def testphoton_range(self):
material = Material.pure(29)
xrayline = XrayLine(29, 'Ka1')
actual = photon_range(20e3,
material,
xrayline,
reference='perkins1991')
self.assertAlmostEqual(8.42816e-7, actual, 10)
def testphoton_range(self):
material = Material.pure(29)
transition = Transition(29, siegbahn='Ka1')
self.assertAlmostEqual(8.4064e-7, photon_range(20e3, material, transition), 10)
def _append_spatial_distribution(self, lines, options, geoinfo, matinfos,
phdets_key_index, phdets_index_keys, *args):
lines.append(self._COMMENT_SPATIALDIST())
# Photon depth detectors
detectors = dict(options.detectors.iterclass(PhotonDepthDetector))
if not detectors:
lines.append(self._COMMENT_SKIP())
return
if len(detectors) != 1:
raise ExporterException("PENEPMA can only have one photon depth detector")
key, detector = next(iter(detectors.items()))
## Get materials
materials = options.geometry.get_materials()
## Get transitions
if not detector.transitions:
zs = set()
for material in materials:
zs |= set(material.composition.keys())
energylow = min(mat.absorption_energy_eV[ELECTRON] for mat in materials)
energyhigh = options.beam.energy_eV
transitions = []
for z in zs:
transitions += get_transitions(z, energylow, energyhigh)
if not transitions:
message = "No transition found for PRZ distribution with high enough probability"
warnings.warn(message, ExporterWarning)
else:
transitions = list(detector.transitions)
transitions.sort(key=attrgetter('probability'), reverse=True)
## Restrain number of transitions to maximum number of PRZ
if len(transitions) > MAX_SPATIAL_DISTRIBUTION // 2:
message = 'Too many transitions (%i). Only the most probable is/are kept.' % \
len(transitions)
warnings.warn(message, ExporterWarning)
transitions = transitions[:MAX_SPATIAL_DISTRIBUTION // 2]
logging.debug('PRZ of the following transitions: %s',
', '.join(map(str, transitions)))
## Retrieve range
e0 = options.beam.energy_eV
safety_factor = 3.0
zmax_m = 1e-08 # PENPEMA forces the minimum depth to be 1e-6 cm
for material in materials:
for transition in transitions:
tmpzmax_m = photon_range(e0, material, transition) * safety_factor
zmax_m = max(zmax_m, tmpzmax_m)
## Create lines
text = ' '.join(map(str, [-3, 3, 1]))
lines.append(self._KEYWORD_GRIDX(text))
text = ' '.join(map(str, [-3, 3, 1]))
lines.append(self._KEYWORD_GRIDY(text))
channels = min(100, detector.channels) # Maximum of 100 channels
text = ' '.join(map(str, [-zmax_m * 1e2, 0, channels]))
lines.append(self._KEYWORD_GRIDZ(text))
index = phdets_key_index[key] + 1
for transition in transitions:
code = int(transition.z * 1e6 + \
transition.dest.index * 1e4 + \
transition.src.index * 1e2)
text = ' '.join(map(str, [code, 0])) # No absorption
lines.append(self._KEYWORD_XRLINE(text))
text = ' '.join(map(str, [code, index])) # With absorption
lines.append(self._KEYWORD_XRLINE(text))
lines.append(self._COMMENT_SKIP())
def test_photon_range():
material = Material.pure(29)
energy_eV = pyxray.xray_transition_energy_eV(29, "Ka1", reference="jeol")
actual = photon_range(20e3, material, 29, energy_eV)
assert actual == pytest.approx(8.4063e-7, abs=1e-10)
def _append_spatial_distribution(self, lines, options, geoinfo, matinfos,
phdets_key_index, phdets_index_keys,
*args):
lines.append(self._COMMENT_SPATIALDIST())
# Photon depth detectors
detectors = dict(options.detectors.iterclass(PhotonDepthDetector))
if not detectors:
lines.append(self._COMMENT_SKIP())
return
if len(detectors) != 1:
raise ExporterException(
"PENEPMA can only have one photon depth detector")
key, detector = next(iter(detectors.items()))
## Get materials
materials = options.geometry.get_materials()
## Get transitions
if not detector.transitions:
zs = set()
for material in materials:
zs |= set(material.composition.keys())
energylow = min(mat.absorption_energy_eV[ELECTRON]
for mat in materials)
energyhigh = options.beam.energy_eV
transitions = []
for z in zs:
transitions += get_transitions(z, energylow, energyhigh)
if not transitions:
message = "No transition found for PRZ distribution with high enough probability"
warnings.warn(message, ExporterWarning)
else:
transitions = list(detector.transitions)
transitions.sort(key=attrgetter('probability'), reverse=True)
## Restrain number of transitions to maximum number of PRZ
if len(transitions) > MAX_SPATIAL_DISTRIBUTION // 2:
message = 'Too many transitions (%i). Only the most probable is/are kept.' % \
len(transitions)
warnings.warn(message, ExporterWarning)
transitions = transitions[:MAX_SPATIAL_DISTRIBUTION // 2]
logging.debug('PRZ of the following transitions: %s',
', '.join(map(str, transitions)))
## Retrieve range
e0 = options.beam.energy_eV
safety_factor = 3.0
zmax_m = 1e-08 # PENPEMA forces the minimum depth to be 1e-6 cm
for material in materials:
for transition in transitions:
tmpzmax_m = photon_range(e0, material,
transition) * safety_factor
zmax_m = max(zmax_m, tmpzmax_m)
## Create lines
text = ' '.join(map(str, [-3, 3, 1]))
lines.append(self._KEYWORD_GRIDX(text))
text = ' '.join(map(str, [-3, 3, 1]))
lines.append(self._KEYWORD_GRIDY(text))
channels = min(100, detector.channels) # Maximum of 100 channels
text = ' '.join(map(str, [-zmax_m * 1e2, 0, channels]))
lines.append(self._KEYWORD_GRIDZ(text))
index = phdets_key_index[key] + 1
for transition in transitions:
code = int(transition.z * 1e6 + \
transition.dest.index * 1e4 + \
transition.src.index * 1e2)
text = ' '.join(map(str, [code, 0])) # No absorption
lines.append(self._KEYWORD_XRLINE(text))
text = ' '.join(map(str, [code, index])) # With absorption
lines.append(self._KEYWORD_XRLINE(text))
lines.append(self._COMMENT_SKIP())