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/src/LinearSolver.h

@@ -8,6 +8,7 @@
 #include "wTag.h"
 #include "wMedium.h"
 #include "wNode.h"
+#include "wMem.h"
 #include "Teuchos_ParameterList.hpp"
 
 #include "wProblem.h"
@@ -110,6 +111,16 @@ protected:
         Teuchos::RCP<RandomField<scalar,Kokkos::DefaultExecutionSpace>> random_field
         )
     {
+        /* @todo [AC] temporary fix for initializing Mem in mrstlnos */
+        for (auto e : pbl.msh->elem) {
+            if (e->type() == ELTYPE::HEX8 || e->type() == ELTYPE::TETRA4) // 3D
+                e->getVMem().update(true);
+            //else // 2D
+            //    e->getVMem().update(false);
+            
+        }
+        /* end temporary fix*/
+
         typedef Tpetra::Vector<>::global_ordinal_type global_ordinal_type;
 
         LinearSolver::getTimers()["write: convert data"].start();