docs(api): link Simulation class page from Simulation module in API index; refresh docs

zasexton · zasexton · commit 106100ce5657 · 2025-09-29T10:51:54.000-07:00
diff --git a/docs/algorithm.html b/docs/algorithm.html
@@ -35,7 +35,7 @@ <h1>svVascularize</h1>
         <a href="index.html#about">About</a>
         <a href="install.html">Installation</a>
         <a class="active" href="doc.html">Documentation</a>
-        <a href="#simulation">Simulation</a>
+        <a href="index.html#simulation">Simulation</a>
         <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
         <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
       </nav>
diff --git a/docs/api/domain.html b/docs/api/domain.html
@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>
diff --git a/docs/api/forest.html b/docs/api/forest.html
@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>
diff --git a/docs/api/index_api.html b/docs/api/index_api.html
@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>
@@ -388,6 +388,15 @@ <h5>1D Models</h5>
                             </div>
                         </div>
 
+                        <div class="api-classes">
+                            <h4>Main Classes</h4>
+                            <ul class="api-class-list">
+                                <li>
+                                    <a href="simulation.html"><code>Simulation</code></a> - Container for generating meshes and simulation files
+                                </li>
+                            </ul>
+                        </div>
+
                         <div class="api-example">
                             <h4>Example Usage</h4>
                             <pre data-copy><code class="language-python">from svv.simulation import Simulation
diff --git a/docs/api/patch.html b/docs/api/patch.html
@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>
diff --git a/docs/api/simulation.html b/docs/api/simulation.html
@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>
diff --git a/docs/api/tree.html b/docs/api/tree.html
@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>
diff --git a/docs/doc.html b/docs/doc.html
@@ -71,6 +71,20 @@ <h3>Community & Support</h3>
       <li><a href="https://github.com/SimVascular/svVascularize/issues" target="_blank" rel="noopener">GitHub Issues</a></li>
     </ul>
 
+    <h3 id="simulation">Simulation Overview</h3>
+    <p>The <code>Simulation</code> module mirrors the capabilities in the library today:</p>
+    <ul>
+      <li><a href="pipeline.html">3-D CFD pipeline</a> &mdash; full workflow from <code>build_meshes()</code> through
+        <code>write_3d_fluid_simulation()</code>, including boundary layer options and multi-tree exports.</li>
+      <li><a href="api/simulation.html">Simulation API reference</a> &mdash; method-by-method detail on mesh storage,
+        face extraction, and svFSI XML generation.</li>
+      <li><a href="quickstart.html#export-0d-simulation-files">0-D exports</a> &mdash; use
+        <code>svv.simulation.fluid.rom.zero_d</code> helpers for fast circuit models; 1-D parameter builders are also
+        included in <code>Simulation.construct_1d_fluid_simulation()</code> for multiscale coupling.</li>
+    </ul>
+    <div class="callout info"><strong>Tip:</strong> 0-D and 1-D solvers are shipped separately; see the installation
+      guide&rsquo;s <a href="install.html#simulation">simulation extras</a> for setup notes.</div>
+
   </main>
 
   <!-- Footer -->
diff --git a/docs/index.html b/docs/index.html
@@ -46,11 +46,31 @@ <h3>About<code>svVascularize</code> </h3>
   </section>
 
 
+  <section id="simulation" class="content">
+    <div class="container">
+      <h3>Simulation Workflows</h3>
+      <p>The <code>svv.simulation.Simulation</code> container turns generated trees and forests into ready-to-run
+        solver input. It automates mesh generation, boundary extraction, and svFSI configuration so you can move from a
+        synthetic network to a 3-D CFD job without leaving Python.</p>
+      <ul>
+        <li><strong>3D CFD:</strong> build watertight tet meshes, optional boundary layers, extract wall/outlet faces,
+          and emit svFSI XML plus surface/volume mesh files.</li>
+        <li><strong>Multi-tree support:</strong> forests are handled tree-by-tree, letting you select which networks to
+          mesh and export.</li>
+        <li><strong>Reduced-order:</strong> direct helpers in <code>svv.simulation.fluid.rom</code> export matching 0-D
+          circuits today, with 1-D parameter generation available for coupling work.</li>
+      </ul>
+      <div class="callout info"><strong>Need details?</strong> The <a href="pipeline.html">3-D pipeline</a> and <a href="api/simulation.html">Simulation API</a> pages walk through every step, from
+        <code>build_meshes()</code> to writing solver files.</div>
+    </div>
+  </section>
+
+
   <footer>
     <div class="container">
       <p>&copy; 2025 SimVascular, Stanford University, The Regents of the University of California, and others —
       <a href="https://opensource.org/license/BSD-3-Clause">BSD 3-Clause License</a><br></p>
     </div>
   </footer>
 </body>
-</html>
+</html>
diff --git a/docs/install.html b/docs/install.html
@@ -47,7 +47,7 @@ <h2>Quick-start</h2>
       <pre data-copy><code class="language-shell">python -m pip install --upgrade pip  # upgrade installer
 python -m pip install svv</code></pre>
       <p>This installs the <em>core</em> pre-built synthetic vascular-generation wheel from PyPI.</p>
-      <div class="callout"><strong>Need hemodynamics solvers?</strong> They are not included by default—see <a href="#optional-solvers">Optional solvers</a>.</div>
+      <div class="callout"><strong>Need hemodynamics solvers?</strong> They are not included by default—see <a href="#simulation">Simulation extras</a>.</div>
     </section>
 
     <!-- REQUIREMENTS -->
@@ -152,11 +152,12 @@ <h2>Building from source</h2>
     </section>
 
