diff --git a/R_lib/kin_r_library.R b/R_lib/kin_r_library.R
index c759bf9e1..273fe6c4f 100644
--- a/R_lib/kin_r_library.R
+++ b/R_lib/kin_r_library.R
@@ -1,4 +1,6 @@
-### Copyright (C) 2018-2022 Marco De Lucia, Max Luebke (GFZ Potsdam)
+## Time-stamp: "Last modified 2023-08-15 11:58:23 delucia"
+
+### Copyright (C) 2018-2023 Marco De Lucia, Max Luebke (GFZ Potsdam)
 ###
 ### POET is free software; you can redistribute it and/or modify it under the
 ### terms of the GNU General Public License as published by the Free Software
@@ -13,51 +15,52 @@
 ### this program; if not, write to the Free Software Foundation, Inc., 51
 ### Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
 
+
 ## Simple function to check file extension. It is needed to check if
 ## the GridFile is SUM (MUFITS format) or rds/RData
 FileExt <- function(x) {
-  pos <- regexpr("\\.([[:alnum:]]+)$", x)
-  ifelse(pos > -1L, substring(x, pos + 1L), "")
+    pos <- regexpr("\\.([[:alnum:]]+)$", x)
+    ifelse(pos > -1L, substring(x, pos + 1L), "")
 }
 
 master_init <- function(setup) {
-  msgm("Process with rank 0 reading GRID properties")
+    msgm("Process with rank 0 reading GRID properties")
 
-  ## Setup the directory where we will store the results
-  verb <- FALSE
-  if (local_rank == 0) {
-    verb <- TRUE ## verbosity loading MUFITS results
-    if (!dir.exists(fileout)) {
-      dir.create(fileout)
-      msgm("created directory ", fileout)
+    ## Setup the directory where we will store the results
+    verb <- FALSE
+    if (local_rank == 0) {
+        verb <- TRUE ## verbosity loading MUFITS results
+        if (!dir.exists(fileout)) {
+            dir.create(fileout)
+            msgm("created directory ", fileout)
+        } else {
+            msgm("dir ", fileout, " already exists, I will overwrite!")
+        }
+        if (!exists("store_result")) {
+            msgm("store_result doesn't exist!")
+        } else {
+            msgm("store_result is ", store_result)
+        }
     } else {
-      msgm("dir ", fileout, " already exists, I will overwrite!")
+        
     }
-    if (!exists("store_result")) {
-      msgm("store_result doesn't exist!")
-    } else {
-      msgm("store_result is ", store_result)
+
+    setup$iter <- 1
+    setup$maxiter <- setup$iterations
+    setup$timesteps <- setup$timesteps
+    setup$simulation_time <- 0
+
+    if (is.null(setup[["store_result"]])) {
+        setup$store_result <- TRUE
     }
-  } else {
-
-  }
-
-  setup$iter <- 1
-  setup$maxiter <- setup$iterations
-  setup$timesteps <- setup$timesteps
-  setup$simulation_time <- 0
-
-  if (is.null(setup[["store_result"]])) {
-    setup$store_result <- TRUE
-  }
-
-  if (setup$store_result) {
-    if (is.null(setup[["out_save"]])) {
-      setup$out_save <- seq(1, setup$iterations)
+    
+    if (setup$store_result) {
+        if (is.null(setup[["out_save"]])) {
+            setup$out_save <- seq(1, setup$iterations)
+        }
     }
-  }
-
-  return(setup)
+    
+    return(setup)
 }
 
 ## This function, called only by master, stores on disk the last
@@ -95,125 +98,125 @@ master_iteration_end <- function(setup) {
 
