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docs(docs): rebuild with more usage examples

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This commit is contained in:
Emily Boudreaux
2025-07-30 15:12:46 -04:00
parent 24870ffcbc
commit cd60ae5c1e
79 changed files with 5050 additions and 4496 deletions
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2
Doxyfile
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@@ -991,7 +991,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.
INPUT = src docs/static/mainpage.md
INPUT = src docs/static/mainpage.md docs/static/usage.md
# This tag can be used to specify the character encoding of the source files
# that Doxygen parses. Internally Doxygen uses the UTF-8 encoding. Doxygen uses

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README.md
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@@ -250,11 +250,29 @@ gridfire::AdaptiveEngineView adaptiveView(baseEngine);
### Python Example
```python
import gridfire
from fourdst.composition import Composition
symbols = ["H-1", ...]
X = [0.708, ...]
comp = Composition()
comp.registerSymbols(symbols)
comp.setMassFraction(X)
comp.finalize(true)
# Initialize GraphEngine with predefined composition
engine = gridfire.GraphEngine(composition="example_composition")
engine = gridfire.GraphEngine(comp)
netIn = gridfire.types.NetIn
netIn.composition = comp
netIn.tMax = 1e-3
netIn.temperature = 1.5e7
netIn.density = 1.6e2
netIn.dt0 = 1e-12
# Perform one integration step
engine.step(dt=1e-3)
print(engine.abundances)
netOut = engine.evaluate(netIn)
print(netOut)
```
## Common Workflow Example
@@ -311,4 +329,4 @@ GridFire integrates with and builds upon several key 4D-STAR libraries:
- [libcomposition](https://github.com/4D-STAR/libcomposition) ([docs](https://4d-star.github.io/libcomposition/)): Composition management toolkit.
- [libconfig](https://github.com/4D-STAR/libconfig): Configuration file parsing utilities.
- [liblogging](https://github.com/4D-STAR/liblogging): Flexible logging framework.
- [libconstants](https://github.com/4D-STAR/libconstants): Physical constants
- [libconstants](https://github.com/4D-STAR/libconstants): Physical constants

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docs/html/classgridfire_1_1_graph_engine-members.html
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@@ -176,9 +176,8 @@ $(function(){initNavTree('classgridfire_1_1_graph_engine.html',''); initResizabl
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197">setUseReverseReactions</a>(bool useReverse)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">syncInternalMaps</a>()</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#a5ac7cff23e70bd07ba7e510b753e2ab6">update</a>(const NetIn &amp;netIn) override</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#aeeafeab40a5f4dbfae78bdc87e25e93f">validateComposition</a>(const fourdst::composition::Composition &amp;composition, double culling, double T9)</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">validateConservation</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
<tr class="odd"><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html#acf4cfccea20f5cb31c9886bf233a28be">validateConservation</a>() const</td><td class="entry"><a class="el" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></td><td class="entry"><span class="mlabel">private</span></td></tr>
<tr class="even"><td class="entry"><a class="el" href="classgridfire_1_1_engine.html#a2e7970bed2100699f226f4141d5db037">~Engine</a>()=default</td><td class="entry"><a class="el" href="classgridfire_1_1_engine.html">gridfire::Engine</a></td><td class="entry"><span class="mlabel">virtual</span></td></tr>
</table></div><!-- contents -->
</div><!-- doc-content -->
<!-- start footer part -->

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@@ -261,9 +261,6 @@ Private Member Functions</h2></td></tr>
<tr class="memitem:acf4cfccea20f5cb31c9886bf233a28be" id="r_acf4cfccea20f5cb31c9886bf233a28be"><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#acf4cfccea20f5cb31c9886bf233a28be">validateConservation</a> () const</td></tr>
<tr class="memdesc:acf4cfccea20f5cb31c9886bf233a28be"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validates mass and charge conservation across all reactions. <br /></td></tr>
<tr class="separator:acf4cfccea20f5cb31c9886bf233a28be"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:aeeafeab40a5f4dbfae78bdc87e25e93f" id="r_aeeafeab40a5f4dbfae78bdc87e25e93f"><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#aeeafeab40a5f4dbfae78bdc87e25e93f">validateComposition</a> (const fourdst::composition::Composition &amp;composition, double culling, double T9)</td></tr>
<tr class="memdesc:aeeafeab40a5f4dbfae78bdc87e25e93f"><td class="mdescLeft">&#160;</td><td class="mdescRight">Validates the composition against the current reaction set. <br /></td></tr>
<tr class="separator:aeeafeab40a5f4dbfae78bdc87e25e93f"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a97f98706b51fbe0d167ed81ffe58c438" id="r_a97f98706b51fbe0d167ed81ffe58c438"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structgridfire_1_1_step_derivatives.html">StepDerivatives</a>&lt; double &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="#a97f98706b51fbe0d167ed81ffe58c438">calculateAllDerivativesUsingPrecomputation</a> (const std::vector&lt; double &gt; &amp;Y_in, const std::vector&lt; double &gt; &amp;bare_rates, const std::vector&lt; double &gt; &amp;bare_reverse_rates, double T9, double rho) const</td></tr>
<tr class="separator:a97f98706b51fbe0d167ed81ffe58c438"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5e96b5a0b34c8932f0e14eabda57f1a4" id="r_a5e96b5a0b34c8932f0e14eabda57f1a4"><td class="memTemplParams" colspan="2">template&lt;IsArithmeticOrAD T&gt; </td></tr>
@@ -358,7 +355,7 @@ Private Attributes</h2></td></tr>
</ul>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="engine__abstract_8h.html" title="Abstract interfaces for reaction network engines in GridFire.">engine_abstract.h</a> </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00101">101</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00100">100</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div><h2 class="groupheader">Constructor &amp; Destructor Documentation</h2>
<a id="afad967546b611d9c005268760feb75d5" name="afad967546b611d9c005268760feb75d5"></a>
<h2 class="memtitle"><span class="permalink"><a href="#afad967546b611d9c005268760feb75d5">&#9670;&#160;</a></span>GraphEngine() <span class="overload">[1/3]</span></h2>
@@ -518,7 +515,7 @@ Private Attributes</h2></td></tr>
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives&lt;ADDouble&gt;</a> containing dY/dt and energy generation rate.</dd></dl>
<p>This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using automatic differentiation. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00616">616</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00594">594</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
</div>
</div>
@@ -566,7 +563,7 @@ Private Attributes</h2></td></tr>
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives&lt;double&gt;</a> containing dY/dt and energy generation rate.</dd></dl>
<p>This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state using double precision arithmetic. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00608">608</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00586">586</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
</div>
</div>
@@ -622,7 +619,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<dl class="section return"><dt>Returns</dt><dd><a class="el" href="structgridfire_1_1_step_derivatives.html" title="Structure holding derivatives and energy generation for a network step.">StepDerivatives&lt;T&gt;</a> containing dY/dt and energy generation rate.</dd></dl>
<p>This method calculates the time derivatives of all species and the specific nuclear energy generation rate for the current state. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00745">745</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00715">715</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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</table>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00470">470</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00448">448</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -724,7 +721,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00645">645</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00623">623</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -786,7 +783,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<dl class="section return"><dt>Returns</dt><dd>Molar flow rate for the reaction (e.g., mol/g/s).</dd></dl>
<p>This method computes the net rate at which the given reaction proceeds under the current state. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00826">826</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00796">796</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00667">667</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00648">648</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00262">262</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00242">242</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00291">291</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00269">269</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00368">368</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00346">346</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00969">969</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00947">947</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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</dl>
