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docs(docs): added extensive docs

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Emily Boudreaux
2025-07-01 15:06:22 -04:00
parent 5b4db3ea43
commit 131f61c9e7
134 changed files with 5101 additions and 2191 deletions
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@@ -107,7 +107,7 @@ $(function(){initNavTree('functions_m.html',''); initResizable(true); });
<li>m_baseEngine&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a4d38b46be9f25c7afe7ddd2b284253f8">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ad8454c98fa9a4bb45dc81059bc51fc81">gridfire::FileDefinedEngineView</a></li>
<li>m_chapter&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#a16f9cbb6269817099d3dc07d4e63da7b">gridfire::reaction::Reaction</a></li>
<li>m_config&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a14171a9ccc45a63996a967c72983de30">gridfire::AdaptiveEngineView</a>, <a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a7a80966c023ae722239491af58609362">gridfire::FileDefinedEngineView</a>, <a class="el" href="classgridfire_1_1_graph_engine.html#a3b17102b143435ddfdc015d7a50c4b18">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.html#aea206c3a7600db8d657666fef88fa20d">gridfire::io::MESANetworkFileParser</a>, <a class="el" href="classgridfire_1_1io_1_1_simple_reaction_list_file_parser.html#a4061e99bd77a3de0d6d9e317bfc74874">gridfire::io::SimpleReactionListFileParser</a>, <a class="el" href="classgridfire_1_1_network.html#a9f8802012728ef5fea0e8cd465044e09">gridfire::Network</a>, <a class="el" href="classgridfire_1_1solver_1_1_direct_network_solver.html#a0d1b52d06b0521e7c556d75cd8d2ffe6">gridfire::solver::DirectNetworkSolver</a>, <a class="el" href="classgridfire_1_1solver_1_1_q_s_e_network_solver.html#a7d19b6e50db34d38c81afec76bbedee1">gridfire::solver::QSENetworkSolver</a></li>
<li>m_constants&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a0837bab6dcd111d9075c9343b90d64f1">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_network.html#adf7002883160101c9f9d1b376b265410">gridfire::Network</a></li>
<li>m_constants&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a10c01bc20ae668c2857efb2a1783098e">gridfire::GraphEngine</a>, <a class="el" href="classgridfire_1_1_network.html#adf7002883160101c9f9d1b376b265410">gridfire::Network</a></li>
<li>m_dt0&#160;:&#160;<a class="el" href="classgridfire_1_1approx8_1_1_approx8_network.html#a6ed8022834e9541b3e547dd867648b0f">gridfire::approx8::Approx8Network</a></li>
<li>m_dynamicSpeciesIndices&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a08ce53701b152f3ce108c1c18ce64de2">gridfire::solver::QSENetworkSolver::EigenFunctor&lt; T &gt;</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a2071ce797f94ae1a3ea6d934748672ce">gridfire::solver::QSENetworkSolver::JacobianFunctor</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a3ac1ef529627d21f7d1ad718dc87f7f9">gridfire::solver::QSENetworkSolver::RHSFunctor</a></li>
<li>m_engine&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a56f8b2b222fb2a7dac190ead0babfdd0">gridfire::solver::DirectNetworkSolver::JacobianFunctor</a>, <a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a04f8c84e46e6fbd0977e50fda4829d1a">gridfire::solver::DirectNetworkSolver::RHSFunctor</a>, <a class="el" href="classgridfire_1_1solver_1_1_network_solver_strategy.html#a724924d94eaf82b67d9988a55c3261e8">gridfire::solver::NetworkSolverStrategy&lt; EngineT &gt;</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a93b46ca95ddf9e4d21d02700621e6285">gridfire::solver::QSENetworkSolver::EigenFunctor&lt; T &gt;</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#aaaa82eff96e6127a6de05444f730e43a">gridfire::solver::QSENetworkSolver::JacobianFunctor</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a0d8d28a6559cfed5e7cd683523d49b2c">gridfire::solver::QSENetworkSolver::RHSFunctor</a></li>
@@ -126,6 +126,7 @@ $(function(){initNavTree('functions_m.html',''); initResizable(true); });
<li>m_numSpecies&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a3f624142212b5e6ff65f5706953fe353">gridfire::solver::DirectNetworkSolver::JacobianFunctor</a>, <a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#ac4a1af03d2a4fbc5cc2407b8a6833147">gridfire::solver::DirectNetworkSolver::RHSFunctor</a></li>
<li>m_parser&#160;:&#160;<a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a0a9b07176cb93b54c677b6ce71fda500">gridfire::FileDefinedEngineView</a></li>
<li>m_peName&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#a6124aa9fc2306349e1dd879a37923248">gridfire::reaction::Reaction</a></li>
<li>m_precomputedReactions&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a5d431d5385b1219ba29689eb29601ea3">gridfire::GraphEngine</a></li>
<li>m_products&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#a4b5607ed413acdf29539b8a57461e49e">gridfire::reaction::Reaction</a></li>
