Fix control_batch naming, metrics workflow and add R visualization script

bin/run_poet.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
-#SBATCH --job-name=proto2_eps01_3_rb
-#SBATCH --output=proto2_eps01_3_rb_%j.out
-#SBATCH --error=proto2_eps01_3_rb_%j.err
+#SBATCH --job-name=proto2_eps0035_no_rb_v2
+#SBATCH --output=proto2_eps0035_no_rb_v2_%j.out
+#SBATCH --error=proto2_eps0035_no_rb_v2%j.err
 #SBATCH --partition=long
 #SBATCH --nodes=6                                                    
 #SBATCH --ntasks-per-node=24 
@@ -15,5 +15,5 @@ module purge
 module load cmake gcc openmpi
 
 #mpirun -n 144 ./poet dolo_fgcs_3.R dolo_fgcs_3.qs2 dolo_only_pqc
-mpirun -n 144 ./poet --interp dolo_fgcs_3_rt.R dolo_fgcs_3.qs2 proto2_eps01_3_rb
+mpirun -n 144 ./poet --interp --rds dolo_fgcs_3_rt.R dolo_fgcs_3.qs2 proto2_eps0035_no_rb_v2
 #mpirun -n 144 ./poet --interp  barite_fgcs_4_new/barite_fgcs_4_new_rt.R barite_fgcs_4_new/barite_fgcs_4_new.qs2 barite

src/Chemistry/ChemistryModule.hpp

@@ -473,7 +473,7 @@ protected:
   bool control_enabled{false};
   bool stab_enabled{false};
   std::unordered_set<uint32_t> ctrl_cell_ids;
-  std::vector<std::vector<double>> control_batch;
+  std::vector<std::vector<double>> ctrl_batch;
 };
 } // namespace poet
 

src/Chemistry/MasterFunctions.cpp

@@ -368,7 +368,7 @@ inline void poet::ChemistryModule::MasterRecvPkgs(worker_list_t &w_list,
         std::vector<double> cell_output(
             recv_buffer.begin() + this->prop_count * i,
             recv_buffer.begin() + this->prop_count * (i + 1));
-        this->control_batch.push_back(std::move(cell_output));
+        this->ctrl_batch.push_back(std::move(cell_output));
       }
       break;
     }
@@ -443,13 +443,11 @@ void poet::ChemistryModule::MasterRunParallel(double dt) {
               MPI_INT);
   }
 
-  // if (control->shouldBcastFlags()) {
   ftype = CHEM_CTRL_FLAGS;
   PropagateFunctionType(ftype);
   uint32_t ctrl_flags = buildCtrlFlags(this->dht_enabled, this->interp_enabled,
                                        this->stab_enabled);
   ChemBCast(&ctrl_flags, 1, MPI_INT);
-  //}
 
   ftype = CHEM_WORK_LOOP;
   PropagateFunctionType(ftype);
@@ -467,8 +465,6 @@ void poet::ChemistryModule::MasterRunParallel(double dt) {
       shuffleField(chem_field.AsVector(), this->n_cells, this->prop_count,
                    wp_sizes_vector.size());
 
-  // this->mpi_surr_buffer.resize(mpi_buffer.size());
-
   /* setup local variables */
   pkg_to_send = wp_sizes_vector.size();
   pkg_to_recv = wp_sizes_vector.size();
@@ -523,39 +519,37 @@ void poet::ChemistryModule::MasterRunParallel(double dt) {
 
   /* do master stuff */
 
-  if (!this->control_batch.empty()) {
-    std::cout << "[Master] Processing " << this->control_batch.size()
+  if (!this->ctrl_batch.empty()) {
+    std::cout << "[Master] Processing " << this->ctrl_batch.size()
               << " control cells for comparison." << std::endl;
 
-    /* using mpi-buffer because we need cell-major layout*/
-    std::vector<std::vector<double>> surrogate_batch;
-    surrogate_batch.reserve(this->control_batch.size());
+    
+    std::vector<std::vector<double>> sur_batch;
+    sur_batch.reserve(this->ctrl_batch.size());
 
-    for (const auto &element : this->control_batch) {
+    for (const auto &element : this->ctrl_batch) {
 
+      /* using mpi-buffer because we need cell-major layout*/
       for (size_t i = 0; i < this->n_cells; i++) {
         uint32_t curr_cell_id = mpi_buffer[this->prop_count * i];
 
         if (curr_cell_id == element[0]) {
-          std::vector<double> surrogate_output(
+          std::vector<double> sur_output(
               mpi_buffer.begin() + this->prop_count * i,
               mpi_buffer.begin() + this->prop_count * (i + 1));
-          surrogate_batch.push_back(surrogate_output);
+          sur_batch.push_back(sur_output);
           break;
         }
       }
     }
 
     metrics_a = MPI_Wtime();
-    control->computeErrorMetrics(this->control_batch, surrogate_batch,
+    control->computeErrorMetrics(this->ctrl_batch, sur_batch,
                                  prop_names, n_cells);
-    control->writeErrorMetrics(ctrl_file_out_dir, prop_names);
-
     metrics_b = MPI_Wtime();
     this->metrics_t += metrics_b - metrics_a;
 
