perf(graph_engine): finished sparsity system for jacobian, major preformance win, roughly 20x faster

essentially all callers can now inform the graph engine about which species they hold active and graph engine then uses those to define a sparsity pattern and only calculate the jacobian along that sparsity pattern

src/include/gridfire/engine/views/engine_defined.h

@@ -65,9 +65,44 @@ namespace gridfire{
          */
         void generateJacobianMatrix(
             const fourdst::composition::Composition& comp,
-            const double T9,
-            const double rho
+            double T9,
+            double rho
         ) const override;
+
+        /**
+         * @brief Generates the Jacobian matrix for the active species.
+         *
+         * @param comp A Composition object containing the current composition of the system
+         * @param T9 The temperature in units of 10^9 K.
+         * @param rho The density in g/cm^3.
+         * @param activeSpecies The vector of active species to include in the Jacobian.
+         *
+         * @throws std::runtime_error If the view is stale.
+         */
+        void generateJacobianMatrix(
+            const fourdst::composition::Composition &comp,
+            double T9,
+            double rho,
+            const std::vector<fourdst::atomic::Species> &activeSpecies
+        ) const override;
+
+        /**
+         * @brief Generates the Jacobian matrix for a given sparsity pattern
+         *
+         * @param comp A Composition object containing the current composition of the system
+         * @param T9 The temperature in units of 10^9 K.
+         * @param rho The density in g/cm^3.
+         * @param sparsityPattern The sparsity pattern to use for the Jacobian matrix.
+         *
+         * @throws std::runtime_error If the view is stale.
+         */
+        void generateJacobianMatrix(
+            const fourdst::composition::Composition &comp,
+            double T9,
+            double rho,
+            const SparsityPattern &sparsityPattern
+        ) const override;
+
         /**
          * @brief Gets an entry from the Jacobian matrix for the active species.
          *