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diff --git a/Equations.html b/Equations.html
@@ -1,22 +1,24 @@
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@@ -83,9 +85,9 @@
            <div itemprop="articleBody">
 
   <section id="equations">
-<span id="id1"></span><h1>Equations<a class="headerlink" href="#equations" title="Permalink to this heading"></a></h1>
+<span id="id1"></span><h1>Equations<a class="headerlink" href="#equations" title="Link to this heading"></a></h1>
 <section id="spray-equations">
-<h2>Spray Equations<a class="headerlink" href="#spray-equations" title="Permalink to this heading"></a></h2>
+<h2>Spray Equations<a class="headerlink" href="#spray-equations" title="Link to this heading"></a></h2>
 <p>This section outlines the modeling and mathematics for the spray routines in <cite>PeleMP</cite>.
 Firstly, spray modeling in <cite>PeleMP</cite> relies on the following assumptions:</p>
 <ul class="simple">
@@ -207,7 +209,7 @@ <h2>Spray Equations<a class="headerlink" href="#spray-equations" title="Permalin
 </ol>
 </section>
 <section id="soot-equations">
-<h2>Soot Equations<a class="headerlink" href="#soot-equations" title="Permalink to this heading"></a></h2>
+<h2>Soot Equations<a class="headerlink" href="#soot-equations" title="Link to this heading"></a></h2>
 <p>In <cite>PeleMP</cite>, soot formation, growth, and oxidation is modeled using the hybrid-method of moments (HMOM) model developed by Mueller et al. <a class="footnote-reference brackets" href="#mueller" id="id5" role="doc-noteref"><span class="fn-bracket">[</span>4<span class="fn-bracket">]</span></a>. This approach combines the numerical ease of the method of moments with interpolative closure (MOMIC) with the ability to capture the bimodal nature of the soot number density function (NDF) provided by the direct quadrature method of moments (DQMOM). <span class="math notranslate nohighlight">\(M_{x,y}\)</span> is the moment of the soot NDF, where <span class="math notranslate nohighlight">\(x\)</span> is the order for volume and <span class="math notranslate nohighlight">\(y\)</span> for surface area; these terms are modeled according to</p>
 <div class="math notranslate nohighlight">
 \[M_{x,y} = N_0 V_0^x S_0^y + \exp{\left(\sum_{r=0}^R \sum_{k = 0}^r a_{r,k} x^k y^{r-k}\right)},\]</div>
@@ -223,23 +225,23 @@ <h2>Soot Equations<a class="headerlink" href="#soot-equations" title="Permalink
 The current formulation ignores the molecular diffusion and thermophoretic effects of the soot, making the first term of the right-hand side zero.</p>
 <p>For more details regarding the HMOM model, users are encouraged to consult the references cited.</p>
 <aside class="footnote-list brackets">
-<aside class="footnote brackets" id="abram" role="note">
+<aside class="footnote brackets" id="abram" role="doc-footnote">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id2">1</a><span class="fn-bracket">]</span></span>
 <p>“Droplet vaporization model for spray combustion calculations”, B. Abramzon and W. A. Sirignano, Int. J. Heat Mass Transf., Vol. 32, No. 9, pp. 1605-1618 (1989)</p>
 </aside>
-<aside class="footnote brackets" id="ton" role="note">
+<aside class="footnote brackets" id="ton" role="doc-footnote">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id3">2</a><span class="fn-bracket">]</span></span>
 <p>“Fuel spray modeling in direct-injection diesel and gasoline engines”, S. Tonini, Dissertation, City University London (2006)</p>
 </aside>
-<aside class="footnote brackets" id="ge" role="note">
+<aside class="footnote brackets" id="ge" role="doc-footnote">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id4">3</a><span class="fn-bracket">]</span></span>
 <p>“Development of a CPU/GPU portable software library for Lagrangian-Eulerian simulations of liquid sprays”, W. Ge and R. Sankaran and J. H. Chen, Int. J. Multiph. Flow, Vol. 128 (2020)</p>
 </aside>
-<aside class="footnote brackets" id="mueller" role="note">
+<aside class="footnote brackets" id="mueller" role="doc-footnote">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id5">4</a><span class="fn-bracket">]</span></span>
 <p>“Hybrid Method of Moments for modeling soot formation and growth”, M. E. Mueller and G. Blanquart and H. Pitsch, Comb. Flame, Vol. 156, No. 6, pp. 1143-1155 (2009)</p>
 </aside>
-<aside class="footnote brackets" id="bisetti" role="note">
+<aside class="footnote brackets" id="bisetti" role="doc-footnote">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id6">5</a><span class="fn-bracket">]</span></span>
 <p>“On the formation and early evolution of soot in turbulent nonpremixed flames”, F. Bisetti and G. Blanquart and M. E. Mueller and H. Pitsch, Comb. Flame, Vol. 159, No. 1, pp. 317-335 (2012)</p>
 </aside>

