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docs(docs): rebuilt docs

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Emily Boudreaux
2025-11-24 09:08:28 -05:00
parent 9fab4fbfae
commit 22c0329de0
2410 changed files with 309008 additions and 146081 deletions
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@@ -102,38 +102,42 @@ $(function(){initNavTree('functions_s.html',''); initResizable(true); });
<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
<h3><a id="index_s" name="index_s"></a>- s -</h3><ul>
<li>seed_species&#160;:&#160;<a class="el" href="structgridfire_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#af2d7e09d940e0fb3ca24a4bc8ec01031">gridfire::MultiscalePartitioningEngineView::QSEGroup</a></li>
<li>seed_species&#160;:&#160;<a class="el" href="structgridfire_1_1engine_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_group.html#a9434050b990ecfa0459feebff3047ee2">gridfire::engine::MultiscalePartitioningEngineView::QSEGroup</a></li>
<li>selectPartitionFunction()&#160;:&#160;<a class="el" href="classgridfire_1_1partition_1_1_composite_partition_function.html#a32f397abf9e9ace9f0c721e4e14eb60b">gridfire::partition::CompositePartitionFunction</a></li>
<li>set()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html#a6fc63f3c5d3fe7a1fd8b0704f2e71e2c">gridfire::engine::NetworkJacobian</a></li>
<li>set_absTol()&#160;:&#160;<a class="el" href="classgridfire_1_1solver_1_1_c_v_o_d_e_solver_strategy.html#aed8907852f77c15bb40d5a8e8f8af9b2">gridfire::solver::CVODESolverStrategy</a></li>
<li>set_callback()&#160;:&#160;<a class="el" href="classgridfire_1_1solver_1_1_c_v_o_d_e_solver_strategy.html#a77638ef3d2279009e5a57bbd3f0eb63b">gridfire::solver::CVODESolverStrategy</a>, <a class="el" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a4d97ee85933d5e5f90d4194bb021a1dc">gridfire::solver::NetworkSolverStrategy&lt; EngineT &gt;</a>, <a class="el" href="class_py_dynamic_network_solver_strategy.html#a112a7babc03858a69d6994a7155370d3">PyDynamicNetworkSolverStrategy</a></li>
<li>set_detailed_step_logging()&#160;:&#160;<a class="el" href="classgridfire_1_1solver_1_1_c_v_o_d_e_solver_strategy.html#a91966d110ca6225af60b633af5521cb4">gridfire::solver::CVODESolverStrategy</a></li>
<li>set_relTol()&#160;:&#160;<a class="el" href="classgridfire_1_1solver_1_1_c_v_o_d_e_solver_strategy.html#a6444290be523ad9fa91fa57c1dd4b6a2">gridfire::solver::CVODESolverStrategy</a></li>
<li>set_stdout_logging_enabled()&#160;:&#160;<a class="el" href="classgridfire_1_1solver_1_1_c_v_o_d_e_solver_strategy.html#a9857665a1198e24aac6add02afc6e306">gridfire::solver::CVODESolverStrategy</a></li>
<li>setFormat()&#160;:&#160;<a class="el" href="classgridfire_1_1_network.html#a787c601f6e4bd06600bf946efbcc98d4">gridfire::Network</a></li>
<li>setNetworkReactions()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#adedc8547568d643473bdfcc86040b488">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#a655e74357cce822c4508069a3bcac2c9">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_dynamic_engine.html#a49025489901e22a20cdf99b455ff2ff0">gridfire::DynamicEngine</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a52288e2629609c8438a3c9bc3f910016">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#af99f5e4871808188d00379c1c35868fe">gridfire::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#af469cba3be850d53f659ec173f0eb4e4">PyDynamicEngine</a></li>
