build based on d36a8cb

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.8.5","generation_timestamp":"2024-02-26T17:34:25","documenter_version":"1.2.1"}}
+{"documenter":{"julia_version":"1.8.5","generation_timestamp":"2024-02-26T19:09:43","documenter_version":"1.2.1"}}

dev/Input/index.html

@@ -42,4 +42,4 @@
   - kinetics: {A: 2.7590590000000007e-08, Ea: 26459.615999999998, n: 3.802, type: Arrhenius}
     products: [oxygen, octane]
     reactants: ['CCC[CH]CCCC', '[O]O']
-    type: ElementaryReaction</code></pre><p>Dashes <code>-</code> denote the beginning of a new <code>key:value</code> pair.  If done in series as above under <code>Species:</code> and under <code>Reactions:</code> this makes an array of dictionaries.  Colons <code>:</code> denote the beginning of a <code>key:value</code> pair within a dictionary.  Key, value pairs following a dash that do not have a dash themselves are part of the same dictionary.  You can also define dictionaries and lists as normal within Julia within the YAML.  </p><h2 id=".rms-File-Format"><a class="docs-heading-anchor" href="#.rms-File-Format">.rms File Format</a><a id=".rms-File-Format-1"></a><a class="docs-heading-anchor-permalink" href="#.rms-File-Format" title="Permalink"></a></h2><p>In YAML RMS amounts to a dictionary of phase dictionaries.  Each phase dictionary has an entry corresponding to &quot;Species&quot;, &quot;Reactions&quot; and &quot;name&quot;.  The &quot;name&quot; corresponds to the name of the phase.  Within &quot;Species&quot; and &quot;Reactions&quot; are associated lists of dictionaries that correspond to Species and Reaction objects.  Beneath &quot;Species&quot; and &quot;Reactions&quot; the structures all follow the same conventions.  </p><p>Each dictionary is assumed to correspond to an object within RMS that should be denoted by the <code>type</code> key and to have key:value maps that correspond to all necessary parameters to construct the object corresponding to the <code>type</code> value.  Thus, the an Arrhenius rate calculator can be defined as {A: 2.7590590000000007e-08, Ea: 26459.615999999998, n: 3.802, type: Arrhenius}.  In that case RMS knows the object from the <code>type</code> value and what to put in the Arrhenius object from the remaining fields.  Of course for more complex objects some of the values will correspond to objects themselves and thus be dictionaries with their own <code>type</code> values.  </p><p>Units can be defined for specific numerical values in the Unitful format <code>1.0u&quot;m^3</code>.  However, currently molecular units are not supported and thus moles must be used (this restriction applies only to <code>.rms</code> files and not to Chemkin format files).  </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Installation/">« Install Julia</a><a class="docs-footer-nextpage" href="../Simulating/">Simulations »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 26 February 2024 17:34">Monday 26 February 2024</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+    type: ElementaryReaction</code></pre><p>Dashes <code>-</code> denote the beginning of a new <code>key:value</code> pair.  If done in series as above under <code>Species:</code> and under <code>Reactions:</code> this makes an array of dictionaries.  Colons <code>:</code> denote the beginning of a <code>key:value</code> pair within a dictionary.  Key, value pairs following a dash that do not have a dash themselves are part of the same dictionary.  You can also define dictionaries and lists as normal within Julia within the YAML.  </p><h2 id=".rms-File-Format"><a class="docs-heading-anchor" href="#.rms-File-Format">.rms File Format</a><a id=".rms-File-Format-1"></a><a class="docs-heading-anchor-permalink" href="#.rms-File-Format" title="Permalink"></a></h2><p>In YAML RMS amounts to a dictionary of phase dictionaries.  Each phase dictionary has an entry corresponding to &quot;Species&quot;, &quot;Reactions&quot; and &quot;name&quot;.  The &quot;name&quot; corresponds to the name of the phase.  Within &quot;Species&quot; and &quot;Reactions&quot; are associated lists of dictionaries that correspond to Species and Reaction objects.  Beneath &quot;Species&quot; and &quot;Reactions&quot; the structures all follow the same conventions.  </p><p>Each dictionary is assumed to correspond to an object within RMS that should be denoted by the <code>type</code> key and to have key:value maps that correspond to all necessary parameters to construct the object corresponding to the <code>type</code> value.  Thus, the an Arrhenius rate calculator can be defined as {A: 2.7590590000000007e-08, Ea: 26459.615999999998, n: 3.802, type: Arrhenius}.  In that case RMS knows the object from the <code>type</code> value and what to put in the Arrhenius object from the remaining fields.  Of course for more complex objects some of the values will correspond to objects themselves and thus be dictionaries with their own <code>type</code> values.  </p><p>Units can be defined for specific numerical values in the Unitful format <code>1.0u&quot;m^3</code>.  However, currently molecular units are not supported and thus moles must be used (this restriction applies only to <code>.rms</code> files and not to Chemkin format files).  </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Installation/">« Install Julia</a><a class="docs-footer-nextpage" href="../Simulating/">Simulations »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 26 February 2024 19:09">Monday 26 February 2024</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/Installation/index.html

@@ -9,4 +9,4 @@
 ENV["CONDA_JL_HOME"] = PATH_TO_YOUR_ENV        
 Pkg.build("Conda")                             
 ENV["PYTHON"] = PATH_TO_PYTHON                 
-Pkg.build(&quot;PyCall&quot;)                            </code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../Input/">Input »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 26 February 2024 17:34">Monday 26 February 2024</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Pkg.build(&quot;PyCall&quot;)                            </code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../Input/">Input »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 26 February 2024 19:09">Monday 26 February 2024</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/Simulating/index.html

@@ -15,4 +15,4 @@
 println("Using $nthreads threads")
 
 soldict = threadedsensitivities(react,indices; odesolver=react.recommendedsolver,senssolver=react.recommendedsolver,
-        odekwargs=Dict([:abstol=&gt;1e-20,:reltol=&gt;1e-6]),senskwargs=Dict([:abstol=&gt;1e-6,:reltol=&gt;1e-3]))</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Input/">« Input</a><a class="docs-footer-nextpage" href="../Analysis/">Analysis »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 26 February 2024 17:34">Monday 26 February 2024</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+        odekwargs=Dict([:abstol=&gt;1e-20,:reltol=&gt;1e-6]),senskwargs=Dict([:abstol=&gt;1e-6,:reltol=&gt;1e-3]))</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Input/">« Input</a><a class="docs-footer-nextpage" href="../Analysis/">Analysis »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 26 February 2024 19:09">Monday 26 February 2024</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>