diff --git a/GettingStarted.html b/GettingStarted.html
@@ -1,22 +1,24 @@
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   <title>Getting Started &mdash; PeleMP 0.1 documentation</title>
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@@ -82,7 +84,7 @@
            <div itemprop="articleBody">
 
   <section id="getting-started">
-<span id="gettingstarted"></span><h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this heading"></a></h1>
+<span id="gettingstarted"></span><h1>Getting Started<a class="headerlink" href="#getting-started" title="Link to this heading"></a></h1>
 <p>The <cite>PeleMP</cite> code can be obtained via <a class="reference external" href="https://github.com/AMReX-Combustion/PeleMP">GitHub</a>.
 <cite>PeleMP</cite> is the repository of multiphysics capabilities for use with other <cite>Pele</cite> codes:</p>
 <ul class="simple">

diff --git a/SootInputs.html b/SootInputs.html
@@ -1,22 +1,24 @@
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@@ -83,7 +85,7 @@
            <div itemprop="articleBody">
 
   <section id="soot-flags-and-inputs">
-<span id="sootinputs"></span><h1>Soot Flags and Inputs<a class="headerlink" href="#soot-flags-and-inputs" title="Permalink to this heading"></a></h1>
+<span id="sootinputs"></span><h1>Soot Flags and Inputs<a class="headerlink" href="#soot-flags-and-inputs" title="Link to this heading"></a></h1>
 <ul class="simple">
 <li><p>In the <code class="docutils literal notranslate"><span class="pre">GNUmakefile</span></code>, specify <code class="docutils literal notranslate"><span class="pre">USE_SOOT</span> <span class="pre">=</span> <span class="pre">TRUE</span></code> and <code class="docutils literal notranslate"><span class="pre">NUM_SOOT_MOMENTS</span> <span class="pre">=</span> <span class="pre">N</span></code> where <code class="docutils literal notranslate"><span class="pre">N</span></code> is the number of moments to be used in the solution, either 3 or 6.</p></li>
 <li><p>Depending on the gas phase solver, soot solving functionality can be turned on in the input file using <code class="docutils literal notranslate"><span class="pre">pelec.add_soot_src</span> <span class="pre">=</span> <span class="pre">1</span></code> or <code class="docutils literal notranslate"><span class="pre">peleLM.do_soot_solve</span> <span class="pre">=</span> <span class="pre">1</span></code>.</p></li>

diff --git a/SprayInputs.html b/SprayInputs.html
@@ -1,22 +1,24 @@
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Spray Flags and Inputs &mdash; PeleMP 0.1 documentation</title>
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@@ -87,7 +89,7 @@
            <div itemprop="articleBody">
 
