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Use the Jupyter Notebook only the analyze the results 11971/head
authorDaniel Garcia-Sanchez <daniel.garcia-sanchez@insp.upmc.fr>
Wed, 21 Apr 2021 19:41:05 +0000 (21:41 +0200)
committerDaniel Garcia-Sanchez <daniel.garcia-sanchez@insp.upmc.fr>
Wed, 21 Apr 2021 19:41:05 +0000 (21:41 +0200)
examples/step-62/doc/results.dox patch | blob | history
examples/step-62/step-62.cc patch | blob | history
examples/step-62/step-62.ipynb patch | blob | history

diff --git a/examples/step-62/doc/results.dox b/examples/step-62/doc/results.dox
index bbe4d34152564546225f626e357818f8a6b8fbb7..888dbecb5f4a8ae7e0371eeb5a7e476851708926 100644 (file)
--- a/examples/step-62/doc/results.dox
+++ b/examples/step-62/doc/results.dox
@@ -132,3 +132,106 @@ which are promising candidates to study macroscopic quantum phenomena.
 The 20GHz mode of a micropillar superlattice cavity is essentially a mechanical harmonic oscillator that is very well isolated
 from the environment. If the device is cooled down to 20mK in a dilution fridge, the mode would then become a
 macroscopic quantum harmonic oscillator.
+
+
+<h3>Possibilities for extensions</h3>
+
+Instead of setting the parameters in the C++ file we could set the parameters
+using a python script and save them in the HDF5 file that we will use for
+the simulations. Then the deal.II program will read the parameters from the
+HDF5 file.
+
+@code{.py}
+import numpy as np
+import h5py
+import matplotlib.pyplot as plt
+import subprocess
+import scipy.constants as constants
+import scipy.optimize
+
+# This considerably reduces the size of the svg data
+plt.rcParams['svg.fonttype'] = 'none'
+
+h5_file = h5py.File('results.h5', 'w')
+data = h5_file.create_group('data')
+displacement = data.create_group('displacement')
+calibration = data.create_group('calibration')
+
+# Set the parameters
+for group in [displacement, calibration]:
+    # Dimensions of the domain
+    # The waveguide length is equal to dimension_x
+    group.attrs['dimension_x'] = 2e-5
+    # The waveguide width is equal to dimension_y
+    group.attrs['dimension_y'] = 2e-8
+
+    # Position of the probe that we use to measure the flux
+    group.attrs['probe_pos_x']   = 8e-6
+    group.attrs['probe_pos_y']   = 0
+    group.attrs['probe_width_y'] = 2e-08
+
+    # Number of points in the probe
+    group.attrs['nb_probe_points'] = 5
+
+    # Global refinement
+    group.attrs['grid_level'] = 1
+
+    # Cavity
+    group.attrs['cavity_resonance_frequency'] = 20e9
+    group.attrs['nb_mirror_pairs']            = 15
+
+    # Material
+    group.attrs['poissons_ratio'] = 0.27
+    group.attrs['youngs_modulus'] = 270000000000.0
+    group.attrs['material_a_rho'] = 3200
+    if group == displacement:
+        group.attrs['material_b_rho'] = 2000
+    else:
+        group.attrs['material_b_rho'] = 3200
+    group.attrs['lambda'] = (group.attrs['youngs_modulus'] * group.attrs['poissons_ratio'] /
+                           ((1 + group.attrs['poissons_ratio']) *
+                           (1 - 2 * group.attrs['poissons_ratio'])))
+    group.attrs['mu']= (group.attrs['youngs_modulus'] / (2 * (1 + group.attrs['poissons_ratio'])))
+
+    # Force
+    group.attrs['max_force_amplitude'] = 1e26
+    group.attrs['force_sigma_x']       = 1e-7
+    group.attrs['force_sigma_y']       = 1
+    group.attrs['max_force_width_x']   = 3e-7
+    group.attrs['max_force_width_y']   = 2e-8
+    group.attrs['force_x_pos']         = -8e-6
+    group.attrs['force_y_pos']         = 0
+
+    # PML
+    group.attrs['pml_x']            = True
+    group.attrs['pml_y']            = False
+    group.attrs['pml_width_x']      = 1.8e-6
+    group.attrs['pml_width_y']      = 5e-7
+    group.attrs['pml_coeff']        = 1.6