<li>setPrecomputation()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a6c5410878496abc349ba30b691cdf0f1">gridfire::GraphEngine</a></li>
<li>setScreeningModel()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_defined_engine_view.html#abf2da57c83c3c4c635cb301f53088258">gridfire::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1_dynamic_engine.html#a3fb44b6f55563a2f590f31916528f2bd">gridfire::DynamicEngine</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a9bc768ca8ca59d442c0d05cb04e36d7c">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a1a0c0a0ade632eb10f0eecab828a059f">gridfire::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#afa3abfd612033336a656f092721c14ac">PyDynamicEngine</a></li>
<li>setStiff()&#160;:&#160;<a class="el" href="classgridfire_1_1approx8_1_1_approx8_network.html#aefed972081514c29cdaaa1efd857ad8d">gridfire::approx8::Approx8Network</a>, <a class="el" href="classgridfire_1_1_network.html#a84de2d691af06c4b62cfab5022b1e8fe">gridfire::Network</a></li>
<li>setUseReverseReactions()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a409991d527ea4d4b05d1af907fe5d197">gridfire::GraphEngine</a></li>
<li>setNetworkReactions()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_adaptive_engine_view.html#a5dbfcafa606c3242dc4ced62c2494a2d">gridfire::engine::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1engine_1_1_defined_engine_view.html#ae89529e13f2b7fd2febcfa5af40d4666">gridfire::engine::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#ab321170954bffc53b1bedaf54f6976be">gridfire::engine::DynamicEngine</a>, <a class="el" href="classgridfire_1_1engine_1_1_graph_engine.html#a90251650123d0d8ce0281e18c4476f45">gridfire::engine::GraphEngine</a>, <a class="el" href="classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view.html#aa378d0e0fa6018b989d83945daa47952">gridfire::engine::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#af469cba3be850d53f659ec173f0eb4e4">PyDynamicEngine</a></li>
<li>setPrecomputation()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_graph_engine.html#a0e0650a14247a7f43623d58de8eedb19">gridfire::engine::GraphEngine</a></li>
<li>setScreeningModel()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_adaptive_engine_view.html#ab050409db954a3fa593633f9d2cd5d89">gridfire::engine::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1engine_1_1_defined_engine_view.html#a68bd0e51d3e127e5f9fd74fdb8180fd9">gridfire::engine::DefinedEngineView</a>, <a class="el" href="classgridfire_1_1engine_1_1_dynamic_engine.html#a50e76977d0dc3cc23d52b51842d35003">gridfire::engine::DynamicEngine</a>, <a class="el" href="classgridfire_1_1engine_1_1_graph_engine.html#af842981deaf84a698b6cbfa66abcb715">gridfire::engine::GraphEngine</a>, <a class="el" href="classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view.html#ad11aa1e168ec03d0c3ed90eeddcefe52">gridfire::engine::MultiscalePartitioningEngineView</a>, <a class="el" href="class_py_dynamic_engine.html#afa3abfd612033336a656f092721c14ac">PyDynamicEngine</a></li>
<li>setUseReverseReactions()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_graph_engine.html#a959928abbef89fd0a20264ef8b79c111">gridfire::engine::GraphEngine</a></li>
<li>shape()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html#a699933e9f807ec196157f92ffb46b9ba">gridfire::engine::NetworkJacobian</a></li>
<li>SimpleReactionListFileParser()&#160;:&#160;<a class="el" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#afc8ed91e8c98205c505e3d9f0cff1993">gridfire::io::SimpleReactionListFileParser</a></li>
