build based on c8f7aaa

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-03T00:21:02","documenter_version":"1.3.0"}}
+{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-03T11:40:43","documenter_version":"1.3.0"}}

dev/internal/index.html

@@ -45,4 +45,4 @@
 </code></pre><p>Interpret the  discrete problem as an ODE/DAE problem. Provide the  rhs function for <a href="../solver/#SciMLBase.ODEFunction-Tuple{VoronoiFVM.AbstractSystem}"><code>ODEFunction</code></a>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.eval_jacobian!" href="#VoronoiFVM.eval_jacobian!"><code>VoronoiFVM.eval_jacobian!</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">eval_jacobian!(J, u, sys, t)
 </code></pre><p>Interpret the  discrete problem as an ODE/DAE problem. Provide the  jacobi matrix calculation function for <a href="../solver/#SciMLBase.ODEFunction-Tuple{VoronoiFVM.AbstractSystem}"><code>ODEFunction</code></a></p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.mass_matrix" href="#VoronoiFVM.mass_matrix"><code>VoronoiFVM.mass_matrix</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">mass_matrix(system)
 </code></pre><p>Calculate the mass matrix for use with <a href="../solver/#SciMLBase.ODEFunction-Tuple{VoronoiFVM.AbstractSystem}"><code>ODEFunction</code></a>. Return a Diagonal matrix if it occurs to be diagonal, otherwise return a SparseMatrixCSC.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.prepare_diffeq!" href="#VoronoiFVM.prepare_diffeq!"><code>VoronoiFVM.prepare_diffeq!</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">prepare_diffeq!(sys, jacval, tjac)
-</code></pre><p>Prepare system for use with VoronoiFVMDiffEq.</p><ul><li><code>jacval</code>: value at which to evaluate jacobian to obtatin prototype</li><li><code>tjac</code>: time moment for jacobian</li></ul><p>Returns a prototype for the jacobian.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../misc/">« Miscellaneous</a><a class="docs-footer-nextpage" href="../allindex/">Index »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Sunday 3 March 2024 00:21">Sunday 3 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre><p>Prepare system for use with VoronoiFVMDiffEq.</p><ul><li><code>jacval</code>: value at which to evaluate jacobian to obtatin prototype</li><li><code>tjac</code>: time moment for jacobian</li></ul><p>Returns a prototype for the jacobian.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../misc/">« Miscellaneous</a><a class="docs-footer-nextpage" href="../allindex/">Index »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Sunday 3 March 2024 11:40">Sunday 3 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/misc/index.html

@@ -4,4 +4,4 @@
 </code></pre><p>Project velocity onto boundary face normals</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><h2 id="Additional-grid-methods"><a class="docs-heading-anchor" href="#Additional-grid-methods">Additional grid methods</a><a id="Additional-grid-methods-1"></a><a class="docs-heading-anchor-permalink" href="#Additional-grid-methods" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.Grid" href="#VoronoiFVM.Grid"><code>VoronoiFVM.Grid</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">Grid=ExtendableGrids.simplexgrid</code></pre><p>Re-Export of ExtendableGrids.simplexgrid</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.cartesian!-Tuple{ExtendableGrid}" href="#VoronoiFVM.cartesian!-Tuple{ExtendableGrid}"><code>VoronoiFVM.cartesian!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">cartesian!(grid)
 </code></pre><p>Set coordinate system in grid to cartesian.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.circular_symmetric!-Tuple{ExtendableGrid}" href="#VoronoiFVM.circular_symmetric!-Tuple{ExtendableGrid}"><code>VoronoiFVM.circular_symmetric!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">circular_symmetric!(grid)
 </code></pre><p>Set coordinate system in grid to circular/cylindrical symmetry.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.spherical_symmetric!-Tuple{ExtendableGrid}" href="#VoronoiFVM.spherical_symmetric!-Tuple{ExtendableGrid}"><code>VoronoiFVM.spherical_symmetric!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">spherical_symmetric!(grid)
-</code></pre><p>Set coordinate system in grid to spherical symmetry.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><h2 id="Exception-types"><a class="docs-heading-anchor" href="#Exception-types">Exception types</a><a id="Exception-types-1"></a><a class="docs-heading-anchor-permalink" href="#Exception-types" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.AssemblyError" href="#VoronoiFVM.AssemblyError"><code>VoronoiFVM.AssemblyError</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">struct AssemblyError &lt;: Exception</code></pre><p>Exception thrown if error occurred during assembly (e.g. domain error)</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.ConvergenceError" href="#VoronoiFVM.ConvergenceError"><code>VoronoiFVM.ConvergenceError</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">struct ConvergenceError &lt;: Exception</code></pre><p>Exception thrown if Newton&#39;s method convergence fails.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.EmbeddingError" href="#VoronoiFVM.EmbeddingError"><code>VoronoiFVM.EmbeddingError</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">struct EmbeddingError &lt;: Exception</code></pre><p>Exception thrown if embedding fails</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.LinearSolverError" href="#VoronoiFVM.LinearSolverError"><code>VoronoiFVM.LinearSolverError</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">struct LinearSolverError &lt;: Exception</code></pre><p>Exception thrown if error occurred during factorization.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../quantities/">« Quantities</a><a class="docs-footer-nextpage" href="../internal/">Internal API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Sunday 3 March 2024 00:21">Sunday 3 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre><p>Set coordinate system in grid to spherical symmetry.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><h2 id="Exception-types"><a class="docs-heading-anchor" href="#Exception-types">Exception types</a><a id="Exception-types-1"></a><a class="docs-heading-anchor-permalink" href="#Exception-types" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.AssemblyError" href="#VoronoiFVM.AssemblyError"><code>VoronoiFVM.AssemblyError</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">struct AssemblyError &lt;: Exception</code></pre><p>Exception thrown if error occurred during assembly (e.g. domain error)</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.ConvergenceError" href="#VoronoiFVM.ConvergenceError"><code>VoronoiFVM.ConvergenceError</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">struct ConvergenceError &lt;: Exception</code></pre><p>Exception thrown if Newton&#39;s method convergence fails.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.EmbeddingError" href="#VoronoiFVM.EmbeddingError"><code>VoronoiFVM.EmbeddingError</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">struct EmbeddingError &lt;: Exception</code></pre><p>Exception thrown if embedding fails</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="VoronoiFVM.LinearSolverError" href="#VoronoiFVM.LinearSolverError"><code>VoronoiFVM.LinearSolverError</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">struct LinearSolverError &lt;: Exception</code></pre><p>Exception thrown if error occurred during factorization.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/j-fu/VoronoiFVM.jl">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../quantities/">« Quantities</a><a class="docs-footer-nextpage" href="../internal/">Internal API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Sunday 3 March 2024 11:40">Sunday 3 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/module_examples/Example001_Solvers/index.html

@@ -142,4 +142,4 @@
         main(; assembly = :cellwise)
     end
 end
-end</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../runexamples/">« About the examples</a><a class="docs-footer-nextpage" href="../Example002_EdgeReaction/">002: check edge reaction »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Sunday 3 March 2024 00:21">Sunday 3 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+end</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../runexamples/">« About the examples</a><a class="docs-footer-nextpage" href="../Example002_EdgeReaction/">002: check edge reaction »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Sunday 3 March 2024 11:40">Sunday 3 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>