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AMReX-Fluids · Apr 16, 2024 · aa4f9a4 · aa4f9a4
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diff --git a/docs_html/.buildinfo b/docs_html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: fbf87383e113e49826fd69fcfcc39358
+config: 59c2e08d271c82216b8e443057f37c02
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs_html/Debugging.html b/docs_html/Debugging.html
@@ -1,20 +1,22 @@
 <!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>Debugging &mdash; incflo 23.00-dev 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_overrides.css" type="text/css" />
+  <title>Debugging &mdash; incflo 24.05-dev documentation</title>
+      <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_overrides.css?v=681a4282" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=0b3700fb"></script>
+        <script src="_static/documentation_options.js?v=18739dcb"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
@@ -35,7 +37,7 @@
             incflo
           </a>
               <div class="version">
-                23.00-dev
+                24.05-dev
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -98,7 +100,7 @@
 <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 <a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/Visualization.html#sec-amrvis" title="(in amrex v23.00-dev)"><span>Amrvis</span></a> in the AMReX documentation).</p>
+<p>and examining it with <code class="docutils literal notranslate"><span class="pre">Amrvis</span></code> (section <a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/Visualization.html#sec-amrvis" title="(in amrex v24.05-dev)"><span>Amrvis</span></a> in the AMReX documentation).</p>
 </li>
 <li><p>You can also use the <code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">print_state</span></code> routine:</p>
 <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>
@@ -124,9 +126,9 @@
 </pre></div>
 </div>
 </div></blockquote>
-<p>Also see AMReX’s documentation on <a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/Debugging.html#sec-basics-debugging" title="(in amrex v23.00-dev)"><span>Debugging</span></a> for further suggestions.</p>
+<p>Also see AMReX’s documentation on <a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/Debugging.html#sec-basics-debugging" title="(in amrex v24.05-dev)"><span>Debugging</span></a> for further suggestions.</p>
 <p>If you believe you’ve encountered a bug or incorrect behavior in incflo, please report the issue
-on incflo’s github page <a class="reference external" href="https://github.com/AMReX-Codes/incflo/issues">here</a> .</p>
+on incflo’s github page <a class="reference external" href="https://github.com/AMReX-Fluids/incflo/issues">here</a> .</p>
 </section>
 
 

diff --git a/docs_html/EB.html b/docs_html/EB.html
@@ -1,20 +1,22 @@
 <!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>Embedded Boundaries &mdash; incflo 23.00-dev 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_overrides.css" type="text/css" />
+  <title>Embedded Boundaries &mdash; incflo 24.05-dev documentation</title>
+      <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_overrides.css?v=681a4282" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=0b3700fb"></script>
+        <script src="_static/documentation_options.js?v=18739dcb"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
@@ -36,7 +38,7 @@
             incflo
           </a>
               <div class="version">
-                23.00-dev
+                24.05-dev
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -92,7 +94,7 @@
 See <a class="reference external" href="https://mfix.netl.doe.gov/gitlab/exa/csg-eb">MFIX’s CSG-EB repository</a> for more details about this format.</p>
 <p>incflo provides several options of embedded boundary geometries. The inputs parameter <code class="docutils literal notranslate"><span class="pre">incflo.geometry</span> <span class="pre">=</span> <span class="pre">XXX</span></code>
 determines which geometry is selected by <code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">incflo</span><span class="o">::</span><span class="n">MakeEBGeometry</span><span class="p">()</span></code> within <code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">incflo</span><span class="o">/</span><span class="n">src</span><span class="o">/</span><span class="n">embedded_boundaries</span></code>.
-The procedure to create your own EB geometry is described in the AMReX documentation on <a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/EB.html#sec-eb-ebinit" title="(in amrex v23.00-dev)"><span>Initializing the Geometric Database</span></a>.
+The procedure to create your own EB geometry is described in the AMReX documentation on <a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/EB.html#sec-eb-ebinit" title="(in amrex v24.05-dev)"><span>Initializing the Geometric Database</span></a>.
 As discussed in the AMReX documentation, note that when constructing the EB, we must specify a
 maxium coarsening level (<code class="docutils literal notranslate"><span class="pre">max_crse_level</span></code>):</p>
 <div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="n">EB2</span><span class="o">::</span><span class="n">Build</span><span class="p">(</span><span class="n">gshop</span><span class="p">,</span><span class="w"> </span><span class="n">geom</span><span class="p">[</span><span class="n">lev</span><span class="p">],</span><span class="w"> </span><span class="n">required_crse_lev</span><span class="p">,</span><span class="w"> </span><span class="n">max_crse_level</span><span class="p">);</span>

