euler_angles_rTiO2_Eg.ipynb

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 "cells": [
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   "cell_type": "code",
   "execution_count": null,
   "metadata": {
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   "outputs": [],
   "source": [
    "# We're going to run MOOSE in a loop for all of the different Euler angles to exploit the maximum phase \n",
    "# difference that will give the maximum band gap splitting\n",
    "# Ideally, we will want to plot the variance of our bandgap distributions as a function of the two euler angles\n",
    "import os\n",
    "import subprocess\n",
    "import numpy as np\n",
    "\n",
    "os.chdir('/home/john/projects/ferret/')\n",
    "\n",
    "# tensor_mechanics does a Z1 X2 Z3 rotation, we can achieve all of the useful combinations of rotations by just modifying \n",
    "# the 2 and 3 euler angles\n",
    "\n",
    "euler_2_vec = np.linspace(0,180,40)  \n",
    "euler_3_vec = np.linspace(0,180,40)  \n",
    "\n",
    "\n",
    "for j in range(0,40):\n",
    "    for k in range(0,40):  \n",
    "        # Define the base file we will be iteratively modifiying #\n",
    "        infile = open('/home/john/projects/ferret/ZnO_rTiO2_eulerMismatch_xstl_shell_def.i')\n",
    "        # Open the out file we will be writing at each step in the iteration #\n",
    "        outfile = open('/home/john/projects/ferret/newZnO_rTiO2_eulerMismatch_xstl_shell-'+repr(j)+'-'+repr(k)+'.i', 'w')\n",
    "        # Note that we are using -'+repr(t)+'.i' in order to for loop the path name. This is used again in the next line.\n",
    "        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)}\n",
    "        for line in infile:\n",
    "            for src, target in replacements.iteritems():\n",
    "                line = line.replace(src, target)\n",
    "            outfile.write(line)\n",
    "        infile.close()\n",
    "        outfile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#MOOSE related stuff ran through script on HORNET:\n",
    "# The below code will harvest the finite-element data using ParaView's excellent filtration options. Here we basically use the volume filter. \n",
    "# MOOSE can probably do it but we'll just use ParaView for now.\n",
    "# a new thing to note. Gnome has a hard time handling folders with a large amount of files. We essentially have 625x120 ~ 75,000 so we need to\n",
    "# iteratively load them. This is very similar to needing to use iter_txt as well. \n",
    "# We load in batches of 25x120, which is much more manageable for this computer.\n",
    "\n",
    "import os\n",
    "import subprocess\n",
    "\n",
    "os.chdir('/home/john/projects/ParaView-bin/bin/')\n",
    "subprocess.call('pvpython /home/john/projects/scripts/MeshEuler-rTiO2-1.py',shell=True)\n",
    "subprocess.call('espeak \"Your pvpython script is done loading the euler data for part 1\"',shell=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
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     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "os.chdir('/home/john/projects/ParaView-bin/bin/')\n",
    "subprocess.call('pvpython /home/john/projects/scripts/MeshEuler-rTiO2-2.py',shell=True)\n",
    "subprocess.call('espeak \"Your pvpython script is done loading the euler data for part 2\"',shell=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
