Gaspard Jankowiak 4 weeks ago
parent
commit
f94ecf4dea

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configs_metrics/gaspard/test_variakb_mu20.yaml View File

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1
+params:
2
+    N: 250 # number of points
3
+    M: 15000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 10 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
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+
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+    c: 1e1 # polymerization speed
14
+
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+    x0_a: 2*0.25 # initial ellipsis width
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+    x0_b: 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: 0.2 # depth
23
+    f_ω0: 8 # pulsation
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+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components
26
+        # 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-4              #friction of MT
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+    MT_potential_power: -2
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+    MT_factor: 1e-2         #strength of MT
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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: 20 # area constraint relaxation
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+    N_target_area: 0.7
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+    N_kb: 1e-3 # bending stiffness
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+    N_ω:  1e-1 # 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-3 # 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:
57
+    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
65
+    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
72
+    nucleus:              true
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+    follow_cam:           false
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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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+    output_prefix: test_ultimaGaspard7bis
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+
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+    plot_period: 20
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+
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+    metrics:
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+        start_iteration: 1
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+        periods: 2
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+
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+    load_state:
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+        do_load: false
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+        filename: "initial_conditions/torino_width_1_x.csv"
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+        do_resample: false
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+        do_recenter: false
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+
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+        init_centro: false
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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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+   

+ 97
- 0
configs_metrics/gaspard/test_variamu.yaml View File

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1
+params:
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+    N: 250 # number of points
3
+    M: 80000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 10 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 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: 0.2 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components
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+        # to approximate a saw-tooth signal
27
+    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-4              #friction of MT
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+    MT_potential_power: -2
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+    MT_factor: 1e-2         #strength of MT
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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
45
+    N_mu: 60 # area constraint relaxation
46
+    N_target_area: 0.7
47
+    N_kb: 5e-3 # bending stiffness
48
+    N_ω:  1e-1 # inplane stiffness
49
+    N_W0: 7e-1  # potential offset
50
+    N_kcont: 5e0 # contact force intensity
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+    N_αcont: 1e1 # contact force sharpness
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+    N_kc: 1e-3 # 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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+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 true
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
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+    write_animation:      true
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+    landscape_plot:       false
67
+    plot_drag:            true
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              true
72
+    follow_cam:           false
73
+    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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+    output_prefix: test_variamu60
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+
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+    plot_period: 20
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+
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+    metrics:
83
+        start_iteration: 1
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+        periods: 2
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+
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+    load_state:
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+        do_load: false
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+        filename: "initial_conditions/torino_width_1_x.csv"
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+        do_resample: false
90
+        do_recenter: false
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+
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+        init_centro: false
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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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+   

+ 97
- 0
configs_metrics/gaspard/varia_KMT.yaml View File

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1
+params:
2
+    N: 250 # number of points
3
+    M: 80000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 10 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.2 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components
26
+        # to approximate a saw-tooth signal
27
+    f_width: 0.4 # mean width
28
+    f_iwidth: 3.0 # inner width, unused
29
+
30
+    drag_gauss_power: 4.0 # drag_gauss_power
31
+    drag_gauss_width: 3.5 # drag_gauss_width
32
+
33
+    mass_gauss_power: 6.0 # mass_gauss_power
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+    mass_gauss_width: 1.0 # mass_gauss_width
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+
36
+    polar_shift: 6.0
37
+
38
+    k_MT: 1e-2              #friction of MT
39
+    MT_potential_power: -2
40
+    MT_factor: 1e-2         #strength of MT
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+    #
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+    # Nucleus related parameters
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+    Nnuc: 200   # number of points on the nucleus
44
+    N_P: -1e0 # pressure
45
+    N_mu: 20 # area constraint relaxation
46
+    N_target_area: 0.7
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+    N_kb: 5e-3 # bending stiffness
48
+    N_ω:  1e-1 # inplane stiffness
49
+    N_W0: 7e-1  # potential offset
50
+    N_kcont: 5e0 # contact force intensity
51
+    N_αcont: 1e1 # contact force sharpness
52
+    N_kc: 1e-3 # centrosome link stiffness
53
+    N_l0c: 5e-1 # centrosome link rest length
54
+    N_r_init: 2.0e-1 # initial nucleus radius
55
+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 true
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
65
+    write_animation:      true
66
+    landscape_plot:       false
67
+    plot_drag:            true
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              true
72
+    follow_cam:           false
73
+    debug:                false
74
+    force_cortex_area:    true
75
+    write_metrics:        true
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+
77
+config:
78
+    output_prefix: test_variaKMT1em2
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+
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+    plot_period: 20
81
+
82
+    metrics:
83
+        start_iteration: 1
84
+        periods: 2
85
+
86
+    load_state:
87
+        do_load: false
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+        filename: "initial_conditions/torino_width_1_x.csv"
89
+        do_resample: false
90
+        do_recenter: false
91
+
92
+        init_centro: false
93
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
94
+
95
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
96
+
97
+   