<li>SimulationTimeTrigger()&#160;:&#160;<a class="el" href="classgridfire_1_1trigger_1_1solver_1_1_c_v_o_d_e_1_1_simulation_time_trigger.html#a235f84a37370a1ca2226fb881b4051c7">gridfire::trigger::solver::CVODE::SimulationTimeTrigger</a></li>
<li>size()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_logical_reaclib_reaction.html#a4c58951d9f7ab252717c226b0da80a9d">gridfire::reaction::LogicalReaclibReaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html#af14cf34d7367cb6a6be5191724c2d4cf">gridfire::reaction::ReactionSet</a>, <a class="el" href="classgridfire_1_1_reaction_set.html#af14cf34d7367cb6a6be5191724c2d4cf">gridfire::ReactionSet</a></li>
<li>solveQSEAbundances()&#160;:&#160;<a class="el" href="classgridfire_1_1_multiscale_partitioning_engine_view.html#a40ce2c18063cd56cffd58419b9ae96bf">gridfire::MultiscalePartitioningEngineView</a></li>
<li>singular()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_network_jacobian.html#a485321469d84b3cf923ec79957044406">gridfire::engine::NetworkJacobian</a></li>
<li>size()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_reaction_set.html#af14cf34d7367cb6a6be5191724c2d4cf">gridfire::engine::ReactionSet</a>, <a class="el" href="classgridfire_1_1policy_1_1_multi_reaction_chain_policy.html#a84fcdc2adab96284d850f8dd43315278">gridfire::policy::MultiReactionChainPolicy</a>, <a class="el" href="classgridfire_1_1reaction_1_1_logical_reaclib_reaction.html#a4c58951d9f7ab252717c226b0da80a9d">gridfire::reaction::LogicalReaclibReaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction_set.html#af14cf34d7367cb6a6be5191724c2d4cf">gridfire::reaction::ReactionSet</a></li>
<li>solve()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_solver.html#aa6f28cf2f5759efad7d428f6794cc151">gridfire::engine::MultiscalePartitioningEngineView::QSESolver</a></li>
<li>solveQSEAbundances()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view.html#a6c785a6334e5fd9593d3e279bafee592">gridfire::engine::MultiscalePartitioningEngineView</a></li>
<li>solver_instance&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_c_v_o_d_e_solver_strategy_1_1_c_v_o_d_e_user_data.html#ad7f3eb9caae25ef25357c41c23d6b392">gridfire::solver::CVODESolverStrategy::CVODEUserData</a></li>
<li>solves()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_solver.html#a420ca8991dd60fac7a9d18fae0eda0c1">gridfire::engine::MultiscalePartitioningEngineView::QSESolver</a></li>
<li>sourceLabel()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_reaclib_reaction.html#a96d4ab87de02e9b0be3c248e2e955b4b">gridfire::reaction::ReaclibReaction</a></li>
<li>sources()&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_logical_reaclib_reaction.html#ad4979f437dc787a5475c3a029804ed99">gridfire::reaction::LogicalReaclibReaction</a></li>
<li>speedOfLight&#160;:&#160;<a class="el" href="structgridfire_1_1rates_1_1weak_1_1_weak_reaction_1_1constants.html#a016c3e02f622e21073f9110707177b76">gridfire::rates::weak::WeakReaction::constants</a></li>
<li>StaleEngineError()&#160;:&#160;<a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_error.html#ade628b2919f3a4c7a8fda2c654029872">gridfire::exceptions::StaleEngineError</a>, <a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html#ad477b6e562bf4167ad327ebaccd4cf10">gridfire::expectations::StaleEngineError</a></li>
<li>StaleEngineTrigger()&#160;:&#160;<a class="el" href="classgridfire_1_1exceptions_1_1_stale_engine_trigger.html#a3c7689e6e1e7269bae7275b099b2f387">gridfire::exceptions::StaleEngineTrigger</a></li>