     <!-- SOLVERS -->
-    <section id="optional-solvers">
-      <h2>Optional Hemodynamic CFD / ROM solvers</h2>
-          <p>The <b>svVascularize</b> Python API is solver-agnostic. For
-     flow analysis you can link to the SimVascular solver
-     family shown in the table:</p>
+    <section id="simulation">
+      <h2>Simulation extras</h2>
+          <p>The <b>svVascularize</b> Python API is solver-agnostic. The
+     <code>Simulation</code> container prepares meshes and svFSI XML files, while helper functions in
+     <code>svv.simulation.fluid.rom</code> emit 0-D circuits. To actually march solutions forward you can link to the
+     SimVascular solvers below:</p>
 
   <table>
     <thead><tr>
@@ -177,6 +178,10 @@ <h2>Optional Hemodynamic CFD / ROM solvers</h2>
           <td>CMake ≥ 3.20, VTK ≥ 9, MPI, BLAS, LAPACK</td></tr>
     </tbody>
   </table>
+        <div class="callout info"><strong>Tip:</strong> After calling <code>Simulation.construct_3d_fluid_simulation()</code>
+          use <code>Simulation.write_3d_fluid_simulation()</code> to emit meshes and <code>fluid_simulation_*.xml</code> files that
+          svFSI consumes directly. The ROM helpers write JSON/<code>.flow</code> data next to the geometry so you can drive
+          multiscale studies from the same tree.</div>
           <!-- 0-D install -->
   <h3 id="solver-0d"><code>svZeroDSolver</code></h3>
   <p>Pre-built wheels do not yet exist for this solver;
@@ -251,4 +256,4 @@ <h2>Troubleshooting &amp; FAQ</h2>
   <!-- Shared interactivity -->
   <script defer src="script.js"></script>
 </body>
-</html>
+</html>
diff --git a/docs/pipeline.html b/docs/pipeline.html
@@ -69,6 +69,33 @@ <h2>End-to-End Pipeline for 3D CFD Simulations</h2>
          These, as well as surface mesh unioning operations, are non-trivial and may take minutes-hours to complete.
          Users can supply custom meshing parameters for their applications to override default values this may result
          in more efficient meshing, but it is recommended that default parameters are attemped first.</div>
+     <p>Once meshes exist, identify wall and outlet patches that become boundary conditions. The
+         <code>Simulation.extract_faces()</code> routine wraps <code>svv.simulation.utils.extract_faces</code> to label
+         surfaces on both the solid model and the tetrahedral mesh.</p>
+     <pre data-copy> <code class="language-python"># Detect walls, outlets, and shared boundaries
+sim.extract_faces(crease_angle=60.0)
+
+# Inspect names stored in the GeneralMesh container
+print(sim.fluid_domain_meshes[0].faces.keys())</code></pre>
+     <p>Finally, assemble the svFSI configuration and write everything to disk. The default output directory is created if
+         it does not exist.</p>
+     <pre data-copy> <code class="language-python"># Build and persist 3-D CFD input files
+sim.construct_3d_fluid_simulation()
+sim.write_3d_fluid_simulation()
+
+# Result: meshes + XML under sim.file_path (e.g. ./simulations/example/)</code></pre>
+     <div class="callout info"><strong>Directory layout:</strong> The export creates a <code>mesh/</code> folder containing
+         the volume grid (<code>.vtu</code> or <code>.vtp</code>), a <code>mesh-surfaces/</code> folder for each named face, and
+         a <code>fluid_simulation_0-0.xml</code> svFSI input file.</div>
+     <p>For rapid prototyping, couple the same tree to the reduced-order solvers shipped with SimVascular.</p>
+     <pre data-copy> <code class="language-python">from svv.simulation.fluid.rom.zero_d.zerod_tree import export_0d_simulation
+
+export_0d_simulation(t, outdir=sim.file_path + "/rom_0d")
+
+# Optionally stage 1-D parameters for multi-scale workflows
+sim.construct_1d_fluid_simulation(time_step_size=1e-3, number_time_steps=2000)</code></pre>
+     <div class="callout warning"><strong>Note:</strong> Writing of 1-D files is not yet automated. The parameter bundle
+         returned by <code>construct_1d_fluid_simulation()</code> can be passed to the SimVascular 1-D solver tools.</div>
  </main>
   <footer>
     <div class="container">
diff --git a/docs/quickstart.html b/docs/quickstart.html
@@ -55,7 +55,7 @@ <h3>Generate and visualise a tree</h3>
       <img src="graphics/quickstart_orbit.gif" alt="Orbit around vascular tree" width="300" />
       <figcaption> Rotating view of the generated vascular tree </figcaption>
     </figure>
-    <h3>Export 0‑D simulation files</h3>
+    <h3 id="export-0d-simulation-files">Export 0‑D simulation files</h3>
     <pre data-copy><code class="language-python">from svv.simulation.fluid.rom.zero_d.zerod_tree import export_0d_simulation
 
 export_0d_simulation(t, outdir="my_tree_0d")
@@ -105,7 +105,7 @@ <h3>Generate and visualise a forest</h3>
       <img src="graphics/quickstart_forest_connected_orbit.gif" alt="Orbit around connected vascular forest" width="400" />
       <figcaption> Rotating view of the connected vascular forest </figcaption>
     </figure>
-  <h3>Export 0-D simulation files</h3>
+  <h3 id="export-0d-forest">Export 0-D simulation files</h3>
       <p>Because a forest object may contain multiple fluid networks, it is important to specify which network a user wants
       to export for simulation as well as the inlet boundaries. These are the second and thrid positional arguments of the
       simulation exporting function, respectively. </p>
