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@@ -590,7 +590,7 @@ <h2> Contents </h2>
 <h1>McCaffrey Plumes<a class="headerlink" href="#mccaffrey-plumes" title="Link to this heading">#</a></h1>
 <section id="setup-description">
 <h2>Setup Description<a class="headerlink" href="#setup-description" title="Link to this heading">#</a></h2>
-<p>The simulations are based on the different setups of the <a class="reference external" href="https://nvlpubs.nist.gov/nistpubs/Legacy/IR/nbsir79-1910.pdf">McCaffrey plume experiments</a>, which are proposed and discussed in the <a class="reference internal" href="../../modelling/03_compartments/03_pool_example.html#extra-task"><span class="std std-ref">Extra Task: Simulation of a purely buoyant diffusion flame</span></a>. The goal is to reproduce aspects of McCaffreys work, like determining the temperature and velocity changes on the plume centre axis over the height.</p>
+<p>The simulations are based on the different setups of the <a class="reference external" href="https://nvlpubs.nist.gov/nistpubs/Legacy/IR/nbsir79-1910.pdf">McCaffrey plume experiments</a>, which are proposed and discussed in the <a class="reference internal" href="#extra-task"><span class="xref myst">Extra Task: Simulation of a purely buoyant diffusion flame</span></a>. The goal is to reproduce aspects of McCaffreys work, like determining the temperature and velocity changes on the plume centre axis over the height.</p>
 <p>In this example, the directory for our project is called <code class="docutils literal notranslate"><span class="pre">FirePlumes</span></code>. Inside the project directory, three other directories are created: one to store the jupyter notebooks <code class="docutils literal notranslate"><span class="pre">RunReports</span></code>, one for the simulations <code class="docutils literal notranslate"><span class="pre">McCaffrey</span></code>, and one for general information <code class="docutils literal notranslate"><span class="pre">GeneralInformation</span></code>.</p>
 <p>The <code class="docutils literal notranslate"><span class="pre">McCaffrey</span></code> directory contains different simulations of the McCaffrey setup. In <code class="docutils literal notranslate"><span class="pre">GeneralInformation</span></code> files containing the extracted experiment data are located. These data series were extracted using the <a class="reference internal" href="../01_basic/04_basic_example_iv.html"><span class="doc std std-doc">WebPlotDigitizer</span></a>. The Jupyter notebooks are to be located in <code class="docutils literal notranslate"><span class="pre">RunReports</span></code>.</p>
 <p>As structure it is recommended that the user creates directories labeled based on the experiment setup, for example <code class="docutils literal notranslate"><span class="pre">14kW</span></code>. This way data can nicely be accessed when following this example here. Furthermore, simulations are performed with differernt resolutions, based on the reference cell. Simulations of these groups are referred to by the resolutin with respect to the reference cell and are stored in according directories. For example the “C5” directory contains simulations for which the reference cell was divided by 5 in each direction.</p>

diff --git a/content/modelling/03_compartments/01_fundamentals.html b/content/modelling/03_compartments/01_fundamentals.html
diff --git a/content/modelling/03_compartments/03_pool_example.html b/content/modelling/03_compartments/03_pool_example.html
diff --git a/content/modelling/03_compartments/04_steckler_example.html b/content/modelling/03_compartments/04_steckler_example.html
@@ -630,22 +630,22 @@ <h3>Step 0 – Reading<a class="headerlink" href="#step-0-reading" title="Link t
 <h3>Step 1 – Opening<a class="headerlink" href="#step-1-opening" title="Link to this heading">#</a></h3>
 <p>Add an opening to the FDS input file, with the extension given by the experimental setup.</p>
 <p>Which grid resolution <span class="math notranslate nohighlight">\(\mf \Delta x\)</span> is defined in the initial FDS setup?</p>
-<p>Check your setup, especially the opening’s width with smokeview by executing FDS with a zero simulation time. It is helpful to display the grid and turn on the projection method to a size preserving mode, see the keyboard shortcut section in <a class="reference internal" href="#../../tools/01_fds_smv/02_smv"><span class="xref myst">SMV Basics</span></a>. <a class="reference internal" href="#fig-steckler-opening"><span class="std std-numref">Fig. 3.26</span></a> illustrates an example of a suitable view on an opening.</p>
