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‎julia-docs/dev/docstrings.html‎

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‎julia-docs/dev/docstrings/medyan.add_fixed_count--51020c406ff1afef.html‎

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‎julia-docs/dev/docstrings/src/context.html‎

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@@ -207,6 +207,7 @@ <h2 id="toc-title">On this page</h2>
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<li><a href="#medyan.chem_adddiffusingcount--2264be341b81a600" id="toc-medyan.chem_adddiffusingcount--2264be341b81a600" class="nav-link" data-scroll-target="#medyan.chem_adddiffusingcount--2264be341b81a600"><code>MEDYAN.chem_adddiffusingcount!</code></a></li>
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<li><a href="#medyan.add_diffusing_count--78fc5fd22c94a7fa" id="toc-medyan.add_diffusing_count--78fc5fd22c94a7fa" class="nav-link" data-scroll-target="#medyan.add_diffusing_count--78fc5fd22c94a7fa"><code>MEDYAN.add_diffusing_count!</code></a></li>
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<li><a href="#medyan.chem_addfixedcount--0286edfebf8ea5e6" id="toc-medyan.chem_addfixedcount--0286edfebf8ea5e6" class="nav-link" data-scroll-target="#medyan.chem_addfixedcount--0286edfebf8ea5e6"><code>MEDYAN.chem_addfixedcount!</code></a></li>
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<li><a href="#medyan.add_fixed_count--51020c406ff1afef" id="toc-medyan.add_fixed_count--51020c406ff1afef" class="nav-link" data-scroll-target="#medyan.add_fixed_count--51020c406ff1afef"><code>MEDYAN.add_fixed_count!</code></a></li>
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<li><a href="#medyan.adddiffusingcount_rand--9d3ddfabbceeef92" id="toc-medyan.adddiffusingcount_rand--9d3ddfabbceeef92" class="nav-link" data-scroll-target="#medyan.adddiffusingcount_rand--9d3ddfabbceeef92"><code>MEDYAN.adddiffusingcount_rand!</code></a></li>
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<li><a href="#medyan.addmembranediffusingcount_rand--7b719dca63a36b1b" id="toc-medyan.addmembranediffusingcount_rand--7b719dca63a36b1b" class="nav-link" data-scroll-target="#medyan.addmembranediffusingcount_rand--7b719dca63a36b1b"><code>MEDYAN.addmembranediffusingcount_rand!</code></a></li>
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<li><a href="#medyan.run_chemistry--dda22fac5c555b9e" id="toc-medyan.run_chemistry--dda22fac5c555b9e" class="nav-link" data-scroll-target="#medyan.run_chemistry--dda22fac5c555b9e"><code>MEDYAN.run_chemistry!</code></a></li>
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</div>
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</div>
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</section>
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<section id="medyan.add_fixed_count--51020c406ff1afef" class="level2">
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<h2 class="anchored" data-anchor-id="medyan.add_fixed_count--51020c406ff1afef"><a href="../../docstrings/medyan.add_fixed_count--51020c406ff1afef.html"><code>MEDYAN.add_fixed_count!</code></a></h2>
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<div class="callout callout-style-simple callout-note no-icon">
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<div class="callout-body d-flex">
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<div class="callout-icon-container">
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<i class="callout-icon no-icon"></i>
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</div>
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<div class="callout-body-container">
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb20"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">add_fixed_count!</span>(c<span class="op">::</span><span class="dt">Context</span>; species, chem_voxel, amount)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<p>Add <code>amount</code> to fixed species <code>species</code> in <code>chem_voxel</code>.</p>
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<p>Only user-defined fixed species (from <a href="../../docstrings/medyan.def_fixed_species--490fb150d53e2870.html"><code>def_fixed_species!</code></a>) can be modified. Internally managed fixed species will throw an error.</p>
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</div>
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</div>
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</div>
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</section>
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<section id="medyan.adddiffusingcount_rand--9d3ddfabbceeef92" class="level2">
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<h2 class="anchored" data-anchor-id="medyan.adddiffusingcount_rand--9d3ddfabbceeef92"><a href="../../docstrings/medyan.adddiffusingcount_rand--9d3ddfabbceeef92.html"><code>MEDYAN.adddiffusingcount_rand!</code></a></h2>
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<div class="callout callout-style-simple callout-note no-icon">
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<i class="callout-icon no-icon"></i>
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</div>
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<div class="callout-body-container">
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb20"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a><span class="fu">adddiffusingcount_rand!</span>(c<span class="op">::</span><span class="dt">Context</span>, dsid, inccount)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb21"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="fu">adddiffusingcount_rand!</span>(c<span class="op">::</span><span class="dt">Context</span>, dsid, inccount)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<p>Distribute the added diffusing species count randomly to compartments weighted by volume.</p>
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<ul>
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<li><code>dsid</code>: diffusing species id.</li>
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</div>
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<div class="callout-body-container">
