def __init__(self, composition, density, thickness=1):
self.composition = composition # ex) SiO2
self.density = density # in g/cm^3
self.thickness = thickness # in cm
self.la = 1.0 #absoprtion length in cm
self.trans = 0.5 # transmission.
self.absrp = 0.5 # absorption
self.delta = 0.1 # index of refraction, real part
self.beta = 0.1 # index of refraction, imaginary part
temp = f1f2.get_ChemName(composition)
AtomList = temp[0]
AtomIndex = temp[1]
AtomWeight = 0
for (ii, atom) in enumerate(AtomList):
AtWt = f1f2.AtSym2AtWt(atom)
index = AtomIndex[ii]
AtomWeight = AtomWeight + index * AtWt
NumberDensity = density * Nav / AtomWeight
self.NumDen = NumberDensity # number of molecules per cm^3
self.AtWt = AtomWeight # weight per mole
def __init__(self, composition, density, thickness=1):
self.composition=composition # ex) SiO2
self.density=density # in g/cm^3
self.thickness=thickness # in cm
self.la=1.0 #absoprtion length in cm
self.trans=0.5 # transmission.
self.absrp=0.5 # absorption
self.delta=0.1 # index of refraction, real part
self.beta=0.1 # index of refraction, imaginary part
temp=f1f2.get_ChemName(composition)
AtomList=temp[0]
AtomIndex=temp[1]
AtomWeight=0
for (ii, atom) in enumerate(AtomList):
AtWt=f1f2.AtSym2AtWt(atom)
index=AtomIndex[ii]
AtomWeight = AtomWeight + index*AtWt
NumberDensity=density*Nav/AtomWeight
self.NumDen=NumberDensity # number of molecules per cm^3
self.AtWt=AtomWeight # weight per mole
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)
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)
