Docs @ 0c772e6

Author: MFC Action

documentation/architecture.html

@@ -384,6 +384,8 @@ <h2 class="doxsection"><a class="anchor" id="autotoc_md10"></a>
 <td class="markdownTableBodyNone"><span class="tt">m_sim_helpers</span>  </td><td class="markdownTableBodyNone">Simulation helper routines for enthalpy computation, CFL calculation, and stability checks  </td></tr>
 <tr class="markdownTableRowEven">
 <td class="markdownTableBodyNone"><span class="tt">m_derived_variables</span>  </td><td class="markdownTableBodyNone">Derives diagnostic flow quantities (vorticity, speed of sound, numerical Schlieren, etc.) from conservative and primitive variables  </td></tr>
+<tr class="markdownTableRowOdd">
+<td class="markdownTableBodyNone"><span class="tt">m_patch_geometries</span>  </td><td class="markdownTableBodyNone">Contains helper functions specific to various patch gemoetries for determining if a grid cell lies inside of or outside of a patch geometry  </td></tr>
 </table>
 <h2 class="doxsection"><a class="anchor" id="autotoc_md11"></a>
 Pre-Process</h2>
@@ -425,7 +427,7 @@ <h1 class="doxsection"><a class="anchor" id="autotoc_md13"></a>
 <li><b>Add the module to <span class="tt">docs/module_categories.json</span></b> so it appears in this page</li>
 </ol>
 <p>Follow the pattern of existing modules like <span class="tt">m_body_forces</span> (simple) or <span class="tt">m_viscous</span> (more involved) as a template.</p>
-<div style="text-align:center; font-size:0.75rem; color:#888; padding:16px 0 0;">Page last updated: 2026-06-16</div> </div></div><!-- contents -->
+<div style="text-align:center; font-size:0.75rem; color:#888; padding:16px 0 0;">Page last updated: 2026-06-17</div> </div></div><!-- contents -->
 </div><!-- PageDoc -->
 </div><!-- doc-content -->
 <div id="page-nav" class="page-nav-panel">

documentation/case.html

@@ -157,7 +157,7 @@
   <div class="headertitle"><div class="title">Case Creator Guide </div></div>
 </div><!--header-->
 <div class="contents">
-<div class="textblock"><h1 class="doxsection"><a class="anchor" id="autotoc_md40"></a>
+<div class="textblock"><h1 class="doxsection"><a class="anchor" id="autotoc_md41"></a>
 Case Creator Guide</h1>
 <blockquote class="doxtable">
 <p><b>Quick reference</b> for building MFC cases: working examples, compatibility rules, and configuration requirements. </p>
@@ -170,7 +170,7 @@ <h2 class="doxsection"><a class="anchor" id="case-design-playbook"></a>
 <blockquote class="doxtable">
 <p><b>Learn by example:</b> The cases below are curated from MFC's <span class="tt">examples/</span> directory and are validated, working configurations. Use them as blueprints for building your own simulations. </p>
 </blockquote>
-<h3 class="doxsection"><a class="anchor" id="autotoc_md41"></a>
+<h3 class="doxsection"><a class="anchor" id="autotoc_md42"></a>
 🟢 Beginner Examples</h3>
 <details >
 <summary >
@@ -196,7 +196,7 @@ <h3 class="doxsection"><a class="anchor" id="autotoc_md41"></a>
 </ul>
 <p></p>
 </details>
-<h3 class="doxsection"><a class="anchor" id="autotoc_md42"></a>
+<h3 class="doxsection"><a class="anchor" id="autotoc_md43"></a>
 🟡 Intermediate Examples</h3>
 <details >
 <summary >
@@ -329,7 +329,7 @@ <h3 class="doxsection"><a class="anchor" id="autotoc_md42"></a>
 </ul>
 <p></p>
 </details>
-<h3 class="doxsection"><a class="anchor" id="autotoc_md43"></a>
+<h3 class="doxsection"><a class="anchor" id="autotoc_md44"></a>
 🔴 Advanced Examples</h3>
 <details >
 <summary >
@@ -1461,7 +1461,7 @@ <h2 class="doxsection"><a class="anchor" id="physics-warnings"></a>
 </table>
 <hr  />
 <p>💡 <b>Tip:</b> If you encounter a validation error, check the relevant section above or review <a href="https://github.com/MFlowCode/MFC/blob/master/toolchain/mfc/case_validator.py"><span class="tt">case_validator.py</span></a> for complete validation logic.</p>
-<div style="text-align:center; font-size:0.75rem; color:#888; padding:16px 0 0;">Page last updated: 2026-06-16</div> </div></div><!-- contents -->
+<div style="text-align:center; font-size:0.75rem; color:#888; padding:16px 0 0;">Page last updated: 2026-06-17</div> </div></div><!-- contents -->
 </div><!-- PageDoc -->
 </div><!-- doc-content -->
 <div id="page-nav" class="page-nav-panel">

