, 47: 0.5}, 'mat')
mat2 = PenelopeMaterial({29: 0.5, 30: 0.5}, 'mat')
ops = Options()
ops.geometry = Inclusion(mat1, mat2, 0.01)
ops.limits.add(TimeLimit(100))
self.c._convert_geometry(ops)
self.e.export_geometry(ops.geometry, self.tmpdir)
# Test
geofilepath = os.path.join(self.tmpdir, 'inclusion.geo')
repfilepath = os.path.join(self.tmpdir, 'geometry.rep')
nmat, nbody = pengeom.init(geofilepath, repfilepath)
self.assertEqual(2, nmat)
self.assertEqual(3, nbody)
matfilepath = os.path.join(self.tmpdir, 'mat1.mat')
self.assertTrue(os.path.exists(matfilepath))
matfilepath = os.path.join(self.tmpdir, 'mat2.mat')
self.assertTrue(os.path.exists(matfilepath))
def testexport_vertical_layers(self):
# Create
mat1 = PenelopeMaterial({79: 0.5, 47: 0.5}, 'mat1')
mat2 = PenelopeMaterial({29: 0.5, 30: 0.5}, 'mat2')
mat3 = PenelopeMaterial({13: 0.5, 14: 0.5}, 'mat3')
ops = Options()
ops.beam.energy_eV = 1234
ops.beam.diameter_m = 25e-9
ops.beam.origin_m = (100e-9, 0, 1)
ops.geometry = VerticalLayers(mat1, mat2)
ops.geometry.add_layer(mat3, 5e-3)
ops.limits.add(TimeLimit(100))
self.c._convert_geometry(ops)
self.e.export_geometry(ops.geometry, self.tmpdir)
# Test
geofilepath = os.path.join(self.tmpdir, 'verticallayers.geo')
repfilepath = os.path.join(self.tmpdir, 'geometry.rep')
nmat, nbody = pengeom.init(geofilepath, repfilepath)
self.assertEqual(3, nmat)
self.assertEqual(4, nbody)
matfilepath = os.path.join(self.tmpdir, 'mat1.mat')
self.assertTrue(os.path.exists(matfilepath))
matfilepath = os.path.join(self.tmpdir, 'mat2.mat')
self.assertTrue(os.path.exists(matfilepath))
matfilepath = os.path.join(self.tmpdir, 'mat3.mat')
self.assertTrue(os.path.exists(matfilepath))
def testexport_inclusion(self):
# Create
mat1 = PenelopeMaterial({79: 0.5, 47: 0.5}, "mat")
mat2 = PenelopeMaterial({29: 0.5, 30: 0.5}, "mat")
ops = Options()
ops.geometry = Inclusion(mat1, mat2, 0.01)
ops.limits.add(TimeLimit(100))
self.c._convert_geometry(ops)
self.e.export_geometry(ops.geometry, self.tmpdir)
# Test
geofilepath = os.path.join(self.tmpdir, "inclusion.geo")
repfilepath = os.path.join(self.tmpdir, "geometry.rep")
nmat, nbody = pengeom.init(geofilepath, repfilepath)
self.assertEqual(2, nmat)
self.assertEqual(3, nbody)
matfilepath = os.path.join(self.tmpdir, "mat1.mat")
self.assertTrue(os.path.exists(matfilepath))
matfilepath = os.path.join(self.tmpdir, "mat2.mat")
self.assertTrue(os.path.exists(matfilepath))
def testexport_vertical_layers(self):
# Create
mat1 = PenelopeMaterial({79: 0.5, 47: 0.5}, "mat1")
mat2 = PenelopeMaterial({29: 0.5, 30: 0.5}, "mat2")
mat3 = PenelopeMaterial({13: 0.5, 14: 0.5}, "mat3")
ops = Options()
ops.beam.energy_eV = 1234
ops.beam.diameter_m = 25e-9
ops.beam.origin_m = (100e-9, 0, 1)
ops.geometry = VerticalLayers(mat1, mat2)
ops.geometry.add_layer(mat3, 5e-3)
ops.limits.add(TimeLimit(100))
self.c._convert_geometry(ops)
self.e.export_geometry(ops.geometry, self.tmpdir)
# Test
geofilepath = os.path.join(self.tmpdir, "verticallayers.geo")
repfilepath = os.path.join(self.tmpdir, "geometry.rep")
nmat, nbody = pengeom.init(geofilepath, repfilepath)
self.assertEqual(3, nmat)
self.assertEqual(4, nbody)
matfilepath = os.path.join(self.tmpdir, "mat1.mat")
self.assertTrue(os.path.exists(matfilepath))
matfilepath = os.path.join(self.tmpdir, "mat2.mat")
self.assertTrue(os.path.exists(matfilepath))
matfilepath = os.path.join(self.tmpdir, "mat3.mat")
self.assertTrue(os.path.exists(matfilepath))
def _run(self, element):
self._update_status(0.1, "Check version")
if self.is_cancelled():
return
version = self._read_version(element)
if version != VERSION:
raise ValueError("Incompatible version: %s != %s" % (version, VERSION))
self._update_status(0.13, "Reading name")
if self.is_cancelled():
return
name = self._read_name(element)
options = Options(name)
self._update_status(0.16, "Reading UUID")
if self.is_cancelled():
return
options._uuid = self._read_uuid(element)
self._update_status(0.2, "Reading programs")
if self.is_cancelled():
return
options.programs.update(self._read_programs(element))
self._update_status(0.3, "Reading beams")
if self.is_cancelled():
return
options.beam = self._read_beams(element)
self._update_status(0.4, "Reading geometries")
if self.is_cancelled():
return
options.geometry = self._read_geometries(element)
self._update_status(0.6, "Reading detectors")
if self.is_cancelled():
return
options.detectors.update(self._read_detectors(element))
self._update_status(0.8, "Reading limits")
if self.is_cancelled():
return
options.limits.update(self._read_limits(element))
self._update_status(0.9, "Reading models")
if self.is_cancelled():
return
options.models.update(self._read_models(element))
return options
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 testexport_substrate(self):
# Create
mat1 = PenelopeMaterial({79: 0.5, 47: 0.5}, 'mat')
ops = Options()
ops.geometry = Substrate(mat1)
ops.limits.add(TimeLimit(100))
self.c._convert_geometry(ops)
self.e.export_geometry(ops.geometry, self.tmpdir)
# Test
geofilepath = os.path.join(self.tmpdir, 'substrate.geo')
repfilepath = os.path.join(self.tmpdir, 'geometry.rep')
nmat, nbody = pengeom.init(geofilepath, repfilepath)
self.assertEqual(1, nmat)
self.assertEqual(2, nbody)
matfilepath = os.path.join(self.tmpdir, 'mat1.mat')
self.assertTrue(os.path.exists(matfilepath))
def testexport_substrate(self):
# Create
mat1 = PenelopeMaterial({79: 0.5, 47: 0.5}, "mat")
ops = Options()
ops.geometry = Substrate(mat1)
ops.limits.add(TimeLimit(100))
self.c._convert_geometry(ops)
self.e.export_geometry(ops.geometry, self.tmpdir)
# Test
geofilepath = os.path.join(self.tmpdir, "substrate.geo")
repfilepath = os.path.join(self.tmpdir, "geometry.rep")
nmat, nbody = pengeom.init(geofilepath, repfilepath)
self.assertEqual(1, nmat)
self.assertEqual(2, nbody)
matfilepath = os.path.join(self.tmpdir, "mat1.mat")
self.assertTrue(os.path.exists(matfilepath))