+    group.attrs['pml_coeff_degree'] = 2
+
+    # Frequency sweep
+    group.attrs['center_frequency']    = 20e9
+    group.attrs['frequency_range']     = 0.5e9
+    group.attrs['start_frequency']     = group.attrs['center_frequency'] - group.attrs['frequency_range'] / 2
+    group.attrs['stop_frequency']      = group.attrs['center_frequency'] + group.attrs['frequency_range'] / 2
+    group.attrs['nb_frequency_points'] = 400
+
+    # Other parameters
+    if group == displacement:
+        group.attrs['simulation_name'] = 'phononic_cavity_displacement'
+    else:
+        group.attrs['simulation_name'] = 'phononic_cavity_calibration'
+    group.attrs['save_vtu_files'] = False
+
+h5_file.close()
+@endcode
+
+In order to read the HDF5 parameters we have to use the
+HDF5::File::FileAccessMode::open flag.
+@code{.py}
+      HDF5::File data_file("results.h5",
+                           HDF5::File::FileAccessMode::open,
+                           MPI_COMM_WORLD);
+      auto       data = data_file.open_group("data");
+@endcode
diff --git a/examples/step-62/step-62.cc b/examples/step-62/step-62.cc
index f321f88b38c05dd79e5ec2e5ab528066bc96cca5..3088dc317e5c42bb78e94c31bca8ca2380360ed7 100644 (file)
--- a/examples/step-62/step-62.cc
+++ b/examples/step-62/step-62.cc
@@ -1370,10 +1370,99 @@ int main(int argc, char *argv[])
 
       Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
 
-      HDF5::File  data_file("results.h5",
-                           HDF5::File::FileAccessMode::open,
+      HDF5::File data_file("results.h5",
+                           HDF5::File::FileAccessMode::create,
                            MPI_COMM_WORLD);
-      HDF5::Group data = data_file.open_group("data");
+      auto       data = data_file.create_group("data");
+
+      // Each of the simulations (displacement and calibration) is stored in a
+      // separate HDF5 group:
+      const std::vector<std::string> group_names = {"displacement",
+                                                    "calibration"};
+      for (auto group_name : group_names)
+        {
+          // For each of these two group names, we now create the group and put
+          // attributes into these groups.
+          // Specifically, these are:
+          // - The dimensions of the waveguide (in $x$ and $y$ directions)
+          // - The position of the probe (in $x$ and $y$ directions)
+          // - The number of points in the probe
+          // - The global refinement level
+          // - The cavity resonance frequency
+          // - The number of mirror pairs
+          // - The material properties
+          // - The force parameters
+          // - The PML parameters
+          // - The frequency parameters
+
+          auto group = data.create_group(group_name);
+
+          group.set_attribute<double>("dimension_x", 2e-5);
+          group.set_attribute<double>("dimension_y", 2e-8);
+          group.set_attribute<double>("probe_pos_x", 8e-6);
+          group.set_attribute<double>("probe_pos_y", 0);
+          group.set_attribute<double>("probe_width_y", 2e-08);
+          group.set_attribute<unsigned int>("nb_probe_points", 5);
+          group.set_attribute<unsigned int>("grid_level", 1);
+          group.set_attribute<double>("cavity_resonance_frequency", 20e9);
+          group.set_attribute<unsigned int>("nb_mirror_pairs", 15);
+
+          group.set_attribute<double>("poissons_ratio", 0.27);
+          group.set_attribute<double>("youngs_modulus", 270000000000.0);
+          group.set_attribute<double>("material_a_rho", 3200);
+
+          if (group_name == std::string("displacement"))
+            group.set_attribute<double>("material_b_rho", 2000);
+          else
+            group.set_attribute<double>("material_b_rho", 3200);
