Merge pull request #4169 from CliMA/oa/fix_trace_gases_new

oalcabes · web-flow · commit 2c6fe62da437 · 2025-12-16T23:11:09.000Z
Refactor trace gases
diff --git a/NEWS.md b/NEWS.md
@@ -4,13 +4,15 @@ ClimaAtmos.jl Release Notes
 main
 -------
 
+v0.33.0
+-------
+- ![#4169](https://github.com/CliMA/ClimaAtmos.jl/pull/4169) [badge-💥breaking]
+Remove the options `co2_model` and `prescribe_ozone`. These are both fixed by
+default now, and can be set to time-varying by including one or both in the
+option `time_varying_trace_gases: ["CO2", "O3]`.
 
 v0.32.0
 -------
-- ![][badge-💥breaking] Remove the options `co2_model` and `prescribe_ozone`.
-These are both fixed by default now, and can be set to time-varying by
-including one or both in the option `time_varying_trace_gases: ["CO2", "O3]`.
-
 - PR [#4162](https://github.com/CliMA/ClimaAtmos.jl/pull/4162) adds an option for
 reproducible restart. It is set to false by default. This shouldn't affect restart
 in the coupler as the coupler save the cache for restarting.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "ClimaAtmos"
 uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
 authors = ["Climate Modeling Alliance"]
-version = "0.32.0"
+version = "0.33.0"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
diff --git a/calibration/experiments/gcm_driven_scm/model_config_diagnostic.yml b/calibration/experiments/gcm_driven_scm/model_config_diagnostic.yml
@@ -23,7 +23,6 @@ z_elem: 60
 z_stretch: true
 dz_bottom: 30
 rad: allskywithclear
-co2_model: fixed
 insolation: "gcmdriven"
 dt: "100secs"
 t_end: "72hours"
diff --git a/calibration/experiments/gcm_driven_scm/model_config_prognostic.yml b/calibration/experiments/gcm_driven_scm/model_config_prognostic.yml
@@ -25,7 +25,6 @@ z_elem: 60
 z_stretch: true
 dz_bottom: 30
 rad: allskywithclear
-co2_model: fixed
 insolation: "gcmdriven"
 perturb_initstate: false
 dt: "10secs"
diff --git a/calibration/test/model_config.yml b/calibration/test/model_config.yml
@@ -8,7 +8,6 @@ output_dir: calibration_end_to_end_test
 output_default_diagnostics: false
 dt_rad: 6hours
 rad: clearsky
-co2_model: fixed
 diagnostics:
   - reduction_time: average
     short_name: rsut
diff --git a/config/default_configs/default_config.yml b/config/default_configs/default_config.yml
@@ -337,12 +337,6 @@ deep_atmosphere:
 restart_file:
   help: "Path to HDF5 file to use as simulation starting point. Note that the simulation can only be restarted in a reproducible way when `reproducible_restart` is true."
   value: ~
-prescribe_ozone:
-  help: "Prescribe time and spatially varying ozone from a file [`false` (default), `true`]"
-  value: false
-co2_model:
-  help: "What CO2 concentration to use for RRTGMP. When fixed, it is set to 397.547 parts per million. Otherwise, it is read from the MaunaLoa measuraments. [`nothing` (default), `Fixed`, `MaunaLoa`]"
-  value: ~
 detect_restart_file:
   help: "When true, try finding a restart file and use it to restart the simulation. Only works with ActiveLink."
   value: false
@@ -352,6 +346,9 @@ reproducible_restart:
 prescribed_aerosols:
   help: "Which aerosols to add. List of keys from the data file (e.g., CB1, CB2)."
   value: []
+time_varying_trace_gases:
+  help: "Trace gases that vary in time, e.g. [\"CO2\", \"O3\"]. Currently, only \"CO2\" and \"O3\" are supported. All other trace gases set fixed to default values from ClimaParams."
