feat: Added rb_limit, rb_interval_limit and condition for bcasting control flags

src/Chemistry/ChemistryModule.hpp

@@ -44,8 +44,7 @@ public:
    * \param wp_size Count of grid cells to fill each work package at maximum.
    * \param communicator MPI communicator to distribute work in.
    */
-  ChemistryModule(uint32_t wp_size,
+  ChemistryModule(uint32_t wp_size, const InitialList::ChemistryInit chem_params,
-                  const InitialList::ChemistryInit chem_params,
                   MPI_Comm communicator);
 
   /**
@@ -71,8 +70,7 @@ public:
   auto GetChemistryTime() const { return this->chem_t; }
 
   void setFilePadding(std::uint32_t maxiter) {
-    this->file_pad =
+    this->file_pad = static_cast<std::uint8_t>(std::ceil(std::log10(maxiter + 1)));
-        static_cast<std::uint8_t>(std::ceil(std::log10(maxiter + 1)));
   }
 
   struct SurrogateSetup {
@@ -105,8 +103,7 @@ public:
     this->ctrl_file_out_dir = setup.dht_out_dir;
 
     if (this->dht_enabled || this->interp_enabled) {
-      this->initializeDHT(setup.dht_size_mb, this->params.dht_species,
+      this->initializeDHT(setup.dht_size_mb, this->params.dht_species, setup.has_het_ids);
-                          setup.has_het_ids);
 
       if (setup.dht_snaps != DHT_SNAPS_DISABLED) {
         this->setDHTSnapshots(setup.dht_snaps, setup.dht_out_dir);
@@ -115,8 +112,7 @@ public:
 
     if (this->interp_enabled) {
       this->initializeInterp(setup.interp_bucket_size, setup.interp_size_mb,
-                             setup.interp_min_entries,
+                             setup.interp_min_entries, this->params.interp_species);
-                             this->params.interp_species);
     }
   }
 
@@ -239,9 +235,7 @@ public:
    *
    * \param enabled True if print progressbar, false if not.
    */
-  void setProgressBarPrintout(bool enabled) {
+  void setProgressBarPrintout(bool enabled) { this->print_progessbar = enabled; };
-    this->print_progessbar = enabled;
-  };
 
   /**
    *  **Master only** Set the ai surrogate validity vector from R
@@ -275,8 +269,7 @@ public:
   }
 
 protected:
-  void initializeDHT(uint32_t size_mb,
+  void initializeDHT(uint32_t size_mb, const NamedVector<std::uint32_t> &key_species,
-                     const NamedVector<std::uint32_t> &key_species,
                      bool has_het_ids);
   void setDHTSnapshots(int type, const std::string &out_dir);
   void setDHTReadFile(const std::string &input_file);
@@ -349,9 +342,8 @@ protected:
   void MasterRunSequential();
 
   void MasterSendPkgs(worker_list_t &w_list, workpointer_t &work_pointer,
-                      workpointer_t &sur_pointer, int &pkg_to_send,
+                      workpointer_t &sur_pointer, int &pkg_to_send, int &count_pkgs,
-                      int &count_pkgs, int &free_workers, double dt,
+                      int &free_workers, double dt, uint32_t iteration,
-                      uint32_t iteration,
                       const std::vector<uint32_t> &wp_sizes_vector);
   void MasterRecvPkgs(worker_list_t &w_list, int &pkg_to_recv, bool to_send,
                       int &free_workers);
@@ -361,8 +353,7 @@ protected:
 
   void WorkerProcessPkgs(struct worker_s &timings, uint32_t &iteration);
 
-  void WorkerDoWork(MPI_Status &probe_status, int double_count,
+  void WorkerDoWork(MPI_Status &probe_status, int double_count, struct worker_s &timings);
-                    struct worker_s &timings);
   void WorkerPostIter(MPI_Status &probe_status, uint32_t iteration);
   void WorkerPostSim(uint32_t iteration);
 
@@ -372,26 +363,23 @@ protected:
   void WorkerPerfToMaster(int type, const struct worker_s &timings);
   void WorkerMetricsToMaster(int type);
 
-  void WorkerRunWorkPackage(WorkPackage &work_package, double dSimTime,
+  void WorkerRunWorkPackage(WorkPackage &work_package, double dSimTime, double dTimestep);
-                            double dTimestep);
 
-  std::vector<uint32_t> CalculateWPSizesVector(uint32_t n_cells,
+  std::vector<uint32_t> CalculateWPSizesVector(uint32_t n_cells, uint32_t wp_size) const;
-                                               uint32_t wp_size) const;
   std::vector<double> shuffleField(const std::vector<double> &in_field,
                                    uint32_t size_per_prop, uint32_t prop_count,
                                    uint32_t wp_count);
-  void unshuffleField(const std::vector<double> &in_buffer,
+  void unshuffleField(const std::vector<double> &in_buffer, uint32_t size_per_prop,
-                      uint32_t size_per_prop, uint32_t prop_count,
+                      uint32_t prop_count, uint32_t wp_count,
-                      uint32_t wp_count, std::vector<double> &out_field);
+                      std::vector<double> &out_field);
   std::vector<std::int32_t>
   parseDHTSpeciesVec(const NamedVector<std::uint32_t> &key_species,
                      const std::vector<std::string> &to_compare) const;
 
   void BCastStringVec(std::vector<std::string> &io);
 
-  void processCtrlPkgs(std::vector<std::vector<double>> &input,
+  void processCtrlPkgs(std::vector<std::vector<double>> &input, double current_sim_time,
-                       double current_sim_time, double dt,
+                       double dt, struct worker_s &timings);
-                       struct worker_s &timings);
 
   void copyPkgs(const WorkPackage &wp, std::vector<double> &mpi_buffer);
 
@@ -408,7 +396,11 @@ protected:
   }
   inline bool hasFlag(int flags, int type) { return (flags & type) != 0; }
 
-  
+  inline void
+  extractCtrlSurVectors(std::unordered_map<uint32_t, std::vector<double>> ctrl_output,
+                        const std::vector<double> &buffer, uint32_t n_cells,
+                        uint32_t prop_count, std::vector<std::vector<double>> &ctrl_vec,
+                        std::vector<std::vector<double>> &sur_vec);
 
   int comm_size, comm_rank;
   MPI_Comm group_comm;
@@ -434,11 +426,7 @@ protected:
     MPI_Bcast(buf, count, datatype, 0, this->group_comm);
   }
 
-  inline void PropagateFunctionType(int &type) const {
+  inline void PropagateFunctionType(int &type) const { ChemBCast(&type, 1, MPI_INT); }
-    ChemBCast(&type, 1, MPI_INT);
-  }
-
-
 
   double simtime = 0.;
   double idle_t = 0.;
@@ -476,7 +464,7 @@ protected:
   bool control_enabled{false};
   bool stab_enabled{false};
   std::unordered_set<uint32_t> ctrl_cell_ids;
-  std::vector<std::vector<double>> ctrl_batch;
+  std::unordered_map<uint32_t, std::vector<double>> ctrl_batch;
 };
 } // namespace poet
 

src/Chemistry/MasterFunctions.cpp

@@ -4,6 +4,8 @@
 #include <cstddef>
 #include <cstdint>
 #include <mpi.h>
+#include <numeric>
+#include <unordered_map>
 #include <vector>
 
 std::vector<uint32_t> poet::ChemistryModule::MasterGatherWorkerMetrics(int type) const {
@@ -12,7 +14,8 @@ std::vector<uint32_t> poet::ChemistryModule::MasterGatherWorkerMetrics(int type)
   uint32_t dummy;
   std::vector<uint32_t> metrics(this->comm_size);
 
-  MPI_Gather(&dummy, 1, MPI_UINT32_T, metrics.data(), 1, MPI_UINT32_T, 0, this->group_comm);
+  MPI_Gather(&dummy, 1, MPI_UINT32_T, metrics.data(), 1, MPI_UINT32_T, 0,
+             this->group_comm);
 
   metrics.erase(metrics.begin());
   return metrics;
@@ -72,8 +75,8 @@ std::vector<uint32_t> poet::ChemistryModule::GetWorkerDHTHits() const {
   MPI_Get_count(&probe, MPI_UINT32_T, &count);
 
   std::vector<uint32_t> ret(count);
-  MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, WORKER_DHT_HITS, this->group_comm,
+  MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, WORKER_DHT_HITS,
-           NULL);
+           this->group_comm, NULL);
 
   return ret;
 }
@@ -114,7 +117,8 @@ std::vector<double> poet::ChemistryModule::GetWorkerInterpolationGatherTimings()
   return MasterGatherWorkerTimings(WORKER_IP_GATHER);
 }
 
-std::vector<double> poet::ChemistryModule::GetWorkerInterpolationFunctionCallTimings() const {
+std::vector<double>
+poet::ChemistryModule::GetWorkerInterpolationFunctionCallTimings() const {
   int type = CHEM_PERF;
   MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
   return MasterGatherWorkerTimings(WORKER_IP_FC);
@@ -132,8 +136,8 @@ std::vector<uint32_t> poet::ChemistryModule::GetWorkerInterpolationCalls() const
   MPI_Get_count(&probe, MPI_UINT32_T, &count);
 
   std::vector<uint32_t> ret(count);
-  MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, WORKER_IP_CALLS, this->group_comm,
+  MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, WORKER_IP_CALLS,
-           NULL);
+           this->group_comm, NULL);
 
   return ret;
 }
@@ -150,13 +154,14 @@ std::vector<uint32_t> poet::ChemistryModule::GetWorkerPHTCacheHits() const {
   MPI_Get_count(&probe, MPI_UINT32_T, &count);
 
   std::vector<uint32_t> ret(count);
-  MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, type, this->group_comm, NULL);
+  MPI_Recv(ret.data(), count, MPI_UINT32_T, probe.MPI_SOURCE, type, this->group_comm,
+           NULL);
 
   return ret;
 }
 
-inline std::vector<int> shuffleVector(const std::vector<int> &in_vector, uint32_t size_per_prop,
+inline std::vector<int> shuffleVector(const std::vector<int> &in_vector,
-                                      uint32_t wp_count) {
+                                      uint32_t size_per_prop, uint32_t wp_count) {
   std::vector<int> out_buffer(in_vector.size());
   uint32_t write_i = 0;
   for (uint32_t i = 0; i < wp_count; i++) {
@@ -168,8 +173,9 @@ inline std::vector<int> shuffleVector(const std::vector<int> &in_vector, uint32_
   return out_buffer;
 }
 
