def testBulkReemission(self):
'''Test bulk reemission
Start a bunch of monoenergetic photons at the center of a wavelength-
shifting sphere, forcing reemission, and check that the final
wavelength distribution matches the wls spectrum.
'''
import scipy.stats
nphotons = 1e5
# set up detector -- a sphere of 'scintillator' surrounded by a
# detecting sphere
scint = Material('scint')
scint.set('refractive_index', 1)
scint.set('absorption_length', 1.0)
scint.set('scattering_length', 1e7)
scint.set('reemission_prob', 1)
x = np.arange(0,1000,10)
norm = scipy.stats.norm(scale=50, loc=600)
pdf = 10 * norm.pdf(x)
cdf = norm.cdf(x)
scint.reemission_cdf = np.array(zip(x, cdf))
detector = Surface('detector')
detector.set('detect', 1)
world = Geometry(vacuum)
world.add_solid(Solid(sphere(1000), vacuum, vacuum, surface=detector))
world.add_solid(Solid(sphere(500), scint, vacuum))
w = create_geometry_from_obj(world, update_bvh_cache=False)
sim = Simulation(w, geant4_processes=0)
# initial photons -- isotropic 250 nm at the origin
pos = np.tile([0,0,0], (nphotons,1)).astype(np.float32)
dir = np.random.rand(nphotons, 3).astype(np.float32) * 2 - 1
dir /= np.sqrt(dir[:,0]**2 + dir[:,1]**2 + dir[:,2]**2)[:,np.newaxis]
pol = np.zeros_like(pos)
t = np.zeros(nphotons, dtype=np.float32)
wavelengths = np.ones(nphotons).astype(np.float32) * 250
photons = Photons(pos=pos, dir=dir, pol=pol, t=t, wavelengths=wavelengths)
# run simulation and extract final wavelengths
event = sim.simulate([photons], keep_photons_end=True).next()
mask = (event.photons_end.flags & SURFACE_DETECT) > 0
final_wavelengths = event.photons_end.wavelengths[mask]
# compare wavelength distribution to scintillator's reemission pdf
hist, edges = np.histogram(final_wavelengths, bins=x)
print 'detected', hist.sum(), 'of', nphotons, 'photons'
hist_norm = 1.0 * hist / (1.0 * hist.sum() / 1000)
pdf /= (1.0 * pdf.sum() / 1000)
chi2 = scipy.stats.chisquare(hist_norm, pdf[:-1])[1]
print 'chi2 =', chi2
# show histogram comparison
#plt.figure(1)
#width = edges[1] - edges[0]
#plt.bar(left=edges, height=pdf, width=width, color='red')
#plt.bar(left=edges[:-1], height=hist_norm, width=width)
#plt.show()
self.assertTrue(chi2 > 0.75)
from chroma.geometry import Material
from chroma.geometry import Surface
from Geant4.hepunit import *
import numpy as np
ls_refractive_index = 1.5
lensmat_refractive_index = 2.0
lensmat_ohara_refractive_index = 1.923
# This is elemental helium - vs. G4_HE
he = Material('He')
he.set('refractive_index', 1.0)
he.set('absorption_length', 1e8)
he.set('scattering_length', 1e8)
he.density = 0.5
he.composition = { 'He' : 1.0 }
lensmat = Material('lensmat')
lensmat.set('refractive_index', lensmat_refractive_index)
lensmat.set('absorption_length', 1e8)
lensmat.set('scattering_length', 1e8)
lensmat_ohara = Material('lensmat_ohara')
lensmat_ohara.set('refractive_index', lensmat_ohara_refractive_index)
lensmat_ohara.set('absorption_length', 1e8)
lensmat_ohara.set('scattering_length', 1e8)
blackhole = Material('blackhole')
blackhole.set('refractive_index', 1.0)
def create_scintillation_material():
global _ls
if _ls is None:
# ls stands for "liquid scintillator"
_ls = Material('liquid-scintillator')
_ls.set('refractive_index', ls_refractive_index)
_ls.set('absorption_length', 1e8)
_ls.set('scattering_length', 1e8)
_ls.density = 0.780
_ls.composition = {'H': 0.663210, 'C': 0.336655, 'N': 1.00996e-4, 'O': 3.36655e-5}
#_ls.set('refractive_index', np.linspace(ls_refractive_index, ls_refractive_index, 38))
# Scintillation properties
energy_scint = list((2 * pi * hbarc / (np.linspace(320, 300, 11).astype(float) * nanometer)))
spect_scint = list([0.04, 0.07, 0.20, 0.49, 0.84, 1.00, 0.83, 0.55, 0.40, 0.17, 0.03])
# See https://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch02s03.html
# Need to validate that the types are being passed through properly. Previously was using list(Scnt_PP.astype(float)
_ls.set_scintillation_property('FASTCOMPONENT', energy_scint, spect_scint)
# TODO: These keys much match the Geant4 pmaterial property names. (Magic strings)
_ls.set_scintillation_property('SCINTILLATIONYIELD', 8000. / MeV) # Was 10000 originally
_ls.set_scintillation_property('RESOLUTIONSCALE', 1.0) # Was 1.0 originally
_ls.set_scintillation_property('FASTTIMECONSTANT', 1. * ns)
_ls.set_scintillation_property('YIELDRATIO', 1.0) # Was 0.8 - I think this is all fast
# Required for scintillation yield per particle
# Commenting out these three lines causes a "malloc: *** error for object 0x1298c02d0: pointer being freed was not allocated" WTF?