+  value: []
 # TODO: remove once https://github.com/CliMA/ClimaAtmos.jl/issues/2873 is closed
 call_cloud_diagnostics_per_stage:
   help: "A temporary Bool for calling cloud diagnostics every stage"
diff --git a/config/gpu_configs/gpu_aquaplanet_dyamond_diag_1process.yml b/config/gpu_configs/gpu_aquaplanet_dyamond_diag_1process.yml
@@ -2,7 +2,6 @@ dt_save_state_to_disk: 12hours
 moist: equil
 precip_model: 0M
 rad: allskywithclear
-co2_model: fixed
 idealized_insolation: false
 dt_rad: 1hours
 vert_diff: "DecayWithHeightDiffusion"
@@ -14,6 +13,6 @@ output_default_diagnostics: false
 diagnostics:
   - short_name: ["pfull", "wa", "va", "rv", "ke"]
     period: "12hours"
-prescribe_ozone: true
+time_varying_trace_gases: ["O3"]
 aerosol_radiation: true
 prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "DST05", "OC1", "OC2", "SO4", "SSLT01", "SSLT02", "SSLT03", "SSLT04", "SSLT05"]
diff --git a/config/gpu_configs/gpu_aquaplanet_dyamond_ss.yml b/config/gpu_configs/gpu_aquaplanet_dyamond_ss.yml
@@ -10,6 +10,6 @@ vert_diff: "DecayWithHeightDiffusion"
 surface_setup: "DefaultMoninObukhov"
 t_end: "1days"
 toml: [toml/longrun_aquaplanet.toml]
-prescribe_ozone: true
+time_varying_trace_gases: ["O3"]
 aerosol_radiation: true
 prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "DST05", "OC1", "OC2", "SO4", "SSLT01", "SSLT02", "SSLT03", "SSLT04", "SSLT05"]
diff --git a/config/gpu_configs/gpu_aquaplanet_dyamond_summer.yml b/config/gpu_configs/gpu_aquaplanet_dyamond_summer.yml
@@ -11,7 +11,7 @@ edmfx_sgs_diffusive_flux: true
 surface_setup: "DefaultMoninObukhov"
 t_end: "1hours"
 toml: [toml/longrun_aquaplanet.toml]
-prescribe_ozone: true
+time_varying_trace_gases: ["O3"]
 aerosol_radiation: true
 prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "DST05", "OC1", "OC2", "SO4", "SSLT01", "SSLT02", "SSLT03", "SSLT04", "SSLT05"]
 start_date: "20160801"
diff --git a/config/gpu_configs/gpu_aquaplanet_dyamond_ws_1process.yml b/config/gpu_configs/gpu_aquaplanet_dyamond_ws_1process.yml
@@ -10,6 +10,6 @@ vert_diff: "DecayWithHeightDiffusion"
 surface_setup: "DefaultMoninObukhov"
 t_end: "1days"
 toml: [toml/longrun_aquaplanet.toml]
-prescribe_ozone: true
+time_varying_trace_gases: ["O3"]
 aerosol_radiation: true
 prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "DST05", "OC1", "OC2", "SO4", "SSLT01", "SSLT02", "SSLT03", "SSLT04", "SSLT05"]
diff --git a/config/gpu_configs/gpu_aquaplanet_dyamond_ws_2process.yml b/config/gpu_configs/gpu_aquaplanet_dyamond_ws_2process.yml
@@ -11,6 +11,6 @@ vert_diff: "DecayWithHeightDiffusion"
 surface_setup: "DefaultMoninObukhov"
 t_end: "1days"
 toml: [toml/longrun_aquaplanet.toml]
-prescribe_ozone: true
+time_varying_trace_gases: ["O3"]
 aerosol_radiation: true
 prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "DST05", "OC1", "OC2", "SO4", "SSLT01", "SSLT02", "SSLT03", "SSLT04", "SSLT05"]
