refactor: Rename IPhreeqcPOET to litephreeqc

refactor: Rename 'poet' directory to 'litephreeqc'

CMakeLists.txt

@@ -220,7 +220,7 @@ target_sources(IPhreeqc
     src/phreeqcpp/UserPunch.cpp
     src/phreeqcpp/UserPunch.h
     src/phreeqcpp/utilities.cpp
-    src/phreeqcpp/GFZ.cpp
+    src/phreeqcpp/litephreeqc_funcs.cpp
     src/thread.h
     src/Var.c
     src/Var.h
@@ -470,7 +470,7 @@ if (STANDALONE_BUILD)
   endif()
 endif()
 
-add_subdirectory(poet)
+add_subdirectory(litephreeqc)
 
 # get_cmake_property(_variableNames VARIABLES)
 # list (SORT _variableNames)

litephreeqc/CMakeLists.txt

@@ -1,4 +1,4 @@
-set(POET_SOURCE_FILES
+set(LPQC_SOURCE_FILES
     src/Engine.cpp
     src/Runner.cpp 
     src/Knobs.cpp
@@ -20,19 +20,19 @@ set(POET_SOURCE_FILES
     src/PhreeqcMatrix/Misc.cpp
 )
 
-add_library(IPhreeqcPOET ${POET_SOURCE_FILES})
+add_library(litephreeqc ${LPQC_SOURCE_FILES})
-target_link_libraries(IPhreeqcPOET PUBLIC IPhreeqc)
+target_link_libraries(litephreeqc PUBLIC IPhreeqc)
-target_include_directories(IPhreeqcPOET PUBLIC
+target_include_directories(litephreeqc PUBLIC
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
     $<INSTALL_INTERFACE:include>)
 
 # Set C++20 standard
-target_compile_features(IPhreeqcPOET PUBLIC cxx_std_20)
+target_compile_features(litephreeqc PUBLIC cxx_std_20)
 
 if (BUILD_TESTING AND STANDALONE_BUILD)
     enable_testing()
 
-    set(POET_TEST_SOURCE_FILES
+    set(LPQC_TEST_SOURCE_FILES
         test/testPhreeqcEngine.cpp
         test/testPhreeqcMatrix.cpp
         test/testPhreeqcRunner.cpp
@@ -40,15 +40,15 @@ if (BUILD_TESTING AND STANDALONE_BUILD)
         test/utils.cpp
     )
 
-    add_executable(poet_test ${POET_TEST_SOURCE_FILES})
+    add_executable(litephreeqc_test ${LPQC_TEST_SOURCE_FILES})
 
     target_link_libraries(
-        poet_test
+        litephreeqc_test
-        IPhreeqcPOET
+        litephreeqc
         GTest::gtest_main
     )
 
-    target_include_directories(poet_test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
+    target_include_directories(litephreeqc_test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
 
     # read file and store in variable
     file(REAL_PATH "${PROJECT_SOURCE_DIR}/database/phreeqc.dat" POET_PHREEQCDAT_DB)
@@ -58,8 +58,8 @@ if (BUILD_TESTING AND STANDALONE_BUILD)
     configure_file("${CMAKE_CURRENT_SOURCE_DIR}/test/testInput.hpp.in" "${CMAKE_CURRENT_BINARY_DIR}/testInput.hpp")
 
     include(GoogleTest)
-    gtest_discover_tests(poet_test)
+    gtest_discover_tests(litephreeqc_test)
 endif()
 
 add_executable(golemrunner test/testGolemRunner.cpp)
-target_link_libraries(golemrunner IPhreeqcPOET)
+target_link_libraries(golemrunner litephreeqc)

litephreeqc/LICENSE.txt

@@ -0,0 +1,10 @@
+This project is subject to the original PHREEQC license. `litephreeqc` is a
+version of the PHREEQC code that has been modified to be used as a library.
+
+It adds a C++ interface on top of the original PHREEQC code, with small changes
+to the original code base. 
+
+Authors of Modifications:
+- Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+- Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+

litephreeqc/include/PhreeqcEngine.hpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #pragma once
 