electron_energy_scint = list([0., 1. * MeV, 10. * MeV, 100. * MeV])
electron_yield = list([0, 8000., 80000., 800000.])
_ls.set_scintillation_property('ELECTRONSCINTILLATIONYIELD', electron_energy_scint, electron_yield)
proton_energy_scint = list([0 * MeV, 0.1 * MeV, 0.5 * MeV, 1 * MeV, 1.5 * MeV, 2 * MeV, 2.5 * MeV, 3 * MeV, 3.5 * MeV, 4 * MeV, 4.4 * MeV, 5 * MeV, 6 * MeV, 7 * MeV, 8 * MeV, 9 * MeV, 10 * MeV, 12 * MeV, 14 * MeV, 16 * MeV, 18 * MeV, 19.9])
proton_yield = list([0, 43, 581, 1637, 2988, 4562, 6316, 8219, 10249, 12389, 14171, 16946, 21809, 26921, 32240, 37736, 43383, 55059, 67150, 79575, 92277, 104558])
_ls.set_scintillation_property('PROTONSCINTILLATIONYIELD', proton_energy_scint , proton_yield)
return _ls
#!/usr/bin/env python
from chroma.geometry import Material, Solid, Surface
import numpy as np
#***************************************************************************
#***************************************************************************
sipm = Material('sipm')
sipm.set('detection', 1)
copper = Material('copper')
copper.set(
'refractive_index', 0.97333
) # 0.87 #https://refractiveindex.info/?shelf=main&book=Cu&page=Werner with wavelength 175nm extrapolated on TREND function excel
copper.set('absorption_length', 50) #1058100
copper.set('scattering_length', 1e6) #10e6
copper.density = 8.96
copper.composition = {'Cu': 1.00}
#***************************************************************************
#***************************************************************************
vacuum = Material('vac')
vacuum.set('refractive_index', 1.0)
vacuum.set('absorption_length', 0)
vacuum.set('scattering_length', 1e6)
vacuum.set('reemission_prob', 0)
#***************************************************************************
#***************************************************************************
LXenon = Material('LXenon')
LXenon.set(
'refractive_index', 1.69
) #https://arxiv.org/ftp/physics/papers/0307/0307044.pdf #possibly 1.57 but lower occurances #1.69
LXenon.set('absorption_length',
1e6) #20000 Changed 364 --> 0 8/9/2018, used 1000mm June 11 2019
import numpy as np
from chroma.geometry import Material, Surface
vacuum = Material('vacuum')
vacuum.set('refractive_index', 1.0)
vacuum.set('absorption_length', 1e6)
vacuum.set('scattering_length', 1e6)
lambertian_surface = Surface('lambertian_surface')
lambertian_surface.set('reflect_diffuse', 1)
black_surface = Surface('black_surface')
black_surface.set('absorb', 1)
shiny_surface = Surface('shiny_surface')
shiny_surface.set('reflect_specular', 1)
glossy_surface = Surface('glossy_surface')
glossy_surface.set('reflect_diffuse', 0.5)
glossy_surface.set('reflect_specular', 0.5)
red_absorb_surface = Surface('red_absorb')
red_absorb_surface.set('absorb', [0.0, 0.0, 1.0], [465, 545, 685])
red_absorb_surface.set('reflect_diffuse', [1.0, 1.0, 0.0], [465, 545, 685])
# r7081hqe photocathode material surface
# source: hamamatsu supplied datasheet for r7081hqe pmt serial number zd0062
r7081hqe_photocathode = Surface('r7081hqe_photocathode')
r7081hqe_photocathode.detect = \
np.array([(260.0, 0.00),
(270.0, 0.04), (280.0, 0.07), (290.0, 0.77), (300.0, 4.57),
def convert_materials(self, debug=False):
"""
#. creates chroma Material instances for each collada material
#. fills in properties from the collada extras
#. records materials in a map keyed by material.name
Chroma materials default to None, 3 settings:
* refractive_index
* absorption_length
* scattering_length
And defaults to zero, 2 settings:
* reemission_prob
* reemission_cdf
G4DAE materials have an extra attribute dict that
contains keys such as
* RINDEX
* ABSLENGTH
* RAYLEIGH
Uncertain of key correspondence, especially REEMISSIONPROB
and what about reemission_cdf ? Possibly the many Scintillator
keys can provide that ?