-    // Clear for next control iteration
-    this->control_batch.clear();
+    this->ctrl_batch.clear();
   }
 
   /* start time measurement of master chemistry */

src/Control/ControlModule.cpp

@@ -7,23 +7,21 @@
 poet::ControlModule::ControlModule(const ControlConfig &config_)
     : config(config_) {}
 
-void poet::ControlModule::beginIteration(ChemistryModule &chem,
-                                         const uint32_t &iter,
+void poet::ControlModule::beginIteration(ChemistryModule &chem, uint32_t &iter,
                                          const bool &dht_enabled,
                                          const bool &interp_enabled) {
 
-  /* dht_enabled and inter_enabled are user settings set before startig the
-   * simulation*/
+  global_iteration = iter;
   double prep_a, prep_b;
 
   prep_a = MPI_Wtime();
 
-  global_iteration = iter;
   updateStabilizationPhase(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::updateStabilizationPhase(ChemistryModule &chem,
                                                    bool dht_enabled,
                                                    bool interp_enabled) {
@@ -31,16 +29,15 @@ void poet::ControlModule::updateStabilizationPhase(ChemistryModule &chem,
     if (disable_surr_counter > 0) {
       --disable_surr_counter;
       flush_request = false;
-      MSG("Rollback counter: " + std::to_string(disable_surr_counter));
+      std::cout << "Rollback counter: " << std::to_string(disable_surr_counter)
+                << std::endl;
     } else {
       rollback_enabled = false;
-      MSG("Rollback stabilization complete, re-enabling surrogates");
+      std::cout << "Rollback stabilization complete, re-enabling surrogate."
+                << std::endl;
     }
   }
 
-  bool prev_stab_state = chem.GetStabEnabled();
-
-  // user requested DHT/INTEP? keep them disabled but enable warmup-phase so
   if (global_iteration <= config.stab_interval || rollback_enabled) {
     chem.SetStabEnabled(true);
     chem.SetDhtEnabled(false);
@@ -50,27 +47,19 @@ void poet::ControlModule::updateStabilizationPhase(ChemistryModule &chem,
     chem.SetDhtEnabled(dht_enabled);
     chem.SetInterpEnabled(interp_enabled);
   }
-
-  // Mark that we need to broadcast flags if stab state changed
-  if (prev_stab_state != chem.GetStabEnabled()) {
-    stab_phase_ended = true;
-  }
 }
 
 void poet::ControlModule::writeCheckpoint(DiffusionModule &diffusion,
                                           uint32_t &iter,
                                           const std::string &out_dir) {
-  double w_check_a, w_check_b;
-
-  w_check_a = MPI_Wtime();
   if (global_iteration % config.checkpoint_interval == 0) {
+    double w_check_a = MPI_Wtime();
     write_checkpoint(out_dir, "checkpoint" + std::to_string(iter) + ".hdf5",
                      {.field = diffusion.getField(), .iteration = iter});
+    double w_check_b = MPI_Wtime();
+    this->w_check_t += w_check_b - w_check_a;
+    last_checkpoint_written = iter;
   }
-  w_check_b = MPI_Wtime();
-  this->w_check_t += w_check_b - w_check_a;
-
-  last_checkpoint_written = iter;
 }
 
 void poet::ControlModule::readCheckpoint(DiffusionModule &diffusion,
@@ -90,18 +79,15 @@ void poet::ControlModule::readCheckpoint(DiffusionModule &diffusion,
 }
 
 void poet::ControlModule::writeErrorMetrics(
-    const std::string &out_dir, const std::vector<std::string> &species) {
-  double stats_a, stats_b;
+    uint32_t &iter, const std::string &out_dir,
+    const std::vector<std::string> &species) {
 
-  stats_a = MPI_Wtime();
+  double stats_a = MPI_Wtime();
   writeSpeciesStatsToCSV(metrics_history, species, out_dir,
                          "species_overview.csv");
-  // writeCellStatsToCSV(cell_metrics_history, species, out_dir,
-  // "cell_overview.csv");
   write_metrics(cell_metrics_history, species, out_dir,
                 "metrics_overview.hdf5");
-  stats_b = MPI_Wtime();
-
+  double stats_b = MPI_Wtime();
   this->stats_t += stats_b - stats_a;
 }
 
@@ -109,19 +95,6 @@ uint32_t poet::ControlModule::getRollbackIter() {
 
   uint32_t last_iter = ((global_iteration - 1) / config.checkpoint_interval) *
                        config.checkpoint_interval;
-
-  /*
-  uint32_t rollback_iter = (last_iter <= last_checkpoint_written)
-                               ? last_iter
-                               : last_checkpoint_written;
-
-  MSG("getRollbackIter: global_iteration=" + std::to_string(global_iteration) +
-      ", checkpoint_interval=" + std::to_string(config.checkpoint_interval) +
-      ", last_checkpoint_written=" + std::to_string(last_checkpoint_written) +
-      ", returning=" + std::to_string(last_checkpoint_written));
-
-  return last_checkpoint_written;
-  */
   return last_iter;
 }
 
