rft: smagorinsky-lilly for future h-v splitting

[haakon-e]

This pull request refactors and extends the Smagorinsky-Lilly subgrid turbulence model implementation, making it more flexible and adding diagnostics and configuration options. The model can now be applied in specific directions (currently only UVW, i.e., all directions), and new diagnostics for horizontal and vertical diffusivities and strain rates are available. The changes affect configuration files, model initialization, diagnostics, and the main turbulence model code.

Key changes:

Smagorinsky-Lilly Model Refactor and Extension

• Refactored the SmagorinskyLilly type to a parametric struct (SmagorinskyLilly{DIR}), allowing specification of which directions the model applies to (currently only :UVW is supported). Added utility functions to check model directionality, enabling more flexible and explicit control over turbulence modeling.
• Updated the Smagorinsky-Lilly turbulence implementation to separately compute and store horizontal and vertical strain rates, eddy viscosities, and diffusivities. The main tendency routines now use these directional quantities, and the precomputation logic has been modularized for clarity and extensibility. [1] [2] [3]

Diagnostics and Postprocessing

• Added new diagnostic variables for horizontal and vertical Smagorinsky diffusivities (Dh_smag, Dv_smag) and strain rate magnitudes (strainh_smag, strainv_smag). These are now available for output and analysis.
• Updated the CI plotting script to include the new Smagorinsky diagnostics and vertical diffusivity in the list of variables plotted, improving postprocessing capabilities.

Configuration and Model Selection

• Changed the configuration options for the Smagorinsky-Lilly model in YAML files: the parameter now accepts "UVW" (all directions) or nothing (disabled), replacing the previous boolean flag. Updated model getter logic to parse and instantiate the correct model variant. [1] [2] [3] [4]

Integration with Other Model Components

• Modified the Jacobian assembly for implicit vertical diffusion to support vertical Smagorinsky-Lilly diffusivity, ensuring correct treatment when the model is active in the vertical direction.

Minor Improvements

• Various code cleanups, improved documentation, and more consistent use of variable names and lazy evaluation for performance and clarity.

These changes collectively make the turbulence modeling more flexible, improve diagnostics, and streamline configuration and code structure.

[haakon-e]

This change is part of the following stack:

• rft: separate vertical and full strain #4073
  • rft: smagorinsky-lilly for future h-v splitting #4074 ◀

_{Change managed by git-spice.}

[haakon-e]

buildkite should pass once #4072 is merged so that ClimaCore is bumped to v0.14.41