#/*##########################################################################
#
# The PyMca X-Ray Fluorescence Toolkit
#
# Copyright (c) 2004-2014 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
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# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
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# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import os
import numpy
from PyMca5.PyMcaIO import specfile
from PyMca5 import PyMcaDataDir
dirname = PyMcaDataDir.PYMCA_DATA_DIR
inputfile = os.path.join(dirname, "MShellRates.dat")
if not os.path.exists(inputfile):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, "MShellRates.dat")
if not os.path.exists(inputfile):
if dirname.lower().endswith(".zip"):
dirname = os.path.dirname(dirname)
inputfile = os.path.join(dirname, "MShellRates.dat")
if not os.path.exists(inputfile):
print("Cannot find inputfile ",inputfile)
raise IOError("Cannot find MShellRates.dat file")
sf=specfile.Specfile(os.path.join(dirname, "MShellRates.dat"))
ElementM1ShellTransitions = sf[0].alllabels()
ElementM2ShellTransitions = sf[1].alllabels()
ElementM3ShellTransitions = sf[2].alllabels()
ElementM4ShellTransitions = sf[3].alllabels()
ElementM5ShellTransitions = sf[4].alllabels()
ElementM1ShellRates = numpy.transpose(sf[0].data()).tolist()
ElementM2ShellRates = numpy.transpose(sf[1].data()).tolist()
ElementM3ShellRates = numpy.transpose(sf[2].data()).tolist()
ElementM4ShellRates = numpy.transpose(sf[3].data()).tolist()
ElementM5ShellRates = numpy.transpose(sf[4].data()).tolist()
sf=specfile.Specfile(os.path.join(dirname, "MShellConstants.dat"))
ElementM1ShellConstants = sf[0].alllabels()
ElementM2ShellConstants = sf[1].alllabels()
ElementM3ShellConstants = sf[2].alllabels()
ElementM4ShellConstants = sf[3].alllabels()
ElementM5ShellConstants = sf[4].alllabels()
ElementM1ShellValues = numpy.transpose(sf[0].data()).tolist()
ElementM2ShellValues = numpy.transpose(sf[1].data()).tolist()
ElementM3ShellValues = numpy.transpose(sf[2].data()).tolist()
ElementM4ShellValues = numpy.transpose(sf[3].data()).tolist()
ElementM5ShellValues = numpy.transpose(sf[4].data()).tolist()
sf=None
EADL97 = False
fname = os.path.join(dirname, "EADL97_MShellConstants.dat")
if os.path.exists(fname):
sf = specfile.Specfile(fname)
EADL97_ElementM1ShellConstants = sf[0].alllabels()
EADL97_ElementM2ShellConstants = sf[1].alllabels()
EADL97_ElementM3ShellConstants = sf[2].alllabels()
EADL97_ElementM4ShellConstants = sf[3].alllabels()
EADL97_ElementM5ShellConstants = sf[4].alllabels()
EADL97_ElementM1ShellValues = numpy.transpose(sf[0].data()).tolist()
EADL97_ElementM2ShellValues = numpy.transpose(sf[1].data()).tolist()
EADL97_ElementM3ShellValues = numpy.transpose(sf[2].data()).tolist()
EADL97_ElementM4ShellValues = numpy.transpose(sf[3].data()).tolist()
EADL97_ElementM5ShellValues = numpy.transpose(sf[4].data()).tolist()
EADL97 = True
sf = None
Elements = ['H', 'He',
'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne',
'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar',
'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe',
'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se',
'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo',
'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn',
'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce',
'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy',
'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W',
'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb',
'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th',
'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf',
'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg',
'Bh', 'Hs', 'Mt']
[docs]def getsymbol(z):
return Elements[z-1]
[docs]def getz(ele):
return Elements.index(ele)+1
#fluorescence yields
[docs]def getomegam1(ele):
zEle = getz(ele)
index = ElementM1ShellConstants.index('omegaM1')
value = ElementM1ShellValues[zEle-1][index]
if (value <= 0.0) and EADL97:
if zEle > 99:
#just to avoid a crash
#I do not expect any fluorescent analysis of these elements ...
zEle = 99
index = EADL97_ElementM1ShellConstants.index('omegaM1')
value = EADL97_ElementM1ShellValues[zEle-1][index]
return value
[docs]def getomegam2(ele):
zEle = getz(ele)
index = ElementM2ShellConstants.index('omegaM2')
value = ElementM2ShellValues[zEle-1][index]
if (value <= 0.0) and EADL97:
if zEle > 99:
#just to avoid a crash
#I do not expect any fluorescent analysis of these elements ...