documentation/case_constraints.html

@@ -157,16 +157,16 @@
   <div class="headertitle"><div class="title">CLI Reference </div></div>
 </div><!--header-->
 <div class="contents">
-<div class="textblock"><h1 class="doxsection"><a class="anchor" id="autotoc_md45"></a>
+<div class="textblock"><h1 class="doxsection"><a class="anchor" id="autotoc_md46"></a>
 CLI Reference</h1>
 <blockquote class="doxtable">
 <p><b>Auto-generated</b> from <span class="tt">toolchain/mfc/cli/commands.py</span></p>
 <p>Regenerate with: <span class="tt">./mfc.sh generate</span> </p>
 </blockquote>
-<h2 class="doxsection"><a class="anchor" id="autotoc_md46"></a>
+<h2 class="doxsection"><a class="anchor" id="autotoc_md47"></a>
 Overview</h2>
 <p>Welcome to the MFC master script. This tool automates and manages building, testing, running, and cleaning of MFC in various configurations on all supported platforms. The README documents this tool and its various commands in more detail. To get started, run <span class="tt">./mfc.sh build -h</span>.</p>
-<h2 class="doxsection"><a class="anchor" id="autotoc_md47"></a>
+<h2 class="doxsection"><a class="anchor" id="autotoc_md48"></a>
 Quick Reference</h2>
 <table class="markdownTable">
 <tr class="markdownTableHead">
@@ -218,7 +218,7 @@ <h2 class="doxsection"><a class="anchor" id="autotoc_md47"></a>
 <tr class="markdownTableRowOdd">
 <td class="markdownTableBodyNone"><code>fp-stability</code>  </td><td class="markdownTableBodyNone">-  </td><td class="markdownTableBodyNone">Run floating-point stability tests using Verrou.  </td></tr>
 </table>
-<h2 class="doxsection"><a class="anchor" id="autotoc_md48"></a>
+<h2 class="doxsection"><a class="anchor" id="autotoc_md49"></a>
 Commands</h2>
 <h3 class="doxsection"><a class="anchor" id="build"></a>
 build</h3>
@@ -503,7 +503,7 @@ <h3 class="doxsection"><a class="anchor" id="validate"></a>
 <div class="line"># Rewrite integer codes to named values</div>
 <div class="line">./mfc.sh validate case.py --migrate</div>
 </div><!-- fragment --><hr  />
-<h2 class="doxsection"><a class="anchor" id="autotoc_md54"></a>
+<h2 class="doxsection"><a class="anchor" id="autotoc_md55"></a>
 Utility Commands</h2>
 <h3 class="doxsection"><a class="anchor" id="new"></a>
 new</h3>
@@ -679,7 +679,7 @@ <h3 class="doxsection"><a class="anchor" id="packer"></a>
 <div class="line"># Compare two packed files</div>
 <div class="line">./mfc.sh packer compare a.pack b.pack</div>
 </div><!-- fragment --><p><b>Subcommands:</b></p>
-<h4 class="doxsection"><a class="anchor" id="autotoc_md58"></a>
+<h4 class="doxsection"><a class="anchor" id="autotoc_md59"></a>
 packer pack</h4>
 <p>Pack a case into a single file.</p>
 <p>Arguments:</p><ul>
@@ -692,7 +692,7 @@ <h4 class="doxsection"><a class="anchor" id="autotoc_md58"></a>
 <tr class="markdownTableRowOdd">
 <td class="markdownTableBodyNone"><span class="tt">-o</span>, <span class="tt">--output</span>  </td><td class="markdownTableBodyNone">Base name of output file.  </td><td class="markdownTableBodyNone">-  </td></tr>
 </table>
-<h4 class="doxsection"><a class="anchor" id="autotoc_md59"></a>
+<h4 class="doxsection"><a class="anchor" id="autotoc_md60"></a>
 packer compare</h4>
 <p>Compare two cases.</p>
 <p>Arguments:</p><ul>
@@ -760,7 +760,7 @@ <h3 class="doxsection"><a class="anchor" id="generate"></a>
 <div class="line"># Generate JSON Schema for IDE support</div>
 <div class="line">./mfc.sh generate --json-schema</div>
 </div><!-- fragment --><hr  />
-<h2 class="doxsection"><a class="anchor" id="autotoc_md64"></a>
+<h2 class="doxsection"><a class="anchor" id="autotoc_md65"></a>
 Development Commands</h2>
 <h3 class="doxsection"><a class="anchor" id="lint"></a>
 lint</h3>
@@ -872,7 +872,7 @@ <h3 class="doxsection"><a class="anchor" id="count_diff"></a>