@@ -129,55 +102,47 @@ std::optional<uint32_t> poet::ControlModule::getRollbackTarget(
     const std::vector<std::string> &species) {
   double r_check_a, r_check_b;
 
-  if (metrics_history.empty()) {
-    MSG("No error history yet, skipping rollback check.");
-    rollback_enabled = false;
-    return std::nullopt;
-  }
-  // Skip threshold checking if already in rollback/stabilization phase
-  if (rollback_enabled) {
+  /* Skip threshold checking if already in stabilization phase*/
+  if (metrics_history.empty() || rollback_enabled) {
     return std::nullopt;
   }
 
-  const auto &s_mape = metrics_history.back().mape;
+  const auto &s_hist = metrics_history.back();
 
+  /* skipping cell_id and id */
   for (size_t sp_i = 2; sp_i < species.size(); sp_i++) {
 
-    // skip charge
-    if (s_mape[sp_i] == 0 || sp_i == 4) {
+    /* check bounds of threshold vector*/
+    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_mape[sp_i] > config.mape_threshold[sp_i]) {
-      if (last_checkpoint_written == 0) {
-        MSG(" Threshold exceeded but no checkpoint exists yet.");
-        return std::nullopt;
-      }
-
-      const auto &c_mape = cell_metrics_history.back().mape;
-      const auto &c_id = cell_metrics_history.back().id;
+    if (s_hist.mape[sp_i] > config.mape_threshold[sp_i]) {
 
+      const auto &c_hist = cell_metrics_history.back();
       auto max_it = std::max_element(
-          c_mape.begin(), c_mape.end(),
+          c_hist.mape.begin(), c_hist.mape.end(),
           [sp_i](const auto &a, const auto &b) { return a[sp_i] < b[sp_i]; });
 
-      size_t max_idx = std::distance(c_mape.begin(), max_it);
-      uint32_t cell_id = c_id[max_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];
 
       rollback_enabled = true;
       flush_request = true;
 
-      MSG("Threshold exceeded for " + species[sp_i] +
-          " with species-level MAPE = " + std::to_string(s_mape[sp_i]) +
-          " exceeding threshold = " +
-          std::to_string(config.mape_threshold[sp_i]) + ". Worst cell: ID=" +
-          std::to_string(cell_id) + " with MAPE=" + std::to_string(cell_mape));
+      std::cout << "Threshold exceeded for " << species[sp_i]
+                << " with species-level MAPE = " << std::to_string(s_hist.mape[sp_i])
+                << " exceeding threshold = "
+                << std::to_string(config.mape_threshold[sp_i])
+                << ". Worst cell: ID=" << std::to_string(cell_id)
+                << ", species= " << species[sp_i] 
+                << " with MAPE=" << std::to_string(cell_mape) << std::endl;
 
       return getRollbackIter();
     }
   }
-  rollback_enabled = false;
-  flush_request = false;
   return std::nullopt;
 }
 
@@ -186,11 +151,6 @@ void poet::ControlModule::computeErrorMetrics(
     std::vector<std::vector<double>> &surrogate_values,
     const std::vector<std::string> &species, const uint32_t size_per_prop) {
 
-  // Skip metric computation if already in rollback/stabilization phase
-  if (rollback_enabled) {
-    return;
-  }
-
   const uint32_t n_cells = reference_values.size();
   const uint32_t n_species = species.size();
   const double ZERO_ABS = config.zero_abs;
@@ -256,7 +216,11 @@ void poet::ControlModule::processCheckpoint(
     DiffusionModule &diffusion, uint32_t &current_iter,
     const std::string &out_dir, const std::vector<std::string> &species) {
 
-  if (flush_request && rollback_count < 3) {
+  // Use max_rollbacks from config, default to 3 if not set
+  // uint32_t max_rollbacks =
+  //  (config.max_rollbacks > 0) ? config.max_rollbacks : 3;
+
+  if (flush_request /* && rollback_count < 3 */) {
     uint32_t target = getRollbackIter();
     readCheckpoint(diffusion, current_iter, target, out_dir);
 
@@ -264,21 +228,10 @@ void poet::ControlModule::processCheckpoint(
     rollback_count++;
     disable_surr_counter = config.stab_interval;
 
-    MSG("Restored checkpoint " + std::to_string(target) +
-        ", surrogates disabled for " + std::to_string(config.stab_interval));
+    std::cout << "Restored checkpoint " << std::to_string(target)
+              << ", surrogate disabled for "
+              << std::to_string(config.stab_interval) << std::endl;
   } else {
     writeCheckpoint(diffusion, global_iteration, out_dir);
   }
-}
-
-bool poet::ControlModule::shouldBcastFlags() {
-  if (global_iteration == 1) {
-    return true;
-  }
-
-  if (stab_phase_ended) {
-    return true;
-  }
-
-  return false;
 }

src/Control/ControlModule.hpp

@@ -19,7 +19,8 @@ class DiffusionModule;
 
 struct ControlConfig {
   uint32_t stab_interval = 0;
-  uint32_t checkpoint_interval = 0;
+  uint32_t checkpoint_interval = 0; // How often to write metrics files
+  //uint32_t max_rb = 0;            // Maximum number of rollbacks allowed
   double zero_abs = 0.0;
   std::vector<double> mape_threshold;
 };
@@ -54,10 +55,10 @@ class ControlModule {
 public:
   explicit ControlModule(const ControlConfig &config);
 
