move the momas example to exampleSystems

Author: frankfeifan

src/reactions/exampleSystems/MoMasBenchmark.hpp

@@ -49,33 +49,35 @@ namespace MomMasBenchmark
   },
 
   // Forward rate constants 
-  { 0.0,
-    0.0, 
-    0.0, 
-    0.0, 
-    0.0, 
-    0.0, 
-    0.0 
+  { 
+    0.0,   // C1 = -X2
+    0.0,   // C2 = X2 + X3
+    0.0,   // C3 = X2 + X4
+    0.0,   // C4 = -4X2 + X3 + 3X4
+    0.0,   // C5 = 4X2 + 3X3 + X4
+    0.0,   // CS1 = 3X2 + X3 + S
+    0.0    // CS2 = -3X2 + X4 + 2S
   },
 
   // Reverse rate constants 
-  { 0.0,
-    0.0, 
-    0.0, 
-    0.0, 
-    0.0, 
-    0.0, 
-    0.0 
+  { 
+    0.0,   // C1 = -X2
+    0.0,   // C2 = X2 + X3
+    0.0,   // C3 = X2 + X4
+    0.0,   // C4 = -4X2 + X3 + 3X4
+    0.0,   // C5 = 4X2 + 3X3 + X4
+    0.0,   // CS1 = 3X2 + X3 + S
+    0.0    // CS2 = -3X2 + X4 + 2S
   },
 
   // Flag of mobile secondary species
-  { 1, // C1 = - X2
+  { 1, // C1 = -X2
     1, // C2 = X2 + X3
     1, // C3 = -X2 + X4
     1, // C4 = -4X2 + X3 + 3X4
     1, // C5 = 4X2 + 3X3 + X4
     0, // CS1 = 3X2 + X3 + S
-    0 // CS2 = -3X2 + X4 + 2S
+    0  // CS2 = -3X2 + X4 + 2S
   }
 };
 

src/reactions/exampleSystems/unitTests/CMakeLists.txt

@@ -2,6 +2,7 @@
 set( testSourceFiles
      testEquilibriumReactions.cpp
      testKineticReactions.cpp
+     testMomasEasyCase.cpp
    )
 
 set( dependencyList hpcReact gtest )

…hemistry/unitTests/testMomasEasyCase.cpp …eSystems/unitTests/testMomasEasyCase.cppsrc/reactions/geochemistry/unitTests/testMomasEasyCase.cpp renamed to src/reactions/exampleSystems/unitTests/testMomasEasyCase.cpp src/reactions/geochemistry/unitTests/testMomasEasyCase.cpp renamed to src/reactions/exampleSystems/unitTests/testMomasEasyCase.cpp

@@ -11,28 +11,12 @@
 
 
 #include "reactions/unitTestUtilities/equilibriumReactionsTestUtilities.hpp"
-#include "../Momas.hpp"
+#include "../MoMasBenchmark.hpp"
 
 using namespace hpcReact;
-using namespace hpcReact::geochemistry;
+using namespace hpcReact::MomMasBenchmark;
 using namespace hpcReact::unitTest_utilities;
 
-
-// //******************************************************************************
-// TEST( testEquilibriumReactions, testEnforceEquilibrium )
-// {
-//   double const initialSpeciesConcentration[] = { 1.0, 1.0e-16, 0.5, 1.0, 1.0e-16 };
-//   double const expectedSpeciesConcentrations[5] = { 3.92138294e-01, 3.03930853e-01, 5.05945481e-01, 7.02014628e-01, 5.95970745e-01 };
-
-
-//   std::cout<<" RESIDUAL_FORM 2:"<<std::endl;
-//   testEnforceEquilibrium< double, 2 >( simpleTestRateParams.equilibriumReactionsParameters(),
-//                                        initialSpeciesConcentration,
-//                                        expectedSpeciesConcentrations );
-
-// }
-
-
 //******************************************************************************
 
 TEST( testEquilibriumReactions, testMoMasAllEquilibrium )
@@ -42,24 +26,24 @@ TEST( testEquilibriumReactions, testMoMasAllEquilibrium )
                                                                            int,
                                                                            int >;
 
-  constexpr int numPrimarySpecies = hpcReact::geochemistry::momasSystemAllEquilibrium.numPrimarySpecies();
+  constexpr int numPrimarySpecies = hpcReact::MomMasBenchmark::simpleSystemParams.numPrimarySpecies();
 
   double const targetAggregatePrimarySpeciesConcentration[numPrimarySpecies] =
   {
-    1.0e-20,     // X1
-    -2.0,    // X2
-    1.0e-20,     // X3
-    2.0,     // X4
-    1.0      // S
+    1.0e-20, // X1
+    -2.0, // X2
+    1.0e-20, // X3
+    2.0, // X4
+    1.0 // S
   };
 
   double const initialPrimarySpeciesConcentration[numPrimarySpecies] =
   {
-    1.0e-20,  // X1
-    0.02,     // X2
-    1.0e-20,  // X3
-    1.0,     // X4
-    1.00      // S
+    1.0e-20, // X1
+    0.02, // X2
+    1.0e-20, // X3
+    1.0, // X4
+    1.00 // S
   };
 
   double const logInitialPrimarySpeciesConcentration[numPrimarySpecies] =
@@ -73,18 +57,18 @@ TEST( testEquilibriumReactions, testMoMasAllEquilibrium )
 
   double logPrimarySpeciesConcentration[numPrimarySpecies];
   EquilibriumReactionsType::enforceEquilibrium_Aggregate( 0,
-                                                          hpcReact::geochemistry::momasSystemAllEquilibrium.equilibriumReactionsParameters(),
+                                                          hpcReact::MomMasBenchmark::simpleSystemParams.equilibriumReactionsParameters(),
                                                           targetAggregatePrimarySpeciesConcentration,
                                                           logInitialPrimarySpeciesConcentration,
                                                           logPrimarySpeciesConcentration );
 
   double const expectedPrimarySpeciesConcentrations[numPrimarySpecies] =
   {
-    9.7051090442170804E-21, // X1
-    5.0023298955833342E-12, // X2
-    1.9327372426296357E-33, // X3
-    7.3929274619958745E-12, // X4
-    9.8708294125907346E-13  // S
+    9.9999999999999919e-21, // X1
+    0.25971841330881928, // X2
+    1.4603613417111526e-24, // X3
+    0.3495378685828045, // X4
+    0.39074371811222675 // S
   };
 
   for( int r=0; r<numPrimarySpecies; ++r )
@@ -100,4 +84,4 @@ int main( int argc, char * * argv )
   ::testing::InitGoogleTest( &argc, argv );
   int const result = RUN_ALL_TESTS();
   return result;
-}
+}

src/reactions/geochemistry/Momas.hpp

@@ -3,7 +3,6 @@ set( testSourceFiles
      testGeochemicalEquilibriumReactions.cpp
      testGeochemicalKineticReactions.cpp
      testGeochemicalMixedReactions.cpp
-     testMomasEasyCase.cpp
      )
 
 set( dependencyList hpcReact gtest )