Euler_angles_rTiO2_final.ipynb

{
 "metadata": {
  "name": "Euler_angles_rTiO2_final"
 }, 
 "nbformat": 2, 
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [
      "# We're going to run MOOSE in a loop for all of the different Euler angles to exploit the maximum phase ", 
      "# difference that will give the maximum band gap splitting", 
      "# Ideally, we will want to plot the variance of our bandgap distributions as a function of the two euler angles", 
      "import os", 
      "import subprocess", 
      "import numpy as np", 
      "", 
      "os.chdir('/home/john/projects/ferret/')", 
      "", 
      "# tensor_mechanics does a Z1 X2 Z3 rotation, we can achieve all of the useful combinations of rotations by just modifying ", 
      "# the 2 and 3 euler angles", 
      "", 
      "euler_2_vec = np.linspace(0,180,40)  ", 
      "euler_3_vec = np.linspace(0,180,40)  ", 
      "", 
      "", 
      "for j in range(0,40):", 
      "    for k in range(0,40):  ", 
      "        # Define the base file we will be iteratively modifiying #", 
      "        infile = open('/home/john/projects/ferret/ZnO_rTiO2_eulerMismatch_xstl_shell_def.i')", 
      "        # Open the out file we will be writing at each step in the iteration #", 
      "        outfile = open('/home/john/projects/ferret/newZnO_rTiO2_eulerMismatch_xstl_shell-'+repr(j)+'-'+repr(k)+'.i', 'w')", 
      "        # Note that we are using -'+repr(t)+'.i' in order to for loop the path name. This is used again in the next line.", 
      "        replacements = {'euler_angle_2 = default':'euler_angle_2 = %s' % euler_2_vec[j],'euler_angle_3 = default':'euler_angle_3 = %s' % euler_3_vec[k],'file_base = out_ZnO_rTiO2_eulerMismatch_xstl_shell':'file_base = out_ZnO_rTiO2_eulerMismatch_xstl_shell-'+repr(j)+'-'+repr(k)}", 
      "        for line in infile:", 
      "            for src, target in replacements.iteritems():", 
      "                line = line.replace(src, target)", 
      "            outfile.write(line)", 
      "        infile.close()", 
      "        outfile.close()", 
      "", 
      "#We have a total of 1600 files, where each file is ~80 Mb"
     ], 
     "language": "python", 
     "outputs": [], 
     "prompt_number": 5
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [
      "#MOOSE related stuff ran through script on HORNET:", 
      "", 
      "# The below code will harvest the finite-element data using ParaView's excellent filtration options. Here we basically use the volume filter. ", 
      "# MOOSE can probably do it but we'll just use ParaView for now.", 
      "# a new thing to note. Gnome has a hard time handling folders with a large amount of files. We essentially have 1600x120 ~ 200,000 so we need to", 
      "# iteratively load them. This is very similar to needing to use iter_txt as well. We'll use 16 partitions of loading.", 
      "# This sub-script will take a long time to run.", 
      "", 
      "import os", 
      "import subprocess", 
      "", 
      "for k in range(1,21):", 
      "    os.chdir('/home/john/projects/ParaView-bin/bin/')", 
      "    subprocess.call('pvpython /media/My\\ Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/scripts-and-out-files/MeshEuler-rTiO2-'+repr(k)+'.py',shell=True)", 
      "    subprocess.call('espeak \"Your pvpython script is done loading the Euler data for part '+repr(k)+'\"',shell=True) #tested, works in this order"
     ], 
     "language": "python", 
     "outputs": [], 
     "prompt_number": 8
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [
      "for k in range(0,40):", 
      "    for j in range(0,2):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-1/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-1/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-1')", 
      "        for t in range(0,12):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "   ", 
      "for k in range(0,40):", 
      "    for j in range(2,4):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-2/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-2/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()       ", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-2')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "            ", 
      "for k in range(0,40):", 
      "    for j in range(4,6):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-3/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-3/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-3')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "            ", 
      "for k in range(0,40):", 