+ 97
- 0
configs_metrics/gaspard/varia_beta_param.yaml View File

@@ -0,0 +1,97 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 80000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 50 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.10 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components to approximate a saw-tooth signal
26
+    f_width: 0.4 # mean width
27
+    f_iwidth: 3.0 # inner width, unused
28
+
29
+    drag_gauss_power: 4.0 # drag_gauss_power
30
+    drag_gauss_width: 3.5 # drag_gauss_width
31
+
32
+    mass_gauss_power: 6.0 # mass_gauss_power
33
+    mass_gauss_width: 1.0 # mass_gauss_width
34
+
35
+    polar_shift: 6.0
36
+
37
+    k_MT: 1e-4              #friction of MT
38
+    MT_potential_power: -2
39
+    MT_factor: 1e-2         #strength of MT
40
+    #
41
+    # Nucleus related parameters
42
+    Nnuc: 200   # number of points on the nucleus
43
+    N_P: -1e0 # pressure
44
+    N_mu: 100 # area constraint relaxation
45
+    N_target_area: 0.7
46
+    N_kb: 5e-4 # bending stiffness
47
+    N_ω:  1e-1 # inplane stiffness
48
+    N_W0: 7e-1  # potential offset
49
+    N_kcont: 5e0 # contact force intensity
50
+    N_αcont: 1e1 # contact force sharpness
51
+    N_kc: 1e-3 # centrosome link stiffness
52
+    N_l0c: 5e-1 # centrosome link rest length
53
+    N_r_init: 2.0e-1 # initial nucleus radius
54
+
55
+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 true
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
65
+    write_animation:      true
66
+    landscape_plot:       false
67
+    plot_drag:            true
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              true
72
+    follow_cam:           false
73
+    debug:                false
74
+    force_cortex_area:    true
75
+    write_metrics:        true
76
+
77
+config:
78
+    output_prefix: test_beta10
79
+
80
+    plot_period: 20
81
+
82
+    metrics:
83
+        start_iteration: 1
84
+        periods: 2
85
+
86
+    load_state:
87
+        do_load: false
88
+        filename: "initial_conditions/torino_width_1_x.csv"
89
+        do_resample: false
90
+        do_recenter: false
91
+
92
+        init_centro: false
93
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
94
+
95
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
96
+
97
+   

+ 97
- 0
configs_metrics/gaspard/varia_kb_mu100.yaml View File

@@ -0,0 +1,97 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 80000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 50 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.2 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components
26
+        # to approximate a saw-tooth signal
27
+    f_width: 0.4 # mean width
28
+    f_iwidth: 3.0 # inner width, unused
29
+
30
+    drag_gauss_power: 4.0 # drag_gauss_power
31
+    drag_gauss_width: 3.5 # drag_gauss_width
32
+
33
+    mass_gauss_power: 6.0 # mass_gauss_power
34
+    mass_gauss_width: 1.0 # mass_gauss_width
35
+
36
+    polar_shift: 6.0
37
+
38
+    k_MT: 1e-4              #friction of MT
39
+    MT_potential_power: -2
40
+    MT_factor: 1e-2         #strength of MT
41
+    #
42
+    # Nucleus related parameters
43
+    Nnuc: 200   # number of points on the nucleus
44
+    N_P: -1e0 # pressure
45
+    N_mu: 100 # area constraint relaxation
46
+    N_target_area: 0.7
47
+    N_kb: 1e-2 # bending stiffness
48
+    N_ω:  1e-1 # inplane stiffness
49
+    N_W0: 7e-1  # potential offset
50
+    N_kcont: 5e0 # contact force intensity
51
+    N_αcont: 1e1 # contact force sharpness
52
+    N_kc: 1e-3 # centrosome link stiffness
53
+    N_l0c: 5e-1 # centrosome link rest length
54
+    N_r_init: 2.0e-1 # initial nucleus radius
55
+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 true
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
65
+    write_animation:      true
66
+    landscape_plot:       false
67
+    plot_drag:            true
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              true
72
+    follow_cam:           false
73
+    debug:                false
74
+    force_cortex_area:    true
75
+    write_metrics:        true
76
+
77
+config:
78
+    output_prefix: test_width1_mu100_variakb1em2
79
+
80
+    plot_period: 20
81
+
82
+    metrics:
83
+        start_iteration: 1
84
+        periods: 2
85
+
86
+    load_state:
87
+        do_load: false
88
+        filename: "initial_conditions/torino_width_1_x.csv"
89
+        do_resample: false
90
+        do_recenter: false
91
+
92
+        init_centro: false
93
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
94
+
95
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
96
+
97
+   

