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#-*- coding: utf-8 -*-
# Written by Zack Gainsforth 2015

# Using the constants from 
#
#		Low-Energy X-ray Interaction Coefficients:
#		Photoabsorption, Scattering, and Reflection
#			E = 30-30,000 eV, Z = 1-92
#
#	        B. L. Henke, E. M. Gullikson, and J. C. Davis
#			Center for X-Ray Optics, 2-400
#			Lawrence Berkeley Laboratory
#			Berkeley, California 94720
#
# To download the nff files used below, go here:
# http://henke.lbl.gov/optical_constants/asf.html

# Using QuickPlot from https://gist.github.com/f16e032f26994d02e480

from pylab import *
import QuickPlot
Mn = genfromtxt('mn.nff')
Fe = genfromtxt('fe.nff')
Co = genfromtxt('co.nff')

Eindexes = range(400,440)
#Eindexes = range(409,450)
E = Mn[Eindexes,0]
Mn = Mn[Eindexes,2]
Fe = Fe[Eindexes,2]
Co = Co[Eindexes,2]

h = 4.135667516e-15
c = 299792458
r0 = 2.8179403268e-15
NAvogadro = 6.02214129e23

muMn = 2 * r0 * h*c/E * Mn/54.93805
muFe = 2 * r0 * h*c/E * Fe/55.84515
muCo = 2 * r0 * h*c/E * Co/58.93320

# My units are m^2/g
# This converts it to cm^2/g
AMn = NAvogadro * muMn * 10000 
AFe = NAvogadro * muFe * 10000 
ACo = NAvogadro * muCo * 10000 

# Now these are photoabsorption cross sections in cm^2/g

QuickPlot.QuickPlot(vstack((E,E,E)), vstack((AMn, AFe, ACo)), boldlevel=3, xlabel='eV', ylabel='$\sigma$ cm$^2$/g')
axvline(x=8048, ymin=0, ymax = 200, linewidth=3, color='k')
legend(['Mn', 'Fe', 'Co'])
tight_layout()

show()