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diff --git a/manual/doctrees/Implementation.doctree b/manual/doctrees/Implementation.doctree
diff --git a/manual/doctrees/LMeXControls.doctree b/manual/doctrees/LMeXControls.doctree
diff --git a/manual/doctrees/Model.doctree b/manual/doctrees/Model.doctree
diff --git a/manual/doctrees/Performances.doctree b/manual/doctrees/Performances.doctree
diff --git a/manual/doctrees/Troubleshooting.doctree b/manual/doctrees/Troubleshooting.doctree
diff --git a/manual/doctrees/Tutorials.doctree b/manual/doctrees/Tutorials.doctree
diff --git a/manual/doctrees/Tutorials_BFSFlame.doctree b/manual/doctrees/Tutorials_BFSFlame.doctree
diff --git a/manual/doctrees/Tutorials_FlameSheet.doctree b/manual/doctrees/Tutorials_FlameSheet.doctree
diff --git a/manual/doctrees/Tutorials_FlowPastCyl.doctree b/manual/doctrees/Tutorials_FlowPastCyl.doctree
diff --git a/manual/doctrees/Tutorials_HotBubble.doctree b/manual/doctrees/Tutorials_HotBubble.doctree
diff --git a/manual/doctrees/Tutorials_SettingUp.doctree b/manual/doctrees/Tutorials_SettingUp.doctree
diff --git a/manual/doctrees/Tutorials_TripleFlame.doctree b/manual/doctrees/Tutorials_TripleFlame.doctree
diff --git a/manual/doctrees/Validation.doctree b/manual/doctrees/Validation.doctree
diff --git a/manual/doctrees/environment.pickle b/manual/doctrees/environment.pickle
diff --git a/manual/doctrees/index.doctree b/manual/doctrees/index.doctree
diff --git a/manual/html/Implementation.html b/manual/html/Implementation.html
@@ -1,13 +1,15 @@
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-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Source code &mdash; PeleLMeX 22.12 documentation</title>
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diff --git a/manual/html/LMeXControls.html b/manual/html/LMeXControls.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>PeleLMeX controls &mdash; PeleLMeX 22.12 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
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@@ -240,9 +242,9 @@ <h2>PeleLMeX derived variables<a class="headerlink" href="#pelelmex-derived-vari
 <table class="docutils align-default" id="id1">
 <caption><span class="caption-number">Table 7 </span><span class="caption-text">PeleLMeX derived variables</span><a class="headerlink" href="#id1" title="Link to this table"></a></caption>
 <colgroup>
-<col style="width: 17%" />
-<col style="width: 17%" />
-<col style="width: 67%" />
+<col style="width: 16.7%" />
+<col style="width: 16.7%" />
+<col style="width: 66.7%" />
 </colgroup>
 <thead>
 <tr class="row-odd"><th class="head"><p>Key</p></th>
@@ -594,8 +596,8 @@ <h2>Run-time control<a class="headerlink" href="#run-time-control" title="Link t
 <table class="docutils align-default" id="id2">
 <caption><span class="caption-number">Table 8 </span><span class="caption-text">PeleLMeX run-time triggers</span><a class="headerlink" href="#id2" title="Link to this table"></a></caption>
 <colgroup>
-<col style="width: 33%" />
-<col style="width: 67%" />
+<col style="width: 33.3%" />
+<col style="width: 66.7%" />
 </colgroup>
 <thead>
 <tr class="row-odd"><th class="head"><p>File</p></th>

diff --git a/manual/html/Model.html b/manual/html/Model.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>The PeleLMeX Model &mdash; PeleLMeX 22.12 documentation</title>
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-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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@@ -137,7 +139,7 @@ <h2>Overview of <cite>PeleLMeX</cite><a class="headerlink" href="#overview-of-pe
 <li><p>Several higher-order Godunov integration schemes for advection</p></li>
 <li><p>Temporally implicit viscosity, species mass diffusion, thermal conductivity, chemical kinetics</p></li>
 <li><p>Closed chamber algorithm enable time-varying background pressure changes</p></li>
-<li><p>Lagrangian spray description using <a class="reference external" href="https://github.com/AMReX-Combustion/PeleMP">PeleMP</a></p></li>
+<li><p>Lagrangian spray description and Hybrid Method of Moments Soot modeling using <a class="reference external" href="https://github.com/AMReX-Combustion/PelePhysics">PelePhysics</a> (formerly these were part of <a class="reference external" href="https://github.com/AMReX-Combustion/PeleMP">PeleMP</a>).</p></li>
 </ul>
 </dd>
 </dl>

diff --git a/manual/html/Performances.html b/manual/html/Performances.html
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+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Performances &mdash; PeleLMeX 22.12 documentation</title>
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diff --git a/manual/html/Troubleshooting.html b/manual/html/Troubleshooting.html
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+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Troubleshooting &mdash; PeleLMeX 22.12 documentation</title>
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diff --git a/manual/html/Tutorials.html b/manual/html/Tutorials.html
@@ -1,13 +1,15 @@
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+<html class="writer-html5" lang="en" data-content_root="./">
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+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Tutorials &mdash; PeleLMeX 22.12 documentation</title>
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diff --git a/manual/html/Tutorials_BFSFlame.html b/manual/html/Tutorials_BFSFlame.html
@@ -1,13 +1,15 @@
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-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Backward facing step anchored premixed flame &mdash; PeleLMeX 22.12 documentation</title>
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-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
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@@ -343,7 +345,7 @@ <h2>Building the executable<a class="headerlink" href="#building-the-executable"
 </div>
 <p>In <cite>PeleLMeX</cite>, the chemistry model (set of species, their thermodynamic and transport properties as well as the description
 of their of chemical interactions) is specified at compile time. Chemistry models available in
-<cite>PelePhysics</cite> can used in <cite>PeleLMeX</cite> by specifying the name of the folder in <cite>PelePhysics/Support/Mechanisms/Models</cite> containing
+<cite>PelePhysics</cite> can used in <cite>PeleLMeX</cite> by specifying the name of the folder in <cite>PelePhysics/Mechanisms</cite> containing
 the relevant files, for example:</p>
 <div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>Chemistry_Model = drm19
 </pre></div>

