05-complex_geometries.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# GDS geometries and MEEP\n",
    "\n",
    "## 2D\n",
    "\n",
    "Some imports and parameters as usual :"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Import meep and mpb (from meep)\n",
    "import meep as mp\n",
    "from meep import mpb\n",
    "\n",
    "# arrays\n",
    "import numpy as np\n",
    "\n",
    "# plotting\n",
    "import matplotlib.pyplot as plt\n",
    "import ipyvolume as ipv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "oxide=mp.Medium(epsilon=2.25)\n",
    "silicon=mp.Medium(epsilon=12)\n",
    "\n",
    "res = 32        # pixels/μm"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Last week you were introduced to zeropdk, a way to create GDS masks. You can directly upload your GDS masks into MEEP for simulation! You just need to add dummy layers to define your simulation ports. It is as easy as calling `mp.get_GDSII_prisms` with a material, GDS file, and layer number (figure from https://meep.readthedocs.io/en/latest/Python_Tutorials/GDSII_Import/) :\n",
    "\n",
    "!['gds_coupler'](https://meep.readthedocs.io/en/latest/images/klayout_schematic.png)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "gdsII_file = 'coupler.gds'\n",
    "\n",
    "CELL_LAYER = 0\n",
    "UPPER_BRANCH_LAYER = 31\n",
    "LOWER_BRANCH_LAYER = 32 # They have two layers of silicon here to parametrize the distance between the branches at this level\n",
    "\n",
    "upper_branch = mp.get_GDSII_prisms(silicon, gdsII_file, UPPER_BRANCH_LAYER)\n",
    "lower_branch = mp.get_GDSII_prisms(silicon, gdsII_file, LOWER_BRANCH_LAYER)\n",
    "\n",
    "cell = mp.GDSII_vol(gdsII_file, CELL_LAYER, zmin=0, zmax=0) # for 2D simulation, don't care about zmin and zmax"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Dummy layers can also be included to precisely denote the positions of the input port for the simulation :"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "SOURCE_LAYER = 5\n",
    "\n",
    "src_vol = mp.GDSII_vol(gdsII_file, SOURCE_LAYER, zmin=0, zmax=0)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Then repeat simulation definition as before :"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "dpml = 1\n",
    "\n",
    "lcen = 1.55\n",
    "fcen = 1/lcen\n",
    "df = 0.2*fcen\n",
    "\n",
    "geometry = upper_branch+lower_branch\n",
    "\n",
    "sources = [mp.EigenModeSource(src=mp.ContinuousSource(fcen,fwidth=df),\n",
    "                              size=src_vol.size,\n",
    "                              center=src_vol.center,\n",
    "                              eig_band=1,\n",
    "                              eig_parity=mp.EVEN_Y+mp.ODD_Z,\n",
    "                              eig_match_freq=True)]\n",
    "\n",
    "sim = mp.Simulation(resolution=res,\n",
    "                    cell_size=cell.size,\n",
    "                    boundary_layers=[mp.PML(dpml)],\n",
    "                    sources=sources,\n",
    "                    geometry=geometry)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-----------\n",
      "Initializing structure...\n",
      "time for choose_chunkdivision = 0.000209093 s\n",
      "Working in 2D dimensions.\n",
      "Computational cell is 34.4062 x 8 x 0 with resolution 32\n",
      "     prism, center = (-9.09425,1.41149,0)\n",
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      "          (-4,0.65,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (9.09425,1.41149,0)\n",
      "          height 0, axis (0,0,1), 174 vertices:\n",
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    {
     "name": "stdout",
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     "text": [
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      "          (4.322,0.155,0)\n",
      "          (4.215,0.152,0)\n",
      "          (4.108,0.151,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (0,0.4,0)\n",
      "          height 0, axis (0,0,1), 4 vertices:\n",
      "          (-4,0.15,0)\n",
      "          (-4,0.65,0)\n",
      "          (4,0.65,0)\n",
      "          (4,0.15,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (-9.09425,-1.41149,0)\n",
      "          height 0, axis (0,0,1), 174 vertices:\n",
      "          (-17.2,-2.65,0)\n",
      "          (-17.2,-2.15,0)\n",
      "          (-14,-2.15,0)\n",
      "          (-13.796,-2.148,0)\n",
      "          (-13.695,-2.145,0)\n",
      "          (-13.593,-2.141,0)\n",
      "          (-13.492,-2.136,0)\n",
      "          (-13.392,-2.13,0)\n",
      "          (-13.291,-2.123,0)\n",
      "          (-13.19,-2.115,0)\n",
      "          (-12.99,-2.095,0)\n",
      "          (-12.89,-2.084,0)\n",
      "          (-12.791,-2.072,0)\n",
      "          (-12.691,-2.06,0)\n",
      "          (-12.592,-2.046,0)\n",
      "          (-12.394,-2.016,0)\n",
      "          (-12.295,-2,0)\n",
      "          (-12.196,-1.983,0)\n",
      "          (-12.098,-1.965,0)\n",
      "          (-11.999,-1.946,0)\n",
      "          (-11.901,-1.927,0)\n",
      "          (-11.802,-1.907,0)\n",
      "          (-11.704,-1.887,0)\n",
      "          (-11.606,-1.866,0)\n",
      "          (-11.508,-1.844,0)\n",
      "          (-11.41,-1.821,0)\n",
      "          (-11.313,-1.798,0)\n",
      "          (-11.215,-1.775,0)\n",
      "          (-11.117,-1.75,0)\n",
      "          (-11.02,-1.726,0)\n",
      "          (-10.922,-1.701,0)\n",
      "          (-10.728,-1.649,0)\n",