 #include "PhreeqcMatrix.hpp"

litephreeqc/include/PhreeqcKnobs.hpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #pragma once
 
 #include <cstdint>

litephreeqc/include/PhreeqcMatrix.hpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #pragma once
 
 #include <map>

litephreeqc/include/PhreeqcRunner.hpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #pragma once
 
 #include "PhreeqcEngine.hpp"

litephreeqc/src/Engine.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "PhreeqcEngine.hpp"
 #include <cstddef>
 #include <iomanip>

litephreeqc/src/Knobs.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "PhreeqcKnobs.hpp"
 
 #include <Phreeqc.h>

litephreeqc/src/PhreeqcMatrix/Access.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include <PhreeqcMatrix.hpp>
 #include <algorithm>
 #include <cstddef>

litephreeqc/src/PhreeqcMatrix/Ctor.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "IPhreeqc.hpp"
 #include "PhreeqcKnobs.hpp"
 #include "PhreeqcMatrix.hpp"

litephreeqc/src/PhreeqcMatrix/Init.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "PhreeqcMatrix.hpp"
 
 #include "../Wrapper/EquilibriumWrapper.hpp"

litephreeqc/src/PhreeqcMatrix/Misc.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "PhreeqcMatrix.hpp"
 
 #include <IPhreeqc.hpp>

litephreeqc/src/Runner.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "PhreeqcEngine.hpp"
 #include "PhreeqcMatrix.hpp"
 #include "PhreeqcRunner.hpp"

litephreeqc/src/Wrapper/EquilibriumCompWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "EquilibriumWrapper.hpp"
 
 EquilibriumWrapper::EquilibriumCompWrapper::EquilibriumCompWrapper(

litephreeqc/src/Wrapper/EquilibriumWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "EquilibriumWrapper.hpp"
 
 #include <algorithm>

litephreeqc/src/Wrapper/EquilibriumWrapper.hpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #pragma once
 
 #include "PPassemblage.h"

litephreeqc/src/Wrapper/ExchangeCompWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "ExchangeWrapper.hpp"
 
 ExchangeWrapper::ExchangeCompWrapper::ExchangeCompWrapper(cxxExchComp &comp)

litephreeqc/src/Wrapper/ExchangeWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "ExchangeWrapper.hpp"
 
 ExchangeWrapper::ExchangeWrapper(cxxExchange *exch,
@@ -21,36 +34,36 @@ ExchangeWrapper::ExchangeWrapper(cxxExchange *exch,
     num_elements += exchange_comps.back()->size();
   }
 
-    // const std::size_t defined_comps = exchange->Get_exchange_comps().size();
+  // const std::size_t defined_comps = exchange->Get_exchange_comps().size();
 
-    // auto header_it = remaining_field_header.begin();
+  // auto header_it = remaining_field_header.begin();
 
-    // while (header_it != remaining_field_header.end() &&
+  // while (header_it != remaining_field_header.end() &&
-    //        exchange_comps.size() < defined_comps) {
+  //        exchange_comps.size() < defined_comps) {
-    //   const std::string formular = *header_it;
+  //   const std::string formular = *header_it;
 
-    //   auto it = std::find_if(exchange->Get_exchange_comps().begin(),
+  //   auto it = std::find_if(exchange->Get_exchange_comps().begin(),
-    //                          exchange->Get_exchange_comps().end(),
+  //                          exchange->Get_exchange_comps().end(),
-    //                          [&](const cxxExchComp &comp) {
+  //                          [&](const cxxExchComp &comp) {
-    //                            return comp.Get_formula() == formular;
+  //                            return comp.Get_formula() == formular;
-    //                          });
+  //                          });
 
-    //   if (it != exchange->Get_exchange_comps().end()) {
+  //   if (it != exchange->Get_exchange_comps().end()) {
-    //     const size_t i = this->exchange_comps.size();
+  //     const size_t i = this->exchange_comps.size();
 
-    //     exchange_comps.push_back(std::make_unique<ExchangeCompWrapper>(*it));
+  //     exchange_comps.push_back(std::make_unique<ExchangeCompWrapper>(*it));
-    //     header_it += this->exchange_comps[i]->size();
+  //     header_it += this->exchange_comps[i]->size();
-    //     num_elements += this->exchange_comps[i]->size();
+  //     num_elements += this->exchange_comps[i]->size();
-    //     continue;
+  //     continue;
-    //   }
+  //   }
 
