def cal_NetYield2(eV0,
Atoms,
xHe=0,
xAl=0,
xKapton=0,
WD=6.0,
xsw=0,
WriteFile='Y',
xsect_resonant=0.0,
sample=''):
# incident energy, list of elements, experimental conditions
# this one tries Ka, Kb, Lg, Lb, La, Lb
angle0 = 45.
textOut = ''
if xsw != 0 and WriteFile == 'Y': print('XSW measurements')
if sample == '':
Include_SelfAbsorption = 'No'
else:
Include_SelfAbsorption = 'Yes'
angle0 = sample.angle / math.pi * 180.
textOut = sample.txt # substrate concentration
NetYield = []
NetTrans = []
Net = []
out2 = ''
net = 0.0
text0 = ''
edges = ['K', 'K', 'L1', 'L1', 'L2', 'L2', 'L2', 'L3', 'L3', 'L3']
Fluo_lines = ['Ka', 'Kb', 'Lb', 'Lg', 'Ln', 'Lb', 'Lg', 'Ll', 'La', 'Lb']
outputfile = 'Elemental_Sensitivity.txt'
if WriteFile == 'Y':
fo = open(outputfile, 'w')
desc = ' '
if xHe == 0: desc = ' not '
if xsw == -1:
out1 = '# 13IDC XRM/XSW using QuadVortex, incident x-ray energy at ' + str(
eV0) + ' eV at ' + str(angle0) + ' degrees \n'
out1+='# Helium path'+desc+'used, '+str(xAl)+' Al attenuators, '+str(xKapton+1)+' Kapton attenuators, '\
+str(WD)+' cm working distance. \n'
else:
out1 = '# 13IDC XRM/XSW using QuadVortex + collimator, incident x-ray energy at ' + str(
eV0) + ' eV at ' + str(angle0) + ' degrees \n'
out1+='# Helium path'+desc+'used, '+str(xAl)+' Al attenuators, '+str(xKapton)+' Kapton attenuators, '\
+str(WD)+' cm working distance. \n'
print(out1)
fo.write(out1)
if sample != '':
for stuff in Atoms:
text1 = '%6.3e %s/cm^3' % (stuff.Conc * sample.Nat1,
stuff.AtSym)
text0 = text0 + ' ' + text1
textOut = textOut + ' ' + text0 # substrate concentration + other concentrations
out1 = '# ' + text0 + '\n'
if print2screen:
print(out1)
fo.write(out1)
out1 = '%s\t%s\t%s \t%s \t%s \t%s \t%s\n' % (
'atom', 'emit', 'emit_energy', 'yield', 'transmission',
'net_sensitivity', 'sensitivity*concentration')
if print2screen:
print(out1)
fo.write(out1)
for (ii, atom) in enumerate(Atoms):
atnum = f1f2.AtSym2AtNum(atom.AtSym)
temp = f1f2.AtNum2f1f2Xsect(atnum, eV0)
xsect = temp[
2] # photo-electric cross-section for fluorescence yield, temp[4] is total for attenuation
con = atom.Conc
for (nn, edge) in enumerate(edges):
emit = Fluo_lines[nn]
#edge='K'; emit='Ka' # check K edge Ka emission
temp = fluo_elem.get_avgElamFY(
atom.AtSym, edge, emit, eV0,
useAvg=1) # July2012: useAvg=1 causes problem
print(emit)
fy = temp[0]
emit_eV = temp[1]
emit_prob = temp[2]
if fy == 0.0 or emit_prob == 0:
continue # try next item if FY=0
else:
if xsect_resonant != 0.0: # use input value near edge
xsect = xsect_resonant # for cross-section near absoprtion edge
#print(xsect,fy,emit_prob)
net_yield = xsect * fy * emit_prob # net_yield --> cross-section, yield, emission_probability
# net transmission --> transmission from surface through detector
## ------------------ [self-absorption] ------------------------------
trans_SelfAbsorp = 1.0 # for self-absorption.
