Update waves

Created by: acrovato

Context

This pull request brings the last developments from the flow module as well as some upgrade to waves.

Major changes in flow

• flow is now able to compute 3D flows
• The Jacobian (tangent) matrix for the Netwton method is now fully analytical
• The adjacent elements identification is now based on ```std::unordered_set````

Major changes in waves

• tbox and fwk are now included in a namespace
• waves is now fully included in a namespace
• All elements now have a private memory (Mem) which can be publicly accessed
• All elements now have a cache including Gauss points (Gauss) which can be publicly accessed
• MshDeformation now uses a linear elasticity solver
• MshCrack class implemented (creates duplicate internal boundaries in meshes)

Test

The ctest battery has been run on gaston, 100% tests passed under 110s.

Future work

• Use automated indentation rules for the whole code
• Move methods using VTK outside of MshData
• Clean tbox (mainly MshData, Tri3, Tera4 and Hex8)

mrstlnos/exe/main.cpp

@@ -254,14 +254,13 @@ template<typename scalar> void test_function(int ensemble_size)
     typedef Tpetra::Vector<>::local_ordinal_type local_ordinal_type;
     typedef Tpetra::Vector<>::global_ordinal_type global_ordinal_type;
 
-    typedef Tpetra::Map<> map_type;
-    typedef Tpetra::Vector<>::scalar_type scalar_type;
-    typedef Tpetra::Vector<>::mag_type magnitude_type;
+    //typedef Tpetra::Map<> map_type;
+    //typedef Tpetra::Vector<>::scalar_type scalar_type;
+    //typedef Tpetra::Vector<>::mag_type magnitude_type;
     typedef Tpetra::MultiVector<scalar,local_ordinal_type,global_ordinal_type> multivector_type;
-    typedef Tpetra::CrsMatrix<scalar,local_ordinal_type,global_ordinal_type> crs_matrix_type;
-    typedef Tpetra::CrsGraph<local_ordinal_type,global_ordinal_type> crs_graph_type;
-
-    typedef Tpetra::Vector<scalar,local_ordinal_type,global_ordinal_type> vector_type;
+    //typedef Tpetra::CrsMatrix<scalar,local_ordinal_type,global_ordinal_type> crs_matrix_type;
+    //typedef Tpetra::CrsGraph<local_ordinal_type,global_ordinal_type> crs_graph_type;
+    //typedef Tpetra::Vector<scalar,local_ordinal_type,global_ordinal_type> vector_type;
 
     int worldsize;
     MPI_Comm_size(MPI_COMM_WORLD, &worldsize);
@@ -285,7 +284,7 @@ template<typename scalar> void test_function(int ensemble_size)
     for(auto n : msh->nodes)
         n->row = n->no-1;
 
-    auto numNodes = msh->nodes.size();
+    //auto numNodes = msh->nodes.size();
     
     
     mrstlnos::Problem pbl(msh, MPI_COMM_WORLD);
@@ -376,7 +375,8 @@ template<typename scalar> void test_function(int ensemble_size)
     RCP<Teuchos::ParameterList> belosParams = rcp(new Teuchos::ParameterList(solverList));
     RCP<Belos::SolverManager<belos_scalar,MV,OP> > blinsolver =
                 rcp(new Belos::PseudoBlockGmresSolMgr<belos_scalar,MV,OP>(blinproblem, belosParams));
-    Belos::ReturnType ret = blinsolver->solve();  
+    //Belos::ReturnType ret = blinsolver->solve();
+    blinsolver->solve();  
     
     auto end = std::chrono::high_resolution_clock::now();
     double total_time = std::chrono::duration_cast<std::chrono::nanoseconds>(end-begin).count();
@@ -390,14 +390,13 @@ template<typename scalar> void test_function2(int ensemble_size)
     typedef Tpetra::Vector<>::local_ordinal_type local_ordinal_type;
     typedef Tpetra::Vector<>::global_ordinal_type global_ordinal_type;
 
-    typedef Tpetra::Map<> map_type;
-    typedef Tpetra::Vector<>::scalar_type scalar_type;
-    typedef Tpetra::Vector<>::mag_type magnitude_type;
-    typedef Tpetra::MultiVector<scalar,local_ordinal_type,global_ordinal_type> multivector_type;
-    typedef Tpetra::CrsMatrix<scalar,local_ordinal_type,global_ordinal_type> crs_matrix_type;
-    typedef Tpetra::CrsGraph<local_ordinal_type,global_ordinal_type> crs_graph_type;
-
-    typedef Tpetra::Vector<scalar,local_ordinal_type,global_ordinal_type> vector_type;
+    //typedef Tpetra::Map<> map_type;
+    //typedef Tpetra::Vector<>::scalar_type scalar_type;
+    //typedef Tpetra::Vector<>::mag_type magnitude_type;
+    //typedef Tpetra::MultiVector<scalar,local_ordinal_type,global_ordinal_type> multivector_type;
+    //typedef Tpetra::CrsMatrix<scalar,local_ordinal_type,global_ordinal_type> crs_matrix_type;
+    //typedef Tpetra::CrsGraph<local_ordinal_type,global_ordinal_type> crs_graph_type;
+    //typedef Tpetra::Vector<scalar,local_ordinal_type,global_ordinal_type> vector_type;
 
     int worldsize;
     MPI_Comm_size(MPI_COMM_WORLD, &worldsize);
@@ -421,7 +420,7 @@ template<typename scalar> void test_function2(int ensemble_size)
     for(auto n : msh->nodes)
         n->row = n->no-1;
 
-    auto numNodes = msh->nodes.size();
+    //auto numNodes = msh->nodes.size();
     
     
     mrstlnos::Problem pbl(msh, MPI_COMM_WORLD);