 ## function for the workers to compute chemistry through PHREEQC
 slave_chemistry <- function(setup, data) {
-  base <- setup$base
-  first <- setup$first
-  prop <- setup$prop
-  immobile <- setup$immobile
-  kin <- setup$kin
-  ann <- setup$ann
-
-  iter <- setup$iter
-  timesteps <- setup$timesteps
-  dt <- timesteps[iter]
-
-  state_T <- data ## not the global field, but the work-package
-
-  ## treat special H+/pH, e-/pe cases
-  state_T <- RedModRphree::Act2pH(state_T)
-
-  ## reduction of the problem
-  if (setup$reduce) {
-    reduced <- ReduceStateOmit(state_T, omit = setup$ann)
-  } else {
-    reduced <- state_T
-  }
-
-  ## form the PHREEQC input script for the current work package
-  inplist <- SplitMultiKin(
-    data = reduced, procs = 1, base = base, first = first,
-    ann = ann, prop = prop, minerals = immobile, kin = kin, dt = dt
-  )
-
-  ## if (local_rank==1 & iter==1)
-  ##         RPhreeWriteInp("FirstInp", inplist)
-
-  tmpC <- RunPQC(inplist, procs = 1, second = TRUE)
-
-  ## recompose after the reduction
-  if (setup$reduce) {
-    state_C <- RecomposeState(tmpC, reduced)
-  } else {
-    state_C <- tmpC
-  }
-
-  ## the next line is needed since we don't need all columns of
-  ## PHREEQC output
-  return(state_C[, prop])
+    base <- setup$base
+    first <- setup$first
+    prop <- setup$prop
+    immobile <- setup$immobile
+    kin <- setup$kin
+    ann <- setup$ann
+    
+    iter <- setup$iter
+    timesteps <- setup$timesteps
+    dt <- timesteps[iter]
+    
+    state_T <- data ## not the global field, but the work-package
+    
+    ## treat special H+/pH, e-/pe cases
+    state_T <- RedModRphree::Act2pH(state_T)
+    
+    ## reduction of the problem
+    if (setup$reduce) {
+        reduced <- ReduceStateOmit(state_T, omit = setup$ann)
+    } else {
+        reduced <- state_T
+    }
+    
+    ## form the PHREEQC input script for the current work package
+    inplist <- SplitMultiKin(
+        data = reduced, procs = 1, base = base, first = first,
+        ann = ann, prop = prop, minerals = immobile, kin = kin, dt = dt
+    )
+    
+    ## if (local_rank==1 & iter==1)
+    ##         RPhreeWriteInp("FirstInp", inplist)
+    
+    tmpC <- RunPQC(inplist, procs = 1, second = TRUE)
+    
+    ## recompose after the reduction
+    if (setup$reduce) {
+        state_C <- RecomposeState(tmpC, reduced)
+    } else {
+        state_C <- tmpC
+    }
+    
+    ## the next line is needed since we don't need all columns of
+    ## PHREEQC output
+    return(state_C[, prop])
 }
 
 ## This function, called by master
 master_chemistry <- function(setup, data) {
-  state_T <- setup$state_T
-
-  msgm(" chemistry iteration", setup$iter)
-
-  ## treat special H+/pH, e-/pe cases
-  state_T <- RedModRphree::Act2pH(state_T)
-
-  ## reduction of the problem
-  if (setup$reduce) {
-    reduced <- ReduceStateOmit(state_T, omit = setup$ann)
-  } else {
-    reduced <- state_T
-  }
-
-  ### inject data from workers
-  res_C <- data
-
-  rownames(res_C) <- NULL
-
-  ## print(res_C)
-
-  if (nrow(res_C) > nrow(reduced)) {
-    res_C <- res_C[seq(2, nrow(res_C), by = 2), ]
-  }
-
-  ## recompose after the reduction
-  if (setup$reduce) {
-    state_C <- RecomposeState(res_C, reduced)
-  } else {
-    state_C <- res_C
-  }
-
-  setup$state_C <- state_C
-  setup$reduced <- reduced
-
-  return(setup)
+    state_T <- setup$state_T
+    
+    msgm(" chemistry iteration", setup$iter)
+    
+    ## treat special H+/pH, e-/pe cases
+    state_T <- RedModRphree::Act2pH(state_T)
+    
+    ## reduction of the problem
+    if (setup$reduce) {
+        reduced <- ReduceStateOmit(state_T, omit = setup$ann)
+    } else {
+        reduced <- state_T
+    }
+    
+    ## inject data from workers
+    res_C <- data
+    
+    rownames(res_C) <- NULL
+    
+    ## print(res_C)
+    
+    if (nrow(res_C) > nrow(reduced)) {
+        res_C <- res_C[seq(2, nrow(res_C), by = 2), ]
+    }
+    
+    ## recompose after the reduction
+    if (setup$reduce) {
+        state_C <- RecomposeState(res_C, reduced)
+    } else {
+        state_C <- res_C
+    }
+    
+    setup$state_C <- state_C
+    setup$reduced <- reduced
+    
+    return(setup)
 }
 
