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refactor(reaction): refactored to an abstract reaction class in prep for weak reactions

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This commit is contained in:
Emily Boudreaux
2025-08-14 13:33:46 -04:00
parent d920a55ba6
commit 0b77f2e269
81 changed files with 1050041 additions and 913 deletions
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36
src/include/gridfire/engine/views/engine_defined.h
View File

@@ -16,14 +16,14 @@ namespace gridfire{
class DefinedEngineView : public DynamicEngine, public EngineView<DynamicEngine> {
public:
DefinedEngineView(const std::vector<std::string>& peNames, DynamicEngine& baseEngine);
const DynamicEngine& getBaseEngine() const override;
[[nodiscard]] const DynamicEngine& getBaseEngine() const override;
// --- Engine Interface ---
/**
* @brief Gets the list of active species in the network defined by the file.
* @return A const reference to the vector of active species.
*/
const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override;
[[nodiscard]] const std::vector<fourdst::atomic::Species>& getNetworkSpecies() const override;
// --- DynamicEngine Interface ---
/**
@@ -37,7 +37,7 @@ namespace gridfire{
*
* @throws std::runtime_error If the view is stale (i.e., `update()` has not been called after `setNetworkFile()`).
*/
std::expected<StepDerivatives<double>, expectations::StaleEngineError> calculateRHSAndEnergy(
[[nodiscard]] std::expected<StepDerivatives<double>, expectations::StaleEngineError> calculateRHSAndEnergy(
const std::vector<double>& Y_defined,
const double T9,
const double rho
@@ -66,7 +66,7 @@ namespace gridfire{
* @throws std::runtime_error If the view is stale.
* @throws std::out_of_range If an index is out of bounds.
*/
double getJacobianMatrixEntry(
[[nodiscard]] double getJacobianMatrixEntry(
const int i_defined,
const int j_defined
) const override;
@@ -86,7 +86,7 @@ namespace gridfire{
* @throws std::runtime_error If the view is stale.
* @throws std::out_of_range If an index is out of bounds.
*/
int getStoichiometryMatrixEntry(
[[nodiscard]] int getStoichiometryMatrixEntry(
const int speciesIndex_defined,
const int reactionIndex_defined
) const override;
@@ -101,7 +101,7 @@ namespace gridfire{
*
* @throws std::runtime_error If the view is stale or if the reaction is not in the active set.
*/
double calculateMolarReactionFlow(
[[nodiscard]] double calculateMolarReactionFlow(
const reaction::Reaction& reaction,
const std::vector<double>& Y_defined,
const double T9,
@@ -114,9 +114,9 @@ namespace gridfire{
*
* @throws std::runtime_error If the view is stale.
*/
const reaction::LogicalReactionSet& getNetworkReactions() const override;
[[nodiscard]] const reaction::ReactionSet& getNetworkReactions() const override;
void setNetworkReactions(const reaction::LogicalReactionSet& reactions) override;
void setNetworkReactions(const reaction::ReactionSet& reactions) override;
/**
* @brief Computes timescales for all active species in the network.
*
@@ -168,7 +168,7 @@ namespace gridfire{
*/
[[nodiscard]] screening::ScreeningType getScreeningModel() const override;
[[nodiscard]] int getSpeciesIndex(const fourdst::atomic::Species &species) const override;
[[nodiscard]] size_t getSpeciesIndex(const fourdst::atomic::Species &species) const override;
[[nodiscard]] std::vector<double> mapNetInToMolarAbundanceVector(const NetIn &netIn) const override;
@@ -181,7 +181,7 @@ namespace gridfire{
///< Active species in the defined engine.
std::vector<fourdst::atomic::Species> m_activeSpecies;
///< Active reactions in the defined engine.
reaction::LogicalReactionSet m_activeReactions;
reaction::ReactionSet m_activeReactions;
///< Maps indices of active species to indices in the full network.
std::vector<size_t> m_speciesIndexMap;
@@ -198,7 +198,7 @@ namespace gridfire{
*
* @throws std::runtime_error If an active species is not found in the base engine's species list.
*/
std::vector<size_t> constructSpeciesIndexMap() const;
[[nodiscard]] std::vector<size_t> constructSpeciesIndexMap() const;
/**
* @brief Constructs the reaction index map.
@@ -210,7 +210,7 @@ namespace gridfire{
*
* @throws std::runtime_error If an active reaction is not found in the base engine's reaction list.
*/
std::vector<size_t> constructReactionIndexMap() const;
[[nodiscard]] std::vector<size_t> constructReactionIndexMap() const;
/**
* @brief Maps a vector of culled abundances to a vector of full abundances.
@@ -219,7 +219,7 @@ namespace gridfire{
* @return A vector of abundances for the full network, with the abundances of the active
* species copied from the defined vector.
*/
std::vector<double> mapViewToFull(const std::vector<double>& defined) const;
[[nodiscard]] std::vector<double> mapViewToFull(const std::vector<double>& defined) const;
/**
* @brief Maps a vector of full abundances to a vector of culled abundances.
@@ -228,7 +228,7 @@ namespace gridfire{
* @return A vector of abundances for the active species, with the abundances of the active
* species copied from the full vector.
*/
std::vector<double> mapFullToView(const std::vector<double>& full) const;
[[nodiscard]] std::vector<double> mapFullToView(const std::vector<double>& full) const;
/**
* @brief Maps a culled species index to a full species index.
@@ -238,7 +238,7 @@ namespace gridfire{
*
* @throws std::out_of_range If the defined index is out of bounds for the species index map.
*/
size_t mapViewToFullSpeciesIndex(size_t definedSpeciesIndex) const;
[[nodiscard]] size_t mapViewToFullSpeciesIndex(size_t definedSpeciesIndex) const;
/**
* @brief Maps a culled reaction index to a full reaction index.
@@ -248,7 +248,7 @@ namespace gridfire{
*
* @throws std::out_of_range If the defined index is out of bounds for the reaction index map.
*/
size_t mapViewToFullReactionIndex(size_t definedReactionIndex) const;
[[nodiscard]] size_t mapViewToFullReactionIndex(size_t definedReactionIndex) const;
void validateNetworkState() const;
@@ -263,8 +263,8 @@ namespace gridfire{
const std::string& fileName,
const io::NetworkFileParser& parser
);
std::string getNetworkFile() const { return m_fileName; }
const io::NetworkFileParser& getParser() const { return m_parser; }
[[nodiscard]] std::string getNetworkFile() const { return m_fileName; }
[[nodiscard]] const io::NetworkFileParser& getParser() const { return m_parser; }
private:
using Config = fourdst::config::Config;
using LogManager = fourdst::logging::LogManager;