Stabilizing CATKE for three-dimensional runs on ImmersedBoundaryGrid

[glwagner]

This PR aims to increase CATKE's stability for three-dimensional runs on ImmersedBoundaryGrid.

One crucial improvement is limiting height_above_bottom to no less than the grid spacing. (We weren't able to limit this by 0, we had to use a small positive number).

A second improvement adds the parameter minimum_convective_buoyancy_flux. This parameter regularizes CATKE's convective mixing length, permitting smoother / less noisy estimates of the surface buoyancy flux. The convective mixing length is only activated if the surface buoyancy flux exceeds minimum_convective_buoyancy_flux.

[glwagner]

New parameters for RiBasedVerticalDiffusivity in this PR as well @simone-silvestri

animate_les_data_with_catke.mp4

Note the TKE variable has no dynamics, just a passive tracer for ri-based.

[glwagner]

CATKE is stunning as usual

animate_les_data_with_catke.mp4

[glwagner]

New default parameters for CATKE:

julia> CATKEVerticalDiffusivity()
CATKEVerticalDiffusivity{VerticallyImplicitTimeDiscretization}
├── maximum_diffusivity: Inf
├── minimum_turbulent_kinetic_energy: 0.0
├── negative_turbulent_kinetic_energy_damping_time_scale: 60.0
├── minimum_convective_buoyancy_flux: 1.0e-11
├── mixing_length: CATKEVerticalDiffusivities.MixingLength
│   ├── Cᵇ:   0.37
│   ├── Cᶜc:  4.8
│   ├── Cᶜe:  1.1
│   ├── Cᵉc:  0.049
│   ├── Cᵉe:  0.0
│   ├── C⁻u:  0.36
│   ├── C⁻c:  0.41
│   ├── C⁻e:  6.7
│   ├── C⁺u:  0.24
│   ├── C⁺c:  0.12
│   ├── C⁺e:  5.4
│   ├── CRiʷ: 0.011
│   └── CRiᶜ: 0.76
└── turbulent_kinetic_energy_equation: CATKEVerticalDiffusivities.TurbulentKineticEnergyEquation
    ├── C⁻D:  4.4
    ├── C⁺D:  3.3
    ├── CᶜD:  0.23
    ├── CᵉD:  0.0
    ├── Cᵂu★: 1.8
    └── CᵂwΔ: 12.0