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diff --git a/docs_html/AGN.html b/docs_html/AGN.html
@@ -27,11 +27,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="index.html" class="icon icon-home"> Nyx
+
+
+
+          <a href="index.html" class="icon icon-home">
+            Nyx
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -73,7 +77,7 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">The AGN Model in Nyx</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/AGN.rst.txt" rel="nofollow"> View page source</a>
@@ -84,31 +88,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-
-<style>
-/* CSS overrides for sphinx_rtd_theme */
-
-/* 24px margin */
-.nbinput.nblast.container,
-.nboutput.nblast.container {
-    margin-bottom: 19px;  /* padding has already 5px */
-}
-
-/* ... except between code cells! */
-.nblast.container + .nbinput.container {
-    margin-top: -19px;
-}
-
-.admonition > p:before {
-    margin-right: 4px;  /* make room for the exclamation icon */
-}
-
-/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
-.math {
-    text-align: unset;
-}
-</style>
-<div class="section" id="the-agn-model-in-nyx">
+  <div class="section" id="the-agn-model-in-nyx">
 <h1>The AGN Model in Nyx<a class="headerlink" href="#the-agn-model-in-nyx" title="Permalink to this headline">¶</a></h1>
 <p>In the AGN model, super-massive black hole (SMBH) particles are formed
 at <em>haloes</em>, where each halo is defined by a connected mass enclosed by

diff --git a/docs_html/Debugging.html b/docs_html/Debugging.html
@@ -29,11 +29,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="index.html" class="icon icon-home"> Nyx
+
+
+
+          <a href="index.html" class="icon icon-home">
+            Nyx
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -75,7 +79,7 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Debugging</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/Debugging.rst.txt" rel="nofollow"> View page source</a>
@@ -86,31 +90,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-
-<style>
-/* CSS overrides for sphinx_rtd_theme */
-
-/* 24px margin */
-.nbinput.nblast.container,
-.nboutput.nblast.container {
-    margin-bottom: 19px;  /* padding has already 5px */
-}
-
-/* ... except between code cells! */
-.nblast.container + .nbinput.container {
-    margin-top: -19px;
-}
-
-.admonition > p:before {
-    margin-right: 4px;  /* make room for the exclamation icon */
-}
-
-/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
-.math {
-    text-align: unset;
-}
-</style>
-<div class="section" id="debugging">
+  <div class="section" id="debugging">
 <span id="chap-debugging"></span><h1>Debugging<a class="headerlink" href="#debugging" title="Permalink to this headline">¶</a></h1>
 <p>Debugging is an art.  Everyone has their own favorite method.  Here we
 offer a few tips we have found to be useful.</p>
@@ -126,21 +106,21 @@
 <ol class="arabic simple">
 <li>Writing a <code class="code cpp c++ docutils literal notranslate"><span class="name"><span class="pre">MultiFab</span></span></code> to disk with</li>
 </ol>
-<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="n">VisMF</span><span class="o">::</span><span class="n">Write</span><span class="p">(</span><span class="k">const</span><span class="w"> </span><span class="n">FabArray</span><span class="o">&lt;</span><span class="n">FArrayBox</span><span class="o">&gt;&amp;</span><span class="w"> </span><span class="n">mf</span><span class="p">,</span><span class="w"> </span><span class="k">const</span><span class="w"> </span><span class="n">std</span><span class="o">::</span><span class="n">string</span><span class="o">&amp;</span><span class="w"> </span><span class="n">name</span><span class="p">);</span><span class="w"></span>
+<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="n">VisMF</span><span class="o">::</span><span class="n">Write</span><span class="p">(</span><span class="k">const</span><span class="w"> </span><span class="n">FabArray</span><span class="o">&lt;</span><span class="n">FArrayBox</span><span class="o">&gt;&amp;</span><span class="w"> </span><span class="n">mf</span><span class="p">,</span><span class="w"> </span><span class="k">const</span><span class="w"> </span><span class="n">std</span><span class="o">::</span><span class="n">string</span><span class="o">&amp;</span><span class="w"> </span><span class="n">name</span><span class="p">);</span>
 </pre></div>
 </div>
 <p>and examining it with <code class="docutils literal notranslate"><span class="pre">Amrvis</span></code> (section <span class="xref std std-ref">sec:amrvis</span> in the AMReX documentation).</p>
 <ol class="arabic simple" start="2">
 <li>You can also use the <code class="code cpp c++ docutils literal notranslate"><span class="name"><span class="pre">print_state</span></span></code> routine:</li>
 </ol>
-<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="kt">void</span><span class="w"> </span><span class="nf">print_state</span><span class="p">(</span><span class="k">const</span><span class="w"> </span><span class="n">MultiFab</span><span class="o">&amp;</span><span class="w"> </span><span class="n">mf</span><span class="p">,</span><span class="w"> </span><span class="k">const</span><span class="w"> </span><span class="n">IntVect</span><span class="o">&amp;</span><span class="w"> </span><span class="n">cell</span><span class="p">,</span><span class="w"> </span><span class="k">const</span><span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">n</span><span class="o">=</span><span class="mi">-1</span><span class="p">);</span><span class="w"></span>
+<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="kt">void</span><span class="w"> </span><span class="nf">print_state</span><span class="p">(</span><span class="k">const</span><span class="w"> </span><span class="n">MultiFab</span><span class="o">&amp;</span><span class="w"> </span><span class="n">mf</span><span class="p">,</span><span class="w"> </span><span class="k">const</span><span class="w"> </span><span class="n">IntVect</span><span class="o">&amp;</span><span class="w"> </span><span class="n">cell</span><span class="p">,</span><span class="w"> </span><span class="k">const</span><span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">n</span><span class="o">=</span><span class="mi">-1</span><span class="p">);</span>
 </pre></div>
 </div>
 <p>which outputs the data for a single cell.</p>
 <ol class="arabic simple" start="3">
 <li>If you want to compare old and new plotfiles,</li>
 </ol>
-<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="n">fcompare</span><span class="w"> </span><span class="o">--</span><span class="n">infile1</span><span class="w"> </span><span class="n">plt00000_run1</span><span class="w"> </span><span class="o">--</span><span class="n">infile2</span><span class="w"> </span><span class="n">plt00000_run2</span><span class="w"> </span><span class="o">--</span><span class="n">diffvar</span><span class="w"> </span><span class="n">u_g</span><span class="w"></span>
+<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="n">fcompare</span><span class="w"> </span><span class="o">--</span><span class="n">infile1</span><span class="w"> </span><span class="n">plt00000_run1</span><span class="w"> </span><span class="o">--</span><span class="n">infile2</span><span class="w"> </span><span class="n">plt00000_run2</span><span class="w"> </span><span class="o">--</span><span class="n">diffvar</span><span class="w"> </span><span class="n">u_g</span>
 </pre></div>
 </div>
 <p>will print out the maximum absolute and relative differences between the two plotfiles