<p>Example usage: </p><div class="fragment"><div class="line">engine.exportToCSV(<span class="stringliteral">&quot;network.csv&quot;</span>);</div>
</div><!-- fragment -->
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00810">810</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00788">788</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Example usage: </p><div class="fragment"><div class="line">engine.exportToDot(<span class="stringliteral">&quot;network.dot&quot;</span>);</div>
</div><!-- fragment -->
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00762">762</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00740">740</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a29bdd4231c29c3a4e524ad6ca66a127d">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00654">654</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00632">632</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Reimplemented from <a class="el" href="classgridfire_1_1_dynamic_engine.html#a818d942efa843959393e4eed3263b7e7">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00687">687</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00665">665</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1250,7 +1247,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aeae6d84ef74d88fd2cdf07b82e98a16f">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00567">567</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00545">545</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Reimplemented from <a class="el" href="classgridfire_1_1_dynamic_engine.html#a04317b66ef14d519264bc30ee69f5bf9">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00456">456</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00434">434</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a05d15ff35a6bc06a2fa7eda19838bd07">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00744">744</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00722">722</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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</dl>
<dl class="section return"><dt>Returns</dt><dd>Map of species to their stoichiometric coefficients. </dd></dl>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00749">749</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00727">727</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00641">641</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00619">619</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a7a203f8e0f3a6744ddc912dfbcfdbcc0">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00629">629</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00607">607</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6ca0f315f75252ca505507a61556dda6">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00883">883</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00861">861</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#ad3d56a8b9161b9cc7f4da51f6bf7e8c9">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00417">417</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00395">395</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6772ac384b4c3d3e91712041e4aaa813">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00864">864</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00842">842</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1648,7 +1645,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#afa108dd5227dbb1045e90d7b3bd8b84f">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00755">755</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00733">733</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00637">637</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00615">615</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1740,7 +1737,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a942e65ced17ca602482cc42e469d6398">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00920">920</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00898">898</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00409">409</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00387">387</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1796,7 +1793,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a55f1b7e5ebe2840e1d7c54665ca5411a">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00421">421</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00399">399</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00982">982</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00960">960</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1912,7 +1909,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a21c34f59c080a853fafa38a25175124e">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00429">429</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00407">407</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1945,7 +1942,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Reimplemented from <a class="el" href="classgridfire_1_1_dynamic_engine.html#a4e2c8b896661b7a89beffe0066cb21cf">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00460">460</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00438">438</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -1981,7 +1978,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00924">924</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00902">902</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00633">633</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00611">611</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -2101,7 +2098,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00624">624</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00602">602</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -2120,7 +2117,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00413">413</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00391">391</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -2193,54 +2190,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Implements <a class="el" href="classgridfire_1_1_dynamic_engine.html#aa799ff785e7e79bf35b11efd55f6282a">gridfire::DynamicEngine</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00908">908</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#aeeafeab40a5f4dbfae78bdc87e25e93f">&#9670;&#160;</a></span>validateComposition()</h2>
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<td class="memname">void gridfire::GraphEngine::validateComposition </td>
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<td class="paramtype">const fourdst::composition::Composition &amp;</td> <td class="paramname"><span class="paramname"><em>composition</em></span>, </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>culling</em></span>, </td>
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<td class="paramtype">double</td> <td class="paramname"><span class="paramname"><em>T9</em></span>&#160;)</td>
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<p>Validates the composition against the current reaction set. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">composition</td><td>The composition to validate. </td></tr>
<tr><td class="paramname">culling</td><td>The culling threshold to use. </td></tr>
<tr><td class="paramname">T9</td><td>The temperature to use.</td></tr>
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<p>This method validates the composition against the current reaction set. If the composition is not compatible with the reaction set, the reaction set is rebuilt from the composition. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00242">242</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l00886">886</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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@@ -2296,7 +2246,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00467">467</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00466">466</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00448">448</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00447">447</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00451">451</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00450">450</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2368,7 +2318,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00476">476</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00475">475</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2394,7 +2344,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Full sparsity pattern for the Jacobian matrix. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00465">465</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00464">464</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2420,7 +2370,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Work object for sparse Jacobian calculations. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00464">464</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00463">463</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2446,7 +2396,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Jacobian matrix (species x species). </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00462">462</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00461">461</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2470,7 +2420,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00449">449</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00448">448</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2496,7 +2446,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Vector of unique species in the network. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00456">456</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00455">455</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2522,7 +2472,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Map from species name to Species object. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00457">457</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00456">456</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2548,7 +2498,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Partition function for the network. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00479">479</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00478">478</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2574,7 +2524,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Precomputed reactions for efficiency. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00478">478</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00477">477</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2600,7 +2550,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Map from reaction ID to REACLIBReaction. //PERF: This makes copies of REACLIBReaction and could be a performance bottleneck. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00454">454</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00453">453</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2626,7 +2576,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Set of REACLIB reactions in the network. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00453">453</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00452">452</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>CppAD function for the right-hand side of the ODE. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00463">463</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00462">462</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00470">470</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00469">469</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Screening type for the reaction network. Default to no screening. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00469">469</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00468">468</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Map from species to their index in the stoichiometry matrix. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00458">458</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00457">457</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Stoichiometry matrix (species x reactions). </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00460">460</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00459">459</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p>Flag to enable or disable using precomputed reactions for efficiency. Mathematically, this should not change the results. Generally end users should not need to change this. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00472">472</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00471">471</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -2806,7 +2756,7 @@ template&lt;IsArithmeticOrAD T&gt; </div>
<p>Flag to enable or disable reverse reactions. If false, only forward reactions are considered. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00474">474</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00473">473</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -53,7 +53,6 @@ var classgridfire_1_1_graph_engine =
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@@ -135,7 +135,7 @@ Private Attributes</h2></td></tr>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00406">406</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00409">409</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00408">408</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01091">1091</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01051">1051</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01100">1100</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01078">1078</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01073">1073</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8cpp_source.html#l01051">1051</a> of file <a class="el" href="engine__graph_8cpp_source.html">engine_graph.cpp</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00445">445</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00444">444</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00444">444</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00443">443</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -332,7 +332,7 @@ Private Attributes</h2></td></tr>
<div class="line"><span class="comment">// The integrator will call calculateRHSAndEnergy, etc. on the multiscaleEngine.</span></div>
<div class="line"><span class="keyword">auto</span> Y_initial = multiscaleEngine.mapNetInToMolarAbundanceVector({equilibratedComp, ...});</div>
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<div class="ttc" id="aclassgridfire_1_1_graph_engine_html"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></div><div class="ttdoc">A reaction network engine that uses a graph-based representation.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00100">engine_graph.h:100</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_multiscale_partitioning_engine_view_html"><div class="ttname"><a href="classgridfire_1_1_multiscale_partitioning_engine_view.html">gridfire::MultiscalePartitioningEngineView</a></div><div class="ttdoc">An engine view that partitions the reaction network into multiple groups based on timescales.</div><div class="ttdef"><b>Definition</b> <a href="engine__multiscale_8h_source.html#l00174">engine_multiscale.h:174</a></div></div>
<div class="ttc" id="astructgridfire_1_1_net_in_html"><div class="ttname"><a href="structgridfire_1_1_net_in.html">gridfire::NetIn</a></div><div class="ttdef"><b>Definition</b> <a href="network_8h_source.html#l00053">network.h:53</a></div></div>
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@@ -510,19 +510,19 @@ $(function(){initNavTree('engine_2bindings_8cpp_source.html',''); initResizable(
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<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_ae0c35d8963b6ed05aeb88089ce301718"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#ae0c35d8963b6ed05aeb88089ce301718">gridfire::FileDefinedEngineView::getNetworkFile</a></div><div class="ttdeci">std::string getNetworkFile() const</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00266">engine_defined.h:266</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_file_defined_engine_view_html_aea834dc382ff1d663040db4532ea928f"><div class="ttname"><a href="classgridfire_1_1_file_defined_engine_view.html#aea834dc382ff1d663040db4532ea928f">gridfire::FileDefinedEngineView::getParser</a></div><div class="ttdeci">const io::NetworkFileParser &amp; getParser() const</div><div class="ttdef"><b>Definition</b> <a href="engine__defined_8h_source.html#l00267">engine_defined.h:267</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a015f8975701f028c29835d3a9794e00f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">gridfire::GraphEngine::isPrecomputationEnabled</a></div><div class="ttdeci">bool isPrecomputationEnabled() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00637">engine_graph.cpp:637</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a01fc9fd5d576b66d07360d05e821c755"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755">gridfire::GraphEngine::calculateReverseRateTwoBody</a></div><div class="ttdeci">double calculateReverseRateTwoBody(const reaction::Reaction &amp;reaction, const double T9, const double forwardRate, const double expFactor) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00291">engine_graph.cpp:291</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a0b7b85f824e1021ae6e56b644db53b28"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28">gridfire::GraphEngine::calculateReverseRate</a></div><div class="ttdeci">double calculateReverseRate(const reaction::Reaction &amp;reaction, double T9) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00262">engine_graph.cpp:262</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a409991d527ea4d4b05d1af907fe5d197"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197">gridfire::GraphEngine::setUseReverseReactions</a></div><div class="ttdeci">void setUseReverseReactions(bool useReverse)</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00413">engine_graph.cpp:413</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a6c5410878496abc349ba30b691cdf0f1"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">gridfire::GraphEngine::setPrecomputation</a></div><div class="ttdeci">void setPrecomputation(bool precompute)</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00633">engine_graph.cpp:633</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a832e2fe066381811a3e0464806ff5e95"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">gridfire::GraphEngine::exportToCSV</a></div><div class="ttdeci">void exportToCSV(const std::string &amp;filename) const</div><div class="ttdoc">Exports the network to a CSV file for analysis.