      "          (-10.63,-1.623,0)\n",
      "          (-10.533,-1.596,0)\n",
      "          (-10.436,-1.568,0)\n",
      "          (-10.338,-1.541,0)\n",
      "          (-10.144,-1.485,0)\n",
      "          (-10.047,-1.456,0)\n",
      "          (-9.949,-1.427,0)\n",
      "          (-9.658,-1.34,0)\n",
      "          (-9.56,-1.31,0)\n",
      "          (-9.463,-1.281,0)\n",
      "          (-9.366,-1.251,0)\n",
      "          (-9.268,-1.221,0)\n",
      "          (-9.074,-1.161,0)\n",
      "          (-8.878,-1.101,0)\n",
      "          (-8.781,-1.071,0)\n",
      "          (-8.585,-1.011,0)\n",
      "          (-8.487,-0.982,0)\n",
      "          (-8.389,-0.952,0)\n",
      "          (-8.291,-0.923,0)\n",
      "          (-8.193,-0.893,0)\n",
      "          (-8.095,-0.864,0)\n",
      "          (-7.996,-0.835,0)\n",
      "          (-7.898,-0.807,0)\n",
      "          (-7.799,-0.778,0)\n",
      "          (-7.7,-0.75,0)\n",
      "          (-7.601,-0.723,0)\n",
      "          (-7.502,-0.695,0)\n",
      "          (-7.403,-0.668,0)\n",
      "          (-7.303,-0.642,0)\n",
      "          (-7.204,-0.615,0)\n",
      "          (-6.904,-0.54,0)\n",
      "          (-6.803,-0.515,0)\n",
      "          (-6.703,-0.492,0)\n",
      "          (-6.501,-0.446,0)\n",
      "          (-6.4,-0.424,0)\n",
      "          (-6.299,-0.403,0)\n",
      "          (-6.197,-0.382,0)\n",
      "          (-6.095,-0.362,0)\n",
      "          (-5.993,-0.343,0)\n",
      "          (-5.891,-0.325,0)\n",
      "          (-5.788,-0.307,0)\n",
      "          (-5.685,-0.29,0)\n",
      "          (-5.582,-0.274,0)\n",
      "          (-5.479,-0.259,0)\n",
      "          (-5.271,-0.231,0)\n",
      "          (-5.167,-0.219,0)\n",
      "          (-5.062,-0.207,0)\n",
      "          (-4.852,-0.187,0)\n",
      "          (-4.747,-0.179,0)\n",
      "          (-4.641,-0.171,0)\n",
      "          (-4.535,-0.165,0)\n",
      "          (-4.429,-0.16,0)\n",
      "          (-4.322,-0.155,0)\n",
      "          (-4.215,-0.152,0)\n",
      "          (-4.108,-0.151,0)\n",
      "          (-4,-0.15,0)\n",
      "          (-4,-0.65,0)\n",
      "          (-4.204,-0.652,0)\n",
      "          (-4.305,-0.655,0)\n",
      "          (-4.407,-0.659,0)\n",
      "          (-4.508,-0.664,0)\n",
      "          (-4.608,-0.67,0)\n",
      "          (-4.709,-0.677,0)\n",
      "          (-4.81,-0.685,0)\n",
      "          (-5.01,-0.705,0)\n",
      "          (-5.11,-0.716,0)\n",
      "          (-5.209,-0.728,0)\n",
      "          (-5.309,-0.74,0)\n",
      "          (-5.408,-0.754,0)\n",
      "          (-5.606,-0.784,0)\n",
      "          (-5.705,-0.8,0)\n",
      "          (-5.804,-0.817,0)\n",
      "          (-5.902,-0.835,0)\n",
      "          (-6.001,-0.854,0)\n",
      "          (-6.099,-0.873,0)\n",
      "          (-6.198,-0.893,0)\n",
      "          (-6.296,-0.913,0)\n",
      "          (-6.394,-0.934,0)\n",
      "          (-6.492,-0.956,0)\n",
      "          (-6.59,-0.979,0)\n",
      "          (-6.687,-1.002,0)\n",
      "          (-6.785,-1.025,0)\n",
      "          (-6.883,-1.05,0)\n",
      "          (-6.98,-1.074,0)\n",
      "          (-7.078,-1.099,0)\n",
      "          (-7.272,-1.151,0)\n",
      "          (-7.37,-1.177,0)\n",
      "          (-7.467,-1.204,0)\n",
      "          (-7.564,-1.232,0)\n",
      "          (-7.662,-1.259,0)\n",
      "          (-7.856,-1.315,0)\n",
      "          (-7.953,-1.344,0)\n",
      "          (-8.051,-1.373,0)\n",
      "          (-8.342,-1.46,0)\n",
      "          (-8.44,-1.49,0)\n",
      "          (-8.537,-1.519,0)\n",
      "          (-8.634,-1.549,0)\n",
      "          (-8.732,-1.579,0)\n",
      "          (-8.926,-1.639,0)\n",
      "          (-9.122,-1.699,0)\n",
      "          (-9.219,-1.729,0)\n",
      "          (-9.415,-1.789,0)\n",
      "          (-9.513,-1.818,0)\n",
      "          (-9.611,-1.848,0)\n",
      "          (-9.709,-1.877,0)\n",
      "          (-9.807,-1.907,0)\n",
      "          (-9.905,-1.936,0)\n",
      "          (-10.004,-1.965,0)\n",
      "          (-10.102,-1.993,0)\n",
      "          (-10.201,-2.022,0)\n",
      "          (-10.3,-2.05,0)\n",
      "          (-10.399,-2.077,0)\n",
      "          (-10.498,-2.105,0)\n",
      "          (-10.597,-2.132,0)\n",
      "          (-10.697,-2.158,0)\n",
      "          (-10.796,-2.185,0)\n",
      "          (-11.096,-2.26,0)\n",
      "          (-11.197,-2.285,0)\n",
      "          (-11.297,-2.308,0)\n",
      "          (-11.499,-2.354,0)\n",
      "          (-11.6,-2.376,0)\n",
      "          (-11.701,-2.397,0)\n",
      "          (-11.803,-2.418,0)\n",
      "          (-11.905,-2.438,0)\n",
      "          (-12.007,-2.457,0)\n",
      "          (-12.109,-2.475,0)\n",
      "          (-12.212,-2.493,0)\n",
      "          (-12.315,-2.51,0)\n",
      "          (-12.418,-2.526,0)\n",
      "          (-12.521,-2.541,0)\n",
      "          (-12.729,-2.569,0)\n",
      "          (-12.833,-2.581,0)\n",
      "          (-12.938,-2.593,0)\n",
      "          (-13.148,-2.613,0)\n",
      "          (-13.253,-2.621,0)\n",
      "          (-13.359,-2.629,0)\n",
      "          (-13.465,-2.635,0)\n",
      "          (-13.571,-2.64,0)\n",
      "          (-13.678,-2.645,0)\n",
      "          (-13.785,-2.648,0)\n",
      "          (-13.892,-2.649,0)\n",