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     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "os.chdir('/home/john/projects/ParaView-bin/bin/')\n",
    "subprocess.call('pvpython /home/john/projects/scripts/MeshEuler-rTiO2-3.py',shell=True)\n",
    "subprocess.call('espeak \"Your pvpython script is done loading the euler data for part 3\"',shell=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
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     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "os.chdir('/home/john/projects/ParaView-bin/bin/')\n",
    "subprocess.call('pvpython /home/john/projects/scripts/MeshEuler-rTiO2-4.py',shell=True)\n",
    "subprocess.call('espeak \"Your pvpython script is done loading the euler data for part 4\"',shell=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "os.chdir('/home/john/projects/ParaView-bin/bin/')\n",
    "subprocess.call('pvpython /home/john/projects/scripts/MeshEuler-rTiO2-5.py',shell=True)\n",
    "subprocess.call('espeak \"Your pvpython script is done loading the euler data for part 5. Freddy is a moron.\"',shell=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# now loop this 25x12 times to get the comp files. We have 5 partitions in the data since we use 25/5\n",
    "# MeshData-k-j-num\n",
    "\n",
    "for k in range(0,6):\n",
    "    for j in range(0,25):\n",
    "        fout=open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv1/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")\n",
    "        for num in range(0,12): #MeshData has 12 csv\n",
    "            f = open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv1/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")\n",
    "            f.next() # skip the header\n",
    "            for line in f:\n",
    "                fout.write(line)\n",
    "            f.close()\n",
    "        fout.close()\n",
    "\n",
    "for k in range(6,11):\n",
    "    for j in range(0,25):\n",
    "        fout=open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv2/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")\n",
    "        for num in range(0,12):\n",
    "            f = open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv2/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")\n",
    "            f.next() # skip the header\n",
    "            for line in f:\n",
    "                fout.write(line)\n",
    "            f.close()\n",
    "        fout.close()\n",
    "        \n",
    "        \n",
    "for k in range(11,16):\n",
    "    for j in range(0,25):\n",
    "        fout=open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv3/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")\n",
    "        for num in range(0,12):\n",
    "            f = open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv3/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")\n",
    "            f.next() # skip the header\n",
    "            for line in f:\n",
    "                fout.write(line)\n",
    "            f.close()\n",
    "        fout.close()\n",
    "        \n",
    "for k in range(16,21):\n",
    "    for j in range(0,25):\n",
    "        fout=open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv4/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")\n",
    "        for num in range(0,12):\n",
    "            f = open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv4/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")\n",
    "            f.next() # skip the header\n",