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb21"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="fu">addmembranediffusingcount_rand!</span>(</span>
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<span id="cb21-2"><a href="#cb21-2" aria-hidden="true" tabindex="-1"></a> c<span class="op">::</span><span class="dt">MEDYAN.Context</span>,</span>
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<span id="cb21-3"><a href="#cb21-3" aria-hidden="true" tabindex="-1"></a> membraneindex<span class="op">::</span><span class="dt">Int64</span>,</span>
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<span id="cb21-4"><a href="#cb21-4" aria-hidden="true" tabindex="-1"></a> speciesindex<span class="op">::</span><span class="dt">Int64</span>,</span>
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<span id="cb21-5"><a href="#cb21-5" aria-hidden="true" tabindex="-1"></a> addcount<span class="op">::</span><span class="dt">Int64</span></span>
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<span id="cb21-6"><a href="#cb21-6" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb22"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="fu">addmembranediffusingcount_rand!</span>(</span>
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<span id="cb22-2"><a href="#cb22-2" aria-hidden="true" tabindex="-1"></a> c<span class="op">::</span><span class="dt">MEDYAN.Context</span>,</span>
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<span id="cb22-3"><a href="#cb22-3" aria-hidden="true" tabindex="-1"></a> membraneindex<span class="op">::</span><span class="dt">Int64</span>,</span>
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<span id="cb22-4"><a href="#cb22-4" aria-hidden="true" tabindex="-1"></a> speciesindex<span class="op">::</span><span class="dt">Int64</span>,</span>
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<span id="cb22-5"><a href="#cb22-5" aria-hidden="true" tabindex="-1"></a> addcount<span class="op">::</span><span class="dt">Int64</span></span>
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<span id="cb22-6"><a href="#cb22-6" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<p>Distribute the added membrane species count randomly to membrane cells, ignoring cell area difference. Does NOT update propensity.</p>
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</div>
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<i class="callout-icon no-icon"></i>
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</div>
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<div class="callout-body-container">
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb22"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="fu">run_chemistry!</span>(c<span class="op">::</span><span class="dt">Context</span>, Δt)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb23"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="fu">run_chemistry!</span>(c<span class="op">::</span><span class="dt">Context</span>, Δt)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<p>Run chemistry for Δt time.</p>
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<p>Update c.time.</p>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb23"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb23-1"><a href="#cb23-1" aria-hidden="true" tabindex="-1"></a><span class="fu">defer_chem_caching!</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>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb24"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="fu">defer_chem_caching!</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>
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<p>This should only be used for advanced optimizations.</p>
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<p>During chemistry, the context mutating functions will typically try to avoid invalidating various cached data needed to quickly sample sites.</p>
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<p>However, if you want to mutate the context outside of chemistry, for example right before or after minimization, you may not want to pay the cost of revalidating all the caches because minimization will already invalidate the caches. Caching will be enabled again and caches will be made valid the next time chemistry is run. Caching can also be manually refreshed and reenabled with: <a href="../../docstrings/medyan.refresh_chem_cache--f90ebca1f896ad2c.html"><code>refresh_chem_cache!</code></a></p>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb24"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb24-1"><a href="#cb24-1" aria-hidden="true" tabindex="-1"></a><span class="fu">refresh_chem_cache!</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>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb25"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a><span class="fu">refresh_chem_cache!</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>
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<p>Normally this isn’t needed as it will happen automatically.</p>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb26"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a><span class="fu">is_chem_cache_valid</span>(c<span class="op">::</span><span class="dt">Context</span>)<span class="op">::</span><span class="dt">Bool</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<p>Return true if the chemistry cache is valid, false otherwise.</p>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb26"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb26-1"><a href="#cb26-1" aria-hidden="true" tabindex="-1"></a><span class="fu">empty!</span>(c<span class="op">::</span><span class="dt">Context</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb27"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a><span class="fu">empty!</span>(c<span class="op">::</span><span class="dt">Context</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<p>Remove all filaments, membranes, links, diffusing species, fixed species, bulk species, chemboundary, and mechboundary.</p>
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‎julia-docs/dev/listings.json‎

