refactor: refactor hpcReact to generalize behavior and introduce solid species and surface complexation. (#5)

* feat: add mixed system.

* Implement mixed ultramafic system with serpentinization rxn

* fix order of constexpr host device

* mixed reactions test working.

* refactor all unitTests.

* add predefined variant for geochem.

* add benchmark system.

* Add Forge system

---------

Co-authored-by: frankfeifan <[email protected]>
Co-authored-by: jkgolla <[email protected]>
Co-authored-by: Randolph Settgast <[email protected]>

Author: 4 people

.gitignore

@@ -1,4 +1,6 @@
 build*
 install*
 cmake/blt*
-.vscode*
+.vscode*
+.DS_Store
+src/.DS_Store

src/CMakeLists.txt

@@ -2,16 +2,23 @@
 set( hpcReact_headers
      common/macros.hpp
      common/CArrayWrapper.hpp
-     reactions/bulkGeneric/EquilibriumReactions.hpp
-     reactions/bulkGeneric/EquilibriumReactionsAggregatePrimaryConcentration_impl.hpp
-     reactions/bulkGeneric/EquilibriumReactionsReactionExtents_impl.hpp
-     reactions/bulkGeneric/KineticReactions.hpp
-     reactions/bulkGeneric/KineticReactions_impl.hpp
-     reactions/bulkGeneric/MixedEquilibriumKineticReactions.hpp
-     reactions/bulkGeneric/MixedEquilibriumKineticReactions_impl.hpp
-     reactions/bulkGeneric/Parameters.hpp
-     reactions/bulkGeneric/ParametersPredefined.hpp
-     reactions/bulkGeneric/SpeciesUtilities.hpp
+     reactions/exampleSystems/BulkGeneric.hpp
+     reactions/geochemistry/Carbonate.hpp
+     reactions/geochemistry/Forge.hpp
+     reactions/geochemistry/GeochemicalSystems.hpp
+     reactions/geochemistry/Ultramafics.hpp
+     reactions/massActions/MassActions.hpp
+     reactions/reactionsSystems/EquilibriumReactions.hpp
+     reactions/reactionsSystems/EquilibriumReactionsAggregatePrimaryConcentration_impl.hpp
+     reactions/reactionsSystems/EquilibriumReactionsReactionExtents_impl.hpp
+     reactions/reactionsSystems/KineticReactions.hpp
+     reactions/reactionsSystems/KineticReactions_impl.hpp
+     reactions/reactionsSystems/MixedEquilibriumKineticReactions.hpp
+     reactions/reactionsSystems/MixedEquilibriumKineticReactions_impl.hpp
+     reactions/reactionsSystems/Parameters.hpp
+     reactions/unitTestUtilities/equilibriumReactionsTestUtilities.hpp
+     reactions/unitTestUtilities/kineticReactionsTestUtilities.hpp
+     reactions/unitTestUtilities/mixedReactionsTestUtilities.hpp
      )
 
 set( hpcReact_sources)
@@ -59,7 +66,9 @@ message(STATUS "HPCReact/src CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DI
 # hpcReact_add_code_checks( PREFIX hpcReact
 #                        EXCLUDES "blt/*" )
 
-add_subdirectory( reactions/bulkGeneric/unitTests )
+add_subdirectory( reactions/exampleSystems/unitTests )
+add_subdirectory( reactions/geochemistry/unitTests )
+add_subdirectory( reactions/massActions/unitTests )
 add_subdirectory( common/unitTests )
 add_subdirectory( docs )
 

src/common/printers.hpp

@@ -1,6 +1,7 @@
 #pragma once
 
 #include <stdio.h>
+#include "CArrayWrapper.hpp"
 
 template< typename T, int N >
 void print( T const (&a)[N], char const * name, int const numDigits )