#/*########################################################################## # # The PyMca X-Ray Fluorescence Toolkit # # Copyright (c) 2004-2016 European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF by the Software group. # # 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: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # 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 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # #############################################################################*/ __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 getDataFile sf=specfile.Specfile(getDataFile("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(getDataFile("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 fname = getDataFile("EADL97_MShellConstants.dat") 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'] def getsymbol(z): return Elements[z-1] def getz(ele): return Elements.index(ele)+1 #fluorescence yields 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 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 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 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 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 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 def getjm1(z): return 1.1 def getjm2(z): return 1.1 def getjm3(z): return 1.2 def getjm4(z): return 1.5 def getjm5(z): return (225.0/z) - 0.35 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 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.float64) ElementMShellRates = numpy.zeros((len(ElementM1ShellRates),len(ElementMShellTransitions)),numpy.float64) ElementMShellRates[:,0] = numpy.arange(len(ElementM1ShellRates)) + 1 n1 = len(ElementM1ShellTransitions) ElementMShellRates[:,2:n1] = numpy.array(ElementM1ShellRates).astype(numpy.float64)[:,2:] * \ numpy.resize(weights[:,0],(nele,1)) n2 = n1 + len(ElementM2ShellTransitions) - 2 ElementMShellRates[:,n1:n2] = numpy.array(ElementM2ShellRates).astype(numpy.float64)[:,2:] * \ numpy.resize(weights[:,1],(nele,1)) n1 = n2 n2 = n1 + len(ElementM3ShellTransitions) - 2 ElementMShellRates[:,n1:n2] = numpy.array(ElementM3ShellRates).astype(numpy.float64)[:,2:] * \ numpy.resize(weights[:,2],(nele,1)) n1 = n2 n2 = n1 + len(ElementM4ShellTransitions) - 2 ElementMShellRates[:,n1:n2] = numpy.array(ElementM4ShellRates).astype(numpy.float64)[:,2:] * \ numpy.resize(weights[:,3],(nele,1)) n1 = n2 n2 = n1 + len(ElementM5ShellTransitions) - 2 ElementMShellRates[:,n1:n2] = numpy.array(ElementM5ShellRates).astype(numpy.float64)[:,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))