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docs(docs): asdded and cleaned up docs

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Emily Boudreaux
2025-07-24 11:10:45 -04:00
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@@ -102,23 +102,34 @@ $(function(){initNavTree('functions_func_c.html',''); initResizable(true); });
<div class="textblock">Here is a list of all functions with links to the classes they belong to:</div>
<h3><a id="index_c" name="index_c"></a>- c -</h3><ul>
<li>calculate_rate()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html#a1d2fb3b6a6a1860ace98b32447d1dd1b">gridfire::reaction::LogicalReaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#ad81e9b2a1773470059ca6989c60556ec">gridfire::reaction::Reaction</a></li>
<li>calculate_forward_rate_log_derivative()&#160;:&#160;<a class="el" href="classgridfire_1_1_reaction.html#a3a8ba9212d76d5ce51f20df6892c6061">gridfire::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html#aa4b8d0d30459f360ff6e29d848e943d5">gridfire::reaction::LogicalReaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#a3a8ba9212d76d5ce51f20df6892c6061">gridfire::reaction::Reaction</a></li>
<li>calculate_rate()&#160;:&#160;<a class="el" href="classgridfire_1_1_reaction.html#ad81e9b2a1773470059ca6989c60556ec">gridfire::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaction.html#a1d2fb3b6a6a1860ace98b32447d1dd1b">gridfire::reaction::LogicalReaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#ad81e9b2a1773470059ca6989c60556ec">gridfire::reaction::Reaction</a></li>
<li>calculateAllDerivatives()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#af41df9ce979b6410e12642cb093916c9">gridfire::GraphEngine</a></li>
<li>calculateAllDerivativesUsingPrecomputation()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a63639f4430d0889605c10839a6f32af9">gridfire::GraphEngine</a></li>
<li>calculateAllDerivativesUsingPrecomputation()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a97f98706b51fbe0d167ed81ffe58c438">gridfire::GraphEngine</a></li>
<li>calculateAllReactionFlows()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#abdbaf4b87629efe43ac1255dad424c0c">gridfire::AdaptiveEngineView</a></li>
<li>calculateFactors_impl()&#160;:&#160;<a class="el" href="classgridfire_1_1screening_1_1_bare_screening_model.html#a6c93b72c8ca34623127f0846d8dee50a">gridfire::screening::BareScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_weak_screening_model.html#a2695206d46b9d2c2503f8e58c44df88f">gridfire::screening::WeakScreeningModel</a></li>
<li>calculateMolarReactionFlow()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ac371fb66fd0a76a04df204c9dd9a05ef">gridfire::FileDefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">gridfire::GraphEngine</a></li>
<li>calculateRHSAndEnergy()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a7b276b7210be588263395bdb0497fc6d">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_engine.html#ac8b56124b6b49cd1802addb74a9a47c2">gridfire::Engine</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a2c1d88b06568f9ea4c65e794d012ebfb">gridfire::FileDefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a8b3baf29829c7ae0a61430ea70632bbf">gridfire::GraphEngine</a></li>
<li>calculateScreeningFactors()&#160;:&#160;<a class="el" href="classgridfire_1_1screening_1_1_bare_screening_model.html#ac35ad34c5da7e1b5087552aa5c83fe60">gridfire::screening::BareScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#aaec9184d80c86a2d8674e395dad81bde">gridfire::screening::ScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_weak_screening_model.html#afbaeaefe6b3ab3ecf81889ddc1cff76c">gridfire::screening::WeakScreeningModel</a></li>
<li>calculateSteadyStateAbundances()&#160;:&#160;<a class="el" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a00d112f6087f6e3a93f4d40a519308d2">gridfire::solver::QSENetworkSolver</a></li>
<li>chapter()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#a5cb438adfefb640e4bc58e09053bd629">gridfire::reaction::Reaction</a></li>
