From 32d35190cbd7a966d98d41bbb9bea0bd69878dd7 Mon Sep 17 00:00:00 2001
From: Max Luebke <mluebke@gfz-potsdam.de>
Date: Tue, 14 Feb 2023 16:37:56 +0100
Subject: [PATCH] fix: write fields using R after chem simulation

---
 app/poet.cpp                     |  1 +
 include/poet/DiffusionModule.hpp |  2 +-
 include/poet/Grid.hpp            |  3 +++
 src/Grid.cpp                     | 19 +++++++++++++++++++
 4 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/app/poet.cpp b/app/poet.cpp
index 69999a82d..097c9ff33 100644
--- a/app/poet.cpp
+++ b/app/poet.cpp
@@ -164,6 +164,7 @@ inline double RunMasterLoop(SimParams &params, RInside &R, Grid &grid,
     chem.RunCells();
     chem_state->mem = chem.GetField();
 
+    grid.WriteFieldsToR(R);
     grid.PreModuleFieldCopy(tick++);
 
     R["req_dt"] = dt;
diff --git a/include/poet/DiffusionModule.hpp b/include/poet/DiffusionModule.hpp
index ce486b9e2..52d0199d0 100644
--- a/include/poet/DiffusionModule.hpp
+++ b/include/poet/DiffusionModule.hpp
@@ -39,7 +39,7 @@ namespace poet {
  *
  */
 
-constexpr const char *DIFFUSION_MODULE_NAME = "state_t";
+constexpr const char *DIFFUSION_MODULE_NAME = "state_T";
 
 class DiffusionModule {
 public:
diff --git a/include/poet/Grid.hpp b/include/poet/Grid.hpp
index 852220919..2ea2068b9 100644
--- a/include/poet/Grid.hpp
+++ b/include/poet/Grid.hpp
@@ -22,6 +22,7 @@
 #define GRID_H
 
 #include "poet/SimParams.hpp"
+#include <RInside.h>
 #include <Rcpp.h>
 #include <array>
 #include <cstddef>
@@ -97,6 +98,8 @@ public:
                         std::string module_name = poet::GRID_MODULE_NAME) const
       -> std::vector<double>;
 
+  void WriteFieldsToR(RInside &R);
+
 private:
   std::vector<FlowInputOutputInfo> flow_vec;
 
diff --git a/src/Grid.cpp b/src/Grid.cpp
index 2fe125d32..ba70e16ee 100644
--- a/src/Grid.cpp
+++ b/src/Grid.cpp
@@ -19,7 +19,9 @@
 */
 
 #include "poet/SimParams.hpp"
+#include <RInside.h>
 #include <Rcpp.h>
+#include <Rcpp/internal/wrap.h>
 #include <algorithm>
 #include <cassert>
 #include <cstdint>
@@ -253,3 +255,20 @@ auto poet::Grid::GetSpeciesByName(std::string name,
   return std::vector<double>(module_memory->mem.begin() + begin_vec,
                              module_memory->mem.begin() + end_vec);
 }
+
+// HACK: Helper function
+void poet::Grid::WriteFieldsToR(RInside &R) {
+
+  for (auto const &elem : this->state_register) {
+    std::string field_name = elem.first;
+    StateMemory *field = elem.second;
+
+    const uint32_t n_cells_per_prop = field->mem.size() / field->props.size();
+
+    R["TMP"] = Rcpp::wrap(field->mem);
+    R["TMP_PROPS"] = Rcpp::wrap(field->props);
+    R.parseEval(std::string(
+        "mysetup$" + field_name + " <- setNames(data.frame(matrix(TMP, nrow=" +
+        std::to_string(n_cells_per_prop) + ")), TMP_PROPS)"));
+  }
+}