<li>StaleJacobianError()&#160;:&#160;<a class="el" href="classgridfire_1_1exceptions_1_1_stale_jacobian_error.html#a0a1f6e905239147ba53b374e62bef505">gridfire::exceptions::StaleJacobianError</a></li>
<li>staleType&#160;:&#160;<a class="el" href="structgridfire_1_1expectations_1_1_stale_engine_error.html#a10bce51a63024715959a66673b909590">gridfire::expectations::StaleEngineError</a></li>
<li>state&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_c_v_o_d_e_solver_strategy_1_1_timestep_context.html#aaae3c42b9172be4d501f022e67f5a6f6">gridfire::solver::CVODESolverStrategy::TimestepContext</a></li>
<li>status&#160;:&#160;<a class="el" href="structgridfire_1_1_priming_report.html#a5fec4b465afb4f2d9bc30cd1cab1b50d">gridfire::PrimingReport</a></li>
<li>status&#160;:&#160;<a class="el" href="structgridfire_1_1engine_1_1_priming_report.html#ac3e0c141e56c7bc41dd89d5fc873fa41">gridfire::engine::PrimingReport</a></li>
<li>step()&#160;:&#160;<a class="el" href="classgridfire_1_1trigger_1_1_and_trigger.html#a8e743e8ebe71f9ded835177db6fad908">gridfire::trigger::AndTrigger&lt; TriggerContextStruct &gt;</a>, <a class="el" href="classgridfire_1_1trigger_1_1_every_nth_trigger.html#a26d0aca39087a1f69e96e0701ca83f81">gridfire::trigger::EveryNthTrigger&lt; TriggerContextStruct &gt;</a>, <a class="el" href="classgridfire_1_1trigger_1_1_not_trigger.html#a5096cb7e70ea357f28e1b9fc8301c793">gridfire::trigger::NotTrigger&lt; TriggerContextStruct &gt;</a>, <a class="el" href="classgridfire_1_1trigger_1_1_or_trigger.html#a95a801aafb5aaa9a22566ebf722a1150">gridfire::trigger::OrTrigger&lt; TriggerContextStruct &gt;</a>, <a class="el" href="classgridfire_1_1trigger_1_1solver_1_1_c_v_o_d_e_1_1_convergence_failure_trigger.html#aaef2090ed67a7c27967821f75a61e524">gridfire::trigger::solver::CVODE::ConvergenceFailureTrigger</a>, <a class="el" href="classgridfire_1_1trigger_1_1solver_1_1_c_v_o_d_e_1_1_off_diagonal_trigger.html#a8b882c6ba6e267d7051031140bbb7ad6">gridfire::trigger::solver::CVODE::OffDiagonalTrigger</a>, <a class="el" href="classgridfire_1_1trigger_1_1solver_1_1_c_v_o_d_e_1_1_simulation_time_trigger.html#aafc7f40bde2c78f4d100b6f9da771831">gridfire::trigger::solver::CVODE::SimulationTimeTrigger</a>, <a class="el" href="classgridfire_1_1trigger_1_1solver_1_1_c_v_o_d_e_1_1_timestep_collapse_trigger.html#a9723e389aeba05fdb3d4fd1dcc1ba07d">gridfire::trigger::solver::CVODE::TimestepCollapseTrigger</a>, <a class="el" href="classgridfire_1_1trigger_1_1_trigger.html#a4b7ffa4d8d31e2118a8e86172be51041">gridfire::trigger::Trigger&lt; TriggerContextStruct &gt;</a></li>
<li>StepDerivatives()&#160;:&#160;<a class="el" href="structgridfire_1_1_step_derivatives.html#a26deeb236e77eddb0119ad368a5d8f1c">gridfire::StepDerivatives&lt; T &gt;</a></li>
<li>stoichiometric_coefficients&#160;:&#160;<a class="el" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#a7a7e9167b19e339e0d69544b9c00e79c">gridfire::GraphEngine::PrecomputedReaction</a></li>
<li>stoichiometry()&#160;:&#160;<a class="el" href="classgridfire_1_1rates_1_1weak_1_1_weak_reaction.html#a8bf7dc26d9f1375625df99bceba08a44">gridfire::rates::weak::WeakReaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaclib_reaction.html#a57b2695d152360a6ba08776cc760e3a1">gridfire::reaction::ReaclibReaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#ad49f4cad024db72c966d949c75f1ce4d">gridfire::reaction::Reaction</a>, <a class="el" href="classgridfire_1_1_reaction.html#a55b7f61d9bde45f2ca485c1b07a05950">gridfire::Reaction</a></li>