diff --git a/docs_html/Development.html b/docs_html/Development.html
@@ -28,11 +28,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="index.html" class="icon icon-home"> Nyx
+
+
+
+          <a href="index.html" class="icon icon-home">
+            Nyx
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -78,7 +82,7 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Work in Progress</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/Development.rst.txt" rel="nofollow"> View page source</a>
@@ -89,31 +93,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-
-<style>
-/* CSS overrides for sphinx_rtd_theme */
-
-/* 24px margin */
-.nbinput.nblast.container,
-.nboutput.nblast.container {
-    margin-bottom: 19px;  /* padding has already 5px */
-}
-
-/* ... except between code cells! */
-.nblast.container + .nbinput.container {
-    margin-top: -19px;
-}
-
-.admonition > p:before {
-    margin-right: 4px;  /* make room for the exclamation icon */
-}
-
-/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
-.math {
-    text-align: unset;
-}
-</style>
-<div class="section" id="work-in-progress">
+  <div class="section" id="work-in-progress">
 <h1>Work in Progress<a class="headerlink" href="#work-in-progress" title="Permalink to this headline">¶</a></h1>
 <p>Here we list work in progress; code pieces related to these efforts are already in the GitHub repo
 but the functionality has not been finished yet and is thus not fomally relesed to the