    "            for line in f:\n",
    "                fout.write(line)\n",
    "            f.close()\n",
    "        fout.close()\n",
    "        \n",
    "for k in range(21,25):\n",
    "    for j in range(0,25):\n",
    "        fout=open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv5/MeshData-\"+repr(k)+\"-\"+repr(j)+\"COMP.csv\",\"a\")\n",
    "        for num in range(0,12):\n",
    "            f = open(\"/home/john/projects/calculations/core_shell/rTiO2-eulercsv5/MeshData-\"+repr(k)+\"-\"+repr(j)+\"-\"+str(num)+\".csv\")\n",
    "            f.next() # skip the header\n",
    "            for line in f:\n",
    "                fout.write(line)\n",
    "            f.close()\n",
    "        fout.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# numpy genfromtxt crashes when loading large files, have to use an iterative loading scheme\n",
    "# Found on stackexchange with some interesting plots on memory. We are essentially using this sceme above with the pvpython scripts\n",
    "\n",
    "import numpy as np\n",
    "\n",
    "def iter_loadtxt(filename, delimiter=',', skiprows=1, dtype=float):\n",
    "    def iter_func():\n",
    "        with open(filename, 'r') as infile:\n",
    "            for _ in range(skiprows):\n",
    "                next(infile)\n",
    "            for line in infile:\n",
    "                line = line.rstrip().split(delimiter)\n",
    "                for item in line:\n",
    "                    yield dtype(item)\n",
    "        iter_loadtxt.rowlength = len(line)\n",
    "\n",
    "    data = np.fromiter(iter_func(), dtype=dtype)\n",
    "    data = data.reshape((-1, iter_loadtxt.rowlength))\n",
    "    return data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
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     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Scratch all the above like four sentences. While it is true, this computer has a finite amount of ram, we have to be careful with how we approach this\n",
    "# at all steps in the loading process. We can't iteratively load all 625 sets of data and store them in memory, but we can iteratively load one set, \n",
    "# save what we want, clear the rest, and then continue.\n",
    "\n",
    "\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "import pylab\n",
    "from matplotlib import rc\n",
    "import os\n",
    "import subprocess\n",
    "\n",
    "fileset_data1 = {}\n",
    "for k in range(0,6):\n",
    "    for j in range(0,25):\n",
    "        fileset_data1[k,j] = iter_loadtxt('/home/john/projects/calculations/core_shell/rTiO2-eulercsv1/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)\n",
    "       \n",
    "     \n",
    "euler_2_vec = np.linspace(0,180,25); euler_3_vec = np.linspace(0,180,25);\n",
    "nbins = 250\n",
    "varSxx = np.zeros((25,25)); varSyy = np.zeros((25,25)); varSzz = np.zeros((25,25)); varEg = np.zeros((25,25));\n",
    "\n",
    "vol1 = {}; Sxx1 = {}; Syy1 = {}; Szz1 = {}; HSxx1 = {}; Eg1 = {}; xedgesSxx1 = {}; yedgesSxx1 = {}; yedgesSxx_up1 = {};\n",
    "xedgesSxx_up1 = {}; vSxxj1 = {}; VSxxj1 = {}; xSxx1 = {}; \n",
    "\n",
    "for k in range(0,6):\n",
    "    for j in range(0,25):\n",
    "        #vol1[k,j] = [row[7] for row in fileset_data1[k,j]]\n",
    "        #Sxx1[k,j] = [row[0] for row in fileset_data1[k,j]]\n",
    "        #Syy1[k,j] = [row[1] for row in fileset_data1[k,j]]\n",
    "        #Szz1[k,j] = [row[2] for row in fileset_data1[k,j]]\n",