zEle = 99
index = EADL97_ElementM2ShellConstants.index('omegaM2')
value = EADL97_ElementM2ShellValues[zEle-1][index]
return value
[docs]def getomegam3(ele):
zEle = getz(ele)
index = ElementM3ShellConstants.index('omegaM3')
value = ElementM3ShellValues[zEle-1][index]
if (value <= 0.0) and EADL97:
if zEle > 99:
#just to avoid a crash
#I do not expect any fluorescent analysis of these elements ...
zEle = 99
index = EADL97_ElementM3ShellConstants.index('omegaM3')
value = EADL97_ElementM3ShellValues[zEle-1][index]
return value
[docs]def getomegam4(ele):
zEle = getz(ele)
index = ElementM4ShellConstants.index('omegaM4')
value = ElementM4ShellValues[zEle-1][index]
if (value <= 0.0) and EADL97:
if zEle > 99:
#just to avoid a crash
#I do not expect any fluorescent analysis of these elements ...
zEle = 99
index = EADL97_ElementM4ShellConstants.index('omegaM4')
value = EADL97_ElementM4ShellValues[zEle-1][index]
return value
[docs]def getomegam5(ele):
zEle = getz(ele)
index = ElementM5ShellConstants.index('omegaM5')
value = ElementM5ShellValues[zEle-1][index]
if (value <= 0.0) and EADL97:
if zEle > 99:
#just to avoid a crash
#I do not expect any fluorescent analysis of these elements ...
zEle = 99
index = EADL97_ElementM5ShellConstants.index('omegaM5')
value = EADL97_ElementM5ShellValues[zEle-1][index]
return value
#Coster Kronig transitions
[docs]def getCosterKronig(ele):
ck = {}
transitions = [ 'f12', 'f13', 'f14', 'f15',
'f23', 'f24', 'f25',
'f34', 'f35',
'f45']
zEle = getz(ele)
if zEle > 99:
#just to avoid a crash
#I do not expect any fluorescent analysis of these elements ...
EADL_z = 99
else:
EADL_z = zEle
ckEADL = {}
ckSum = 0.0
for t in transitions:
if t in ElementM1ShellConstants:
index = ElementM1ShellConstants.index(t)
ck[t] = ElementM1ShellValues[zEle-1][index]
if EADL97:
#try to extend with EADL97 values
index = EADL97_ElementM1ShellConstants.index(t)
ckEADL[t] = EADL97_ElementM1ShellValues[EADL_z-1][index]
elif t in ElementM2ShellConstants:
index = ElementM2ShellConstants.index(t)
ck[t] = ElementM2ShellValues[zEle-1][index]
if EADL97:
#try to extend with EADL97 values
index = EADL97_ElementM2ShellConstants.index(t)
ckEADL[t] = EADL97_ElementM2ShellValues[EADL_z-1][index]
elif t in ElementM3ShellConstants:
index = ElementM3ShellConstants.index(t)
ck[t] = ElementM3ShellValues[zEle-1][index]
if EADL97:
#try to extend with EADL97 values
index = EADL97_ElementM3ShellConstants.index(t)
ckEADL[t] = EADL97_ElementM3ShellValues[EADL_z-1][index]
elif t in ElementM4ShellConstants:
index = ElementM4ShellConstants.index(t)
ck[t] = ElementM4ShellValues[zEle-1][index]
if EADL97:
#try to extend with EADL97 values
index = EADL97_ElementM4ShellConstants.index(t)
ckEADL[t] = EADL97_ElementM4ShellValues[EADL_z-1][index]
else:
print("%s not in M-Shell Coster-Kronig transitions" % t)
continue
ckSum += ck[t]
if ckSum > 0.0:
#I do not force EADL97 because of compatibility
#with previous versions. I may offer forcing to
#EADL97 in the future.