      "          (-14,-2.65,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (9.09425,-1.41149,0)\n",
      "          height 0, axis (0,0,1), 174 vertices:\n",
      "          (14,-2.65,0)\n",
      "          (13.892,-2.649,0)\n",
      "          (13.785,-2.648,0)\n",
      "          (13.678,-2.645,0)\n",
      "          (13.571,-2.64,0)\n",
      "          (13.465,-2.635,0)\n",
      "          (13.359,-2.629,0)\n",
      "          (13.253,-2.621,0)\n",
      "          (13.148,-2.613,0)\n",
      "          (12.938,-2.593,0)\n",
      "          (12.833,-2.581,0)\n",
      "          (12.729,-2.569,0)\n",
      "          (12.521,-2.541,0)\n",
      "          (12.418,-2.526,0)\n",
      "          (12.315,-2.51,0)\n",
      "          (12.212,-2.493,0)\n",
      "          (12.109,-2.475,0)\n",
      "          (12.007,-2.457,0)\n",
      "          (11.905,-2.438,0)\n",
      "          (11.803,-2.418,0)\n",
      "          (11.701,-2.397,0)\n",
      "          (11.6,-2.376,0)\n",
      "          (11.499,-2.354,0)\n",
      "          (11.297,-2.308,0)\n",
      "          (11.197,-2.285,0)\n",
      "          (11.096,-2.26,0)\n",
      "          (10.796,-2.185,0)\n",
      "          (10.697,-2.158,0)\n",
      "          (10.597,-2.132,0)\n",
      "          (10.498,-2.105,0)\n",
      "          (10.399,-2.077,0)\n",
      "          (10.3,-2.05,0)\n",
      "          (10.201,-2.022,0)\n",
      "          (10.102,-1.993,0)\n",
      "          (10.004,-1.965,0)\n",
      "          (9.905,-1.936,0)\n",
      "          (9.807,-1.907,0)\n",
      "          (9.709,-1.877,0)\n",
      "          (9.611,-1.848,0)\n",
      "          (9.513,-1.818,0)\n",
      "          (9.415,-1.789,0)\n",
      "          (9.219,-1.729,0)\n",
      "          (9.122,-1.699,0)\n",
      "          (8.926,-1.639,0)\n",
      "          (8.732,-1.579,0)\n",
      "          (8.634,-1.549,0)\n",
      "          (8.537,-1.519,0)\n",
      "          (8.44,-1.49,0)\n",
      "          (8.342,-1.46,0)\n",
      "          (8.051,-1.373,0)\n",
      "          (7.953,-1.344,0)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "          (7.856,-1.315,0)\n",
      "          (7.662,-1.259,0)\n",
      "          (7.564,-1.232,0)\n",
      "          (7.467,-1.204,0)\n",
      "          (7.37,-1.177,0)\n",
      "          (7.272,-1.151,0)\n",
      "          (7.078,-1.099,0)\n",
      "          (6.98,-1.074,0)\n",
      "          (6.883,-1.05,0)\n",
      "          (6.785,-1.025,0)\n",
      "          (6.687,-1.002,0)\n",
      "          (6.59,-0.979,0)\n",
      "          (6.492,-0.956,0)\n",
      "          (6.394,-0.934,0)\n",
      "          (6.296,-0.913,0)\n",
      "          (6.198,-0.893,0)\n",
      "          (6.099,-0.873,0)\n",
      "          (6.001,-0.854,0)\n",
      "          (5.902,-0.835,0)\n",
      "          (5.804,-0.817,0)\n",
      "          (5.705,-0.8,0)\n",
      "          (5.606,-0.784,0)\n",
      "          (5.408,-0.754,0)\n",
      "          (5.309,-0.74,0)\n",
      "          (5.209,-0.728,0)\n",
      "          (5.11,-0.716,0)\n",
      "          (5.01,-0.705,0)\n",
      "          (4.81,-0.685,0)\n",
      "          (4.709,-0.677,0)\n",
      "          (4.608,-0.67,0)\n",
      "          (4.508,-0.664,0)\n",
      "          (4.407,-0.659,0)\n",
      "          (4.305,-0.655,0)\n",
      "          (4.204,-0.652,0)\n",
      "          (4,-0.65,0)\n",
      "          (4,-0.15,0)\n",
      "          (4.108,-0.151,0)\n",
      "          (4.215,-0.152,0)\n",
      "          (4.322,-0.155,0)\n",
      "          (4.429,-0.16,0)\n",
      "          (4.535,-0.165,0)\n",
      "          (4.641,-0.171,0)\n",
      "          (4.747,-0.179,0)\n",
      "          (4.852,-0.187,0)\n",
      "          (5.062,-0.207,0)\n",
      "          (5.167,-0.219,0)\n",
      "          (5.271,-0.231,0)\n",
      "          (5.479,-0.259,0)\n",
      "          (5.582,-0.274,0)\n",
      "          (5.685,-0.29,0)\n",
      "          (5.788,-0.307,0)\n",
      "          (5.891,-0.325,0)\n",
      "          (5.993,-0.343,0)\n",
      "          (6.095,-0.362,0)\n",
      "          (6.197,-0.382,0)\n",
      "          (6.299,-0.403,0)\n",
      "          (6.4,-0.424,0)\n",
      "          (6.501,-0.446,0)\n",
      "          (6.703,-0.492,0)\n",
      "          (6.803,-0.515,0)\n",
      "          (6.904,-0.54,0)\n",
      "          (7.204,-0.615,0)\n",
      "          (7.303,-0.642,0)\n",
      "          (7.403,-0.668,0)\n",
      "          (7.502,-0.695,0)\n",
      "          (7.601,-0.723,0)\n",
      "          (7.7,-0.75,0)\n",
      "          (7.799,-0.778,0)\n",
      "          (7.898,-0.807,0)\n",
      "          (7.996,-0.835,0)\n",
      "          (8.095,-0.864,0)\n",
      "          (8.193,-0.893,0)\n",
      "          (8.291,-0.923,0)\n",
      "          (8.389,-0.952,0)\n",
      "          (8.487,-0.982,0)\n",
      "          (8.585,-1.011,0)\n",
      "          (8.781,-1.071,0)\n",
      "          (8.878,-1.101,0)\n",
      "          (9.074,-1.161,0)\n",
      "          (9.268,-1.221,0)\n",
      "          (9.366,-1.251,0)\n",
      "          (9.463,-1.281,0)\n",
      "          (9.56,-1.31,0)\n",
      "          (9.658,-1.34,0)\n",
      "          (9.949,-1.427,0)\n",
      "          (10.047,-1.456,0)\n",
      "          (10.144,-1.485,0)\n",
      "          (10.338,-1.541,0)\n",
      "          (10.436,-1.568,0)\n",
      "          (10.533,-1.596,0)\n",
      "          (10.63,-1.623,0)\n",