diff --git a/config/gpu_configs/gpu_aquaplanet_dyamond_ws_4process.yml b/config/gpu_configs/gpu_aquaplanet_dyamond_ws_4process.yml
@@ -13,6 +13,6 @@ vert_diff: "DecayWithHeightDiffusion"
 surface_setup: "DefaultMoninObukhov"
 t_end: "1days"
 toml: [toml/longrun_aquaplanet.toml]
-prescribe_ozone: true
+time_varying_trace_gases: ["O3"]
 aerosol_radiation: true
 prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "DST05", "OC1", "OC2", "SO4", "SSLT01", "SSLT02", "SSLT03", "SSLT04", "SSLT05"]
diff --git a/config/longrun_configs/amip_target_diagedmf.yml b/config/longrun_configs/amip_target_diagedmf.yml
@@ -5,8 +5,7 @@ rad: "allskywithclear"
 dt_rad: "1hours"
 dt_cloud_fraction: "1hours"
 insolation: "timevarying"
-co2_model: maunaloa
-prescribe_ozone: true
+time_varying_trace_gases: ["CO2", "O3"]
 aerosol_radiation: true
 prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "DST05", "OC1", "OC2", "SO4", "SSLT01", "SSLT02", "SSLT03", "SSLT04", "SSLT05"]
 surface_setup: "DefaultMoninObukhov"
diff --git a/config/longrun_configs/amip_target_edonly.yml b/config/longrun_configs/amip_target_edonly.yml
@@ -5,8 +5,7 @@ rad: "allskywithclear"
 dt_rad: "1hours"
 dt_cloud_fraction: "1hours"
 insolation: "timevarying"
-co2_model: maunaloa
-prescribe_ozone: true
+time_varying_trace_gases: ["CO2", "O3"]
 aerosol_radiation: true
 edmfx_sgs_diffusive_flux: true
 prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "DST05", "OC1", "OC2", "SO4", "SSLT01", "SSLT02", "SSLT03", "SSLT04", "SSLT05"]
diff --git a/config/model_configs/aquaplanet_nonequil_allsky_gw_res.yml b/config/model_configs/aquaplanet_nonequil_allsky_gw_res.yml
@@ -14,7 +14,7 @@ insolation: "timevarying"
 non_orographic_gravity_wave: true
 orographic_gravity_wave: "gfdl_restart"
 surface_setup: "DefaultMoninObukhov"
-prescribe_ozone: true
+time_varying_trace_gases: ["O3"]
 reproducibility_test: true
 prescribed_aerosols: ["SO4", "CB1", "OC1", "DST01", "SSLT01"]
 toml: [toml/sphere_aquaplanet_1M.toml]
diff --git a/config/model_configs/aquaplanet_nonequil_allsky_gw_res_2M.yml b/config/model_configs/aquaplanet_nonequil_allsky_gw_res_2M.yml
@@ -13,7 +13,7 @@ insolation: "timevarying"
 non_orographic_gravity_wave: true
 orographic_gravity_wave: "gfdl_restart"
 surface_setup: "DefaultMoninObukhov"
-prescribe_ozone: true
+time_varying_trace_gases: ["O3"]
 reproducibility_test: true
 prescribed_aerosols: ["SO4", "CB1", "OC1", "DST01", "SSLT01", "SSLT02", "SSLT03", "SSLT04", "SSLT05"]
 diagnostics:
diff --git a/config/model_configs/diagnostic_edmfx_aquaplanet.yml b/config/model_configs/diagnostic_edmfx_aquaplanet.yml
@@ -2,7 +2,6 @@ dt: 120secs
 viscous_sponge: false
 surface_setup: DefaultMoninObukhov
 rad: clearsky
-co2_model: fixed
 turbconv: diagnostic_edmfx
 prognostic_tke: true
 edmfx_entr_model: "Generalized"
diff --git a/config/model_configs/diagnostic_edmfx_aquaplanet_gpu.yml b/config/model_configs/diagnostic_edmfx_aquaplanet_gpu.yml
@@ -1,7 +1,6 @@
