From 7c97f29fa6fc371c1ab7f50a945aeb8dcd9fe6c3 Mon Sep 17 00:00:00 2001
From: rastogi <rastogi@hpc-login.hpc.cs.uni-potsdam.de>
Date: Thu, 30 Oct 2025 21:36:03 +0100
Subject: [PATCH] Added ctrl_cell_ids

---
 src/Control/ControlModule.hpp |  5 +++++
 src/poet.cpp                  |  3 +++
 src/poet.hpp.in               | 12 ++++--------
 3 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/src/Control/ControlModule.hpp b/src/Control/ControlModule.hpp
index 01c76ccb9..2631e937a 100644
--- a/src/Control/ControlModule.hpp
+++ b/src/Control/ControlModule.hpp
@@ -52,6 +52,7 @@ public:
     std::uint32_t control_interval;
     std::vector<std::string> species_names;
     std::vector<double> mape_threshold;
+    std::vector<double> ctrl_cell_ids;
   };
 
   void enableControlLogic(const ControlSetup &setup) {
@@ -60,6 +61,7 @@ public:
     this->control_interval = setup.control_interval;
     this->species_names = setup.species_names;
     this->mape_threshold = setup.mape_threshold;
+    this->ctrl_cell_ids = setup.ctrl_cell_ids;
   }
 
   bool getControlIntervalEnabled() const {
@@ -78,6 +80,8 @@ public:
 
   std::vector<double> getMapeThreshold() const { return this->mape_threshold; }
 
+  std::vector<uint32_t> getCtrlCellIds() const { return this->ctrl_cell_ids; }
+
   /* Profiling getters */
 
   auto getUpdateCtrlLogicTime() const { return this->prep_t; }
@@ -100,6 +104,7 @@ private:
   std::uint32_t rollback_count = 0;
   std::uint32_t sur_disabled_counter = 0;
   std::vector<double> mape_threshold;
+  std::vector<uint32_t> ctrl_cell_ids;
 
   std::vector<std::string> species_names;
   std::string out_dir;
diff --git a/src/poet.cpp b/src/poet.cpp
index 5f7a92e82..bf04da0a8 100644
--- a/src/poet.cpp
+++ b/src/poet.cpp
@@ -250,10 +250,13 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
 
     params.timesteps =
         Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("timesteps"));
+    params.checkpoint_interval = Rcpp::as<uint32_t>(global_rt_setup->operator[]("checkpoint_interval"));
     params.control_interval =
         Rcpp::as<uint32_t>(global_rt_setup->operator[]("control_interval"));
     params.mape_threshold = Rcpp::as<std::vector<double>>(
         global_rt_setup->operator[]("mape_threshold"));
+    params.ctrl_cell_ids =  Rcpp::as<std::vector<uint32_t>>(
+        global_rt_setup->operator[]("ctrl_cell_ids"));
 
     catch (const std::exception &e) {
       ERRMSG("Error while parsing R scripts: " + std::string(e.what()));
diff --git a/src/poet.hpp.in b/src/poet.hpp.in
index a5b82c150..d92f35bc2 100644
--- a/src/poet.hpp.in
+++ b/src/poet.hpp.in
@@ -41,7 +41,6 @@ static const inline std::string r_runtime_parameters = "mysetup";
 struct RuntimeParameters {
   std::string out_dir;
   std::vector<double> timesteps;
-  std::vector<double> species_epsilon;
 
   Rcpp::List init_params;
 
@@ -52,13 +51,10 @@ struct RuntimeParameters {
 
   bool print_progress = false;
 
-  std::uint32_t penalty_iteration = 0;
-  std::uint32_t max_penalty_iteration = 0;
-  std::uint32_t penalty_counter = 0;
-  std::uint32_t next_penalty_check = 0;
-  bool rollback_simulation = false;
-  bool control_iteration_active = false;
-  std::uint32_t control_iteration = 1;
+  std::uint32_t checkpoint_interval = 0;
+  std::uint32_t control_interval = 0;
+  std::vector<double> mape_threshold;
+  std::vector<double> ctrl_cell_ids;
 
   static constexpr std::uint32_t WORK_PACKAGE_SIZE_DEFAULT = 32;
   std::uint32_t work_package_size = WORK_PACKAGE_SIZE_DEFAULT;