    "        Eg1[k,j] = [row[3] for row in fileset_data1[k,j]]\n",
    "        #HSxx1[k,j], xedgesSxx1[k,j], yedgesSxx1[k,j] = np.histogram2d(Sxx1[k,j][1:len(Sxx1[k,j])],vol1[k,j][1:len(vol1[k,j])],bins=nbins) \n",
    "        #HSxx1[k,j] = np.rot90(HSxx1[k,j])\n",
    "        #HSxx1[k,j] = np.flipud(HSxx1[k,j])\n",
    "        #yedgesSxx_up1[k,j] = yedgesSxx1[k,j][0:len(yedgesSxx1[k,j])-1]+(yedgesSxx1[k,j][1:len(yedgesSxx1[k,j])]-yedgesSxx1[k,j][0:len(yedgesSxx1[k,j])-1])/2\n",
    "        #vSxxj1[k,j] = np.einsum('ij,i',HSxx1[k,j],yedgesSxx_up1[k,j])\n",
    "        #VSxxj1[k,j] = vSxxj1[k,j]/sum(vSxxj1[k,j])*100\n",
    "        #xSxx1[k,j] = xedgesSxx1[k,j][0:len(xedgesSxx1[k,j])-1]+(xedgesSxx1[k,j][1:len(xedgesSxx1[k,j])]-xedgesSxx1[k,j][0:len(xedgesSxx1[k,j])-1])/2\n",
    "        #varSxx[k,j] = np.var(Sxx1[k,j])\n",
    "        #varSyy[k,j] = np.var(Syy1[k,j])\n",
    "        #varSzz[k,j] = np.var(Szz1[k,j])\n",
    "        varEg[k,j] = np.var(Eg1[k,j])\n",
    "\n",
    "%xdel fileset_data1 \n",
    "#%xdel Sxx1\n",
    "#%xdel Syy1\n",
    "#%xdel Szz1\n",
    "%xdel Eg1\n",
    "\n",
    "subprocess.call('espeak \"Loading is complete.\"',shell=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fileset_data2 = {}\n",
    "for k in range(6,11):\n",
    "    for j in range(0,25):\n",
    "        fileset_data2[k,j] = iter_loadtxt('/home/john/projects/calculations/core_shell/rTiO2-eulercsv2/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)\n",
    "\n",
    "\n",
    "vol2 = {}; Sxx2 = {}; Syy2 = {}; Szz2 = {}; HSxx2 = {}; xedgesSxx2 = {}; yedgesSxx2 = {}; yedgesSxx_up2 = {};\n",
    "xedgesSxx_up2 = {}; vSxxj2 = {}; VSxxj2 = {}; xSxx2 = {}; Eg2 = {};\n",
    "\n",
    "for k in range(6,11):\n",
    "    for j in range(0,25):\n",
    "        #vol2[k,j] = [row[7] for row in fileset_data2[k,j]]\n",
    "        #Sxx2[k,j] = [row[0] for row in fileset_data2[k,j]]\n",
    "        #Syy2[k,j] = [row[1] for row in fileset_data2[k,j]]\n",
    "        #Szz2[k,j] = [row[2] for row in fileset_data2[k,j]]\n",
    "        Eg2[k,j]= [row[3] for row in fileset_data2[k,j]]\n",
    "        #HSxx2[k,j], xedgesSxx2[k,j], yedgesSxx2[k,j] = np.histogram2d(Sxx2[k,j][1:len(Sxx2[k,j])],vol2[k,j][1:len(vol2[k,j])],bins=nbins) \n",
    "        #HSxx2[k,j] = np.rot90(HSxx2[k,j])\n",
    "        #HSxx2[k,j] = np.flipud(HSxx2[k,j])\n",
    "        #yedgesSxx_up2[k,j] = yedgesSxx2[k,j][0:len(yedgesSxx2[k,j])-1]+(yedgesSxx2[k,j][1:len(yedgesSxx2[k,j])]-yedgesSxx2[k,j][0:len(yedgesSxx2[k,j])-1])/2\n",
    "        #vSxxj2[k,j] = np.einsum('ij,i',HSxx2[k,j],yedgesSxx_up2[k,j])\n",
    "        #VSxxj2[k,j] = vSxxj2[k,j]/sum(vSxxj2[k,j])*100\n",
    "        #xSxx2[k,j] = xedgesSxx2[k,j][0:len(xedgesSxx2[k,j])-1]+(xedgesSxx2[k,j][1:len(xedgesSxx2[k,j])]-xedgesSxx2[k,j][0:len(xedgesSxx2[k,j])-1])/2\n",
    "        #varSxx[k,j] = np.var(Sxx2[k,j])\n",
    "        #varSyy[k,j] = np.var(Syy2[k,j])\n",
    "        #varSzz[k,j] = np.var(Szz2[k,j])\n",
    "        varEg[k,j] = np.var(Eg2[k,j])\n",
    "\n",
    "%xdel fileset_data2\n",
    "#%xdel Sxx2\n",
    "#%xdel Syy2\n",
    "#%xdel Szz2\n",
    "%xdel Eg2\n",
    "\n",
    "subprocess.call('espeak \"Loading is complete.\"',shell=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fileset_data3 = {}\n",
    "for k in range(11,16):\n",
    "    for j in range(0,25):\n",