-inline std::vector<double> shuffleField(const std::vector<double> &in_field, uint32_t size_per_prop,
+inline std::vector<double> shuffleField(const std::vector<double> &in_field,
-                                        uint32_t species_count, uint32_t wp_count) {
+                                        uint32_t size_per_prop, uint32_t species_count,
+                                        uint32_t wp_count) {
   std::vector<double> out_buffer(in_field.size());
   uint32_t write_i = 0;
   for (uint32_t i = 0; i < wp_count; i++) {
@@ -216,20 +222,45 @@ inline void printProgressbar(int count_pkgs, int n_wp, int barWidth = 70) {
   std::cout.flush();
   /* end visual progress */
 }
+inline void poet::ChemistryModule::extractCtrlSurVectors(
+    std::unordered_map<uint32_t, std::vector<double>> ctrl_output,
+    const std::vector<double> &buffer, uint32_t n_cells, uint32_t prop_count,
+    std::vector<std::vector<double>> &ctrl_vec,
+    std::vector<std::vector<double>> &sur_vec) {
+  ctrl_vec.reserve(ctrl_output.size());
+  sur_vec.reserve(ctrl_output.size());
 
-/*
+  for (const auto &item : ctrl_output) {
+    const uint32_t id = item.first;
+    const auto &data = item.second;
 
-std::vector<std::vector<double>> extractSurCells(){
+    ctrl_vec.push_back(data);
 
+    /* extract matching surrogate output*/
+    bool found = false;
+    for (uint32_t i = 0; i < n_cells; i++) {
+      uint32_t curr_id = static_cast<uint32_t>(buffer[prop_count * i]);
+
+      if (curr_id == id) {
+        sur_vec.emplace_back(buffer.begin() + prop_count * i,
+                             buffer.begin() + prop_count * (i + 1));
+        found = true;
+        break;
+      }
+    }
+    if (!found) {
+      /* keep alignment if missing */
+      std::vector<double> vec(prop_count, 0.0);
+      vec[0] = static_cast<double>(id);
+      sur_vec.emplace_back(vec);
+    }
+  }
 }
-*/
 
-inline void poet::ChemistryModule::MasterSendPkgs(worker_list_t &w_list,
+inline void poet::ChemistryModule::MasterSendPkgs(
-                                                  workpointer_t &work_pointer,
+    worker_list_t &w_list, workpointer_t &work_pointer, workpointer_t &sur_pointer,
-                                                  workpointer_t &sur_pointer, int &pkg_to_send,
+    int &pkg_to_send, int &count_pkgs, int &free_workers, double dt, uint32_t iteration,
-                                                  int &count_pkgs, int &free_workers, double dt,
+    const std::vector<uint32_t> &wp_sizes_vector) {
-                                                  uint32_t iteration,
-                                                  const std::vector<uint32_t> &wp_sizes_vector) {
   /* declare variables */
   int local_work_package_size;
 
@@ -243,8 +274,8 @@ inline void poet::ChemistryModule::MasterSendPkgs(worker_list_t &w_list,
       local_work_package_size = (int)wp_sizes_vector[count_pkgs];
       count_pkgs++;
 
-      uint32_t wp_start_index = std::accumulate(wp_sizes_vector.begin(),
+      uint32_t wp_start_index = std::accumulate(
-                                                std::next(wp_sizes_vector.begin(), count_pkgs), 0);
+          wp_sizes_vector.begin(), std::next(wp_sizes_vector.begin(), count_pkgs), 0);
 
       /* note current processed work package in workerlist */
       w_list[p].send_addr = work_pointer.base();
@@ -273,12 +304,6 @@ inline void poet::ChemistryModule::MasterSendPkgs(worker_list_t &w_list,
       send_buffer[end_of_wp + 4] = wp_start_index;
       // control flags (bitmask)
 
-      /*
-      int flags = (this->interp_enabled ? 1 : 0) | (this->dht_enabled ? 2 : 0) |
-                  (this->warmup_enabled ? 4 : 0) |
-                  (this->control_enabled ? 8 : 0);
-      send_buffer[end_of_wp + 5] = static_cast<double>(flags);
-      */
       /* ATTENTION Worker p has rank p+1 */
       // MPI_Send(send_buffer, end_of_wp + BUFFER_OFFSET, MPI_DOUBLE, p + 1,
       //          LOOP_WORK, this->group_comm);
@@ -311,11 +336,12 @@ inline void poet::ChemistryModule::MasterRecvPkgs(worker_list_t &w_list, int &pk
     // only of there are still packages to send and free workers are available
     if (to_send && free_workers > 0)
       // non blocking probing
-      MPI_Iprobe(MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD, &need_to_receive, &probe_status);
+      MPI_Iprobe(MPI_ANY_SOURCE, MPI_ANY_TAG, this->group_comm, &need_to_receive,
+                 &probe_status);
     else {
       idle_a = MPI_Wtime();
       // blocking probing
-      MPI_Probe(MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD, &probe_status);
+      MPI_Probe(MPI_ANY_SOURCE, MPI_ANY_TAG, this->group_comm, &probe_status);
       idle_b = MPI_Wtime();
       this->idle_t += idle_b - idle_a;
     }
@@ -354,7 +380,11 @@ inline void poet::ChemistryModule::MasterRecvPkgs(worker_list_t &w_list, int &pk
       for (std::size_t i = 0; i < cells_per_batch; i++) {
         std::vector<double> cell_output(recv_buffer.begin() + this->prop_count * i,
                                         recv_buffer.begin() + this->prop_count * (i + 1));
-        this->ctrl_batch.push_back(cell_output);
+
+        if (!cell_output.empty()) {
+          uint32_t id = static_cast<uint32_t>(cell_output[0]);
+          this->ctrl_batch[id] = cell_output;
+        }
       }
       break;
     }
@@ -422,19 +452,19 @@ void poet::ChemistryModule::MasterRunParallel(double dt) {
   if (this->ai_surrogate_enabled) {
     ftype = CHEM_AI_BCAST_VALIDITY;
     PropagateFunctionType(ftype);
-    this->ai_surrogate_validity_vector =
+    this->ai_surrogate_validity_vector = shuffleVector(
-        shuffleVector(this->ai_surrogate_validity_vector, this->n_cells, wp_sizes_vector.size());
+        this->ai_surrogate_validity_vector, this->n_cells, wp_sizes_vector.size());
     ChemBCast(&this->ai_surrogate_validity_vector.front(), this->n_cells, MPI_INT);
   }
 
-  ftype = CHEM_CTRL_FLAGS;
+  if (control->needsFlagBcast()) {
-  PropagateFunctionType(ftype);
+    ftype = CHEM_CTRL_FLAGS;
-  uint32_t ctrl_flags = buildCtrlFlags(this->dht_enabled, this->interp_enabled, this->stab_enabled);
+    PropagateFunctionType(ftype);
-  ChemBCast(&ctrl_flags, 1, MPI_UINT32_T);
+    uint32_t ctrl_flags =
-  // std::cout << "[Master] Flags mask=" << ctrl_flags
+        buildCtrlFlags(this->dht_enabled, this->interp_enabled, this->stab_enabled);
-  //           << " dht=" << this->dht_enabled
+    ChemBCast(&ctrl_flags, 1, MPI_UINT32_T);
-  //           << " ip=" << this->interp_enabled
+  }
-  //           << " stab=" << this->stab_enabled << std::endl;
+  this->ctrl_batch.clear();
 
   ftype = CHEM_WORK_LOOP;
   PropagateFunctionType(ftype);
@@ -448,8 +478,8 @@ void poet::ChemistryModule::MasterRunParallel(double dt) {
 
   /* shuffle grid */
   // grid.shuffleAndExport(mpi_buffer);
-  std::vector<double> mpi_buffer =
+  std::vector<double> mpi_buffer = shuffleField(chem_field.AsVector(), this->n_cells,
-      shuffleField(chem_field.AsVector(), this->n_cells, this->prop_count, wp_sizes_vector.size());
+                                                this->prop_count, wp_sizes_vector.size());
 
   /* setup local variables */
   pkg_to_send = wp_sizes_vector.size();
@@ -479,8 +509,8 @@ void poet::ChemistryModule::MasterRunParallel(double dt) {
     // while there are still packages to send
     if (pkg_to_send > 0) {
       // send packages to all free workers ...
-      MasterSendPkgs(worker_list, work_pointer, sur_pointer, pkg_to_send, i_pkgs, free_workers, dt,
+      MasterSendPkgs(worker_list, work_pointer, sur_pointer, pkg_to_send, i_pkgs,
-                     iteration, wp_sizes_vector);
+                     free_workers, dt, iteration, wp_sizes_vector);
     }
     // ... and try to receive them from workers who has finished their work
     MasterRecvPkgs(worker_list, pkg_to_recv, pkg_to_send > 0, free_workers);
@@ -499,7 +529,8 @@ void poet::ChemistryModule::MasterRunParallel(double dt) {
   /* unshuffle grid */
   // grid.importAndUnshuffle(mpi_buffer);
   std::vector<double> out_vec{mpi_buffer};
-  unshuffleField(mpi_buffer, this->n_cells, this->prop_count, wp_sizes_vector.size(), out_vec);
+  unshuffleField(mpi_buffer, this->n_cells, this->prop_count, wp_sizes_vector.size(),
+                 out_vec);
   chem_field = out_vec;
 
   /* do master stuff */
@@ -508,31 +539,42 @@ void poet::ChemistryModule::MasterRunParallel(double dt) {
     std::cout << "[Master] Processing " << this->ctrl_batch.size()
               << " control cells for comparison." << std::endl;
 
-    std::vector<std::vector<double>> sur_batch;
+    std::vector<std::vector<double>> ctrl_vec;
-    sur_batch.reserve(this->ctrl_batch.size());
+    std::vector<std::vector<double>> sur_vec;
 
-    for (const auto &element : this->ctrl_batch) {
+    extractCtrlSurVectors(this->ctrl_batch, mpi_buffer, this->n_cells, this->prop_count,
+                          ctrl_vec, sur_vec);
 
-      /* using mpi-buffer because we need cell-major layout*/
+    // Diagnostics: iterate map correctly
-      for (size_t i = 0; i < this->n_cells; i++) {
+    if (this->ctrl_batch.size() > this->ctrl_cell_ids.size()) {
-        uint32_t curr_cell_id = mpi_buffer[this->prop_count * i];
+      std::cout << "[Master] Warning: ctrl_batch (" << this->ctrl_batch.size()
+                << ") is larger than ctrl_cell_ids (" << this->ctrl_cell_ids.size()
+                << "). Dumping IDs and species concentrations:" << std::endl;
 