-  void beginIteration(ChemistryModule &chem, const uint32_t &iter,
+  void beginIteration(ChemistryModule &chem, uint32_t &iter,
                       const bool &dht_enabled, const bool &interp_enaled);
 
-  void writeErrorMetrics(const std::string &out_dir,
+  void writeErrorMetrics(uint32_t &iter, const std::string &out_dir,
                          const std::vector<std::string> &species);
 
   std::optional<uint32_t> getRollbackTarget();

src/poet.cpp

@@ -254,8 +254,7 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
         Rcpp::as<uint32_t>(global_rt_setup->operator[]("checkpoint_interval"));
     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.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"));
     params.ctrl_cell_ids = Rcpp::as<std::vector<uint32_t>>(
@@ -415,9 +414,9 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
     MSG("End of *coupling* iteration " + std::to_string(iter) + "/" +
         std::to_string(maxiter));
 
+    control.writeErrorMetrics(iter, params.out_dir, chem.getField().GetProps());
     control.processCheckpoint(diffusion, iter, params.out_dir,
                               chem.getField().GetProps());
-
     // MSG();
   } // END SIMULATION LOOP
 
@@ -434,13 +433,22 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
   Rcpp::List diffusion_profiling;
   diffusion_profiling["simtime"] = diffusion.getTransportTime();
 
-  if (params.use_dht) {
-    chem_profiling["dht_hits"] = Rcpp::wrap(chem.GetWorkerDHTHits());
-    chem_profiling["dht_evictions"] = Rcpp::wrap(chem.GetWorkerDHTEvictions());
-    chem_profiling["dht_get_time"] = Rcpp::wrap(chem.GetWorkerDHTGetTimings());
-    chem_profiling["dht_fill_time"] =
-        Rcpp::wrap(chem.GetWorkerDHTFillTimings());
-  }
+  Rcpp::List ctrl_profiling;
+  ctrl_profiling["compute_metrics_master"] = chem.GetMasterCtrlMetricsTime();
+  ctrl_profiling["unshuffle_field_master"] = chem.GetMasterUnshuffleTime();
+  ctrl_profiling["w_checkpoint_master"] = control.getWriteCheckpointTime();
+  ctrl_profiling["r_checkpoint_master"] = control.getReadCheckpointTime();
+  ctrl_profiling["write_stats"] = control.getWriteMetricsTime();
+  ctrl_profiling["ctrl_logic_master"] = control.getUpdateCtrlLogicTime();
+  ctrl_profiling["recv_data_master"] = chem.GetMasterRecvCtrlDataTime();
+  ctrl_profiling["worker"] = Rcpp::wrap(chem.GetWorkerControlTimings());
+
+  // if (params.use_dht) {
+  chem_profiling["dht_hits"] = Rcpp::wrap(chem.GetWorkerDHTHits());
+  chem_profiling["dht_evictions"] = Rcpp::wrap(chem.GetWorkerDHTEvictions());
+  chem_profiling["dht_get_time"] = Rcpp::wrap(chem.GetWorkerDHTGetTimings());
+  chem_profiling["dht_fill_time"] = Rcpp::wrap(chem.GetWorkerDHTFillTimings());
+  //}
 
   if (params.use_interp) {
     chem_profiling["interp_w"] =
@@ -460,6 +468,7 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
   profiling["simtime"] = dSimTime;
   profiling["chemistry"] = chem_profiling;
   profiling["diffusion"] = diffusion_profiling;
+  profiling["control"] = ctrl_profiling;
 
   chem.MasterLoopBreak();
 

src/poet.hpp.in

@@ -52,6 +52,7 @@ struct RuntimeParameters {
   bool print_progress = false;
   std::uint32_t stab_interval = 0;
   std::uint32_t checkpoint_interval = 0;
+  std::uint32_t max_rb = 0;
   double zero_abs = 0.0;
   std::vector<double> mape_threshold;
   std::vector<uint32_t> ctrl_cell_ids;