      "          (10.728,-1.649,0)\n",
      "          (10.922,-1.701,0)\n",
      "          (11.02,-1.726,0)\n",
      "          (11.117,-1.75,0)\n",
      "          (11.215,-1.775,0)\n",
      "          (11.313,-1.798,0)\n",
      "          (11.41,-1.821,0)\n",
      "          (11.508,-1.844,0)\n",
      "          (11.606,-1.866,0)\n",
      "          (11.704,-1.887,0)\n",
      "          (11.802,-1.907,0)\n",
      "          (11.901,-1.927,0)\n",
      "          (11.999,-1.946,0)\n",
      "          (12.098,-1.965,0)\n",
      "          (12.196,-1.983,0)\n",
      "          (12.295,-2,0)\n",
      "          (12.394,-2.016,0)\n",
      "          (12.592,-2.046,0)\n",
      "          (12.691,-2.06,0)\n",
      "          (12.791,-2.072,0)\n",
      "          (12.89,-2.084,0)\n",
      "          (12.99,-2.095,0)\n",
      "          (13.19,-2.115,0)\n",
      "          (13.291,-2.123,0)\n",
      "          (13.392,-2.13,0)\n",
      "          (13.492,-2.136,0)\n",
      "          (13.593,-2.141,0)\n",
      "          (13.695,-2.145,0)\n",
      "          (13.796,-2.148,0)\n",
      "          (14,-2.15,0)\n",
      "          (17.2,-2.15,0)\n",
      "          (17.2,-2.65,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (0,-0.4,0)\n",
      "          height 0, axis (0,0,1), 4 vertices:\n",
      "          (-4,-0.65,0)\n",
      "          (-4,-0.15,0)\n",
      "          (4,-0.15,0)\n",
      "          (4,-0.65,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "subpixel-averaging is 68.224% done, 1.87819 s remaining\n",
      "subpixel-averaging is 68.224% done, 1.87065 s remaining\n"
     ]
    }
   ],
   "source": [
    "sim.init_sim()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Look at the geometry before simulating :"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "f = plt.figure(dpi=100)\n",
    "sim.plot2D(ax=f.gca())\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Simulate for the fields :"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sim.run(until=400)  # arbitrary long run time to ensure that fields have reached steady state"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Plot the result :"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "eps_data = sim.get_epsilon()\n",
    "ez_data = np.real(sim.get_efield_z())\n",
    "\n",
    "plt.figure(dpi=200)\n",
    "plt.imshow(np.transpose(eps_data), interpolation='spline36', cmap='binary')\n",
    "plt.imshow(np.flipud(np.transpose(ez_data)), interpolation='spline36', cmap='RdBu', alpha=0.9)\n",
    "plt.axis('off')\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Extruding to 3D\n",
    "\n",
    "We can also give a $z_{min}$ and $z_{max}$ argument to the layers when we load them for 3D simulations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "sim.reset_meep()\n",
    "\n",
    "t_oxide = 1.0\n",
    "t_Si = 0.22\n",
    "t_air = 0.78\n",
    "\n",
    "cell_thickness = dpml+t_oxide+t_Si+t_air+dpml\n",
    "si_zmin = 0\n",
    "\n",
    "cell_zmax = 0.5*cell_thickness\n",
    "cell_zmin = -0.5*cell_thickness\n",
    "si_zmax = t_Si"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "upper_branch = mp.get_GDSII_prisms(silicon, gdsII_file, UPPER_BRANCH_LAYER, si_zmin, si_zmax)\n",
    "lower_branch = mp.get_GDSII_prisms(silicon, gdsII_file, LOWER_BRANCH_LAYER, si_zmin, si_zmax)\n",
    "geometry = upper_branch+lower_branch\n",
    "\n",
    "cell = mp.GDSII_vol(gdsII_file, CELL_LAYER, cell_zmin, cell_zmax)\n",
    "src_vol = mp.GDSII_vol(gdsII_file, SOURCE_LAYER, si_zmin, si_zmax)\n",
    "\n",
    "oxide_center = mp.Vector3(z=-0.5*t_oxide)\n",
    "oxide_size = mp.Vector3(cell.size.x,cell.size.y,t_oxide)\n",
    "oxide_layer = [mp.Block(material=oxide, center=oxide_center, size=oxide_size)]\n",
    "geometry = geometry+oxide_layer\n",
    "\n",
    "# Uncomment this to setup the simulations. Takes a while to run!\n",
    "sources = [mp.EigenModeSource(src=mp.GaussianSource(fcen,fwidth=df),\n",
    "                             size=src_vol.size,\n",
    "                             center=src_vol.center,\n",
    "                             eig_band=1,\n",
    "                             eig_parity=mp.NO_PARITY,\n",
    "                             eig_match_freq=True)]\n",
    "\n",
    "# Display simulation object\n",
    "sim = mp.Simulation(resolution=res,\n",
    "                   eps_averaging=False,\n",
    "                   subpixel_maxeval=1,\n",
    "                   subpixel_tol=1,\n",
    "                   cell_size=cell.size,\n",
    "                   boundary_layers=[mp.PML(dpml)],\n",
    "                   sources=sources,\n",
    "                   geometry=geometry)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-----------\n",
      "Initializing structure...\n",
      "time for choose_chunkdivision = 0.000842094 s\n",
      "Working in 3D dimensions.\n",
      "Computational cell is 34.4062 x 8 x 4 with resolution 32\n",
      "     prism, center = (-9.09425,1.41149,0.11)\n",
      "          height 0.22, axis (0,0,1), 174 vertices:\n",
      "          (-4,0.15,0)\n",
      "          (-4.108,0.151,0)\n",
      "          (-4.215,0.152,0)\n",
      "          (-4.322,0.155,0)\n",
      "          (-4.429,0.16,0)\n",
      "          (-4.535,0.165,0)\n",
      "          (-4.641,0.171,0)\n",
      "          (-4.747,0.179,0)\n",
      "          (-4.852,0.187,0)\n",
      "          (-5.062,0.207,0)\n",
      "          (-5.167,0.219,0)\n",
