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docs(docs): rebuilt docs with loads more detail for triggers and weak reactions

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Emily Boudreaux
2025-10-08 11:17:09 -04:00
parent 8a0b5b2c36
commit 274c566726
600 changed files with 39207 additions and 9125 deletions
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docs/html/classgridfire_1_1_adaptive_engine_view.js
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@@ -3,27 +3,28 @@ var classgridfire_1_1_adaptive_engine_view =
[ "ReactionFlow", "structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow.html", "structgridfire_1_1_adaptive_engine_view_1_1_reaction_flow" ],
[ "Config", "classgridfire_1_1_adaptive_engine_view.html#afec39b2faa34ea65c5488dd8e11ba3c3", null ],
[ "LogManager", "classgridfire_1_1_adaptive_engine_view.html#a5eaf7c3a4e28cd3a4f34979b88a80103", null ],
[ "RescueSet", "classgridfire_1_1_adaptive_engine_view.html#a4ff60b5214ec0bdaf683feb6615573a5", null ],
[ "RescueSet", "classgridfire_1_1_adaptive_engine_view.html#ac674338ddcbae4c33dd84b0441631806", null ],
[ "AdaptiveEngineView", "classgridfire_1_1_adaptive_engine_view.html#ad599363cdd457e72e2e2937b0222c455", null ],
[ "calculateAllReactionFlows", "classgridfire_1_1_adaptive_engine_view.html#abdbaf4b87629efe43ac1255dad424c0c", null ],
[ "calculateMolarReactionFlow", "classgridfire_1_1_adaptive_engine_view.html#a048d4b1d41ecb4125a558d1b9ed7cb31", null ],
[ "calculateRHSAndEnergy", "classgridfire_1_1_adaptive_engine_view.html#af703ad17ea65ffff4b75bf8ccc00e5d5", null ],
[ "calculateAllReactionFlows", "classgridfire_1_1_adaptive_engine_view.html#ab5397d217039f096acededd4d2779780", null ],
[ "calculateEpsDerivatives", "classgridfire_1_1_adaptive_engine_view.html#a5d1b50afd2fba6af75e976a4f9c9dcbc", null ],
[ "calculateMolarReactionFlow", "classgridfire_1_1_adaptive_engine_view.html#a3c1e27b45051c4ba481a2b87513982ed", null ],
[ "calculateRHSAndEnergy", "classgridfire_1_1_adaptive_engine_view.html#ac5545d546166de94514871d7ad7b8669", null ],
[ "constructReactionIndexMap", "classgridfire_1_1_adaptive_engine_view.html#a89614f4a48f60c4170a0197f45303e7c", null ],
[ "constructSpeciesIndexMap", "classgridfire_1_1_adaptive_engine_view.html#a896d29325b4233e83d9298850b617a2d", null ],
[ "cullReactionsByFlow", "classgridfire_1_1_adaptive_engine_view.html#a42417e96fe9fd623458af109401daf08", null ],
[ "finalizeActiveSet", "classgridfire_1_1_adaptive_engine_view.html#aa79fb382c98461b02a2c30668491e6c5", null ],
[ "cullReactionsByFlow", "classgridfire_1_1_adaptive_engine_view.html#a95fbfb7f2bdbf80195f1ea0aff8d62fb", null ],
[ "finalizeActiveSet", "classgridfire_1_1_adaptive_engine_view.html#a7b8b3a786b973e4383e721358e61b7ed", null ],
[ "findReachableSpecies", "classgridfire_1_1_adaptive_engine_view.html#a0ed21f7e7c1034fc87b40d4116c4221b", null ],
[ "generateJacobianMatrix", "classgridfire_1_1_adaptive_engine_view.html#a03fc187d3d306b9058103b9522cbbaeb", null ],
[ "generateJacobianMatrix", "classgridfire_1_1_adaptive_engine_view.html#a8da7664cf483cba7f979f855a74c3559", null ],
[ "generateStoichiometryMatrix", "classgridfire_1_1_adaptive_engine_view.html#a231193a61ba5a31e8eb92b0d4ce69111", null ],
[ "getBaseEngine", "classgridfire_1_1_adaptive_engine_view.html#aee095b30a9dce5fcb5ae2fa1d2aa192c", null ],
[ "getJacobianMatrixEntry", "classgridfire_1_1_adaptive_engine_view.html#a4710d218c8a0fd161e994ecd60b48e58", null ],
[ "getNetworkReactions", "classgridfire_1_1_adaptive_engine_view.html#a12cc2f352678fba9688363ba1876ab9c", null ],
