From e5588a2ee973976f3ba9504879457db9591e9b2b Mon Sep 17 00:00:00 2001
From: Max Luebke <mluebke@gfz-potsdam.de>
Date: Wed, 18 Dec 2024 17:34:46 +0100
Subject: [PATCH] feat: add support for redox in PhreeqcMatrix initialization

---
 ext/iphreeqc             |  2 +-
 src/Init/GridInit.cpp    | 10 +++++++++-
 src/Init/InitialList.hpp |  7 ++++---
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/ext/iphreeqc b/ext/iphreeqc
index 2c8c31193..6e727e2f8 160000
--- a/ext/iphreeqc
+++ b/ext/iphreeqc
@@ -1 +1 @@
-Subproject commit 2c8c311934cd54f0923d8b92dcccd9894825ce1b
+Subproject commit 6e727e2f896e853745b4dd123c5772a9b40ad705
diff --git a/src/Init/GridInit.cpp b/src/Init/GridInit.cpp
index 6b0e4ae15..52ce6943a 100644
--- a/src/Init/GridInit.cpp
+++ b/src/Init/GridInit.cpp
@@ -179,7 +179,15 @@ PhreeqcMatrix InitialList::prepareGrid(const Rcpp::List &grid_input,
     throw std::runtime_error("Grid size must be positive.");
   }
 
-  PhreeqcMatrix pqc_mat = PhreeqcMatrix(database, script, include_h0_o0);
+  bool with_redox =
+      grid_input.containsElementNamed(
+          GRID_MEMBER_STR(GridMembers::PQC_WITH_REDOX))
+          ? Rcpp::as<bool>(
+                grid_input[GRID_MEMBER_STR(GridMembers::PQC_WITH_REDOX)])
+          : false;
+
+  PhreeqcMatrix pqc_mat =
+      PhreeqcMatrix(database, script, include_h0_o0, with_redox);
 
   this->transport_names = pqc_mat.getSolutionNames();
 
diff --git a/src/Init/InitialList.hpp b/src/Init/InitialList.hpp
index d3d1bf871..03132983e 100644
--- a/src/Init/InitialList.hpp
+++ b/src/Init/InitialList.hpp
@@ -75,6 +75,7 @@ private:
   enum class GridMembers {
     PQC_SCRIPT_STRING,
     PQC_SCRIPT_FILE,
+    PQC_WITH_REDOX,
     PQC_DB_STRING,
     PQC_DB_FILE,
     GRID_DEF,
@@ -88,9 +89,9 @@ private:
       static_cast<std::size_t>(InitialList::GridMembers::ENUM_SIZE);
 
   static constexpr std::array<const char *, size_GridMembers>
-      GridMembersString = {"pqc_in_string",  "pqc_in_file", "pqc_db_string",
-                           "pqc_db_file",    "grid_def",    "grid_size",
-                           "constant_cells", "porosity"};
+      GridMembersString = {"pqc_in_string", "pqc_in_file",    "pqc_with_redox",
+                           "pqc_db_string", "pqc_db_file",    "grid_def",
+                           "grid_size",     "constant_cells", "porosity"};
 
   constexpr const char *GRID_MEMBER_STR(GridMembers member) const {
     return GridMembersString[static_cast<std::size_t>(member)];