From eb09cd2725635eba7285d7a9c60866283097ea3c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Max=20L=C3=BCbke?= <mluebke@uni-potsdam.de>
Date: Thu, 19 Dec 2024 08:59:56 +0100
Subject: [PATCH] feat: add with_h0_o0 and with_redox parameters to
 ChemistryModule and related classes

---
 src/Chemistry/ChemistryModule.cpp | 3 ++-
 src/Init/ChemistryInit.cpp        | 2 ++
 src/Init/GridInit.cpp             | 3 +++
 src/Init/InitialList.cpp          | 8 ++++++++
 src/Init/InitialList.hpp          | 6 ++++++
 5 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/src/Chemistry/ChemistryModule.cpp b/src/Chemistry/ChemistryModule.cpp
index 32c14be90..c95796b79 100644
--- a/src/Chemistry/ChemistryModule.cpp
+++ b/src/Chemistry/ChemistryModule.cpp
@@ -171,7 +171,8 @@ poet::ChemistryModule::ChemistryModule(
 
   if (!is_master) {
     PhreeqcMatrix pqc_mat =
-        PhreeqcMatrix(chem_params.database, chem_params.pqc_script);
+        PhreeqcMatrix(chem_params.database, chem_params.pqc_script,
+                      chem_params.with_h0_o0, chem_params.with_redox);
 
     this->pqc_runner =
         std::make_unique<PhreeqcRunner>(pqc_mat.subset(chem_params.pqc_ids));
diff --git a/src/Init/ChemistryInit.cpp b/src/Init/ChemistryInit.cpp
index b399671ed..db0b098d0 100644
--- a/src/Init/ChemistryInit.cpp
+++ b/src/Init/ChemistryInit.cpp
@@ -69,6 +69,8 @@ InitialList::ChemistryInit InitialList::getChemistryInit() const {
   chem_init.database = database;
   chem_init.pqc_script = pqc_script;
   chem_init.pqc_ids = pqc_ids;
+  chem_init.with_h0_o0 = with_h0_o0;
+  chem_init.with_redox = with_redox;
   // chem_init.pqc_scripts = pqc_scripts;
   // chem_init.pqc_ids = pqc_ids;
 
diff --git a/src/Init/GridInit.cpp b/src/Init/GridInit.cpp
index 52ce6943a..63b33a628 100644
--- a/src/Init/GridInit.cpp
+++ b/src/Init/GridInit.cpp
@@ -186,6 +186,9 @@ PhreeqcMatrix InitialList::prepareGrid(const Rcpp::List &grid_input,
                 grid_input[GRID_MEMBER_STR(GridMembers::PQC_WITH_REDOX)])
           : false;
 
+  this->with_h0_o0 = include_h0_o0;
+  this->with_redox = with_redox;
+
   PhreeqcMatrix pqc_mat =
       PhreeqcMatrix(database, script, include_h0_o0, with_redox);
 
diff --git a/src/Init/InitialList.cpp b/src/Init/InitialList.cpp
index 88452a8c4..c6282977d 100644
--- a/src/Init/InitialList.cpp
+++ b/src/Init/InitialList.cpp
@@ -57,6 +57,10 @@ void InitialList::importList(const Rcpp::List &setup, bool minimal) {
       Rcpp::as<std::string>(setup[static_cast<int>(ExportList::CHEM_DATABASE)]);
   this->pqc_script = Rcpp::as<std::string>(
       setup[static_cast<int>(ExportList::CHEM_PQC_SCRIPT)]);
+  this->with_h0_o0 =
+      Rcpp::as<bool>(setup[static_cast<int>(ExportList::CHEM_PQC_WITH_H0_O0)]);
+  this->with_redox =
+      Rcpp::as<bool>(setup[static_cast<int>(ExportList::CHEM_PQC_WITH_REDOX)]);
   this->field_header = Rcpp::as<std::vector<std::string>>(
       setup[static_cast<int>(ExportList::CHEM_FIELD_HEADER)]);
   this->pqc_ids = Rcpp::as<std::vector<int>>(
@@ -113,6 +117,10 @@ Rcpp::List InitialList::exportList() {
   out[static_cast<int>(ExportList::CHEM_DATABASE)] = Rcpp::wrap(this->database);
   out[static_cast<int>(ExportList::CHEM_PQC_SCRIPT)] =
       Rcpp::wrap(this->pqc_script);
+  out[static_cast<int>(ExportList::CHEM_PQC_WITH_H0_O0)] =
+      Rcpp::wrap(this->with_h0_o0);
+  out[static_cast<int>(ExportList::CHEM_PQC_WITH_REDOX)] =
+      Rcpp::wrap(this->with_redox);
   out[static_cast<int>(ExportList::CHEM_FIELD_HEADER)] =
       Rcpp::wrap(this->field_header);
   out[static_cast<int>(ExportList::CHEM_PQC_IDS)] = Rcpp::wrap(this->pqc_ids);
diff --git a/src/Init/InitialList.hpp b/src/Init/InitialList.hpp
index 03132983e..64c2fd08c 100644
--- a/src/Init/InitialList.hpp
+++ b/src/Init/InitialList.hpp
@@ -52,6 +52,8 @@ private:
     DIFFU_ALPHA_Y,
     CHEM_DATABASE,
     CHEM_PQC_SCRIPT,
+    CHEM_PQC_WITH_H0_O0,
+    CHEM_PQC_WITH_REDOX,
     CHEM_PQC_IDS,
     CHEM_FIELD_HEADER,
     // CHEM_PQC_SCRIPTS,
@@ -190,6 +192,8 @@ private:
 
   std::string database;
   std::string pqc_script;
+  bool with_h0_o0{false};
+  bool with_redox{false};
   // std::vector<std::string> pqc_scripts;
   std::vector<int> pqc_ids;
 
@@ -220,6 +224,8 @@ public:
 
     std::string database;
     std::string pqc_script;
+    bool with_h0_o0;
+    bool with_redox;
     std::vector<int> pqc_ids;
 
     // std::map<int, std::string> pqc_input;