      "          (-5.271,0.231,0)\n",
      "          (-5.479,0.259,0)\n",
      "          (-5.582,0.274,0)\n",
      "          (-5.685,0.29,0)\n",
      "          (-5.788,0.307,0)\n",
      "          (-5.891,0.325,0)\n",
      "          (-5.993,0.343,0)\n",
      "          (-6.095,0.362,0)\n",
      "          (-6.197,0.382,0)\n",
      "          (-6.299,0.403,0)\n",
      "          (-6.4,0.424,0)\n",
      "          (-6.501,0.446,0)\n",
      "          (-6.703,0.492,0)\n",
      "          (-6.803,0.515,0)\n",
      "          (-6.904,0.54,0)\n",
      "          (-7.204,0.615,0)\n",
      "          (-7.303,0.642,0)\n",
      "          (-7.403,0.668,0)\n",
      "          (-7.502,0.695,0)\n",
      "          (-7.601,0.723,0)\n",
      "          (-7.7,0.75,0)\n",
      "          (-7.799,0.778,0)\n",
      "          (-7.898,0.807,0)\n",
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      "          (-8.291,0.923,0)\n",
      "          (-8.389,0.952,0)\n",
      "          (-8.487,0.982,0)\n",
      "          (-8.585,1.011,0)\n",
      "          (-8.781,1.071,0)\n",
      "          (-8.878,1.101,0)\n",
      "          (-9.074,1.161,0)\n",
      "          (-9.268,1.221,0)\n",
      "          (-9.366,1.251,0)\n",
      "          (-9.463,1.281,0)\n",
      "          (-9.56,1.31,0)\n",
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      "          (-10.338,1.541,0)\n",
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      "          (-10.922,1.701,0)\n",
      "          (-11.02,1.726,0)\n",
      "          (-11.117,1.75,0)\n",
      "          (-11.215,1.775,0)\n",
      "          (-11.313,1.798,0)\n",
      "          (-11.41,1.821,0)\n",
      "          (-11.508,1.844,0)\n",
      "          (-11.606,1.866,0)\n",
      "          (-11.704,1.887,0)\n",
      "          (-11.802,1.907,0)\n",
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      "          (-11.999,1.946,0)\n",
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      "          (-14,2.15,0)\n",
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      "          (-14,2.65,0)\n",
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      "          (-13.678,2.645,0)\n",
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      "          (-10.3,2.05,0)\n",
      "          (-10.201,2.022,0)\n",
      "          (-10.102,1.993,0)\n",
      "          (-10.004,1.965,0)\n",
      "          (-9.905,1.936,0)\n",
      "          (-9.807,1.907,0)\n",
      "          (-9.709,1.877,0)\n",
      "          (-9.611,1.848,0)\n",
      "          (-9.513,1.818,0)\n",
      "          (-9.415,1.789,0)\n",
      "          (-9.219,1.729,0)\n",
      "          (-9.122,1.699,0)\n",
      "          (-8.926,1.639,0)\n",
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      "          (-8.537,1.519,0)\n",
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      "          (-8.051,1.373,0)\n",
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      "          (-7.856,1.315,0)\n",
      "          (-7.662,1.259,0)\n",
      "          (-7.564,1.232,0)\n",
      "          (-7.467,1.204,0)\n",
      "          (-7.37,1.177,0)\n",
      "          (-7.272,1.151,0)\n",
      "          (-7.078,1.099,0)\n",
      "          (-6.98,1.074,0)\n",
      "          (-6.883,1.05,0)\n",
      "          (-6.785,1.025,0)\n",
      "          (-6.687,1.002,0)\n",
      "          (-6.59,0.979,0)\n",
      "          (-6.492,0.956,0)\n",
      "          (-6.394,0.934,0)\n",
      "          (-6.296,0.913,0)\n",
      "          (-6.198,0.893,0)\n",
      "          (-6.099,0.873,0)\n",
      "          (-6.001,0.854,0)\n",
      "          (-5.902,0.835,0)\n",
      "          (-5.804,0.817,0)\n",
      "          (-5.705,0.8,0)\n",
      "          (-5.606,0.784,0)\n",
      "          (-5.408,0.754,0)\n",
      "          (-5.309,0.74,0)\n",
      "          (-5.209,0.728,0)\n",
      "          (-5.11,0.716,0)\n",
      "          (-5.01,0.705,0)\n",
      "          (-4.81,0.685,0)\n",
      "          (-4.709,0.677,0)\n",
      "          (-4.608,0.67,0)\n",
      "          (-4.508,0.664,0)\n",
      "          (-4.407,0.659,0)\n",
      "          (-4.305,0.655,0)\n",
      "          (-4.204,0.652,0)\n",
      "          (-4,0.65,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (9.09425,1.41149,0.11)\n",
      "          height 0.22, axis (0,0,1), 174 vertices:\n",
      "          (4,0.15,0)\n",
      "          (4,0.65,0)\n",
      "          (4.204,0.652,0)\n",
      "          (4.305,0.655,0)\n",
      "          (4.407,0.659,0)\n",
      "          (4.508,0.664,0)\n",
      "          (4.608,0.67,0)\n",
      "          (4.709,0.677,0)\n",
      "          (4.81,0.685,0)\n",
      "          (5.01,0.705,0)\n",
      "          (5.11,0.716,0)\n",
      "          (5.209,0.728,0)\n",
      "          (5.309,0.74,0)\n",
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      "          (5.705,0.8,0)\n",
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      "          (5.902,0.835,0)\n",
      "          (6.001,0.854,0)\n",
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      "          (6.296,0.913,0)\n",
      "          (6.394,0.934,0)\n",
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      "          (6.59,0.979,0)\n",
      "          (6.687,1.002,0)\n",
      "          (6.785,1.025,0)\n",
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      "          (7.37,1.177,0)\n",