+ 97
- 0
configs_metrics/gaspard/varia_kb_mu60.yaml View File

@@ -0,0 +1,97 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 80000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 10 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.2 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components
26
+        # to approximate a saw-tooth signal
27
+    f_width: 0.4 # mean width
28
+    f_iwidth: 3.0 # inner width, unused
29
+
30
+    drag_gauss_power: 4.0 # drag_gauss_power
31
+    drag_gauss_width: 3.5 # drag_gauss_width
32
+
33
+    mass_gauss_power: 6.0 # mass_gauss_power
34
+    mass_gauss_width: 1.0 # mass_gauss_width
35
+
36
+    polar_shift: 6.0
37
+
38
+    k_MT: 1e-4              #friction of MT
39
+    MT_potential_power: -2
40
+    MT_factor: 1e-2         #strength of MT
41
+    #
42
+    # Nucleus related parameters
43
+    Nnuc: 200   # number of points on the nucleus
44
+    N_P: -1e0 # pressure
45
+    N_mu: 60 # area constraint relaxation
46
+    N_target_area: 0.7
47
+    N_kb: 5e-2 # bending stiffness
48
+    N_ω:  1e-1 # inplane stiffness
49
+    N_W0: 7e-1  # potential offset
50
+    N_kcont: 5e0 # contact force intensity
51
+    N_αcont: 1e1 # contact force sharpness
52
+    N_kc: 1e-2 # centrosome link stiffness
53
+    N_l0c: 5e-1 # centrosome link rest length
54
+    N_r_init: 2.0e-1 # initial nucleus radius
55
+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 true
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
65
+    write_animation:      true
66
+    landscape_plot:       false
67
+    plot_drag:            true
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              true
72
+    follow_cam:           false
73
+    debug:                false
74
+    force_cortex_area:    true
75
+    write_metrics:        true
76
+
77
+config:
78
+    output_prefix: test_width1_mu60_variakb5em2
79
+
80
+    plot_period: 20
81
+
82
+    metrics:
83
+        start_iteration: 1
84
+        periods: 2
85
+
86
+    load_state:
87
+        do_load: false
88
+        filename: "initial_conditions/torino_width_1_x.csv"
89
+        do_resample: false
90
+        do_recenter: false
91
+
92
+        init_centro: false
93
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
94
+
95
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
96
+
97
+   

+ 99
- 0
configs_metrics/gaspard/varia_omega.yaml View File

@@ -0,0 +1,99 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 50000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 2*5e-2 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 0 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 6.5*8e-1 # polymerization speed
14
+
15
+    x0_a: 0.2 # initial ellipsis width
16
+    x0_b: 0.2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.1 # depth
23
+    f_ω0: 8.0 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components
26
+        # to approximate a saw-tooth signal
27
+    f_width: 0.4 # mean width
28
+    f_iwidth: 3.0 # inner width, unused
29
+
30
+    drag_gauss_power: 4.0 # drag_gauss_power
31
+    drag_gauss_width: 3.5 # drag_gauss_width
32
+
33
+    mass_gauss_power: 6.0 # mass_gauss_power
34
+    mass_gauss_width: 1.0 # mass_gauss_width
35
+
36
+    polar_shift: 6.0
37
+
38
+    k_MT: 1e-4
39
+    MT_potential_power: -2
40
+    MT_factor: 1e-2
41
+    #
42
+    # Nucleus related parameters
43
+    Nnuc: 200   # number of points on the nucleus
44
+    N_P: -1e0 # pressure
45
+    N_mu: 100 # area constraint relaxation
46
+    N_target_area: 0.5
47
+    N_kb: 5e-4 # bending stiffness
48
+    N_ω:  1e-1 # inplane stiffness
49
+    N_W0: 7e-1  # potential offset
50
+    N_kcont: 5e0 # contact force intensity
51
+    N_αcont: 1e1 # contact force sharpness
52
+    N_kc: 1e-3 # centrosome link stiffness
53
+    N_l0c: 5e-1 # centrosome link rest length
54
+    N_r_init: 2.0e-1 # initial nucleus radius
55
+
56
+flags:
57
+    confine:              true
58
+    adjust_drag:          false
59
+    polymerize:           true
60
+    dryrun:               true
61
+    plot:                 true
62
+    pretty:               false
63
+    continuous:           true
64
+    innerloop:            false
65
+    weighted_confinement: true
66
+    write_animation:      true
67
+    landscape_plot:       false
68
+    plot_drag:            true
69
+    circular_wall:        false
70
+    cortex:               true
71
+    centrosome:           true
72
+    nucleus:              true
73
+    follow_cam:           false
74
+    debug:                false
75
+    force_cortex_area:    true
76
+    write_metrics:        true
77
+
78
+config:
79
+    output_prefix: test_omega
80
+
81
+    plot_period: 20
82
+
83
+    metrics:
84
+        start_iteration: 1
85
+        post_init_periods: 1
86
+        periods: 2
87
+
88
+    load_state:
89
+        do_load: false
90
+        filename: "initial_conditions/torino_width_1_x.csv"
91
+        do_resample: false
92
+        do_recenter: false
93
+
94
+        init_centro: false
95
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
96
+
97
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
98
+
99
+   

