From 1250dc59d9e55b0149be315630d5fae7f2412009 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Max=20L=C3=BCbke?= <mluebke@gfz-potsdam.de>
Date: Wed, 6 Mar 2024 11:59:12 +0100
Subject: [PATCH] Add Macros.hpp and RInsidePOET.hpp*** ***Add RInsidePOET
 class and RHookFunction template*** ***Update include paths in
 SimParams.hpp*** ***Update CMakeLists.txt to link poetlib*** ***Update
 DHT_Wrapper.hpp include path*** ***Update DiffusionModule.cpp include path***
 ***Update poet.cpp include paths*** ***Add poet.hpp.in

---
 src/{ => Base}/Macros.hpp                     |  0
 src/{ => Base}/RInsidePOET.hpp                |  0
 src/Base/SimParams.hpp                        |  4 +-
 src/CMakeLists.txt                            | 39 ++++++++++++-------
 src/Chemistry/SurrogateModels/DHT_Wrapper.hpp |  2 +-
 src/Transport/DiffusionModule.cpp             |  2 +-
 src/poet.cpp                                  |  6 +--
 src/{poet.h.in => poet.hpp.in}                |  0
 8 files changed, 33 insertions(+), 20 deletions(-)
 rename src/{ => Base}/Macros.hpp (100%)
 rename src/{ => Base}/RInsidePOET.hpp (100%)
 rename src/{poet.h.in => poet.hpp.in} (100%)

diff --git a/src/Macros.hpp b/src/Base/Macros.hpp
similarity index 100%
rename from src/Macros.hpp
rename to src/Base/Macros.hpp
diff --git a/src/RInsidePOET.hpp b/src/Base/RInsidePOET.hpp
similarity index 100%
rename from src/RInsidePOET.hpp
rename to src/Base/RInsidePOET.hpp
diff --git a/src/Base/SimParams.hpp b/src/Base/SimParams.hpp
index 212ec9948..523b5b105 100644
--- a/src/Base/SimParams.hpp
+++ b/src/Base/SimParams.hpp
@@ -22,8 +22,8 @@
 #define PARSER_H
 
 #include "../DataStructures/DataStructures.hpp"
-#include "../Macros.hpp"
-#include "../RInsidePOET.hpp"
+#include "Macros.hpp"
+#include "RInsidePOET.hpp"
 
 #include "argh.hpp" // Argument handler https://github.com/adishavit/argh
 
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index addb7c11b..51261c39a 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,20 +1,27 @@
-file(GLOB_RECURSE poet_lib_SRC
-  CONFIGURE_DEPENDS
-  "*.cpp" "*.c")
+add_library(poetlib
+  Base/Grid.cpp
+  Base/SimParams.cpp
+  Chemistry/ChemistryModule.cpp
+  Chemistry/MasterFunctions.cpp 
+  Chemistry/WorkerFunctions.cpp 
+  Chemistry/SurrogateModels/DHT_Wrapper.cpp 
+  Chemistry/SurrogateModels/DHT.c 
+  Chemistry/SurrogateModels/HashFunctions.cpp 
+  Chemistry/SurrogateModels/InterpolationModule.cpp 
+  Chemistry/SurrogateModels/ProximityHashTable.cpp
+  DataStructures/Field.cpp
+  Transport/DiffusionModule.cpp
+)
 
-configure_file(poet.h.in poet.h)
-
-add_executable(poet ${poet_lib_SRC})
-target_link_libraries(poet 
-  MPI::MPI_CXX 
+target_link_libraries(poetlib PUBLIC
+  MPI::MPI_C 
   ${MATH_LIBRARY} 
   RRuntime 
   PhreeqcRM 
   tug
 )
-target_include_directories(poet PRIVATE "${CMAKE_CURRENT_BINARY_DIR}")
 
-target_compile_definitions(poet PRIVATE STRICT_R_HEADERS OMPI_SKIP_MPICXX)
+target_compile_definitions(poetlib PUBLIC STRICT_R_HEADERS)
 
 mark_as_advanced(PHREEQCRM_BUILD_MPI PHREEQCRM_DISABLE_OPENMP)
 set(PHREEQCRM_DISABLE_OPENMP ON CACHE BOOL "" FORCE)
@@ -22,13 +29,19 @@ set(PHREEQCRM_DISABLE_OPENMP ON CACHE BOOL "" FORCE)
 option(POET_DHT_DEBUG "Build with DHT debug info" OFF)
 
 if(POET_DHT_DEBUG)
-  target_compile_definitions(poet PRIVATE DHT_STATISTICS)
+  target_compile_definitions(poetlib PRIVATE DHT_STATISTICS)
 endif()
 
 option(POET_PHT_ADDITIONAL_INFO "Enables additional information in the PHT" OFF)
 
 if (POET_PHT_ADDITIONAL_INFO)
-  target_compile_definitions(poet PRIVATE POET_PHT_ADD)
+  target_compile_definitions(poetlib PRIVATE POET_PHT_ADD)
 endif()
 
-install(TARGETS poet DESTINATION bin)
\ No newline at end of file
+configure_file(poet.hpp.in poet.hpp)
+
+add_executable(poet poet.cpp)
+target_link_libraries(poet PRIVATE poetlib MPI::MPI_C RRuntime)
+target_include_directories(poet PRIVATE "${CMAKE_CURRENT_BINARY_DIR}")
+
+install(TARGETS poet DESTINATION bin)
diff --git a/src/Chemistry/SurrogateModels/DHT_Wrapper.hpp b/src/Chemistry/SurrogateModels/DHT_Wrapper.hpp
index 083fe9d25..791be2d1b 100644
--- a/src/Chemistry/SurrogateModels/DHT_Wrapper.hpp
+++ b/src/Chemistry/SurrogateModels/DHT_Wrapper.hpp
@@ -23,9 +23,9 @@
 #ifndef DHT_WRAPPER_H
 #define DHT_WRAPPER_H
 
+#include "../../Base/RInsidePOET.hpp"
 #include "../../Base/SimParams.hpp"
 #include "../../DataStructures/DataStructures.hpp"
-#include "../../RInsidePOET.hpp"
 #include "../enums.hpp"
 #include "HashFunctions.hpp"
 #include "LookupKey.hpp"
diff --git a/src/Transport/DiffusionModule.cpp b/src/Transport/DiffusionModule.cpp
index b02f5ca0b..abbecce95 100644
--- a/src/Transport/DiffusionModule.cpp
+++ b/src/Transport/DiffusionModule.cpp
@@ -19,7 +19,7 @@
 */
 
 #include "DiffusionModule.hpp"
-#include "../Macros.hpp"
+#include "../Base/Macros.hpp"
 
 #include <tug/BoundaryCondition.hpp>
 #include <tug/Diffusion.hpp>
diff --git a/src/poet.cpp b/src/poet.cpp
index aa6c22cb6..c4996dc97 100644
--- a/src/poet.cpp
+++ b/src/poet.cpp
@@ -19,13 +19,13 @@
 */
 
 #include "Base/Grid.hpp"
+#include "Base/Macros.hpp"
+#include "Base/RInsidePOET.hpp"
 #include "Base/SimParams.hpp"
 #include "Chemistry/ChemistryModule.hpp"
-#include "Macros.hpp"
-#include "RInsidePOET.hpp"
 #include "Transport/DiffusionModule.hpp"
 
-#include <poet.h>
+#include <poet.hpp>
 
 #include <Rcpp.h>
 #include <cstdint>
diff --git a/src/poet.h.in b/src/poet.hpp.in
similarity index 100%
rename from src/poet.h.in
rename to src/poet.hpp.in