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/tests/meshDef.py

@@ -45,7 +45,6 @@ def main():
     mshCrck = tbox.MshCrack(msh, dim, "wake", ["field", "field_", "airfoil", "airfoil_", "downstream", "downstream_"])
     pbl = f.Problem(msh, dim, alpha0, M_inf, c_ref, c_ref, xc, 0., 0.)
     # create mesh deformation handler
-    #mshDef = tbox.MshDeformation(msh, dim, "field", ["upstream", "side", "downstream"], ["airfoil"], ["wake", "wake_"])
     mshDef = tbox.MshDeformation(msh, dim)
     mshDef.setField("field")
     mshDef.setFixed(["upstream", "side", "downstream"])