    "        fileset_data3[k,j] = iter_loadtxt('/home/john/projects/calculations/core_shell/rTiO2-eulercsv3/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)\n",
    "        \n",
    "vol3 = {}; Sxx3 = {}; Syy3 = {}; Szz3 = {}; HSxx3 = {}; xedgesSxx3 = {}; yedgesSxx3 = {}; yedgesSxx_up3 = {};\n",
    "xedgesSxx_up3 = {}; vSxxj3 = {}; VSxxj3 = {}; xSxx3 = {}; Eg3 = {};\n",
    "\n",
    "for k in range(11,16):\n",
    "    for j in range(0,25):\n",
    "        #vol3[k,j] = [row[7] for row in fileset_data3[k,j]]\n",
    "        #Sxx3[k,j] = [row[0] for row in fileset_data3[k,j]]\n",
    "        #Syy3[k,j] = [row[1] for row in fileset_data3[k,j]]\n",
    "        #Szz3[k,j] = [row[2] for row in fileset_data3[k,j]]\n",
    "        Eg3[k,j] = [row[3] for row in fileset_data3[k,j]]\n",
    "        #HSxx3[k,j], xedgesSxx3[k,j], yedgesSxx3[k,j] = np.histogram2d(Sxx3[k,j][1:len(Sxx3[k,j])],vol3[k,j][1:len(vol3[k,j])],bins=nbins) \n",
    "        #HSxx3[k,j] = np.rot90(HSxx3[k,j])\n",
    "        #HSxx3[k,j] = np.flipud(HSxx3[k,j])\n",
    "        #yedgesSxx_up3[k,j] = yedgesSxx3[k,j][0:len(yedgesSxx3[k,j])-1]+(yedgesSxx3[k,j][1:len(yedgesSxx3[k,j])]-yedgesSxx3[k,j][0:len(yedgesSxx3[k,j])-1])/2\n",
    "        #vSxxj3[k,j] = np.einsum('ij,i',HSxx3[k,j],yedgesSxx_up3[k,j])\n",
    "        #VSxxj3[k,j] = vSxxj3[k,j]/sum(vSxxj3[k,j])*100\n",
    "        #xSxx3[k,j] = xedgesSxx3[k,j][0:len(xedgesSxx3[k,j])-1]+(xedgesSxx3[k,j][1:len(xedgesSxx3[k,j])]-xedgesSxx3[k,j][0:len(xedgesSxx3[k,j])-1])/2\n",
    "        #varSxx[k,j] = np.var(Sxx3[k,j])\n",
    "        #varSyy[k,j] = np.var(Syy3[k,j])\n",
    "        #varSzz[k,j] = np.var(Szz3[k,j])\n",
    "        varEg[k,j] = np.var(Eg3[k,j])\n",
    "\n",
    "        \n",
    "%xdel fileset_data3\n",
    "#%xdel Sxx3\n",
    "#%xdel Syy3\n",
    "#%xdel Szz3\n",
    "%xdel Eg3\n",
    "\n",
    "subprocess.call('espeak \"Loading is complete.\"',shell=True)     "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
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   "outputs": [
    {
     "data": {
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     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fileset_data4 = {}\n",
    "for k in range(16,21):\n",
    "    for j in range(0,25):\n",
    "        fileset_data4[k,j] = iter_loadtxt('/home/john/projects/calculations/core_shell/rTiO2-eulercsv4/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)\n",
    "\n",
    "vol4 = {}; Sxx4 = {}; Syy4 = {}; Szz4 = {}; HSxx4 = {}; xedgesSxx4 = {}; yedgesSxx4 = {}; yedgesSxx_up4 = {};\n",
    "xedgesSxx_up4 = {}; vSxxj4 = {}; VSxxj4 = {}; xSxx4 = {}; Eg4 = {};\n",
    "\n",
    "for k in range(16,21):\n",
    "    for j in range(0,25):\n",
    "        #vol4[k,j] = [row[7] for row in fileset_data4[k,j]]\n",
    "        #Sxx4[k,j] = [row[0] for row in fileset_data4[k,j]]\n",
    "        #Syy4[k,j] = [row[1] for row in fileset_data4[k,j]]\n",
    "        #Szz4[k,j] = [row[2] for row in fileset_data4[k,j]]\n",
    "        Eg4[k,j] = [row[3] for row in fileset_data4[k,j]]\n",
    "        #HSxx4[k,j], xedgesSxx4[k,j], yedgesSxx4[k,j] = np.histogram2d(Sxx4[k,j][1:len(Sxx4[k,j])],vol4[k,j][1:len(vol4[k,j])],bins=nbins) \n",
    "        #HSxx4[k,j] = np.rot90(HSxx4[k,j])\n",
    "        #HSxx4[k,j] = np.flipud(HSxx4[k,j])\n",
    "        #yedgesSxx_up4[k,j] = yedgesSxx4[k,j][0:len(yedgesSxx4[k,j])-1]+(yedgesSxx4[k,j][1:len(yedgesSxx4[k,j])]-yedgesSxx4[k,j][0:len(yedgesSxx4[k,j])-1])/2\n",
    "        #vSxxj4[k,j] = np.einsum('ij,i',HSxx4[k,j],yedgesSxx_up4[k,j])\n",
