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miniPBL v4.0.0

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@samfrederick samfrederick released this 09 Feb 03:25
· 6 commits to main since this release
v4.0.0
7ca33dd

Addition of advanced physics parameterizations to miniPBL: vertical grid stretching, Deardorff prognostic TKE subgrid closure, Monin-Obukhov similarity theory surface layer, Rayleigh sponge damping, and large-scale subsidence. All operators updated to support variable vertical spacing. Existing 1D, 2D, and 3D modes are fully backward-compatible.

New Features

Vertical Grid Stretching

  • Optional geometric stretching of the vertical grid with configurable stretch_factor (ratio between successive cell thicknesses) and nz_uniform (number of uniform cells near the surface before stretching begins)
  • New grid arrays dz_center[k] (cell thickness) and dz_face[k] (distance between cell centers) replace the scalar dz throughout all operators
  • When stretch_factor = 1.0 (default), the grid is identical to the previous uniform spacing

Variable-dz Support in All Operators

  • Diffusion: flux F[k] = -K[k] * (f[k] - f[k-1]) / dz_face[k]; tendency (F[k+1] - F[k]) / dz_center[k]
  • Advection: flux divergence uses local dz_center[k] and dz_face[k]
  • Pressure Poisson solver: tridiagonal coefficients a[k] = 1/(dz_c[k]*dz_f[k]), c[k] = 1/(dz_c[k]*dz_f[k+1]) for variable spacing
  • Divergence and pressure gradient correction use position-dependent spacing
  • Boundary conditions (top gradient, surface stress) use local cell thickness

Deardorff TKE Subgrid-Scale Closure

  • Prognostic TKE equation: de/dt = Shear + Buoyancy - Dissipation + Diffusion
  • Shear production: S = K_m * (|du/dz|^2 + |dv/dz|^2)
  • Buoyancy production/destruction: B = -(g/theta_ref) * K_h * dtheta/dz
  • Dissipation: eps = c_eps * e^(3/2) / l with c_eps = 0.19 + 0.51*l/Delta
  • Stability-dependent mixing length: l = min(c_l * sqrt(e) / N, Delta) (Delta for unstable conditions)
  • Eddy viscosity: K_m = c_m * l * sqrt(e); eddy diffusivity: K_h = (1 + 2*l/Delta) * K_m
  • TKE advanced by RK3 alongside theta, u, v, w; clamped to configurable minimum
  • Column-by-column computation for 2D and 3D fields
  • Activated by setting scheme: "deardorff-tke" in the turbulence config

Monin-Obukhov Similarity Theory (MOST) Surface Layer

  • Iterative solver for friction velocity (u_star) and temperature scale (theta_star) given wind speed and temperature at the first grid level
  • Businger-Dyer stability functions for momentum (psi_m) and heat (psi_h) under both stable and unstable conditions
  • Surface heat flux: w'theta'_sfc = -u_star * theta_star
  • Surface momentum flux: tau = -u_star^2 * (u,v) / |V|
  • Replaces both the prescribed surface heat flux and the no-slip surface stress approximation when activated
  • Activated by setting surface_flux_scheme: "most" in the physics config

Rayleigh Sponge Damping Layer

  • Rayleigh damping in the upper domain: d(phi)/dt += -alpha(z) * (phi - phi_ref)
  • Damping profile: alpha(z) = alpha_max * sin^2(pi/2 * (z - z_sponge) / (Lz - z_sponge))
  • Applied to theta (relaxed toward horizontal mean), u and v (horizontal mean), w and TKE (zero)
  • Configurable sponge_fraction (default 0.25) and sponge_alpha_max (default 0, i.e. off)

Large-Scale Subsidence

  • Prescribed subsidence profile: w_s(z) = -D * z where D is the divergence rate
  • Theta tendency: d(theta)/dt += -w_s * d(theta)/dz
  • Prevents unbounded boundary layer growth in long simulations
  • Activated by setting subsidence_divergence > 0 in the physics config

Configuration Changes

GridConfig

  • stretch_factor: float = 1.0 — geometric stretch ratio (1.0 = uniform)
  • nz_uniform: int = 0 — uniform cells near surface before stretching

PhysicsConfig

  • surface_flux_scheme: str = "prescribed" — "prescribed" or "most"
  • theta_surface: float = 302.0 — surface temperature for MOST (K)
  • subsidence_divergence: float = 0.0 — large-scale divergence rate (1/s)
  • sponge_fraction: float = 0.25 — fraction of domain for sponge layer
  • sponge_alpha_max: float = 0.01 — maximum Rayleigh damping rate (1/s)

TurbulenceConfig

  • scheme now supports "k-profile" (existing) and "deardorff-tke" (new)
  • tke_c_m: float = 0.1 — eddy viscosity coefficient
  • tke_c_eps_base: float = 0.19 — base dissipation coefficient
  • tke_c_l: float = 0.76 — mixing length coefficient
  • tke_min: float = 1e-4 — minimum TKE floor (m^2/s^2)

Backward Compatibility

All new features default to off. Existing configurations produce identical results:

  • stretch_factor = 1.0: uniform grid (identical to v3.0.0)
  • scheme = "k-profile": diagnostic K-profile closure (unchanged)
  • surface_flux_scheme = "prescribed": fixed surface heat flux (unchanged)
  • sponge_alpha_max = 0.0: no sponge damping
  • subsidence_divergence = 0.0: no subsidence

Files Added

  • minipbl/tke_closure.py — Deardorff prognostic TKE closure
  • minipbl/surface_layer.py — Monin-Obukhov similarity theory surface fluxes
  • minipbl/forcing.py — Rayleigh sponge damping and large-scale subsidence

Dependencies

  • numpy, scipy, matplotlib, pyyaml
Assets 2
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