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Centralize JCB variable lists #2171

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58ecf8a
Initial commit
Jun 2, 2026
2d6c0c6
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DavidNew-NOAA Jun 3, 2026
a414d71
Finished atmosphere and aerosol templates
DavidNew-NOAA Jun 3, 2026
54ecb4f
Finished prototype for snow and soil
DavidNew-NOAA Jun 5, 2026
0bc5423
Finished marine prototype
DavidNew-NOAA Jun 5, 2026
bb943a0
Slight renaming
DavidNew-NOAA Jun 10, 2026
60b88ea
Clean up
DavidNew-NOAA Jun 10, 2026
2e66337
some re-refactoring
DavidNew-NOAA Jun 11, 2026
47c4638
cleanup
DavidNew-NOAA Jun 11, 2026
68adb8c
Save changes
DavidNew-NOAA Jun 11, 2026
aaf6400
Almost done save marine
DavidNew-NOAA Jun 11, 2026
1b4ae5e
Almost done save marine
DavidNew-NOAA Jun 11, 2026
2cbf840
Final changes
DavidNew-NOAA Jun 12, 2026
119f674
Merge branch 'develop' into feature/jcb-gdas-refactor
DavidNew-NOAA Jun 12, 2026
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75 changes: 65 additions & 10 deletions parm/aero/jcb-base.yaml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -24,19 +24,74 @@ minimizer: DRPCG
final_diagnostics_departures: anlmob
final_prints_frequency: PT3H
number_of_outer_loops: 1
analysis_variables: [mass_fraction_of_sulfate_in_air,
mass_fraction_of_hydrophobic_black_carbon_in_air,
mass_fraction_of_hydrophilic_black_carbon_in_air,
mass_fraction_of_hydrophobic_organic_carbon_in_air,
mass_fraction_of_hydrophilic_organic_carbon_in_air,
mass_fraction_of_dust001_in_air, mass_fraction_of_dust002_in_air,
mass_fraction_of_dust003_in_air, mass_fraction_of_dust004_in_air,
mass_fraction_of_dust005_in_air, mass_fraction_of_sea_salt001_in_air,
mass_fraction_of_sea_salt002_in_air, mass_fraction_of_sea_salt003_in_air,
mass_fraction_of_sea_salt004_in_air]
{% set _analysis_vars = ['mass_fraction_of_sulfate_in_air',
'mass_fraction_of_hydrophobic_black_carbon_in_air',
'mass_fraction_of_hydrophilic_black_carbon_in_air',
'mass_fraction_of_hydrophobic_organic_carbon_in_air',
'mass_fraction_of_hydrophilic_organic_carbon_in_air',
'mass_fraction_of_dust001_in_air',
'mass_fraction_of_dust002_in_air',
'mass_fraction_of_dust003_in_air',
'mass_fraction_of_dust004_in_air',
'mass_fraction_of_dust005_in_air',
'mass_fraction_of_sea_salt001_in_air',
'mass_fraction_of_sea_salt002_in_air',
'mass_fraction_of_sea_salt003_in_air',
'mass_fraction_of_sea_salt004_in_air'] %}
analysis_variables: {{ _analysis_vars }}

# Model things
# ------------

# Variables
aero_det_state_variables: {{ _analysis_vars + ['air_temperature',
'air_pressure_thickness',
'water_vapor_mixing_ratio_wrt_moist_air'] }}
aero_bmat_state_variables: {{ _analysis_vars + ['mass_fraction_of_sea_salt005_in_air'] }}

# Increment variables:
aero_det_increment_variables: {{ _analysis_vars }}

# Variable IO names
aero_field_io_names:
air_temperature: T
air_pressure_thickness: delp
water_vapor_mixing_ratio_wrt_moist_air: sphum
mass_fraction_of_sulfate_in_air: so4
mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
mass_fraction_of_dust001_in_air: dust1
mass_fraction_of_dust002_in_air: dust2
mass_fraction_of_dust003_in_air: dust3
mass_fraction_of_dust004_in_air: dust4
mass_fraction_of_dust005_in_air: dust5
mass_fraction_of_sea_salt001_in_air: seas1
mass_fraction_of_sea_salt002_in_air: seas2
mass_fraction_of_sea_salt003_in_air: seas3
mass_fraction_of_sea_salt004_in_air: seas4
mass_fraction_of_sea_salt005_in_air: seas5
slmsk: slmsk
aero_field_io_names_crtm:
air_temperature: T
air_pressure_thickness: delp
water_vapor_mixing_ratio_wrt_moist_air: sphum
mass_fraction_of_sulfate_in_air: so4
mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
mass_fraction_of_dust001_in_air: dust1
mass_fraction_of_dust002_in_air: dust2
mass_fraction_of_dust003_in_air: dust3
mass_fraction_of_dust004_in_air: dust4
mass_fraction_of_dust005_in_air: dust5
mass_fraction_of_sea_salt001_in_air: seas2
mass_fraction_of_sea_salt002_in_air: seas3
mass_fraction_of_sea_salt003_in_air: seas4
mass_fraction_of_sea_salt004_in_air: seas5