return ck
elif EADL97:
#extended values if defined
#for instance, the region from Mg to Cl
return ckEADL
else:
return ck
#Jump ratios following Veigele: Atomic Data Tables 5 (1973) 51-111. p 54 and 55
[docs]def getjm1(z):
return 1.1
[docs]def getjm2(z):
return 1.1
[docs]def getjm3(z):
return 1.2
[docs]def getjm4(z):
return 1.5
[docs]def getjm5(z):
return (225.0/z) - 0.35
[docs]def getwjump(ele,excitedshells=[1.0,1.0,1.0,1.0,1.0]):
"""
wjump represents the probability for a vacancy to be created
on the respective M-Shell by direct photoeffect on that shell
"""
z = getz(ele)
#weights due to photoeffect
jm = [getjm1(z), getjm2(z), getjm3(z), getjm4(z), getjm5(z)]
wjump = []
i = 0
cum = 0.00
for jump in jm:
v = excitedshells[i]*(jump-1.0)/jump
wjump.append(v)
cum += v
i+=1
for i in range(len(wjump)):
wjump[i] = wjump[i] / cum
return wjump
[docs]def getweights(ele,excitedshells=None):
if type(ele) == type(" "):
pass
else:
ele = getsymbol(int(ele))
if excitedshells == None:excitedshells=[1.0,1.0,1.0,1.0,1.0]
w = getwjump(ele,excitedshells)
#weights due to Coster Kronig transitions and fluorescence yields
ck= getCosterKronig(ele)
w[0] *= 1.0
w[1] *= (1.0 + ck['f12'] * w[0])
w[2] *= (1.0 + ck['f13'] * w[0] + ck['f23'] * w[1])
w[3] *= (1.0 + ck['f14'] * w[0] + ck['f24'] * w[1] + ck['f34'] * w[2])
w[4] *= (1.0 + ck['f15'] * w[0] + ck['f25'] * w[1] + ck['f35'] * w[2] + ck['f45'] * w[3])
omega = [ getomegam1(ele), getomegam2(ele), getomegam3(ele), getomegam4(ele), getomegam5(ele)]
for i in range(len(w)):
w[i] *= omega[i]
cum = sum(w)
for i in range(len(w)):
if cum > 0.0:
w[i] /= cum
return w
ElementMShellTransitions = ElementM1ShellTransitions + \
ElementM2ShellTransitions[2:] + \
ElementM3ShellTransitions[2:] + \
ElementM4ShellTransitions[2:] + \
ElementM5ShellTransitions[2:]
nele = len(ElementM1ShellRates)
elements = range(1,nele+1)
weights = []
for ele in elements:
weights.append(getweights(ele))
weights = numpy.array(weights).astype(numpy.float)
ElementMShellRates = numpy.zeros((len(ElementM1ShellRates),len(ElementMShellTransitions)),numpy.float)
ElementMShellRates[:,0] = numpy.arange(len(ElementM1ShellRates)) + 1
n1 = len(ElementM1ShellTransitions)
ElementMShellRates[:,2:n1] = numpy.array(ElementM1ShellRates).astype(numpy.float)[:,2:] * \
numpy.resize(weights[:,0],(nele,1))
n2 = n1 + len(ElementM2ShellTransitions) - 2
ElementMShellRates[:,n1:n2] = numpy.array(ElementM2ShellRates).astype(numpy.float)[:,2:] * \
numpy.resize(weights[:,1],(nele,1))
n1 = n2
n2 = n1 + len(ElementM3ShellTransitions) - 2
ElementMShellRates[:,n1:n2] = numpy.array(ElementM3ShellRates).astype(numpy.float)[:,2:] * \
numpy.resize(weights[:,2],(nele,1))
n1 = n2
n2 = n1 + len(ElementM4ShellTransitions) - 2
ElementMShellRates[:,n1:n2] = numpy.array(ElementM4ShellRates).astype(numpy.float)[:,2:] * \
numpy.resize(weights[:,3],(nele,1))
n1 = n2
n2 = n1 + len(ElementM5ShellTransitions) - 2
ElementMShellRates[:,n1:n2] = numpy.array(ElementM5ShellRates).astype(numpy.float)[:,2:] * \
numpy.resize(weights[:,4],(nele,1))
if __name__ == "__main__":
import sys
if len(sys.argv) > 1:
ele = sys.argv[1]
if ele in Elements:
z = getz(ele)
print("Atomic Number = ",z)
print("M1-shell yield = ",getomegam1(ele))
print("M2-shell yield = ",getomegam2(ele))
print("M3-shell yield = ",getomegam3(ele))
print("M4-shell yield = ",getomegam4(ele))
print("M5-shell yield = ",getomegam5(ele))
print("M1-shell jump = ",getjm1(z))
print("M2-shell jump = ",getjm2(z))
print("M3-shell jump = ",getjm3(z))
print("M4-shell jump = ",getjm4(z))
print("M5-shell jump = ",getjm5(z))
print("Coster-Kronig = ",getCosterKronig(ele))
EADL97 = False
print("Coster-Kronig no EADL97 = ",getCosterKronig(ele))