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00810">engine_graph.cpp:810</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8c29d8bbde407e913be5eb77efb2c0c9"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">gridfire::GraphEngine::getNetReactionStoichiometry</a></div><div class="ttdeci">static std::unordered_map&lt; fourdst::atomic::Species, int &gt; getNetReactionStoichiometry(const reaction::Reaction &amp;reaction)</div><div class="ttdoc">Gets the net stoichiometry for a given reaction.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00749">engine_graph.cpp:749</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a015f8975701f028c29835d3a9794e00f"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a015f8975701f028c29835d3a9794e00f">gridfire::GraphEngine::isPrecomputationEnabled</a></div><div class="ttdeci">bool isPrecomputationEnabled() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00615">engine_graph.cpp:615</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a01fc9fd5d576b66d07360d05e821c755"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755">gridfire::GraphEngine::calculateReverseRateTwoBody</a></div><div class="ttdeci">double calculateReverseRateTwoBody(const reaction::Reaction &amp;reaction, const double T9, const double forwardRate, const double expFactor) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00269">engine_graph.cpp:269</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a0b7b85f824e1021ae6e56b644db53b28"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28">gridfire::GraphEngine::calculateReverseRate</a></div><div class="ttdeci">double calculateReverseRate(const reaction::Reaction &amp;reaction, double T9) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00242">engine_graph.cpp:242</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a409991d527ea4d4b05d1af907fe5d197"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197">gridfire::GraphEngine::setUseReverseReactions</a></div><div class="ttdeci">void setUseReverseReactions(bool useReverse)</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00391">engine_graph.cpp:391</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a6c5410878496abc349ba30b691cdf0f1"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">gridfire::GraphEngine::setPrecomputation</a></div><div class="ttdeci">void setPrecomputation(bool precompute)</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00611">engine_graph.cpp:611</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a832e2fe066381811a3e0464806ff5e95"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a832e2fe066381811a3e0464806ff5e95">gridfire::GraphEngine::exportToCSV</a></div><div class="ttdeci">void exportToCSV(const std::string &amp;filename) const</div><div class="ttdoc">Exports the network to a CSV file for analysis.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00788">engine_graph.cpp:788</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_a8c29d8bbde407e913be5eb77efb2c0c9"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#a8c29d8bbde407e913be5eb77efb2c0c9">gridfire::GraphEngine::getNetReactionStoichiometry</a></div><div class="ttdeci">static std::unordered_map&lt; fourdst::atomic::Species, int &gt; getNetReactionStoichiometry(const reaction::Reaction &amp;reaction)</div><div class="ttdoc">Gets the net stoichiometry for a given reaction.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00727">engine_graph.cpp:727</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_aa6202cee0c3c481eda77cc9a91bc126b"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#aa6202cee0c3c481eda77cc9a91bc126b">gridfire::GraphEngine::involvesSpecies</a></div><div class="ttdeci">bool involvesSpecies(const fourdst::atomic::Species &amp;species) const</div><div class="ttdoc">Checks if a given species is involved in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00179">engine_graph.cpp:179</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad049a295e2bb0f3e97b76d5742875119"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">gridfire::GraphEngine::generateJacobianMatrix</a></div><div class="ttdeci">void generateJacobianMatrix(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</div><div class="ttdoc">Generates the Jacobian matrix for the current state.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00654">engine_graph.cpp:654</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_adac8c7d62bae76e17fc060e86dadd929"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">gridfire::GraphEngine::exportToDot</a></div><div class="ttdeci">void exportToDot(const std::string &amp;filename) const</div><div class="ttdoc">Exports the network to a DOT file for visualization.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00762">engine_graph.cpp:762</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_add98ece49ec5c538bddf3cc77004fe44"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#add98ece49ec5c538bddf3cc77004fe44">gridfire::GraphEngine::getPartitionFunction</a></div><div class="ttdeci">const partition::PartitionFunction &amp; getPartitionFunction() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00641">engine_graph.cpp:641</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ae7a210d9ab13ad5fb0c612f027acabd0"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ae7a210d9ab13ad5fb0c612f027acabd0">gridfire::GraphEngine::isUsingReverseReactions</a></div><div class="ttdeci">bool isUsingReverseReactions() const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00409">engine_graph.cpp:409</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_af28950c5af3a92eb03a1a64ed0f913e7"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7">gridfire::GraphEngine::calculateReverseRateTwoBodyDerivative</a></div><div class="ttdeci">double calculateReverseRateTwoBodyDerivative(const reaction::Reaction &amp;reaction, const double T9, const double reverseRate) const</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00368">engine_graph.cpp:368</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_ad049a295e2bb0f3e97b76d5742875119"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#ad049a295e2bb0f3e97b76d5742875119">gridfire::GraphEngine::generateJacobianMatrix</a></div><div class="ttdeci">void generateJacobianMatrix(const std::vector&lt; double &gt; &amp;Y_dynamic, const double T9, const double rho) const override</div><div class="ttdoc">Generates the Jacobian matrix for the current state.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00632">engine_graph.cpp:632</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html_adac8c7d62bae76e17fc060e86dadd929"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html#adac8c7d62bae76e17fc060e86dadd929">gridfire::GraphEngine::exportToDot</a></div><div class="ttdeci">void exportToDot(const std::string &amp;filename) const</div><div class="ttdoc">Exports the network to a DOT file for visualization.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8cpp_source.html#l00740">engine_graph.cpp:740</a></div></div>
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<div class="ttc" id="aclassgridfire_1_1_multiscale_partitioning_engine_view_html_a1e04e8cb8c84b1bd033ac599accf0888"><div class="ttname"><a href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1e04e8cb8c84b1bd033ac599accf0888">gridfire::MultiscalePartitioningEngineView::getDynamicSpecies</a></div><div class="ttdeci">const std::vector&lt; fourdst::atomic::Species &gt; &amp; getDynamicSpecies() const</div><div class="ttdoc">Gets the dynamic species in the network.</div><div class="ttdef"><b>Definition</b> <a href="engine__multiscale_8cpp_source.html#l00789">engine_multiscale.cpp:789</a></div></div>
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AdaptiveEngineView Example</h2>

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<p><img src="../../assets/logo/GridFire.png" alt="GridFire Logo" class="inline"/></p>
<hr />
<p>GridFire is a C++ library designed to perform general nuclear network evolution using the Reaclib library. It is part of the larger SERiF project within the 4D-STAR collaboration.</p>
<p><b>Design Philosophy and Workflow:</b> GridFire is architected to balance physical fidelity, computational efficiency, and extensibility when simulating complex nuclear reaction networks. Users begin by defining a composition, which is used to construct a full GraphEngine representation of the reaction network. To manage the inherent stiffness and multi-scale nature of these networks, GridFire employs a layered view strategy: partitioning algorithms isolate fast and slow processes, adaptive culling removes negligible reactions at runtime, and implicit solvers stably integrate the remaining stiff system. This modular pipeline allows researchers to tailor accuracy versus performance trade-offs, reuse common engine components, and extend screening or partitioning models without modifying core integration routines.</p>
<p> GridFire is a C++ library designed to perform general nuclear network evolution using the Reaclib library. It is part of the larger SERiF project within the 4D-STAR collaboration. GridFire is primarily focused on modeling the most relevant burning stages for stellar evolution modeling. Currently, there is limited support for inverse reactions. Therefore, GridFire has a limited set of tools to evolves a fusing plasma in NSE; however, this is not the primary focus of the library and has therefor not had significant development. For those interested in modeling super nova, neutron star mergers, or other high-energy astrophysical phenomena, we <b>strongly</b> recomment using <a href="https://bitbucket.org/jlippuner/skynet/src/master/">SkyNet</a>.</p>