-    //   header_it++;
+  //   header_it++;
-    // }
+  // }
 
-    // if (exchange_comps.size() != defined_comps) {
+  // if (exchange_comps.size() != defined_comps) {
-    //   throw std::runtime_error(
+  //   throw std::runtime_error(
-    //       "Not all exchange components found in Phreeqc variables");
+  //       "Not all exchange components found in Phreeqc variables");
-    // }
+  // }
 }
 
 void ExchangeWrapper::get(std::span<LDBLE> &exchange) const {

litephreeqc/src/Wrapper/ExchangeWrapper.hpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #pragma once
 
 #include "ExchComp.h"

litephreeqc/src/Wrapper/KineticCompWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "KineticWrapper.hpp"
 #include <cstddef>
 #include <string>

litephreeqc/src/Wrapper/KineticWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "KineticWrapper.hpp"
 #include <vector>
 

litephreeqc/src/Wrapper/KineticWrapper.hpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #pragma once
 
 #include "KineticsComp.h"

litephreeqc/src/Wrapper/SolutionWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "SolutionWrapper.hpp"
 #include "NameDouble.h"
 #include <set>

litephreeqc/src/Wrapper/SolutionWrapper.hpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #pragma once
 
 #include "Solution.h"

litephreeqc/src/Wrapper/SurfaceChargeWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "SurfaceWrapper.hpp"
 
 SurfaceWrapper::SurfaceChargeWrapper::SurfaceChargeWrapper(

litephreeqc/src/Wrapper/SurfaceCompWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "SurfaceWrapper.hpp"
 
 SurfaceWrapper::SurfaceCompWrapper::SurfaceCompWrapper(cxxSurfaceComp &comp)

litephreeqc/src/Wrapper/SurfaceWrapper.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "SurfaceWrapper.hpp"
 #include "SurfaceComp.h"
 

litephreeqc/src/Wrapper/SurfaceWrapper.hpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #pragma once
 
 #include "Surface.h"

litephreeqc/src/Wrapper/WrapperBase.hpp

@@ -0,0 +1,31 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
+#pragma once
+
+#include <phrqtype.h>
+#include <span>
+
+class WrapperBase {
+public:
+  virtual ~WrapperBase() = default;
+
+  std::size_t size() const { return this->num_elements; };
+
+  virtual void get(std::span<LDBLE> &data) const = 0;
+
+  virtual void set(const std::span<LDBLE> &data) = 0;
+
+protected:
+  std::size_t num_elements = 0;
+};