[ "getJacobianMatrixEntry", "classgridfire_1_1_adaptive_engine_view.html#adf3b8a5734983509ca02b7a1a480119f", null ],
[ "getNetworkReactions", "classgridfire_1_1_adaptive_engine_view.html#a3247c1e6a76de5622223ee7b5ca3452a", null ],
[ "getNetworkSpecies", "classgridfire_1_1_adaptive_engine_view.html#ac83a8efe25c0e5b9bf7756ac3a500bb1", null ],
[ "getScreeningModel", "classgridfire_1_1_adaptive_engine_view.html#a0ab1199f900a58f309c3c36532c9164f", null ],
[ "getSpeciesDestructionTimescales", "classgridfire_1_1_adaptive_engine_view.html#a522e78bce9ff062939572248d57f8cea", null ],
[ "getSpeciesIndex", "classgridfire_1_1_adaptive_engine_view.html#a9055feb245524a5a9549ace935f059ff", null ],
[ "getSpeciesTimescales", "classgridfire_1_1_adaptive_engine_view.html#a4e856d6d4d2fc220952bbb7e6b2f85d9", null ],
[ "getStoichiometryMatrixEntry", "classgridfire_1_1_adaptive_engine_view.html#a67b4ea8cad115394bb4a42cc39d696f9", null ],
[ "getSpeciesDestructionTimescales", "classgridfire_1_1_adaptive_engine_view.html#aa861db5f6fc4e85fb51f524e4e1367c6", null ],
[ "getSpeciesIndex", "classgridfire_1_1_adaptive_engine_view.html#abb811382522c31f6456787edd4f59ace", null ],
[ "getSpeciesTimescales", "classgridfire_1_1_adaptive_engine_view.html#a57a218c5a145f589531777c8615b7408", null ],
[ "getStoichiometryMatrixEntry", "classgridfire_1_1_adaptive_engine_view.html#abe2ca6426e10cc6a10090eecf7098dbe", null ],
[ "isStale", "classgridfire_1_1_adaptive_engine_view.html#ad268c9942655e5c9605148fe07718e88", null ],
[ "mapCulledToFull", "classgridfire_1_1_adaptive_engine_view.html#a68695f056b660e91285b7e5a931612e1", null ],
[ "mapCulledToFullReactionIndex", "classgridfire_1_1_adaptive_engine_view.html#a91e742642d8a8d9ec0620779927e5101", null ],
@@ -31,12 +32,12 @@ var classgridfire_1_1_adaptive_engine_view =
[ "mapFullToCulled", "classgridfire_1_1_adaptive_engine_view.html#a3d9d8e862d1c2f0a8ba460c57f6a7f44", null ],
[ "mapNetInToMolarAbundanceVector", "classgridfire_1_1_adaptive_engine_view.html#a7d0237956bf3ec7230bc51d88e7f8019", null ],
[ "primeEngine", "classgridfire_1_1_adaptive_engine_view.html#a70005361262bc180d4417b608661e3c3", null ],
[ "rescueEdgeSpeciesDestructionChannel", "classgridfire_1_1_adaptive_engine_view.html#a823c665ba89452aa2b3d5422fa5d313f", null ],
[ "setNetworkReactions", "classgridfire_1_1_adaptive_engine_view.html#a7b3a6b3ab0a52f0f84d2b142e74ea672", null ],
[ "rescueEdgeSpeciesDestructionChannel", "classgridfire_1_1_adaptive_engine_view.html#a0439f464865b4c01bad0f6be6055c3fc", null ],
[ "setNetworkReactions", "classgridfire_1_1_adaptive_engine_view.html#adedc8547568d643473bdfcc86040b488", null ],
[ "setScreeningModel", "classgridfire_1_1_adaptive_engine_view.html#aae4ddbef1c4e2202fd236221a4bf376b", null ],
[ "update", "classgridfire_1_1_adaptive_engine_view.html#a2a7ecf985a326b4bea43e00cf9ee43dd", null ],
[ "validateState", "classgridfire_1_1_adaptive_engine_view.html#aedc0dedb51c81e03f253cc409a5d5c40", null ],
[ "m_activeReactions", "classgridfire_1_1_adaptive_engine_view.html#a19fc7e02e216b797aa643fa35e429800", null ],
[ "m_activeReactions", "classgridfire_1_1_adaptive_engine_view.html#ab5ab06941bf6d97007d0a76658bf2aa6", null ],
[ "m_activeSpecies", "classgridfire_1_1_adaptive_engine_view.html#af4bc9fc6e4afcd6a53c49ca6e2a95940", null ],
[ "m_baseEngine", "classgridfire_1_1_adaptive_engine_view.html#a4d38b46be9f25c7afe7ddd2b284253f8", null ],
[ "m_config", "classgridfire_1_1_adaptive_engine_view.html#a14171a9ccc45a63996a967c72983de30", null ],