+ 97
- 0
configs_metrics/gaspard/varia_omega_param.yaml View File

@@ -0,0 +1,97 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 80000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 50 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.20 # depth
23
+    f_ω0: 6 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components to approximate a saw-tooth signal
26
+    f_width: 0.4 # mean width
27
+    f_iwidth: 3.0 # inner width, unused
28
+
29
+    drag_gauss_power: 4.0 # drag_gauss_power
30
+    drag_gauss_width: 3.5 # drag_gauss_width
31
+
32
+    mass_gauss_power: 6.0 # mass_gauss_power
33
+    mass_gauss_width: 1.0 # mass_gauss_width
34
+
35
+    polar_shift: 6.0
36
+
37
+    k_MT: 1e-4              #friction of MT
38
+    MT_potential_power: -2
39
+    MT_factor: 1e-2         #strength of MT
40
+    #
41
+    # Nucleus related parameters
42
+    Nnuc: 200   # number of points on the nucleus
43
+    N_P: -1e0 # pressure
44
+    N_mu: 100 # area constraint relaxation
45
+    N_target_area: 0.7
46
+    N_kb: 5e-4 # bending stiffness
47
+    N_ω:  1e-1 # inplane stiffness
48
+    N_W0: 7e-1  # potential offset
49
+    N_kcont: 5e0 # contact force intensity
50
+    N_αcont: 1e1 # contact force sharpness
51
+    N_kc: 1e-3 # centrosome link stiffness
52
+    N_l0c: 5e-1 # centrosome link rest length
53
+    N_r_init: 2.0e-1 # initial nucleus radius
54
+
55
+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 true
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
65
+    write_animation:      true
66
+    landscape_plot:       false
67
+    plot_drag:            true
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              true
72
+    follow_cam:           false
73
+    debug:                false
74
+    force_cortex_area:    true
75
+    write_metrics:        true
76
+
77
+config:
78
+    output_prefix: test_omega6
79
+
80
+    plot_period: 20
81
+
82
+    metrics:
83
+        start_iteration: 1
84
+        periods: 2
85
+
86
+    load_state:
87
+        do_load: false
88
+        filename: "initial_conditions/torino_width_1_x.csv"
89
+        do_resample: false
90
+        do_recenter: false
91
+
92
+        init_centro: false
93
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
94
+
95
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
96
+
97
+   

+ 97
- 0
configs_metrics/gaspard/varia_width_param.yaml View File

@@ -0,0 +1,97 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 80000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 50 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.20 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components to approximate a saw-tooth signal
26
+    f_width: 0.4 # mean width
27
+    f_iwidth: 3.0 # inner width, unused
28
+
29
+    drag_gauss_power: 4.0 # drag_gauss_power
30
+    drag_gauss_width: 3.5 # drag_gauss_width
31
+
32
+    mass_gauss_power: 6.0 # mass_gauss_power
33
+    mass_gauss_width: 1.0 # mass_gauss_width
34
+
35
+    polar_shift: 6.0
36
+
37
+    k_MT: 1e-4              #friction of MT
38
+    MT_potential_power: -2
39
+    MT_factor: 1e-2         #strength of MT
40
+    #
41
+    # Nucleus related parameters
42
+    Nnuc: 200   # number of points on the nucleus
43
+    N_P: -1e0 # pressure
44
+    N_mu: 100 # area constraint relaxation
45
+    N_target_area: 0.7
46
+    N_kb: 5e-4 # bending stiffness
47
+    N_ω:  1e-1 # inplane stiffness
48
+    N_W0: 7e-1  # potential offset
49
+    N_kcont: 5e0 # contact force intensity
50
+    N_αcont: 1e1 # contact force sharpness
51
+    N_kc: 1e-3 # centrosome link stiffness
52
+    N_l0c: 5e-1 # centrosome link rest length
53
+    N_r_init: 2.0e-1 # initial nucleus radius
54
+
55
+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 false
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
65
+    write_animation:      false
66
+    landscape_plot:       false
67
+    plot_drag:            true
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              true
72
+    follow_cam:           false
73
+    debug:                false
74
+    force_cortex_area:    true
75
+    write_metrics:        true
76
+
77
+config:
78
+    output_prefix: test_wdith1234
79
+
80
+    plot_period: 20
81
+
82
+    metrics:
83
+        start_iteration: 1
84
+        periods: 2
85
+
86
+    load_state:
87
+        do_load: false
88
+        filename: "initial_conditions/torino_width_1_x.csv"
89
+        do_resample: false
90
+        do_recenter: false
91
+
92
+        init_centro: false
93
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
94
+
95
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
96
+
97
+   

+ 97
- 0
configs_metrics/gaspard/varia_width_param.yaml.in View File

@@ -0,0 +1,97 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 80000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 50 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.20 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components to approximate a saw-tooth signal
26
+    f_width: §§W§§ # mean width
27
+    f_iwidth: 3.0 # inner width, unused
28
+
29
+    drag_gauss_power: 4.0 # drag_gauss_power
30
+    drag_gauss_width: 3.5 # drag_gauss_width
31
+
32
+    mass_gauss_power: 6.0 # mass_gauss_power
33
+    mass_gauss_width: 1.0 # mass_gauss_width
34
+
35
+    polar_shift: 6.0
36
+
37
+    k_MT: 1e-4              #friction of MT
38
+    MT_potential_power: -2
39
+    MT_factor: 1e-2         #strength of MT
40
+    #
41
+    # Nucleus related parameters
42
+    Nnuc: 200   # number of points on the nucleus
43
+    N_P: -1e0 # pressure
44
+    N_mu: 100 # area constraint relaxation
45
+    N_target_area: 0.7
46
+    N_kb: 5e-4 # bending stiffness
47
+    N_ω:  1e-1 # inplane stiffness
48
+    N_W0: 7e-1  # potential offset
49
+    N_kcont: 5e0 # contact force intensity
50
+    N_αcont: 1e1 # contact force sharpness
51
+    N_kc: 1e-3 # centrosome link stiffness
52
+    N_l0c: 5e-1 # centrosome link rest length
53
+    N_r_init: 2.0e-1 # initial nucleus radius
54
+
55
+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 false
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
65
+    write_animation:      false
66
+    landscape_plot:       false
67
+    plot_drag:            true
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              false
72
+    follow_cam:           false
73
+    debug:                false
74
+    force_cortex_area:    true
75
+    write_metrics:        true
76
+
77
+config:
78
+    output_prefix: test_width/v2
79
+
80
+    plot_period: 20
81
+
82
+    metrics:
83
+        start_iteration: 1
84
+        post_init_periods: 1
85
+        periods: 2
86
+
87
+    load_state:
88
+        do_load: false
89
+        filename: "initial_conditions/torino_width_1_x.csv"
90
+        do_resample: false
91
+        do_recenter: false
92
+
93
+        init_centro: false
94
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
95
+
96
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
97
+