 dt: 120secs
 surface_setup: DefaultMoninObukhov
 rad: clearsky
-co2_model: fixed
 turbconv: diagnostic_edmfx
 prognostic_tke: true
 edmfx_entr_model: "Generalized"
diff --git a/config/model_configs/diagnostic_edmfx_era5_initial_condition.yml b/config/model_configs/diagnostic_edmfx_era5_initial_condition.yml
@@ -18,7 +18,6 @@ vorticity_hyperdiffusion_coefficient: 0.1857
 insolation: "timevarying"
 surface_setup: DefaultMoninObukhov
 rad: allskywithclear
-co2_model: fixed
 turbconv: diagnostic_edmfx
 implicit_diffusion: true
 approximate_linear_solve_iters: 2
diff --git a/config/model_configs/edonly_edmfx_aquaplanet.yml b/config/model_configs/edonly_edmfx_aquaplanet.yml
@@ -1,7 +1,6 @@
 dt: 120secs
 surface_setup: DefaultMoninObukhov
 rad: allskywithclear
-co2_model: fixed
 edmfx_sgs_diffusive_flux: true
 turbconv: edonly_edmfx
 moist: equil
diff --git a/config/model_configs/prognostic_edmfx_aquaplanet.yml b/config/model_configs/prognostic_edmfx_aquaplanet.yml
@@ -5,7 +5,6 @@ dz_bottom: 500.0
 dt: 20secs
 surface_setup: DefaultMoninObukhov
 rad: clearsky
-co2_model: fixed
 turbconv: prognostic_edmfx
 prognostic_tke: true
 edmfx_entr_model: "Generalized"
diff --git a/config/model_configs/prognostic_edmfx_aquaplanet_dense_autodiff.yml b/config/model_configs/prognostic_edmfx_aquaplanet_dense_autodiff.yml
@@ -7,7 +7,6 @@ viscous_sponge: false
 dt: 20secs
 surface_setup: DefaultMoninObukhov
 rad: clearsky
-co2_model: fixed
 turbconv: prognostic_edmfx
 prognostic_tke: true
 edmfx_entr_model: "Generalized"
diff --git a/config/model_configs/prognostic_edmfx_aquaplanet_gpu.yml b/config/model_configs/prognostic_edmfx_aquaplanet_gpu.yml
@@ -7,7 +7,6 @@ viscous_sponge: false
 dt: 20secs
 surface_setup: DefaultMoninObukhov
 rad: clearsky
-co2_model: fixed
 turbconv: prognostic_edmfx
 prognostic_tke: true
 edmfx_entr_model: "Generalized"
diff --git a/config/model_configs/prognostic_edmfx_aquaplanet_gpu_dense_autodiff.yml b/config/model_configs/prognostic_edmfx_aquaplanet_gpu_dense_autodiff.yml
@@ -7,7 +7,6 @@ viscous_sponge: false
 dt: 20secs
 surface_setup: DefaultMoninObukhov
 rad: clearsky
-co2_model: fixed
 turbconv: prognostic_edmfx
 prognostic_tke: true
 edmfx_entr_model: "Generalized"
diff --git a/config/model_configs/prognostic_edmfx_aquaplanet_gpu_sparse_autodiff.yml b/config/model_configs/prognostic_edmfx_aquaplanet_gpu_sparse_autodiff.yml
@@ -7,7 +7,6 @@ viscous_sponge: false
 dt: 20secs
 surface_setup: DefaultMoninObukhov
 rad: clearsky
-co2_model: fixed
 turbconv: prognostic_edmfx
 prognostic_tke: true
 edmfx_entr_model: "Generalized"
diff --git a/config/model_configs/prognostic_edmfx_aquaplanet_sparse_autodiff.yml b/config/model_configs/prognostic_edmfx_aquaplanet_sparse_autodiff.yml
@@ -7,7 +7,6 @@ viscous_sponge: false
 dt: 20secs
 surface_setup: DefaultMoninObukhov
 rad: clearsky
-co2_model: fixed
 turbconv: prognostic_edmfx
 prognostic_tke: true