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"/docstrings/medyan.add_diffusing_count--78fc5fd22c94a7fa.html",
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"/docstrings/medyan.add_diffusion_coeff--a77d1ef833cfdedd.html",
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"/docstrings/medyan.add_filament_params--74c7d0081157ca31.html",
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"/docstrings/medyan.add_fixed_count--51020c406ff1afef.html",
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"/docstrings/medyan.add_membranesitereaction--59d1fe245302e071.html",
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"/docstrings/medyan.adddiffusingcount_rand--9d3ddfabbceeef92.html",
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"/docstrings/medyan.addfilamentendsite--95612d72d1fda05f.html",

‎julia-docs/dev/reference/fileformats.html‎

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<pre class="{julia}"><code>collect(group["chem/fc"])</code></pre>
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<p>Default: Empty</p>
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<p>A 4D array of <code>Int64</code> indexed by [species id, cartesian index] to give count. The count is a fixed point number <code>Q31f32</code> reinterpreted as an integer. To get the count, divide the integers stored by 2^32.</p>
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See <a href="../docstrings/medyan.chem_addfixedcount--0286edfebf8ea5e6.html"><code>MEDYAN.chem_addfixedcount!</code></a>
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See <a href="../docstrings/medyan.add_fixed_count--51020c406ff1afef.html"><code>MEDYAN.add_fixed_count!</code></a>
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</details>
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<details>
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<summary>

‎julia-docs/dev/reference/index.html‎

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<li><p><a href="../docstrings/src/trajectory-io/snapshot.html#medyan.load_snapshot--e534be293ce74465" title="/docstrings/src/trajectory-io/snapshot.qmd#load_snapshot!"><code>load_snapshot!</code></a></p></li>
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<li><p><a href="../docstrings/src/context.html#medyan.add_diffusing_count--78fc5fd22c94a7fa" title="/docstrings/src/context.qmd#add_diffusing_count!"><code>add_diffusing_count!</code></a></p></li>
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<li><p><a href="../docstrings/src/context.html#medyan.chem_addfixedcount--0286edfebf8ea5e6" title="/docstrings/src/context.qmd#chem_addfixedcount!"><code>chem_addfixedcount!</code></a></p></li>
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<li><p><a href="../docstrings/src/context.html#medyan.add_fixed_count--51020c406ff1afef" title="/docstrings/src/context.qmd#add_fixed_count!"><code>add_fixed_count!</code></a></p></li>
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<li><p><a href="../docstrings/src/context.html#medyan.adddiffusingcount_rand--9d3ddfabbceeef92" title="/docstrings/src/context.qmd#adddiffusingcount_rand!"><code>adddiffusingcount_rand!</code></a></p></li>
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<li><p><a href="../docstrings/src/context.html#medyan.set_time--a6dd8f73f68a3759" title="/docstrings/src/context.qmd#set_time!"><code>set_time!</code></a></p></li>
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<li><p><a href="../docstrings/src/context.html#medyan.set_enable_collision--ff3352f0a3c63ab0" title="/docstrings/src/context.qmd#set_enable_collision!"><code>set_enable_collision!</code></a></p></li>

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