vary_hydroP_ZnO_iso.ipynb

{
 "metadata": {
  "name": "vary_hydroP_ZnO_iso"
 }, 
 "nbformat": 2, 
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [
      "import os", 
      "import subprocess", 
      "import numpy as np", 
      "", 
      "os.chdir('/home/john/projects/ferret/')", 
      "", 
      "pressure_vec = np.linspace(-1.0e-08,1.0e-08,121)  ", 
      "", 
      "for t in range(0,121):", 
      "    # Define the base file we will be iteratively modifiying #", 
      "    infile = open('/home/john/projects/ferret/vary_hydroP_ZnO_iso.i')", 
      "    # Open the out file we will be writing at each step in the iteration #", 
      "    outfile = open('/home/john/projects/ferret/newvary_hydroP_ZnO_iso-'+repr(t)+'.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 = {'pressure = def':'pressure = %s' % pressure_vec[t],'file_base = out_0_Zn_ZnO_xstl000_core_iso_shell_P-def':'file_base = out_0_Zn_ZnO_xstl000_core_iso_shell_P-'+repr(t)}", 
      "    for line in infile:", 
      "        for src, target in replacements.iteritems():", 
      "            line = line.replace(src, target)", 
      "        outfile.write(line)", 
      "    infile.close()", 
      "    outfile.close()"
     ], 
     "language": "python", 
     "outputs": [], 
     "prompt_number": 1
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [
      "import os", 
      "import subprocess", 
      "", 
      "os.chdir('/home/john/projects/ParaView-bin/bin/')", 
      "subprocess.call('pvpython /home/john/projects/calculations/core_shell/final_plots/vary_hydroP_ZnO_iso/scripts-and-out-files/MeshData.py',shell=True)", 
      "os.chdir('/home/john/projects/calculations/core_shell/final_plots/vary_hydroP_ZnO_iso/')", 
      "for k in range(0,121):", 
      "    for t in range(1,8):", 
      "        subprocess.call('rm MeshData-'+repr(k)+'-'+repr(t)+'.csv',shell=True)"
     ], 
     "language": "python", 
     "outputs": [], 
     "prompt_number": 3
    }, 
    {
     "cell_type": "code", 
     "collapsed": false, 
     "input": [
      "import numpy as np", 
      "import os", 
      "import subprocess", 
      "", 
      "EgBinEdges = np.linspace(0.0,6.0,122)", 
      "volBinEdges=np.linspace(0,0.5,len(EgBinEdges))", 
      "", 
      "for k in range(0,121):    ", 
      "    data_SigmaVolume = np.genfromtxt('/home/john/projects/calculations/core_shell/final_plots/vary_hydroP_ZnO_iso/MeshData-'+str(k)+'-0.csv',delimiter=',', dtype = float)", 
      "    Eg = [row[9] for row in data_SigmaVolume]", 
      "    vol = [row[13] for row in data_SigmaVolume] ", 
      "    ", 
      "    Hbg, xEdges, yEdges = np.histogram2d(Eg[1:len(Eg)],vol[1:len(vol)], bins = (EgBinEdges, volBinEdges))", 
      "    Hbg = np.rot90(Hbg)", 
      "    Hbg = np.flipud(Hbg)", 
      "    ", 
      "    yedgesbg_up = yEdges[0:len(yEdges)-1]+(yEdges[1:len(yEdges)]-yEdges[0:len(yEdges)-1])/2 ", 
      "    vEgj = np.einsum('ij,i',Hbg,yedgesbg_up)", 
      "    VEgj = vEgj/sum(vEgj)*100", 
      "    x_bg = xEdges[0:len(xEdges)-1]+(xEdges[1:len(xEdges)]-xEdges[0:len(xEdges)-1])/2", 
      "    ", 
      "    np.savetxt(\"/home/john/projects/calculations/core_shell/final_plots/vary_hydroP_ZnO_iso/data_for_animation-\"+str(k)+\".csv\",[x_bg,VEgj],delimiter=\",\") ", 