+ 98
- 0
configs_metrics/nucleus/varia_kb_mu20.yaml View File

@@ -0,0 +1,98 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 15000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 10 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.2 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components
26
+        # to approximate a saw-tooth signal
27
+    f_width: 0.4 # mean width
28
+    f_iwidth: 3.0 # inner width, unused
29
+
30
+    drag_gauss_power: 4.0 # drag_gauss_power
31
+    drag_gauss_width: 3.5 # drag_gauss_width
32
+
33
+    mass_gauss_power: 6.0 # mass_gauss_power
34
+    mass_gauss_width: 1.0 # mass_gauss_width
35
+
36
+    polar_shift: 6.0
37
+
38
+    k_MT: 1e-4              #friction of MT
39
+    MT_potential_power: -2
40
+    MT_factor: 1e-2         #strength of MT
41
+    #
42
+    # Nucleus related parameters
43
+    Nnuc: 200   # number of points on the nucleus
44
+    N_P: -1e0 # pressure
45
+    N_mu: 20 # area constraint relaxation
46
+    N_target_area: 0.7
47
+    N_kb: 1e-3 # bending stiffness
48
+    N_ω:  1e-1 # inplane stiffness
49
+    N_W0: 7e-1  # potential offset
50
+    N_kcont: 5e0 # contact force intensity
51
+    N_αcont: 1e1 # contact force sharpness
52
+    N_kc: 1e-3 # centrosome link stiffness
53
+    N_l0c: 5e-1 # centrosome link rest length
54
+    N_r_init: 2.0e-1 # initial nucleus radius
55
+
56
+flags:
57
+    confine:              true
58
+    adjust_drag:          false
59
+    polymerize:           true
60
+    dryrun:               true
61
+    plot:                 true
62
+    pretty:               false
63
+    continuous:           true
64
+    innerloop:            false
65
+    weighted_confinement: true
66
+    write_animation:      true
67
+    landscape_plot:       false
68
+    plot_drag:            true
69
+    circular_wall:        false
70
+    cortex:               true
71
+    centrosome:           true
72
+    nucleus:              true
73
+    follow_cam:           false
74
+    debug:                false
75
+    force_cortex_area:    true
76
+    write_metrics:        true
77
+
78
+config:
79
+    output_prefix: test_ultimaGaspard7bis
80
+
81
+    plot_period: 20
82
+
83
+    metrics:
84
+        start_iteration: 1
85
+        periods: 2
86
+
87
+    load_state:
88
+        do_load: false
89
+        filename: "initial_conditions/torino_width_1_x.csv"
90
+        do_resample: false
91
+        do_recenter: false
92
+
93
+        init_centro: false
94
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
95
+
96
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
97
+
98
+   

+ 100
- 0
configs_metrics/nucleus/varia_mu.yaml View File

@@ -0,0 +1,100 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 80000 # max. number of iterations
4
+
5
+    δt: 2e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 10 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.2 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components
26
+        # to approximate a saw-tooth signal
27
+    f_width: 0.4 # mean width
28
+    f_iwidth: 3.0 # inner width, unused
29
+
30
+    drag_gauss_power: 4.0 # drag_gauss_power
31
+    drag_gauss_width: 3.5 # drag_gauss_width
32
+
33
+    mass_gauss_power: 6.0 # mass_gauss_power
34
+    mass_gauss_width: 1.0 # mass_gauss_width
35
+
36
+    polar_shift: 6.0
37
+
38
+    k_MT: 1e-4              #friction of MT
39
+    MT_potential_power: -2
40
+    MT_factor: 1e-2         #strength of MT
41
+    #
42
+    # Nucleus related parameters
43
+    Nnuc: 200   # number of points on the nucleus
44
+    N_P: -1e0 # pressure
45
+    N_mu: 60 # area constraint relaxation
46
+    N_target_area: 0.7
47
+    N_kb: 5e-3 # bending stiffness
48
+    N_ω:  1e-1 # inplane stiffness
49
+    N_W0: 7e-1  # potential offset
50
+    N_kcont: 5e0 # contact force intensity
51
+    N_αcont: 1e1 # contact force sharpness
52
+    N_kc: 1e-3 # centrosome link stiffness
53
+    N_l0c: 5e-1 # centrosome link rest length
54
+    N_r_init: 2.0e-1 # initial nucleus radius
55
+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 true
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
65
+    write_animation:      true
66
+    landscape_plot:       false
67
+    plot_drag:            false
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              true
72
+    follow_cam:           true
73
+    debug:                false
74
+    force_cortex_area:    true
75
+    write_metrics:        true
76
+    explicit_mt_force:    false
77
+
78
+config:
79
+    output_prefix: nuc_variamu60
80
+
81
+    plot_period: 20
82
+
83
+    recompute_nucleus_each: 5
84
+
85
+    metrics:
86
+        start_iteration: 1
87
+        periods: 2
88
+
89
+    load_state:
90
+        do_load: false
91
+        filename: "initial_conditions/torino_width_1_x.csv"
92
+        do_resample: false
93
+        do_recenter: false
94
+
95
+        init_centro: false
96
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
97
+
98
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
99
+
100
+   

