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)

flow/src/wMedium.cpp

@@ -8,7 +8,6 @@ Medium::Medium(std::shared_ptr<MshData> _msh, int no, Fct0 &_rho, Fct0 &_mach,
                 Fct0 &_cP, Fun0PosPhiInf &_phiInf) : Group(_msh, no), rho(_rho),
                 mach(_mach), cP(_cP), phiInf(_phiInf)
 {
-    initialize();
     createMap();
     std::cout << "tag=" << *tag << std::endl;
 }
@@ -17,28 +16,10 @@ Medium::Medium(std::shared_ptr<MshData> _msh, std::string const &name,
                 Fct0 &_rho, Fct0 &_mach, Fct0 &_cP, Fun0PosPhiInf &_phiInf) :
                 Group(_msh, name), rho(_rho), mach(_mach), cP(_cP), phiInf(_phiInf)
 {
-    initialize();
     createMap();
     std::cout << "tag=" << *tag << std::endl;
 }
 
-/**
- * @brief Compute volume and center of gravity for each elements
- * @authors Adrien Crovato
- */
-void Medium::initialize()
-{
-    // Compute CG of current element
-    for (auto e : tag->elems) {
-        Pt cg(0,0,0);
-        for (auto n : e->nodes) {
-            cg += n->pos;
-        }
-        cg /= e->nodes.size();
-        cgE[e] = cg;
-    }
-}
-
 /**
  * @brief Create data structure
  *