      "    for j in range(6,8):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-4/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-4/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-4')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(8,10):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-5/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-5/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-5')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(10,12):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-6/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-6/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-6')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(12,14):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-7/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-7/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-7')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(14,16):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-8/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-8/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-8')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(16,18):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-9/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-9/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-9')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(18,20):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-10/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-10/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-10')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(20,22):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-11/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-11/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-11')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(22,24):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-12/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-12/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-12')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(24,26):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-13/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-13/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-13')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(26,28):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-14/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-14/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-14')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(28,30):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-15/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-15/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-15')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(30,32):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-16/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-16/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-16')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(32,34):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-17/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-17/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-17')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(34,36):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-18/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-18/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-18')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(36,38):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-19/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-19/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-19')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "        ", 
      "for k in range(0,40):", 
      "    for j in range(38,40):", 
      "        fout=open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-20/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")", 
      "        for num in range(0,12): #MeshData has 12 csv", 
      "            f = open(\"/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-20/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")", 
      "            f.next() # skip the header", 
      "            for line in f:", 
      "                fout.write(line)", 
      "            f.close()", 
      "        fout.close()", 
      "        os.chdir('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-20')", 
      "        for t in range(0,125):", 
      "            subprocess.call('rm MeshData-'+repr(k)+'-'+repr(j)+'-'+repr(t)+'.csv',shell=True)", 
      "      "
     ], 
     "language": "python", 
     "outputs": [], 
     "prompt_number": 9
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [
      "# numpy genfromtxt crashes when loading large files, have to use an iterative loading scheme", 
      "# Found on stackexchange with some interesting plots on memory. We are essentially using this sceme above with the pvpython scripts", 
      "", 
      "import numpy as np", 
      "", 
      "def iter_loadtxt(filename, delimiter=',', skiprows=1, dtype=float):", 
      "    def iter_func():", 
      "        with open(filename, 'r') as infile:", 
      "            for _ in range(skiprows):", 
      "                next(infile)", 
      "            for line in infile:", 
      "                line = line.rstrip().split(delimiter)", 
      "                for item in line:", 
      "                    yield dtype(item)", 
      "        iter_loadtxt.rowlength = len(line)", 
      "", 
      "    data = np.fromiter(iter_func(), dtype=dtype)", 
      "    data = data.reshape((-1, iter_loadtxt.rowlength))", 
      "    return data"
     ], 
     "language": "python", 
     "outputs": [], 
     "prompt_number": 1
    }, 
    {
     "cell_type": "code", 
     "collapsed": false, 
     "input": [
      "import subprocess", 
      "", 
      "euler_2_vec = np.linspace(0,180,40); euler_3_vec = np.linspace(0,180,40);", 
      "", 
      "Eg1 = {}; Eg2 = {}; Eg3 = {}; Eg4 = {}; Eg5 = {}; Eg6 = {}; Eg7 = {}; Eg8 = {}; Eg9 = {}; Eg10 = {};", 
