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feat(GraphNetwork): started templating for auto diff

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This commit is contained in:
Emily Boudreaux
2025-06-19 15:20:37 -04:00
parent cd5a6b200b
commit e0704dcafe
2 changed files with 16 additions and 10 deletions
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15
src/network/private/netgraph.cpp
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@@ -20,7 +20,8 @@
namespace serif::network { namespace serif::network {
GraphNetwork::GraphNetwork( template <typename GeneralScalarType>
GraphNetwork<GeneralScalarType>::GraphNetwork(
const serif::composition::Composition &composition const serif::composition::Composition &composition
): ):
Network(REACLIB), Network(REACLIB),
@@ -32,7 +33,8 @@ namespace serif::network {
syncInternalMaps(); syncInternalMaps();
} }
GraphNetwork::GraphNetwork( template <typename GeneralScalarType>
GraphNetwork<GeneralScalarType>::GraphNetwork(
const serif::composition::Composition &composition, const serif::composition::Composition &composition,
const double cullingThreshold, const double cullingThreshold,
const double T9 const double T9
@@ -46,14 +48,16 @@ namespace serif::network {
syncInternalMaps(); syncInternalMaps();
} }
void GraphNetwork::syncInternalMaps() { template <typename GeneralScalarType>
void GraphNetwork<GeneralScalarType>::syncInternalMaps() {
collectNetworkSpecies(); collectNetworkSpecies();
populateReactionIDMap(); populateReactionIDMap();
populateSpeciesToIndexMap(); populateSpeciesToIndexMap();
} }
// --- Network Graph Construction Methods --- // --- Network Graph Construction Methods ---
void GraphNetwork::collectNetworkSpecies() { template <typename GeneralScalarType>
void GraphNetwork<GeneralScalarType>::collectNetworkSpecies() {
m_networkSpecies.clear(); m_networkSpecies.clear();
m_networkSpeciesMap.clear(); m_networkSpeciesMap.clear();
@@ -81,7 +85,8 @@ namespace serif::network {
} }
void GraphNetwork::populateReactionIDMap() { template <typename GeneralScalarType>
void GraphNetwork<GeneralScalarType>::populateReactionIDMap() {
LOG_INFO(m_logger, "Populating reaction ID map for REACLIB graph network (serif::network::GraphNetwork)..."); LOG_INFO(m_logger, "Populating reaction ID map for REACLIB graph network (serif::network::GraphNetwork)...");
m_reactionIDMap.clear(); m_reactionIDMap.clear();
for (const auto& reaction: m_reactions) { for (const auto& reaction: m_reactions) {

11
src/network/public/netgraph.h
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@@ -18,6 +18,7 @@
// REACLIBReactions are quite large data structures, so this could be a performance bottleneck. // REACLIBReactions are quite large data structures, so this could be a performance bottleneck.
namespace serif::network { namespace serif::network {
template <typename GeneralScalarType>
class GraphNetwork final : public Network { class GraphNetwork final : public Network {
public: public:
explicit GraphNetwork(const serif::composition::Composition &composition); explicit GraphNetwork(const serif::composition::Composition &composition);
@@ -38,15 +39,15 @@ namespace serif::network {
reaclib::REACLIBReactionSet m_reactions; ///< Set of REACLIB reactions for the network. reaclib::REACLIBReactionSet m_reactions; ///< Set of REACLIB reactions for the network.
serif::composition::Composition m_initialComposition; serif::composition::Composition m_initialComposition;
serif::composition::Composition m_currentComposition; serif::composition::Composition m_currentComposition;
double m_cullingThreshold; ///< Threshold for culling reactions. GeneralScalarType m_cullingThreshold; ///< Threshold for culling reactions.
double m_T9; ///< Temperature in T9 units to evaluate culling. GeneralScalarType m_T9; ///< Temperature in T9 units to evaluate culling.
std::vector<serif::atomic::Species> m_networkSpecies; ///< The species in the network. std::vector<serif::atomic::Species> m_networkSpecies; ///< The species in the network.
std::unordered_map<std::string_view, serif::atomic::Species> m_networkSpeciesMap; std::unordered_map<std::string_view, serif::atomic::Species> m_networkSpeciesMap;
std::unordered_map<std::string_view, const reaclib::REACLIBReaction> m_reactionIDMap; ///< Map of reaction IDs to REACLIB reactions. std::unordered_map<std::string_view, const reaclib::REACLIBReaction> m_reactionIDMap; ///< Map of reaction IDs to REACLIB reactions.
boost::numeric::ublas::compressed_matrix<int> m_stoichiometryMatrix; ///< Stoichiometry matrix for the network. boost::numeric::ublas::compressed_matrix<int> m_stoichiometryMatrix; ///< Stoichiometry matrix for the network.
boost::numeric::ublas::compressed_matrix<double> m_jacobianMatrix; ///< Jacobian matrix for the network. boost::numeric::ublas::compressed_matrix<GeneralScalarType> m_jacobianMatrix; ///< Jacobian matrix for the network.
std::unordered_map<serif::atomic::Species, size_t> m_speciesToIndexMap; ///< Map of species to their index in the stoichiometry matrix. std::unordered_map<serif::atomic::Species, size_t> m_speciesToIndexMap; ///< Map of species to their index in the stoichiometry matrix.
@@ -62,8 +63,8 @@ namespace serif::network {
void generateStoichiometryMatrix(); void generateStoichiometryMatrix();
void generateJacobianMatrix(); void generateJacobianMatrix();
std::vector<double> calculateRHS(const std::vector<double>& Y, const double T9, const double rho) const; std::vector<GeneralScalarType> calculateRHS(const std::vector<GeneralScalarType>& Y, const GeneralScalarType T9, const GeneralScalarType rho) const;
double calculateReactionRate(const reaclib::REACLIBReaction &reaction, const std::vector<double>& Y, const double T9, const double rho) const; GeneralScalarType calculateReactionRate(const reaclib::REACLIBReaction &reaction, const std::vector<GeneralScalarType>& Y, const GeneralScalarType T9, const GeneralScalarType rho) const;
void pruneNetworkGraph(); void pruneNetworkGraph();
}; };