-        if (curr_cell_id == element[0]) {
+      for (const auto &kv : this->ctrl_batch) {
-          std::vector<double> sur_output(mpi_buffer.begin() + this->prop_count * i,
+        const uint32_t id = kv.first;
-                                         mpi_buffer.begin() + this->prop_count * (i + 1));
+        const auto &row = kv.second;
-          sur_batch.push_back(sur_output);
+        if (row.empty())
-          break;
+          continue;
+
+        // Print all columns with names, starting from k = 0
+        for (std::size_t k = 0; k < row.size(); ++k) {
+          std::string name = (k < prop_names.size())
+                                 ? prop_names[k] // species_names/prop_names
+                                 : ("prop" + std::to_string(k)); // fallback
+          std::cout << name << "=" << row[k];
+          if (k + 1 < row.size())
+            std::cout << ", ";
         }
+        std::cout << std::endl;
       }
     }
 
     metrics_a = MPI_Wtime();
-    control->computeMetrics(this->ctrl_batch, sur_batch, prop_names, ctrl_cell_ids.size(),
+    control->computeMetrics(ctrl_vec, sur_vec, prop_names, ctrl_cell_ids.size(),
                             ctrl_file_out_dir);
     metrics_b = MPI_Wtime();
     this->metrics_t += metrics_b - metrics_a;
-
-    this->ctrl_batch.clear();
   }
 
   /* start time measurement of master chemistry */
@@ -543,7 +585,12 @@ void poet::ChemistryModule::MasterRunParallel(double dt) {
   this->seq_t += seq_d - seq_c;
 
   /* end time measurement of whole chemistry simulation */
-  std::optional<uint32_t> target = control->findRbTarget(prop_names);
+
+  std::optional<uint32_t> target = std::nullopt;
+
+  if (!this->ctrl_batch.empty()) {
+    target = control->findRbTarget(prop_names);
+  }
   int flush = target.has_value() ? 1 : 0;
 
   /* advise workers to end chemistry iteration */
@@ -566,8 +613,8 @@ void poet::ChemistryModule::MasterLoopBreak() {
   MPI_Bcast(&type, 1, MPI_INT, 0, this->group_comm);
 }
 
-std::vector<uint32_t> poet::ChemistryModule::CalculateWPSizesVector(uint32_t n_cells,
+std::vector<uint32_t>
-                                                                    uint32_t wp_size) const {
+poet::ChemistryModule::CalculateWPSizesVector(uint32_t n_cells, uint32_t wp_size) const {
   bool mod_pkgs = (n_cells % wp_size) != 0;
   uint32_t n_packages = (uint32_t)(n_cells / wp_size) + static_cast<int>(mod_pkgs);
 

src/Chemistry/WorkerFunctions.cpp

@@ -13,6 +13,7 @@
 #include <mpi.h>
 #include <stdexcept>
 #include <string>
+#include <unordered_map>
 #include <vector>
 
 namespace poet {
@@ -93,7 +94,8 @@ void poet::ChemistryModule::WorkerLoop() {
   }
 }
 
-void poet::ChemistryModule::WorkerProcessPkgs(struct worker_s &timings, uint32_t &iteration) {
+void poet::ChemistryModule::WorkerProcessPkgs(struct worker_s &timings,
+                                              uint32_t &iteration) {
   MPI_Status probe_status;
   bool loop = true;
 
@@ -123,7 +125,8 @@ void poet::ChemistryModule::WorkerProcessPkgs(struct worker_s &timings, uint32_t
   }
 }
 
-void poet::ChemistryModule::copyPkgs(const WorkPackage &wp, std::vector<double> &mpi_buffer) {
+void poet::ChemistryModule::copyPkgs(const WorkPackage &wp,
+                                     std::vector<double> &mpi_buffer) {
 
   for (std::size_t wp_i = 0; wp_i < wp.size; wp_i++) {
     std::copy(wp.output[wp_i].begin(), wp.output[wp_i].end(),
@@ -153,8 +156,8 @@ void poet::ChemistryModule::processCtrlPkgs(std::vector<std::vector<double>> &in
   copyPkgs(control_wp, mpi_buffer);
 
   MPI_Request send_req;
-  MPI_Isend(mpi_buffer.data(), mpi_buffer.size(), MPI_DOUBLE, 0, LOOP_CTRL, MPI_COMM_WORLD,
+  MPI_Isend(mpi_buffer.data(), mpi_buffer.size(), MPI_DOUBLE, 0, LOOP_CTRL,
-            &send_req);
+            this->group_comm, &send_req);
   MPI_Wait(&send_req, MPI_STATUS_IGNORE);
 }
 
@@ -175,14 +178,12 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status, int double_co
   int flags;
   std::vector<double> mpi_buffer(count);
 
-  static int ctrl_cells_processed = 0;
-  static std::vector<std::vector<double>> ctrl_batch;
-
   const int CL_INDEX = 7;
   const double CL_THRESHOLD = 1e-10;
 
   /* receive */
-  MPI_Recv(mpi_buffer.data(), count, MPI_DOUBLE, 0, LOOP_WORK, this->group_comm, MPI_STATUS_IGNORE);
+  MPI_Recv(mpi_buffer.data(), count, MPI_DOUBLE, 0, LOOP_WORK, this->group_comm,
+           MPI_STATUS_IGNORE);
 
   /* decrement count of work_package by BUFFER_OFFSET */
   count -= BUFFER_OFFSET;
@@ -205,19 +206,18 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status, int double_co
   wp_start_index = mpi_buffer[count + 4];
 
   for (std::size_t wp_i = 0; wp_i < s_curr_wp.size; wp_i++) {
-    s_curr_wp.input[wp_i] = std::vector<double>(mpi_buffer.begin() + this->prop_count * wp_i,
+    s_curr_wp.input[wp_i] =
-                                                mpi_buffer.begin() + this->prop_count * (wp_i + 1));
+        std::vector<double>(mpi_buffer.begin() + this->prop_count * wp_i,
+                            mpi_buffer.begin() + this->prop_count * (wp_i + 1));
   }
 
   /* skip simulation of cells cells where Cl concentration is below threshold */
-  /*
   for (std::size_t wp_i = 0; wp_i < s_curr_wp.size; wp_i++) {
     if (s_curr_wp.input[wp_i][CL_INDEX] < CL_THRESHOLD) {
       s_curr_wp.mapping[wp_i] = CHEM_SKIP;
       s_curr_wp.output[wp_i] = s_curr_wp.input[wp_i];
     }
   }
-  */
 
   // std::cout << this->comm_rank << ":" << counter++ << std::endl;
   if (dht_enabled || interp_enabled || stab_enabled) {
@@ -245,26 +245,29 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status, int double_co
     }
   }
 
-  //  if (!this->stab_enabled) { /* process cells to be monitored in a seperate workpackage */
+  if (!this->stab_enabled) {
-  for (std::size_t wp_i = 0; wp_i < s_curr_wp.size; wp_i++) {
+    std::unordered_map<uint32_t, std::vector<double>> ctrl_cells_wp;
-    uint32_t cell_id = s_curr_wp.input[wp_i][0];
+    for (std::size_t wp_i = 0; wp_i < s_curr_wp.size; wp_i++) {
+      uint32_t id = static_cast<uint32_t>(s_curr_wp.input[wp_i][0]);
 
-    bool is_ctrl_cell = this->ctrl_cell_ids.find(cell_id) != this->ctrl_cell_ids.end();
+      bool is_ctrl_cell = this->ctrl_cell_ids.find(id) != this->ctrl_cell_ids.end();
-    bool used_sur = (s_curr_wp.mapping[wp_i] != CHEM_PQC) && (s_curr_wp.mapping[wp_i] != CHEM_SKIP);
+      bool used_sur =
+          (s_curr_wp.mapping[wp_i] != CHEM_PQC) && (s_curr_wp.mapping[wp_i] != CHEM_SKIP);
 
-    if (is_ctrl_cell && used_sur) {
+      if (is_ctrl_cell && used_sur) {
-      ctrl_batch.push_back(s_curr_wp.input[wp_i]);
+        ctrl_cells_wp[id] = s_curr_wp.input[wp_i];
-      ctrl_cells_processed++;
-
-      if (ctrl_batch.size() == s_curr_wp.size ||
-          ctrl_cells_processed == this->ctrl_cell_ids.size()) {
-        processCtrlPkgs(ctrl_batch, current_sim_time, dt, timings);
-        ctrl_batch.clear();
-        ctrl_cells_processed = 0;
       }
     }
+
+    if (!ctrl_cells_wp.empty()) {
+      std::vector<std::vector<double>> batch;
+      batch.reserve(ctrl_cells_wp.size());
+      for (auto &kv : ctrl_cells_wp) {
+        batch.push_back(kv.second);
+      }
+      processCtrlPkgs(batch, current_sim_time, dt, timings);
+    }
   }
-  // }
 
   phreeqc_time_start = MPI_Wtime();
 
@@ -276,7 +279,8 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status, int double_co
 
   /* send results to master */
   MPI_Request send_req;
-  MPI_Isend(mpi_buffer.data(), count, MPI_DOUBLE, 0, LOOP_WORK, MPI_COMM_WORLD, &send_req);
+  MPI_Isend(mpi_buffer.data(), count, MPI_DOUBLE, 0, LOOP_WORK, this->group_comm,
+            &send_req);
 
   if (dht_enabled || interp_enabled || stab_enabled) {
     /* write results to DHT */
@@ -299,8 +303,8 @@ void poet::ChemistryModule::WorkerPostIter(MPI_Status &probe_status, uint32_t it
   MPI_Get_count(&probe_status, MPI_INT, &size);
 
   if (size == 1) {
-    MPI_Recv(&flush_request, size, MPI_INT, probe_status.MPI_SOURCE, LOOP_END, this->group_comm,
+    MPI_Recv(&flush_request, size, MPI_INT, probe_status.MPI_SOURCE, LOOP_END,
-             MPI_STATUS_IGNORE);
+             this->group_comm, MPI_STATUS_IGNORE);
   } else {
     MPI_Recv(NULL, 0, MPI_INT, probe_status.MPI_SOURCE, LOOP_END, this->group_comm,
              MPI_STATUS_IGNORE);
@@ -322,8 +326,8 @@ void poet::ChemistryModule::WorkerPostIter(MPI_Status &probe_status, uint32_t it
     interp->resetCounter();
     interp->writePHTStats();
     if (this->dht_snaps_type == DHT_SNAPS_ITEREND) {
-      out << this->dht_file_out_dir << "/iter_" << std::setfill('0') << std::setw(this->file_pad)
+      out << this->dht_file_out_dir << "/iter_" << std::setfill('0')
-          << iteration << ".pht";
+          << std::setw(this->file_pad) << iteration << ".pht";
       interp->dumpPHTState(out.str());
     }
 
