#/*########################################################################## # # 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("LShellRates.dat")) ElementL1ShellTransitions = sf[0].alllabels() ElementL2ShellTransitions = sf[1].alllabels() ElementL3ShellTransitions = sf[2].alllabels() ElementL1ShellRates = numpy.transpose(sf[0].data()).tolist() ElementL2ShellRates = numpy.transpose(sf[1].data()).tolist() ElementL3ShellRates = numpy.transpose(sf[2].data()).tolist() sf=specfile.Specfile(getDataFile("LShellConstants.dat")) ElementL1ShellConstants = sf[0].alllabels() ElementL2ShellConstants = sf[1].alllabels() ElementL3ShellConstants = sf[2].alllabels() ElementL1ShellValues = numpy.transpose(sf[0].data()).tolist() ElementL2ShellValues = numpy.transpose(sf[1].data()).tolist() ElementL3ShellValues = numpy.transpose(sf[2].data()).tolist() sf=None fname = getDataFile("EADL97_LShellConstants.dat") sf = specfile.Specfile(fname) EADL97_ElementL1ShellConstants = sf[0].alllabels() EADL97_ElementL2ShellConstants = sf[1].alllabels() EADL97_ElementL3ShellConstants = sf[2].alllabels() EADL97_ElementL1ShellValues = numpy.transpose(sf[0].data()).tolist() EADL97_ElementL2ShellValues = numpy.transpose(sf[1].data()).tolist() EADL97_ElementL3ShellValues = numpy.transpose(sf[2].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 getomegal1(ele): zEle = getz(ele) index = ElementL1ShellConstants.index('omegaL1') value = ElementL1ShellValues[zEle-1][index] if (value <= 0.0) and EADL97: #extend with EADL97 values if zEle > 99: #just to avoid a crash #I do not expect any fluorescent analysis of these elements ... zEle = 99 index = EADL97_ElementL1ShellConstants.index('omegaL1') value = EADL97_ElementL1ShellValues[zEle-1][index] return value def getomegal2(ele): zEle = getz(ele) index = ElementL2ShellConstants.index('omegaL2') value = ElementL2ShellValues[zEle-1][index] if (value <= 0.0) and EADL97: #extend with EADL97 values if zEle > 99: #just to avoid a crash #I do not expect any fluorescent analysis of these elements ... zEle = 99 index = EADL97_ElementL2ShellConstants.index('omegaL2') value = EADL97_ElementL2ShellValues[zEle-1][index] return value def getomegal3(ele): zEle = getz(ele) index = ElementL3ShellConstants.index('omegaL3') value = ElementL3ShellValues[zEle-1][index] if (value <= 0.0) and EADL97: #extend with EADL97 values if zEle > 99: #just to avoid a crash #I do not expect any fluorescent analysis of these elements ... zEle = 99 index = EADL97_ElementL3ShellConstants.index('omegaL3') value = EADL97_ElementL3ShellValues[zEle-1][index] return value def getCosterKronig(ele): ck = {} transitions = [ 'f12', 'f13', 'f23'] 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 ElementL1ShellConstants: index = ElementL1ShellConstants.index(t) ck[t] = ElementL1ShellValues[zEle-1][index] if EADL97: #extend with EADL97 values index = EADL97_ElementL1ShellConstants.index(t) ckEADL[t] = EADL97_ElementL1ShellValues[EADL_z-1][index] elif t in ElementL2ShellConstants: index = ElementL2ShellConstants.index(t) ck[t] = ElementL2ShellValues[zEle-1][index] if EADL97: #extend with EADL97 values index = EADL97_ElementL2ShellConstants.index(t) ckEADL[t] = EADL97_ElementL2ShellValues[EADL_z-1][index] elif t in ElementL3ShellConstants: index = ElementL3ShellConstants.index(t) ck[t] = ElementL3ShellValues[zEle-1][index] if EADL97: #extend with EADL97 values index = EADL97_ElementL3ShellConstants.index(t) ckEADL[t] = EADL97_ElementL3ShellValues[EADL_z-1][index] else: print("%s not in L-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 getjl1(z): return 1.2 def getjl2(z): return 1.4 def getjl3(z): return (80.0/z) + 1.5 def getwjump(ele,excitedshells=[1.0,1.0,1.0]): """ wjump represents the probability for a vacancy to be created on the respective L-Shell by direct photoeffect on that shell """ z = getz(ele) #weights due to photoeffect jl = [getjl1(z), getjl2(z), getjl3(z)] wjump = [] i = 0 cum = 0.00 for jump in jl: 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] 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]) omega = [ getomegal1(ele), getomegal2(ele), getomegal3(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 if 'TOTAL' in ElementL1ShellTransitions: labeloffset = 2 else: labeloffset = 1 ElementLShellTransitions = ElementL1ShellTransitions + \ ElementL2ShellTransitions[labeloffset:] + \ ElementL3ShellTransitions[labeloffset:] for i in range(len(ElementLShellTransitions)): ElementLShellTransitions[i]+="*" nele = len(ElementL1ShellRates) elements = range(1,nele+1) weights = [] for ele in elements: weights.append(getweights(ele)) weights = numpy.array(weights).astype(numpy.float64) ElementLShellRates = numpy.zeros((len(ElementL1ShellRates), len(ElementLShellTransitions)), numpy.float64) ElementLShellRates[:,0] = numpy.arange(len(ElementL1ShellRates)) + 1 n1 = len(ElementL1ShellTransitions) lo = labeloffset ElementLShellRates[:,lo:n1] = numpy.array(ElementL1ShellRates).astype(numpy.float64)[:,lo:] * \ numpy.resize(weights[:,0],(nele,1)) n2 = n1 + len(ElementL2ShellTransitions) - lo ElementLShellRates[:,n1:n2] = numpy.array(ElementL2ShellRates).astype(numpy.float64)[:,lo:]* \ numpy.resize(weights[:,1],(nele,1)) n1 = n2 n2 = n1 + len(ElementL3ShellTransitions) - lo ElementLShellRates[:,n1:n2] = numpy.array(ElementL3ShellRates).astype(numpy.float64)[:,lo:]* \ numpy.resize(weights[:,2],(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("L1-shell yield = ",getomegal1(ele)) print("L2-shell yield = ",getomegal2(ele)) print("L3-shell yield = ",getomegal3(ele)) print("L1-shell jump = ",getjl1(z)) print("L2-shell jump = ",getjl2(z)) print("L3-shell jump = ",getjl3(z)) print("Coster-Kronig = ",getCosterKronig(ele))