    "        #VSxxj4[k,j] = vSxxj4[k,j]/sum(vSxxj4[k,j])*100\n",
    "        #xSxx4[k,j] = xedgesSxx4[k,j][0:len(xedgesSxx4[k,j])-1]+(xedgesSxx4[k,j][1:len(xedgesSxx4[k,j])]-xedgesSxx4[k,j][0:len(xedgesSxx4[k,j])-1])/2\n",
    "        #varSxx[k,j] = np.var(Sxx4[k,j])\n",
    "        #varSyy[k,j] = np.var(Syy4[k,j])\n",
    "        #varSzz[k,j] = np.var(Szz4[k,j])\n",
    "        varEg[k,j] = np.var(Eg4[k,j])\n",
    "\n",
    "\n",
    "%xdel fileset_data4\n",
    "#%xdel Sxx4\n",
    "#%xdel Syy4\n",
    "#%xdel Szz4\n",
    "%xdel Eg4\n",
    "        \n",
    "subprocess.call('espeak \"Loading is complete.\"',shell=True)      "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fileset_data5 = {}\n",
    "\n",
    "for k in range(21,25):\n",
    "    for j in range(0,25):\n",
    "        fileset_data5[k,j] = iter_loadtxt('/home/john/projects/calculations/core_shell/rTiO2-eulercsv5/MeshData-'+repr(k)+'-'+repr(j)+'COMP.csv',delimiter=',',skiprows=1,dtype=float)\n",
    "\n",
    "vol5 = {}; Sxx5 = {}; Syy5 = {}; Szz5 = {}; HSxx5 = {}; xedgesSxx5 = {}; yedgesSxx5 = {}; yedgesSxx_up5 = {};\n",
    "xedgesSxx_up5 = {}; vSxxj5 = {}; VSxxj5 = {}; xSxx5 = {}; Eg5 = {};\n",
    "\n",
    "for k in range(21,25):\n",
    "    for j in range(0,25):\n",
    "        #vol5[k,j] = [row[7] for row in fileset_data5[k,j]]\n",
    "        #Sxx5[k,j] = [row[0] for row in fileset_data5[k,j]]\n",
    "        #Syy5[k,j] = [row[1] for row in fileset_data5[k,j]]\n",
    "        #Szz5[k,j] = [row[2] for row in fileset_data5[k,j]]\n",
    "        Eg5[k,j] = [row[3] for row in fileset_data5[k,j]]\n",
    "        #HSxx5[k,j], xedgesSxx5[k,j], yedgesSxx5[k,j] = np.histogram2d(Sxx5[k,j][1:len(Sxx5[k,j])],vol5[k,j][1:len(vol5[k,j])],bins=nbins) \n",
    "        #HSxx5[k,j] = np.rot90(HSxx5[k,j])\n",
    "        #HSxx5[k,j] = np.flipud(HSxx5[k,j])\n",
    "        #yedgesSxx_up5[k,j] = yedgesSxx5[k,j][0:len(yedgesSxx5[k,j])-1]+(yedgesSxx5[k,j][1:len(yedgesSxx5[k,j])]-yedgesSxx5[k,j][0:len(yedgesSxx5[k,j])-1])/2\n",
    "        #vSxxj5[k,j] = np.einsum('ij,i',HSxx5[k,j],yedgesSxx_up5[k,j])\n",
    "        #VSxxj5[k,j] = vSxxj5[k,j]/sum(vSxxj5[k,j])*100\n",
    "        #xSxx5[k,j] = xedgesSxx5[k,j][0:len(xedgesSxx5[k,j])-1]+(xedgesSxx5[k,j][1:len(xedgesSxx5[k,j])]-xedgesSxx5[k,j][0:len(xedgesSxx5[k,j])-1])/2\n",
    "        #varSxx[k,j] = np.var(Sxx5[k,j])\n",
    "        #varSyy[k,j] = np.var(Syy5[k,j])\n",
    "        #varSzz[k,j] = np.var(Szz5[k,j])\n",
    "        varEg[k,j] = np.var(Eg5[k,j])\n",
    "\n",
    "\n",
    "%xdel fileset_data5\n",
    "#%xdel Sxx5\n",
    "#%xdel Syy5\n",
    "#%xdel Szz5\n",
    "%xdel Eg5\n",
    "        \n",
    "subprocess.call('espeak \"Final loading is complete.\"',shell=True)      "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    " # Plot 2D histogram using pcolor\n",
    "\n",
    "plt.pcolormesh(euler_2_vec,euler_3_vec,varSet*np.power(10,5))\n",
    "plt.ylabel('$\\phi_3$',fontsize=16)\n",
    "plt.xlabel('$\\Phi_2$',fontsize= 16)\n",
    "#%xdel cbar1\n",
    "cbar1 = plt.colorbar()\n",
    "cbar1.ax.set_ylabel('$\\mathrm{var}( E_{g}) 10^{-5} \\mathrm{eV}$')\n",
    "plt.xlim([0,180])\n",
    "tick_vals = np.linspace(0,180,3)\n",
    "tick_labels = [tick_vals[i] for i in range(len(tick_vals))]\n",
    "tick_labels[0] = '0'\n",
    "tick_labels[1] = '$\\pi/2$'\n",
    "tick_labels[2] = '$\\pi$'\n",
    "plt.xticks(tick_vals, tick_labels)\n",
    "plt.ylim([0,180])\n",