      "Eg11 = {}; Eg12 = {}; Eg13 = {}; Eg14 = {}; Eg15 = {}; Eg16 = {}; Eg17 = {}; Eg18 = {}; Eg19 = {}; Eg20 = {};", 
      "vol1 = {}; vol2 = {}; vol3 = {}; vol4 = {}; vol5 = {}; vol6 = {}; vol7 = {}; vol8 = {}; vol9 = {}; vol10 = {};", 
      "vol11 = {}; vol12 = {}; vol13 = {}; vol14 = {}; vol15 = {}; vol16 = {}; vol17 = {}; vol18 = {}; vol19 = {}; vol20 = {};", 
      "Sxx1 = {}; Sxx2 = {}; Sxx3 = {}; Sxx4 = {}; Sxx5 = {}; Sxx6 = {}; Sxx7 = {};Sxx8 = {}; Sxx9 = {}; Sxx10 = {}; ", 
      "Sxx11 = {}; Sxx12 = {}; Sxx13 = {}; Sxx14 = {}; Sxx15 = {}; Sxx16 = {}; Sxx17 = {}; Sxx18 = {}; Sxx19 = {}; Sxx20 = {};  ", 
      "Szz1 = {}; Szz2 = {}; Szz3 = {}; Szz4 = {}; Szz5 = {}; Szz6 = {}; Szz7 = {};Szz8 = {}; Szz9 = {}; Szz10 = {}; ", 
      "Szz11 = {}; Szz12 = {}; Szz13 = {}; Szz14 = {}; Szz15 = {}; Szz16 = {}; Szz17 = {}; Szz18 = {}; Szz19 = {}; Szz20 = {};  ", 
      "", 
      "varEg = np.zeros((40,40));", 
      "varEg_weighted = np.zeros((40,40));", 
      "meanEg_weighted = np.zeros((40,40));", 
      "varSxx_weighted = np.zeros((40,40));", 
      "varSzz_weighted = np.zeros((40,40,));", 
      "vol_total_stored = np.zeros((40,40));", 
      "", 
      "fileset_data1 = {}; fileset_data2 = {}; fileset_data3 = {}; fileset_data4 = {}; fileset_data5 = {};", 
      "fileset_data6 = {}; fileset_data7 = {}; fileset_data8 = {}; fileset_data9 = {}; fileset_data10 = {};", 
      "fileset_data11 = {}; fileset_data12 = {}; fileset_data13 = {}; fileset_data14 = {}; fileset_data15 = {};", 
      "fileset_data16 = {}; fileset_data17 = {}; fileset_data18 = {}; fileset_data19 = {}; fileset_data20 = {};", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(0,2):", 
      "        fileset_data1[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-1/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(0,2):", 
      "        Eg1 = [row[9] for row in fileset_data1[k,j]]", 
      "        Sxx1 = [row[0] for row in fileset_data1[k,j]]", 
      "        Szz1 = [row[2] for row in fileset_data1[k,j]]", 
      "        vol1 = [row[13] for row in fileset_data1[k,j]]", 
      "        varEg[k,j] = np.var(Eg1)", 
      "        vol1_total = sum(vol1)", 
      "        vol_total_stored[k,j] = vol1_total", 
      "        vol1_norm = vol1/vol1_total", 
      "        meanEg1_weighted = np.einsum('i,i',vol1_norm,Eg1)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol1_norm,Eg1)", 
      "        meanSxx1_weighted = np.einsum('i,i',vol1_norm,Sxx1)", 
      "        meanSzz1_weighted = np.einsum('i,i',vol1_norm,Szz1)", 
      "        varSxx_weighted[k,j] = sum(vol1_norm * np.power((Sxx1 - meanSxx1_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol1_norm * np.power((Szz1 - meanSzz1_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol1_norm * np.power((Eg1 - meanEg1_weighted),2))", 
      "        ", 
      "%xdel fileset_data1 ", 
      "%xdel Eg1", 
      "%xdel vol1", 
      "%xdel Sxx1", 
      "%xdel Szz1", 
      "", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(2,4):", 
      "        fileset_data2[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-2/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(2,4):", 
      "        Eg2 = [row[9] for row in fileset_data2[k,j]]", 
      "        Sxx2 = [row[0] for row in fileset_data2[k,j]]", 
      "        Szz2 = [row[2] for row in fileset_data2[k,j]]", 
      "        vol2 = [row[13] for row in fileset_data2[k,j]]", 
      "        varEg[k,j] = np.var(Eg2)", 
      "        vol2_total = sum(vol2)", 
      "        vol_total_stored[k,j] = vol2_total", 
      "        vol2_norm = vol2/vol2_total", 
      "        meanEg2_weighted = np.einsum('i,i',vol2_norm,Eg2)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol2_norm,Eg2)", 
      "        meanSxx2_weighted = np.einsum('i,i',vol2_norm,Sxx2)", 
      "        meanSzz2_weighted = np.einsum('i,i',vol2_norm,Szz2)", 
      "        varSxx_weighted[k,j] = sum(vol2_norm * np.power((Sxx2 - meanSxx2_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol2_norm * np.power((Szz2 - meanSzz2_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol2_norm * np.power((Eg2 - meanEg2_weighted),2))", 
      "        ", 
      "%xdel fileset_data2 ", 
      "%xdel Eg2", 
      "%xdel vol2", 
      "%xdel Sxx2", 
      "%xdel Szz2", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(4,6):", 
      "        fileset_data3[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-3/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(4,6):", 
      "        Eg3 = [row[9] for row in fileset_data3[k,j]]", 
      "        Sxx3 = [row[0] for row in fileset_data3[k,j]]", 
      "        Szz3 = [row[2] for row in fileset_data3[k,j]]", 
      "        vol3 = [row[13] for row in fileset_data3[k,j]]", 
      "        varEg[k,j] = np.var(Eg3)", 
      "        vol3_total = sum(vol3)", 
      "        vol_total_stored[k,j] = vol3_total", 
      "        vol3_norm = vol3/vol3_total", 
      "        meanEg3_weighted = np.einsum('i,i',vol3_norm,Eg3)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol3_norm,Eg3)", 
      "        meanSxx3_weighted = np.einsum('i,i',vol3_norm,Sxx3)", 
      "        meanSzz3_weighted = np.einsum('i,i',vol3_norm,Szz3)", 