 
 ## Adapted version for "reduction"
 ReduceStateOmit <- function(data, omit = NULL, sign = 6) {
-  require(mgcv)
+    require(mgcv)
+    
+    rem <- colnames(data)
+    if (is.list(omit)) {
+        indomi <- match(names(omit), colnames(data))
+        datao <- data[, -indomi]
+    } else {
+        datao <- data
+    }
+    
+    datao <- signif(datao, sign)
+    red <- mgcv::uniquecombs(datao)
+    inds <- attr(red, "index")
+    now <- ncol(red)
+    
+    
+    ## reattach the omitted column(s)
+    ## FIXME: control if more than one ann is present
+    if (is.list(omit)) {
+        red <- cbind(red, rep(data[1, indomi], nrow(red)))
 
-  rem <- colnames(data)
-  if (is.list(omit)) {
-    indomi <- match(names(omit), colnames(data))
-    datao <- data[, -indomi]
-  } else {
-    datao <- data
-  }
+        colnames(red)[now + 1] <- names(omit)
 
-  datao <- signif(datao, sign)
-  red <- mgcv::uniquecombs(datao)
-  inds <- attr(red, "index")
-  now <- ncol(red)
-
-
-  ## reattach the omitted column(s)
-  ## FIXME: control if more than one ann is present
-  if (is.list(omit)) {
-    red <- cbind(red, rep(data[1, indomi], nrow(red)))
-
-    colnames(red)[now + 1] <- names(omit)
-
-    ret <- red[, colnames(data)]
-  } else {
-    ret <- red
-  }
-  rownames(ret) <- NULL
-  attr(ret, "index") <- inds
-  return(ret)
+        ret <- red[, colnames(data)]
+    } else {
+        ret <- red
+    }
+    rownames(ret) <- NULL
+    attr(ret, "index") <- inds
+    return(ret)
 }
 
 
@@ -221,67 +224,70 @@ ReduceStateOmit <- function(data, omit = NULL, sign = 6) {
 ## Attach the name of the calling function to the message displayed on
 ## R's stdout
 msgm <- function(...) {
-  if (local_rank == 0) {
-    fname <- as.list(sys.call(-1))[[1]]
-    prefix <- paste0("R: ", fname, " ::")
-    cat(paste(prefix, ..., "\n"))
-  }
-  invisible()
+    if (local_rank == 0) {
+        fname <- as.list(sys.call(-1))[[1]]
+        prefix <- paste0("R: ", fname, " ::")
+        cat(paste(prefix, ..., "\n"))
+    }
+    invisible()
 }
 
 
 ## Function called by master R process to store on disk all relevant
 ## parameters for the simulation
 StoreSetup <- function(setup) {
-  to_store <- vector(mode = "list", length = 3)
-  # names(to_store) <- c("Sim", "Flow", "Transport", "Chemistry", "DHT")
-  names(to_store) <- c("Sim", "Transport", "DHT")
 
-  ## read the setup R file, which is sourced in kin.cpp
-  tmpbuff <- file(filesim, "r")
-  setupfile <- readLines(tmpbuff)
-  close.connection(tmpbuff)
+    to_store <- vector(mode = "list", length = 4)
+    ## names(to_store) <- c("Sim", "Flow", "Transport", "Chemistry", "DHT")
+    names(to_store) <- c("Sim", "Transport", "DHT", "Cmdline")
+    
+    ## read the setup R file, which is sourced in kin.cpp
+    tmpbuff <- file(filesim, "r")
+    setupfile <- readLines(tmpbuff)
+    close.connection(tmpbuff)
+    
+    to_store$Sim <- setupfile
+    
+    ## to_store$Flow <- list(
+    ##     snapshots  = setup$snapshots,
+    ##     gridfile   = setup$gridfile,
+    ##     phase      = setup$phase,
+    ##     density    = setup$density,
+    ##     dt_differ  = setup$dt_differ,
+    ##     prolong    = setup$prolong,
+    ##     maxiter    = setup$maxiter,
+    ##     saved_iter = setup$iter_output,
+    ##     out_save   = setup$out_save )
 