+<p>Check your setup, especially the opening’s width with smokeview by executing FDS with a zero simulation time. It is helpful to display the grid and turn on the projection method to a size preserving mode, see the keyboard shortcut section in <a class="reference internal" href="#../../tools/01_fds_smv/02_smv"><span class="xref myst">SMV Basics</span></a>. <a class="reference internal" href="#fig-steckler-opening"><span class="std std-numref">Fig. 3.9</span></a> illustrates an example of a suitable view on an opening.</p>
 <figure class="align-default" id="fig-steckler-opening">
 <a class="reference internal image-reference" href="../../../_images/steckler_opening.png"><img alt="../../../_images/steckler_opening.png" src="../../../_images/steckler_opening.png" style="width: 60%;" /></a>
 <figcaption>
-<p><span class="caption-number">Fig. 3.26 </span><span class="caption-text">Check for the opening size.</span><a class="headerlink" href="#fig-steckler-opening" title="Link to this image">#</a></p>
+<p><span class="caption-number">Fig. 3.9 </span><span class="caption-text">Check for the opening size.</span><a class="headerlink" href="#fig-steckler-opening" title="Link to this image">#</a></p>
 </figcaption>
 </figure>
 </section>
 <section id="step-2-hrr">
 <h3>Step 2 – HRR<a class="headerlink" href="#step-2-hrr" title="Link to this heading">#</a></h3>
 <p>In the initial setup, there is already a surface property defined. Adopt the specific heat release rate to match the one in test number 13 and add a surface tempertaure of <span class="math notranslate nohighlight">\(\mf 100~^\circ C\)</span>. This elevated temperature represents the hot surface of the burner.</p>
-<p>Plot the heat release rate like in <a class="reference internal" href="#fig-steckler-20cm-hrr"><span class="std std-numref">Fig. 3.27</span></a>, where the curve is shown for the full simulation time.</p>
+<p>Plot the heat release rate like in <a class="reference internal" href="#fig-steckler-20cm-hrr"><span class="std std-numref">Fig. 3.10</span></a>, where the curve is shown for the full simulation time.</p>
 <figure class="align-default" id="fig-steckler-20cm-hrr">
 <a class="reference internal image-reference" href="../../../_images/steckler_20cm_hrr.svg"><img alt="../../../_images/steckler_20cm_hrr.svg" src="../../../_images/steckler_20cm_hrr.svg" width="80%" /></a>
 <figcaption>
-<p><span class="caption-number">Fig. 3.27 </span><span class="caption-text">Comparison of the targeted heat realease rate and the one achieved in the simulations.</span><a class="headerlink" href="#fig-steckler-20cm-hrr" title="Link to this image">#</a></p>
+<p><span class="caption-number">Fig. 3.10 </span><span class="caption-text">Comparison of the targeted heat realease rate and the one achieved in the simulations.</span><a class="headerlink" href="#fig-steckler-20cm-hrr" title="Link to this image">#</a></p>
 </figcaption>
 </figure>
 </section>
@@ -658,35 +658,35 @@ <h3>Step 3 – Output<a class="headerlink" href="#step-3-output" title="Link to
 <li><p>A set of individual devices, or</p></li>
 <li><p>with a linear array of devices, see section 21.2.2 (Linear Array of Point Devices) in <span id="id4">[<a class="reference internal" href="../../overview/03_references.html#id11" title="Kevin McGrattan, Simo Hostikka, Jason Floyd, Randall McDermott, and Marcos Vanella. Fire Dynamics Simulator User's Guide – Version 6.7.5. Technical Report, NIST, 2020. URL: https://github.com/firemodels/fds/releases/download/FDS6.7.5/FDS_User_Guide.pdf.">MHF+20d</a>]</span>.</p></li>
 </ul>
-<p>Check their positions with Smokeview. They are indicated as green dots, see <a class="reference internal" href="#fig-steckler-devices"><span class="std std-numref">Fig. 3.28</span></a>.</p>
+<p>Check their positions with Smokeview. They are indicated as green dots, see <a class="reference internal" href="#fig-steckler-devices"><span class="std std-numref">Fig. 3.11</span></a>.</p>
 <figure class="align-default" id="fig-steckler-devices">
 <a class="reference internal image-reference" href="../../../_images/steckler_devices.png"><img alt="../../../_images/steckler_devices.png" src="../../../_images/steckler_devices.png" style="width: 60%;" /></a>
 <figcaption>
-<p><span class="caption-number">Fig. 3.28 </span><span class="caption-text">Check for the device positioning.</span><a class="headerlink" href="#fig-steckler-devices" title="Link to this image">#</a></p>
+<p><span class="caption-number">Fig. 3.11 </span><span class="caption-text">Check for the device positioning.</span><a class="headerlink" href="#fig-steckler-devices" title="Link to this image">#</a></p>
 </figcaption>
 </figure>
-<p>Additionally, check if the quasi steady-state is reached in the simulations, like shown in <a class="reference internal" href="#fig-steckler-20cm-temp-devc"><span class="std std-numref">Fig. 3.29</span></a>.</p>
