NuMRI/kalman/input_files/aorta.yaml

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

io:
    write_path: 'results/aorta_1ms'
    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: 1
        type: 'dirichlet'
        value: ['0','0','0']
    - 
        id: 2
        type: 'dirichlet'
        value: ['0','0','-U*sin(DOLFIN_PI*t/Th)*(t<=Th) + (Th<t)*(-3.67949466208*U*sin(9*DOLFIN_PI*t/Th)*exp(-t*10))']
        parameters:
            U: 100
            Th: 0.35
            t: 0   
    - 
        id: 3
        type: 'windkessel'
        parameters:
            R_p: 10
            C: 0.0008
            R_d: 2400
            p0: 80
            conv: 1333.223874   
    - 
        id: 4
        type: 'windkessel'
        parameters:
            R_p: 60
            C: 0.00034
            R_d: 4200
            p0: 80
            conv: 1333.223874   
    - 
        id: 5
        type: 'windkessel'
        parameters:
            R_p: 220
            C: 0.00034
            R_d: 11000
            p0: 80
            conv: 1333.223874   
    - 
        id: 6
        type: 'windkessel'
        parameters:
            R_p: 160
            C: 0.00034
            R_d: 7800
            p0: 80
            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: 0.04
    checkpoint_dt:  0.04 # <= 0: only last; else value + last
    report: 1   # 0: print nothing, 1: print time step and writeout, 2: 1 + flux

# 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: False
            boundaries: [6]
            gamma: 10
        backflow_boundaries: [3,4,5,6]
        streamline_diffusion:
            enabled: False
            parameter: 'standard'   # standard, shakib, codina, klr
            length_scale: 'metric' # 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'

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


    measurements:
        -
            #mesh: '/home/yeye/NuMRI/kalman/meshes/coaortaH3_leo2.0.h5'
            mesh: './meshes/coaortaH1.h5'
            fe_degree: 1
            xdmf_file: 'measurements/aorta/u_all.xdmf'
            file_root: 'measurements/aorta/u{i}.h5'
            indices: 0 # indices of checkpoints to be processed. 0 == all
            velocity_direction: ~
            noise_stddev: 0     # standard deviation of Gaussian noise
    
    roukf:
        particles: 'simplex' # unique or simplex
        observation_operator: 'postprocessing'         #state or postprocessing
        reparameterize: True
        ODV_functional:
            enable: False
            VENC: 102    #  102,120%   59,70%   42 50%,   21,25%