 <td class="markdownTableBodyNone"><span class="tt">--reldebug</span>, <span class="tt">--no-reldebug</span>  </td><td class="markdownTableBodyNone">Build with lightweight debug flags (CI)  </td><td class="markdownTableBodyNone"><span class="tt">false</span>  </td></tr>
 </table>
 <hr  />
-<h2 class="doxsection"><a class="anchor" id="autotoc_md71"></a>
+<h2 class="doxsection"><a class="anchor" id="autotoc_md72"></a>
 CI Commands</h2>
 <h3 class="doxsection"><a class="anchor" id="bench"></a>
 bench</h3>
@@ -938,7 +938,7 @@ <h3 class="doxsection"><a class="anchor" id="bench_diff"></a>
 <td class="markdownTableBodyNone"><span class="tt">--reldebug</span>, <span class="tt">--no-reldebug</span>  </td><td class="markdownTableBodyNone">Build with lightweight debug flags (CI)  </td><td class="markdownTableBodyNone"><span class="tt">false</span>  </td></tr>
 </table>
 <hr  />
-<h2 class="doxsection"><a class="anchor" id="autotoc_md74"></a>
+<h2 class="doxsection"><a class="anchor" id="autotoc_md75"></a>
 Other Commands</h2>
 <h3 class="doxsection"><a class="anchor" id="load"></a>
 load</h3>
@@ -956,10 +956,10 @@ <h3 class="doxsection"><a class="anchor" id="interactive"></a>
 <p>Launch an interactive menu for MFC operations.</p>
 <p><b>Usage:</b> <span class="tt">./mfc.sh interactive [OPTIONS]</span></p>
 <hr  />
-<h2 class="doxsection"><a class="anchor" id="autotoc_md77"></a>
+<h2 class="doxsection"><a class="anchor" id="autotoc_md78"></a>
 Common Options</h2>
 <p>Many commands share common option sets:</p>
-<h3 class="doxsection"><a class="anchor" id="autotoc_md78"></a>
+<h3 class="doxsection"><a class="anchor" id="autotoc_md79"></a>
 Target Selection (<span class="tt">-t, --targets</span>)</h3>
 <p>Available targets:</p><ul>
 <li><span class="tt">pre_process</span> - Pre-processor</li>
@@ -968,7 +968,7 @@ <h3 class="doxsection"><a class="anchor" id="autotoc_md78"></a>
 <li><span class="tt">syscheck</span> - System check utility</li>
 <li><span class="tt">documentation</span> - Build documentation</li>
 </ul>
-<h3 class="doxsection"><a class="anchor" id="autotoc_md79"></a>
+<h3 class="doxsection"><a class="anchor" id="autotoc_md80"></a>
 Build Configuration Flags</h3>
 <table class="markdownTable">
 <tr class="markdownTableHead">
@@ -988,18 +988,18 @@ <h3 class="doxsection"><a class="anchor" id="autotoc_md79"></a>
 <tr class="markdownTableRowOdd">
 <td class="markdownTableBodyNone"><span class="tt">--mixed</span> / <span class="tt">--no-mixed</span>  </td><td class="markdownTableBodyNone">Mixed precision  </td></tr>
 </table>
-<h3 class="doxsection"><a class="anchor" id="autotoc_md80"></a>
+<h3 class="doxsection"><a class="anchor" id="autotoc_md81"></a>
 Verbosity (<span class="tt">-v, --verbose</span>)</h3>
 <p>Controls output verbosity level:</p>
 <ul>
 <li><span class="tt">-v</span> - Basic verbose output</li>
 <li><span class="tt">-vv</span> - Show build commands</li>
 <li><span class="tt">-vvv</span> - Full verbose output including CMake details</li>
 </ul>
-<h3 class="doxsection"><a class="anchor" id="autotoc_md81"></a>
+<h3 class="doxsection"><a class="anchor" id="autotoc_md82"></a>
 Debug Logging (<span class="tt">-d, --debug-log</span>)</h3>
 <p>Enables debug logging for the Python toolchain (mfc.sh internals). This is for troubleshooting the build system, not the MFC simulation code.</p>
-<div style="text-align:center; font-size:0.75rem; color:#888; padding:16px 0 0;">Page last updated: 2026-06-16</div> </div></div><!-- contents -->
+<div style="text-align:center; font-size:0.75rem; color:#888; padding:16px 0 0;">Page last updated: 2026-06-17</div> </div></div><!-- contents -->
 </div><!-- PageDoc -->
 </div><!-- doc-content -->
 <div id="page-nav" class="page-nav-panel">