+
+          group.set_attribute(
+            "lambda",
+            group.get_attribute<double>("youngs_modulus") *
+              group.get_attribute<double>("poissons_ratio") /
+              ((1 + group.get_attribute<double>("poissons_ratio")) *
+               (1 - 2 * group.get_attribute<double>("poissons_ratio"))));
+          group.set_attribute("mu",
+                              group.get_attribute<double>("youngs_modulus") /
+                                (2 * (1 + group.get_attribute<double>(
+                                            "poissons_ratio"))));
+
+          group.set_attribute<double>("max_force_amplitude", 1e26);
+          group.set_attribute<double>("force_sigma_x", 1e-7);
+          group.set_attribute<double>("force_sigma_y", 1);
+          group.set_attribute<double>("max_force_width_x", 3e-7);
+          group.set_attribute<double>("max_force_width_y", 2e-8);
+          group.set_attribute<double>("force_x_pos", -8e-6);
+          group.set_attribute<double>("force_y_pos", 0);
+
+          group.set_attribute<bool>("pml_x", true);
+          group.set_attribute<bool>("pml_y", false);
+          group.set_attribute<double>("pml_width_x", 1.8e-6);
+          group.set_attribute<double>("pml_width_y", 5e-7);
+          group.set_attribute<double>("pml_coeff", 1.6);
+          group.set_attribute<unsigned int>("pml_coeff_degree", 2);
+
+          group.set_attribute<double>("center_frequency", 20e9);
+          group.set_attribute<double>("frequency_range", 0.5e9);
+          group.set_attribute<double>(
+            "start_frequency",
+            group.get_attribute<double>("center_frequency") -
+              group.get_attribute<double>("frequency_range") / 2);
+          group.set_attribute<double>(
+            "stop_frequency",
+            group.get_attribute<double>("center_frequency") +
+              group.get_attribute<double>("frequency_range") / 2);
+          group.set_attribute<unsigned int>("nb_frequency_points", 400);
+
+          if (group_name == std::string("displacement"))
+            group.set_attribute<std::string>(
+              "simulation_name", std::string("phononic_cavity_displacement"));
+          else
+            group.set_attribute<std::string>(
+              "simulation_name", std::string("phononic_cavity_calibration"));
+
+          group.set_attribute<bool>("save_vtu_files", false);
+        }
 
       {
         // Displacement simulation. The parameters are read from the
diff --git a/examples/step-62/step-62.ipynb b/examples/step-62/step-62.ipynb
index 2639aeb0d2d30c9fa2cefcea1755a527747a9eed..fe9b17f4c6129fd708834639d5c310060e25c858 100644 (file)
--- a/examples/step-62/step-62.ipynb
+++ b/examples/step-62/step-62.ipynb
@@ -1,157 +1,9 @@
 {
  "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Step-62"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Set parameters"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [],
-   "source": [
-    "%config InlineBackend.figure_formats = ['svg']\n",
-    "%matplotlib inline\n",
-    "import numpy as np\n",
-    "import h5py\n",
-    "import matplotlib.pyplot as plt\n",
-    "import subprocess\n",
-    "import scipy.constants as constants\n",
-    "import scipy.optimize\n",
-    "\n",
-    "# This considerably reduces the size of the svg data\n",
-    "plt.rcParams['svg.fonttype'] = 'none'\n",
-    "\n",
-    "h5_file = h5py.File('results.h5', 'w')\n",
-    "data = h5_file.create_group('data')\n",
-    "displacement = data.create_group('displacement')\n",
-    "calibration = data.create_group('calibration')\n",
-    "\n",
-    "# Set the parameters\n",
-    "for group in [displacement, calibration]:\n",
-    "    # Dimensions of the domain\n",
-    "    # The waveguide length is equal to dimension_x\n",