@@ -347,16 +351,16 @@ void poet::ChemistryModule::WorkerPostSim(uint32_t iteration) {
   }
   if (this->interp_enabled && this->dht_snaps_type >= DHT_SNAPS_ITEREND) {
     std::stringstream out;
-    out << this->dht_file_out_dir << "/iter_" << std::setfill('0') << std::setw(this->file_pad)
+    out << this->dht_file_out_dir << "/iter_" << std::setfill('0')
-        << iteration << ".pht";
+        << std::setw(this->file_pad) << iteration << ".pht";
     interp->dumpPHTState(out.str());
   }
 }
 
 void poet::ChemistryModule::WorkerWriteDHTDump(uint32_t iteration) {
   std::stringstream out;
-  out << this->dht_file_out_dir << "/iter_" << std::setfill('0') << std::setw(this->file_pad)
+  out << this->dht_file_out_dir << "/iter_" << std::setfill('0')
-      << iteration << ".dht";
+      << std::setw(this->file_pad) << iteration << ".dht";
   int res = dht->tableToFile(out.str().c_str());
   if (res != DHT_SUCCESS && this->comm_rank == 2)
     std::cerr << "CPP: Worker: Error in writing current state of DHT to file.\n";
@@ -377,13 +381,13 @@ void poet::ChemistryModule::WorkerReadDHTDump(const std::string &dht_input_file)
     }
   } else {
     if (this->comm_rank == 2)
-      std::cout << "CPP: Worker: Successfully loaded state of DHT from file " << dht_input_file
+      std::cout << "CPP: Worker: Successfully loaded state of DHT from file "
-                << "\n";
+                << dht_input_file << "\n";
   }
 }
 
-void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package, double dSimTime,
+void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package,
-                                                 double dTimestep) {
+                                                 double dSimTime, double dTimestep) {
 
   std::vector<std::vector<double>> inout_chem = work_package.input;
   std::vector<std::size_t> to_ignore;
@@ -399,7 +403,8 @@ void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package, doub
 
   this->pqc_runner->run(inout_chem, dTimestep, to_ignore);
 
-  //std::cout << "Ignored " << to_ignore.size() << " cells out of " << wp_size << "." << std::endl;
+  // std::cout << "Ignored " << to_ignore.size() << " cells out of " << wp_size << "." <<
+  // std::endl;
 
   for (std::size_t wp_id = 0; wp_id < work_package.size; wp_id++) {
     if (work_package.mapping[wp_id] == CHEM_PQC) {
@@ -415,7 +420,8 @@ void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package, doub
 void poet::ChemistryModule::WorkerPerfToMaster(int type, const struct worker_s &timings) {
   switch (type) {
   case WORKER_PHREEQC: {
-    MPI_Gather(&timings.phreeqc_t, 1, MPI_DOUBLE, NULL, 1, MPI_DOUBLE, 0, this->group_comm);
+    MPI_Gather(&timings.phreeqc_t, 1, MPI_DOUBLE, NULL, 1, MPI_DOUBLE, 0,
+               this->group_comm);
     break;
   }
   case WORKER_CTRL_ITER: {
@@ -427,7 +433,8 @@ void poet::ChemistryModule::WorkerPerfToMaster(int type, const struct worker_s &
     break;
   }
   case WORKER_DHT_FILL: {
-    MPI_Gather(&timings.dht_fill, 1, MPI_DOUBLE, NULL, 1, MPI_DOUBLE, 0, this->group_comm);
+    MPI_Gather(&timings.dht_fill, 1, MPI_DOUBLE, NULL, 1, MPI_DOUBLE, 0,
+               this->group_comm);
     break;
   }
   case WORKER_IDLE: {
@@ -470,8 +477,8 @@ void poet::ChemistryModule::WorkerMetricsToMaster(int type) {
   auto reduce_and_send = [&worker_rank, &worker_comm,
                           &group_comm](std::vector<std::uint32_t> &send_buffer, int tag) {
     std::vector<uint32_t> to_master(send_buffer.size());
-    MPI_Reduce(send_buffer.data(), to_master.data(), send_buffer.size(), MPI_UINT32_T, MPI_SUM, 0,
+    MPI_Reduce(send_buffer.data(), to_master.data(), send_buffer.size(), MPI_UINT32_T,
-               worker_comm);
+               MPI_SUM, 0, worker_comm);
 
     if (worker_rank == 0) {
       MPI_Send(to_master.data(), to_master.size(), MPI_UINT32_T, 0, tag, group_comm);

src/Control/ControlModule.cpp

@@ -5,26 +5,22 @@
 #include <cmath>
 #include <numeric>
 
-poet::ControlModule::ControlModule(const ControlConfig &config_) : config(config_) {}
+poet::ControlModule::ControlModule(const ControlConfig &config_, ChemistryModule &chem)
-
+    : config(config_), chem_(chem) {}
-void poet::ControlModule::beginIteration(ChemistryModule &chem, uint32_t &iter,
-                                         const bool &dht_enabled, const bool &interp_enabled) {
 
+void poet::ControlModule::beginIteration(uint32_t &iter, const bool &dht_enabled,
+                                         const bool &interp_enabled) {
   global_iter = iter;
   double prep_a, prep_b;
-
   prep_a = MPI_Wtime();
-
+  updateSurrState(dht_enabled, interp_enabled);
-  updateSurrState(chem, dht_enabled, interp_enabled);
   prep_b = MPI_Wtime();
   this->prep_t += prep_b - prep_a;
 }
 
-/* Disables dht and/or interp during stabilzation phase */
+void poet::ControlModule::updateSurrState(bool dht_enabled, bool interp_enabled) {
-void poet::ControlModule::updateSurrState(ChemistryModule &chem, bool dht_enabled,
-                                          bool interp_enabled) {
   bool in_warmup = (global_iter <= config.stab_interval);
-  bool rb_limit_reached = (rb_count >= config.rb_limit);
+  bool rb_limit_reached = rbLimitReached();
 
   if (rb_enabled && stab_countdown > 0) {
     --stab_countdown;
@@ -32,48 +28,56 @@ void poet::ControlModule::updateSurrState(ChemistryModule &chem, bool dht_enable
     if (stab_countdown == 0) {
       rb_enabled = false;
     }
-    flush_request = false;
   }
-
+  /* disables surrogate during warmup, active rollback or after rollback limit is reached
-  /* disable surrogates during warmup, active rollback or after limit */
+   */
   if (in_warmup || rb_enabled || rb_limit_reached) {
-    chem.SetStabEnabled(!rb_limit_reached);
+    chem_.SetStabEnabled(!rb_limit_reached);
-    chem.SetDhtEnabled(false);
+    chem_.SetDhtEnabled(false);
-    chem.SetInterpEnabled(false);
+    chem_.SetInterpEnabled(false);
 
     if (rb_limit_reached) {
-      std::cout << "Interpolation completly disabled." << std::endl;
+      std::cout << "Interpolation completely disabled." << std::endl;
     } else {
       std::cout << "In stabilization phase." << std::endl;
     }
     return;
   }
 
+  if (rb_count > 0 && !rb_enabled && !in_warmup) {
+    surr_active++;
+    if (surr_active > config.rb_interval_limit) {
+      surr_active = 0;
+      rb_count -= 1;
+      std::cout << "Rollback count reset to: " << rb_count << "." << std::endl;
+    }
+  }
+
   /* enable user-requested surrogates */
-  chem.SetStabEnabled(false);
+  chem_.SetStabEnabled(false);
-  chem.SetDhtEnabled(dht_enabled);
+  chem_.SetDhtEnabled(dht_enabled);
-  chem.SetInterpEnabled(interp_enabled);
+  chem_.SetInterpEnabled(interp_enabled);
   std::cout << "Interpolating." << std::endl;
 }
 
-void poet::ControlModule::writeCheckpoint(DiffusionModule &diffusion, uint32_t &iter,
+void poet::ControlModule::writeCheckpoint(uint32_t &iter, const std::string &out_dir) {
-                                          const std::string &out_dir) {
   if (global_iter % config.chkpt_interval == 0) {
     double w_check_a = MPI_Wtime();
     write_checkpoint(out_dir, "checkpoint" + std::to_string(iter) + ".hdf5",
-                     {.field = diffusion.getField(), .iteration = iter});
+                     {.field = chem_.getField(), .iteration = iter});
     double w_check_b = MPI_Wtime();
     this->w_check_t += w_check_b - w_check_a;
   }
 }
 
-void poet::ControlModule::readCheckpoint(DiffusionModule &diffusion, uint32_t &current_iter,
+void poet::ControlModule::readCheckpoint(uint32_t &current_iter, uint32_t rollback_iter,
-                                         uint32_t rollback_iter, const std::string &out_dir) {
+                                         const std::string &out_dir) {
   double r_check_a, r_check_b;
 
   r_check_a = MPI_Wtime();
-  Checkpoint_s checkpoint_read{.field = diffusion.getField()};
+  Checkpoint_s checkpoint_read{.field = chem_.getField()};
-  read_checkpoint(out_dir, "checkpoint" + std::to_string(rollback_iter) + ".hdf5", checkpoint_read);
+  read_checkpoint(out_dir, "checkpoint" + std::to_string(rollback_iter) + ".hdf5",
+                  checkpoint_read);
   current_iter = checkpoint_read.iteration;
   r_check_b = MPI_Wtime();
   r_check_t += r_check_b - r_check_a;
@@ -81,168 +85,91 @@ void poet::ControlModule::readCheckpoint(DiffusionModule &diffusion, uint32_t &c
 
 void poet::ControlModule::writeMetrics(uint32_t &iter, const std::string &out_dir,
                                        const std::vector<std::string> &species) {
-
-  if (rb_count >= config.rb_limit || global_iter <= config.stab_interval) {
-    return;
-  }
-
-  if (rb_enabled) {
-    return;
-  }
-
   double stats_a = MPI_Wtime();
   writeSpeciesStatsToCSV(s_history, species, out_dir, "species_overview.csv");
-  write_metrics(c_history, species, out_dir, "metrics_overview.hdf5");
+  if (global_iter % (config.chkpt_interval / 2) == 0) {
+    write_metrics(c_history, species, out_dir, "metrics_overview.hdf5");
+  }
   double stats_b = MPI_Wtime();
   this->stats_t += stats_b - stats_a;
 }
 
 uint32_t poet::ControlModule::calcRbIter() {
-  uint32_t last_iter = ((global_iter - 1) / config.chkpt_interval) * config.chkpt_interval;
+  uint32_t last_iter =
+      ((global_iter - 1) / config.chkpt_interval) * config.chkpt_interval;
   return last_iter;
 }
 