<li>calculateMolarReactionFlow()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a142725470f96cba3edb48a29f1264032">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_dynamic_engine.html#a6633b1757c41dd9e1c397333f4f9e785">gridfire::DynamicEngine</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a9245642b741f215e52861d00e756fb3f">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a79eb9c108d694a27ec913ed0143aa044">gridfire::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#a6224f546ba66b1257506b1fc9f47195a">PyDynamicEngine</a></li>
<li>calculateReverseMolarReactionFlow()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a17774cd9ffcf1ba94019df766a0984a0">gridfire::GraphEngine</a></li>
<li>calculateReverseRate()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a0b7b85f824e1021ae6e56b644db53b28">gridfire::GraphEngine</a></li>
<li>calculateReverseRateTwoBody()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a01fc9fd5d576b66d07360d05e821c755">gridfire::GraphEngine</a></li>
<li>calculateReverseRateTwoBodyDerivative()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#af28950c5af3a92eb03a1a64ed0f913e7">gridfire::GraphEngine</a></li>
<li>calculateRHSAndEnergy()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#af703ad17ea65ffff4b75bf8ccc00e5d5">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a4b0d71367cb1d4c06bcd01251bbeb60d">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_engine.html#a89f714d19b84a93a004a7afbb487a6cb">gridfire::Engine</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#aaed3743a52246b0f7bf03995e1c12081">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a716d7357e944e8394d8b8e0b5e7625eb">gridfire::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#a5b7f0cfe327c634ec125303256de8b9a">PyDynamicEngine</a>, <a class="el" href="class_py_engine.html#a2f92602ecf210414b46838fc0a9ae26d">PyEngine</a></li>
<li>calculateScreeningFactors()&#160;:&#160;<a class="el" href="classgridfire_1_1screening_1_1_bare_screening_model.html#ac35ad34c5da7e1b5087552aa5c83fe60">gridfire::screening::BareScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_screening_model.html#aaec9184d80c86a2d8674e395dad81bde">gridfire::screening::ScreeningModel</a>, <a class="el" href="classgridfire_1_1screening_1_1_weak_screening_model.html#afbaeaefe6b3ab3ecf81889ddc1cff76c">gridfire::screening::WeakScreeningModel</a>, <a class="el" href="class_py_screening.html#a2b8756c197eb89e77cb6dd231c979315">PyScreening</a></li>
<li>chapter()&#160;:&#160;<a class="el" href="classgridfire_1_1_reaction.html#a5cb438adfefb640e4bc58e09053bd629">gridfire::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#a5cb438adfefb640e4bc58e09053bd629">gridfire::reaction::Reaction</a></li>
<li>clear()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html#a05f71d318564d880079fd6c96d59ae21">gridfire::reaction::TemplatedReactionSet&lt; ReactionT &gt;</a></li>
<li>clone()&#160;:&#160;<a class="el" href="classgridfire_1_1partition_1_1_composite_partition_function.html#a7b000d55c7d1f489e54a57f7f4e3808a">gridfire::partition::CompositePartitionFunction</a>, <a class="el" href="classgridfire_1_1partition_1_1_ground_state_partition_function.html#ade2b0f92a3d9b74968166793466a11e4">gridfire::partition::GroundStatePartitionFunction</a>, <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html#a677a90f992fd56b8718e36655c33ce6d">gridfire::partition::PartitionFunction</a>, <a class="el" href="classgridfire_1_1partition_1_1_rauscher_thielemann_partition_function.html#ad229cac0a84df5ebbcaf0550f83debf6">gridfire::partition::RauscherThielemannPartitionFunction</a>, <a class="el" href="class_py_partition_function.html#af918b357e38fb82499ad53584557c43d">PyPartitionFunction</a></li>
<li>collect()&#160;:&#160;<a class="el" href="classgridfire_1_1_defined_engine_view.html#adbc64284b5f5a3256867be46fa87c69e">gridfire::DefinedEngineView</a></li>
<li>collectAtomicReverseRateAtomicBases()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a29b338630c959449c15881935ac30746">gridfire::GraphEngine</a></li>
<li>collectNetworkSpecies()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#aedf42d83bfcc28313b6b6454034d2efa">gridfire::GraphEngine</a></li>
<li>constructReactionIndexMap()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a89614f4a48f60c4170a0197f45303e7c">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#aebb3f3548f8781506f31580706810a4e">gridfire::FileDefinedEngineView</a></li>