if Include_SelfAbsorption == 'Yes':
sample.getPenetration(eV0) # incident x-ray attenuation
if fy * emit_eV * emit_prob == 0: # any one of three is zero
break # skip
sample.getLa(emit_eV)
# account for incident x-ray attenuation, emitted x-ray attenuation
trans_SelfAbsorp = sample.scale # for elements that are not part of substrate
if (atom in sample.ElemListFY):
if atom.tag == 'substrate1':
trans_SelfAbsorp = sample.scale1 # for elements that are part of top substrate
if atom.tag == 'substrate2':
trans_SelfAbsorp = sample.scale2 # for elements that are part of bottom substrate
## ----------------------------------------------------------------------------
net_trans = Assemble_Detector(emit_eV, xHe, xAl, xKapton, WD, xsw)
net = net_yield * net_trans * trans_SelfAbsorp # elemental sensitivity
inten = net * con # sensitivity * concentration
if WriteFile == 'Y':
out1 = '%s\t%s\t%6.1f \t%.3e \t%.3e \t%.3e \t%.3e\n' % (
atom.AtSym + '_' + edge, emit, emit_eV, net_yield,
net_trans, net, inten)
fo.write(out1)
if print2screen:
print('%s %s %6.1f net_yield=%.3e net_trans=%.3e net=%.3e\t' %
(atom.AtSym + '_' + edge, emit, emit_eV, net_yield,
net_trans, net))
#print(out1)+' %s, depth-dependent factor= %6.4f' % (atom.tag, trans_SelfAbsorp)
if emit == 'Kb' and fy != 0: # if above K edge, don't bother trying L edges
break
return textOut
def sim_spectra(eV0, Atoms, xHe=0, xAl=0, xKapton=0, WD=6.0, xsw=0, sample=''):
# sample=sample matrix with object attribues to add self-absorption effect
# Atoms is a list with elements that have attributes AtSym, Conc, tag
if xsw == -1: xKapton = xKapton - 1 # no collimator
Include_SelfAbsorption = 'Yes'
Print2Screen = 'No'
if sample == '': Include_SelfAbsorption = 'No'
if xsw != 0: print('XSW measurements')
xx = []
yy = []
tag = []
intensity_max = -10.0
LoLimit = 1e-10
angle0 = ''
text1 = ''
if sample != '': # sample matrix option is used
angle0 = str(sample.angle * 180. / math.pi)
angle0 = angle0[:5]
for (ii, item) in enumerate(
sample.ElemListFY): # add matrix elements to the lists
Atoms.append(item)
outputfile = 'simSpectrum_table.txt'
fo = open(outputfile, 'w')
out1 = '#incident x-ray at ' + str(eV0) + ' eV and ' + angle0 + ' Deg.\n'
if Print2Screen == 'Yes': print(out1)
fo.write(out1)
out1 = '#Emission\tenergy(eV)\tintensity \n'
if Print2Screen == 'Yes': print(out1)
fo.write(out1)
out2 = '#'
for (ix, atom) in enumerate(Atoms):
atnum = f1f2.AtSym2AtNum(atom.AtSym)
# con=Conc[ix]
con = atom.Conc
out2 = out2 + atom.AtSym + '[' + str(con) + '] '
for edge in ['K', 'L1', 'L2', 'L3']:
temp = f1f2.AtNum2f1f2Xsect(atnum, eV0)
xsect = temp[
2] # photoelectric crosssection for each element at incident x-ray, fluorescence yield
temp = elam.use_ElamFY(atom.AtSym, edge)
edge_eV = float(temp[2]) # absorption edge
if eV0 > edge_eV:
fy = float(temp[3])
for EmitLine in temp[4]:
EmitName = EmitLine[1]
emit_eV = float(EmitLine[2])
emit_prob = float(EmitLine[3])
if emit_eV < fluo_emit_min:
continue # ignore fluorescence below fluo_emit_min (global variable)
name = atom.AtSym + '_' + EmitName
# net transmission --> transmission from surface through detector
## ------------------ [self-absorption] ------------------------------
trans_SelfAbsorp = 1.0 # for self-absorption.