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      "          (10.3,2.05,0)\n",
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      "          (11.297,2.308,0)\n",
      "          (11.499,2.354,0)\n",
      "          (11.6,2.376,0)\n",
      "          (11.701,2.397,0)\n",
      "          (11.803,2.418,0)\n",
      "          (11.905,2.438,0)\n",
      "          (12.007,2.457,0)\n",
      "          (12.109,2.475,0)\n",
      "          (12.212,2.493,0)\n",
      "          (12.315,2.51,0)\n",
      "          (12.418,2.526,0)\n",
      "          (12.521,2.541,0)\n",
      "          (12.729,2.569,0)\n",
      "          (12.833,2.581,0)\n",
      "          (12.938,2.593,0)\n",
      "          (13.148,2.613,0)\n",
      "          (13.253,2.621,0)\n",
      "          (13.359,2.629,0)\n",
      "          (13.465,2.635,0)\n",
      "          (13.571,2.64,0)\n",
      "          (13.678,2.645,0)\n",
      "          (13.785,2.648,0)\n",
      "          (13.892,2.649,0)\n",
      "          (14,2.65,0)\n",
      "          (17.2,2.65,0)\n",
      "          (17.2,2.15,0)\n",
      "          (14,2.15,0)\n",
      "          (13.796,2.148,0)\n",
      "          (13.695,2.145,0)\n",
      "          (13.593,2.141,0)\n",
      "          (13.492,2.136,0)\n",
      "          (13.392,2.13,0)\n",
      "          (13.291,2.123,0)\n",
      "          (13.19,2.115,0)\n",
      "          (12.99,2.095,0)\n",
      "          (12.89,2.084,0)\n",
      "          (12.791,2.072,0)\n",
      "          (12.691,2.06,0)\n",
      "          (12.592,2.046,0)\n",
      "          (12.394,2.016,0)\n",
      "          (12.295,2,0)\n",
      "          (12.196,1.983,0)\n",
      "          (12.098,1.965,0)\n",
      "          (11.999,1.946,0)\n",
      "          (11.901,1.927,0)\n",
      "          (11.802,1.907,0)\n",
      "          (11.704,1.887,0)\n",
      "          (11.606,1.866,0)\n",
      "          (11.508,1.844,0)\n",
      "          (11.41,1.821,0)\n",
      "          (11.313,1.798,0)\n",
      "          (11.215,1.775,0)\n",
      "          (11.117,1.75,0)\n",
      "          (11.02,1.726,0)\n",
      "          (10.922,1.701,0)\n",
      "          (10.728,1.649,0)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "          (10.63,1.623,0)\n",
      "          (10.533,1.596,0)\n",
      "          (10.436,1.568,0)\n",
      "          (10.338,1.541,0)\n",
      "          (10.144,1.485,0)\n",
      "          (10.047,1.456,0)\n",
      "          (9.949,1.427,0)\n",
      "          (9.658,1.34,0)\n",
      "          (9.56,1.31,0)\n",
      "          (9.463,1.281,0)\n",
      "          (9.366,1.251,0)\n",
      "          (9.268,1.221,0)\n",
      "          (9.074,1.161,0)\n",
      "          (8.878,1.101,0)\n",
      "          (8.781,1.071,0)\n",
      "          (8.585,1.011,0)\n",
      "          (8.487,0.982,0)\n",
      "          (8.389,0.952,0)\n",
      "          (8.291,0.923,0)\n",
      "          (8.193,0.893,0)\n",
      "          (8.095,0.864,0)\n",
      "          (7.996,0.835,0)\n",
      "          (7.898,0.807,0)\n",
      "          (7.799,0.778,0)\n",
      "          (7.7,0.75,0)\n",
      "          (7.601,0.723,0)\n",
      "          (7.502,0.695,0)\n",
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      "          (7.303,0.642,0)\n",
      "          (7.204,0.615,0)\n",
      "          (6.904,0.54,0)\n",
      "          (6.803,0.515,0)\n",
      "          (6.703,0.492,0)\n",
      "          (6.501,0.446,0)\n",
      "          (6.4,0.424,0)\n",
      "          (6.299,0.403,0)\n",
      "          (6.197,0.382,0)\n",
      "          (6.095,0.362,0)\n",
      "          (5.993,0.343,0)\n",
      "          (5.891,0.325,0)\n",
      "          (5.788,0.307,0)\n",
      "          (5.685,0.29,0)\n",
      "          (5.582,0.274,0)\n",
      "          (5.479,0.259,0)\n",
      "          (5.271,0.231,0)\n",
      "          (5.167,0.219,0)\n",
      "          (5.062,0.207,0)\n",
      "          (4.852,0.187,0)\n",
      "          (4.747,0.179,0)\n",
      "          (4.641,0.171,0)\n",
      "          (4.535,0.165,0)\n",
      "          (4.429,0.16,0)\n",
      "          (4.322,0.155,0)\n",
      "          (4.215,0.152,0)\n",
      "          (4.108,0.151,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (0,0.4,0.11)\n",
      "          height 0.22, axis (0,0,1), 4 vertices:\n",
      "          (-4,0.15,0)\n",
      "          (-4,0.65,0)\n",
      "          (4,0.65,0)\n",
      "          (4,0.15,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (-9.09425,-1.41149,0.11)\n",
      "          height 0.22, axis (0,0,1), 174 vertices:\n",
      "          (-17.2,-2.65,0)\n",
      "          (-17.2,-2.15,0)\n",
      "          (-14,-2.15,0)\n",
      "          (-13.796,-2.148,0)\n",
      "          (-13.695,-2.145,0)\n",
      "          (-13.593,-2.141,0)\n",
      "          (-13.492,-2.136,0)\n",
      "          (-13.392,-2.13,0)\n",
      "          (-13.291,-2.123,0)\n",
      "          (-13.19,-2.115,0)\n",
      "          (-12.99,-2.095,0)\n",
      "          (-12.89,-2.084,0)\n",
      "          (-12.791,-2.072,0)\n",
      "          (-12.691,-2.06,0)\n",
      "          (-12.592,-2.046,0)\n",
      "          (-12.394,-2.016,0)\n",
      "          (-12.295,-2,0)\n",
      "          (-12.196,-1.983,0)\n",
      "          (-12.098,-1.965,0)\n",
      "          (-11.999,-1.946,0)\n",
      "          (-11.901,-1.927,0)\n",
      "          (-11.802,-1.907,0)\n",