# Geometry
aero_layout_x: {{ layout_x | default(1, true) }}
aero_layout_y: {{ layout_y | default(1, true) }}
Expand Down
121 changes: 119 additions & 2 deletions parm/atm/jcb-base.yaml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -31,10 +31,110 @@ atmosphere_ninner_1: {{ NINNER_LOOP1 | default(2, true) }}
atmosphere_grad_red_1: 1e-10
atmosphere_ninner_2: {{ NINNER_LOOP2 | default(4, true) }}
atmosphere_grad_red_2: 1e-10
analysis_variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,snow_water,rain_water,graupel,ozone_mass_mixing_ratio]

# Analysis variables
{% set _shared_vars = ['eastward_wind',
'northward_wind',
'air_temperature',
'water_vapor_mixing_ratio_wrt_moist_air',
'cloud_liquid_ice',
'cloud_liquid_water'] %}
{% set _analysis_vars = _shared_vars + ['air_pressure_at_surface',
'ozone_mass_mixing_ratio',
'snow_water',
'rain_water',
'graupel'] %}
{% set _analysis_vars_molesO3 = _shared_vars + ['air_pressure_at_surface',
'mole_fraction_of_ozone_in_air',
'snow_water',
'rain_water',
'graupel'] %}
{% set _analysis_vars_noprecip = _shared_vars + ['air_pressure_at_surface',
'ozone_mass_mixing_ratio'] %}
{% set _analysis_vars_molesO3_noprecip = _shared_vars + ['air_pressure_at_surface',
'mole_fraction_of_ozone_in_air'] %}
{% set _fv3_increment_vars = _shared_vars + ['air_pressure_thickness',
'layer_thickness',
'ozone_mass_mixing_ratio',
'snow_water',
'rain_water',
'graupel'] %}

analysis_variables: {{ _analysis_vars }}

# Model things
# ------------

# State variables
atmosphere_det_state_variables: {{ _analysis_vars + ['geopotential_height_at_surface',
'cloud_ice_number_concentration',
'rain_number_concentration',
'slmsk',
'sheleg',
'skin_temperature_at_surface',
'vtype',
'stype',
'vfrac',
'soilt',
'soilm',
'totalSnowDepthMeters',
'eastward_wind_at_surface',
'northward_wind_at_surface',
'f10m',
'air_pressure_thickness'] }}
atmosphere_jedi2fv3inc_state_variables: {{ _analysis_vars + ['geopotential_height_at_surface'] }}

# Increment variables
atmosphere_det_increment_variables: {{ _analysis_vars }}
atmosphere_det_increment_variables_molesO3: {{ _analysis_vars_molesO3 }}
atmosphere_det_increment_variables_noprecip: {{ _analysis_vars_noprecip }}
atmosphere_det_increment_variables_molesO3_noprecip: {{ _analysis_vars_molesO3_noprecip }}
atmosphere_fv3_increment_variables: {{ _fv3_increment_vars }}

# Variable IO names
atmosphere_background_field_io_names:
eastward_wind: ugrd
northward_wind: vgrd
air_temperature: tmp
layer_thickness: delz
air_pressure_thickness: dpres
air_pressure_at_surface: pressfc
water_vapor_mixing_ratio_wrt_moist_air: spfh
cloud_liquid_ice: icmr
cloud_liquid_water: clwmr
snow_water: snmr
rain_water: rwmr
graupel: grle
cloud_ice_number_concentration: nccice
rain_number_concentration: nconrd
ozone_mass_mixing_ratio: o3mr
geopotential_height_at_surface: hgtsfc
slmsk: land
sheleg: weasd
skin_temperature_at_surface: tmpsfc
stype: sotyp
vfrac: veg
totalSnowDepthMeters: snod
eastward_wind_at_surface: ugrd_hyblev1
northward_wind_at_surface: vgrd_hyblev1
soilm: soilw1
soilt: soilt1
soilMoistureVolumetric: smc
atmosphere_increment_field_io_names:
eastward_wind: u_inc
northward_wind: v_inc
air_temperature: T_inc
water_vapor_mixing_ratio_wrt_moist_air: sphum_inc
cloud_liquid_water: liq_wat_inc
ozone_mass_mixing_ratio: o3mr_inc
cloud_liquid_ice: icmr_inc
snow_water: snmr_inc
rain_water: rwmr_inc
graupel: grle_inc
air_pressure_thickness: delp_inc
layer_thickness: delz_inc
air_pressure_at_surface: pressfc_inc