litephreeqc/test/testGolemRunner.cpp

@@ -0,0 +1,174 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
+//  Time-stamp: "Last modified 2024-12-02 17:37:08 delucia"
+#include <algorithm>
+#include <cmath>
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+#include <iterator>
+#include <linux/limits.h>
+#include <memory>
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "PhreeqcEngine.hpp"
+#include "PhreeqcMatrix.hpp"
+#include "PhreeqcRunner.hpp"
+
+std::string readFile(const std::string &path) {
+  std::string string_rpath(PATH_MAX, '\0');
+
+  if (realpath(path.c_str(), string_rpath.data()) == nullptr) {
+    throw std::runtime_error(":: Failed to resolve the realpath to file " +
+                             path);
+  }
+
+  std::ifstream file(string_rpath);
+
+  if (!file.is_open()) {
+    throw std::runtime_error(":: Failed to open file: " + path);
+  }
+
+  std::stringstream buffer;
+  buffer << file.rdbuf();
+
+  return buffer.str();
+}
+
+// pretty print a vector, standard implementation from stackoverflow
+template <typename T>
+std::ostream &operator<<(std::ostream &os, std::vector<T> vec) {
+  os << "{ ";
+  std::copy(vec.begin(), vec.end(), std::ostream_iterator<T>(os, ", "));
+  os << " }";
+  return os;
+}
+
+int main(int argc, char *argv[]) {
+
+  if (argc < 3) {
+    std::cout << "::" << argv[0] << ": two args needed, script and database\n";
+    return 1;
+  }
+
+  ////// INITIALISATION
+  // read Script and Database and put it in a std::string
+  auto script = readFile(argv[1]);
+  auto db = readFile(argv[2]);
+
+  // Create the matrix directly from database and init script
+  PhreeqcMatrix pqc_mat(db, script);
+
+  // How many different SOLUTIONS ("CELLS") are defined in the script?
+  const auto ids = pqc_mat.getIds();
+
+  int n = ids.size();
+
+  std::cout << ":: Found " << n << " distinct PHREEQC problems \n";
+  std::cout << ids << "\n";
+
+  const auto solutes = pqc_mat.getSolutionNames();
+  std::cout << ":: These are the common solutes across all the " << n
+            << " problems: \n";
+  std::cout << solutes << "\n";
+
+  // iterate on the ids (THEY start at 1!!)
+  for (const auto &i : ids) {
+    auto pphases = pqc_mat.getEquilibriumNames(i);
+    if (!pphases.empty()) {
+      std::cout << ":: Equilibrium phases [" << (int)i << "]: \n";
+      std::cout << pphases << "\n";
+    }
+
+    auto kinetics = pqc_mat.getKineticsNames(i);
+    if (!kinetics.empty()) {
+      std::cout << ":: Kinetics [" << i << "]: \n";
+      std::cout << kinetics << "\n";
+    }
+  }
+
+  // The exported data type holds the matrix in a "STL format" with
+  // a "header" of names and their accompanying values. The values
+  // are stored in a row-major order per default.
+  auto exported_mat = pqc_mat.get();
+  // Get the total number of solutes
+  const int len = exported_mat.names.size();
+  // Get the values as reference to modify them in place
+  std::vector<double> &cell_values = exported_mat.values;
+
+  std::cout << ":: Values in the PhreeqcMatrix: \n";
+
+  // std::cout << exported_mat.names  << "\n";
+  // std::cout << cell_values << "\n";
+  // END INIT
+
+  //// Phreeqc RUN through the new Runner class
+
+  // optional SUBSET the matrix (i.e., the unique ids defined in
+  // golem map as input)
+  // const auto subsetted_pqc_mat = pqc_mat.subset({1, 2});
+  PhreeqcRunner runner(pqc_mat);
+
+  const auto stl_mat = pqc_mat.get();
+  const auto matrix_values = stl_mat.values;
+  const auto num_columns = stl_mat.names.size();
+  const auto spec_names = stl_mat.names;
+
+  // container to pass in/out
+  std::vector<std::vector<double>> simulationInOut;
+
+  // grid cells
+  const std::size_t num_cells = 10;
+  const std::size_t half_cells = 5;
+
+  // copy the values to the InOut vector. We replicate cell 1
+  for (std::size_t index = 0; index < num_cells; ++index) {
+    if (index < half_cells) {
+      simulationInOut.push_back(std::vector<double>(
+          matrix_values.begin(), matrix_values.begin() + num_columns));
+    } else {
+      simulationInOut.push_back(std::vector<double>(
+          matrix_values.begin() + num_columns, matrix_values.end()));
+    }
+  }
+
+  const double timestep = 100.;
+
+  // compute 1 timestep
+  runner.run(simulationInOut, timestep);
+
+  for (std::size_t cell_index = 0; cell_index < simulationInOut.size();
+       ++cell_index) {
+    const bool is_first_half = cell_index < half_cells;
+    if (is_first_half) {
+      std::cout << "Grid element: " << cell_index << " \n";
+      for (std::size_t spec = 0; spec < num_columns; ++spec) {
+        std::cout << ":" << spec_names[spec] << "="
+                  << simulationInOut[cell_index][spec];
+      }
+      std::cout << "\n";
+    }
+  }
+
+  return 0;
+}
+
+// Oneliner for rz-vm278 relative to iphreeqc/poet/test!!
+
+// g++ testGolemRunner.cpp -o testG -Wall -I../../poet/include -I../../src
+// -I../../src/phreeqcpp -I../../src/phreeqcpp/common
+// -I../../src/phreeqcpp/PhreeqcKeywords -lIPhreeqc -lIPhreeqcPOET
+// -L../../bbuild/ -L../../bbuild/poet

litephreeqc/test/testPhreeqcEngine.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include <stdexcept>
 