      "    ", 
      "subprocess.call('espeak \"Complete\"',shell=True)"
     ], 
     "language": "python", 
     "outputs": [
      {
       "ename": "SyntaxError", 
       "evalue": "invalid syntax (<ipython-input-2-108bff2781e5>, line 24)", 
       "output_type": "pyerr", 
       "traceback": [
        "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-2-108bff2781e5>\"\u001b[0;36m, line \u001b[0;32m24\u001b[0m\n\u001b[0;31m    subprocess.call('espeak \"Complete\"',shell=True)import numpy as np\u001b[0m\n\u001b[0m                                                        ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
       ]
      }
     ], 
     "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", 
      "import itertools", 
      "from matplotlib import cm", 
      "", 
      "rad2_vec = 12.5", 
      "rad1_vec = np.linspace(2.5,11,121);", 
      "pressure_vec = np.linspace(-1.0e-08,1.0e-08,121)*np.power(10,9)", 
      "", 
      "EgBinEdges = np.linspace(0.0,6.0,121) #need to fix this", 
      "VEgj_vec = np.zeros((121,121))", 
      "", 
      "#Technically we don't have data for 399 of the rad2_vec, but we can extrapolate it with this method.. I think.", 
      "", 
      "#stv = 3/r:", 
      "#original stv differs from new stv due to relaxation of the surface", 
      "", 
      "    ", 
      "for k in range(0,121):", 
      "    data_vec = np.genfromtxt(\"/home/john/projects/calculations/core_shell/final_plots/vary_hydroP_ZnO_iso/data_for_animation-\"+str(k)+\".csv\",delimiter=',',dtype = float)", 
      "    VEgj_vec[k,:] = data_vec[1,:]", 
      "", 
      "    ", 
      "fig = plt.figure()", 
      "#ax = fig.add_subplot(111, projection='3d')", 
      "", 
      "x = EgBinEdges", 
      "y = pressure_vec", 
      "", 
      "plt.pcolormesh(x,y,VEgj_vec)", 
      "", 
      "plt.xlabel('$ E_g\\,\\, [\\mathrm{eV}]$',fontsize=20)", 
      "plt.ylabel('$\\mathrm{Pressure}\\,\\,[\\mathrm{GPa}]$',fontsize=20)", 
      "", 
      "#%xdel cbar1", 
      "cbar1 = plt.colorbar()", 
      "cbar1.ax.set_ylabel('$\\mathrm{Shell}\\,\\, \\mathrm{volume}\\,\\, [\\%]$',fontsize=20)", 
      "#tick_vals = np.linspace(0.0,6.0,7)", 
      "#tick_labels = [tick_vals[i] for i in range(len(tick_vals))]", 
      "#tick_labels[0] = ''", 
      "#tick_labels[1] = '-0.07'", 
      "#tick_labels[2] = ''", 
      "#tick_labels[3] = '-0.06'", 
      "#tick_labels[4] = ''", 
      "#tick_labels[5] = '-0.05'", 
      "#tick_labels[6] = ''", 
      "#tick_labels[7] = '-0.04'", 
      "#plt.xticks(tick_vals, tick_labels)", 
      "plt.tick_params(axis='both', which='major', labelsize=18)", 
      "plt.axis([x.min(),x.max(),y.min(),y.max()])", 
      "#plt.title('$E_g$ dependence on D for ZnO shell')", 
      "plt.savefig(\"/home/john/projects/Eg_hydroP_ZnO_iso.eps\",format='eps',dpi=600)", 
      "", 
      "plt.show()"
     ], 
     "language": "python", 
     "outputs": [], 
     "prompt_number": 8
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [], 
     "language": "python", 
     "outputs": []
    }, 
    {
     "cell_type": "code", 
     "collapsed": true, 
     "input": [], 
     "language": "python", 
     "outputs": []
    }
   ]
  }
 ]
}