def setUp(self):
super().setUp()
self.testdatadir = os.path.join(os.path.dirname(__file__), '..',
'testdata', 'pengeom')
self.geo = Geometry('Test Geometry')
surface1 = zplane(1e-8)
surface2 = zplane(-1e-1)
surface3 = cylinder(1.0)
surface4 = xplane(0.0)
self.mat1 = Material('copper', {29: 1.0}, 8.9)
self.module1 = Module(self.mat1)
self.module1.add_surface(surface1, SIDEPOINTER_NEGATIVE)
self.module1.add_surface(surface2, SIDEPOINTER_POSITIVE)
self.module1.add_surface(surface3, SIDEPOINTER_NEGATIVE)
self.module1.add_surface(surface4, SIDEPOINTER_POSITIVE)
self.geo.add_module(self.module1)
self.mat2 = Material('zinc', {30: 1.0}, 7.14)
self.module2 = Module(self.mat2)
self.module2.add_surface(surface1, SIDEPOINTER_NEGATIVE)
self.module2.add_surface(surface2, SIDEPOINTER_POSITIVE)
self.module2.add_surface(surface3, SIDEPOINTER_NEGATIVE)
self.module2.add_module(self.module1)
self.geo.add_module(self.module2)
self.geo.tilt_deg = 45
def create_example1_disc():
# Create materials
material_cu = Material('Cu', {29: 1.0}, 8.9)
# Create geometry
module = Module(material_cu, 'Solid cylinder')
module.add_surface(zplane(0.0), SIDEPOINTER_POSITIVE)
module.add_surface(zplane(0.005), SIDEPOINTER_NEGATIVE)
module.add_surface(cylinder(1.0), SIDEPOINTER_NEGATIVE)
geometry = Geometry('A solid cylinder.')
geometry.add_module(module)
# Create input
input = PenmainInput()
input.TITLE.set('Point source and a homogeneous cylinder.')
input.SKPAR.set(1)
input.SENERG.set(40e3)
input.SPOSIT.set(0.0, 0.0, -0.0001)
input.SCONE.set(0.0, 0.0, 5.0)
input.materials.add(1, material_cu.filename, 1e3, 1e3, 1e3, 0.05, 0.05,
1e3, 1e3)
input.GEOMFN.set('disc.geo')
input.PARINP.add(1, 0.005)
input.PARINP.add(2, 0.01)
input.DSMAX.add(1, 1e-4)
input.IFORCE.add(1, 1, 4, 2000, 0.1, 2.0)
input.IFORCE.add(1, 1, 5, 200, 0.1, 2.0)
input.IBRSPL.add(1, 2)
input.IXRSPL.add(1, 2)
input.NBE.set(0, 0, 100)
input.NBANGL.set(45, 18)
detector = input.impact_detectors.add(0.0, 0.0, 100, 0, 2)
detector.IDBODY.add(1)
detector = input.energy_deposition_detectors.add(0, 0, 100)
detector.EDBODY.add(1)
input.GRIDZ.set(0, 0.005, 100)
input.GRIDR.set(0.01, 50)
input.RESUME.set('dump.dat')
input.DUMPTO.set('dump.dat')
input.DUMPP.set(60)
input.NSIMSH.set(2e9)
input.TIME.set(600)
return input
def _export_sample_inclusion(self, sample, options, erracc, geometry,
dsmaxs):
self._validate_sample_inclusion(sample, options, erracc)
# Surface
inclusion_diameter_m = apply_lazy(sample.inclusion_diameter_m, sample,
options)
surface_cylinder = cylinder(100.0) # 100 cm radius
surface_top = zplane(0.0) # z = 0
surface_bottom = zplane(-100.0) # z = -100 cm
surface_sphere = sphere(inclusion_diameter_m / 2.0 * 100.0)
# Inclusion module
inclusion_material = apply_lazy(sample.inclusion_material, sample,
options)
penmaterial = self._export_material(inclusion_material,
options,
erracc,
index=1)
module_inclusion = Module(penmaterial, "Inclusion")
module_inclusion.add_surface(surface_top, SidePointer.NEGATIVE)
module_inclusion.add_surface(surface_sphere, SidePointer.NEGATIVE)
dsmaxs[module_inclusion] = inclusion_diameter_m
# Substrate module
substrate_material = apply_lazy(sample.substrate_material, sample,
options)
penmaterial = self._export_material(substrate_material,
options,
erracc,
index=2)
module_substrate = Module(penmaterial, "Substrate")
module_substrate.add_surface(surface_cylinder, SidePointer.NEGATIVE)
module_substrate.add_surface(surface_top, SidePointer.NEGATIVE)
module_substrate.add_surface(surface_bottom, SidePointer.POSITIVE)
module_substrate.add_module(module_inclusion)
# Geometry
geometry.title = "Inclusion"
geometry.add_module(module_substrate)
geometry.add_module(module_inclusion)
geometry.tilt_rad = apply_lazy(sample.tilt_rad, sample, options)
geometry.rotation_rad = apply_lazy(sample.azimuth_rad, sample, options)