+<p>Additionally, check if the quasi steady-state is reached in the simulations, like shown in <a class="reference internal" href="#fig-steckler-20cm-temp-devc"><span class="std std-numref">Fig. 3.12</span></a>.</p>
 <figure class="align-default" id="fig-steckler-20cm-temp-devc">
 <a class="reference internal image-reference" href="../../../_images/steckler_20cm_temp-devc.svg"><img alt="../../../_images/steckler_20cm_temp-devc.svg" src="../../../_images/steckler_20cm_temp-devc.svg" width="80%" /></a>
 <figcaption>
-<p><span class="caption-number">Fig. 3.29 </span><span class="caption-text">Time series of a point temperature measurement in the opening.</span><a class="headerlink" href="#fig-steckler-20cm-temp-devc" title="Link to this image">#</a></p>
+<p><span class="caption-number">Fig. 3.12 </span><span class="caption-text">Time series of a point temperature measurement in the opening.</span><a class="headerlink" href="#fig-steckler-20cm-temp-devc" title="Link to this image">#</a></p>
 </figcaption>
 </figure>
 </section>
 <section id="step-4-comparison-with-the-experiment">
 <h3>Step 4 – Comparison with the Experiment<a class="headerlink" href="#step-4-comparison-with-the-experiment" title="Link to this heading">#</a></h3>
 <p>Plot the simulation results for temperature and velocity as time averaged values during the quasi steady-state. Add to these plots the experimental data stated by the study, here you can use the central values (in x-direction). A common representation is to use the y-axis of the plot for the height and the x-axis for the values.</p>
-<p>Your results may look like those in <a class="reference internal" href="#fig-steckler-20cm-temp-exp"><span class="std std-numref">Fig. 3.30</span></a> and <a class="reference internal" href="#fig-steckler-20cm-velo-exp"><span class="std std-numref">Fig. 3.31</span></a>.</p>
+<p>Your results may look like those in <a class="reference internal" href="#fig-steckler-20cm-temp-exp"><span class="std std-numref">Fig. 3.13</span></a> and <a class="reference internal" href="#fig-steckler-20cm-velo-exp"><span class="std std-numref">Fig. 3.14</span></a>.</p>
 <figure class="align-default" id="fig-steckler-20cm-temp-exp">
 <a class="reference internal image-reference" href="../../../_images/steckler_20cm_temp-exp.svg"><img alt="../../../_images/steckler_20cm_temp-exp.svg" src="../../../_images/steckler_20cm_temp-exp.svg" width="80%" /></a>
 <figcaption>
-<p><span class="caption-number">Fig. 3.30 </span><span class="caption-text">Comparison of the predicted temperature profile with experimental data.</span><a class="headerlink" href="#fig-steckler-20cm-temp-exp" title="Link to this image">#</a></p>
+<p><span class="caption-number">Fig. 3.13 </span><span class="caption-text">Comparison of the predicted temperature profile with experimental data.</span><a class="headerlink" href="#fig-steckler-20cm-temp-exp" title="Link to this image">#</a></p>
 </figcaption>
 </figure>
 <figure class="align-default" id="fig-steckler-20cm-velo-exp">
 <a class="reference internal image-reference" href="../../../_images/steckler_20cm_velo-exp.svg"><img alt="../../../_images/steckler_20cm_velo-exp.svg" src="../../../_images/steckler_20cm_velo-exp.svg" width="80%" /></a>
 <figcaption>
-<p><span class="caption-number">Fig. 3.31 </span><span class="caption-text">Comparison of the predicted velocity profile with experimental data.</span><a class="headerlink" href="#fig-steckler-20cm-velo-exp" title="Link to this image">#</a></p>
+<p><span class="caption-number">Fig. 3.14 </span><span class="caption-text">Comparison of the predicted velocity profile with experimental data.</span><a class="headerlink" href="#fig-steckler-20cm-velo-exp" title="Link to this image">#</a></p>
 </figcaption>
 </figure>
 </section>
@@ -699,13 +699,13 @@ <h3>Step 5 – Grid Resolution<a class="headerlink" href="#step-5-grid-resolutio
 <figure class="align-default" id="fig-steckler-20cm-temp-grid-sensitivity">
 <a class="reference internal image-reference" href="../../../_images/steckler_20cm_temp-grid-sensitivity.svg"><img alt="../../../_images/steckler_20cm_temp-grid-sensitivity.svg" src="../../../_images/steckler_20cm_temp-grid-sensitivity.svg" width="80%" /></a>
 <figcaption>
-<p><span class="caption-number">Fig. 3.32 </span><span class="caption-text">Grid sensitivity of the temperature profile.</span><a class="headerlink" href="#fig-steckler-20cm-temp-grid-sensitivity" title="Link to this image">#</a></p>
+<p><span class="caption-number">Fig. 3.15 </span><span class="caption-text">Grid sensitivity of the temperature profile.</span><a class="headerlink" href="#fig-steckler-20cm-temp-grid-sensitivity" title="Link to this image">#</a></p>
 </figcaption>
 </figure>
 <figure class="align-default" id="fig-steckler-20cm-velo-grid-sensitivity">