-std::optional<uint32_t> poet::ControlModule::findRbTarget(const std::vector<std::string> &species) {
+std::optional<uint32_t>
-
+poet::ControlModule::findRbTarget(const std::vector<std::string> &species) {
-  double r_check_a, r_check_b;
 
   /* Skip threshold checking if already in stabilization phase*/
   if (s_history.empty() || rb_enabled) {
     return std::nullopt;
   }
-
   const auto &s_hist = s_history.back();
 
   /* skipping cell_id and id */
-  for (size_t sp_i = 2; sp_i < species.size(); sp_i++) {
+  for (size_t sp_idx = 2; sp_idx < species.size(); sp_idx++) {
-
+    /* skip Charge */
-    /* check bounds of threshold vector*/
+    if (sp_idx == 4) {
-    if (sp_i >= config.mape_threshold.size()) {
-      std::cerr << "Warning: No threshold defined for species " << species[sp_i] << " at index "
-                << std::to_string(sp_i) << std::endl;
       continue;
     }
-    if (s_hist.mape[sp_i] > config.mape_threshold[sp_i]) {
+    if (sp_idx >= config.mape_threshold.size()) {
-
+      std::cerr << "Warning: No threshold defined for species " << species[sp_idx]
-      const auto &c_hist = c_history.back();
+                << " at index " << std::to_string(sp_idx) << std::endl;
-      auto max_it =
+      continue;
-          std::max_element(c_hist.mape.begin(), c_hist.mape.end(),
+    }
-                           [sp_i](const auto &a, const auto &b) { return a[sp_i] < b[sp_i]; });
+    const double sp_mape = s_hist.mape[sp_idx];
-
+    const double sp_thr = config.mape_threshold[sp_idx];
-      size_t max_idx = std::distance(c_hist.mape.begin(), max_it);
-      uint32_t cell_id = c_hist.id[max_idx];
-      double cell_mape = (*max_it)[sp_i];
 
+    if (sp_mape > sp_thr) {
       flush_request = true;
+      std::cout << "Species " << species[sp_idx]
+                << " exceeded threshold (MAPE=" << sp_mape << " > thr=" << sp_thr
+                << "). Offending cells:" << std::endl;
 
-      std::cout << "Threshold exceeded for " << species[sp_i]
+      if (!c_history.empty()) {
-                << " with species-level MAPE = " << std::to_string(s_hist.mape[sp_i])
+        const auto &c_hist = c_history.back();
-                << " exceeding threshold = " << std::to_string(config.mape_threshold[sp_i])
+        printExceedingCells(c_hist, sp_idx, sp_thr);
-                << ". Worst cell: ID=" << std::to_string(cell_id)
+      }
-                << " with MAPE=" << std::to_string(cell_mape) << std::endl;
-
       return calcRbIter();
     }
   }
   return std::nullopt;
 }
 
-void poet::ControlModule::computeMetrics(std::vector<std::vector<double>> &reference_values,
+void poet::ControlModule::printExceedingCells(const CellMetrics &c_hist, size_t sp_idx,
-                                         std::vector<std::vector<double>> &surrogate_values,
+                                              double sp_thr) {
-                                         const std::vector<std::string> &species,
+  for (size_t cell_idx = 0; cell_idx < c_hist.mape.size(); ++cell_idx) {
-                                         const uint32_t size_per_prop, const std::string &out_dir) {
+    const double mape = c_hist.mape[cell_idx][sp_idx];
-  if (rb_count >= config.rb_limit) {
+    if (mape > sp_thr) {
-    return;
+      const uint32_t id = c_hist.id[cell_idx];
+      std::cout << "  cell_id=" << id << " mape=" << mape << std::endl;
+    }
   }
+}
 
-  const uint32_t n_cells = reference_values.size();
+void poet::ControlModule::computeMetrics(std::vector<std::vector<double>> &ref_values,
+                                         std::vector<std::vector<double>> &sur_values,
+                                         const std::vector<std::string> &species,
+                                         const uint32_t size_per_prop,
+                                         const std::string &out_dir) {
+
+  std::cout << "DEBUG: computeMetrics called at iteration " << global_iter
+            << ", rb_count=" << rb_count << "/" << config.rb_limit << std::endl;
+
+  const uint32_t n_cells = ref_values.size();
   const uint32_t n_species = species.size();
-  const double ZERO_ABS = config.zero_abs;
 
   CellMetrics c_metrics(n_cells, n_species, global_iter, rb_count);
   SpeciesMetrics s_metrics(n_species, global_iter, rb_count);
 
-  std::vector<double> species_err_sum(n_species, 0.0);
+  /* compute cell-level metrics */
-  std::vector<double> species_sqr_sum(n_species, 0.0);
+  computeCellMetrics(ref_values, sur_values, c_metrics);
 
-  for (size_t cell_i = 0; cell_i < n_cells; cell_i++) {
+  /* compute species-level metrics */
-
+  computeSpeciesMetrics(ref_values, sur_values, species, size_per_prop, s_metrics);
-    c_metrics.id.push_back(reference_values[cell_i][0]);
-    c_metrics.mape[cell_i][0] = reference_values[cell_i][0];
-    c_metrics.rrmse[cell_i][0] = reference_values[cell_i][0];
-
-    for (size_t sp_i = 2; sp_i < n_species; sp_i++) {
-      const double ref_value = reference_values[cell_i][sp_i];
-      const double sur_value = surrogate_values[cell_i][sp_i];
-
-      if (std::isnan(ref_value) || std::isnan(sur_value)) {
-        // Initialize to 0 for NaN cases to avoid uninitialized values
-        c_metrics.mape[cell_i][sp_i] = 0.0;
-        c_metrics.rrmse[cell_i][sp_i] = 0.0;
-
-        std::cout << "WARNING: NaN detected - Cell=" << reference_values[cell_i][0]
-                  << ", Species=" << species[sp_i]
-                  << ", Ref=" << (std::isnan(ref_value) ? "NaN" : std::to_string(ref_value))
-                  << ", Sur=" << (std::isnan(sur_value) ? "NaN" : std::to_string(sur_value))
-                  << std::endl;
-        continue;
-      }
-      if (std::abs(ref_value) < ZERO_ABS) {
-        if (std::abs(sur_value) >= ZERO_ABS) {
-
-          species_err_sum[sp_i] += 1.0;
-          species_sqr_sum[sp_i] += 1.0;
-
-          c_metrics.mape[cell_i][sp_i] = 100.0;
-          c_metrics.rrmse[cell_i][sp_i] = 1.0;
-        } else {
-          // Both values are near zero, initialize to 0
-          c_metrics.mape[cell_i][sp_i] = 0.0;
-          c_metrics.rrmse[cell_i][sp_i] = 0.0;
-        }
-      } else {
-        double alpha = 1.0 - (sur_value / ref_value);
-
-        species_err_sum[sp_i] += std::abs(alpha);
-        species_sqr_sum[sp_i] += alpha * alpha;
-
-        c_metrics.mape[cell_i][sp_i] = 100.0 * std::abs(alpha);
-        c_metrics.rrmse[cell_i][sp_i] = alpha * alpha;
-        // Log extreme MAPE values for debugging
-        if (c_metrics.mape[cell_i][sp_i] > 100.0) {
-          std::cout << "WARNING: High MAPE detected - Cell=" << c_metrics.id[cell_i]
-                    << ", Species=" << species[sp_i] << ", MAPE=" << c_metrics.mape[cell_i][sp_i]
-                    << "%, Ref=" << ref_value << ", Sur=" << sur_value << ", Alpha=" << alpha
-                    << std::endl;
-        }
-      }
-    }
-  }
-  for (size_t sp_i = 2; sp_i < n_species; sp_i++) {
-    s_metrics.mape[sp_i] = 100.0 * (species_err_sum[sp_i] / size_per_prop);
-    s_metrics.rrmse[sp_i] = std::sqrt(species_sqr_sum[sp_i] / size_per_prop);
-  }
-
-  // Sort cell metrics by ID
-  std::vector<size_t> indices(n_cells);
-  std::iota(indices.begin(), indices.end(), 0);
-  std::sort(indices.begin(), indices.end(),
-            [&c_metrics](size_t a, size_t b) { return c_metrics.id[a] < c_metrics.id[b]; });
-
-  // Reorder cell metrics based on sorted indices
-  std::vector<uint32_t> sorted_ids(n_cells);
-  std::vector<std::vector<double>> sorted_mape(n_cells, std::vector<double>(n_species));
-  std::vector<std::vector<double>> sorted_rrmse(n_cells, std::vector<double>(n_species));
-
-  for (size_t i = 0; i < n_cells; i++) {
-    sorted_ids[i] = c_metrics.id[indices[i]];
-    sorted_mape[i] = c_metrics.mape[indices[i]];
-    sorted_rrmse[i] = c_metrics.rrmse[indices[i]];
-  }
-
-  c_metrics.id = std::move(sorted_ids);
-  c_metrics.mape = std::move(sorted_mape);
-  c_metrics.rrmse = std::move(sorted_rrmse);
 
   s_history.push_back(s_metrics);
   c_history.push_back(c_metrics);
@@ -250,30 +177,105 @@ void poet::ControlModule::computeMetrics(std::vector<std::vector<double>> &refer
   writeMetrics(global_iter, out_dir, species);
 }
 