util/data_evaluation/RFun_Eval_qs2.R

@@ -0,0 +1,452 @@
+## Simple library of functions to assess and visualize the results of the coupled simulations
+## Modified to work with .qs2 files (qs2 package format)
+
+## Time-stamp: "Last modified 2025-11-25"
+
+require(qs2)  ## for reading .qs2 files
+require(stringr)
+
+# Note: RedModRphree, Rmufits, and Rcpp functions for DHT/PHT reading are kept
+# but you'll need those packages only if you use ReadAllDHT/ReadAllPHT functions
+
+curdir <- dirname(sys.frame(1)$ofile) ##path.expand(".")
+
+print(paste("RFun_Eval_qs2.R is in ", curdir))
+
+## ============================================================================
+## NEW: Functions for reading .qs2 simulation outputs
+## ============================================================================
+
+## function which reads all simulation results in a given directory (.qs2 format)
+ReadRTSims_qs2 <- function(dir) {
+    pattern <- "^iter_.*\\.qs2$"
+    files_full <- list.files(dir, pattern = pattern, full.names = TRUE)
+    files_name <- list.files(dir, pattern = pattern, full.names = FALSE)
+    
+    if (length(files_full) == 0) {
+        warning(paste("No .qs2 files found in", dir, "with pattern", pattern))
+        return(NULL)
+    }
+    
+    res <- lapply(files_full, qs2::qs_read)
+    names(res) <- gsub(".qs2", "", files_name, perl = TRUE)
+    
+    return(res[str_sort(names(res), numeric = TRUE)])
+}
+## Read a single .qs2 file
+ReadQS2 <- function(file) {
+    if (!file.exists(file)) {
+        stop(paste("File not found:", file))
+    }
+    qs2::qs_read(file)
+}
+
+## Extract chemistry field data from .qs2 iteration file
+## Assumes structure similar to old .rds format with $C (chemistry) and $T (transport)
+ExtractChemistry <- function(qs2_data) {
+    if ("C" %in% names(qs2_data)) {
+        return(qs2_data$C)
+    } else if (is.data.frame(qs2_data)) {
+        return(qs2_data)
+    } else {
+        warning("Could not find chemistry data in expected format")
+        return(qs2_data)
+    }
+}
+
+## Extract transport field data from .qs2 iteration file
+ExtractTransport <- function(qs2_data) {
+    if ("T" %in% names(qs2_data)) {
+        return(qs2_data$T)
+    } else {
+        warning("Could not find transport data in expected format")
+        return(NULL)
+    }
+}
+
+## ============================================================================
+## ORIGINAL: DHT/PHT reading functions (kept for surrogate analysis)
+## ============================================================================
+
+# Only load these if needed (requires Rcpp compilation)
+if (requireNamespace("Rcpp", quietly = TRUE) && file.exists(paste0(curdir, "/interpret_keys.cpp"))) {
+    library(Rcpp)
+    sourceCpp(file = paste0(curdir, "/interpret_keys.cpp"))
+    
+    # Wrapper around previous sourced Rcpp function
+    ConvertDHTKey <- function(value) {
+      rcpp_key_convert(value)
+    }
+    
+    ConvertToUInt64 <- function(double_data) {
+      rcpp_uint64_convert(double_data)
+    }
+} else {
+    if (!requireNamespace("Rcpp", quietly = TRUE)) {
+        message("Note: Rcpp not available. DHT/PHT reading functions will not work.")
+    }
+    # Create dummy functions so the rest of the script doesn't break
+    ConvertDHTKey <- function(value) {
+      stop("Rcpp not available. Cannot convert DHT keys.")
+    }
+    ConvertToUInt64 <- function(double_data) {
+      stop("Rcpp not available. Cannot convert to UInt64.")
+    }
+}
+
+## function which reads all successive DHT stored in a given directory
+ReadAllDHT <- function(dir, new_scheme = TRUE) {
+    files_full <- list.files(dir, pattern="iter.*\\.dht$", full.names=TRUE)
+    files_name <- list.files(dir, pattern="iter.*\\.dht$", full.names=FALSE)
+    
+    if (length(files_full) == 0) {
+        warning(paste("No .dht files found in", dir))
+        return(NULL)
+    }
+    
+    res <- lapply(files_full, ReadDHT, new_scheme = new_scheme)
+    names(res) <- gsub("\\.dht$","",files_name)
+    return(res)
+}
+
+## function which reads one .dht file and gives a matrix
+ReadDHT <- function(file, new_scheme = TRUE) {
+    conn <- file(file, "rb")  ## open for reading in binary mode
+    if (!isSeekable(conn))
+        stop("Connection not seekable")
+
+    ## we first reposition ourselves to the end of the file...
+    tmp <- seek(conn, where=0, origin = "end")
+    ## ... and then back to the origin so to store the length in bytes
+    flen <- seek(conn, where=0, origin = "start")
+
+    ## we read the first 2 integers (4 bytes each) containing dimensions in bytes
+    dims <- readBin(conn, what="integer", n=2)
+
+    ## compute dimensions of the data
+    tots <- sum(dims)
+    ncol <- tots/8
+    nrow <- (flen - 8)/tots ## 8 here is 2*sizeof("int")
+    buff <- readBin(conn, what="double", n=ncol*nrow)
+    ## close connection
+    close(conn)
+    res <- matrix(buff, nrow=nrow, ncol=ncol, byrow=TRUE)
+
+    if (new_scheme) {
+      nkeys <- dims[1] / 8
+      keys <- res[, 1:nkeys]
+
+      conv <- apply(keys, 2, ConvertDHTKey)
+      res[, 1:nkeys] <- conv
+    }
+
+    return(res)
+}
+
+## function which reads all successive PHT stored in a given directory
+ReadAllPHT <- function(dir, with_info = FALSE) {
