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add example configuration

Gaspard Jankowiak 11 months ago
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071f512a05
1 changed files with 120 additions and 0 deletions
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      example_config.yaml

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example_config.yaml View File

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+params:
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+    N: 250 # number of points
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+    M: 40000 # max. number of iterations
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+
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+    δt: 2e-4 # time step # 2e-4
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+
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+    P: 4*6.15e-1 # pressure
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+    K: 2*5e-2 # membrane elasticity
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+    Ka: 1 # cortex viscosity
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+    mu: 0 # area constraint relaxation constant
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+    target_area: 1.8 # cortex target area
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+
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+    c: 6.5*8e-1 # polymerization speed
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+
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+    x0_a: 0.2 # initial ellipsis width
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+    x0_b: 0.2 # initial ellipsis height
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+    x0_shift: 0.0 # initial vertical shift
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+
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+    # Confinement field
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+
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+    f_α: 2e1 # sharpness
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+    f_β: 0.1 # depth
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+    f_ω0: 8.0 # pulsation
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+    f_σ: 1 # direction
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+    f_nk: 1 # number of Fourier components
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+        # to approximate a saw-tooth signal
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+    f_width: 0.4 # mean width
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+    f_iwidth: 3.0 # inner width, unused
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+
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+    drag_gauss_power: 4.0 # drag_gauss_power
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+    drag_gauss_width: 3.5 # drag_gauss_width
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+
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+    mass_gauss_power: 6.0 # mass_gauss_power
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+    mass_gauss_width: 1.0 # mass_gauss_width
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+
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+    polar_shift: 6.0
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+
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+    k_MT: 1e-2
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+    MT_potential_power: -2
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+    MT_factor: 1e1
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+    #
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+    # Nucleus related parameters
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+    Nnuc: 200   # number of points on the nucleus
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+    N_P: -1e0 # pressure
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+    N_mu: 100 # area constraint relaxation
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+    N_target_area: 0.5
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+    N_kb: 5e-4 # bending stiffness
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+    N_ω:  2e1 # inplane stiffness
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+    N_W0: 7e-1  # potential offset
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+    N_kcont: 5e0 # contact force intensity
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+    N_αcont: 1e1 # contact force sharpness
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+    N_kc: 1e-2 # centrosome link stiffness
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+    N_l0c: 5e-1 # centrosome link rest length
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+    N_r_init: 2.0e-1 # initial nucleus radius
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+
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+flags:
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+    confine:              true
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+    adjust_drag:          false
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+    polymerize:           true
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+    dryrun:               true
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+    plot:                 true
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+    pretty:               false
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+    continuous:           true
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+    innerloop:            false
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+    weighted_confinement: true
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+    write_animation:      true
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+    landscape_plot:       false
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+    plot_drag:            true
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+    circular_wall:        false
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+    cortex:               true
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+    centrosome:           true
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+    nucleus:              true
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+    follow_cam:           true
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+    follow_nucleus:       true
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+    debug:                false
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+    force_cortex_area:    true
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+    write_metrics:        true
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+
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+config:
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+    # directory where results will be store
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+    output_prefix: test_output
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+
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+    # how often to update the plot (in iterations)
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+    plot_period: 20
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+
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+    # how often should the nucleus coordinates be recomputed (in iterations)
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+    recompute_nucleus_each: 5
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+
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+    metrics:
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+        # at which iteration to start metrics (if no nucleus)
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+        start_iteration: 1
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+
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+        # how many periods to wait before starting metrics
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+        # (counted from the time the back of the cell hits the nucleus)
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+        post_init_periods: 1
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+
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+        # over how many periods should metrics be computed
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+        periods: 1
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+
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+    load_state:
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+        # should the initial condition (cortex) should be loaded from a file?
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+        # if not, it is computed automatically
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+        do_load: false
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+
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+        # file to load the cortex data from
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+        filename: "initial_conditions/torino_width_1_x.csv"
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+
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+        # should points be redistributed over the cortex
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+        # (useful if N changes)
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+        do_resample: false
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+
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+        # should the centrosome also be loaded from a file?
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+        init_centro: false
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+
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+        # file to load the centrosome data from
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+        filename: "initial_conditions/torino_width_1_x.csv"
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+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
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+
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+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
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+

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