def _export_sample_substrate(self, sample, options, erracc, geometry,
dsmaxs):
self._validate_sample_substrate(sample, options, erracc)
# Geometry
surface_cylinder = cylinder(100) # 100 cm radius
surface_top = zplane(0.0) # z = 0
surface_bottom = zplane(-100) # z = -100 cm
material = apply_lazy(sample.material, sample, options)
penmaterial = self._export_material(material, options, erracc, index=1)
module = Module(penmaterial, "Substrate")
module.add_surface(surface_cylinder, SidePointer.NEGATIVE)
module.add_surface(surface_top, SidePointer.NEGATIVE)
module.add_surface(surface_bottom, SidePointer.POSITIVE)
geometry.title = "Substrate"
geometry.add_module(module)
geometry.tilt_rad = apply_lazy(sample.tilt_rad, sample, options)
geometry.rotation_rad = apply_lazy(sample.azimuth_rad, sample, options)
def create_epma2():
# Create geometry
surface_top = zplane(0.0)
surface_bottom = zplane(-0.1)
surface_cylinder = cylinder(1.0)
surface_divider = xplane(0.0)
module_right = Module(MATERIAL_CU, 'Right half of the sample')
module_right.add_surface(surface_top, SIDEPOINTER_NEGATIVE)
module_right.add_surface(surface_bottom, SIDEPOINTER_POSITIVE)
module_right.add_surface(surface_cylinder, SIDEPOINTER_NEGATIVE)
module_right.add_surface(surface_divider, SIDEPOINTER_POSITIVE)
module_left = Module(MATERIAL_FE, 'Left half of the sample')
module_left.add_surface(surface_top, SIDEPOINTER_NEGATIVE)
module_left.add_surface(surface_bottom, SIDEPOINTER_POSITIVE)
module_left.add_surface(surface_cylinder, SIDEPOINTER_NEGATIVE)
module_left.add_module(module_right)
geometry = Geometry('Cylindrical homogeneous foil')
geometry.add_module(module_right)
geometry.add_module(module_left)
index_lookup = geometry.indexify()
index_lookup[MATERIAL_CU] = 1
index_lookup[MATERIAL_FE] = 2
# Create input
input = PenepmaInput()
input.TITLE.set('A CU-Fe couple')
input.SENERG.set(15e3)
input.SPOSIT.set(2e-5, 0.0, 1.0)
input.SDIREC.set(180, 0.0)
input.SAPERT.set(0.0)
input.materials.add(index_lookup[MATERIAL_FE], MATERIAL_FE.filename, 1e3,
1e3, 1e3, 0.2, 0.2, 1e3, 1e3) # Note inversion
input.materials.add(index_lookup[MATERIAL_CU], MATERIAL_CU.filename, 1e3,
1e3, 1e3, 0.2, 0.2, 1e3, 1e3)
input.GEOMFN.set('epma2.geo')
input.DSMAX.add(index_lookup[module_right], 1e-4)
input.DSMAX.add(index_lookup[module_left], 1e-4)
input.IFORCE.add(index_lookup[module_right], 1, 4, -5, 0.9, 1.0)
input.IFORCE.add(index_lookup[module_right], 1, 5, -250, 0.9, 1.0)
input.IFORCE.add(index_lookup[module_right], 2, 2, 10, 1e-3, 1.0)
input.IFORCE.add(index_lookup[module_right], 2, 3, 10, 1e-3, 1.0)
input.IFORCE.add(index_lookup[module_left], 1, 4, -5, 0.9, 1.0)
input.IFORCE.add(index_lookup[module_left], 1, 5, -7, 0.9, 1.0)
input.IFORCE.add(index_lookup[module_left], 2, 2, 10, 1e-3, 1.0)
input.IFORCE.add(index_lookup[module_left], 2, 3, 10, 1e-3, 1.0)
input.IBRSPL.add(index_lookup[module_right], 2)
input.IBRSPL.add(index_lookup[module_left], 2)
input.IXRSPL.add(index_lookup[module_right], 2)
input.IXRSPL.add(index_lookup[module_left], 2)
input.NBE.set(0, 0, 300)
input.NBANGL.set(45, 30)
input.photon_detectors.add(0, 90, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(5, 15, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(15, 25, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(25, 35, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(35, 45, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(45, 55, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(55, 65, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(65, 75, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(75, 85, 0, 360, 0, 0.0, 0.0, 1000)
input.GRIDX.set(-1e-5, 5e-5, 60)
input.GRIDY.set(-3e-5, 3e-5, 60)
input.GRIDZ.set(-6e-5, 0.0, 60)
input.XRLINE.add(26010300)
input.XRLINE.add(29010300)
input.RESUME.set('dump2.dat')