      "        varSxx_weighted[k,j] = sum(vol3_norm * np.power((Sxx3 - meanSxx3_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol3_norm * np.power((Szz3 - meanSzz3_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol3_norm * np.power((Eg3 - meanEg3_weighted),2))", 
      "        ", 
      "%xdel fileset_data3 ", 
      "%xdel Eg3", 
      "%xdel vol3", 
      "%xdel Sxx3", 
      "%xdel Szz3", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(6,8):", 
      "        fileset_data4[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-4/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(6,8):", 
      "        Eg4 = [row[9] for row in fileset_data4[k,j]]", 
      "        Sxx4 = [row[0] for row in fileset_data4[k,j]]", 
      "        Szz4 = [row[2] for row in fileset_data4[k,j]]", 
      "        vol4 = [row[13] for row in fileset_data4[k,j]]", 
      "        varEg[k,j] = np.var(Eg4)", 
      "        vol4_total = sum(vol4)", 
      "        vol_total_stored[k,j] = vol4_total", 
      "        vol4_norm = vol4/vol4_total", 
      "        meanEg4_weighted = np.einsum('i,i',vol4_norm,Eg4)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol4_norm,Eg4)", 
      "        meanSxx4_weighted = np.einsum('i,i',vol4_norm,Sxx4)", 
      "        meanSzz4_weighted = np.einsum('i,i',vol4_norm,Szz4)", 
      "        varSxx_weighted[k,j] = sum(vol4_norm * np.power((Sxx4 - meanSxx4_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol4_norm * np.power((Szz4 - meanSzz4_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol4_norm * np.power((Eg4 - meanEg4_weighted),2))", 
      "        ", 
      "%xdel fileset_data4", 
      "%xdel Eg4", 
      "%xdel vol4", 
      "%xdel Sxx4", 
      "%xdel Szz4", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(8,10):", 
      "        fileset_data5[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-5/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(8,10):", 
      "        Eg5 = [row[9] for row in fileset_data5[k,j]]", 
      "        Sxx5 = [row[0] for row in fileset_data5[k,j]]", 
      "        Szz5 = [row[2] for row in fileset_data5[k,j]]", 
      "        vol5 = [row[13] for row in fileset_data5[k,j]]", 
      "        varEg[k,j] = np.var(Eg5)", 
      "        vol5_total = sum(vol5)", 
      "        vol_total_stored[k,j] = vol5_total", 
      "        vol5_norm = vol5/vol5_total", 
      "        meanEg5_weighted = np.einsum('i,i',vol5_norm,Eg5)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol5_norm,Eg5)", 
      "        meanSxx5_weighted = np.einsum('i,i',vol5_norm,Sxx5)", 
      "        meanSzz5_weighted = np.einsum('i,i',vol5_norm,Szz5)", 
      "        varSxx_weighted[k,j] = sum(vol5_norm * np.power((Sxx5 - meanSxx5_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol5_norm * np.power((Szz5 - meanSzz5_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol5_norm * np.power((Eg5 - meanEg5_weighted),2))", 
      "        ", 
      "%xdel fileset_data5 ", 
      "%xdel Eg5", 
      "%xdel vol5", 
      "%xdel Sxx5", 
      "%xdel Szz5", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(10,12):", 
      "        fileset_data6[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-6/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(10,12):", 
      "        Eg6 = [row[9] for row in fileset_data6[k,j]]", 
      "        Sxx6 = [row[0] for row in fileset_data6[k,j]]", 
      "        Szz6 = [row[2] for row in fileset_data6[k,j]]", 
      "        vol6 = [row[13] for row in fileset_data6[k,j]]", 
      "        varEg[k,j] = np.var(Eg6)", 
      "        vol6_total = sum(vol6)", 
      "        vol_total_stored[k,j] = vol6_total", 
      "        vol6_norm = vol6/vol6_total", 
      "        meanEg6_weighted = np.einsum('i,i',vol6_norm,Eg6)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol6_norm,Eg6)", 
      "        meanSxx6_weighted = np.einsum('i,i',vol6_norm,Sxx6)", 
      "        meanSzz6_weighted = np.einsum('i,i',vol6_norm,Szz6)", 
      "        varSxx_weighted[k,j] = sum(vol6_norm * np.power((Sxx6 - meanSxx6_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol6_norm * np.power((Szz6 - meanSzz6_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol6_norm * np.power((Eg6 - meanEg6_weighted),2))", 
      "        ", 
      "%xdel fileset_data6 ", 
      "%xdel Eg6", 
      "%xdel vol6", 
      "%xdel Sxx6", 
      "%xdel Szz6", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(12,14):", 
      "        fileset_data7[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-7/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(12,14):", 
      "        Eg7 = [row[9] for row in fileset_data7[k,j]]", 
      "        Sxx7 = [row[0] for row in fileset_data7[k,j]]", 
      "        Szz7 = [row[2] for row in fileset_data7[k,j]]", 
      "        vol7 = [row[13] for row in fileset_data7[k,j]]", 
      "        varEg[k,j] = np.var(Eg7)", 
      "        vol7_total = sum(vol7)", 
      "        vol_total_stored[k,j] = vol7_total", 
      "        vol7_norm = vol7/vol7_total", 
      "        meanEg7_weighted = np.einsum('i,i',vol7_norm,Eg7)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol7_norm,Eg7)", 
      "        meanSxx7_weighted = np.einsum('i,i',vol7_norm,Sxx7)", 
      "        meanSzz7_weighted = np.einsum('i,i',vol7_norm,Szz7)", 