-    "    group.attrs['dimension_x'] = 2e-5\n",
-    "    # The waveguide width is equal to dimension_y\n",
-    "    group.attrs['dimension_y'] = 2e-8\n",
-    "    \n",
-    "    # Position of the probe that we use to measure the flux\n",
-    "    group.attrs['probe_pos_x']   = 8e-6\n",
-    "    group.attrs['probe_pos_y']   = 0\n",
-    "    group.attrs['probe_width_y'] = 2e-08\n",
-    "    \n",
-    "    # Number of points in the probe\n",
-    "    group.attrs['nb_probe_points'] = 5\n",
-    "    \n",
-    "    # Global refinement\n",
-    "    group.attrs['grid_level'] = 1\n",
-    "\n",
-    "    # Cavity\n",
-    "    group.attrs['cavity_resonance_frequency'] = 20e9\n",
-    "    group.attrs['nb_mirror_pairs']            = 15\n",
-    "\n",
-    "    # Material\n",
-    "    group.attrs['poissons_ratio'] = 0.27\n",
-    "    group.attrs['youngs_modulus'] = 270000000000.0\n",
-    "    group.attrs['material_a_rho'] = 3200\n",
-    "    if group == displacement:\n",
-    "        group.attrs['material_b_rho'] = 2000\n",
-    "    else:\n",
-    "        group.attrs['material_b_rho'] = 3200   \n",
-    "    group.attrs['lambda'] = (group.attrs['youngs_modulus'] * group.attrs['poissons_ratio'] /\n",
-    "                           ((1 + group.attrs['poissons_ratio']) *\n",
-    "                           (1 - 2 * group.attrs['poissons_ratio'])))\n",
-    "    group.attrs['mu']= (group.attrs['youngs_modulus'] / (2 * (1 + group.attrs['poissons_ratio'])))\n",
-    "\n",
-    "    # Force\n",
-    "    group.attrs['max_force_amplitude'] = 1e26\n",
-    "    group.attrs['force_sigma_x']       = 1e-7\n",
-    "    group.attrs['force_sigma_y']       = 1\n",
-    "    group.attrs['max_force_width_x']   = 3e-7\n",
-    "    group.attrs['max_force_width_y']   = 2e-8\n",
-    "    group.attrs['force_x_pos']         = -8e-6\n",
-    "    group.attrs['force_y_pos']         = 0\n",
-    "\n",
-    "    # PML\n",
-    "    group.attrs['pml_x']            = True\n",
-    "    group.attrs['pml_y']            = False\n",
-    "    group.attrs['pml_width_x']      = 1.8e-6\n",
-    "    group.attrs['pml_width_y']      = 5e-7\n",
-    "    group.attrs['pml_coeff']        = 1.6\n",
-    "    group.attrs['pml_coeff_degree'] = 2\n",
-    "\n",
-    "    # Frequency sweep\n",
-    "    group.attrs['center_frequency']    = 20e9\n",
-    "    group.attrs['frequency_range']     = 0.5e9\n",
-    "    group.attrs['start_frequency']     = group.attrs['center_frequency'] - group.attrs['frequency_range'] / 2\n",
-    "    group.attrs['stop_frequency']      = group.attrs['center_frequency'] + group.attrs['frequency_range'] / 2\n",
-    "    group.attrs['nb_frequency_points'] = 400\n",
-    "\n",
-    "    # Other parameters\n",
-    "    if group == displacement:\n",
-    "        group.attrs['simulation_name'] = 'phononic_cavity_displacement'\n",
-    "    else:\n",
-    "        group.attrs['simulation_name'] = 'phononic_cavity_calibration'\n",
-    "    group.attrs['save_vtu_files'] = False\n",
-    "    \n",
-    "h5_file.close()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Run simulation"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {
-    "collapsed": false
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "CompletedProcess(args=['mpiexec', './step-62'], returncode=0)"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "# Now you can run your simulation locally or in a cluster\n",
-    "subprocess.run(['mpiexec','./step-62'])"
-   ]
-  },
-  {
-   "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "## Analyze data"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {
-    "collapsed": false
-   },
    "outputs": [
     {
      "data": {
@@ -159,8 +11,8 @@