diff --git a/docs_html/FluidEquations.html b/docs_html/FluidEquations.html
@@ -1,20 +1,22 @@
 <!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>Fluid Variables &mdash; incflo 23.00-dev 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_overrides.css" type="text/css" />
+  <title>Fluid Variables &mdash; incflo 24.05-dev documentation</title>
+      <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_overrides.css?v=681a4282" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=0b3700fb"></script>
+        <script src="_static/documentation_options.js?v=18739dcb"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
@@ -37,7 +39,7 @@
             incflo
           </a>
               <div class="version">
-                23.00-dev
+                24.05-dev
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -135,11 +137,14 @@ <h1>Fluid Equations<a class="headerlink" href="#fluid-equations" title="Link to
 <p>Incompressibility constraint:</p>
 <div class="math notranslate nohighlight">
 \[\nabla \cdot U = 0\]</div>
-<p>Tracer(s):</p>
+<p>Tracer(s): for conservative,</p>
 <div class="math notranslate nohighlight">
 \[\frac{\partial \rho s}{\partial t} + \nabla \cdot (\rho U s)  =  \nabla \cdot \mu_s \nabla s + \rho H_s\]</div>
+<p>or, for non-conservative,</p>
+<div class="math notranslate nohighlight">
+\[\frac{\partial s}{\partial t} + U \cdot \nabla s  =  \nabla \cdot \mu_s \nabla s + H_s\]</div>
 <p>By default, <span class="math notranslate nohighlight">\(H_s = 0\)</span> and <span class="math notranslate nohighlight">\({\bf H}_U = {\bf 0}\)</span>.
-If gravity is set during runtime, then <span class="math notranslate nohighlight">\({\bf H}_U\)</span> defaults to <span class="math notranslate nohighlight">\(\rho {\bf g}\)</span></p>
+If gravity is set during runtime, then <span class="math notranslate nohighlight">\({\bf H}_U\)</span> defaults to <span class="math notranslate nohighlight">\(\rho {\bf g}\)</span>.</p>
 </section>
 
 

diff --git a/docs_html/Fluids_Chapter.html b/docs_html/Fluids_Chapter.html
@@ -1,20 +1,22 @@
 <!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>Solving the Fluid Equations &mdash; incflo 23.00-dev 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_overrides.css" type="text/css" />
+  <title>Solving the Fluid Equations &mdash; incflo 24.05-dev documentation</title>
+      <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_overrides.css?v=681a4282" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=0b3700fb"></script>
+        <script src="_static/documentation_options.js?v=18739dcb"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
@@ -36,7 +38,7 @@
             incflo
           </a>
               <div class="version">
-                23.00-dev
+                24.05-dev
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">

diff --git a/docs_html/GettingStarted.html b/docs_html/GettingStarted.html
@@ -1,20 +1,22 @@
 <!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>Getting Started &mdash; incflo 23.00-dev 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_overrides.css" type="text/css" />
+  <title>Getting Started &mdash; incflo 24.05-dev documentation</title>
+      <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_overrides.css?v=681a4282" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=0b3700fb"></script>
+        <script src="_static/documentation_options.js?v=18739dcb"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
@@ -36,7 +38,7 @@
             incflo
           </a>
               <div class="version">
-                23.00-dev
+                24.05-dev
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -116,13 +118,13 @@
 For additional information on downloading the AMReX source code see <a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/GettingStarted.html">AMReX user guide - Downloading the code</a>.</p>
 </li>
 <li><p>Download the AMReX-Hydro repository by typing:</p>
-<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/AMReX-Codes/AMReX-Hydro.git
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/AMReX-Fluids/AMReX-Hydro.git
 </pre></div>
 </div>
 <p>This will create a folder called <code class="docutils literal notranslate"><span class="pre">AMReX-Hydro/</span></code> on your machine.</p>
 </li>
 <li><p>Download the incflo repository by typing:</p>
-<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/AMReX-Codes/incflo.git
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/AMReX-Fluids/incflo.git
 </pre></div>
 </div>
 <p>This will create a folder called <code class="docutils literal notranslate"><span class="pre">incflo/</span></code> on your machine.</p>
@@ -436,11 +438,11 @@ <h2>Running the code<a class="headerlink" href="#running-the-code" title="Link t
 <code class="docutils literal notranslate"><span class="pre">chk00010</span></code>, etc. These are called plotfiles and checkpoint
 files. The plotfiles are used for visualization of derived fields; the checkpoint
 files are used for restarting the code. For more information see the AMReX Documentation on
-<a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/IO_Chapter.html#chap-io" title="(in amrex v23.00-dev)"><span>I/O (Plotfile, Checkpoint)</span></a>.</p>
+<a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/IO_Chapter.html#chap-io" title="(in amrex v24.05-dev)"><span>I/O (Plotfile, Checkpoint)</span></a>.</p>
 </section>
 <section id="visualizing-the-results">
 <h2>Visualizing the Results<a class="headerlink" href="#visualizing-the-results" title="Link to this heading"></a></h2>
-<p>Options for visualizing the data are discussed in the AMReX Documenation on <a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/Visualization_Chapter.html#chap-visualization" title="(in amrex v23.00-dev)"><span>Visualization</span></a>.</p>
+<p>Options for visualizing the data are discussed in the AMReX Documenation on <a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/Visualization_Chapter.html#chap-visualization" title="(in amrex v24.05-dev)"><span>Visualization</span></a>.</p>
 </section>
 </section>