# Set of default parameters for steady Navier-Stokes
mesh:       '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
density: 1.2
dynamic_viscosity: 0.035
stokes: False

io:
    write_hdf5: True
    write_hdf5_timeseries: False
    write_xdmf: True
    write_path: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/roukf'
    restart:
        path: ''  # './projects/nse_coa3d/results/test_restart2/' 
        time: 0
    write_checkpoints: True
    write_velocity: 'update'     # tentative
    log: False
    write_outlets: False
    outlets_path: '/home/yeye/Desktop/PhD/AORTA/outlets/'


boundary_conditions: 
    - id: 2
      type: 'dirichlet'
      value: ['0','0','-0.5*U*(fabs( sin(2*DOLFIN_PI*t/Th)) + sin(2*DOLFIN_PI*t/Th) )*(t<0.7)']
      degree: 3
      parameters: 
              U: 60   # 60 original
              Th: 0.7   # 0.7 original 
              t: 0
    - id: 1
      type: 'dirichlet'
      value: ['0','0','0']
      degree: 2
    - id: 3
      type: 'windkessel'
      value: [100,0.01,1000]
    - id: 4
      type: 'windkessel'
      value: [250,0.0001,8000]    # [R,C,R_d]
    - id: 5
      type: 'windkessel'
      value: [250,0.00001,8000]    # [R,C,R_d]
    - id: 6
      type: 'windkessel'
      value: [250,0.0001,8000]    # [R,C,R_d]


timemarching:
    velocity_pressure_coupling: 'fractionalstep'    # monolithic, fractionalstep

    monolithic:
        timescheme: 'gmp'   # generalized midpoint, steady FIXME TODO
        theta: 1            # 1: Euler, 0.5: implicit midpoint rule (one-legged)
        nonlinear:
            method: 'constant_extrapolation'   # constant_extrapolation, linear_extrapolation, newton, picard, snes
            maxit: 20
            init_steps: 30
            use_aitken: 1   #  0: False, 1: Picard only, 2: all
            report: 1       # 0: None, 1: residuals, 2: residuals and energy (inflow/driving/forcing via ESSENTIAL Dbcs!)
            atol: 1.e-6    # note: dot required!!
            rtol: 1.e-16
            stol: 0.0

    fractionalstep:
        scheme: 'CT'      # CT, IPCS
        coupled_velocity: False     # False faster, True needed if robin_bc implicit
        robin_bc_velocity_scheme: 'implicit' # explicit, semi-implicit, implicit
        transpiration_bc_projection: 'robin'      # robin, dirichlet
        flux_report_normalize_boundary: 1

    T: 0.9       # end time
    dt: 0.01
    write_dt: 0.01
    checkpoint_dt:  0.01 # <= 0: only last; else value + last
    report: 1   # 0: print nothing, 1: print time step and writeout, 2: 1 + flux

estimation:
    boundary_conditions:
        - id: 2
          type: 'dirichlet'
          initial_stddev: [10]
          parameters: [U]

    measurements:
        -
            mesh: '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
            fe_degree: 1
            xdmf_file: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/measurements/meas.xdmf'
            file_root: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/measurements/u{i}.h5'
            indices: 0 # indices of checkpoints to be processed. 0 == all
            noise_stddev: 20     # standard deviation of Gaussian noise
    
    roukf:
        particles: 'simplex' # unique or simplex
        observation_operator: 'state'         #state or postprocessing
        reparameterize: False
        
    #observations:
    #    mesh: '/home/yeye/Desktop/PhD/AORTA/MESH/aorta_coarse/aorta_coarse_marked.h5'
    #    timeseries: '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse2/measurements'
    #    stddev: 10.   # noiselevel x VENC

# solver setup
fem:
    velocity_space: p1  # p1 p1b/p1+ p2
    pressure_space: p1  # p1 p0/dg0 dg1

    strain_symmetric: 0
    convection_skew_symmetric: 1    # aka Temam term
    stabilization:
        backflow_boundaries: [2,3,4,5,6]
        streamline_diffusion:
            enabled: False
            parameter: 'shakib'   # standard, shakib, codina, klr
            length_scale: 'metric' # average, max, metric
            consistent: False   # deprecated
            Cinv: ~
        monolithic:
            infsup: False    # pspg, pressure-stabilization
            graddiv: False
            consistent: False
            pressure_stab_constant: 1.

    fix_pressure: False
    fix_pressure_point: [0., 0. , 0.]

linear_solver:
    method: 'lu'
    # inputfile: './projects/nse_coa3d/input/pc/MUMPS_default.yaml'
    # inputfile: './input/pc/fgmres_gamg_rtol1e-6.yaml'