        "<?xml version=\"1.0\" encoding=\"utf-8\" standalone=\"no\"?>\n",
        "<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\"\n",
        "  \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n",
-       "<!-- Created with matplotlib (http://matplotlib.org/) -->\n",
-       "<svg height=\"290pt\" version=\"1.1\" viewBox=\"0 0 389 290\" width=\"389pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
+       "<!-- Created with matplotlib (https://matplotlib.org/) -->\n",
+       "<svg height=\"290.75175pt\" version=\"1.1\" viewBox=\"0 0 389.28125 290.75175\" width=\"389.28125pt\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
        " <defs>\n",
        "  <style type=\"text/css\">\n",
        "*{stroke-linecap:butt;stroke-linejoin:round;}\n",
@@ -190,58 +42,58 @@
        "      <defs>\n",
        "       <path d=\"M 0 0 \n",
        "L 0 3.5 \n",
-       "\" id=\"mb3d45af095\" style=\"stroke:#000000;stroke-width:0.8;\"/>\n",
+       "\" id=\"m6b8c65b599\" style=\"stroke:#000000;stroke-width:0.8;\"/>\n",
        "      </defs>\n",
        "      <g>\n",
-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"89.435795\" xlink:href=\"#mb3d45af095\" y=\"253.1955\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"89.435795\" xlink:href=\"#m6b8c65b599\" y=\"253.1955\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_1\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:middle;\" transform=\"rotate(-0, 89.435795, 267.793937)\" x=\"89.435795\" y=\"267.793937\">19.8</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:middle;\" transform=\"rotate(-0, 89.435795, 267.793937)\" x=\"89.435795\" y=\"267.793937\">19.8</text>\n",
        "     </g>\n",
        "    </g>\n",
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-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"219.560938\" xlink:href=\"#m71cbb29084\" y=\"253.1955\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"219.560938\" xlink:href=\"#m25d1b9ad14\" y=\"253.1955\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_3\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:middle;\" transform=\"rotate(-0, 219.560938, 267.793937)\" x=\"219.560938\" y=\"267.793937\">20.0</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:middle;\" transform=\"rotate(-0, 219.560938, 267.793937)\" x=\"219.560938\" y=\"267.793937\">20.0</text>\n",
        "     </g>\n",
        "    </g>\n",
        "    <g id=\"xtick_4\">\n",
        "     <g id=\"line2d_4\">\n",
        "      <g>\n",
-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"280.433665\" xlink:href=\"#m71cbb29084\" y=\"253.1955\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"280.433665\" xlink:href=\"#m25d1b9ad14\" y=\"253.1955\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_4\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:middle;\" transform=\"rotate(-0, 280.433665, 267.793937)\" x=\"280.433665\" y=\"267.793937\">20.1</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:middle;\" transform=\"rotate(-0, 280.433665, 267.793937)\" x=\"280.433665\" y=\"267.793937\">20.1</text>\n",
        "     </g>\n",
        "    </g>\n",
        "    <g id=\"xtick_5\">\n",
        "     <g id=\"line2d_5\">\n",
        "      <g>\n",
-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"341.306392\" xlink:href=\"#m71cbb29084\" y=\"253.1955\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"341.306392\" xlink:href=\"#m25d1b9ad14\" y=\"253.1955\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_5\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:middle;\" transform=\"rotate(-0, 341.306392, 267.793937)\" x=\"341.306392\" y=\"267.793937\">20.2</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:middle;\" transform=\"rotate(-0, 341.306392, 267.793937)\" x=\"341.306392\" y=\"267.793937\">20.2</text>\n",