 #include <testInput.hpp>

litephreeqc/test/testPhreeqcKnobs.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include <gtest/gtest.h>
 #include <testInput.hpp>
 

litephreeqc/test/testPhreeqcMatrix.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include <cmath>
 #include <gtest/gtest.h>
 #include <string>

litephreeqc/test/testPhreeqcRunner.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "PhreeqcRunner.hpp"
 #include "utils.hpp"
 

litephreeqc/test/utils.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "utils.hpp"
 
 #include <fstream>

litephreeqc/test/utils.hpp

@@ -0,0 +1,18 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
+#pragma once
+
+#include <string>
+
+std::string readFile(const std::string &path);

poet/src/Wrapper/WrapperBase.hpp

@@ -1,18 +0,0 @@
-#pragma once
-
-#include <phrqtype.h>
-#include <span>
-
-class WrapperBase {
-public:
-  virtual ~WrapperBase() = default;
-
-  std::size_t size() const { return this->num_elements; };
-
-  virtual void get(std::span<LDBLE> &data) const = 0;
-
-  virtual void set(const std::span<LDBLE> &data) = 0;
-
-protected:
-  std::size_t num_elements = 0;
-};

poet/test/testGolemRunner.cpp

@@ -1,161 +0,0 @@
-//  Time-stamp: "Last modified 2024-12-02 17:37:08 delucia"
-#include <iostream>
-#include <iomanip>
-#include <linux/limits.h>
-#include <sstream>
-#include <fstream>
-#include <algorithm>
-#include <iterator>
-#include <vector>
-#include <string>
-#include <memory>
-#include <cmath>
-
-#include "PhreeqcMatrix.hpp"
-#include "PhreeqcEngine.hpp"
-#include "PhreeqcRunner.hpp"
-
-
-std::string readFile(const std::string &path) {
-  std::string string_rpath(PATH_MAX, '\0');
-
-  if (realpath(path.c_str(), string_rpath.data()) == nullptr) {
-    throw std::runtime_error(":: Failed to resolve the realpath to file " + path);
-  }
-
-  std::ifstream file(string_rpath);
-
-  if (!file.is_open()) {
-    throw std::runtime_error(":: Failed to open file: " + path);
-  }
-
-  std::stringstream buffer;
-  buffer << file.rdbuf();
-
-  return buffer.str();
-}
-
-// pretty print a vector, standard implementation from stackoverflow 
-template<typename T>
-std::ostream & operator<<(std::ostream & os, std::vector<T> vec)
-{
-    os << "{ ";
-    std::copy(vec.begin(), vec.end(), std::ostream_iterator<T>(os, ", "));
-    os << " }";
-    return os;
-}
-
-
-int main(int argc, char *argv[]) {
-    
-    if (argc < 3) {
-	std::cout << "::" << argv[0] << ": two args needed, script and database\n";
-	return 1;
-    }
-
-
-    ////// INITIALISATION
-    // read Script and Database and put it in a std::string
-    auto script = readFile(argv[1]);
-    auto db     = readFile(argv[2]);
-
-    // Create the matrix directly from database and init script
-    PhreeqcMatrix pqc_mat(db, script);
-    
-    // How many different SOLUTIONS ("CELLS") are defined in the script?
-    const auto ids = pqc_mat.getIds();
-    
-    int n = ids.size();
-    
-    std::cout << ":: Found " << n << " distinct PHREEQC problems \n";
-    std::cout << ids << "\n";
-
-    const auto solutes  = pqc_mat.getSolutionNames();
-    std::cout << ":: These are the common solutes across all the " << n << " problems: \n";
-    std::cout << solutes << "\n";
-    
-    // iterate on the ids (THEY start at 1!!)
-    for (const auto & i : ids) {
-	auto pphases  = pqc_mat.getEquilibriumNames(i);
-	if (!pphases.empty()) {
-	    std::cout << ":: Equilibrium phases [" << (int) i <<  "]: \n";
-	    std::cout << pphases << "\n";