      "        varSxx_weighted[k,j] = sum(vol7_norm * np.power((Sxx7 - meanSxx7_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol7_norm * np.power((Szz7 - meanSzz7_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol7_norm * np.power((Eg7 - meanEg7_weighted),2))", 
      "        ", 
      "%xdel fileset_data7 ", 
      "%xdel Eg7", 
      "%xdel vol7", 
      "%xdel Sxx7", 
      "%xdel Szz7", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(14,16):", 
      "        fileset_data8[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-8/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(14,16):", 
      "        Eg8 = [row[9] for row in fileset_data8[k,j]]", 
      "        Sxx8 = [row[0] for row in fileset_data8[k,j]]", 
      "        Szz8 = [row[2] for row in fileset_data8[k,j]]", 
      "        vol8 = [row[13] for row in fileset_data8[k,j]]", 
      "        varEg[k,j] = np.var(Eg8)", 
      "        vol8_total = sum(vol8)", 
      "        vol_total_stored[k,j] = vol8_total", 
      "        vol8_norm = vol8/vol8_total", 
      "        meanEg8_weighted = np.einsum('i,i',vol8_norm,Eg8) ", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol8_norm,Eg8)", 
      "        meanSxx8_weighted = np.einsum('i,i',vol8_norm,Sxx8)", 
      "        meanSzz8_weighted = np.einsum('i,i',vol8_norm,Szz8)", 
      "        varSxx_weighted[k,j] = sum(vol8_norm * np.power((Sxx8 - meanSxx8_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol8_norm * np.power((Szz8 - meanSzz8_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol8_norm * np.power((Eg8 - meanEg8_weighted),2))", 
      "        ", 
      "%xdel fileset_data8 ", 
      "%xdel Eg8", 
      "%xdel vol8", 
      "%xdel Sxx8", 
      "%xdel Szz8", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(16,18):", 
      "        fileset_data9[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-9/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(16,18):", 
      "        Eg9 = [row[9] for row in fileset_data9[k,j]]", 
      "        Sxx9 = [row[0] for row in fileset_data9[k,j]]", 
      "        Szz9 = [row[2] for row in fileset_data9[k,j]]", 
      "        vol9 = [row[13] for row in fileset_data9[k,j]]", 
      "        varEg[k,j] = np.var(Eg9)", 
      "        vol9_total = sum(vol9)", 
      "        vol_total_stored[k,j] = vol9_total", 
      "        vol9_norm = vol9/vol9_total", 
      "        meanEg9_weighted = np.einsum('i,i',vol9_norm,Eg9)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol9_norm,Eg9)", 
      "        meanSxx9_weighted = np.einsum('i,i',vol9_norm,Sxx9)", 
      "        meanSzz9_weighted = np.einsum('i,i',vol9_norm,Szz9)", 
      "        varSxx_weighted[k,j] = sum(vol9_norm * np.power((Sxx9 - meanSxx9_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol9_norm * np.power((Szz9 - meanSzz9_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol9_norm * np.power((Eg9 - meanEg9_weighted),2))", 
      "        ", 
      "%xdel fileset_data9 ", 
      "%xdel Eg9", 
      "%xdel vol9", 
      "%xdel Sxx9", 
      "%xdel Szz9", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(18,20):", 
      "        fileset_data10[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-10/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(18,20):", 
      "        Eg10 = [row[9] for row in fileset_data10[k,j]]", 
      "        Sxx10 = [row[0] for row in fileset_data10[k,j]]", 
      "        Szz10 = [row[2] for row in fileset_data10[k,j]]", 
      "        vol10 = [row[13] for row in fileset_data10[k,j]]", 
      "        varEg[k,j] = np.var(Eg10)", 
      "        vol10_total = sum(vol10)", 
      "        vol_total_stored[k,j] = vol10_total", 
      "        vol10_norm = vol10/vol10_total", 
      "        meanEg10_weighted = np.einsum('i,i',vol10_norm,Eg10)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol10_norm,Eg10)", 
      "        meanSxx10_weighted = np.einsum('i,i',vol10_norm,Sxx10)", 
      "        meanSzz10_weighted = np.einsum('i,i',vol10_norm,Szz10)", 
      "        varSxx_weighted[k,j] = sum(vol10_norm * np.power((Sxx10 - meanSxx10_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol10_norm * np.power((Szz10 - meanSzz10_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol10_norm * np.power((Eg10 - meanEg10_weighted),2))", 
      "        ", 
      "%xdel fileset_data10 ", 
      "%xdel Eg10", 
      "%xdel vol10", 
      "%xdel Sxx10", 
      "%xdel Szz10", 
      "", 
      "subprocess.call('espeak \"Load half complete\"',shell=True)", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(20,22):", 
      "        fileset_data11[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-11/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(20,22):", 
      "        Eg11 = [row[9] for row in fileset_data11[k,j]]", 
      "        Sxx11 = [row[0] for row in fileset_data11[k,j]]", 
      "        Szz11 = [row[2] for row in fileset_data11[k,j]]", 
      "        vol11 = [row[13] for row in fileset_data11[k,j]]", 
      "        varEg[k,j] = np.var(Eg11)", 
      "        vol11_total = sum(vol11)", 
      "        vol_total_stored[k,j] = vol11_total", 
      "        vol11_norm = vol11/vol11_total", 
      "        meanEg11_weighted = np.einsum('i,i',vol11_norm,Eg11)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol11_norm,Eg11)", 
      "        meanSxx11_weighted = np.einsum('i,i',vol11_norm,Sxx11)", 