<li>m_QSESpeciesIndices&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#abaf28fdd93e881ef56c24f541be7492d">gridfire::solver::QSENetworkSolver::EigenFunctor&lt; T &gt;</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a1b92391170eb46771bd499aa8d115334">gridfire::solver::QSENetworkSolver::JacobianFunctor</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a6be7259897a47ce480b289144b06e269">gridfire::solver::QSENetworkSolver::RHSFunctor</a></li>
<li>m_qValue&#160;:&#160;<a class="el" href="classgridfire_1_1reaction_1_1_reaction.html#a59122a2898bb9af640cc3e9aeb49028b">gridfire::reaction::Reaction</a></li>
@@ -149,6 +150,7 @@ $(function(){initNavTree('functions_m.html',''); initResizable(true); });
<li>m_stoichiometryMatrix&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#ad1cb5fd32efc37668e2d9ecf0c72ad24">gridfire::GraphEngine</a></li>
<li>m_T9&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_jacobian_functor.html#a88f5fc48a555b369f1e2688d6bb67b83">gridfire::solver::DirectNetworkSolver::JacobianFunctor</a>, <a class="el" href="structgridfire_1_1solver_1_1_direct_network_solver_1_1_r_h_s_functor.html#a082844f1eae0609e66620575210e8823">gridfire::solver::DirectNetworkSolver::RHSFunctor</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a6771ae56ddd9058954b42ee92a378309">gridfire::solver::QSENetworkSolver::EigenFunctor&lt; T &gt;</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_jacobian_functor.html#a85f88639447a9a706008efece82ff289">gridfire::solver::QSENetworkSolver::JacobianFunctor</a>, <a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a35026100163c7cc6fdb4c2e4d988b8cb">gridfire::solver::QSENetworkSolver::RHSFunctor</a></li>
<li>m_tMax&#160;:&#160;<a class="el" href="classgridfire_1_1approx8_1_1_approx8_network.html#a6fadf388f07c160f1887a3cb72eaa869">gridfire::approx8::Approx8Network</a></li>
<li>m_usePrecomputation&#160;:&#160;<a class="el" href="classgridfire_1_1_graph_engine.html#a191cff35402d3c97c82c5c966a39d0de">gridfire::GraphEngine</a></li>
<li>m_y&#160;:&#160;<a class="el" href="classgridfire_1_1approx8_1_1_approx8_network.html#abf9f13ff532917ddac4a7d987698836d">gridfire::approx8::Approx8Network</a></li>
<li>m_Y_QSE&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_r_h_s_functor.html#a02c23ef20d616bf5a591a274b66cd75a">gridfire::solver::QSENetworkSolver::RHSFunctor</a></li>
<li>m_YFull&#160;:&#160;<a class="el" href="structgridfire_1_1solver_1_1_q_s_e_network_solver_1_1_eigen_functor.html#a2dca32a9e0bea5aea2a565f94b99a8de">gridfire::solver::QSENetworkSolver::EigenFunctor&lt; T &gt;</a></li>
@@ -157,9 +159,9 @@ $(function(){initNavTree('functions_m.html',''); initResizable(true); });
<li>mapCulledToFullSpeciesIndex()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a256d14a333f9401039b826cc889761a8">gridfire::AdaptiveEngineView</a></li>
<li>mapFullToCulled()&#160;:&#160;<a class="el" href="classgridfire_1_1_adaptive_engine_view.html#a3d9d8e862d1c2f0a8ba460c57f6a7f44">gridfire::AdaptiveEngineView</a></li>
<li>mapFullToView()&#160;:&#160;<a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a97e5ee4651dbe6754678fe96e4702fee">gridfire::FileDefinedEngineView</a></li>
<li>mapViewToFull()&#160;:&#160;<a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ac231044e37e0962f664f8465e1ccb022">gridfire::FileDefinedEngineView</a></li>
<li>mapViewToFullReactionIndex()&#160;:&#160;<a class="el" href="classgridfire_1_1_file_defined_engine_view.html#ae7d6f0ff9076d59d1245c047bbd1bdb9">gridfire::FileDefinedEngineView</a></li>
<li>mapViewToFullSpeciesIndex()&#160;:&#160;<a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a8d2c6b9a33b9c8c172bbd2c2e2e9ffaf">gridfire::FileDefinedEngineView</a></li>
<li>mapViewToFull()&#160;:&#160;<a class="el" href="classgridfire_1_1_file_defined_engine_view.html#adba3c11b11a04b2907c1635210d73dee">gridfire::FileDefinedEngineView</a></li>
<li>mapViewToFullReactionIndex()&#160;:&#160;<a class="el" href="classgridfire_1_1_file_defined_engine_view.html#a74217a1f8fd8e6daff969cb17885315c">gridfire::FileDefinedEngineView</a></li>
<li>mapViewToFullSpeciesIndex()&#160;:&#160;<a class="el" href="classgridfire_1_1_file_defined_engine_view.html#aa2373955ef5b0eabf7a57c7208e38bb1">gridfire::FileDefinedEngineView</a></li>
<li>MESANetworkFileParser()&#160;:&#160;<a class="el" href="classgridfire_1_1io_1_1_m_e_s_a_network_file_parser.html#ac5963d0da6780de753df996b490f8d2c">gridfire::io::MESANetworkFileParser</a></li>
<li>mIon&#160;:&#160;<a class="el" href="structgridfire_1_1approx8_1_1_approx8_net.html#a928b7810cb2993d59d40aa73c2faef18">gridfire::approx8::Approx8Net</a></li>
<li>MolarAbundance()&#160;:&#160;<a class="el" href="structgridfire_1_1_net_in.html#a47781e8d5503e3b4f12d669e2cbcfb65">gridfire::NetIn</a></li>