diff --git a/docs_html/GridCreation.html b/docs_html/GridCreation.html
@@ -29,11 +29,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="index.html" class="icon icon-home"> Nyx
+
+
+
+          <a href="index.html" class="icon icon-home">
+            Nyx
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -81,7 +85,7 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="ManagingGridHierarchy_Chapter.html">Gridding and Load Balancing</a></li>
       <li class="breadcrumb-item active">Grid Creation</li>
       <li class="wy-breadcrumbs-aside">
@@ -93,31 +97,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-
-<style>
-/* CSS overrides for sphinx_rtd_theme */
-
-/* 24px margin */
-.nbinput.nblast.container,
-.nboutput.nblast.container {
-    margin-bottom: 19px;  /* padding has already 5px */
-}
-
-/* ... except between code cells! */
-.nblast.container + .nbinput.container {
-    margin-top: -19px;
-}
-
-.admonition > p:before {
-    margin-right: 4px;  /* make room for the exclamation icon */
-}
-
-/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
-.math {
-    text-align: unset;
-}
-</style>
-<div class="section" id="grid-creation">
+  <div class="section" id="grid-creation">
 <span id="sec-grid-creation"></span><h1>Grid Creation<a class="headerlink" href="#grid-creation" title="Permalink to this headline">¶</a></h1>
 <p>To run Nyx you must specify <code class="code cpp c++ docutils literal notranslate"><span class="name"><span class="pre">n_cell</span></span></code> in the inputs file –
 this is the number of cells spanning the domain in each coordinate direction at level 0.</p>

diff --git a/docs_html/ICs.html b/docs_html/ICs.html
@@ -29,11 +29,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="index.html" class="icon icon-home"> Nyx
+
+
+
+          <a href="index.html" class="icon icon-home">
+            Nyx
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -90,7 +94,7 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Initial conditions</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/ICs.rst.txt" rel="nofollow"> View page source</a>
@@ -101,31 +105,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-
-<style>
-/* CSS overrides for sphinx_rtd_theme */
-
-/* 24px margin */
-.nbinput.nblast.container,
-.nboutput.nblast.container {
-    margin-bottom: 19px;  /* padding has already 5px */
-}
-
-/* ... except between code cells! */
-.nblast.container + .nbinput.container {
-    margin-top: -19px;
-}
-
-.admonition > p:before {
-    margin-right: 4px;  /* make room for the exclamation icon */
-}
-
-/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
-.math {
-    text-align: unset;
-}
-</style>
-<div class="section" id="initial-conditions">
+  <div class="section" id="initial-conditions">
 <h1>Initial conditions<a class="headerlink" href="#initial-conditions" title="Permalink to this headline">¶</a></h1>
 <p>There are a couple main ways in which initial conditions can be set in Nyx:
 using an ASCII particle file, using binary particle file(s), using

diff --git a/docs_html/InSitu.html b/docs_html/InSitu.html
@@ -29,11 +29,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="index.html" class="icon icon-home"> Nyx
+
+
+
+          <a href="index.html" class="icon icon-home">
+            Nyx
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -80,7 +84,7 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="index.html" class="icon icon-home"></a></li>
+      <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">In situ Analysis</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/InSitu.rst.txt" rel="nofollow"> View page source</a>
@@ -91,31 +95,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-
-<style>
-/* CSS overrides for sphinx_rtd_theme */
-
-/* 24px margin */
-.nbinput.nblast.container,
-.nboutput.nblast.container {
-    margin-bottom: 19px;  /* padding has already 5px */
-}
-
-/* ... except between code cells! */
-.nblast.container + .nbinput.container {
-    margin-top: -19px;
-}
-
-.admonition > p:before {
-    margin-right: 4px;  /* make room for the exclamation icon */
-}
-
-/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
-.math {
-    text-align: unset;
-}
-</style>
-<div class="section" id="in-situ-analysis">
+  <div class="section" id="in-situ-analysis">
 <span id="insitu"></span><h1>In situ Analysis<a class="headerlink" href="#in-situ-analysis" title="Permalink to this headline">¶</a></h1>
 <p>Nyx supports in situ visualization using Ascent, and can leverage AMReX’s Sensei visualization pipeline. Additionally, Nyx supports in situ halo finding using Reeber2. This is useful both as
 in situ analysis tool, and for subgrid models, like AGN (under development).</p>