<p><b>Design Philosophy and Workflow:</b> GridFire is architected to balance physical fidelity, computational efficiency, and extensibility when simulating complex nuclear reaction networks. Users begin by defining a composition, which is used to construct a full GraphEngine representation of the reaction network. To manage the inherent stiffness and multiscale nature of these networks, GridFire employs a layered view strategy: partitioning algorithms isolate fast and slow processes, adaptive culling removes negligible reactions at runtime, and implicit solvers stably integrate the remaining stiff system. This modular pipeline allows researchers to tailor accuracy versus performance trade-offs, reuse common engine components, and extend screening or partitioning models without modifying core integration routines.</p>
<h2><a class="anchor" id="autotoc_md1"></a>
Funding</h2>
<p>GridFire is a part of the 4D-STAR collaboration.</p>
<p>4D-STAR is funded by European Research Council (ERC) under the Horizon Europe programme (Synergy Grant agreement No. 101071505: 4D-STAR) Work for this project is funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research.</p>
<p>4D-STAR is funded by European Research Council (ERC) under the Horizon Europe programme (Synergy Grant agreement No. 101071505: 4D-STAR) Work for this project is funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council.</p>
<h2><a class="anchor" id="autotoc_md2"></a>
Build and Installation Instructions</h2>
<h3><a class="anchor" id="autotoc_md3"></a>
@@ -123,8 +123,10 @@ Prerequisites</h3>
<li>Boost libraries (&gt;= 1.75.0) installed system-wide</li>
</ul>
<blockquote class="doxtable">
<p>Note: Boost is the only external library dependency; no additional libraries are required beyond a C++ compiler, Meson, Python, and Boost.</p>
<p>Windows is not supported at this time. </p>
<p><b>Note:</b> Boost is the only external library dependency; no additional libraries are required beyond a C++ compiler, Meson, Python, and Boost. </p>
</blockquote>
<blockquote class="doxtable">
<p><b>Note:</b> Windows is not supported at this time and <em>there are no plans to support it in the future</em>. Windows users are encouraged to use WSL2 or a Linux VM. </p>
</blockquote>
<h3><a class="anchor" id="autotoc_md4"></a>
Dependency Installation on Common Platforms</h3>
@@ -161,13 +163,16 @@ Developer Workflow</h3>
</ol>
<h2><a class="anchor" id="autotoc_md9"></a>
Code Architecture and Logical Flow</h2>
<p>GridFire is organized into modular components that collaborate to simulate nuclear reaction networks with high fidelity:</p>
<p>GridFire is organized into a series of composable modules, each responsible for a specific aspect of nuclear reaction network modeling. The core components include:</p>
<ul>
<li><b>Engine Module:</b> Core interfaces and implementations (e.g., <code>GraphEngine</code>) that evaluate reaction network rate equations and energy generation.</li>
<li><b>Screening Module:</b> Implements nuclear reaction screening corrections (<code>WeakScreening</code>, <code>BareScreening</code>, etc.) affecting reaction rates.</li>
<li><b>Rates Module:</b> Parses and manages Reaclib reaction rate data, providing temperature- and density-dependent rate evaluations.</li>
<li><b>Python Interface:</b> Exposes C++ functionality to Python, enabling rapid prototyping and integration into workflows.</li>
<li><b>Reaction Module:</b> Parses and manages Reaclib reaction rate data, providing temperature- and density-dependent rate evaluations.</li>
<li><b>Partition Module:</b> Implements partition functions (e.g., <code>GroundStatePartitionFunction</code>, <code>RauscherThielemannPartitionFunction</code>) to weight reaction rates based on nuclear properties.</li>
<li><b>Solver Module:</b> Defines numerical integration strategies (e.g., <code>DirectNetworkSolver</code>) for solving the stiff ODE systems arising from reaction networks.</li>
<li><b>Python Interface:</b> Exposes <em>almost</em> all C++ functionality to Python, allowing users to define compositions, configure engines, and run simulations directly from Python scripts.</li>
</ul>
<p>Generally a user will start by selecting a base engine (currently we only offer <code>GraphEngine</code>), which constructs the full reaction network graph from a given composition. The user can then apply various engine views to adapt the network topology, such as partitioning fast and slow reactions, adaptively culling low-flow pathways, or priming the network with specific species. Finally, a numerical solver is selected to integrate the network over time, producing updated abundances and diagnostics.</p>
<h3><a class="anchor" id="autotoc_md10"></a>
GraphEngine Configuration Options</h3>
<p>GraphEngine exposes runtime configuration methods to tailor network construction and rate evaluations:</p>
@@ -269,7 +274,7 @@ C++ Example: GraphEngine Initialization</h3>
<div class="line"><span class="comment">// Define a composition and initialize the engine</span></div>
<div class="line">fourdst::composition::Composition comp;</div>
<div class="line"><a class="code hl_class" href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a> engine(comp);</div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></div><div class="ttdoc">A reaction network engine that uses a graph-based representation.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00101">engine_graph.h:101</a></div></div>
<div class="ttc" id="aclassgridfire_1_1_graph_engine_html"><div class="ttname"><a href="classgridfire_1_1_graph_engine.html">gridfire::GraphEngine</a></div><div class="ttdoc">A reaction network engine that uses a graph-based representation.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00100">engine_graph.h:100</a></div></div>
<div class="ttc" id="aengine__graph_8h_html"><div class="ttname"><a href="engine__graph_8h.html">engine_graph.h</a></div></div>
</div><!-- fragment --><h3><a class="anchor" id="autotoc_md19"></a>
C++ Example: Adaptive Network View</h3>
@@ -285,12 +290,31 @@ C++ Example: Adaptive Network View</h3>
</div><!-- fragment --><h3><a class="anchor" id="autotoc_md20"></a>
Python Example</h3>
<div class="fragment"><div class="line"><span class="keyword">import</span> gridfire</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="keyword">from</span> fourdst.composition <span class="keyword">import</span> Composition</div>
<div class="line"> </div>
<div class="line">symbols = [<span class="stringliteral">&quot;H-1&quot;</span>, ...]</div>
<div class="line">X = [0.708, ...]</div>
<div class="line"> </div>
<div class="line">comp = Composition()</div>
<div class="line">comp.registerSymbols(symbols)</div>
<div class="line">comp.setMassFraction(X)</div>
<div class="line">comp.finalize(true)</div>
<div class="line"><span class="comment"># Initialize GraphEngine with predefined composition</span></div>
<div class="line">engine = <a class="code hl_class" href="classgridfire_1_1_graph_engine.html">gridfire.GraphEngine</a>(composition=<span class="stringliteral">&quot;example_composition&quot;</span>)</div>
<div class="line">engine = <a class="code hl_class" href="classgridfire_1_1_graph_engine.html">gridfire.GraphEngine</a>(comp)</div>
<div class="line">netIn = gridfire.types.NetIn</div>
<div class="line">netIn.composition = comp</div>
<div class="line">netIn.tMax = 1e-3</div>
<div class="line">netIn.temperature = 1.5e7</div>
<div class="line">netIn.density = 1.6e2</div>
<div class="line">netIn.dt0 = 1e-12</div>
<div class="line"> </div>
<div class="line"><span class="comment"># Perform one integration step</span></div>
<div class="line">engine.step(dt=1e-3)</div>
<div class="line">print(engine.abundances)</div>
</div><!-- fragment --><h2><a class="anchor" id="autotoc_md21"></a>
<div class="line">netOut = engine.evaluate(netIn)</div>
<div class="line">print(netOut)</div>
</div><!-- fragment --><p>More detailed python usage can be found <a class="el" href="md_docs_2static_2usage.html">here</a></p>
<h2><a class="anchor" id="autotoc_md21"></a>
Common Workflow Example</h2>
<p>A representative workflow often composes multiple engine views to balance accuracy, stability, and performance when integrating stiff nuclear networks:</p>
<div class="fragment"><div class="line"><span class="preprocessor">#include &quot;<a class="code" href="engine__graph_8h.html">gridfire/engine/engine_graph.h</a>&quot;</span></div>

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<div class="textblock"><p><a class="anchor" id="autotoc_md23"></a></p>
<p>This tutorial walks you through installing GridFire’s Python bindings, choosing engines and views thoughtfully, running a simulation, and visualizing your results.</p>
<hr />
<h1><a class="anchor" id="autotoc_md25"></a>
1. Installation</h1>
<h2><a class="anchor" id="autotoc_md26"></a>
1.1 PyPI Release</h2>
<p>The quickest way to get started is: </p><div class="fragment"><div class="line">pip install gridfire</div>
</div><!-- fragment --><h2><a class="anchor" id="autotoc_md27"></a>
1.2 Development from Source</h2>
<p>If you want the cutting-edge features or need to hack the C++ backend: </p><div class="fragment"><div class="line">git clone https://github.com/4DSTAR/GridFire.git</div>
<div class="line">cd GridFire</div>