+    files_full <- list.files(dir, pattern="iter.*\\.pht$", full.names=TRUE)
+    files_name <- list.files(dir, pattern="iter.*\\.pht$", full.names=FALSE)
+    
+    if (length(files_full) == 0) {
+        warning(paste("No .pht files found in", dir))
+        return(NULL)
+    }
+    
+    res <- lapply(files_full, ReadPHT, with_info = with_info)
+    names(res) <- gsub("\\.pht$","",files_name)
+    return(res)
+}
+
+## function which reads one .pht file and gives a matrix
+ReadPHT <- function(file, with_info = FALSE) {
+    conn <- file(file, "rb")  ## open for reading in binary mode
+    if (!isSeekable(conn))
+        stop("Connection not seekable")
+
+    ## we first reposition ourselves to the end of the file...
+    tmp <- seek(conn, where=0, origin = "end")
+    ## ... and then back to the origin so to store the length in bytes
+    flen <- seek(conn, where=0, origin = "start")
+
+    ## we read the first 2 integers (4 bytes each) containing dimensions in bytes
+    dims <- readBin(conn, what="integer", n=2)
+
+    ## compute dimensions of the data
+    tots <- sum(dims)
+    ncol <- tots/8
+    nrow <- (flen - 8)/tots ## 8 here is 2*sizeof("int")
+    buff <- readBin(conn, what="double", n=ncol*nrow)
+    ## close connection
+    close(conn)
+    res <- matrix(buff, nrow=nrow, ncol=ncol, byrow=TRUE)
+
+    nkeys <- dims[1] / 8
+    keys <- res[, 1:nkeys]
+
+    timesteps <- res[, nkeys + 1]
+    conv <- apply(keys, 2, ConvertDHTKey)
+
+    ndata <- dims[2] / 8
+    fill_rate <- ConvertToUInt64(res[, nkeys + 2])
+
+    buff <- c(conv, timesteps, fill_rate)
+
+    if (with_info) {
+      ndata <- dims[2]/8
+      visit_count <- ConvertToUInt64(res[, nkeys + ndata])
+      buff <- c(buff, visit_count)
+    }
+
+    res <- matrix(buff, nrow = nrow, byrow = FALSE)
+
+    return(res)
+}
+
+## ============================================================================
+## PLOTTING and ANALYSIS functions (work with both .rds and .qs2 data)
+## ============================================================================
+
+## Scatter plots of each variable in the iteration 
+PlotScatter <- function(sam1, sam2, which=NULL, labs=c("NO DHT", "DHT"), pch=".", cols=3, ...) {
+    if ((!is.data.frame(sam1)) & ("T" %in% names(sam1)))
+        sam1 <- sam1$C
+    if ((!is.data.frame(sam2)) & ("T" %in% names(sam2)))
+        sam2 <- sam2$C
+    if (is.numeric(which))
+        inds <- which
+    else if (is.character(which))
+        inds <- match(which, colnames(sam1))
+    else if (is.null(which))
+        inds <- seq_along(colnames(sam1))
+
+    rows <- ceiling(length(inds) / cols)
+    par(mfrow=c(rows, cols))
+    a <- lapply(inds, function(x) {
+        plot(sam1[,x], sam2[,x], main=colnames(sam1)[x],  xlab=labs[1], ylab=labs[2], pch=pch, col="red", ...)
+        abline(0,1, col="grey", lwd=1.5)
+    })
+    invisible()
+}
+
+##### Some metrics for relative comparison
+
+## Root Mean Square Error
+RMSE <- function(pred, obs)
+    sqrt(mean((pred - obs)^2, na.rm = TRUE))
+
+## Using range as norm
+RranRMSE <- function(pred, obs)
+    sqrt(mean((pred - obs)^2, na.rm = TRUE))/abs(max(pred, na.rm = TRUE) - min(pred, na.rm = TRUE))
+
+## Using max val as norm
+RmaxRMSE <- function(pred, obs)
+    sqrt(mean((pred - obs)^2, na.rm = TRUE))/abs(max(pred, na.rm = TRUE))
+
+## Using sd as norm
+RsdRMSE <- function(pred, obs)
+    sqrt(mean((pred - obs)^2, na.rm = TRUE))/sd(pred, na.rm = TRUE)
+
+## Using mean as norm
+RmeanRMSE <- function(pred, obs)
+    sqrt(mean((pred - obs)^2, na.rm = TRUE))/mean(pred, na.rm = TRUE)
+
+## Using mean as norm
+RAEmax <- function(pred, obs)
+    mean(abs(pred - obs), na.rm = TRUE)/max(pred, na.rm = TRUE)
+
+## Max absolute error
+MAE <- function(pred, obs)
+    max(abs(pred - obs), na.rm = TRUE)
+
+## Mean Absolute Percentage Error
+MAPE <- function(pred, obs)
+    mean(abs((obs - pred) / obs) * 100, na.rm = TRUE)
+
+## workhorse function for ComputeErrors and its use with mapply
+AppliedFun <- function(a, b, .fun) {
+    # Extract chemistry data if needed
+    if (!is.data.frame(a) && "C" %in% names(a)) a <- a$C
+    if (!is.data.frame(b) && "C" %in% names(b)) b <- b$C
+    
+    mapply(.fun, as.list(a), as.list(b))
+}
+
+## Compute the diffs between two simulation, iter by iter,
+## with a given metric (passed in form of function name to this function)
+ComputeErrors <- function(sim1, sim2, FUN=RMSE) {
+    if (length(sim1)!= length(sim2)) {
+        cat("The simulations do not have the same length, subsetting to the shortest\n")
+        a <- min(length(sim1), length(sim2))
+        sim1 <- sim1[1:a]
+        sim2 <- sim2[1:a]
+    }
+    if (!is.function(match.fun(FUN))) {
+        stop("Invalid function\n")
+    }
+
+    t(mapply(AppliedFun, sim1, sim2, MoreArgs=list(.fun=FUN)))
+}
+
+## Function to display the error progress between 2 simulations
+ErrorProgress <- function(mat, ignore, colors, metric, ...) {
+    if (is.null(mat)) {
+        stop("Cannot plot: matrix is NULL")
+    }
+    
+    # Convert to matrix if it's a vector or data frame
+    if (is.vector(mat)) {
+        stop("Cannot plot: input is a vector (need at least 2 columns). Check that your data has multiple columns.")
+    }