      "        meanSzz11_weighted = np.einsum('i,i',vol11_norm,Szz11)", 
      "        varSxx_weighted[k,j] = sum(vol11_norm * np.power((Sxx11 - meanSxx11_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol11_norm * np.power((Szz11 - meanSzz11_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol11_norm * np.power((Eg11 - meanEg11_weighted),2))", 
      "", 
      "%xdel fileset_data11 ", 
      "%xdel Eg11", 
      "%xdel vol11", 
      "%xdel Sxx11", 
      "%xdel Szz11", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(22,24):", 
      "        fileset_data12[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-12/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(22,24):", 
      "        Eg12 = [row[9] for row in fileset_data12[k,j]]", 
      "        Sxx12 = [row[0] for row in fileset_data12[k,j]]", 
      "        Szz12 = [row[2] for row in fileset_data12[k,j]]", 
      "        vol12 = [row[13] for row in fileset_data12[k,j]]", 
      "        varEg[k,j] = np.var(Eg12)", 
      "        vol12_total = sum(vol12)", 
      "        vol_total_stored[k,j] = vol12_total", 
      "        vol12_norm = vol12/vol12_total", 
      "        meanEg12_weighted = np.einsum('i,i',vol12_norm,Eg12)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol12_norm,Eg12)", 
      "        meanSxx12_weighted = np.einsum('i,i',vol12_norm,Sxx12)", 
      "        meanSzz12_weighted = np.einsum('i,i',vol12_norm,Szz12)", 
      "        varSxx_weighted[k,j] = sum(vol12_norm * np.power((Sxx12 - meanSxx12_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol12_norm * np.power((Szz12 - meanSzz12_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol12_norm * np.power((Eg12 - meanEg12_weighted),2))", 
      "        ", 
      "%xdel fileset_data12 ", 
      "%xdel Eg12", 
      "%xdel vol12", 
      "%xdel Sxx12", 
      "%xdel Szz12", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(24,26):", 
      "        fileset_data13[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-13/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(24,26):", 
      "        Eg13 = [row[9] for row in fileset_data13[k,j]]", 
      "        Sxx13 = [row[0] for row in fileset_data13[k,j]]", 
      "        Szz13 = [row[2] for row in fileset_data13[k,j]]", 
      "        vol13 = [row[13] for row in fileset_data13[k,j]]", 
      "        varEg[k,j] = np.var(Eg13)", 
      "        vol13_total = sum(vol13)", 
      "        vol_total_stored[k,j] = vol13_total", 
      "        vol13_norm = vol13/vol13_total", 
      "        meanEg13_weighted = np.einsum('i,i',vol13_norm,Eg13)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol13_norm,Eg13)", 
      "        meanSxx13_weighted = np.einsum('i,i',vol13_norm,Sxx13)", 
      "        meanSzz13_weighted = np.einsum('i,i',vol13_norm,Szz13)", 
      "        varSxx_weighted[k,j] = sum(vol13_norm * np.power((Sxx13 - meanSxx13_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol13_norm * np.power((Szz13 - meanSzz13_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol13_norm * np.power((Eg13 - meanEg13_weighted),2))", 
      "        ", 
      "%xdel fileset_data13 ", 
      "%xdel Eg13", 
      "%xdel vol13", 
      "%xdel Sxx13", 
      "%xdel Szz13", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(26,28):", 
      "        fileset_data14[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-14/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(26,28):", 
      "        Eg14 = [row[9] for row in fileset_data14[k,j]]", 
      "        Sxx14 = [row[0] for row in fileset_data14[k,j]]", 
      "        Szz14 = [row[2] for row in fileset_data14[k,j]]", 
      "        vol14 = [row[13] for row in fileset_data14[k,j]]", 
      "        varEg[k,j] = np.var(Eg14)", 
      "        vol14_total = sum(vol14)", 
      "        vol_total_stored[k,j] = vol14_total", 
      "        vol14_norm = vol14/vol14_total", 
      "        meanEg14_weighted = np.einsum('i,i',vol14_norm,Eg14)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol14_norm,Eg14)", 
      "        meanSxx14_weighted = np.einsum('i,i',vol14_norm,Sxx14)", 
      "        meanSzz14_weighted = np.einsum('i,i',vol14_norm,Szz14)", 
      "        varSxx_weighted[k,j] = sum(vol14_norm * np.power((Sxx14 - meanSxx14_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol14_norm * np.power((Szz14 - meanSzz14_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol14_norm * np.power((Eg14 - meanEg14_weighted),2))", 
      "        ", 
      "%xdel fileset_data14 ", 
      "%xdel Eg14", 
      "%xdel vol14", 
      "%xdel Sxx14", 
      "%xdel Szz14", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(28,30):", 
      "        fileset_data15[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-15/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(28,30):", 
      "        Eg15 = [row[9] for row in fileset_data15[k,j]]", 
      "        Sxx15 = [row[0] for row in fileset_data15[k,j]]", 
      "        Szz15 = [row[2] for row in fileset_data15[k,j]]", 
      "        vol15 = [row[13] for row in fileset_data15[k,j]]", 
      "        varEg[k,j] = np.var(Eg15)", 
      "        vol15_total = sum(vol15)", 
      "        vol_total_stored[k,j] = vol15_total", 
      "        vol15_norm = vol15/vol15_total", 