<li>success&#160;:&#160;<a class="el" href="structgridfire_1_1_priming_report.html#afa4dd791ddd9df84039554524b681fb3">gridfire::PrimingReport</a></li>
<li>StepDerivatives()&#160;:&#160;<a class="el" href="structgridfire_1_1engine_1_1_step_derivatives.html#ab6f82eeaf31cdb66fb40267838b19a34">gridfire::engine::StepDerivatives&lt; T &gt;</a></li>
<li>stoichiometric_coefficients&#160;:&#160;<a class="el" href="structgridfire_1_1engine_1_1_graph_engine_1_1_precomputed_reaction.html#a333e30364947d83549b20d857641d646">gridfire::engine::GraphEngine::PrecomputedReaction</a></li>
<li>stoichiometry()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_reaction.html#a55b7f61d9bde45f2ca485c1b07a05950">gridfire::engine::Reaction</a>, <a class="el" href="classgridfire_1_1rates_1_1weak_1_1_weak_reaction.html#a8bf7dc26d9f1375625df99bceba08a44">gridfire::rates::weak::WeakReaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaclib_reaction.html#a57b2695d152360a6ba08776cc760e3a1">gridfire::reaction::ReaclibReaction</a>, <a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#ad49f4cad024db72c966d949c75f1ce4d">gridfire::reaction::Reaction</a></li>
<li>success&#160;:&#160;<a class="el" href="structgridfire_1_1engine_1_1_priming_report.html#a68aa5f346f5d9d598bf921e175c49239">gridfire::engine::PrimingReport</a></li>
<li>supports()&#160;:&#160;<a class="el" href="classgridfire_1_1partition_1_1_composite_partition_function.html#ae8908a78f087ea516cdd5a4cdd449a9c">gridfire::partition::CompositePartitionFunction</a>, <a class="el" href="classgridfire_1_1partition_1_1_ground_state_partition_function.html#a49b18aae58eb6250aaa23d43d55f02bd">gridfire::partition::GroundStatePartitionFunction</a>, <a class="el" href="classgridfire_1_1partition_1_1_partition_function.html#a6df4191d10516477371a0384e1e55bf5">gridfire::partition::PartitionFunction</a>, <a class="el" href="classgridfire_1_1partition_1_1_rauscher_thielemann_partition_function.html#a588a11c654751765b04d6425c99041f5">gridfire::partition::RauscherThielemannPartitionFunction</a>, <a class="el" href="class_py_partition_function.html#a0f288a01a3ed7fb92fff5d9fd7d56aa8">PyPartitionFunction</a></li>
<li>symmetry_factor&#160;:&#160;<a class="el" href="structgridfire_1_1_graph_engine_1_1_precomputed_reaction.html#ac42504e868c0b9fd9ac9a405ea739f0e">gridfire::GraphEngine::PrecomputedReaction</a></li>
<li>syncInternalMaps()&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#acdce8d87e23a2cd1504bc9472e538c0f">gridfire::GraphEngine</a></li>
<li>symmetry_factor&#160;:&#160;<a class="el" href="structgridfire_1_1engine_1_1_graph_engine_1_1_precomputed_reaction.html#aa4ae79e03a28fd221759ea93bda389d5">gridfire::engine::GraphEngine::PrecomputedReaction</a></li>
<li>syncInternalMaps()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_graph_engine.html#a9af928bf8a5327d3cb45254c0e59f914">gridfire::engine::GraphEngine</a></li>
<li>sys_func()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_solver.html#a58b7b2ac01c40084cc839309267e400e">gridfire::engine::MultiscalePartitioningEngineView::QSESolver</a></li>
<li>sys_jac()&#160;:&#160;<a class="el" href="classgridfire_1_1engine_1_1_multiscale_partitioning_engine_view_1_1_q_s_e_solver.html#a9a34e36baa074c1b39b230e0b5010a82">gridfire::engine::MultiscalePartitioningEngineView::QSESolver</a></li>
</ul>
</div><!-- contents -->
</div><!-- doc-content -->