      "          (-11.704,-1.887,0)\n",
      "          (-11.606,-1.866,0)\n",
      "          (-11.508,-1.844,0)\n",
      "          (-11.41,-1.821,0)\n",
      "          (-11.313,-1.798,0)\n",
      "          (-11.215,-1.775,0)\n",
      "          (-11.117,-1.75,0)\n",
      "          (-11.02,-1.726,0)\n",
      "          (-10.922,-1.701,0)\n",
      "          (-10.728,-1.649,0)\n",
      "          (-10.63,-1.623,0)\n",
      "          (-10.533,-1.596,0)\n",
      "          (-10.436,-1.568,0)\n",
      "          (-10.338,-1.541,0)\n",
      "          (-10.144,-1.485,0)\n",
      "          (-10.047,-1.456,0)\n",
      "          (-9.949,-1.427,0)\n",
      "          (-9.658,-1.34,0)\n",
      "          (-9.56,-1.31,0)\n",
      "          (-9.463,-1.281,0)\n",
      "          (-9.366,-1.251,0)\n",
      "          (-9.268,-1.221,0)\n",
      "          (-9.074,-1.161,0)\n",
      "          (-8.878,-1.101,0)\n",
      "          (-8.781,-1.071,0)\n",
      "          (-8.585,-1.011,0)\n",
      "          (-8.487,-0.982,0)\n",
      "          (-8.389,-0.952,0)\n",
      "          (-8.291,-0.923,0)\n",
      "          (-8.193,-0.893,0)\n",
      "          (-8.095,-0.864,0)\n",
      "          (-7.996,-0.835,0)\n",
      "          (-7.898,-0.807,0)\n",
      "          (-7.799,-0.778,0)\n",
      "          (-7.7,-0.75,0)\n",
      "          (-7.601,-0.723,0)\n",
      "          (-7.502,-0.695,0)\n",
      "          (-7.403,-0.668,0)\n",
      "          (-7.303,-0.642,0)\n",
      "          (-7.204,-0.615,0)\n",
      "          (-6.904,-0.54,0)\n",
      "          (-6.803,-0.515,0)\n",
      "          (-6.703,-0.492,0)\n",
      "          (-6.501,-0.446,0)\n",
      "          (-6.4,-0.424,0)\n",
      "          (-6.299,-0.403,0)\n",
      "          (-6.197,-0.382,0)\n",
      "          (-6.095,-0.362,0)\n",
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      "          (-5.705,-0.8,0)\n",
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      "          (-7.662,-1.259,0)\n",
      "          (-7.856,-1.315,0)\n",
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      "          (-8.051,-1.373,0)\n",
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      "          (-8.634,-1.549,0)\n",
      "          (-8.732,-1.579,0)\n",
      "          (-8.926,-1.639,0)\n",
      "          (-9.122,-1.699,0)\n",
      "          (-9.219,-1.729,0)\n",
      "          (-9.415,-1.789,0)\n",
      "          (-9.513,-1.818,0)\n",
      "          (-9.611,-1.848,0)\n",
      "          (-9.709,-1.877,0)\n",
      "          (-9.807,-1.907,0)\n",
      "          (-9.905,-1.936,0)\n",
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      "          (-10.102,-1.993,0)\n",
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      "          (-10.3,-2.05,0)\n",
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      "          (-10.498,-2.105,0)\n",
      "          (-10.597,-2.132,0)\n",
      "          (-10.697,-2.158,0)\n",
      "          (-10.796,-2.185,0)\n",
      "          (-11.096,-2.26,0)\n",
      "          (-11.197,-2.285,0)\n",
      "          (-11.297,-2.308,0)\n",
      "          (-11.499,-2.354,0)\n",
      "          (-11.6,-2.376,0)\n",
      "          (-11.701,-2.397,0)\n",
      "          (-11.803,-2.418,0)\n",
      "          (-11.905,-2.438,0)\n",
      "          (-12.007,-2.457,0)\n",
      "          (-12.109,-2.475,0)\n",
      "          (-12.212,-2.493,0)\n",
      "          (-12.315,-2.51,0)\n",
      "          (-12.418,-2.526,0)\n",
      "          (-12.521,-2.541,0)\n",
      "          (-12.729,-2.569,0)\n",
      "          (-12.833,-2.581,0)\n",
      "          (-12.938,-2.593,0)\n",
      "          (-13.148,-2.613,0)\n",
      "          (-13.253,-2.621,0)\n",
      "          (-13.359,-2.629,0)\n",
      "          (-13.465,-2.635,0)\n",
      "          (-13.571,-2.64,0)\n",
      "          (-13.678,-2.645,0)\n",
      "          (-13.785,-2.648,0)\n",
      "          (-13.892,-2.649,0)\n",
      "          (-14,-2.65,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (9.09425,-1.41149,0.11)\n",
      "          height 0.22, axis (0,0,1), 174 vertices:\n",
      "          (14,-2.65,0)\n",
      "          (13.892,-2.649,0)\n",
      "          (13.785,-2.648,0)\n",
      "          (13.678,-2.645,0)\n",
      "          (13.571,-2.64,0)\n",
      "          (13.465,-2.635,0)\n",
      "          (13.359,-2.629,0)\n",
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      "          (13.148,-2.613,0)\n",
      "          (12.938,-2.593,0)\n",
      "          (12.833,-2.581,0)\n",
      "          (12.729,-2.569,0)\n",
      "          (12.521,-2.541,0)\n",
      "          (12.418,-2.526,0)\n",
      "          (12.315,-2.51,0)\n",
      "          (12.212,-2.493,0)\n",
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      "          (10.498,-2.105,0)\n",
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      "          (10.3,-2.05,0)\n",
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      "          (9.709,-1.877,0)\n",
      "          (9.611,-1.848,0)\n",
      "          (9.513,-1.818,0)\n",
      "          (9.415,-1.789,0)\n",
      "          (9.219,-1.729,0)\n",
      "          (9.122,-1.699,0)\n",
      "          (8.926,-1.639,0)\n",
      "          (8.732,-1.579,0)\n",
      "          (8.634,-1.549,0)\n",
      "          (8.537,-1.519,0)\n",
      "          (8.44,-1.49,0)\n",