if Include_SelfAbsorption == 'Yes':
sample.getPenetration(
eV0) # incident x-ray attenuation
eV0str = str(eV0)
text1 = ' absorption_length1(%seV)= %2.2e%s \
absorption_length2(%seV)= %2.2e%s' % (
eV0str, sample.la1 * 1.e4, 'microns', eV0str,
sample.la2 * 1.e4, 'microns')
# text1 is added to sample.txt later
sample.getLa(
emit_eV) # emitted fluorescence attenuation
trans_SelfAbsorp = sample.scale # for elements that are not part of substrate
if (atom in sample.ElemListFY):
if atom.tag == 'substrate1':
trans_SelfAbsorp = sample.scale1 # for elements that are part of top substrate
if atom.tag == 'substrate2':
trans_SelfAbsorp = sample.scale2 # for elements that are part of bottom substrate
## ----------------------------------------------------------------------------
trans = Assemble_Detector(emit_eV, xHe, xAl, xKapton, WD,
xsw)
intensity = con * fy * emit_prob * xsect * trans * trans_SelfAbsorp
if intensity < LoLimit:
continue # skip weak emission, arbtraray limit =1e-10.
if intensity > intensity_max: intensity_max = intensity
xx.append(emit_eV)
yy.append(intensity)
tag.append(name)
for ix in range(len(yy)):
yy[ix] = yy[
ix] / intensity_max * 100.00 # makes the strongest line to 100.0
out1 = '%s\t%f\t%f \n' % (tag[ix], xx[ix], yy[ix])
if Print2Screen == 'Yes': print(out1)
fo.write(out1)
if Print2Screen == 'Yes': print(out2)
fo.write(out2)
fo.close()
out1 = sim_GaussPeaks(
xx, yy, det_res, eV0
) # det_res: detector resoultion for Gaussian width (global variable)
if Include_SelfAbsorption == 'Yes':
sample.txt = sample.txt + text1 # sample.txt is combined to output of cal_NetYield
text = cal_NetYield2(
eV0, Atoms, xHe, xAl, xKapton, WD, xsw,
sample=sample) # calculate net yield with weight-averaged emission
print(out2)
return text # cal_NetYield2 output is str with number densities of elements
def __init__(self, composition1='Si', density1=2.33, thickness1=0.1, \
composition2='Si', density2=2.33, thickness2=0.1, angle0=45.0, option='surface'):
self.composition1 = composition1 # ex) Fe2O3
out = f1f2.get_ChemName(composition1) # output from get_ChemName
self.ElemList1 = out[
0] # list of elments in matrix: 'Fe', 'O' for Fe2O3
self.ElemInd1 = out[1] # list of index: 2, 3 for Fe2O3
self.ElemFrt1 = out[2] # list of fraction: 0.4, 0.6 for Fe2O3
self.density1 = density1 # in g/cm^3
self.thickness1 = thickness1 # top layer thickness in cm
self.composition2 = composition2
out = f1f2.get_ChemName(composition2)
self.ElemList2 = out[0] # for the bottom substrate
self.ElemInd2 = out[1]
self.ElemFrt2 = out[2]
self.density2 = density2
self.thickness2 = thickness2 # bottom layer thickness in cm
self.angle = angle0 * math.pi / 180. # in radian, incident beam angle, surface normal =pi/2
self.option = option # option for fluorescing element location, surface/top/bottom
self.la1 = 1.0 # absoprtion length in cm
self.delta1 = 0.1 # index of refraction, real part correction
self.beta1 = 0.1 # index of refraction, imaginary part
self.Nat1 = 1.0 # atomic number density of the Fe2O3, 1e22 Fe2O3 atoms /cm^3
self.la2 = 1.0
self.delta2 = 0.1
self.beta2 = 0.1
self.Nat2 = 1.0 # atomic number density of the first element, 1e22 Fe2O3 atoms/cm^3
self.scale = 1.0 # weighted average over the depth range: sum of (trans*factors)