# Geometry
atmosphere_layout_x: {{ layout_x | default(1, true) }}
atmosphere_layout_y: {{ layout_y | default(1, true) }}
Expand Down Expand Up @@ -127,7 +227,24 @@ bias_files_dict:
# -------------------------
local_ensemble_da_solver: Deterministic GETKF

increment_variables: [eastward_wind,northward_wind,layer_thickness,air_pressure_thickness,air_temperature,air_pressure_at_surface,water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,snow_water,rain_water,graupel,ozone_mass_mixing_ratio]
{% set _increment_vars = _analysis_vars + ['air_pressure_thickness',
'layer_thickness'] %}

atmosphere_ens_state_variables: {{ _increment_vars + ['geopotential_height_at_surface',
'cloud_ice_number_concentration',
'rain_number_concentration',
'slmsk',
'sheleg',
'skin_temperature_at_surface',
'vtype',
'stype',
'vfrac',
'soilt',
'soilm',
'totalSnowDepthMeters',
'eastward_wind_at_surface',
'northward_wind_at_surface',
'f10m'] }}

atm_enkfonly: {{ DOENKFONLY_ATM | default(false, true) }}

Expand Down
4 changes: 2 additions & 2 deletions parm/jcb-gdas/algorithm/aero/aero_addincrement.yaml.j2
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Original file line number Diff line number Diff line change
Expand Up @@ -24,13 +24,13 @@ increment geometry:
field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
state:
datetime: '{{ aero_background_time_iso }}'
state variables: {{ analysis_variables }}
state variables: {{ aero_det_increment_variables }}
filetype: cube sphere history
provider: ufs
datapath: ./
filename: {{ aero_variational_history_prefix }}cubed_sphere_grid_atmf006.nc
increment:
added variables: {{ analysis_variables }}
added variables: {{ aero_det_increment_variables }}
filetype: fms restart
datapath: ./
filename is datetime templated: true
Expand Down
51 changes: 3 additions & 48 deletions parm/jcb-gdas/algorithm/aero/aero_convert_background.yaml.j2
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Expand Up @@ -24,38 +24,8 @@ states:
- input:
datetime: '{{ aero_background_error_time_iso }}'
filetype: fms restart
state variables:
- mass_fraction_of_sulfate_in_air
- mass_fraction_of_hydrophobic_black_carbon_in_air
- mass_fraction_of_hydrophilic_black_carbon_in_air
- mass_fraction_of_hydrophobic_organic_carbon_in_air
- mass_fraction_of_hydrophilic_organic_carbon_in_air
- mass_fraction_of_dust001_in_air
- mass_fraction_of_dust002_in_air
- mass_fraction_of_dust003_in_air
- mass_fraction_of_dust004_in_air
- mass_fraction_of_dust005_in_air
- mass_fraction_of_sea_salt001_in_air
- mass_fraction_of_sea_salt002_in_air
- mass_fraction_of_sea_salt003_in_air
- mass_fraction_of_sea_salt004_in_air
- mass_fraction_of_sea_salt005_in_air
field io names:
mass_fraction_of_dust001_in_air: dust1
mass_fraction_of_dust002_in_air: dust2
mass_fraction_of_dust003_in_air: dust3
mass_fraction_of_dust004_in_air: dust4
mass_fraction_of_dust005_in_air: dust5
mass_fraction_of_sea_salt001_in_air: seas1
mass_fraction_of_sea_salt002_in_air: seas2
mass_fraction_of_sea_salt003_in_air: seas3
mass_fraction_of_sea_salt004_in_air: seas4
mass_fraction_of_sea_salt005_in_air: seas5
mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
mass_fraction_of_sulfate_in_air: so4
state variables: {{ aero_bmat_state_variables }}
field io names: {{ aero_field_io_names }}
datapath: {{ aero_background_path }}
filename_core: '{{ aero_background_error_time_fv3 }}.fv_core.res.nc'
filename_trcr: '{{ aero_background_error_time_fv3 }}.fv_tracer.res.nc'
Expand All @@ -66,19 +36,4 @@ states:
filename_core: 'anlres.fv_core.res.nc'
filename_trcr: 'anlres.fv_tracer.res.nc'
filename_cplr: 'anlres.coupler.res'
field io names:
mass_fraction_of_dust001_in_air: dust1
mass_fraction_of_dust002_in_air: dust2
mass_fraction_of_dust003_in_air: dust3
mass_fraction_of_dust004_in_air: dust4
mass_fraction_of_dust005_in_air: dust5
mass_fraction_of_sea_salt001_in_air: seas1
mass_fraction_of_sea_salt002_in_air: seas2
mass_fraction_of_sea_salt003_in_air: seas3
mass_fraction_of_sea_salt004_in_air: seas4
mass_fraction_of_sea_salt005_in_air: seas5
mass_fraction_of_hydrophobic_black_carbon_in_air: bc1
mass_fraction_of_hydrophilic_black_carbon_in_air: bc2
mass_fraction_of_hydrophobic_organic_carbon_in_air: oc1
mass_fraction_of_hydrophilic_organic_carbon_in_air: oc2
mass_fraction_of_sulfate_in_air: so4
field io names: {{ aero_field_io_names }}
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