input.DUMPTO.set('dump2.dat')
input.DUMPP.set(60)
input.RSEED.set(-10, 1)
input.REFLIN.set(26010300, 1, 1.5e-3)
input.NSIMSH.set(2e9)
input.TIME.set(2e9)
return input
def create_epma1():
# Create geometry
module = Module(MATERIAL_CU, 'Sample')
module.add_surface(zplane(0.0), SIDEPOINTER_NEGATIVE)
module.add_surface(zplane(-0.1), SIDEPOINTER_POSITIVE)
module.add_surface(cylinder(1.0), SIDEPOINTER_NEGATIVE)
geometry = Geometry('Cylindrical homogeneous foil')
geometry.add_module(module)
index_lookup = geometry.indexify()
# Create input
input = PenepmaInput()
input.TITLE.set('A Cu slab')
input.SENERG.set(15e3)
input.SPOSIT.set(0.0, 0.0, 1.0)
input.SDIREC.set(180, 0.0)
input.SAPERT.set(0.0)
input.materials.add(index_lookup[MATERIAL_CU], MATERIAL_CU.filename, 1e3,
1e3, 1e3, 0.2, 0.2, 1e3, 1e3)
input.GEOMFN.set('epma1.geo')
input.DSMAX.add(index_lookup[module], 1e-4)
input.IFORCE.add(index_lookup[module], 1, 4, -5, 0.9, 1.0)
input.IFORCE.add(index_lookup[module], 1, 5, -250, 0.9, 1.0)
input.IFORCE.add(index_lookup[module], 2, 2, 10, 1e-3, 1.0)
input.IFORCE.add(index_lookup[module], 2, 3, 10, 1e-3, 1.0)
input.IBRSPL.add(index_lookup[module], 2)
input.IXRSPL.add(index_lookup[module], 2)
input.NBE.set(0, 0, 300)
input.NBANGL.set(45, 30)
input.photon_detectors.add(0, 90, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(5, 15, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(15, 25, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(25, 35, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(35, 45, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(45, 55, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(55, 65, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(65, 75, 0, 360, 0, 0.0, 0.0, 1000)
input.photon_detectors.add(75, 85, 0, 360, 0, 0.0, 0.0, 1000)
input.GRIDX.set(-4e-5, 4e-5, 60)
input.GRIDY.set(-4e-5, 4e-5, 60)
input.GRIDZ.set(-6e-5, 0.0, 60)
input.XRLINE.set(29010300)
input.RESUME.set('dump1.dat')
input.DUMPTO.set('dump1.dat')
input.DUMPP.set(60)
input.RSEED.set(-10, 1)
input.REFLIN.set(29010300, 1, 1.25e-3)
input.NSIMSH.set(2e9)
input.TIME.set(2e9)
return input
def _export_sample_verticallayers(self, sample, options, erracc, geometry,
dsmaxs):
self._validate_sample_verticallayers(sample, options, erracc)
layers = apply_lazy(sample.layers, sample, options)
xpositions_m = sample.layers_xpositions_m
# Surfaces
surface_cylinder = cylinder(100) # 100 cm radius
surface_top = zplane(0.0) # z = 0
depth_m = apply_lazy(sample.depth_m, sample, options)
if math.isfinite(depth_m):
surface_bottom = zplane(-depth_m * 100.0)
else:
surface_bottom = zplane(-100.0) # z = -100 cm
surface_layers = []
if layers:
for layer, (xmin_m, _xmax_m) in zip(layers, xpositions_m):
surface = xplane(xmin_m * 100.0)
surface_layers.append(surface)
_xmin_m, xmax_m = xpositions_m[-1]
surface = xplane(xmax_m * 100.0)
surface_layers.append(surface)
else:
surface = xplane(0.0)
surface_layers.append(surface)
# Modules
index = 1
## Left substrate
left_material = apply_lazy(sample.left_material, sample, options)
penmaterial = self._export_material(left_material, options, erracc,
index)
module = Module(penmaterial, "Left substrate")
module.add_surface(surface_cylinder, SidePointer.NEGATIVE)
module.add_surface(surface_top, SidePointer.NEGATIVE)
module.add_surface(surface_bottom, SidePointer.POSITIVE)
module.add_surface(surface_layers[0], SidePointer.NEGATIVE)
if math.isfinite(depth_m):
dsmaxs[module] = depth_m
geometry.add_module(module)
index += 1
## Layers
for layer, (surface_left,
surface_right) in zip(layers, _pairwise(surface_layers)):
material = apply_lazy(layer.material, layer, options)
penmaterial = self._export_material(material, options, erracc,
index)
module = Module(penmaterial, "Layer {}".format(index - 1))
module.add_surface(surface_cylinder, SidePointer.NEGATIVE)