   <section id="spray-flags-and-inputs">
-<span id="sprayinputs"></span><h1>Spray Flags and Inputs<a class="headerlink" href="#spray-flags-and-inputs" title="Permalink to this heading"></a></h1>
+<span id="sprayinputs"></span><h1>Spray Flags and Inputs<a class="headerlink" href="#spray-flags-and-inputs" title="Link to this heading"></a></h1>
 <ul class="simple">
 <li><p>In the <code class="docutils literal notranslate"><span class="pre">GNUmakefile</span></code>, specify <code class="docutils literal notranslate"><span class="pre">USE_PARTICLES</span> <span class="pre">=</span> <span class="pre">TRUE</span></code> and <code class="docutils literal notranslate"><span class="pre">SPRAY_FUEL_NUM</span> <span class="pre">=</span> <span class="pre">N</span></code> where <code class="docutils literal notranslate"><span class="pre">N</span></code> is the number of liquid species being used in the simulation.</p></li>
 <li><p>Depending on the gas phase solver, spray solving functionality can be turned on in the input file using <code class="docutils literal notranslate"><span class="pre">pelec.do_spray_particles</span> <span class="pre">=</span> <span class="pre">1</span></code> or <code class="docutils literal notranslate"><span class="pre">peleLM.do_spray_particles</span> <span class="pre">=</span> <span class="pre">1</span></code>.</p></li>
@@ -240,7 +242,7 @@
 </li>
 </ul>
 <section id="spray-injection">
-<h2>Spray Injection<a class="headerlink" href="#spray-injection" title="Permalink to this heading"></a></h2>
+<h2>Spray Injection<a class="headerlink" href="#spray-injection" title="Link to this heading"></a></h2>
 <p>Templates to facilitate and simplify spray injection are available in <cite>PeleMP</cite>. To use them, changes must be made to the input and <code class="docutils literal notranslate"><span class="pre">SprayParticlesInitInsert.cpp</span></code> files. Inputs related to injection use the <code class="docutils literal notranslate"><span class="pre">spray.</span></code> parser name. To create a jet in the domain, modify the <code class="docutils literal notranslate"><span class="pre">InitSprayParticles()</span></code> function in <code class="docutils literal notranslate"><span class="pre">SprayParticleInitInsert.cpp</span></code>. Here is an example:</p>
 <div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>void
 SprayParticleContainer::InitSprayParticles(
@@ -262,9 +264,9 @@ <h2>Spray Injection<a class="headerlink" href="#spray-injection" title="Permalin
 <p>No two jets may have the same name. If an injector is constructed using only a name and geometry, the injection parameters are read from the input file. Here is a list of injection related inputs:</p>
 <table class="docutils align-default">
 <colgroup>
-<col style="width: 25%" />
-<col style="width: 50%" />
-<col style="width: 25%" />
+<col style="width: 25.0%" />
+<col style="width: 50.0%" />
+<col style="width: 25.0%" />
 </colgroup>
 <thead>
 <tr class="row-odd"><th class="head"><p>Input</p></th>
@@ -349,7 +351,7 @@ <h2>Spray Injection<a class="headerlink" href="#spray-injection" title="Permalin
 <figure class="align-center" id="id1" style="width: 60%">
 <img alt="_images/inject_transform.png" src="_images/inject_transform.png" />
 <figcaption>
-<p><span class="caption-text">Demonstration of injection angles. <span class="math notranslate nohighlight">\(\phi_J\)</span> varies uniformly from <span class="math notranslate nohighlight">\([0, 2 \pi]\)</span></span><a class="headerlink" href="#id1" title="Permalink to this image"></a></p>
+<p><span class="caption-text">Demonstration of injection angles. <span class="math notranslate nohighlight">\(\phi_J\)</span> varies uniformly from <span class="math notranslate nohighlight">\([0, 2 \pi]\)</span></span><a class="headerlink" href="#id1" title="Link to this image"></a></p>
 </figcaption>
 </figure>
 <p>Care must be taken to ensure the amount of mass injected during a time step matches the desired mass flow rate. For smaller time steps, the risk of over-injecting mass increases. To mitigate this issue, each jet accounts for three values: <span class="math notranslate nohighlight">\(N_{P,\min}\)</span>, <span class="math notranslate nohighlight">\(m_{\rm{acc}}\)</span>, and <span class="math notranslate nohighlight">\(t_{\rm{acc}}\)</span> (labeled in the code as <code class="docutils literal notranslate"><span class="pre">m_minParcel</span></code>, <code class="docutils literal notranslate"><span class="pre">m_sumInjMass</span></code>, and <code class="docutils literal notranslate"><span class="pre">m_sumInjTime</span></code>, respectively). <span class="math notranslate nohighlight">\(N_{P,\min}\)</span> is the minimum number of parcels that must be injected over the course of an injection event; this must be greater than or equal to one. <span class="math notranslate nohighlight">\(m_{\rm{acc}}\)</span> is the amount of uninjected mass accumulated over the time period <span class="math notranslate nohighlight">\(t_{\rm{acc}}\)</span>. The injection routine steps are as follows:</p>