      "        meanEg15_weighted = np.einsum('i,i',vol15_norm,Eg15)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol15_norm,Eg15)", 
      "        meanSxx15_weighted = np.einsum('i,i',vol15_norm,Sxx15)", 
      "        meanSzz15_weighted = np.einsum('i,i',vol15_norm,Szz15)", 
      "        varSxx_weighted[k,j] = sum(vol15_norm * np.power((Sxx15 - meanSxx15_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol15_norm * np.power((Szz15 - meanSzz15_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol15_norm * np.power((Eg15 - meanEg15_weighted),2))", 
      "        ", 
      "%xdel fileset_data15 ", 
      "%xdel Eg15", 
      "%xdel vol15", 
      "%xdel Sxx15", 
      "%xdel Szz15", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(30,32):", 
      "        fileset_data16[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-16/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(30,32):", 
      "        Eg16 = [row[9] for row in fileset_data16[k,j]]", 
      "        Sxx16 = [row[0] for row in fileset_data16[k,j]]", 
      "        Szz16 = [row[2] for row in fileset_data16[k,j]]", 
      "        vol16 = [row[13] for row in fileset_data16[k,j]]", 
      "        varEg[k,j] = np.var(Eg16)", 
      "        vol16_total = sum(vol16)", 
      "        vol_total_stored[k,j] = vol16_total", 
      "        vol16_norm = vol16/vol16_total", 
      "        meanEg16_weighted = np.einsum('i,i',vol16_norm,Eg16)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol16_norm,Eg16)", 
      "        meanSxx16_weighted = np.einsum('i,i',vol16_norm,Sxx16)", 
      "        meanSzz16_weighted = np.einsum('i,i',vol16_norm,Szz16)", 
      "        varSxx_weighted[k,j] = sum(vol16_norm * np.power((Sxx16 - meanSxx16_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol16_norm * np.power((Szz16 - meanSzz16_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol16_norm * np.power((Eg16 - meanEg16_weighted),2))", 
      "        ", 
      "%xdel fileset_data16 ", 
      "%xdel Eg16", 
      "%xdel vol16", 
      "%xdel Sxx16", 
      "%xdel Szz16", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(32,34):", 
      "        fileset_data17[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-17/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(32,34):", 
      "        Eg17 = [row[9] for row in fileset_data17[k,j]]", 
      "        Sxx17 = [row[0] for row in fileset_data17[k,j]]", 
      "        Szz17 = [row[2] for row in fileset_data17[k,j]]", 
      "        vol17 = [row[13] for row in fileset_data17[k,j]]", 
      "        varEg[k,j] = np.var(Eg17)", 
      "        vol17_total = sum(vol17)", 
      "        vol_total_stored[k,j] = vol17_total", 
      "        vol17_norm = vol17/vol17_total", 
      "        meanEg17_weighted = np.einsum('i,i',vol17_norm,Eg17)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol17_norm,Eg17)", 
      "        meanSxx17_weighted = np.einsum('i,i',vol17_norm,Sxx17)", 
      "        meanSzz17_weighted = np.einsum('i,i',vol17_norm,Szz17)", 
      "        varSxx_weighted[k,j] = sum(vol17_norm * np.power((Sxx17 - meanSxx17_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol17_norm * np.power((Szz17 - meanSzz17_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol17_norm * np.power((Eg17 - meanEg17_weighted),2))", 
      "        ", 
      "%xdel fileset_data17", 
      "%xdel Eg17", 
      "%xdel vol17", 
      "%xdel Sxx17", 
      "%xdel Szz17", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(34,36):", 
      "        fileset_data18[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-18/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(34,36):", 
      "        Eg18 = [row[9] for row in fileset_data18[k,j]]", 
      "        Sxx18 = [row[0] for row in fileset_data18[k,j]]", 
      "        Szz18 = [row[2] for row in fileset_data18[k,j]]", 
      "        vol18 = [row[13] for row in fileset_data18[k,j]]", 
      "        varEg[k,j] = np.var(Eg18)", 
      "        vol18_total = sum(vol18)", 
      "        vol_total_stored[k,j] = vol18_total", 
      "        vol18_norm = vol18/vol18_total", 
      "        meanEg18_weighted = np.einsum('i,i',vol18_norm,Eg18)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol18_norm,Eg18)", 
      "        meanSxx18_weighted = np.einsum('i,i',vol18_norm,Sxx18)", 
      "        meanSzz18_weighted = np.einsum('i,i',vol18_norm,Szz18)", 
      "        varSxx_weighted[k,j] = sum(vol18_norm * np.power((Sxx18 - meanSxx18_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol18_norm * np.power((Szz18 - meanSzz18_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol18_norm * np.power((Eg18 - meanEg18_weighted),2))", 
      "        ", 
      "%xdel fileset_data18", 
      "%xdel Eg18", 
      "%xdel vol18", 
      "%xdel Sxx18", 
      "%xdel Szz18", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(36,38):", 
      "        fileset_data19[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-19/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(36,38):", 
      "        Eg19 = [row[9] for row in fileset_data19[k,j]]", 
      "        Sxx19 = [row[0] for row in fileset_data19[k,j]]", 
      "        Szz19 = [row[2] for row in fileset_data19[k,j]]", 
      "        vol19 = [row[13] for row in fileset_data19[k,j]]", 
      "        varEg[k,j] = np.var(Eg19)", 