        "     </g>\n",
        "    </g>\n",
        "    <g id=\"text_6\">\n",
-       "     <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:middle;\" transform=\"rotate(-0, 219.560938, 281.472062)\" x=\"219.560938\" y=\"281.472062\">frequency (GHz)</text>\n",
+       "     <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:middle;\" transform=\"rotate(-0, 219.560938, 281.472062)\" x=\"219.560938\" y=\"281.472062\">frequency (GHz)</text>\n",
        "    </g>\n",
        "   </g>\n",
        "   <g id=\"matplotlib.axis_2\">\n",
@@ -541,72 +395,72 @@
        "      <defs>\n",
        "       <path d=\"M 0 0 \n",
        "L -3.5 0 \n",
-       "\" id=\"m02a51f3213\" style=\"stroke:#000000;stroke-width:0.8;\"/>\n",
+       "\" id=\"mb1005e1430\" style=\"stroke:#000000;stroke-width:0.8;\"/>\n",
        "      </defs>\n",
        "      <g>\n",
-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#m02a51f3213\" y=\"222.90313\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#mb1005e1430\" y=\"222.90313\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_7\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 226.702349)\" x=\"45.160938\" y=\"226.702349\">−1.0</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 226.702349)\" x=\"45.160938\" y=\"226.702349\">−1.0</text>\n",
        "     </g>\n",
        "    </g>\n",
        "    <g id=\"ytick_2\">\n",
        "     <g id=\"line2d_7\">\n",
        "      <g>\n",
-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#m02a51f3213\" y=\"186.940536\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#mb1005e1430\" y=\"186.940536\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_8\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 190.739755)\" x=\"45.160938\" y=\"190.739755\">−0.5</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 190.739755)\" x=\"45.160938\" y=\"190.739755\">−0.5</text>\n",
        "     </g>\n",
        "    </g>\n",
        "    <g id=\"ytick_3\">\n",
        "     <g id=\"line2d_8\">\n",
        "      <g>\n",
-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#m02a51f3213\" y=\"150.977942\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#mb1005e1430\" y=\"150.977942\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_9\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 154.777161)\" x=\"45.160938\" y=\"154.777161\">0.0</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 154.777161)\" x=\"45.160938\" y=\"154.777161\">0.0</text>\n",
        "     </g>\n",
        "    </g>\n",
        "    <g id=\"ytick_4\">\n",
        "     <g id=\"line2d_9\">\n",
        "      <g>\n",
-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#m02a51f3213\" y=\"115.015348\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#mb1005e1430\" y=\"115.015348\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_10\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 118.814566)\" x=\"45.160938\" y=\"118.814566\">0.5</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 118.814566)\" x=\"45.160938\" y=\"118.814566\">0.5</text>\n",
        "     </g>\n",
        "    </g>\n",
        "    <g id=\"ytick_5\">\n",
        "     <g id=\"line2d_10\">\n",
        "      <g>\n",
-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#m02a51f3213\" y=\"79.052753\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#mb1005e1430\" y=\"79.052753\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_11\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 82.851972)\" x=\"45.160938\" y=\"82.851972\">1.0</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 82.851972)\" x=\"45.160938\" y=\"82.851972\">1.0</text>\n",
        "     </g>\n",
        "    </g>\n",
        "    <g id=\"ytick_6\">\n",