-	}
-	
-	auto kinetics = pqc_mat.getKineticsNames(i);
-	if (!kinetics.empty()) {
-	    std::cout << ":: Kinetics [" << i <<  "]: \n";
-	    std::cout << kinetics << "\n";
-	}
-    }
-
-    // The exported data type holds the matrix in a "STL format" with
-    // a "header" of names and their accompanying values. The values
-    // are stored in a row-major order per default.
-    auto exported_mat = pqc_mat.get();
-    // Get the total number of solutes
-    const int len = exported_mat.names.size();
-    // Get the values as reference to modify them in place
-    std::vector<double> &cell_values = exported_mat.values;
-
-    std::cout << ":: Values in the PhreeqcMatrix: \n";
-
-    // std::cout << exported_mat.names  << "\n";
-    // std::cout << cell_values << "\n";
-    // END INIT
-
-
-    
-    //// Phreeqc RUN through the new Runner class 
-
-    // optional SUBSET the matrix (i.e., the unique ids defined in
-    // golem map as input)
-    // const auto subsetted_pqc_mat = pqc_mat.subset({1, 2});
-    PhreeqcRunner runner(pqc_mat);
-
-    const auto stl_mat = pqc_mat.get();
-    const auto matrix_values = stl_mat.values;
-    const auto num_columns = stl_mat.names.size();
-    const auto spec_names = stl_mat.names;
-
-    // container to pass in/out
-    std::vector<std::vector<double>> simulationInOut;
-
-    // grid cells
-    const std::size_t num_cells = 10;
-    const std::size_t half_cells = 5;
-
-    // copy the values to the InOut vector. We replicate cell 1 
-    for (std::size_t index = 0; index < num_cells; ++index) {
-	if (index < half_cells) {
-	    simulationInOut.push_back(std::vector<double>(
-            matrix_values.begin(), matrix_values.begin() + num_columns));
-	} else {
-	    simulationInOut.push_back(std::vector<double>(
-            matrix_values.begin() + num_columns, matrix_values.end()));
-	}
-    }
-
-    const double timestep = 100.;
-
-    // compute 1 timestep
-    runner.run(simulationInOut, timestep);
-
-    for (std::size_t cell_index = 0; cell_index < simulationInOut.size(); ++cell_index) {
-	const bool is_first_half = cell_index < half_cells;
-	if (is_first_half) {
-	    std::cout << "Grid element: " << cell_index << " \n";
-	    for (std::size_t spec = 0; spec < num_columns; ++spec) {
-		std::cout << ":" << spec_names[spec] << "=" << simulationInOut[cell_index][spec];
-	    }
-	    std::cout << "\n";
-	}
-    }
-
-    
-    return 0;
-}
-
-// Oneliner for rz-vm278 relative to iphreeqc/poet/test!!
-
-// g++ testGolemRunner.cpp -o testG -Wall -I../../poet/include -I../../src -I../../src/phreeqcpp -I../../src/phreeqcpp/common -I../../src/phreeqcpp/PhreeqcKeywords -lIPhreeqc -lIPhreeqcPOET -L../../bbuild/ -L../../bbuild/poet

poet/test/utils.hpp

@@ -1,5 +0,0 @@
-#pragma once
-
-#include <string>
-
-std::string readFile(const std::string &path);

src/phreeqcpp/litephreeqc_funcs.cpp

@@ -1,3 +1,16 @@
+/*
+ * This project is subject to the original PHREEQC license. `litephreeqc` is a
+ * version of the PHREEQC code that has been modified to be used as a library.
+ *
+ * It adds a C++ interface on top of the original PHREEQC code, with small
+ * changes to the original code base.
+ *
+ * Authors of Modifications:
+ * - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
+ * - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
+ *
+ */
+
 #include "Phreeqc.h"
 #include <set>
 
@@ -85,4 +98,4 @@ std::vector<std::string> Phreeqc::find_all_valence_states(
   }
 
   return solution_with_valences;
-}
+}