module.add_surface(surface_top, SidePointer.NEGATIVE)
module.add_surface(surface_bottom, SidePointer.POSITIVE)
module.add_surface(surface_left, SidePointer.POSITIVE)
module.add_surface(surface_right, SidePointer.NEGATIVE)
thickness_m = apply_lazy(layer.thickness_m, layer, options)
dsmaxs[module] = min(thickness_m, depth_m)
geometry.add_module(module)
index += 1
## Right substrate
right_material = apply_lazy(sample.right_material, sample, options)
penmaterial = self._export_material(right_material, options, erracc,
index)
module = Module(penmaterial, "Right substrate")
module.add_surface(surface_cylinder, SidePointer.NEGATIVE)
module.add_surface(surface_top, SidePointer.NEGATIVE)
module.add_surface(surface_bottom, SidePointer.POSITIVE)
module.add_surface(surface_layers[-1], SidePointer.POSITIVE)
if math.isfinite(depth_m):
dsmaxs[module] = depth_m
geometry.title = "Vertical layers"
geometry.add_module(module)
geometry.tilt_rad = apply_lazy(sample.tilt_rad, sample, options)
geometry.rotation_rad = apply_lazy(sample.azimuth_rad, sample, options)
def _export_sample_horizontallayers(self, sample, options, erracc,
geometry, dsmaxs):
self._validate_sample_horizontallayers(sample, options, erracc)
layers = apply_lazy(sample.layers, sample, options)
zpositions_m = sample.layers_zpositions_m
# Surfaces
surface_cylinder = cylinder(100) # 100 cm radius
surface_layers = [zplane(0.0)]
for layer, (zmin_m, _zmax_m) in zip(layers, zpositions_m):
surface = zplane(zmin_m * 100.0)
surface_layers.append(surface)
# Modules
index = 0
tmpgrouping = []
for layer, (surface_top,
surface_bottom) in zip(layers, _pairwise(surface_layers)):
material = apply_lazy(layer.material, layer, options)
penmaterial = self._export_material(material, options, erracc,
index)
module = Module(penmaterial, "Layer {}".format(index))
module.add_surface(surface_cylinder, SidePointer.NEGATIVE)
module.add_surface(surface_top, SidePointer.NEGATIVE)
module.add_surface(surface_bottom, SidePointer.POSITIVE)
thickness_m = apply_lazy(layer.thickness_m, layer, options)
dsmaxs[module] = thickness_m
geometry.add_module(module)
tmpgrouping.append((module, surface_bottom))
index += 1
if sample.has_substrate():
surface_top = surface_layers[-1]
surface_bottom = zplane(surface_top.shift.z_cm -
100) # 100 cm below last layer
substrate_material = apply_lazy(sample.substrate_material, sample,
options)
penmaterial = self._export_material(substrate_material, options,
erracc, index)
module = Module(penmaterial, "Substrate")
module.add_surface(surface_cylinder, SidePointer.NEGATIVE)
module.add_surface(surface_top, SidePointer.NEGATIVE)
module.add_surface(surface_bottom, SidePointer.POSITIVE)
geometry.add_module(module)
tmpgrouping.append((module, surface_bottom))
# Grouping
# G0: s0, s2, m0, m1
# G1: s0, s3, m2, g0
# G2: s0, s4, m3, g1
# etc.
if len(tmpgrouping) <= 2: # no grouping required if only 2 modules
return
module, surface_bottom = tmpgrouping[1]
group = Module(PENELOPE_VACUUM, "grouping")
group.add_surface(surface_cylinder, SidePointer.NEGATIVE)
group.add_surface(surface_layers[0],
SidePointer.NEGATIVE) # top z = 0.0
group.add_surface(surface_bottom, SidePointer.POSITIVE)
group.add_module(tmpgrouping[0][0]) # m0
group.add_module(module) # m1
geometry.add_module(group)
for module, surface_bottom in tmpgrouping[2:]:
oldgroup = group
group = Module(PENELOPE_VACUUM, "grouping")
group.add_surface(surface_cylinder, SidePointer.NEGATIVE)
group.add_surface(surface_layers[0],
SidePointer.NEGATIVE) # top z = 0.0
group.add_surface(surface_bottom, SidePointer.POSITIVE)
group.add_module(module)
group.add_module(oldgroup)
geometry.add_module(group)
geometry.title = "Horizontal layers"
geometry.tilt_rad = apply_lazy(sample.tilt_rad, sample, options)
geometry.rotation_rad = apply_lazy(sample.azimuth_rad, sample, options)