        "     <g id=\"line2d_11\">\n",
        "      <g>\n",
-       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#m02a51f3213\" y=\"43.090159\"/>\n",
+       "       <use style=\"stroke:#000000;stroke-width:0.8;\" x=\"52.160938\" xlink:href=\"#mb1005e1430\" y=\"43.090159\"/>\n",
        "      </g>\n",
        "     </g>\n",
        "     <g id=\"text_12\">\n",
-       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 46.889378)\" x=\"45.160938\" y=\"46.889378\">1.5</text>\n",
+       "      <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:end;\" transform=\"rotate(-0, 45.160938, 46.889378)\" x=\"45.160938\" y=\"46.889378\">1.5</text>\n",
        "     </g>\n",
        "    </g>\n",
        "    <g id=\"text_13\">\n",
-       "     <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:400;text-anchor:middle;\" transform=\"rotate(-90, 14.798438, 144.4755)\" x=\"14.798438\" y=\"144.4755\">phase (rad)</text>\n",
+       "     <text style=\"font-family:DejaVu Sans;font-size:10px;font-style:normal;font-weight:normal;text-anchor:middle;\" transform=\"rotate(-90, 14.798438, 144.4755)\" x=\"14.798438\" y=\"144.4755\">phase (rad)</text>\n",
        "    </g>\n",
        "   </g>\n",
        "   <g id=\"line2d_12\">\n",
-       "    <path clip-path=\"url(#pbed3d3adf0)\" d=\"M 67.379119 166.088347 \n",
+       "    <path clip-path=\"url(#p75b59b16f3)\" d=\"M 67.379119 166.088347 \n",
        "L 130.692858 202.273193 \n",
        "L 159.679871 218.610148 \n",
        "L 176.461826 227.843396 \n",
@@ -681,27 +535,41 @@
        "\" style=\"fill:none;stroke:#000000;stroke-linecap:square;stroke-linejoin:miter;stroke-width:0.8;\"/>\n",
        "   </g>\n",
        "   <g id=\"text_14\">\n",
-       "    <text style=\"font-family:DejaVu Sans;font-size:12px;font-style:normal;font-weight:400;\" transform=\"translate(123.457813 16.318125)\">Phase (transmission coefficient)</text>\n",
-       "    <text style=\"font-family:DejaVu Sans;font-size:12px;font-style:normal;font-weight:400;\" transform=\"translate(219.560938 29.7555)\"/>\n",
+       "    <text style=\"font-family:DejaVu Sans;font-size:12px;font-style:normal;font-weight:normal;\" transform=\"translate(123.457813 16.318125)\">Phase (transmission coefficient)</text>\n",
+       "    <text style=\"font-family:DejaVu Sans;font-size:12px;font-style:normal;font-weight:normal;\" transform=\"translate(219.560938 29.7555)\"/>\n",
        "   </g>\n",
        "  </g>\n",
        " </g>\n",
        " <defs>\n",
-       "  <clipPath id=\"pbed3d3adf0\">\n",
+       "  <clipPath id=\"p75b59b16f3\">\n",
        "   <rect height=\"217.44\" width=\"334.8\" x=\"52.160938\" y=\"35.7555\"/>\n",
        "  </clipPath>\n",
        " </defs>\n",
        "</svg>\n"
       ],
       "text/plain": [
-       "<matplotlib.figure.Figure at 0x7f785eabc5c0>"
+       "<Figure size 432x288 with 1 Axes>"
       ]
      },
-     "metadata": {},
+     "metadata": {
+      "needs_background": "light"
+     },
      "output_type": "display_data"
     }
    ],
    "source": [
+    "%config InlineBackend.figure_formats = ['svg']\n",
+    "%matplotlib inline\n",
+    "import numpy as np\n",
+    "import h5py\n",
+    "import matplotlib.pyplot as plt\n",
+    "import subprocess\n",
+    "import scipy.constants as constants\n",
+    "import scipy.optimize\n",
+    "\n",
+    "# This considerably reduces the size of the svg data\n",
+    "plt.rcParams['svg.fonttype'] = 'none'\n",
+    "\n",
     "h5_file = h5py.File('results.h5', 'r')\n",
     "data = h5_file['data']\n",
     "\n",
@@ -772,7 +640,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.3"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,
Mirror of the development repository for deal.II

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