feat: integrate PhreeqcKnobs into PhreeqcMatrix; add getKnobs method and update Engine initialization

poet/include/PhreeqcMatrix.hpp

@@ -7,6 +7,7 @@
 #include <vector>
 
 #include "IPhreeqc.hpp"
+#include "PhreeqcKnobs.hpp"
 
 /**
  * @brief Class for storing information from Phreeqc
@@ -273,6 +274,16 @@ public:
    */
   bool checkIfExists(int cell_id) const;
 
+  /**
+   * @brief Retrieves the current PhreeqcKnobs settings.
+   *
+   * This function returns a copy of the PhreeqcKnobs object that contains
+   * the current configuration settings for the Phreeqc instance.
+   *
+   * @return PhreeqcKnobs The current configuration settings.
+   */
+  PhreeqcKnobs getKnobs() const { return *_m_knobs; }
+
 private:
   std::map<int, std::vector<element>> _m_map;
   std::map<int, std::vector<base_names>> _m_internal_names;
@@ -284,5 +295,7 @@ private:
   void remove_NaNs();
 
   std::shared_ptr<IPhreeqc> _m_pqc;
+  std::shared_ptr<PhreeqcKnobs> _m_knobs;
+
   std::string _m_database;
 };

poet/src/Engine.cpp

@@ -10,6 +10,7 @@
 #include <string>
 #include <vector>
 
+#include "PhreeqcKnobs.hpp"
 #include "PhreeqcMatrix.hpp"
 #include "Wrapper/EquilibriumWrapper.hpp"
 #include "Wrapper/ExchangeWrapper.hpp"
@@ -87,6 +88,8 @@ PhreeqcEngine::Impl::Impl(const PhreeqcMatrix &pqc_mat, const int cell_id) {
 
   this->LoadDatabaseString(pqc_mat.getDatabase().c_str());
 
+  pqc_mat.getKnobs().writeKnobs(this->PhreeqcPtr);
+
   const std::string pqc_string =
       replaceRawKeywordID(pqc_mat.getDumpStringsPQI(cell_id));
 

poet/src/PhreeqcMatrix/Ctor.cpp

@@ -1,9 +1,11 @@
 #include "IPhreeqc.hpp"
+#include "PhreeqcKnobs.hpp"
 #include "PhreeqcMatrix.hpp"
 
 #include <Phreeqc.h>
 #include <Solution.h>
 #include <cmath>
+#include <memory>
 #include <string>
 
 PhreeqcMatrix::PhreeqcMatrix(const std::string &database,
@@ -14,6 +16,9 @@ PhreeqcMatrix::PhreeqcMatrix(const std::string &database,
   this->_m_pqc->LoadDatabaseString(database.c_str());
   this->_m_pqc->RunString(input_script.c_str());
 
+  this->_m_knobs =
+      std::make_shared<PhreeqcKnobs>(this->_m_pqc.get()->GetPhreeqcPtr());
+
   this->initialize();
 }