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+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="Introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="GettingStarted.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Inputs_Chapter.html">Run-time Inputs</a></li>
+<li class="toctree-l1"><a class="reference internal" href="ManagingGridHierarchy_Chapter.html">Gridding and Load Balancing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Fluids_Chapter.html">Solving the Fluid Equations</a></li>
+<li class="toctree-l1"><a class="reference internal" href="EB.html">Embedded Boundaries</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Debugging</a></li>
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+
+  <section id="debugging">
+<span id="chap-debugging"></span><h1>Debugging<a class="headerlink" href="#debugging" title="Link to this heading"></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>
+<p>Compiling in debug mode (e.g., <code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">make</span><span class="w"> </span><span class="n">DEBUG</span><span class="o">=</span><span class="n">TRUE</span></code> for gmake users;
+<code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">cmake</span><span class="w"> </span><span class="o">-</span><span class="n">DDEBUG</span></code> for cmake users) and running with
+<code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">amrex</span><span class="p">.</span><span class="n">fpe_trap_invalid</span><span class="o">=</span><span class="mi">1</span></code> in the inputs file can be helpful.
+In debug mode, many compiler debugging flags are turned on and all
+<code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">MultiFab</span></code> s are initialized to signaling NaNs.  The
+<code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">amrex</span><span class="p">.</span><span class="n">fpe_trap_invalid</span></code> parameter will result in backtrace files
+when a floating point exception occurs.  One can then examine those
+files to track down the origin of the issue.</p>
+<p>Several ways to look at the data include:</p>
+<ol class="arabic">
+<li><p>Writing a <code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">MultiFab</span></code> to disk with</p>
+<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 v24.04-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>
+</pre></div>
+</div>
+<p>which outputs the data for a single cell.</p>
+</li>
+<li><p>If you want to compare old and new plotfiles,</p>
+<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
+for each variable and will also create a new plotfile “diffs” that contains the difference
+in u_g (in this case) between the two plotfiles.</p>
+<p>The <code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">fcompare</span></code> executable can be built in AMReX (go to amrex/Tools/Plotfile and type “make”).</p>
+</li>
+</ol>
+<p>Valgrind is another useful debugging tool.  Note that for runs using
+more than one MPI process, one can tell valgrind to output to different
+files for different processes.  For example,</p>
+<blockquote>
+<div><div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">mpiexec -n 4 valgrind --leak-check=yes --track-origins=yes --log-file=vallog.%p ./incflo.exe ...</span>
+</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 v24.04-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-Fluids/incflo/issues">here</a> .</p>
+</section>
+
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+<li class="toctree-l1"><a class="reference internal" href="Introduction.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="GettingStarted.html">Getting Started</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="ManagingGridHierarchy_Chapter.html">Gridding and Load Balancing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Fluids_Chapter.html">Solving the Fluid Equations</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Embedded Boundaries</a></li>
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+  <section id="embedded-boundaries">
+<span id="chap-eb"></span><h1>Embedded Boundaries<a class="headerlink" href="#embedded-boundaries" title="Link to this heading"></a></h1>
+<p>incflo follows AMReX’s approach to embedded boundaries (EB), which is described in the
+<a class="reference external" href="https://amrex-codes.github.io/amrex/docs_html/EB_Chapter.html">AMReX EB documentation</a>.
+By default, incflo uses AMReX’s constructive solid geometry framework defined in the namespace <code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">amrex</span><span class="o">::</span><span class="n">EB2</span></code>.
+Alternatively, the constructive solid geometry can also be created using OpenSCAD’s CSG file format by installing
+the <code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">csg</span><span class="o">-</span><span class="n">eb</span></code> library. To use this option, incflo must be built with the flag
+<code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">USE_CSG</span><span class="o">=</span><span class="n">TRUE</span></code> and <code class="code highlight cpp c++ docutils literal highlight-c++"><span class="n">CSGEB_HOME</span></code> must be set to where the library was installed.
+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 v24.04-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>
+</pre></div>
+</div>
+<p>This specifies to which level of coarseness the EB is still defined. It might not be
+immediately obvious, but the multigrid solver (used in the fluid solve) also
+depends indirectly on this parameters. Choosing a value of <code class="docutils literal notranslate"><span class="pre">max_crse_level</span></code> that is too small might restrict
+how many levels the MLMG solver can use, and therefore give slightly different answers in the fluid solve.</p>
+</section>
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