    "tick_vals = np.linspace(0,180,3)\n",
    "tick_labels = [tick_vals[i] for i in range(len(tick_vals))]\n",
    "tick_labels[0] = '0'\n",
    "tick_labels[1] = '$\\pi/2$'\n",
    "tick_labels[2] = '$\\pi$'\n",
    "plt.yticks(tick_vals, tick_labels)\n",
    "plt.title('variance of band gap for rTiO2 shell')\n",
    "plt.savefig(\"/home/john/projects/varEg_euler_rTiO2.pdf\")\n",
    "#plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "from mpl_toolkits.mplot3d import Axes3D\n",
    "import matplotlib.pyplot as plt\n",
    "from matplotlib import rc\n",
    "\n",
    "fig = plt.figure()\n",
    "ax = fig.add_subplot(111, projection='3d')\n",
    "x = y = euler_2_vec\n",
    "X, Y = np.meshgrid(x, y)\n",
    "zs = varSet*np.power(10,5)\n",
    "Z = zs.reshape(X.shape)\n",
    "\n",
    "ax.plot_surface(X, Y, Z, rstride=1, cstride=1,alpha = 0.4,color='b')\n",
    "\n",
    "ax.set_xlabel('$\\phi_2$',fontsize=20)\n",
    "ax.set_ylabel('$\\Phi_3$',fontsize=20)\n",
    "ax.set_zlabel('$\\mathrm{var}(E_{g}) 10^{-5} \\mathrm{eV}$',fontsize=20)\n",
    "\n",
    "plt.xlim([0,180])\n",
    "tick_vals = np.linspace(0,180,3)\n",
    "tick_labels = [tick_vals[i] for i in range(len(tick_vals))]\n",
    "tick_labels[0] = '0'\n",
    "tick_labels[1] = '$\\pi/2$'\n",
    "tick_labels[2] = '$\\pi$'\n",
    "plt.xticks(tick_vals, tick_labels)\n",
    "plt.ylim([0,180])\n",
    "tick_vals = np.linspace(0,180,3)\n",
    "tick_labels = [tick_vals[i] for i in range(len(tick_vals))]\n",
    "tick_labels[0] = '0'\n",
    "tick_labels[1] = '$\\pi/2$'\n",
    "tick_labels[2] = '$\\pi$'\n",
    "plt.yticks(tick_vals, tick_labels)\n",
    "\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
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       "          7.02418685e-06],\n",
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       "          4.36190019e-06,   5.63689042e-06,   6.53583928e-06,\n",
       "          6.82029386e-06,   6.43799878e-06,   5.51082639e-06,\n",
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       "          1.83984289e-06,   2.17484686e-06,   3.11678574e-06,\n",
       "          4.41947578e-06,   5.71252135e-06,   6.62494386e-06,\n",
       "          6.91376185e-06],\n",
       "       [  6.88232887e-06,   6.50096652e-06,   5.55684347e-06,\n",
       "          4.30031544e-06,   3.04929332e-06,   2.12145011e-06,\n",
       "          1.76464831e-06,   2.09228651e-06,   3.03773451e-06,\n",
       "          4.34996058e-06,   5.65508657e-06,   6.58096919e-06,\n",
       "          6.88232888e-06,   6.50096651e-06,   5.55684345e-06,\n",
       "          4.30031543e-06,   3.04929331e-06,   2.12145012e-06,\n",
       "          1.76464831e-06,   2.09228650e-06,   3.03773450e-06,\n",
       "          4.34996056e-06,   5.65508655e-06,   6.58096920e-06,\n",
       "          6.88232886e-06]])"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "varEg"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
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    "          6.88232886e-06]]);"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
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       "          6.88232886e-06]])"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
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   "execution_count": null,
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   "outputs": [],
   "source": []
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