Probably many the scintillator keys are only relevant to photon
production rather than photon propagation, so they are irrelevant
to Chroma.
Which materials have each::
EFFICIENCY [1 ] Bialkali
-------------- assumed to not apply to optical photons ---------
FASTTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator
SLOWTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator
YIELDRATIO [2 ] GdDopedLS,LiquidScintillator
GammaFASTTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator
GammaSLOWTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator
GammaYIELDRATIO [2 ] GdDopedLS,LiquidScintillator
AlphaFASTTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator
AlphaSLOWTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator
AlphaYIELDRATIO [2 ] GdDopedLS,LiquidScintillator
NeutronFASTTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator
NeutronSLOWTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator
NeutronYIELDRATIO [2 ] GdDopedLS,LiquidScintillator
SCINTILLATIONYIELD [2 ] GdDopedLS,LiquidScintillator
RESOLUTIONSCALE [2 ] GdDopedLS,LiquidScintillator
---------------------------------------------------------------------
ReemissionFASTTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator for opticalphoton
ReemissionSLOWTIMECONSTANT [2 ] GdDopedLS,LiquidScintillator
ReemissionYIELDRATIO [2 ] GdDopedLS,LiquidScintillator
FASTCOMPONENT [2 ] GdDopedLS,LiquidScintillator "Fast_Intensity"
SLOWCOMPONENT [2 ] GdDopedLS,LiquidScintillator "Slow_Intensity"
REEMISSIONPROB [2 ] GdDopedLS,LiquidScintillator "Reemission_Prob"
------------------------------------------------------------------------
RAYLEIGH [5 ] GdDopedLS,Acrylic,Teflon,LiquidScintillator,MineralOil
RINDEX [14] Air,GdDopedLS,Acrylic,Teflon,LiquidScintillator,Bialkali,
Vacuum,Pyrex,MineralOil,Water,NitrogenGas,IwsWater,OwsWater,DeadWater
ABSLENGTH [20] PPE,Air,GdDopedLS,Acrylic,Teflon,LiquidScintillator,Bialkali,
Vacuum,Pyrex,UnstStainlessSteel,StainlessSteel,
ESR,MineralOil,Water,NitrogenGas,IwsWater,ADTableStainlessSteel,Tyvek,OwsWater,DeadWater
Observations:
#. no RAYLEIGH for water
"""
keymap = {
"RINDEX": 'refractive_index',
"ABSLENGTH": 'absorption_length',
"RAYLEIGH": 'scattering_length',
"REEMISSIONPROB": 'reemission_prob',
}
keymat = {}
collada = self.nodecls.orig
for dmaterial in collada.materials:
material = Material(dmaterial.id)
if DEBUG:
material.dae = dmaterial
# vacuum like defaults ? is that appropriate ? what is the G4 equivalent ?
material.set('refractive_index', 1.0)
material.set('absorption_length', 1e6)
material.set('scattering_length', 1e6)
if dmaterial.extra is not None:
props = dmaterial.extra.properties
for dkey, dval in props.items():
if dkey not in keymat:
keymat[dkey] = []
keymat[dkey].append(
material.name
) # record of materials that have each key
if dkey in keymap:
key = keymap[dkey]
material.set(key, dval[:, 1], wavelengths=dval[:, 0])
log.debug(
"for material %s set Chroma prop %s from G4DAE prop %s vals %s "
% (material.name, key, dkey, len(dval)))
else:
log.debug(
"for material %s skipping G4DAE prop %s vals %s " %
(material.name, dkey, len(dval)))
pass
self.setup_cdf(material, props)
pass
pass
self.materials[material.name] = material
pass
log.debug("convert_materials G4DAE keys encountered : %s " %
len(keymat))
if debug:
for dkey in sorted(keymat, key=lambda _: len(keymat[_])):
mats = keymat[dkey]
print " %-30s [%-2s] %s " % (dkey, len(mats), ",".join(
map(matshorten, mats)))
import numpy as np
from chroma.geometry import Material, Surface
from chroma.demo.optics import vacuum, r7081hqe_photocathode
import math
glass = Material('glass')
glass.set('refractive_index', 1.49)
glass.absorption_length = \
np.array([(200, 0.1e-6), (300, 1000), (330, 1000.0), (500, 2000.0), (600, 1000.0), (770, 500.0), (800, 0.1e-6)])
glass.set('scattering_length', 1e6)
silica = np.array([(180, .9), (200, .93), (220,.94), (240, .95), (260, .95), (280, .95), (800,.95)])
gel = np.array([(180, 0.0), (260, 0.0),(280, .09),(300.,.4), (320, .83), (365,.98), (404.7,0.99), (480,1.0), (800,1.0)])
mirror = np.array([(180, 0), (220, 0), (240,.0), (260, .1), (280, .4), (300, .7), (340,.88), (360, .95), (400, .97), (550, .97), (600, .95), (700, .92), (800, .87)])
mcp_boro_photocathode = Surface('mcp_boro_photocathode')
mcp_silica_photocathode = Surface('mcp_silica_photocathode')
'''
mcp_boro_photocathode.detect = \
np.array([(240.0, 0.00), (250.0, 0.04), (260.0, 2),
(270.0, 8.77), (280.0, 24), (290.0, 26), (300.0, 27),
(310.0, 28.00), (320.0, 28.8), (330.0, 29.7), (340.0, 30.1),
(350.0, 30.52), (360.0, 31.0), (370.0, 31.30), (380.0, 31.20),
(390.0, 31.00), (400.0, 30.90), (410.0, 30.50), (420.0, 30.16),
(430.0, 29.24), (440.0, 28.31), (450.0, 27.41), (460.0, 26.25),
(470.0, 24.90), (480.0, 23.05), (490.0, 21.58), (500.0, 19.94),
(510.0, 18.48), (520.0, 17.01), (530.0, 15.34), (540.0, 12.93),
(550.0, 10.17), (560.0, 7.86), (570.0, 6.23), (580.0, 5.07),
(590.0, 4.03), (600.0, 3.18), (610.0, 2.38), (620.0, 1.72),
(630.0, 0.95), (640.0, 0.71), (650.0, 0.44), (660.0, 0.25),
import numpy as np
from chroma.geometry import Material, Surface
vacuum = Material('vacuum')
vacuum.set('refractive_index', 1.0)
vacuum.set('absorption_length', 1e6)
vacuum.set('scattering_length', 1e6)
lambertian_surface = Surface('lambertian_surface')
lambertian_surface.set('reflect_diffuse', 1)
black_surface = Surface('black_surface')
black_surface.set('absorb', 1)
shiny_surface = Surface('shiny_surface')
shiny_surface.set('reflect_specular', 1)
glossy_surface = Surface('glossy_surface')
glossy_surface.set('reflect_diffuse', 0.5)
glossy_surface.set('reflect_specular', 0.5)
red_absorb_surface = Surface('red_absorb')
red_absorb_surface.set('absorb', [0.0, 0.0, 1.0], [465, 545, 685])
red_absorb_surface.set('reflect_diffuse', [1.0, 1.0, 0.0], [465, 545, 685])
# r7081hqe photocathode material surface
# source: hamamatsu supplied datasheet for r7081hqe pmt serial number zd0062
r7081hqe_photocathode = Surface('r7081hqe_photocathode')
r7081hqe_photocathode.detect = \
np.array([(260.0, 0.00),
(270.0, 0.04), (280.0, 0.07), (290.0, 0.77), (300.0, 4.57),