diff --git a/manual/html/Tutorials_FlameSheet.html b/manual/html/Tutorials_FlameSheet.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Premixed flame sheet with harmonic perturbations &mdash; PeleLMeX 22.12 documentation</title>
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-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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@@ -358,7 +360,7 @@ <h2>Building the executable<a class="headerlink" href="#building-the-executable"
 The compiler (<code class="docutils literal notranslate"><span class="pre">gnu</span></code>) and the parallelism paradigm (in the present case only MPI is used) are then selected. If MPI is not available on your
 platform, please set <code class="docutils literal notranslate"><span class="pre">USE_MPI</span> <span class="pre">=</span> <span class="pre">FALSE</span></code>.
 Note that on OSX platform, one should update the compiler to <code class="docutils literal notranslate"><span class="pre">llvm</span></code>.</p>
-<p>In <cite>PeleLMeX</cite>, the chemistry model (set of species, their thermodynamic and transport properties as well as the description of their of chemical interactions) is specified at compile time. Chemistry models available in <cite>PelePhysics</cite> can used in <cite>PeleLMeX</cite> by specifying the name of the folder in <cite>PelePhysics/Support/Mechanisms/Models</cite> containing the relevant files, for example:</p>
+<p>In <cite>PeleLMeX</cite>, the chemistry model (set of species, their thermodynamic and transport properties as well as the description of their of chemical interactions) is specified at compile time. Chemistry models available in <cite>PelePhysics</cite> can used in <cite>PeleLMeX</cite> by specifying the name of the folder in <cite>PelePhysics/Mechanisms</cite> containing the relevant files, for example:</p>
 <div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>Chemistry_Model = drm19
 </pre></div>
 </div>

diff --git a/manual/html/Tutorials_FlowPastCyl.html b/manual/html/Tutorials_FlowPastCyl.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Non-reacting flow past a cylinder &mdash; PeleLMeX 22.12 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
-      <link rel="stylesheet" href="_static/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="_static/theme.css?v=df66b05f" />
+
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@@ -296,7 +298,7 @@ <h2>Building the executable<a class="headerlink" href="#building-the-executable"
 </pre></div>
 </div>
 <p>It allows the user to specify the number of spatial dimensions (2D), trigger the compilation of the EB source code, the compiler (<code class="docutils literal notranslate"><span class="pre">gnu</span></code>) and the parallelism paradigm (in the present case only MPI is used). The other options can be activated for debugging and profiling purposes. Note that on OSX platform, one should update the compiler to <code class="docutils literal notranslate"><span class="pre">llvm</span></code>.</p>
-<p>In <cite>PeleLMeX</cite>, the chemistry model (set of species, their thermodynamic and transport properties as well as the description of their of chemical interactions) is specified at compile time. Chemistry models available in <cite>PelePhysics</cite> can used in <cite>PeleLMeX</cite> by specifying the name of the folder in <cite>PelePhysics/Support/Mechanisms/Models</cite> containing the relevant files, for example:</p>
+<p>In <cite>PeleLMeX</cite>, the chemistry model (set of species, their thermodynamic and transport properties as well as the description of their of chemical interactions) is specified at compile time. Chemistry models available in <cite>PelePhysics</cite> can used in <cite>PeleLMeX</cite> by specifying the name of the folder in <cite>PelePhysics/Mechanisms</cite> containing the relevant files, for example:</p>
 <div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>Chemistry_Model = air
 </pre></div>
 </div>

diff --git a/manual/html/Tutorials_HotBubble.html b/manual/html/Tutorials_HotBubble.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Rising light bubble &mdash; PeleLMeX 22.12 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
-      <link rel="stylesheet" href="_static/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
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+
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@@ -305,7 +307,7 @@ <h2>Building the executable<a class="headerlink" href="#building-the-executable"
 (in the present case only MPI is used) are then selected. Note that on OSX platform, one should update the compiler to <code class="docutils literal notranslate"><span class="pre">llvm</span></code>.</p>
 <p>In <cite>PeleLMeX</cite>, the chemistry model (set of species, their thermodynamic and transport properties as well as the description
 of their of chemical interactions) is specified at compile time. Chemistry models available in
-<cite>PelePhysics</cite> can used in <cite>PeleLMeX</cite> by specifying the name of the folder in <cite>PelePhysics/Support/Mechanisms/Models</cite> containing
+<cite>PelePhysics</cite> can used in <cite>PeleLMeX</cite> by specifying the name of the folder in <cite>PelePhysics/Mechanisms</cite> containing
 the relevant files, for example:</p>
 <div class="highlight-rst notranslate"><div class="highlight"><pre><span></span>Chemistry_Model = air
 </pre></div>

diff --git a/manual/html/Tutorials_SettingUp.html b/manual/html/Tutorials_SettingUp.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Setting-up your environment &mdash; PeleLMeX 22.12 documentation</title>
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