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)

README.md

@@ -34,8 +34,7 @@ sudo apt-get install libmumps-seq-dev libopenblas-dev
 sudo apt-get install gmsh
 sudo apt-get install python-dev python-mpi4py
 sudo apt-get install swig
-sudo apt-get install python-pyqt5
-sudo apt-get install python-vtk6 libvtk6.3
+sudo apt-get install libvtk6.3 libvtk6-dev libvtk6-qt-dev python-vtk6 python-pyqt5
 sudo apt-get install python-numpy python-scipy python-matplotlib
 ```
 Optional packages