remove Diagnostics module

[juliasloan25]

Purpose

Remove Diagnostics module in favor of ClimaDiagnostics and ClimaAnalysis

closes #954

will supersede #875 and #517

Content

This PR touches a lot of files, but most of it is just propagating a few main changes:

• delete the ClimaCoupler Diagnostics module, tests, docs
• use ClimaAtmos.Diagnostics to output atmos diagnostics, and ClimaDiagnostics to output coupler diagnostics
  • coupler diagnostics are defined in user_io/amip_diagnostics.jl
  • the diagnostics handler is added to our CoupledSimulation object, which results in changes in many files
• add default AMIP diagnostics in driver
• user_io/ci_plots.jl is generalized to meet the needs of our updated diagnostic plotting
• artifacts are now output to a subdirectory of the run name, i.e. run_name/artifacts/, rather than an adjacent directory run_name_artifacts/
  • this isn't necessary for the other changes of the PR, but I found that it made more sense as I was looking at run outputs

To-do

• generalize make_ci_plots to work for AMIP plots as well; update amip_paperplots function to use this
• recreate AMIP paperplots using existing ClimaAtmos diagnostics defined in https://github.com/CliMA/ClimaAtmos.jl/blob/main/src/diagnostics/core_diagnostics.jl
  • coupler symbol -> atmos symbol:
  • ":T" -> "ta"
  • ":u" -> "ua"
  • ":q_tot" -> "hus"
  • ":q_liq_ice" -> "clw"
  • ":precipitation_rate" -> "pr"
  • ":T_sfc" -> "ts"
• remove output_short_name, output_long_name
• for the few quantities that aren't already computed in ClimaAtmos diagnostics, add new variables in climaatmos_extra_diags.jl
  • ":toa_fluxes": sum fluxes that can be accessed from atmos cache
  • ":turbulent_energy_fluxes": access calculated value from CoupledSimulation (requires extending ClimaDiagnostics functions)
• remove amip_visualizer.jl
• remove diagnostics from CoupledSimulation object
• remove use_coupler_diagnostics flag
• remove Diagnostics module and tests

Output checks

• check slabplanet_atmos_diags now outputs toa_fluxes_net, previous coupler-added atmos diagnostics, and default diagnostics from atmos
• check all amip runs output F_turb_energy
• check plots are created for amip runs
  • atmos and coupled diagnostics

Previous output: AMIP paperplots

New output:

atmos_summary_2D.pdf

atmos_summary_3D.pdf (averaged over lon)

coupler_summary_2D.pdf

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• I have read and checked the items on the review checklist.

[juliasloan25]

we need to include amip_diags_handler in the cs object so we have access to it inside the coupling loop without creating a closure

[juliasloan25]

these previously weren't being correctly imported but it wasn't caught because we were including files that did import these

[Sbozzolo]

Look good to me! Maybe I'd just add a section in the docs to discuss how to add new diagnostics and give some links to the example you added and to the docs for ClimaDiagnostics and ClimaAnalysis