      "          (8.342,-1.46,0)\n",
      "          (8.051,-1.373,0)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "          (7.953,-1.344,0)\n",
      "          (7.856,-1.315,0)\n",
      "          (7.662,-1.259,0)\n",
      "          (7.564,-1.232,0)\n",
      "          (7.467,-1.204,0)\n",
      "          (7.37,-1.177,0)\n",
      "          (7.272,-1.151,0)\n",
      "          (7.078,-1.099,0)\n",
      "          (6.98,-1.074,0)\n",
      "          (6.883,-1.05,0)\n",
      "          (6.785,-1.025,0)\n",
      "          (6.687,-1.002,0)\n",
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      "          (6.394,-0.934,0)\n",
      "          (6.296,-0.913,0)\n",
      "          (6.198,-0.893,0)\n",
      "          (6.099,-0.873,0)\n",
      "          (6.001,-0.854,0)\n",
      "          (5.902,-0.835,0)\n",
      "          (5.804,-0.817,0)\n",
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      "          (6.803,-0.515,0)\n",
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      "          (7.403,-0.668,0)\n",
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      "          (11.508,-1.844,0)\n",
      "          (11.606,-1.866,0)\n",
      "          (11.704,-1.887,0)\n",
      "          (11.802,-1.907,0)\n",
      "          (11.901,-1.927,0)\n",
      "          (11.999,-1.946,0)\n",
      "          (12.098,-1.965,0)\n",
      "          (12.196,-1.983,0)\n",
      "          (12.295,-2,0)\n",
      "          (12.394,-2.016,0)\n",
      "          (12.592,-2.046,0)\n",
      "          (12.691,-2.06,0)\n",
      "          (12.791,-2.072,0)\n",
      "          (12.89,-2.084,0)\n",
      "          (12.99,-2.095,0)\n",
      "          (13.19,-2.115,0)\n",
      "          (13.291,-2.123,0)\n",
      "          (13.392,-2.13,0)\n",
      "          (13.492,-2.136,0)\n",
      "          (13.593,-2.141,0)\n",
      "          (13.695,-2.145,0)\n",
      "          (13.796,-2.148,0)\n",
      "          (14,-2.15,0)\n",
      "          (17.2,-2.15,0)\n",
      "          (17.2,-2.65,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     prism, center = (0,-0.4,0.11)\n",
      "          height 0.22, axis (0,0,1), 4 vertices:\n",
      "          (-4,-0.65,0)\n",
      "          (-4,-0.15,0)\n",
      "          (4,-0.15,0)\n",
      "          (4,-0.65,0)\n",
      "          dielectric constant epsilon diagonal = (12,12,12)\n",
      "     block, center = (0,0,-0.5)\n",
      "          size (34.4,8,1)\n",
      "          axes (1,0,0), (0,1,0), (0,0,1)\n",
      "          dielectric constant epsilon diagonal = (2.25,2.25,2.25)\n",
      "subpixel-averaging is 65.5774% done, 2.09988 s remaining\n",
      "subpixel-averaging is 66.548% done, 2.01084 s remaining\n",
      "subpixel-averaging is 66.5239% done, 2.01298 s remaining\n",
      "time for set_epsilon = 32.579 s\n",
      "-----------\n",
      "MPB solved for omega_1(2.2349,0,0) = 0.740287 after 42 iters\n",
      "MPB solved for omega_1(1.91466,0,0) = 0.645103 after 18 iters\n",
      "MPB solved for omega_1(1.91485,0,0) = 0.645161 after 5 iters\n",
      "MPB solved for omega_1(1.91485,0,0) = 0.645161 after 1 iters\n"
     ]
    }
   ],
   "source": [
    "sim.init_sim()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Usually (say on your own machine), you can use Mayavi to easily visualize in 3D with `sim.plot3D`. The graphical backend of the cluster doesn't allow for Mayavi, so we can look at cuts :"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<Figure size 432x288 with 2 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "fig, ax = plt.subplots(figsize=(6, 4))\n",
    "\n",
    "eps = sim.get_epsilon()\n",
    "eps = eps[dpml*res:-1*dpml*res, dpml*res:-1*dpml*res, dpml*res:-1*dpml*res] # Trim PMLs\n",
    "eps_xy = eps[:,:,0]\n",
    "\n",
    "pos = ax.imshow(eps_xy.T, cmap='gray_r', interpolation='none', extent=(0, np.shape(eps_xy)[0]/res, 0, np.shape(eps_xy)[1]/res))\n",
    "cbar = fig.colorbar(pos, ax=ax)\n",
    "cbar.set_label('eps')\n",
    "ax.set_title('xy cut for bottom of simulation')\n",
    "ax.set_xlabel('x')\n",
    "ax.set_ylabel('y')\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<Figure size 432x288 with 2 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "fig, ax = plt.subplots(figsize=(6, 4))\n",
    "\n",
    "eps_xy = eps[:,:,32]\n",
    "\n",
    "pos = ax.imshow(eps_xy.T, cmap='gray_r', interpolation='none', extent=(0, np.shape(eps_xy)[0]/res, 0, np.shape(eps_xy)[1]/res))\n",
    "cbar = fig.colorbar(pos, ax=ax)\n",
    "cbar.set_label('eps')\n",
    "ax.set_title('xy cut for middle of simulation')\n",
    "ax.set_xlabel('x')\n",
    "ax.set_ylabel('y')\n",
    "plt.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Ipyvolume can also be used as an alternative (the mp environment has the right widget, on regular Jupyter Notebooks)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b35376fcefa4480a964c6a4a63d4704e",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(VBox(children=(HBox(children=(Label(value='levels:'), FloatSlider(value=1.0, max=1.0, step=0.00…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import ipyvolume as ipv\n",
    "ipv.quickvolshow(eps.T, level=[2.25,12], extent=[[0, np.shape(eps)[0]/res],[0, np.shape(eps)[1]/res],[cell_zmin, cell_zmax]])\n",
    "ipv.show()"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "mp [~/home/ELE559/anaconda3/envs/mp/]",
   "language": "python",
   "name": "conda_mp"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}