+ 100
- 0
configs_metrics/nucleus/varia_mu_dt=5e-5.yaml View File

@@ -0,0 +1,100 @@
1
+params:
2
+    N: 250 # number of points
3
+    M: 200000 # max. number of iterations
4
+
5
+    δt: 1e-4 # time step
6
+
7
+    P: 4*6.15e-1 # pressure
8
+    K: 3e-1 # membrane elasticity
9
+    Ka: 1 # cortex viscosity
10
+    mu: 10 # area constraint relaxation constant
11
+    target_area: 1.8 # cortex target area
12
+
13
+    c: 1e1 # polymerization speed
14
+
15
+    x0_a: 2*0.25 # initial ellipsis width
16
+    x0_b: 2 # initial ellipsis height
17
+    x0_shift: 0.0 # initial vertical shift
18
+
19
+    # Confinement field
20
+
21
+    f_α: 2e1 # sharpness
22
+    f_β: 0.2 # depth
23
+    f_ω0: 8 # pulsation
24
+    f_σ: 1 # direction
25
+    f_nk: 1 # number of Fourier components
26
+        # to approximate a saw-tooth signal
27
+    f_width: 0.4 # mean width
28
+    f_iwidth: 3.0 # inner width, unused
29
+
30
+    drag_gauss_power: 4.0 # drag_gauss_power
31
+    drag_gauss_width: 3.5 # drag_gauss_width
32
+
33
+    mass_gauss_power: 6.0 # mass_gauss_power
34
+    mass_gauss_width: 1.0 # mass_gauss_width
35
+
36
+    polar_shift: 6.0
37
+
38
+    k_MT: 1e-4              #friction of MT
39
+    MT_potential_power: -2
40
+    MT_factor: 1e-2         #strength of MT
41
+    #
42
+    # Nucleus related parameters
43
+    Nnuc: 200   # number of points on the nucleus
44
+    N_P: -1e0 # pressure
45
+    N_mu: 60 # area constraint relaxation
46
+    N_target_area: 0.7
47
+    N_kb: 5e-3 # bending stiffness
48
+    N_ω:  1e-1 # inplane stiffness
49
+    N_W0: 7e-1  # potential offset
50
+    N_kcont: 5e0 # contact force intensity
51
+    N_αcont: 1e1 # contact force sharpness
52
+    N_kc: 1e-3 # centrosome link stiffness
53
+    N_l0c: 5e-1 # centrosome link rest length
54
+    N_r_init: 2.0e-1 # initial nucleus radius
55
+flags:
56
+    confine:              true
57
+    adjust_drag:          false
58
+    polymerize:           true
59
+    dryrun:               true
60
+    plot:                 true
61
+    pretty:               false
62
+    continuous:           true
63
+    innerloop:            false
64
+    weighted_confinement: true
65
+    write_animation:      true
66
+    landscape_plot:       false
67
+    plot_drag:            false
68
+    circular_wall:        false
69
+    cortex:               true
70
+    centrosome:           true
71
+    nucleus:              true
72
+    follow_cam:           true
73
+    debug:                false
74
+    force_cortex_area:    true
75
+    write_metrics:        true
76
+    explicit_mt_force:    false
77
+
78
+config:
79
+    output_prefix: nuc_variamu60
80
+
81
+    plot_period: 20
82
+
83
+    recompute_nucleus_each: 5
84
+
85
+    metrics:
86
+        start_iteration: 1
87
+        periods: 2
88
+
89
+    load_state:
90
+        do_load: false
91
+        filename: "initial_conditions/torino_width_1_x.csv"
92
+        do_resample: false
93
+        do_recenter: false
94
+
95
+        init_centro: false
96
+        filename_centro: "initial_conditions/torino_width_1_centro.csv"
97
+
98
+        # shift_nucleus: 0.25 # 3/4 of a period = 3/4 * 2π / f.ω0
99
+
100
+   

+ 17
- 0
metrics.jl View File

@@ -0,0 +1,17 @@
1
+import JankoUtils
2
+
3
+d_depth = 0.1
4
+d_w0 = 8
5
+d_width = 0.4
6
+
7
+width = d_width
8
+depth = d_depth
9
+prefix="w0"
10
+
11
+w0_range = collect(range(4, stop=12; step=0.25))
12
+
13
+for (i,w0) in enumerate(w0_range)
14
+    outputfile = "autoconfigs/metrics_$(width)_$(depth)_$(w0).yaml"
15
+    run(pipeline(`sed -e s/§§prefix§§/$prefix/ -e s/§§width§§/$width/ -e s/§§w0§§/$w0/ -e s/§§depth§§/$depth/ metrics.yaml.in`, stdout=outputfile))
16
+    go(outputfile)
17
+end