+    if (is.data.frame(mat)) {
+        mat <- as.matrix(mat)
+    }
+    
+    if (nrow(mat) == 0 || ncol(mat) == 0) {
+        stop("Cannot plot: matrix is empty")
+    }
+    
+    if (missing(colors))
+        colors <- sample(rainbow(ncol(mat)))
+
+    if (missing(metric))
+        metric <- "Metric"
+
+    ## if the optional argument "ignore" (a character vector) is
+    ## passed, we remove the matching column names
+    if (!missing(ignore)) {
+        to_remove <- match(ignore, colnames(mat))
+        to_remove <- to_remove[!is.na(to_remove)]  # Remove NAs
+        if (length(to_remove) > 0) {
+            mat <- mat[, -to_remove, drop = FALSE]
+            colors <- colors[-to_remove]
+        }
+    }
+    
+    yc <- mat[nrow(mat),]
+    par(mar=c(5,4,2,8))
+    matplot(mat, type="l", lty=1, lwd=2, col=colors, xlab="iteration", ylab=metric, ...)
+    mtext(colnames(mat), side = 4, line = 0.5, outer = FALSE, at = yc, adj = 0, col = colors, las=2, cex=0.7)
+}
+
+## Function which exports all simulations to ParaView's .vtu 
+## Requires package RcppVTK
+ExportToParaview <- function(vtu, nameout, results) {
+    if (!requireNamespace("RcppVTK", quietly = TRUE)) {
+        stop("Package RcppVTK is required for this function")
+    }
+    require(RcppVTK)
+    
+    n <- length(results)
+    vars <- colnames(results[[1]])
+    ## strip eventually present ".vtu" from nameout
+    nameout <- sub(".vtu", "", nameout, fixed=TRUE)
+    namesteps <- paste0(nameout,  ".", sprintf("%04d",seq(1,n)), ".vtu")
+    for (step in seq_along(results)) {
+        file.copy(from=vtu, to=namesteps[step], overwrite = TRUE)
+        cat(paste("Saving step ", step, " in file ", namesteps[step], "\n"))
+        ret <- ExportMatrixToVTU (fin=vtu, fout=namesteps[step], names=colnames(results[[step]]), mat=results[[step]])
+    }
+    invisible(ret)
+}
+
+
+## Version of Rmufits::PlotCartCellData with the ability to fix the
+## "breaks" for color coding of 2D simulations
+Plot2DCellData <- function (data, grid, nx, ny, contour = TRUE,
+                            nlevels = 12, breaks, palette = "heat.colors",
+                            rev.palette = TRUE, scale = TRUE, plot.axes=TRUE, ...) {
+    if (!missing(grid)) {
+        xc <- unique(sort(grid$cell$XCOORD))
+        yc <- unique(sort(grid$cell$YCOORD))
+        nx <- length(xc)
+        ny <- length(yc)
+        if (!length(data) == nx * ny) 
+            stop("Wrong nx, ny or grid")
+    } else {
+        xc <- seq(1, nx)
+        yc <- seq(1, ny)
+    }
+    z <- matrix(round(data, 6), ncol = nx, nrow = ny, byrow = TRUE)
+    pp <- t(z[rev(seq(1, nrow(z))), ])
+
+    if (missing(breaks)) {
+        breaks <- pretty(data, n = nlevels)
+    }
+    
+    breakslen <- length(breaks)
+    colors <- do.call(palette, list(n = breakslen - 1))
+    if (rev.palette) 
+        colors <- rev(colors)
+    if (scale) {
+        par(mfrow = c(1, 2))
+        nf <- layout(matrix(c(1, 2), 1, 2, byrow = TRUE), widths = c(4, 
+            1))
+    }
+    par(las = 1, mar = c(5, 5, 3, 1))
+    image(xc, yc, pp, xlab = "X [m]", ylab = "Y[m]", las = 1, asp = 1,
+          breaks = breaks, col = colors, axes = FALSE, ann=plot.axes,
+          ...)
+
+    if (plot.axes) {
+        axis(1)
+        axis(2)
+    }
+    if (contour) 
+        contour(unique(sort(xc)), unique(sort(yc)), pp, breaks = breaks, 
+            add = TRUE)
+    if (scale) {
+        par(las = 1, mar = c(5, 1, 5, 5))
+        if (requireNamespace("Rmufits", quietly = TRUE)) {
+            Rmufits::PlotImageScale(data, breaks = breaks, add.axis = FALSE, 
+                axis.pos = 4, col = colors)
+        }
+        axis(4, at = breaks)
+    }
+    invisible(pp)
+}
+
+PlotAsMP4 <- function(data, nx, ny, to_plot, out_dir, name,
+                      contour = FALSE, scale = FALSE, framerate = 30) {
+  sort_data <- data[str_sort(names(data), numeric = TRUE)]
+  plot_data <- lapply(sort_data, function(x) {
+      if (!is.data.frame(x) && "C" %in% names(x)) {
+          return(x$C[[to_plot]])
+      } else {
+          return(x[[to_plot]])
+      }
+  })
+  pad_size <- ceiling(log10(length(plot_data)))
+
+  dir.create(out_dir, showWarnings = FALSE)
+  output_files <- paste0(out_dir, "/", name, "_%0", pad_size, "d.png")
+  output_mp4 <- paste0(out_dir, "/", name, ".mp4")
+
+  png(output_files,
+    width = 297, height = 210, units = "mm",
+    res = 100
+  )
+
+  for (i in 1:length(plot_data)) {
+    if (requireNamespace("Rmufits", quietly = TRUE)) {
+        Rmufits::PlotCartCellData(plot_data[[i]], nx = nx, ny = ny, contour = contour, scale = scale)
+    } else {
+        Plot2DCellData(plot_data[[i]], nx = nx, ny = ny, contour = contour, scale = scale)
+    }
+  }
+  dev.off()
+
+  ffmpeg_command <- paste(
+    "ffmpeg -y -framerate", framerate, "-i", output_files,
+    "-c:v libx264 -crf 22", output_mp4
+  )
+
+  system(ffmpeg_command)
+  message(paste("Created video:", output_mp4))
+}
+
+cat("\n=== RFun_Eval_qs2.R loaded successfully ===\n")
+cat("New functions for .qs2 files:\n")
+cat("  - ReadRTSims_qs2(dir)  : Read all iteration .qs2 files\n")
+cat("  - ReadQS2(file)        : Read single .qs2 file\n")
+cat("All other functions work as before!\n\n")