 edmfx_entr_model: "Generalized"
diff --git a/config/model_configs/prognostic_edmfx_diurnal_scm_imp.yml b/config/model_configs/prognostic_edmfx_diurnal_scm_imp.yml
@@ -29,7 +29,6 @@ edmfx_vertical_diffusion: false
 edmfx_filter: true
 prognostic_tke: true
 precip_model: "0M"
-prescribe_ozone: false
 moist: "equil"
 config: "column"
 z_max: 60e3
diff --git a/config/model_configs/prognostic_edmfx_gcmdriven_column.yml b/config/model_configs/prognostic_edmfx_gcmdriven_column.yml
@@ -33,7 +33,6 @@ netcdf_output_at_levels: true
 netcdf_interpolation_num_points: [2, 2, 60]
 output_default_diagnostics: false
 rad: allskywithclear
-co2_model: fixed
 insolation: "gcmdriven"
 diagnostics:
   - short_name: [ts, ta, thetaa, ha, pfull, rhoa, ua, va, wa, hur, hus, cl, clw, cli, hussfc, evspsbl, pr]
diff --git a/config/model_configs/prognostic_edmfx_tv_era5driven_column.yml b/config/model_configs/prognostic_edmfx_tv_era5driven_column.yml
@@ -20,7 +20,6 @@ edmfx_vertical_diffusion: true
 edmfx_filter: true
 prognostic_tke: true
 precip_model: "0M"
-prescribe_ozone: false
 moist: "equil"
 config: "column"
 z_max: 45e3
diff --git a/config/model_configs/rcemipii_box_CRM_1M.yml b/config/model_configs/rcemipii_box_CRM_1M.yml
@@ -5,7 +5,6 @@ insolation: rcemipii
 initial_condition: RCEMIPIIProfile_300
 config: box
 rad: allskywithclear
-co2_model: fixed
 approximate_linear_solve_iters: 2  # only valid when implicit_diffusion=true
 rayleigh_sponge: true  # set sponge level in toml file
 smagorinsky_lilly: "UV"
diff --git a/config/model_configs/rcemipii_sphere_diagnostic_edmfx.yml b/config/model_configs/rcemipii_sphere_diagnostic_edmfx.yml
@@ -1,7 +1,6 @@
 surface_setup: DefaultMoninObukhov
 surface_temperature: RCEMIPII
 rad: allskywithclear
-co2_model: fixed
 turbconv: diagnostic_edmfx
 insolation: rcemipii
 prognostic_tke: true
diff --git a/docs/src/tracers.md b/docs/src/tracers.md
@@ -1,13 +1,13 @@
 # Aerosols
 
-`ClimaAtmos` implements two modes for ozone profiles. These are only relevant
-for the radiation transfer, and only when RRTMGP is used.
+# Trace Gases
+`ClimaAtmos` implements two modes for each ozone and carbon dioxide: one time varying and one time invariant. These are only relevant for the radiation transfer, and only when RRTMGP is used. All other atmospheric gases are held fixed with default values from RRTMPG that can be changed in the toml file.
 
-### Idealized Ozone Profile
+### Time Invariant Ozone Profile
 
-The `IdealizedOzone` type of ozone uses the `idealized_ozone` function to
-compute an idealized ozone profile based on the work of `Wing2018`. This
-profile is not time-varying.
+The time invariant type of ozone uses the `idealized_ozone` function to
+compute an idealized ozone profile based on the work of `Wing2018`.
+This option is default.
 
 The `idealized_ozone` function returns the ozone concentration in volume mixing
 ratio (VMR) at a given altitude `z`.