-void poet::ControlModule::processCheckpoint(DiffusionModule &diffusion, uint32_t &current_iter,
+inline double poet::ControlModule::computeAlpha(double ref, double sur) const {
-                                            const std::string &out_dir,
+  const double zero_abs = config.zero_abs;
-                                            const std::vector<std::string> &species) {
+  if (std::isnan(ref) || std::isnan(sur)) {
-  if (rb_count >= config.rb_limit) {
+    return 0.0;
+  }
+  if (std::abs(ref) < zero_abs) {
+    return (std::abs(sur) < zero_abs) ? 0.0 : 1.0;
+  }
+  return 1.0 - (sur / ref);
+}
+
+void poet::ControlModule::computeSpeciesMetrics(
+    const std::vector<std::vector<double>> &ref_values,
+    const std::vector<std::vector<double>> &sur_values,
+    const std::vector<std::string> &species, uint32_t size_per_prop,
+    SpeciesMetrics &s_metrics) {
+
+  const size_t n_cells = ref_values.size();
+  const size_t n_species = species.size();
+  std::vector<double> err_sum(n_species, 0.0);
+  std::vector<double> sqr_sum(n_species, 0.0);
+
+  for (size_t cell_idx = 0; cell_idx < n_cells; cell_idx++) {
+    for (size_t sp_idx = 2; sp_idx < n_species; sp_idx++) {
+      const double alpha =
+          computeAlpha(ref_values[cell_idx][sp_idx], sur_values[cell_idx][sp_idx]);
+      err_sum[sp_idx] += std::abs(alpha);
+      sqr_sum[sp_idx] += alpha * alpha;
+    }
+  }
+
+  for (size_t sp_idx = 2; sp_idx < n_species; sp_idx++) {
+    s_metrics.mape[sp_idx] =
+        100.0 * (err_sum[sp_idx] / static_cast<double>(size_per_prop));
+    s_metrics.rrmse[sp_idx] =
+        std::sqrt(sqr_sum[sp_idx] / static_cast<double>(size_per_prop));
+  }
+}
+
+void poet::ControlModule::computeCellMetrics(
+    const std::vector<std::vector<double>> &ref_values,
+    const std::vector<std::vector<double>> &sur_values, CellMetrics &c_metrics) {
+
+  const size_t n_cells = ref_values.size();
+  // Use ref_values to get n_species instead of accessing potentially uninitialized mape
+  const size_t n_species = (n_cells > 0) ? ref_values[0].size() : 0;
+
+  if (n_cells == 0 || n_species == 0) {
+    std::cerr << "Warning: computeCellMetrics called with empty data" << std::endl;
     return;
   }
-  if (flush_request && rb_count < config.rb_limit) {
+
+  for (size_t cell_idx = 0; cell_idx < n_cells; ++cell_idx) {
+    // Assign the per-cell id correctly
+    c_metrics.id[cell_idx] = static_cast<uint32_t>(ref_values[cell_idx][0]);
+
+    for (size_t sp_idx = 2; sp_idx < n_species; ++sp_idx) {
+
+      const double alpha =
+          computeAlpha(ref_values[cell_idx][sp_idx], sur_values[cell_idx][sp_idx]);
+      c_metrics.mape[cell_idx][sp_idx] = 100.0 * std::abs(alpha);
+      c_metrics.rrmse[cell_idx][sp_idx] = alpha * alpha;
+      c_metrics.conc[cell_idx][sp_idx] = ref_values[cell_idx][sp_idx];
+    }
+  }
+
+  /* cell_ID and ID columns */
+}
+
+void poet::ControlModule::processCheckpoint(uint32_t &current_iter,
+                                            const std::string &out_dir,
+                                            const std::vector<std::string> &species) {
+  if (rbLimitReached()) {
+    return;
+  }
+  if (flush_request) {
     uint32_t target = calcRbIter();
-    readCheckpoint(diffusion, current_iter, target, out_dir);
+    readCheckpoint(current_iter, target, out_dir);
 
     rb_enabled = true;
     rb_count++;
     stab_countdown = config.stab_interval;
+    flush_request = false;
 
-    std::cout << "Restored checkpoint " << std::to_string(target) << ", surrogate disabled for "
+    std::cout << "Restored checkpoint " << std::to_string(target)
-              << std::to_string(config.stab_interval) << std::endl;
+              << ", surrogate disabled for " << std::to_string(config.stab_interval)
+              << std::endl;
   } else {
-    writeCheckpoint(diffusion, global_iter, out_dir);
+    writeCheckpoint(global_iter, out_dir);
   }
 }
 
 bool poet::ControlModule::needsFlagBcast() const {
-  if (rb_count >= config.rb_limit) {
+  return (config.rb_limit > 0) && !rbLimitReached();
-    return false;
-  }
-  return true;
 }
+
+inline bool poet::ControlModule::rbLimitReached() const {
+  /* rollback is completly disabled */
+  if (config.rb_limit == 0)
+    return false;
+  return rb_count >= config.rb_limit;
+}

src/Control/ControlModule.hpp

@@ -4,7 +4,6 @@
 #include "Base/Macros.hpp"
 #include "Chemistry/ChemistryModule.hpp"
 #include "IO/HDF5Functions.hpp"
-#include "Transport/DiffusionModule.hpp"
 #include "poet.hpp"
 
 #include <cstdint>
@@ -21,6 +20,7 @@ struct ControlConfig {
   uint32_t stab_interval = 0;
   uint32_t chkpt_interval = 0;
   uint32_t rb_limit = 0;
+  uint32_t rb_interval_limit = 0;
   double zero_abs = 0.0;
   std::vector<double> mape_threshold;
 };
@@ -29,12 +29,15 @@ struct CellMetrics {
   std::vector<std::uint32_t> id;
   std::vector<std::vector<double>> mape;
   std::vector<std::vector<double>> rrmse;
+  std::vector<std::vector<double>> conc;
   uint32_t iteration = 0;
   uint32_t rb_count = 0;
 
   CellMetrics(uint32_t n_cells, uint32_t n_species, uint32_t iter, uint32_t rb_count)
-      : mape(n_cells, std::vector<double>(n_species, 0.0)),
+      : id(n_cells, 0), mape(n_cells, std::vector<double>(n_species, 0.0)),
-        rrmse(n_cells, std::vector<double>(n_species, 0.0)), iteration(iter), rb_count(rb_count) {}
+        rrmse(n_cells, std::vector<double>(n_species, 0.0)),
+        conc(n_cells, std::vector<double>(n_species, 0.0)), iteration(iter),
+        rb_count(rb_count) {}
 };
 
 struct SpeciesMetrics {
@@ -50,22 +53,24 @@ struct SpeciesMetrics {
 class ControlModule {
 
 public:
-  explicit ControlModule(const ControlConfig &config);
+  explicit ControlModule(const ControlConfig &config, ChemistryModule &chem);
 
-  void beginIteration(ChemistryModule &chem, uint32_t &iter, const bool &dht_enabled,
+  /* store global iteration, dht and pht settings */
-                      const bool &interp_enaled);
+  void beginIteration(uint32_t &iter, const bool &dht_enabled, const bool &interp_enaled);
 
   void writeMetrics(uint32_t &iter, const std::string &out_dir,
                     const std::vector<std::string> &species);
 
   void computeMetrics(std::vector<std::vector<double>> &reference_values,
                       std::vector<std::vector<double>> &surrogate_values,
-                      const std::vector<std::string> &species, const uint32_t size_per_prop,
+                      const std::vector<std::string> &species,
-                      const std::string &out_dir);
+                      const uint32_t size_per_prop, const std::string &out_dir);
 
-  void processCheckpoint(DiffusionModule &diffusion, uint32_t &current_iter,
+  void processCheckpoint(uint32_t &current_iter, const std::string &out_dir,
-                         const std::string &out_dir, const std::vector<std::string> &species);
+                         const std::vector<std::string> &species);
 
+  /* Returnn rollback target or nullopt and sets flush_request when threshold is exceeded.
+  It reports the cells which exceed the threshold. */
   std::optional<uint32_t> findRbTarget(const std::vector<std::string> &species);
 
   bool getFlushRequest() const { return flush_request; }
@@ -88,20 +93,38 @@ public:
   auto getMetricsWriteTime() const { return stats_t; }
 
 private:
-  void updateSurrState(ChemistryModule &chem, bool dht_enabled, bool interp_enabled);
+  void updateSurrState(bool dht_enabled, bool interp_enabled);
 
-  void readCheckpoint(DiffusionModule &diffusion, uint32_t &current_iter, uint32_t rollback_iter,
+  void readCheckpoint(uint32_t &current_iter, uint32_t rollback_iter,
                       const std::string &out_dir);
-  void writeCheckpoint(DiffusionModule &diffusion, uint32_t &iter, const std::string &out_dir);
+  void writeCheckpoint(uint32_t &iter, const std::string &out_dir);
 
   uint32_t calcRbIter();
 
+  void computeSpeciesMetrics(const std::vector<std::vector<double>> &ref_values,
+                             const std::vector<std::vector<double>> &sur_values,
+                             const std::vector<std::string> &species,
+                             uint32_t size_per_prop, SpeciesMetrics &s_metrics);
+
+  void computeCellMetrics(const std::vector<std::vector<double>> &ref_values,
+                          const std::vector<std::vector<double>> &sur_values,
+                          CellMetrics &c_metrics);
+
+  inline double computeAlpha(double ref, double sur) const;
+
+  static void printExceedingCells(const CellMetrics &c_hist, size_t sp_idx,
+                                  double sp_thr);
+
+  inline bool rbLimitReached() const;
+
   ControlConfig config;
+  ChemistryModule &chem_;
 
   std::uint32_t global_iter = 0;
   std::uint32_t rb_count = 0;
   std::uint32_t rb_limit = 0;
   std::uint32_t stab_countdown = 0;
+  std::uint32_t surr_active = 0;
   std::vector<uint32_t> ctrl_cell_ids;
 
   bool rb_enabled = false;

src/IO/StatsIO.cpp

@@ -8,7 +8,9 @@
 #include <highfive/highfive.hpp>
 #include <iomanip>
 #include <iostream>
+#include <limits>
 #include <string>
+#include <unordered_map>
 #include <vector>
 
 namespace fs = std::filesystem;
@@ -16,65 +18,98 @@ namespace fs = std::filesystem;
 int write_metrics(const std::vector<poet::CellMetrics> &metrics_history,
                   const std::vector<std::string> &species_names,
                   const std::string &dir_path, const std::string &file_name) {
-
   if (!fs::exists(dir_path)) {
     std::cerr << "Directory does not exist: " << dir_path << std::endl;
     return -1;
   }
+
   fs::path file_path = fs::path(dir_path) / file_name;
 
-  // Use a std::string path to avoid filesystem path conversion issues.
+  const std::size_t n_species = species_names.size();
-  H5Easy::File file(file_path.string(), H5Easy::File::Truncate);
+  if (n_species == 0) {
+    std::cerr << "Species names list is empty; skipping HDF5 metrics dump.\n";
+    return -1;
+  }
 