util/data_evaluation/run_vis.R

@@ -0,0 +1,50 @@
+# Load the new functions
+source("/mnt/beegfs/home/rastogi/poet/util/data_evaluation/RFun_Eval.R")
+
+# Set base path
+base_dir <- "/mnt/beegfs/home/rastogi/poet/bin"
+
+sim1 <- ReadRTSims(file.path(base_dir, "proto2_eps01_no_rb_v2"))
+sim2 <- ReadRTSims(file.path(base_dir, "proto2_eps0035_no_rb_v2"))
+
+
+# ========================================
+# Compare two simulations
+# ========================================
+rmse_errors <- ComputeErrors(sim1, sim2, FUN = RMSE)
+mape_errors <- ComputeErrors(sim1, sim2, FUN = MAPE)
+
+# Print summary
+cat("RMSE errors computed for", ncol(rmse_errors), "variables\n")
+cat("MAPE errors computed for", ncol(mape_errors), "variables\n")
+cat("Number of iterations compared:", nrow(rmse_errors), "\n\n")
+
+# Set output path explicitly
+output_pdf <- file.path(base_dir, "comparison_plots.pdf")
+cat("Saving plots to:", output_pdf, "\n")
+
+# Save plots to PDF
+pdf(output_pdf, width = 10, height = 6)
+
+# Plot error progression
+cat("Creating ErrorProgress plot...\n")
+ErrorProgress(rmse_errors, ignore = c("Charge"), metric = "RMSE")
+
+# Scatter plot for specific iteration (if that iteration exists)
+if (length(sim1) >= 10 && length(sim2) >= 10) {
+  cat("Creating scatter plot for iteration 10...\n")
+  PlotScatter(sim1[[10]], sim2[[10]], 
+              labs = c("Proto2 Eps=0.01%", "Proto2 Eps=0.0035%"),
+              which = c("Ca", "Mg", "Cl", "C"))
+} else {
+  cat("Not enough iterations for scatter plot\n")
+}
+
+dev.off()
+cat("Plots saved successfully to:", output_pdf, "\n")
+
+# ========================================
+# DHT/PHT analysis (if you have snapshot files)
+# ========================================
+#dht_snaps <- ReadAllDHT("poet/bin/proto1_only_interp")
+#pht_snaps <- ReadAllPHT("poet/bin/proto1_only_interp")