      "        vol19_total = sum(vol19)", 
      "        vol_total_stored[k,j] = vol19_total", 
      "        vol19_norm = vol19/vol19_total", 
      "        meanEg19_weighted = np.einsum('i,i',vol19_norm,Eg19)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol19_norm,Eg19)", 
      "        meanSxx19_weighted = np.einsum('i,i',vol19_norm,Sxx19)", 
      "        meanSzz19_weighted = np.einsum('i,i',vol19_norm,Szz19)", 
      "        varSxx_weighted[k,j] = sum(vol19_norm * np.power((Sxx19 - meanSxx19_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol19_norm * np.power((Szz19 - meanSzz19_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol19_norm * np.power((Eg19 - meanEg19_weighted),2))", 
      "        ", 
      "%xdel fileset_data19 ", 
      "%xdel Eg19", 
      "%xdel vol19", 
      "%xdel Sxx19", 
      "%xdel Szz19", 
      "", 
      "for k in range(0,40):", 
      "    for j in range(38,40):", 
      "        fileset_data20[k,j] = iter_loadtxt('/media/My Passport/Linux/projects/calculations/core_shell/final_plots/vary_Euler_rTiO2/secondary-20/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)", 
      "for k in range(0,40):", 
      "    for j in range(38,40):", 
      "        Eg20 = [row[9] for row in fileset_data20[k,j]]", 
      "        Sxx20 = [row[0] for row in fileset_data20[k,j]]", 
      "        Szz20 = [row[2] for row in fileset_data20[k,j]]", 
      "        vol20 = [row[13] for row in fileset_data20[k,j]]", 
      "        varEg[k,j] = np.var(Eg20)", 
      "        vol20_total = sum(vol20)", 
      "        vol_total_stored[k,j] = vol20_total", 
      "        vol20_norm = vol20/vol20_total", 
      "        meanEg20_weighted = np.einsum('i,i',vol20_norm,Eg20)", 
      "        meanEg_weighted[k,j] = np.einsum('i,i',vol20_norm,Eg20)", 
      "        meanSxx20_weighted = np.einsum('i,i',vol20_norm,Sxx20)", 
      "        meanSzz20_weighted = np.einsum('i,i',vol20_norm,Szz20)", 
      "        varSxx_weighted[k,j] = sum(vol20_norm * np.power((Sxx20 - meanSxx20_weighted),2))", 
      "        varSzz_weighted[k,j] = sum(vol20_norm * np.power((Szz20 - meanSzz20_weighted),2))", 
      "        varEg_weighted[k,j] = sum(vol20_norm * np.power((Eg20 - meanEg20_weighted),2))", 
      "        ", 
      "%xdel fileset_data20 ", 
      "%xdel Eg20", 
      "%xdel vol20", 
      "%xdel Sxx20", 
      "%xdel Szz20", 
      "", 
      "subprocess.call('espeak \"Load complete\"',shell=True)"
     ], 
     "language": "python", 
     "outputs": [
      {
       "output_type": "pyout", 
       "prompt_number": 2, 
       "text": [
        "0"
       ]
      }
     ], 
     "prompt_number": 2
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [
      "import numpy as np", 
      "from mpl_toolkits.mplot3d import Axes3D", 
      "import matplotlib.pyplot as plt", 
      "from matplotlib import rc", 
      "", 
      "plt.pcolormesh(euler_2_vec,euler_3_vec,(varEg)*np.power(10,8))", 
      "#use \\theta \\phi \\Psi convention", 
      "plt.ylabel('$\\phi$',fontsize=18)", 
      "plt.xlabel('$\\Psi$',fontsize= 18)", 
      "#%xdel cbar3", 
      "cbar3 = plt.colorbar()", 
      "cbar3.ax.set_ylabel('$\\mathrm{var} ( E_{g} )\\,\\,\\,10^{-8} \\,\\,[\\mathrm{eV}^2]$',fontsize=18)", 
      "plt.xlim([0,180])", 
      "tick_vals = np.linspace(0,180,3)", 
      "tick_labels = [tick_vals[i] for i in range(len(tick_vals))]", 
      "tick_labels[0] = ''", 
      "tick_labels[1] = '$\\pi/2$'", 
      "tick_labels[2] = '$\\pi$'", 
      "plt.xticks(tick_vals, tick_labels)", 
      "plt.ylim([0,180])", 
      "tick_vals = np.linspace(0,180,3)", 
      "tick_labels = [tick_vals[i] for i in range(len(tick_vals))]", 
      "tick_labels[0] = '0'", 
      "tick_labels[1] = '$\\pi/2$'", 
      "tick_labels[2] = '$\\pi$'", 
      "plt.yticks(tick_vals, tick_labels)", 
      "plt.tick_params(axis='both', which='major', labelsize=18)", 
      "#plt.title('volume weighted variance of band gap for ZnO shell')", 
      "plt.savefig(\"/home/john/varEg_weighted_rTiO2_shell.eps\",format='eps',dpi=600,bbox_inches = 'tight')", 
      "plt.show()"
     ], 
     "language": "python", 
     "outputs": [], 
     "prompt_number": 3
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [
      "from mpl_toolkits.mplot3d import axes3d", 
      "import matplotlib.pyplot as plt", 
      "import numpy as np", 
      "", 
      "fig = plt.figure()", 
      "ax = fig.add_subplot(111, projection='3d')", 
      "X, Y, Z = axes3d.get_test_data(0.05)", 
      "ax.plot_wireframe(X, Y, Z, rstride=10, cstride=10)", 
      "", 
      "plt.show()"
     ], 
     "language": "python", 
     "outputs": [], 
     "prompt_number": 15
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [], 
     "language": "python", 
     "outputs": []
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [], 
     "language": "python", 
     "outputs": []
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [], 
     "language": "python", 
     "outputs": []
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [], 
     "language": "python", 
     "outputs": []
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [], 
     "language": "python", 
     "outputs": []
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [], 
     "language": "python", 
     "outputs": []
    }
   ]
  }
 ]
}