<div class="line"># Create a virtualenv to isolate dependencies</div>
<div class="line">python3 -m venv .venv &amp;&amp; source .venv/bin/activate</div>
<div class="line"> </div>
<div class="line"># Install Python bindings (meson-python &amp; pybind11 under the hood)</div>
<div class="line">pip install .</div>
</div><!-- fragment --><p>You can also build manually with Meson (generally end users will not need to do this): </p><div class="fragment"><div class="line">meson setup build-python</div>
<div class="line">meson compile -C build_gridfire</div>
</div><!-- fragment --><hr />
<h1><a class="anchor" id="autotoc_md29"></a>
2. Why These Engines and Views?</h1>
<p>GridFire’s design balances physical fidelity and performance. Here’s why we pick each component:</p>
<ol type="1">
<li><b>GraphEngine</b>: Constructs the <b>full</b> reaction network from Reaclib rates and composition. Use this when:<ul>
<li>You need maximum physical accuracy (no reactions are omitted). <br />
</li>
<li>You are exploring new burning pathways or validating against literature. <br />
</li>
</ul>
</li>
<li><b>MultiscalePartitioningEngineView</b>: Implements the Hix &amp; Thielemann partitioning strategy:<ul>
<li><b>Fast reactions</b> vs <b>slow reactions</b> are split onto separate kernels. <br />
</li>
<li>This reduces stiffness by isolating processes on very different timescales. <br />
</li>
<li>Choose when your network spans orders of magnitude in timescales (e.g., rapid proton captures vs. slow beta decays). <br />
</li>
</ul>
</li>
<li><b>AdaptiveEngineView</b>: Dynamically culls low-flow reactions at runtime:<ul>
<li>At each timestep, reactions with negligible contribution are temporarily removed. <br />
</li>
<li>This greatly accelerates large networks without significant loss of accuracy. <br />
</li>
<li>Ideal for long integrations where the active set evolves over time. <br />
</li>
</ul>
</li>
<li><b>Leading-Edge Views</b>: <br />
<ul>
<li><code>NetworkPrimingEngineView</code> to inject seed species and study ignition phenomena. <br />
</li>
<li><code>DefinedEngineView</code> to freeze the network to a user-specified subset (e.g., focus on the CNO cycle). <br />
</li>
</ul>
</li>
</ol>
<p>By composing these views in sequence, you can tailor accuracy vs performance for your scientific question. Commonly one might use a flow like <b>GraphEngine → Partitioning → Adaptive</b> to capture both full-network physics and manageable stiffness.</p>
<hr />
<h1><a class="anchor" id="autotoc_md31"></a>
3. Step-by-Step Example</h1>
<p>Adapted from <a href="../../tests/python/test.py"><code>tests/python/test.py</code></a>. Comments explain each choice.</p>
<div class="fragment"><div class="line"><span class="keyword">import</span> matplotlib.pyplot <span class="keyword">as</span> plt</div>
<div class="line"><span class="keyword">from</span> gridfire.engine <span class="keyword">import</span> GraphEngine, MultiscalePartitioningEngineView, AdaptiveEngineView</div>
<div class="line"><span class="keyword">from</span> <a class="code hl_namespace" href="namespacegridfire_1_1solver.html">gridfire.solver</a> <span class="keyword">import</span> DirectNetworkSolver</div>
<div class="line"><span class="keyword">from</span> gridfire.type <span class="keyword">import</span> NetIn</div>
<div class="line"><span class="keyword">from</span> fourdst.composition <span class="keyword">import</span> Composition</div>
<div class="line"> </div>
<div class="line"><span class="comment"># 1. Define your composition (e.g., M-dwarf surface mix)</span></div>
<div class="line">symbols = [<span class="stringliteral">&quot;H-1&quot;</span>,<span class="stringliteral">&quot;He-3&quot;</span>,<span class="stringliteral">&quot;He-4&quot;</span>,<span class="stringliteral">&quot;C-12&quot;</span>,<span class="stringliteral">&quot;N-14&quot;</span>,<span class="stringliteral">&quot;O-16&quot;</span>,<span class="stringliteral">&quot;Ne-20&quot;</span>,<span class="stringliteral">&quot;Mg-24&quot;</span>]</div>
<div class="line">abundances = [0.708,2.94e-5,0.276,0.003,0.0011,9.62e-3,1.62e-3,5.16e-4]</div>
<div class="line">comp = Composition()</div>
<div class="line">comp.registerSymbols(symbols)</div>
<div class="line">comp.setMassFraction(symbols, abundances)</div>
<div class="line">comp.finalize(normalize=<span class="keyword">True</span>) <span class="comment"># scale to total mass = 1</span></div>
<div class="line"> </div>
<div class="line"><span class="comment"># 2. Prepare the NetIn object</span></div>
<div class="line">netIn = NetIn()</div>
<div class="line">netIn.composition = comp</div>
<div class="line">netIn.temperature = 1.5e7 <span class="comment"># Kelvin</span></div>
<div class="line">netIn.density = 1.6e2 <span class="comment"># g/cm³</span></div>
<div class="line">netIn.tMax = 3.15e7 <span class="comment"># seconds to evolve (~1yr)</span></div>
<div class="line">netIn.dt0 = 1e-12 <span class="comment"># initial timestep</span></div>
<div class="line"> </div>
<div class="line"><span class="comment"># 3. Construct the full network engine</span></div>
<div class="line">build_depth = 2 <span class="comment"># shallow test network for speed; Full = -1</span></div>
<div class="line">baseEngine = GraphEngine(comp, buildDepth=build_depth)</div>
<div class="line">baseEngine.setUseReverseReactions(<span class="keyword">False</span>) <span class="comment"># At these temps we can turn off reverse reactions</span></div>
<div class="line"> </div>
<div class="line"><span class="comment"># 4. Partition fast/slow reactions (reduces stiffness)</span></div>
<div class="line">partitionedEngine = MultiscalePartitioningEngineView(baseEngine)</div>
<div class="line"> </div>
<div class="line"><span class="comment"># 5. Adaptively cull negligible flows (improves speed)</span></div>
<div class="line">adaptiveEngine = AdaptiveEngineView(partitionedEngine)</div>
<div class="line"> </div>
<div class="line"><span class="comment"># 6. Choose an ODE solver (implicit Rosenbrock4)</span></div>
<div class="line">solver = DirectNetworkSolver(adaptiveEngine, absTol=1e-12, relTol=1e-8)</div>
<div class="line"> </div>
<div class="line"><span class="comment"># 7. Run the integration</span></div>
<div class="line"> </div>
<div class="line">netOut = solver.evaluate(netIn)</div>
<div class="line"> </div>
<div class="line"><span class="comment"># 8. Final result:</span></div>
<div class="line">print(f<span class="stringliteral">&quot;Final H-1 fraction: {netOut.composition.getMassFraction(&#39;H-1&#39;)}&quot;</span>)</div>
<div class="ttc" id="anamespacegridfire_1_1solver_html"><div class="ttname"><a href="namespacegridfire_1_1solver.html">gridfire::solver</a></div><div class="ttdef"><b>Definition</b> <a href="solver_8h_source.html#l00015">solver.h:15</a></div></div>
</div><!-- fragment --><p><b>Why these choices?</b> <br />
</p><ul>
<li><b>buildDepth=2</b>: In Emily’s preliminary tests, depth=2 captures key reaction loops without the overhead of a full network. <br />
</li>
<li><b>Partition &amp; Adaptive Views</b>: Partitioning reduces stiffness between rapid charged-particle captures and slower β-decays; adaptive culling keeps the working set minimal. <br />
</li>
<li><b>Implicit solver</b>: Rosenbrock4 handles stiff systems robustly, letting you push to longer <code>tMax</code>.</li>
</ul>
<hr />
<h1><a class="anchor" id="autotoc_md33"></a>
4. Visualizing Reaction Networks</h1>
<p>GridFire engines and views provide built-in export methods for Graphviz DOT and CSV formats:</p>
<div class="fragment"><div class="line"><span class="comment"># Export the base network to DOT for Graphviz</span></div>
<div class="line">baseEngine.exportToDot(<span class="stringliteral">&#39;network.dot&#39;</span>)</div>
<div class="line"><span class="comment"># Optionally generate a PNG (shell):</span></div>
<div class="line"><span class="comment"># dot -Tpng network.dot -o network.png</span></div>
<div class="line"> </div>
<div class="line"><span class="comment"># Export a partitioned view of the network</span></div>
<div class="line">partitionedEngine.exportToDot(<span class="stringliteral">&#39;partitioned.dot&#39;</span>)</div>
<div class="line"> </div>
<div class="line"><span class="comment"># Export to CSV for programmatic analysis</span></div>
<div class="line">baseEngine.exportToCSV(<span class="stringliteral">&#39;network.csv&#39;</span>)</div>
</div><!-- fragment --><p> You can then use tools like Graphviz or pandas: </p><div class="fragment"><div class="line"># Convert DOT to PNG</div>
<div class="line">dot -Tpng network.dot -o network.png</div>
</div><!-- fragment --> <div class="fragment"><div class="line"><span class="keyword">import</span> pandas <span class="keyword">as</span> pd</div>
<div class="line"> </div>
<div class="line"><span class="comment"># Load and inspect reaction list</span></div>
<div class="line">df = pd.read_csv(<span class="stringliteral">&#39;network.csv&#39;</span>)</div>
<div class="line">print(df.head())</div>
</div><!-- fragment --><p> For time-series data, record intermediates with an observer and save with pandas or numpy: </p><div class="fragment"><div class="line"><span class="keyword">import</span> pandas <span class="keyword">as</span> pd</div>
<div class="line"> </div>
<div class="line"><span class="comment"># Build a DataFrame of time vs species fraction</span></div>
<div class="line">df = pd.DataFrame({<span class="stringliteral">&#39;time&#39;</span>: t, <span class="stringliteral">&#39;H-1&#39;</span>: X_H1})</div>
