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

@@ -39,7 +39,7 @@ void Medium::createMap()
         std::vector<Element *> vAdjE;
         for (auto n : e->nodes)
             vAdjE.insert(vAdjE.end(), neMap.at(n).begin(), neMap.at(n).end());
-        // // Sort vector as function of cg x-location and remove duplicates
+        // Sort and remove duplicates
         std::sort(vAdjE.begin(), vAdjE.end());
         auto iterator = std::unique(vAdjE.begin(), vAdjE.end());
         vAdjE.resize(std::distance(vAdjE.begin(),iterator));