feat(Comoposition-Tracking): updated GridFire to use new, molar-abundance based, version of libcomposition (v2.0.6)

This entailed a major rewrite of the composition handling from each engine and engine view along with the solver and primer. The intent here is to let Compositions be constructed from the same extensive property which the solver tracks internally. This addressed C0 discontinuity issues in the tracked molar abundances of species which were introduced by repeadidly swaping from molar abundance space to mass fraction space and back. This also allowed for a simplification of the primeNetwork method. Specifically the mass borrowing system was dramatically simplified as molar abundances are extensive.

src/include/gridfire/engine/engine_abstract.h

@@ -10,6 +10,8 @@
 
 #include "gridfire/expectations/expected_engine.h"
 
+#include "fourdst/composition/composition_abstract.h"
+
 #include <vector>
 #include <unordered_map>
 #include <utility>
@@ -58,7 +60,7 @@ namespace gridfire {
      */
     template <IsArithmeticOrAD T>
     struct StepDerivatives {
-        std::map<fourdst::atomic::Species, T> dydt; ///< Derivatives of abundances (dY/dt for each species).
+        std::map<fourdst::atomic::Species, T> dydt{}; ///< Derivatives of abundances (dY/dt for each species).
         T nuclearEnergyGenerationRate = T(0.0); ///< Specific energy generation rate (e.g., erg/g/s).
 
         StepDerivatives() : dydt(), nuclearEnergyGenerationRate(T(0.0)) {}
@@ -120,7 +122,7 @@ namespace gridfire {
          * rate for the current state.
          */
         [[nodiscard]] virtual std::expected<StepDerivatives<double>, expectations::StaleEngineError> calculateRHSAndEnergy(
-            const fourdst::composition::Composition& comp,
+            const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho
         ) const = 0;
@@ -153,20 +155,20 @@ namespace gridfire {
          * for the current state. The matrix can then be accessed via getJacobianMatrixEntry().
          */
         virtual void generateJacobianMatrix(
-            const fourdst::composition::Composition& comp,
+            const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho
         ) const = 0;
 
         virtual void generateJacobianMatrix(
-            const fourdst::composition::Composition& comp,
+            const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho,
             const std::vector<fourdst::atomic::Species>& activeSpecies
         ) const = 0;
 
         virtual void generateJacobianMatrix(
-            const fourdst::composition::Composition& comp,
+            const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho,
             const SparsityPattern& sparsityPattern
@@ -223,7 +225,7 @@ namespace gridfire {
          */
         [[nodiscard]] virtual double calculateMolarReactionFlow(
             const reaction::Reaction& reaction,
-            const fourdst::composition::Composition& comp,
+            const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho
         ) const = 0;
@@ -240,7 +242,7 @@ namespace gridfire {
          * generation rate with respect to temperature and density for the current state.
          */
         [[nodiscard]] virtual EnergyDerivatives calculateEpsDerivatives(
-            const fourdst::composition::Composition& comp,
+            const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho
         ) const = 0;
@@ -266,13 +268,13 @@ namespace gridfire {
          * which can be used for timestep control, diagnostics, and reaction network culling.
          */
         [[nodiscard]] virtual std::expected<std::unordered_map<fourdst::atomic::Species, double>, expectations::StaleEngineError> getSpeciesTimescales(
-            const fourdst::composition::Composition& comp,
+            const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho
         ) const = 0;
 
         [[nodiscard]] virtual std::expected<std::unordered_map<fourdst::atomic::Species, double>, expectations::StaleEngineError> getSpeciesDestructionTimescales(
-            const fourdst::composition::Composition& comp,
+            const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho
         ) const = 0;
@@ -390,7 +392,7 @@ namespace gridfire {
          * which may involve adding or removing species and reactions based on the
          * specified depth. However, not all engines support this operation.
          */
-        virtual void rebuild(const fourdst::composition::Composition& comp, BuildDepthType depth) {
+        virtual void rebuild(const fourdst::composition::CompositionAbstract &comp, BuildDepthType depth) {
             throw std::logic_error("Setting network depth not supported by this engine.");
             // ReSharper disable once CppDFAUnreachableCode
         }
@@ -408,7 +410,7 @@ namespace gridfire {
          * example, by either QSE partitioning or reaction flow rate culling
          */
         virtual fourdst::composition::Composition collectComposition(
-            fourdst::composition::Composition& comp
+            fourdst::composition::CompositionAbstract &comp
         ) const = 0;
 
     };