<li>constructSpeciesIndexMap()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a896d29325b4233e83d9298850b617a2d">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a51ba09ff01fdcac1125d42f276c9a0a7">gridfire::FileDefinedEngineView</a></li>
<li>contains()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#ab92785f331a446e51a0960b75d60b37b">gridfire::reaction::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html#a7777ecd0f594fdf66ce57d22610fad3c">gridfire::reaction::TemplatedReactionSet&lt; ReactionT &gt;</a></li>
<li>contains_product()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#a074d3cd2421fd5d0133e47f0522403e2">gridfire::reaction::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html#a443ec5d7138764b32975232e13071ccf">gridfire::reaction::TemplatedReactionSet&lt; ReactionT &gt;</a></li>
<li>contains_reactant()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#abbe243affa61ba9b2cd2a7b905cd5e45">gridfire::reaction::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html#ac42606350d7557106f7954b1f114c128">gridfire::reaction::TemplatedReactionSet&lt; ReactionT &gt;</a></li>
<li>CompositePartitionFunction()&#160;:&#160;<a class="el" href="classgridfire_1_1partition_1_1_composite_partition_function.html#ad80743933712de627c6a69d06d42ceb5">gridfire::partition::CompositePartitionFunction</a></li>
<li>compute_and_cache()&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_manager.html#a595aa16333693ee2bbcac35aa85a1c2a">gridfire::solver::DirectNetworkSolver::RHSManager</a></li>
<li>constructCandidateGroups()&#160;:&#160;<a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#ac206840057bac65b7f7738e6dfd1047a">gridfire::MultiscalePartitioningEngineView</a></li>
<li>constructPrimingReactionSet()&#160;:&#160;<a class="el" href="classgridfire_1_1_network_priming_engine_view.html#a91f60d8a6bd92dc5d5f6fcda8e89408f">gridfire::NetworkPrimingEngineView</a></li>
<li>constructReactionIndexMap()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a89614f4a48f60c4170a0197f45303e7c">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#ab2514984afaaf8590c28ab71943fbe68">gridfire::DefinedEngineView</a></li>
<li>constructSpeciesIndexMap()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a896d29325b4233e83d9298850b617a2d">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a9ea4812bc697fe43f8aded14f8aa0985">gridfire::DefinedEngineView</a></li>
<li>contains()&#160;:&#160;<a class="el" href="classgridfire_1_1_reaction.html#ab92785f331a446e51a0960b75d60b37b">gridfire::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#ab92785f331a446e51a0960b75d60b37b">gridfire::reaction::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html#a7777ecd0f594fdf66ce57d22610fad3c">gridfire::reaction::TemplatedReactionSet&lt; ReactionT &gt;</a></li>
<li>contains_product()&#160;:&#160;<a class="el" href="classgridfire_1_1_reaction.html#a074d3cd2421fd5d0133e47f0522403e2">gridfire::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#a074d3cd2421fd5d0133e47f0522403e2">gridfire::reaction::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html#a443ec5d7138764b32975232e13071ccf">gridfire::reaction::TemplatedReactionSet&lt; ReactionT &gt;</a></li>
<li>contains_reactant()&#160;:&#160;<a class="el" href="classgridfire_1_1_reaction.html#abbe243affa61ba9b2cd2a7b905cd5e45">gridfire::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#abbe243affa61ba9b2cd2a7b905cd5e45">gridfire::reaction::Reaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html#ac42606350d7557106f7954b1f114c128">gridfire::reaction::TemplatedReactionSet&lt; ReactionT &gt;</a></li>
<li>contains_species()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_templated_reaction_set.html#ad870856d206d93f27125c88d44ff9e34">gridfire::reaction::TemplatedReactionSet&lt; ReactionT &gt;</a></li>
<li>convert_netIn()&#160;:&#160;<a class="el" href="classgridfire_1_1approx8_1_1_approx8_network.html#a56426da6f1af7eb8a6d1cc70bc8e742a">gridfire::approx8::Approx8Network</a></li>
<li>cullReactionsByFlow()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a42417e96fe9fd623458af109401daf08">gridfire::AdaptiveEngineView</a></li>