NuMRI/kalman/input_files/aorta.yaml

mesh: './meshes/coaortaH1.h5'
# Physical parameters of the fluid  
fluid:
    density: 1.2
    dynamic_viscosity: 0.035
    stokes: False
    state_velocity: 'update'

io:
    write_path: 'results/aorta'
    restart:
        path: ''  # './projects/nse_coa3d/results/test_restart2/' 
        time: 0
    write_xdmf: True
    write_checkpoints: True 
    write_hdf5_timeseries: False
    write_velocity: 'update'     # update or tentative

boundary_conditions:
    - 
        id: 2
        type: 'dirichlet'
        #value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (t<0.8)*(Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta)) +
        #                 -U*sin(DOLFIN_PI*(t-0.8)/Th)*(t<= 0.8+Th )*(t>0.8) + (t<1.6)*(0.8+Th<t)*(U*DOLFIN_PI/Th*(t-0.8-Th)*exp(-(t-0.8-Th)*beta)) +
        #                 -U*sin(DOLFIN_PI*(t-1.6)/Th)*(t<= 1.6+Th )*(t>1.6) + (t<2.4)*(1.6+Th<t)*(U*DOLFIN_PI/Th*(t-1.6-Th)*exp(-(t-1.6-Th)*beta))' ]
        value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(U*DOLFIN_PI/Th*(t-Th)*exp(-(t-Th)*beta))']
        parameters:
            U: 75  #REFERENCE
            Th: 0.36
            beta: 70
            t: 0
    - 
        id: 1
        type: 'dirichlet'
        value: ['0','0','0']
    - 
        id: 3
        type: 'windkessel'
        parameters:
            R_p: 200
            C: 0.0004
            R_d: 4800
            p0: 85
            conv: 1333.223874   
    - 
        id: 4
        type: 'windkessel'
        parameters:
            R_p: 480
            C: 0.0004  # REFERENCE
            #R_d: 7200  # REFERENCE
            R_d:  8760  #Pa
            #R_d: 17520 #Pb x2
            #R_d: 4000  #Pc
            p0: 85
            conv: 1333.223874   
    - 
        id: 5
        type: 'windkessel'
        parameters:
            R_p: 520
            C: 0.0003 # REFERENCE
            #R_d: 11520 # REFERENCE
            R_d:  8760  #Pa
            #R_d: 17520 #Pb x2
            #R_d: 4000 #Pc
            p0: 85
            conv: 1333.223874   
    - 
        id: 6
        type: 'windkessel'
        parameters:
            R_p: 520
            C: 0.0003 # REFERENCE
            #R_d: 11520 # REFERENCE
            R_d:  8760 #Pa
            #R_d: 17520 #Pb x2
            #R_d: 4000 #Pc
            p0: 85
            conv: 1333.223874   

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: 0.8       # end time
    dt: 0.001
    write_dt: 0.03
    checkpoint_dt:  0.03 # <= 0: only last; else value + last
    report: 1   # 0: print nothing, 1: print time step and writeout, 2: 1 + flux

windkessel:
    implicit: True
    # low rank update formulation can run in parallel.
    # note that fgmres or similar has to be selected for the pressure solve, as
    # matrix is not explicitly formed.
    low_rank_update: False

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

    strain_symmetric: False
    convection_skew_symmetric: True    # aka Temam term
    stabilization:
        forced_normal:
            enabled: True
            boundaries: [3,4,5,6]
            gamma: 20
        backflow_boundaries: [3,4,5,6]
        streamline_diffusion:
            enabled: False
            parameter: 'standard'   # standard, shakib, codina, klr
            length_scale: 'average' # average, max, metric
            parameter_element_constant: True
            Cinv: ~
        monolithic:
            infsup: 'pspg'    # 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: 'input_files/fracstep_p-gmres_u-LU_WK-LRC.yaml'

estimation:
    boundary_conditions:
        #- 
        #    id: 3
        #    type: 'windkessel'
        #    mode: 'Rd'
        #    initial_stddev: 1
        - 
            id: 4
            type: 'windkessel'
            mode: 'Rd'
            initial_stddev: 0.5
        #- 
        #    id: 5
        #    type: 'windkessel'
        #    mode: 'Rd'
        #    initial_stddev: 0.5
        #- 
        #    id: 6
        #    type: 'windkessel'
        #    mode: 'Rd'
        #    initial_stddev: 0.5
        #- 
        #    id: 2
        #    type: 'dirichlet'
        #    parameters: 'U'
        #    initial_stddev: 0.5


    measurements:
        -
            mesh: '/home/yeye/NuMRI/kalman/meshes/slice_Hz2.3.h5'
            fe_degree: 0
            xdmf_file: 'measurements/slice/u_all.xdmf'
            file_root: 'measurements/slice/u{i}.h5'
            indices: 0 # indices of checkpoints to be processed. 0 == all
            velocity_direction: ~
            noise_stddev: 10
            VENC: 0
            module_meas_file_root: ''

    
    roukf:
        particles: 'simplex' # unique or simplex
        observation_operator: 'postprocessing'         #state or postprocessing
        reparameterize: True
        MAG_functional: False