@@ -26,34 +26,28 @@ ozone = ClimaAtmos.idealized_ozone.(z)
 lines(ozone, z)
 ```
 
-### Prescribed Ozone Profile
+### Time Varying Ozone Profile
 
-The `PrescribedOzone` type of ozone uses CMIP6 forcing data to prescribe ozone
+The time varying ozone profile uses CMIP6 forcing data to prescribe ozone
 as read from files. A high-resolution, multi-year file is available in the
 `ozone_concentrations` artifact. This file is not small, so you have to obtain
 independently. Please, refer to `ClimaArtifacts` for more information. If the
 file is not found, a low-resolution, single-year version is used. This is not
-advised for production simulations.
+advised for production simulations. This option is enabled with by adding `"O3"`
+to the `time_varying_gases` config argument list, ie: `time_varying_gases: ["O3"]`.
 
 We interpolate the data from file in time every time radiation is called. The
 interpolation used is the `LinerPeriodFilling` from `ClimaUtilities`. This is a
 linear period-aware interpolation that preserves the annual cycle.
 
-### Prescribed CO2 Profile
+### Time Invariant CO2 Profile
 
-In addition to ozone, `ClimaAtmos` can prescribe CO2 concentration using data
-from [Mauna Loa CO2 measurements](https://gml.noaa.gov/ccgg/trends/data.html).
-This option is enabled with `MaunaLoaCO2`. Alternatively, `FixedCO2`
-utilizes a constant value that can be prescribed (by default, 397.547 ppm).
-
-### More docstrings
+By default, CO2 concentrations are set to 397.547 ppm. The number can be altered
+by changing the `CO2_fixed_value` parameter in the toml file.
 
-```@docs
-ClimaAtmos.AbstractOzone
-ClimaAtmos.IdealizedOzone
-ClimaAtmos.PrescribedOzone
+### Time Varying CO2 Profile
 
-ClimaAtmos.AbstractCO2
-ClimaAtmos.FixedCO2
-ClimaAtmos.MaunaLoaCO2
-```
+`ClimaAtmos` can prescribe CO2 concentration using data
+from [Mauna Loa CO2 measurements](https://gml.noaa.gov/ccgg/trends/data.html).
+This option is enabled with by adding `"CO2"` to the `time_varying_gases`
+config argument list, ie: `time_varying_gases: ["CO2"]`.
diff --git a/reproducibility_tests/ref_counter.jl b/reproducibility_tests/ref_counter.jl
@@ -1,4 +1,4 @@
-288
+289
 
 # **README**
 #
@@ -20,6 +20,10 @@
 
 
 #=
+289
+- Merging the trace gases PR again, which does change behavior slightly as a
+result of reading values from params rather than from a file.
+
 288
 - Revert PR 4153, which changed ref_counter to 287
 
diff --git a/src/cache/cache.jl b/src/cache/cache.jl
diff --git a/src/cache/tracer_cache.jl b/src/cache/tracer_cache.jl
diff --git a/src/parameterized_tendencies/radiation/radiation.jl b/src/parameterized_tendencies/radiation/radiation.jl
diff --git a/src/parameterized_tendencies/radiation/update_inputs.jl b/src/parameterized_tendencies/radiation/update_inputs.jl
diff --git a/src/parameters/Parameters.jl b/src/parameters/Parameters.jl
diff --git a/src/parameters/create_parameters.jl b/src/parameters/create_parameters.jl
diff --git a/src/solver/model_getters.jl b/src/solver/model_getters.jl
diff --git a/src/solver/type_getters.jl b/src/solver/type_getters.jl
diff --git a/src/solver/types.jl b/src/solver/types.jl
diff --git a/test/restart.jl b/test/restart.jl
diff --git a/test/solver/atmos_model_constructor.jl b/test/solver/atmos_model_constructor.jl
diff --git a/toml/rcemipii_box.toml b/toml/rcemipii_box.toml
