build based on 30665a8

Author: Documenter.jl

julia-docs/dev/docstrings.html

@@ -208,10 +208,10 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.context--4896731d1a77eb1c"><co
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-<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb1"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">apply_chem_boundary!</span>(c<span class="op">::</span><span class="dt">Context</span>; oversampling_factor<span class="op">::</span><span class="dt">Int</span>=<span class="fl">16</span>)<span class="op">::</span><span class="dt">Nothing</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb1"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">apply_chem_boundary!</span>(c<span class="op">::</span><span class="dt">Context</span>)<span class="op">::</span><span class="dt">Nothing</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <p>Update chem voxel volumes and diffusion rates.</p>
 <p>The chem boundary is the intersection of any boundary set by <a href="../docstrings/medyan.set_chem_boundary--8446b49a230e3146.html"><code>set_chem_boundary!</code></a> and membranes with <code>chem_boundary=true</code>.</p>
-<p><code>oversampling_factor</code> can be increased to improve the accuracy at the expense of increased memory use.</p>
+<p><a href="../docstrings/medyan.set_chem_boundary_oversampling_factor--dd246eef62c89b5f.html"><code>set_chem_boundary_oversampling_factor!</code></a> can be used to increase the boundary sampling resolution at the expense of increased memory use.</p>
 <p>Calling this will invalidate the chem cache.</p>
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julia-docs/dev/docstrings/medyan.apply_chem_boundary--86fcf1aed37adaf6.html

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 <li><p><code>func_membranespeciespotentialenergy::Any</code>: Membrane species potential energy function. See docs on default function for more info.</p></li>
 <li><p><code>external_energy_forces!::Any</code>: External energy/force expressions. This should be a mutating function taking a <code>(fc::MEDYAN.ForceContext, vectorized_x)</code>, which adds to <code>fc.forces, fc.energies, and fc.energy</code>. The energy and force must be consistent, and this is not checked. This can be used as ad-hoc solutions to experiment with uncommon forces, such as specifically designed attachments, etc. If this variable is used often, consider moving it into MEDYAN.</p></li>
 <li><p><code>chemboundary::MEDYAN.Boundary</code>: chemical boundary, updates compartment volumes and diffusion rates</p></li>
+<li><p><code>chem_boundary_oversampling_factor::Int64</code>: Oversampling factor for chem boundary TSDF computation. Default is 4.</p></li>
+<li><p><code>chem_boundary_tsdf_max_distance::Float64</code>: Maximum distance for TSDF truncation (nm). Actual max is max(this, 2.5*grid_spacing). Default is 312.5 nm.</p></li>
+<li><p><code>chem_boundary_tsdf_cache::Union{Nothing, Array{Float64, 3}}</code>: Cached truncated signed distance field for chem boundary. <code>nothing</code> means cache is invalid.</p></li>
 <li><p><code>mechboundary::MEDYAN.Boundary</code>: mechanical boundary</p></li>
 <li><p><code>sharedtypedconfigs::MEDYAN.SharedTypedConfigs</code>: Shared configurations stored in type parameters.</p></li>
 <li><p><code>validflags::MEDYAN.ValidFlags</code>: Interval system consistency validation flags.</p></li>