<div class="line">df.to_csv(<span class="stringliteral">&#39;H1_evolution.csv&#39;</span>, index=<span class="keyword">False</span>)</div>
</div><!-- fragment --><p> Then plot in pandas or Excel for custom figures.</p>
<hr />
<h1><a class="anchor" id="autotoc_md35"></a>
5. Beyond the Basics</h1>
<ul>
<li><b>Custom Partition Functions</b>: In Python, subclass <code><a class="el" href="classgridfire_1_1partition_1_1_partition_function.html" title="Abstract interface for evaluating nuclear partition functions.">gridfire.partition.PartitionFunction</a></code>, override <code>evaluate</code>, <code>supports</code>, and <code>clone</code> to implement new weighting schemes. <br />
</li>
<li><b>Parameter Studies</b>: Loop over <code>buildDepth</code>, solver tolerances, or initial compositions to get a sense of the sensitity of the network to input conditions or build a monte carlo grid. <br />
</li>
<li><b>Error Handling</b>: <div class="fragment"><div class="line"><span class="keywordflow">try</span>:</div>
<div class="line"> results = solver.evaluate(netIn)</div>
<div class="line"><span class="keywordflow">except</span> GridFireRuntimeError <span class="keyword">as</span> e:</div>
<div class="line"> print(<span class="stringliteral">&#39;Fatal engine error:&#39;</span>, e)</div>
<div class="line"><span class="keywordflow">except</span> GridFireValueError <span class="keyword">as</span> e:</div>
<div class="line"> print(<span class="stringliteral">&#39;Invalid input:&#39;</span>, e)</div>
</div><!-- fragment --></li>
</ul>
<p>For full API details, consult the docstrings in <code>src/python/</code> and the C++ implementation in <code>src/lib/</code>. Enjoy exploring nuclear astrophysics with GridFire! </p>
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<p>Alias for CppAD AD type for double precision. </p>
<p>This alias simplifies the use of the CppAD automatic differentiation type. </p>
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<p>Minimum abundance threshold below which species are ignored. </p>
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<p>Minimum density threshold below which reactions are ignored. </p>
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<p>Minimum value for Jacobian matrix entries. </p>
<p>Jacobian matrix entries with absolute values below this threshold are treated as zero to maintain sparsity and improve performance. </p>
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@@ -358,7 +358,7 @@ $(function(){initNavTree('solver_8cpp_source.html',''); initResizable(true); });
<div class="ttc" id="aengine__graph_8h_html"><div class="ttname"><a href="engine__graph_8h.html">engine_graph.h</a></div></div>
<div class="ttc" id="aerror__engine_8h_html"><div class="ttname"><a href="error__engine_8h.html">error_engine.h</a></div></div>
<div class="ttc" id="anamespacegridfire_1_1solver_html"><div class="ttname"><a href="namespacegridfire_1_1solver.html">gridfire::solver</a></div><div class="ttdef"><b>Definition</b> <a href="solver_8h_source.html#l00015">solver.h:15</a></div></div>
<div class="ttc" id="anamespacegridfire_html_a96c062f94713921e5d7568ecedcdcb06"><div class="ttname"><a href="namespacegridfire.html#a96c062f94713921e5d7568ecedcdcb06">gridfire::MIN_ABUNDANCE_THRESHOLD</a></div><div class="ttdeci">static constexpr double MIN_ABUNDANCE_THRESHOLD</div><div class="ttdoc">Minimum abundance threshold below which species are ignored.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00067">engine_graph.h:67</a></div></div>
<div class="ttc" id="anamespacegridfire_html_a96c062f94713921e5d7568ecedcdcb06"><div class="ttname"><a href="namespacegridfire.html#a96c062f94713921e5d7568ecedcdcb06">gridfire::MIN_ABUNDANCE_THRESHOLD</a></div><div class="ttdeci">static constexpr double MIN_ABUNDANCE_THRESHOLD</div><div class="ttdoc">Minimum abundance threshold below which species are ignored.</div><div class="ttdef"><b>Definition</b> <a href="engine__graph_8h_source.html#l00066">engine_graph.h:66</a></div></div>
<div class="ttc" id="anetwork_8h_html"><div class="ttname"><a href="network_8h.html">network.h</a></div></div>
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<div class="ttc" id="astructgridfire_1_1_net_in_html"><div class="ttname"><a href="structgridfire_1_1_net_in.html">gridfire::NetIn</a></div><div class="ttdef"><b>Definition</b> <a href="network_8h_source.html#l00053">network.h:53</a></div></div>

20
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@@ -132,7 +132,7 @@ Public Attributes</h2></td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00385">385</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00384">384</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a3e2e67e532970738d20491ea56b170f3">&#9670;&#160;</a></span>affected_species_indices</h2>
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<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00390">390</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div>
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@@ -164,7 +164,7 @@ Public Attributes</h2></td></tr>
<p>Powers of each unique product in the reverse reaction. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00396">396</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00395">395</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div>
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@@ -180,7 +180,7 @@ Public Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00389">389</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00388">388</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div>
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@@ -196,7 +196,7 @@ Public Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00387">387</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00386">386</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div>
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@@ -214,7 +214,7 @@ Public Attributes</h2></td></tr>
<p>Symmetry factor for reverse reactions. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00397">397</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00396">396</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div>
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@@ -230,7 +230,7 @@ Public Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00392">392</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00391">391</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div>
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@@ -246,7 +246,7 @@ Public Attributes</h2></td></tr>
</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00390">390</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00389">389</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div>
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@@ -264,7 +264,7 @@ Public Attributes</h2></td></tr>
<p>Unique product indices for reverse reactions. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00395">395</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00394">394</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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</table>
</div><div class="memdoc">
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00388">388</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00387">387</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -123,7 +123,7 @@ Public Attributes</h2></td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock">
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00400">400</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00399">399</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div><h2 class="groupheader">Member Data Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a8bea6e348699c1aea93d17bb56739306">&#9670;&#160;</a></span>c</h2>
@@ -139,7 +139,7 @@ Public Attributes</h2></td></tr>
<p>Speed of light in cm/s. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00403">403</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00402">402</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
</div>
</div>
@@ -157,7 +157,7 @@ Public Attributes</h2></td></tr>
<p>Boltzmann constant in erg/K. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00404">404</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00403">403</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -175,7 +175,7 @@ Public Attributes</h2></td></tr>
<p>Avogadro's number. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00402">402</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00401">401</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -193,7 +193,7 @@ Public Attributes</h2></td></tr>
<p>Atomic mass unit in g. </p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00401">401</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
<p class="definition">Definition at line <a class="el" href="engine__graph_8h_source.html#l00400">400</a> of file <a class="el" href="engine__graph_8h_source.html">engine_graph.h</a>.</p>
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@@ -0,0 +1,115 @@
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<div id="projectname">GridFire<span id="projectnumber">&#160;0.0.1a</span>
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<div id="projectbrief">General Purpose Nuclear Network</div>
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@@ -216,13 +216,33 @@ gridfire::AdaptiveEngineView adaptiveView(baseEngine);
### Python Example
```python
import gridfire
from fourdst.composition import Composition
symbols = ["H-1", ...]
