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/case/config.py

@@ -14,18 +14,21 @@ def getParam():
     p['Pars'] = {'xLength' : 5, 'yLength' : 5, 'sEleFar' : 1.0, 'sEleAirfTE' : 0.01, 'sEleAirfLE' : 0.005} # Parameters for input file model
     p['Dim'] = 2 # Problem dimension
     # Markers
-    p['Fluid'] = 'internalField' # Name of physical group containing the fluid
-    p['Farfield'] = ['upstream', 'side', 'downstream'] # Name of physical group containing the farfield boundaries
+    p['Fluid'] = 'field' # Name of physical group containing the fluid
+    p['Farfield'] = ['upstream', 'side', 'downstream'] # Name of physical group containing the farfield boundaries (downstream should be last element)
+    p['Symmetry'] = [] # Name of physical group containing the symmetry boundaries (none for 2D)
     p['Slip'] = 'airfoil' # Name of physical group containing the (solid) slip boundary
-    p['Wake'] = ['wakeUp', 'wakeLw'] # Name of physical group containing the upper and lower sides of the wake
-    p['Kutta'] =  ['teUp', 'teLw'] # Name of physical group containing the upper and lower sides of the trailing edge
+    p['Wake'] = 'wake' # Name of physical group containing the wake
+    p['Te'] =  'te' # Name of physical group containing the trailing edge
+    p['wakeTip'] = [] # Name of physical group containing the edge of the wake (none for 2D)
+    p['TeTip'] = [] # Name of physical group containing the edge of the wake and the trailing edge (none for 2D)
     # Freestream
     p['M_inf'] = 0.3 # Freestream Mach number
     p['AoA_begin'] = -3. # Freestream angle of attack (begin)
     p['AoA_end'] = 3. # Freestream angle of attack (end)
     p['AoA_step'] = 1. # Freestream angle of attack (step)
     # Geometry
-    p['C_ref'] = 1. # Reference chord length
+    p['S_ref'] = 1. # Reference chord/surface length
     # Numerical
     p['nthreads'] = args.k # Number of threads
     p['Rel_tol'] = 1e-6 # Relative tolerance on solver residual
@@ -33,7 +36,7 @@ def getParam():
     p['LS_tol'] = 1e-6 # Tolerance on linesearch residual
     p['Max_it'] = 50 # Solver maximum number of iterations
     p['Max_it_LS'] = 10 # Linesearch maximum number of iterations
-    p['AV_thrsh'] = 1e-3 # Residual threshold below which the artificial viscosity is decreased
+    p['AV_thrsh'] = 1e-2 # Residual threshold below which the artificial viscosity is decreased
     p['M_crit'] = 5. # Critical Mach number above which density is damped
     # Thermodynamic
     p['gamma'] = 1.4 # Specific heat ratio