-  to_store$Sim <- setupfile
+    to_store$Transport <- setup$diffusion
 
-  # to_store$Flow <- list(
-  #     snapshots  = setup$snapshots,
-  #     gridfile   = setup$gridfile,
-  #     phase      = setup$phase,
-  #     density    = setup$density,
-  #     dt_differ  = setup$dt_differ,
-  #     prolong    = setup$prolong,
-  #     maxiter    = setup$maxiter,
-  #     saved_iter = setup$iter_output,
-  #     out_save   = setup$out_save )
+    ## to_store$Chemistry <- list(
+    ##    nprocs   = n_procs,
+    ##    wp_size  = work_package_size,
+    ##    base     = setup$base,
+    ##    first    = setup$first,
+    ##    init     = setup$initsim,
+    ##    db       = db,
+    ##    kin      = setup$kin,
+    ##    ann      = setup$ann)
 
-  to_store$Transport <- setup$diffusion
-  # to_store$Chemistry <- list(
-  #    nprocs   = n_procs,
-  #    wp_size  = work_package_size,
-  #    base     = setup$base,
-  #    first    = setup$first,
-  #    init     = setup$initsim,
-  #    db       = db,
-  #    kin      = setup$kin,
-  #    ann      = setup$ann)
+    if (dht_enabled) {
+        to_store$DHT <- list(
+            enabled   = dht_enabled,
+            log       = dht_log
+            ## signif    = dht_final_signif,
+            ## proptype  = dht_final_proptype
+        )
+    } else {
+        to_store$DHT <- FALSE
+    }
 
-  if (dht_enabled) {
-    to_store$DHT <- list(
-      enabled   = dht_enabled,
-      log       = dht_log
-      #signif    = dht_final_signif,
-      #proptype  = dht_final_proptype
-    )
-  } else {
-    to_store$DHT <- FALSE
-  }
-
-  saveRDS(to_store, file = paste0(fileout, "/setup.rds"))
-  msgm("initialization stored in ", paste0(fileout, "/setup.rds"))
+    to_store$Cmdline <- commandArgs(trailingOnly=FALSE)
+    saveRDS(to_store, file = paste0(fileout, "/setup.rds"))
+    msgm("initialization stored in ", paste0(fileout, "/setup.rds"))
 }
 
 GetWorkPackageSizesVector <- function(n_packages, package_size, len) {
-  ids <- rep(1:n_packages, times=package_size, each = 1)[1:len]
-  return(as.integer(table(ids)))
+    ids <- rep(1:n_packages, times=package_size, each = 1)[1:len]
+    return(as.integer(table(ids)))
 }
diff --git a/src/SimParams.cpp b/src/SimParams.cpp
index fd77dde20..0a81c5b73 100644
--- a/src/SimParams.cpp
+++ b/src/SimParams.cpp
@@ -1,8 +1,10 @@
+//  Time-stamp: "Last modified 2023-08-15 12:12:36 delucia"
+
 /*
 ** Copyright (C) 2018-2021 Alexander Lindemann, Max Luebke (University of
 ** Potsdam)
 **
-** Copyright (C) 2018-2022 Marco De Lucia, Max Luebke (GFZ Potsdam)
+** Copyright (C) 2018-2023 Marco De Lucia, Max Luebke (GFZ Potsdam)
 **
 ** POET is free software; you can redistribute it and/or modify it under the
 ** terms of the GNU General Public License as published by the Free Software
@@ -144,9 +146,9 @@ int SimParams::parseFromCmdl(char *argv[], RInsidePOET &R) {
 
   simparams.print_progressbar = cmdl[{"P", "progress"}];
 
-  simparams.print_progressbar = cmdl[{"P", "progress"}];
+  // simparams.print_progressbar = cmdl[{"P", "progress"}];
 
-  /*Parse DHT arguments*/
+  /* Parse DHT arguments */
   chem_params.use_dht = cmdl["dht"];
   chem_params.use_interp = cmdl["interp"];
   // cout << "CPP: DHT is " << ( dht_enabled ? "ON" : "OFF" ) << '\n';