X = [0.708, ...]
comp = Composition()
comp.registerSymbols(symbols)
comp.setMassFraction(X)
comp.finalize(true)
# Initialize GraphEngine with predefined composition
engine = gridfire.GraphEngine(composition="example_composition")
engine = gridfire.GraphEngine(comp)
netIn = gridfire.types.NetIn
netIn.composition = comp
netIn.tMax = 1e-3
netIn.temperature = 1.5e7
netIn.density = 1.6e2
netIn.dt0 = 1e-12
# Perform one integration step
engine.step(dt=1e-3)
print(engine.abundances)
netOut = engine.evaluate(netIn)
print(netOut)
```
More detailed python usage can be found [here](usage.md)
## Common Workflow Example
A representative workflow often composes multiple engine views to balance accuracy, stability, and performance when integrating stiff nuclear networks:
@@ -277,4 +297,4 @@ GridFire integrates with and builds upon several key 4D-STAR libraries:
- [libcomposition](https://github.com/4D-STAR/libcomposition) ([docs](https://4d-star.github.io/libcomposition/)): Composition management toolkit.
- [libconfig](https://github.com/4D-STAR/libconfig): Configuration file parsing utilities.
- [liblogging](https://github.com/4D-STAR/liblogging): Flexible logging framework.
- [libconstants](https://github.com/4D-STAR/libconstants): Physical constants
- [libconstants](https://github.com/4D-STAR/libconstants): Physical constants

164
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@@ -0,0 +1,164 @@
# GridFire Python Usage Guide
This tutorial walks you through installing GridFire’s Python bindings, choosing engines and views thoughtfully, running a simulation, and visualizing your results.
---
## 1. Installation
### 1.1 PyPI Release
The quickest way to get started is:
```bash
pip install gridfire
```
### 1.2 Development from Source
If you want the cutting-edge features or need to hack the C++ backend:
```bash
git clone https://github.com/4DSTAR/GridFire.git
cd GridFire
# Create a virtualenv to isolate dependencies
python3 -m venv .venv && source .venv/bin/activate
# Install Python bindings (meson-python & pybind11 under the hood)
pip install .
```
You can also build manually with Meson (generally end users will not need to do this):
```bash
meson setup build-python
meson compile -C build_gridfire
```
---
## 2. Why These Engines and Views?
GridFire’s design [balances physical fidelity and performance](../README.md). Here’s why we pick each component:
1. **GraphEngine**: Constructs the **full** reaction network from Reaclib rates and composition. Use this when:
- You need maximum physical accuracy (no reactions are omitted).
- You are exploring new burning pathways or validating against literature.
2. **MultiscalePartitioningEngineView**: Implements the Hix & Thielemann partitioning strategy:
- **Fast reactions** vs **slow reactions** are split onto separate kernels.
- This reduces stiffness by isolating processes on very different timescales.
- Choose when your network spans orders of magnitude in timescales (e.g., rapid proton captures vs. slow beta decays).
3. **AdaptiveEngineView**: Dynamically culls low-flow reactions at runtime:
- At each timestep, reactions with negligible contribution are temporarily removed.
- This greatly accelerates large networks without significant loss of accuracy.
- Ideal for long integrations where the active set evolves over time.
4. **Leading-Edge Views**:
- `NetworkPrimingEngineView` to inject seed species and study ignition phenomena.
- `DefinedEngineView` to freeze the network to a user-specified subset (e.g., focus on the CNO cycle).
By composing these views in sequence, you can tailor accuracy vs performance for your scientific question. Commonly one might use a flow like **GraphEngine → Partitioning → Adaptive** to capture both full-network physics and manageable stiffness.
---
## 3. Step-by-Step Example
Adapted from [`tests/python/test.py`](../../tests/python/test.py). Comments explain each choice.
```python
import matplotlib.pyplot as plt
from gridfire.engine import GraphEngine, MultiscalePartitioningEngineView, AdaptiveEngineView
from gridfire.solver import DirectNetworkSolver
from gridfire.type import NetIn
from fourdst.composition import Composition
# 1. Define your composition (e.g., M-dwarf surface mix)
symbols = ["H-1","He-3","He-4","C-12","N-14","O-16","Ne-20","Mg-24"]
abundances = [0.708,2.94e-5,0.276,0.003,0.0011,9.62e-3,1.62e-3,5.16e-4]
comp = Composition()
comp.registerSymbols(symbols)
comp.setMassFraction(symbols, abundances)
comp.finalize(normalize=True) # scale to total mass = 1
# 2. Prepare the NetIn object
netIn = NetIn()
netIn.composition = comp
netIn.temperature = 1.5e7 # Kelvin
netIn.density = 1.6e2 # g/cm³
netIn.tMax = 3.15e7 # seconds to evolve (~1yr)
netIn.dt0 = 1e-12 # initial timestep
# 3. Construct the full network engine
build_depth = 2 # shallow test network for speed; Full = -1
baseEngine = GraphEngine(comp, buildDepth=build_depth)
baseEngine.setUseReverseReactions(False) # At these temps we can turn off reverse reactions
# 4. Partition fast/slow reactions (reduces stiffness)
partitionedEngine = MultiscalePartitioningEngineView(baseEngine)
# 5. Adaptively cull negligible flows (improves speed)
adaptiveEngine = AdaptiveEngineView(partitionedEngine)
# 6. Choose an ODE solver (implicit Rosenbrock4)
solver = DirectNetworkSolver(adaptiveEngine, absTol=1e-12, relTol=1e-8)
# 7. Run the integration
netOut = solver.evaluate(netIn)
# 8. Final result:
print(f"Final H-1 fraction: {netOut.composition.getMassFraction('H-1')}")
```
**Why these choices?**
- **buildDepth=2**: In Emily’s preliminary tests, depth=2 captures key reaction loops without the overhead of a full network.
- **Partition & Adaptive Views**: Partitioning reduces stiffness between rapid charged-particle captures and slower β-decays; adaptive culling keeps the working set minimal.
- **Implicit solver**: Rosenbrock4 handles stiff systems robustly, letting you push to longer `tMax`.
---
## 4. Visualizing Reaction Networks
GridFire engines and views provide built-in export methods for Graphviz DOT and CSV formats:
```python
# Export the base network to DOT for Graphviz
baseEngine.exportToDot('network.dot')
# Optionally generate a PNG (shell):
# dot -Tpng network.dot -o network.png
# Export a partitioned view of the network
partitionedEngine.exportToDot('partitioned.dot')
# Export to CSV for programmatic analysis
baseEngine.exportToCSV('network.csv')
```
You can then use tools like Graphviz or pandas:
```bash
# Convert DOT to PNG
dot -Tpng network.dot -o network.png
```
```python
import pandas as pd
# Load and inspect reaction list
df = pd.read_csv('network.csv')
print(df.head())
```
For time-series data, record intermediates with an observer and save with pandas or numpy:
```python
import pandas as pd
# Build a DataFrame of time vs species fraction
df = pd.DataFrame({'time': t, 'H-1': X_H1})
df.to_csv('H1_evolution.csv', index=False)
```
Then plot in pandas or Excel for custom figures.
---
## 5. Beyond the Basics
- **Custom Partition Functions**: In Python, subclass `gridfire.partition.PartitionFunction`, override `evaluate`, `supports`, and `clone` to implement new weighting schemes.
- **Parameter Studies**: Loop over `buildDepth`, solver tolerances, or initial compositions to get a sense of the sensitity of the network to input conditions or build a monte carlo grid.
- **Error Handling**:
```python
try:
results = solver.evaluate(netIn)
except GridFireRuntimeError as e:
print('Fatal engine error:', e)
except GridFireValueError as e:
print('Invalid input:', e)
```
For full API details, consult the docstrings in `src/python/` and the C++ implementation in `src/lib/`. Enjoy exploring nuclear astrophysics with GridFire!