+ 19
- 0
metrics_depth.jl View File

@@ -0,0 +1,19 @@
1
+import JankoUtils
2
+
3
+d_depth = 0.1
4
+d_w0 = 8
5
+d_width = 0.4
6
+
7
+width = d_width
8
+depth = d_depth
9
+w0 = d_w0
10
+prefix="depth"
11
+
12
+for dd in range(0, stop=0.7; step=0.0125)
13
+    width = 0.3 + dd
14
+    depth = dd
15
+    outputfile = "autoconfigs/metrics_$(width)_$(depth)_$(w0).yaml"
16
+    run(pipeline(`sed -e s/§§prefix§§/$prefix/ -e s/§§width§§/$width/ -e s/§§w0§§/$w0/ -e s/§§depth§§/$depth/ metrics.yaml.in`, stdout=outputfile))
17
+    go(outputfile)
18
+end
19
+

+ 49
- 0
metrics_nuc_beta.jl View File

@@ -0,0 +1,49 @@
1
+push!(LOAD_PATH, "src")
2
+
3
+import CellSim
4
+import Dates
5
+
6
+# The configuration file from which parameters are taken
7
+base_config = "configs_metrics/nucleus/varia_beta_param.yaml"
8
+
9
+# The output prefix, this overrides the one set in the configuration file
10
+output_prefix = "nuc_beta"
11
+
12
+# Load configuration
13
+P, F, config = CellSim.read_config(base_config)
14
+
15
+# Override the output prefix and create it
16
+config["output_prefix"] = output_prefix
17
+mkpath(output_prefix)
18
+
19
+# Set batch mode (only closes Figures at the end to avoid clutter)
20
+config["batch"] = true
21
+
22
+# Log file, used to list parameter value so we don't have to
23
+# compute them by hand. We cannot use the YAML files as Julia can
24
+# only read YAML files, not write to them.
25
+
26
+# Log file name
27
+parameter_log_file = string(output_prefix, "/parameter_log.txt")
28
+
29
+# Open the log file and write the date on top
30
+param_log = open(parameter_log_file, "a")
31
+date = string(Dates.now())
32
+write(param_log, string("\n", date, "\n\n"))
33
+
34
+# The range in which the varying parameter is taken
35
+betas = collect(range(0.0, 0.3; length=21))[2:end]
36
+
37
+# Loop
38
+for beta in betas
39
+    # Set the parameter value
40
+    P.f_β = beta
41
+
42
+    # Write the current value to the log file
43
+    write(param_log, string(beta, "\n"))
44
+
45
+    # Run the simulation
46
+    CellSim.launch(P, F, config)
47
+end
48
+
49
+close(param_log)

+ 51
- 0
metrics_nuc_mu.jl View File

@@ -0,0 +1,51 @@
1
+push!(LOAD_PATH, "src")
2
+
3
+import CellSim
4
+import Dates
5
+
6
+# The configuration file from which parameters are taken
7
+base_config = "configs_metrics/nucleus/varia_mu.yaml"
8
+
9
+# The output prefix, this overrides the one set in the configuration file
10
+output_prefix = "nuc_mu_3"
11
+
12
+# Load configuration
13
+P, F, config = CellSim.read_config(base_config)
14
+
15
+# Override the output prefix and create it
16
+config["output_prefix"] = output_prefix
17
+mkpath(output_prefix)
18
+
19
+# Set batch mode (only closes Figures at the end to avoid clutter)
20
+config["batch"] = true
21
+
22
+# Log file, used to list parameter value so we don't have to
23
+# compute them by hand. We cannot use the YAML files as Julia can
24
+# only read YAML files, not write to them.
25
+
26
+# Log file name
27
+parameter_log_file = string(output_prefix, "/parameter_log.txt")
28
+
29
+# Open the log file and write the date on top
30
+param_log = open(parameter_log_file, "a")
31
+date = string(Dates.now())
32
+write(param_log, string("\n", date, "\n\n"))
33
+
34
+# The range in which the varying parameter is taken
35
+# mus = 10 .^range(-4, log10.(400); length=20)
36
+mus = [3, 10, 25, 50, 100, 200, 300, 400]
37
+mus = collect(range(1, stop=50, length=25))
38
+
39
+# Loop
40
+for mu in mus
41
+    # Set the parameter value
42
+    P.N_mu = mu
43
+
44
+    # Write the current value to the log file
45
+    write(param_log, string(mu, "\n"))
46
+
47
+    # Run the simulation
48
+    CellSim.launch(P, F, config)
49
+end
50
+
51
+close(param_log)

