command line options
fcpu -------------------------------------------------
  -debug <0>: The debugging level (fcpu)
  -base_filename <3d>: The base filename for mesh files (fcpu)
  -vel_order <2>: The order of velocity elements (fcpu:setupDiscretization())
  -interpolation: <TRUE> whether to interpolate the grid to generate edges and faces (fcpu:USG())
  -Re <1>: Reynolds number (fcpu:NSSolver())
  -Fr <1>: Fround number (fcpu:NSSolver())
  -unitGravityDirectionX <0>: Unit Gravity Vector Component in X Direction (fcpu:ParticulateFlow::addRHSGravity() )
  -unitGravityDirectionY <0>: Unit Gravity Vector Component in Y Direction (fcpu:ParticulateFlow::addRHSGravity() )
  -unitGravityDirectionZ <-1>: Unit Gravity Vector Component in Z Direction (fcpu:ParticulateFlow::addRHSGravity() )
  -dt <0.1>: time step (fcpu:NSSolver())
  -NSteps <0>: number of second-order time updates (fcpu:NSSolver())
  -dumpStep <100>: dump filed every dumpStep in the second-order time updates (fcpu:NSSolver())
  -identicalVelStructure: <TRUE> whether the three components have the same structure (either bc or free for all three)  (fcpu:CFD(), fcpu:NSSolver::computeConvectionVecInWeakForm())
  -identicalVelBC: <TRUE> whether the three components have the same BC values  (fcpu:CFD(), fcpu:NSSolver::computeConvectionVecInWeakForm())
  -zeroVelBC: <TRUE> whether the velocity bcs are all 0 so that we can save time on bc vector construction (fcpu:CFD(), fcpu:CFD::CreateMatrices())
  -particleFileName <3d.particles>: file name of the particle input (fcpu:ParticulateFlow())
  -subSteps <1>: number of substeps for collision correction (fcpu:ParticulateFlow::order2Update)
  -maxIter <100>: maximum number of iterations for omega (fcpu:ParticulateFlow::FictitiousDomainCorrectionWeak())
  -RKOrder <4>: order of Runge-Kutta update in convection for second order steps (fcpu:ParticulateFlow::order2UpdateNew())
  -updateOrder <3>: order of update (fcpu:ParticulateFlow::run())
  -generateMesh: <FALSE> whether To generate the mesh instead of loading them from files (fcpu:USG())
  -refinementLimit <0>: dx for refinement. <=0 not to refine (fcpu:USG())
  -outputSieve: <FALSE> whether To dump sieve to files (fcpu:USG())
  -loadSieve: <FALSE> whether To load sieve from files (fcpu:USG())
  -outputSieveOnly: <FALSE> whether To dump sieve to files and then exit (fcpu:USG())
  -matrixCreation <1>: methods to create matrices: 0:dump, 1:create, 2: load (fcpu:CFD:Matrix)
  -useLumpedMass <-3>: whether To precondition with the lumped mass matrix,0-none, 1-row sum, 2-diagonal scaling, 3-quadrature (fcpu:CFD::CreateSolvers())
  -Umax <0>: Maxmum prescribed velocity in the fully developed profile (fcpu:BC )
  -flowType <0>: whether sedimentation/fluidizedbed (fcpu)
  -movingRF: <FALSE> whether to move the frame of reference (fcpu:ParticulateFlow:)
  -evenZ: <TRUE> whether the Z spacing is even/need to load from file? (fcpu:USG)
  -restart: <FALSE> whether to restart from restart/ ? (fcpu)
  -curvedBC: <FALSE> whether to use curved BC with 2nd order elements (fcpu)
  -outputGmsh: <TRUE> whether to output gmsh mesh/pos files (fcpu)
  -doMesh: <FALSE> whether to use bodyfitted mesh for particles (fcpu)
  -omegaMethod <0>: methods to compute particle angular velocity: 0-crul, 1-cross (fcpu)
  -dumpMatrices: <FALSE> whether to dump Mat/VecBC (fcpu:CFD)
  -cacheIndices: <TRUE> whether to cache indices (fcpu:USG)
  -cacheConnectivity: <TRUE> whether to cache Connectivity Table (fcpu:USG)
  -moc: <FALSE> whether to use the method of characteristic to update the convection equation (fcpu:NSSolver)
  -CboxSize <0>: cell size for the collision box (fcpu:CollisionBox )
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