Source code for PyMca5.PyMcaPhysics.xrf.LShell

#/*##########################################################################
#
# 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
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# 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
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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, "LShellRates.dat")
if not os.path.exists(inputfile):
    dirname = os.path.dirname(dirname)
    inputfile = os.path.join(dirname, "LShellRates.dat")
    if dirname.lower().endswith(".zip"):
        dirname = os.path.dirname(dirname)
        inputfile = os.path.join(dirname, "LShellRates.dat")
    if not os.path.exists(inputfile):
        print("Cannot find inputfile ",inputfile)
        raise IOError("Cannot find LShellRates.dat file")
sf=specfile.Specfile(os.path.join(dirname, "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(os.path.join(dirname, "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

EADL97 = False
fname = os.path.join(dirname, "EADL97_LShellConstants.dat")
if os.path.exists(fname):
    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']


[docs]def getsymbol(z): return Elements[z-1]
[docs]def getz(ele): return Elements.index(ele)+1
#fluorescence yields
[docs]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
[docs]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
[docs]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
[docs]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
[docs]def getjl1(z): return 1.2
[docs]def getjl2(z): return 1.4
[docs]def getjl3(z): return (80.0/z) + 1.5
[docs]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
[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] 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.float) ElementLShellRates = numpy.zeros((len(ElementL1ShellRates), len(ElementLShellTransitions)), numpy.float) ElementLShellRates[:,0] = numpy.arange(len(ElementL1ShellRates)) + 1 n1 = len(ElementL1ShellTransitions) lo = labeloffset ElementLShellRates[:,lo:n1] = numpy.array(ElementL1ShellRates).astype(numpy.float)[:,lo:] * \ numpy.resize(weights[:,0],(nele,1)) n2 = n1 + len(ElementL2ShellTransitions) - lo ElementLShellRates[:,n1:n2] = numpy.array(ElementL2ShellRates).astype(numpy.float)[:,lo:]* \ numpy.resize(weights[:,1],(nele,1)) n1 = n2 n2 = n1 + len(ElementL3ShellTransitions) - lo ElementLShellRates[:,n1:n2] = numpy.array(ElementL3ShellRates).astype(numpy.float)[:,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))