+ 75
- 0
metrics_nuc_mu_kb.jl View File

@@ -0,0 +1,75 @@
1
+push!(LOAD_PATH, "src")
2
+
3
+import CellSim
4
+import Dates
5
+
6
+# The configuration file from which parameters are taken
7
+# base_config = "configs_metrics/nucleus/varia_mu.yaml"
8
+base_config = "configs_metrics/nucleus/varia_mu.yaml"
9
+
10
+# The output prefix, this overrides the one set in the configuration file
11
+output_prefix = "nuc_mu_kb_fine_1"
12
+
13
+# Load configuration
14
+P, F, config = CellSim.read_config(base_config)
15
+
16
+# Override the output prefix and create it
17
+config["output_prefix"] = output_prefix
18
+mkpath(output_prefix)
19
+
20
+# Set batch mode (only closes Figures at the end to avoid clutter)
21
+config["batch"] = true
22
+
23
+# Log file, used to list parameter value so we don't have to
24
+# compute them by hand. We cannot use the YAML files as Julia can
25
+# only read YAML files, not write to them.
26
+
27
+# Log file name
28
+parameter_log_file = string(output_prefix, "/parameter_log.txt")
29
+
30
+# Open the log file and write the date on top
31
+param_log = open(parameter_log_file, "a")
32
+date = string(Dates.now())
33
+write(param_log, string("\n", date, "\n\n"))
34
+
35
+# The range in which the varying parameter is taken
36
+# mus = 10 .^range(-4, log10.(400); length=20)
37
+# mus = collect(range(1, stop=50, length=15))
38
+# kbs = 10 .^range(log10.(5e-4), log10.(0.5); length=15)
39
+#
40
+mus = collect(range(1, stop=50, length=15))[11]
41
+kbs = 10 .^range(log10.(5e-4), log10.(0.5); length=15)[10]
42
+
43
+# fine 1
44
+mus = collect(range(23.6, stop=34, length=8))
45
+kbs = 10 .^range(log10.(0.0204), log10.(0.035); length=4)
46
+
47
+# fine 2
48
+# mus = collect(range(34.3, stop=50, length=6))
49
+# kbs = 10 .^range(log10.(0.035), log10.(0.0575); length=4)
50
+
51
+param_range = Base.Iterators.product(kbs, mus)
52
+# param_range = Base.Iterators.drop(param_range, 72)
53
+
54
+
55
+# Loop
56
+for (kb, mu) in param_range
57
+    println("kb: ", kb, ", mu: ", mu)
58
+
59
+    # Set the parameter value
60
+    P.N_mu = mu
61
+    P.N_kb = kb
62
+
63
+    # Write the current value to the log file
64
+    date = string(Dates.now())
65
+    write(param_log, string(date, "\t", mu, "\t", kb, "\n"))
66
+
67
+    # Run the simulation
68
+    try
69
+        CellSim.launch(P, F, config)
70
+    catch
71
+        println("error")
72
+    end
73
+end
74
+
75
+close(param_log)

+ 50
- 0
metrics_nuc_width.jl View File

@@ -0,0 +1,50 @@
1
+push!(LOAD_PATH, "src")
2
+
3
+import CellSim
4
+import Dates
5
+
6
+# The configuration file from which parameters are taken
7
+base_config = "configs_metrics/nucleus/varia_width_param.yaml"
8
+
9
+# The output prefix, this overrides the one set in the configuration file
10
+output_prefix = "nuc_width"
11
+
12
+# Load configuration
13
+P, F, config = CellSim.read_config(base_config)
14
+
15
+# Override the output prefix and create it
16
+config["output_prefix"] = output_prefix
17
+mkpath(output_prefix)
18
+
19
+# Set batch mode (only closes Figures at the end to avoid clutter)
20
+config["batch"] = true
21
+
22
+# Log file, used to list parameter value so we don't have to
23
+# compute them by hand. We cannot use the YAML files as Julia can
24
+# only read YAML files, not write to them.
25
+
26
+# Log file name
27
+parameter_log_file = string(output_prefix, "/parameter_log.txt")
28
+
29
+# Open the log file and write the date on top
30
+# If it already exists, we do not delete it, but write at the end
31
+param_log = open(parameter_log_file, "a")
32
+date = string(Dates.now())
33
+write(param_log, string("\n", date, "\n\n"))
34
+
35
+# The range in which the varying parameter is taken
36
+ws = range(0.3, 0.8; length=20)[10:end]
37
+
38
+# Loop
39
+for w in ws
40
+    # Set the parameter value
41
+    P.f_width = w
42
+
43
+    # Write the current value to the log file
44
+    write(param_log, string(w, "\n"))
45
+
46
+    # Run the simulation
47
+    CellSim.launch(P, F, config)
48
+end
49
+
50
+close(param_log)

+ 18
- 0
metrics_runs.jl View File

@@ -0,0 +1,18 @@
1
+push!(LOAD_PATH, "src")
2
+
3
+import CellSim
4
+
5
+base_config = "configs_metrics/without_nucleus/varia_width_param.yaml"
6
+
7
+output_prefix = "nonuc_width"
8
+
9
+P, F, config = CellSim.read_config(base_config)
10
+
11
+config["output_prefix"] = output_prefix
12
+
13
+ws = range(4, 14; length=20)
14
+
15
+for w in ws
16
+    P.f_ω0 = w
17
+    CellSim.launch(P, F, config)
18
+end

+ 8
- 0
metrics_width.jl View File

@@ -0,0 +1,8 @@
1
+import JankoUtils
2
+
3
+for w in range(0.3, stop=0.7; length=20)
4
+    width = w
5
+    outputfile = "autoconfigs/nucleus_metrics_$(width).yaml"
6
+    run(pipeline(`sed -e s/§§W§§/$width/ configs_metrics/gaspard/varia_width_param.yaml.in`, stdout=outputfile))
7
+    go(outputfile)
8
+end

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