self.scale1 = 1.0 # sum of (trans*1.0) this is for substrate element in top layer
self.scale2 = 1.0 # sum of (trans*thickness2/thickness1) for substrate element in bottom layer
self.ElemListFY = [] # fluorescing element
self.ElemFrtFY = [] # fraction for fluorescing element
self.Nat1 = 1 # atomic number density in atoms/cc, for example # of Fe2O3/cm^3 for Fe2O3 substrate
self.Nat2 = 1 # atomic number density in atoms/cc
substrate1_material = Material(composition1, density1)
AtNumDen1 = substrate1_material.NumDen # substrate1
substrate2_material = Material(composition2, density2)
AtNumDen2 = substrate2_material.NumDen # substrate2, fixed 8/12/10
self.Nat1 = AtNumDen1
self.Nat2 = AtNumDen2
self.txt = ''
text1 = 'substrate1:%6.3e %s/cm^3' % (AtNumDen1, composition1)
#print(text1)
text2 = 'substrate2:%6.3e %s/cm^3' % (AtNumDen2, composition2)
self.txt = text1 + ' ' + text2
print(self.txt)
# atom.conc is normalized to the number density of substrate1 molecule
for (ii, item) in enumerate(self.ElemList1):
if f1f2.AtSym2AtNum(item) >= 12: # ignore elements below Mg
#atom=ElemFY(item, self.ElemFrt1[ii], 'substrate1')
atom = ElemFY(item, self.ElemInd1[ii], 'substrate1')
# eg. for Fe2O3, Fe concentration is 2 (=2 x Fe2O3 number density)
self.ElemListFY.append(atom)
for (ii, item) in enumerate(self.ElemList2):
if f1f2.AtSym2AtNum(item) >= 12: # ignore elements below Mg
#atom=ElemFY(item, self.ElemFrt2[ii], 'substrate2')
atom = ElemFY(item, self.ElemInd2[ii] * AtNumDen2 / AtNumDen1,
'substrate2')
self.ElemListFY.append(atom)
numLayer = 100 # each layer is sliced into 100 sublayers.
self.depths = [] # depth values for calculation
for ii in range(numLayer):
step = 1.0 / numLayer
self.depths.append(step * ii * self.thickness1)
for ii in range(numLayer):
step = 1.0 / numLayer
self.depths.append(step * ii * self.thickness2 + self.thickness1)
self.factors = [] # 1 or pre if element present at each depth
pre = self.thickness2 / self.thickness1 # prefactor, if two layers have different thickness
if self.option == 'surface': # fluorescecing atoms present in only on the surface
for ii in range(len(self.depths)):
if ii == 0:
self.factors.append(1.0)
else:
self.factors.append(0.0)
if self.option == 'all': # fluorescecing atoms present throughout
for ii in range(len(self.depths)):
if self.depths[ii] < self.thickness1:
self.factors.append(1.0)
else:
self.factors.append(pre)
if self.option == 'top': # fluorescecing atoms present only in the top layer
for ii in range(len(self.depths)):
if self.depths[ii] < self.thickness1:
self.factors.append(1.0)
else:
self.factors.append(0.0)
if self.option == 'bottom': # fluorescecing atoms present only in the bottom layer
for ii in range(len(self.depths)):
if self.depths[ii] < self.thickness1:
self.factors.append(0.0)
else:
self.factors.append(pre)
# note: fluorescing substrate atoms present throughout regardless of the option.
self.trans = [] # transmission to surface for emitted fluorescence
self.absrp = [] # absorption until surface for emitted fluorescence
self.inten0 = [] # incident x-ray intensity at each depth
for ii in range(len(self.depths)):
self.trans.append(0.5)
self.absrp.append(0.5)
self.inten0.append(0.5)