From 1c004dfda9951e013ee8d483f46b633c37dc619d Mon Sep 17 00:00:00 2001
From: Max Luebke <mluebke@gfz-potsdam.de>
Date: Tue, 2 Apr 2024 11:39:59 +0000
Subject: [PATCH] Update dependencies and refactor code

---
 ext/iphreeqc    |  2 +-
 src/poet.cpp    | 29 +++++++++++------------------
 src/poet.hpp.in |  4 ++++
 3 files changed, 16 insertions(+), 19 deletions(-)

diff --git a/ext/iphreeqc b/ext/iphreeqc
index f69561987..daeecf112 160000
--- a/ext/iphreeqc
+++ b/ext/iphreeqc
@@ -1 +1 @@
-Subproject commit f695619875fcf43e411af67d592c05b199f41a15
+Subproject commit daeecf11263dbeb08cb13b43df81d5d9dcc22060
diff --git a/src/poet.cpp b/src/poet.cpp
index 1f6be971f..ecb5b5bf8 100644
--- a/src/poet.cpp
+++ b/src/poet.cpp
@@ -22,27 +22,21 @@
 
 #include "Base/Macros.hpp"
 #include "Base/RInsidePOET.hpp"
-// #include "Chemistry/ChemistryModule.hpp"
 #include "Chemistry/ChemistryModule.hpp"
 #include "DataStructures/Field.hpp"
 #include "Init/InitialList.hpp"
 #include "Transport/DiffusionModule.hpp"
 
 #include <RInside.h>
-#include <R_ext/Boolean.h>
-#include <Rcpp/DataFrame.h>
-#include <Rcpp/vector/instantiation.h>
-#include <poet.hpp>
-
 #include <Rcpp.h>
 #include <cstdlib>
-
+#include <mpi.h>
 #include <string>
 
-#include <mpi.h>
-
 #include "Base/argh.hpp"
 
+#include <poet.hpp>
+
 using namespace std;
 using namespace poet;
 using namespace Rcpp;
@@ -110,9 +104,11 @@ ParseRet parseInitValues(char **argv, RInsidePOET &R,
     }
   }
 
-  // simparams.print_progressbar = cmdl[{"P", "progress"}];
+  params.print_progressbar = cmdl[{"P", "progress"}];
 
-  // // simparams.print_progressbar = cmdl[{"P", "progress"}];
+  /*Parse work package size*/
+  cmdl("work-package-size", CHEM_DEFAULT_WORK_PACKAGE_SIZE) >>
+      params.work_package_size;
 
   // /* Parse DHT arguments */
   // chem_params.use_dht = cmdl["dht"];
@@ -136,9 +132,6 @@ ParseRet parseInitValues(char **argv, RInsidePOET &R,
   // /*Parse output options*/
   // simparams.store_result = !cmdl["ignore-result"];
 
-  // /*Parse work package size*/
-  // cmdl("work-package-size", WORK_PACKAGE_SIZE_DEFAULT) >> simparams.wp_size;
-
   // chem_params.use_interp = cmdl["interp"];
   // cmdl("interp-size", 100) >> chem_params.pht_size;
   // cmdl("interp-min", 5) >> chem_params.interp_min_entries;
@@ -446,10 +439,12 @@ int main(int argc, char *argv[]) {
 
   MSG("RInside initialized on process " + std::to_string(world_rank));
 
+  ChemistryModule chemistry(run_params.work_package_size,
+                            init_list.getChemistryInit(), MPI_COMM_WORLD);
+
   if (world_rank > 0) {
 
-    ChemistryModule worker(1, init_list.getChemistryInit(), MPI_COMM_WORLD);
-    worker.WorkerLoop();
+    chemistry.WorkerLoop();
 
     MPI_Barrier(MPI_COMM_WORLD);
 
@@ -483,8 +478,6 @@ int main(int argc, char *argv[]) {
   DiffusionModule diffusion(init_list.getDiffusionInit(),
                             init_list.getInitialGrid());
 
-  ChemistryModule chemistry(1, init_list.getChemistryInit(), MPI_COMM_WORLD);
-
   chemistry.masterSetField(init_list.getInitialGrid());
 
   Rcpp::List profiling = RunMasterLoop(R, run_params, diffusion, chemistry);
diff --git a/src/poet.hpp.in b/src/poet.hpp.in
index 99b3e7a58..dcf71b972 100644
--- a/src/poet.hpp.in
+++ b/src/poet.hpp.in
@@ -22,6 +22,7 @@
 
 #pragma once
 
+#include <cstdint>
 #include <set>
 #include <string>
 #include <vector>
@@ -43,10 +44,13 @@ const std::set<std::string> paramlist{
     "work-package-size", "dht-strategy", "dht-size",   "dht-snaps",
     "dht-file",          "interp-size",  "interp-min", "interp-bucket-entries"};
 
+constexpr uint32_t CHEM_DEFAULT_WORK_PACKAGE_SIZE = 32;
+
 struct RuntimeParameters {
   std::vector<double> timesteps;
 
   bool print_progressbar;
+  uint32_t work_package_size;
 
   Rcpp::List init_params;