 <a class="reference internal image-reference" href="../../../_images/steckler_20cm_velo-grid-sensitivity.svg"><img alt="../../../_images/steckler_20cm_velo-grid-sensitivity.svg" src="../../../_images/steckler_20cm_velo-grid-sensitivity.svg" width="80%" /></a>
 <figcaption>
-<p><span class="caption-number">Fig. 3.33 </span><span class="caption-text">Grid sensitivity of the velocity profile.</span><a class="headerlink" href="#fig-steckler-20cm-velo-grid-sensitivity" title="Link to this image">#</a></p>
+<p><span class="caption-number">Fig. 3.16 </span><span class="caption-text">Grid sensitivity of the velocity profile.</span><a class="headerlink" href="#fig-steckler-20cm-velo-grid-sensitivity" title="Link to this image">#</a></p>
 </figcaption>
 </figure>
 </section>

diff --git a/content/tools/03_analysis/03_example_mccaffreyplumes.html b/content/tools/03_analysis/03_example_mccaffreyplumes.html
@@ -567,7 +567,7 @@ <h2> Contents </h2>
 <section id="introduction">
 <h2>Introduction<a class="headerlink" href="#introduction" title="Link to this heading">#</a></h2>
 <p>Here, we provide a proposal as to how one could organise their simulation projects. Projects can be anything, from work for a thesis or in context of a simulation campaign in the industry.</p>
-<p>In this example, the directory for our project is called <code class="docutils literal notranslate"><span class="pre">FirePlumes</span></code>. Inside the project directory, three other directories are created: one to store the jupyter notebooks <code class="docutils literal notranslate"><span class="pre">RunReports</span></code>, one for the simulations <code class="docutils literal notranslate"><span class="pre">McCaffrey</span></code>, and one for general information <code class="docutils literal notranslate"><span class="pre">GeneralInformation</span></code>. The simulations are based on the different setups of the <a class="reference external" href="https://nvlpubs.nist.gov/nistpubs/Legacy/IR/nbsir79-1910.pdf">McCaffrey plume experiments</a>, which are proposed and discussed in the <a class="reference internal" href="../../modelling/03_compartments/03_pool_example.html#extra-task"><span class="std std-ref">Extra Task: Simulation of a purely buoyant diffusion flame</span></a>.</p>
+<p>In this example, the directory for our project is called <code class="docutils literal notranslate"><span class="pre">FirePlumes</span></code>. Inside the project directory, three other directories are created: one to store the jupyter notebooks <code class="docutils literal notranslate"><span class="pre">RunReports</span></code>, one for the simulations <code class="docutils literal notranslate"><span class="pre">McCaffrey</span></code>, and one for general information <code class="docutils literal notranslate"><span class="pre">GeneralInformation</span></code>. The simulations are based on the different setups of the <a class="reference external" href="https://nvlpubs.nist.gov/nistpubs/Legacy/IR/nbsir79-1910.pdf">McCaffrey plume experiments</a>, which are proposed and discussed in the <a class="reference internal" href="#extra-task"><span class="xref myst">Extra Task: Simulation of a purely buoyant diffusion flame</span></a>.</p>
 <p>In general, it could be useful to distribute different aspects of the project over different jupyter notebooks. Consider, for example, one were to compare experiment data to simulation results. One notebook could be used to pre-process the data from the experiment, one could be used to prepare the simulation input and one could be used to compare the results.</p>
 <p>In <code class="docutils literal notranslate"><span class="pre">RunReports</span></code>, sub-directories are created by the notebooks to store their respective results. File and directory labels are used to control the flow of reading the data. The data is organised in Python dictionaries. An external Python script is provided to store functions used in the notebook in an effort to keep it relatively clean. The <code class="docutils literal notranslate"><span class="pre">reload</span></code> module from the <code class="docutils literal notranslate"><span class="pre">importlib</span></code> package is used to reload the <code class="docutils literal notranslate"><span class="pre">Processing.py</span></code> script during runtime of the notebook. This allows to add functions to <code class="docutils literal notranslate"><span class="pre">Processing.py</span></code>, while designing the content of the <code class="docutils literal notranslate"><span class="pre">RunReport</span></code> notebook and load them without need to restart the respective kernel.</p>
 <div class="cell docutils container">

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