-  for (size_t idx = 0; idx < metrics_history.size(); ++idx) {
+  // Always start from a clean file: no stale datasets, no mismatched shapes.
-    const auto &metrics = metrics_history[idx];
+  HighFive::File file(file_path.string(), HighFive::File::Truncate);
-    /*
-    std::string grp = "entry_" + std::to_string(idx) + "_iter_" +
-                      std::to_string(metrics.iteration) + "_rb_" +
-                      std::to_string(metrics.rollback_count);
-    */
-    std::string grp = "iter_" + std::to_string(metrics.iteration) + "_rb_" +
-                      std::to_string(metrics.rb_count);
 
-    size_t n_cells = metrics.id.size();
+  // cell_id -> all rows over time
-    // Use provided species_names as the source of truth to avoid OOB when mape is empty.
+  using Row = std::vector<double>;
-    size_t n_species = species_names.size();
+  using Matrix = std::vector<Row>;
+  std::unordered_map<std::uint32_t, Matrix> mape_per_cell;
+  std::unordered_map<std::uint32_t, Matrix> rrmse_per_cell;
+  std::unordered_map<std::uint32_t, Matrix> conc_per_cell;
 
-    // Create a scalar dataset "meta" and attach attributes to it (no explicit groups).
+  // Build per-cell time series from the *entire* history.
-    H5Easy::dump(file, grp + "/meta", 0, H5Easy::DumpMode::Overwrite);
+  for (const auto &metrics : metrics_history) {
+    const std::uint32_t iter = metrics.iteration;
 
-    H5Easy::dumpAttribute(file, grp + "/meta", "species_names", species_names,
+    for (std::size_t cell_idx = 0; cell_idx < metrics.id.size(); ++cell_idx) {
-                          H5Easy::DumpMode::Overwrite);
+      const auto cell_id = metrics.id[cell_idx];
-    H5Easy::dumpAttribute(file, grp + "/meta", "iteration", metrics.iteration,
-                          H5Easy::DumpMode::Overwrite);
-    H5Easy::dumpAttribute(file, grp + "/meta", "rollback_count",
-                          metrics.rb_count, H5Easy::DumpMode::Overwrite);
-    H5Easy::dumpAttribute(file, grp + "/meta", "n_cells", n_cells,
-                          H5Easy::DumpMode::Overwrite);
-    H5Easy::dumpAttribute(file, grp + "/meta", "n_species", n_species,
-                          H5Easy::DumpMode::Overwrite);
 
-    // Dump only if data is non-empty to avoid corrupting the file on failures.
+      // --- MAPE row: [iteration, mape...]
-    if (!metrics.mape.empty()) {
+      Row mape_row;
-      H5Easy::dump(file, grp + "/mape", metrics.mape,
+      mape_row.reserve(1 + n_species);
-                   H5Easy::DumpMode::Overwrite);
+      mape_row.push_back(static_cast<double>(iter));
-    }
+
-    if (!metrics.rrmse.empty()) {
+      const auto &src_m = metrics.mape[cell_idx];
-      H5Easy::dump(file, grp + "/rrmse", metrics.rrmse,
+      const std::size_t len_m = std::min(src_m.size(), n_species);
-                   H5Easy::DumpMode::Overwrite);
+      mape_row.insert(mape_row.end(), src_m.begin(), src_m.begin() + len_m);
+      if (len_m < n_species) {
+        mape_row.resize(1 + n_species, std::numeric_limits<double>::quiet_NaN());
+      }
+
+      // --- RRMSE row: [iteration, rrmse...]
+      Row rrmse_row;
+      rrmse_row.reserve(1 + n_species);
+      rrmse_row.push_back(static_cast<double>(iter));
+
+      const auto &src_r = metrics.rrmse[cell_idx];
+      const std::size_t len_r = std::min(src_r.size(), n_species);
+      rrmse_row.insert(rrmse_row.end(), src_r.begin(), src_r.begin() + len_r);
+      if (len_r < n_species) {
+        rrmse_row.resize(1 + n_species, std::numeric_limits<double>::quiet_NaN());
+      }
+
+      Row conc_row;
+      conc_row.reserve(1 + n_species);
+      conc_row.push_back(static_cast<double>(iter));
+
+      const auto &src_c = metrics.conc[cell_idx];
+      const std::size_t len_c = std::min(src_c.size(), n_species);
+      conc_row.insert(conc_row.end(), src_c.begin(), src_c.begin() + len_c);
+      if (len_c < n_species) {
+        conc_row.resize(1 + n_species, std::numeric_limits<double>::quiet_NaN());
+      }
+
+      // Append to per-cell matrices
+      mape_per_cell[cell_id].push_back(std::move(mape_row));
+      rrmse_per_cell[cell_id].push_back(std::move(rrmse_row));
+      conc_per_cell[cell_id].push_back(std::move(conc_row));
     }
   }
 
-  // Ensure all buffers are flushed to disk.
+  // Now dump each cell’s full time series
-  file.flush();
+  for (const auto &kv : mape_per_cell) {
+    const auto cell_id = kv.first;
+    const auto &mape_matrix = kv.second;
+    const auto &rrmse_matrix = rrmse_per_cell[cell_id];
+    const auto &conc_matrix = conc_per_cell[cell_id];
+
+    const std::string cell_grp = "cells/" + std::to_string(cell_id);
+
+    H5Easy::dump(file, cell_grp + "/mape", mape_matrix, H5Easy::DumpMode::Overwrite);
+    H5Easy::dump(file, cell_grp + "/rrmse", rrmse_matrix, H5Easy::DumpMode::Overwrite);
+    H5Easy::dump(file, cell_grp + "/conc", conc_matrix, H5Easy::DumpMode::Overwrite);
+  }
 
   return 0;
 }
 
 void writeCellStatsToCSV(const std::vector<poet::CellMetrics> &all_stats,
                          const std::vector<std::string> &species_names,
-                         const std::string &out_dir,
+                         const std::string &out_dir, const std::string &filename) {
-                         const std::string &filename) {
   std::ofstream out(std::filesystem::path(out_dir) / filename);
   if (!out.is_open()) {
     std::cerr << "Could not open " << filename << " !" << std::endl;
@@ -83,8 +118,8 @@ void writeCellStatsToCSV(const std::vector<poet::CellMetrics> &all_stats,
 
   // Header
   out << std::left << std::setw(15) << "CellID" << std::setw(15) << "Iteration"
-      << std::setw(15) << "Rollback" << std::setw(15) << "Species"
+      << std::setw(15) << "Rollback" << std::setw(15) << "Species" << std::setw(15)
-      << std::setw(15) << "MAPE" << std::setw(15) << "RRMSE"
+      << "MAPE" << std::setw(15) << "RRMSE"
       << "\n"
       << std::string(90, '-') << "\n";
 
@@ -92,25 +127,21 @@ void writeCellStatsToCSV(const std::vector<poet::CellMetrics> &all_stats,
   for (const auto &metrics : all_stats) {
     for (size_t cell_idx = 0; cell_idx < metrics.id.size(); ++cell_idx) {
       for (size_t sp_idx = 0; sp_idx < species_names.size(); ++sp_idx) {
-        out << std::left << std::setw(15) << metrics.id[cell_idx]
+        out << std::left << std::setw(15) << metrics.id[cell_idx] << std::setw(15)
-            << std::setw(15) << metrics.iteration
+            << metrics.iteration << std::setw(15) << metrics.rb_count << std::setw(15)
-            << std::setw(15) << metrics.rb_count
+            << species_names[sp_idx] << std::setw(15) << metrics.mape[cell_idx][sp_idx]
-            << std::setw(15) << species_names[sp_idx]
-            << std::setw(15) << metrics.mape[cell_idx][sp_idx]
             << std::setw(15) << metrics.rrmse[cell_idx][sp_idx] << "\n";
       }
     }
     out << "\n";
   }
   out.close();
-  std::cout << "Cell error metrics written to " << out_dir << "/" << filename
+  std::cout << "Cell error metrics written to " << out_dir << "/" << filename << "\n";
-            << "\n";
 }
 
-void writeSpeciesStatsToCSV(
+void writeSpeciesStatsToCSV(const std::vector<poet::SpeciesMetrics> &all_stats,
-    const std::vector<poet::SpeciesMetrics> &all_stats,
+                            const std::vector<std::string> &species_names,
-    const std::vector<std::string> &species_names, const std::string &out_dir,
+                            const std::string &out_dir, const std::string &filename) {
-    const std::string &filename) {
   std::ofstream out(std::filesystem::path(out_dir) / filename);
   if (!out.is_open()) {
     std::cerr << "Could not open " << filename << " !" << std::endl;
@@ -118,9 +149,8 @@ void writeSpeciesStatsToCSV(
   }
 
   // Header
-  out << std::left << std::setw(15) << "Iteration" << std::setw(15)
+  out << std::left << std::setw(15) << "Iteration" << std::setw(15) << "Rollback"
-      << "Rollback" << std::setw(15) << "Species" << std::setw(15) << "MAPE"
+      << std::setw(15) << "Species" << std::setw(15) << "MAPE" << std::setw(15) << "RRMSE"
-      << std::setw(15) << "RRMSE"
       << "\n"
       << std::string(75, '-') << "\n";
 
@@ -128,13 +158,11 @@ void writeSpeciesStatsToCSV(
   for (const auto &metrics : all_stats) {
     for (size_t sp_idx = 0; sp_idx < species_names.size(); ++sp_idx) {
       out << std::left << std::setw(15) << metrics.iteration << std::setw(15)
-          << metrics.rb_count << std::setw(15) << species_names[sp_idx]
+          << metrics.rb_count << std::setw(15) << species_names[sp_idx] << std::setw(15)
-          << std::setw(15) << metrics.mape[sp_idx] << std::setw(15)
+          << metrics.mape[sp_idx] << std::setw(15) << metrics.rrmse[sp_idx] << "\n";
-          << metrics.rrmse[sp_idx] << "\n";
     }
     out << "\n";
   }
   out.close();
-  std::cout << "Species error metrics written to " << out_dir << "/" << filename
+  std::cout << "Species error metrics written to " << out_dir << "/" << filename << "\n";
-            << "\n";
 }

src/IO/StatsIO.hpp

@@ -1,13 +1,17 @@
+#pragma once
+
+#include "Control/ControlModule.hpp"
 #include <string>
 #include <vector>
 
-void writeSpeciesStatsToCSV(
+int write_metrics(const std::vector<poet::CellMetrics> &metrics_history,
-    const std::vector<poet::SpeciesMetrics> &all_stats,
+                  const std::vector<std::string> &species_names,
-    const std::vector<std::string> &species_names, const std::string &out_dir,
+                  const std::string &dir_path, const std::string &file_name);
-    const std::string &filename);
+
-    
 void writeCellStatsToCSV(const std::vector<poet::CellMetrics> &all_stats,
                          const std::vector<std::string> &species_names,
-                         const std::string &out_dir,
+                         const std::string &out_dir, const std::string &filename);
-                         const std::string &filename);
+
-// namespace poet
+void writeSpeciesStatsToCSV(const std::vector<poet::SpeciesMetrics> &all_stats,
+                            const std::vector<std::string> &species_names,
+                            const std::string &out_dir, const std::string &filename);

src/poet.cpp

@@ -117,11 +117,13 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
   // cout << "CPP: DHT size per process (Byte) = " << dht_size_per_process <<
   // endl;
 
-  dht_group->add_option("--dht-snaps", params.dht_snaps,
+  dht_group->add_option(
-                        "Save snapshots of DHT to disk: \n0 = disabled (default)\n1 = After "
+      "--dht-snaps", params.dht_snaps,
-                        "simulation\n2 = After each iteration");
+      "Save snapshots of DHT to disk: \n0 = disabled (default)\n1 = After "
+      "simulation\n2 = After each iteration");
 
-  auto *interp_group = app.add_option_group("Interpolation", "Interpolation related options");
+  auto *interp_group =
+      app.add_option_group("Interpolation", "Interpolation related options");
 
   interp_group->add_flag("--interp", params.use_interp, "Enable interpolation");
   interp_group
@@ -143,7 +145,8 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
   app.add_flag("--ai-surrogate", params.use_ai_surrogate,
                "Enable AI surrogate for chemistry module");
 
-  app.add_flag("--rds", params.as_rds, "Save output as .rds file instead of default .qs2");
+  app.add_flag("--rds", params.as_rds,
+               "Save output as .rds file instead of default .qs2");
 
   app.add_flag("--qs", params.as_qs, "Save output as .qs file instead of default .qs2");
 
@@ -159,7 +162,8 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
       ->required()
       ->check(CLI::ExistingFile);
 
-  app.add_option("out_dir", params.out_dir, "Output directory of the simulation")->required();
+  app.add_option("out_dir", params.out_dir, "Output directory of the simulation")
+      ->required();
 
   try {
     app.parse(argc, argv);
@@ -234,10 +238,15 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
     // MDL add "out_ext" for output format to R setup
     (*global_rt_setup)["out_ext"] = params.out_ext;
 
-    params.timesteps = Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("timesteps"));
+    params.timesteps =
-    params.chkpt_interval = Rcpp::as<uint32_t>(global_rt_setup->operator[]("chkpt_interval"));
+        Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("timesteps"));
+    params.chkpt_interval =
+        Rcpp::as<uint32_t>(global_rt_setup->operator[]("chkpt_interval"));
     params.rb_limit = Rcpp::as<uint32_t>(global_rt_setup->operator[]("rb_limit"));
-    params.stab_interval = Rcpp::as<uint32_t>(global_rt_setup->operator[]("stab_interval"));
+    params.rb_interval_limit =
+        Rcpp::as<uint32_t>(global_rt_setup->operator[]("rb_interval_limit"));
+    params.stab_interval =
+        Rcpp::as<uint32_t>(global_rt_setup->operator[]("stab_interval"));
     params.zero_abs = Rcpp::as<double>(global_rt_setup->operator[]("zero_abs"));
     params.mape_threshold =
         Rcpp::as<std::vector<double>>(global_rt_setup->operator[]("mape_threshold"));
@@ -258,7 +267,8 @@ void call_master_iter_end(RInside &R, const Field &trans, const Field &chem) {
   R["TMP"] = Rcpp::wrap(trans.AsVector());
   R["TMP_PROPS"] = Rcpp::wrap(trans.GetProps());
   R.parseEval(std::string("state_T <- setNames(data.frame(matrix(TMP, nrow=" +
-                          std::to_string(trans.GetRequestedVecSize()) + ")), TMP_PROPS)"));
+                          std::to_string(trans.GetRequestedVecSize()) +
+                          ")), TMP_PROPS)"));
 
   R["TMP"] = Rcpp::wrap(chem.AsVector());
   R["TMP_PROPS"] = Rcpp::wrap(chem.GetProps());
@@ -286,7 +296,7 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
 
   double dSimTime{0};
   for (uint32_t iter = 1; iter < maxiter + 1; iter++) {
-    control.beginIteration(chem, iter, params.use_dht, params.use_interp);
+    control.beginIteration(iter, params.use_dht, params.use_interp);
 
     double start_t = MPI_Wtime();
 
@@ -295,7 +305,8 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
     std::cout << std::endl;
 
     /* displaying iteration number, with C++ and R iterator */
-    MSG("Going through iteration " + std::to_string(iter) + "/" + std::to_string(maxiter));
+    MSG("Going through iteration " + std::to_string(iter) + "/" +
+        std::to_string(maxiter));
 
     MSG("Current time step is " + std::to_string(dt));
 
@@ -334,13 +345,14 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
       chem.set_ai_surrogate_validity_vector(R.parseEval("validity_vector"));
 
       MSG("AI TempField");
-      std::vector<std::vector<double>> RTempField = R.parseEval("set_valid_predictions(predictors,\
+      std::vector<std::vector<double>> RTempField =
+          R.parseEval("set_valid_predictions(predictors,\
                        aipreds,\
                        validity_vector)");
 
       MSG("AI Set Field");
-      Field predictions_field =
+      Field predictions_field = Field(R.parseEval("nrow(predictors)"), RTempField,
-          Field(R.parseEval("nrow(predictors)"), RTempField, R.parseEval("colnames(predictors)"));
+                                      R.parseEval("colnames(predictors)"));
 
       MSG("AI Update");
       chem.getField().update(predictions_field);
@@ -386,9 +398,10 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
 
     diffusion.getField().update(chem.getField());
 
-    MSG("End of *coupling* iteration " + std::to_string(iter) + "/" + std::to_string(maxiter));
+    MSG("End of *coupling* iteration " + std::to_string(iter) + "/" +
+        std::to_string(maxiter));
 
-    control.processCheckpoint(diffusion, iter, params.out_dir, chem.getField().GetProps());
+    control.processCheckpoint(iter, params.out_dir, chem.getField().GetProps());
     // MSG();
   } // END SIMULATION LOOP
 
@@ -426,7 +439,8 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
     chem_profiling["interp_w"] = Rcpp::wrap(chem.GetWorkerInterpolationWriteTimings());
     chem_profiling["interp_r"] = Rcpp::wrap(chem.GetWorkerInterpolationReadTimings());
     chem_profiling["interp_g"] = Rcpp::wrap(chem.GetWorkerInterpolationGatherTimings());
-    chem_profiling["interp_fc"] = Rcpp::wrap(chem.GetWorkerInterpolationFunctionCallTimings());
+    chem_profiling["interp_fc"] =
+        Rcpp::wrap(chem.GetWorkerInterpolationFunctionCallTimings());
     chem_profiling["interp_calls"] = Rcpp::wrap(chem.GetWorkerInterpolationCalls());
     chem_profiling["interp_cached"] = Rcpp::wrap(chem.GetWorkerPHTCacheHits());
   }
@@ -481,8 +495,8 @@ std::vector<std::string> getSpeciesNames(const Field &&field, int root, MPI_Comm
     for (std::uint32_t i = 0; i < n_elements; i++) {
       n_string_size = field.GetProps()[i].size();
       MPI_Bcast(&n_string_size, 1, MPI_UINT32_T, root, MPI_COMM_WORLD);
-      MPI_Bcast(const_cast<char *>(field.GetProps()[i].c_str()), n_string_size, MPI_CHAR, root,
+      MPI_Bcast(const_cast<char *>(field.GetProps()[i].c_str()), n_string_size, MPI_CHAR,
-                MPI_COMM_WORLD);
+                root, MPI_COMM_WORLD);
     }
 
     return field.GetProps();
@@ -626,8 +640,8 @@ int main(int argc, char *argv[]) {
       // // if (MY_RANK == 0) { // get timestep vector from
       // // grid_init function ... //
 
-      *global_rt_setup =
+      *global_rt_setup = master_init_R(*global_rt_setup, run_params.out_dir,
-          master_init_R(*global_rt_setup, run_params.out_dir, init_list.getInitialGrid().asSEXP());
+                                       init_list.getInitialGrid().asSEXP());
 
       // MDL: store all parameters
       // MSG("Calling R Function to store calling parameters");
@@ -658,12 +672,12 @@ int main(int argc, char *argv[]) {
 
       DiffusionModule diffusion(init_list.getDiffusionInit(), init_list.getInitialGrid());
 
-      ControlConfig config(run_params.stab_interval, run_params.chkpt_interval, run_params.rb_limit,
-                           run_params.zero_abs, run_params.mape_threshold);
-
-      ControlModule control(config);
-
       chemistry.masterSetField(init_list.getInitialGrid());
+
+      ControlConfig config(run_params.stab_interval, run_params.chkpt_interval,
+                           run_params.rb_limit, run_params.rb_interval_limit,
+                           run_params.zero_abs, run_params.mape_threshold);
+      ControlModule control(config, chemistry);
       chemistry.SetControlModule(&control);
 
       Rcpp::List profiling = RunMasterLoop(R, run_params, diffusion, chemistry, control);
@@ -679,8 +693,8 @@ int main(int argc, char *argv[]) {
                    "'/timings.', setup$out_ext));";
       R.parseEval(r_vis_code);
 
-      MSG("Done! Results are stored as R objects into <" + run_params.out_dir + "/timings." +
+      MSG("Done! Results are stored as R objects into <" + run_params.out_dir +
-          run_params.out_ext);
+          "/timings." + run_params.out_ext);
     }
   }
 

src/poet.hpp.in

@@ -53,6 +53,7 @@ struct RuntimeParameters {
   std::uint32_t stab_interval = 0;
   std::uint32_t chkpt_interval = 0;
   std::uint32_t rb_limit = 0;
+  std::uint32_t rb_interval_limit = 0;
   double zero_abs = 0.0;
   std::vector<double> mape_threshold;
   std::vector<uint32_t> ctrl_cell_ids;