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Add workflow and tasks for performing 3DVar (tested with SOCA) (#152)
* Add shell for the new tasks (#133) * add shell for all the new tasaks * rename b clim task * update registry Co-authored-by: danholdaway <[email protected]> * Feature/3dvar generateb (#136) * fetch bump or execution with seg fault * Feature/3dvar standalone godas (#138) * Add the basis for running standalone 3DVar * add bclim to flow * changes in executable * 3dvar is executing now, seg fault is fixed * hofx fix * changes in eva * GODAS observations and golden period * SPECIAL case in executable and modifications for 3dvar EVA * changes in flow * changes in flow and codestyle fixes * trailing spaces Co-authored-by: danholdaway <[email protected]> * write logs in the executable tasks * update YAML files to ioda v3 * Feature/3dvar bump eva (#140) * Add the basis for running standalone 3DVar * add bclim to flow * changes in executable * 3dvar is executing now, seg fault is fixed * hofx fix * changes in eva * GODAS observations and golden period * SPECIAL case in executable and modifications for 3dvar EVA * changes in flow * changes in flow and codestyle fixes * trailing spaces * bump SABER update works * ioda_v3 changes * changes in eva * yaml fixes * yaml fixes --------- Co-authored-by: danholdaway <[email protected]> * refactor eva to allow plotting jedi log things * fixes to workflow files * add new task for generating static b by linking (#147) * add new task for generating static b by linking. * remove prints * correct py norms * yaml norms --------- Co-authored-by: danholdaway <[email protected]> * Feature/3dvar lowres (#151) * fixing workflow * linking changes * lowres works * hofx working * 3dvar workflow running * DA recommended changes --------- Co-authored-by: danholdaway <[email protected]> Co-authored-by: Doruk Ardağ <[email protected]>
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‎src/swell/__init__.py

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repo_directory = os.path.dirname(__file__)
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# Set the version for swell
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__version__ = '1.1.3'
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__version__ = '1.2.0'

‎src/swell/configuration/jedi/interfaces/geos_atmosphere/model/stage.yaml

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- link_files:
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directories:
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- ['{{swell_static_files}}/jedi/fv3-jedi/geos_atmosphere/GEOS_CRTM_Surface/geos.crtmsrf.{{horizontal_resolution}}.nc4', '{{experiment_dir}}/stage/fv3-jedi/geos_atmosphere/bkg/']
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- ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/GEOS_CRTM_Surface/geos.crtmsrf.{{horizontal_resolution}}.nc4', '{{experiment_dir}}/stage/fv3-jedi/geos_atmosphere/bkg/']
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- ['{{experiment_dir}}/jedi_bundle/source/fv3-jedi/test/Data/fieldmetadata/*', '{{experiment_dir}}/stage/fv3-jedi/geos_atmosphere/fieldmetadata/']
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- ['{{experiment_dir}}/jedi_bundle/source/fv3-jedi/test/Data/fv3files/*', '{{experiment_dir}}/stage/fv3-jedi/geos_atmosphere/fv3files/']

‎src/swell/configuration/jedi/interfaces/geos_ocean/geos_ocean.yaml

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@@ -3,3 +3,4 @@ executables:
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hofx3d: soca_hofx3d.x
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hofx: soca_hofx.x
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var: soca_var.x
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bump: soca_staticbinit.x

‎src/swell/configuration/jedi/interfaces/geos_ocean/model/analysis.yaml

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datadir: ./
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exp: {{experiment_id}}
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type: an

‎src/swell/configuration/jedi/interfaces/geos_ocean/model/background.yaml

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date: '{{local_background_time_iso}}'
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read_from_file: 1
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basename: '{{cycle_dir}}/'
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basename: './'
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ocn_filename: 'MOM6.res.{{local_background_time}}.nc'
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state variables: [socn, tocn, ssh, hocn, uocn, vocn]
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state variables: [socn, tocn, ssh, hocn, mld, layer_depth]

‎src/swell/configuration/jedi/interfaces/geos_ocean/model/background_error.yaml

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covariance model: 'SocaError'
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analysis variables: {{analysis_variables}}
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date: '{{local_background_time_iso}}'
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bump:
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io:
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data directory: '{{cycle_dir}}/background_error_model/'
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drivers:
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multivariate strategy: 'univariate'
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read local nicas: true
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correlation:
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- name: 'ocn'
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variables: {{analysis_variables}}
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linear variable change:
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input variables: {{analysis_variables}}
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output variables: {{analysis_variables}}
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linear variable changes:
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- linear variable change name: BkgErrFILT
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ocean_depth_min: 1000 # [m]
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rescale_bkgerr: 1.0
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efold_z: 2500.0 # [m]
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- linear variable change name: BkgErrGODAS
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sst_bgerr_file: '{{cycle_dir}}/soca/godas_sst_bgerr.nc'
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t_min: 0.1
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t_max: 2.0
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t_dz: 20.0
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t_efold: 500.0
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s_min: 0.0
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s_max: 0.25
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ssh_min: 0.0 # value at EQ
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ssh_max: 0.1 # value in Extratropics
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ssh_phi_ex: 20 # lat of transition from extratropics
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cicen_min: 0.1
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cicen_max: 0.5
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hicen_min: 10.0
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hicen_max: 100.0
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- linear variable change name: VertConvSOCA
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Lz_min: 2.0
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Lz_mld: 1
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Lz_mld_max: 500.0
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scale_layer_thick: 1.5

‎src/swell/configuration/jedi/interfaces/geos_ocean/model/background_error_init.yaml

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covariance model: 'SocaError'
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analysis variables: {{analysis_variables}}
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date: '{{local_background_time_iso}}'
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bump:
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io:
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data directory: '{{cycle_dir}}/background_error_model'
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drivers:
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multivariate strategy: 'univariate'
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compute nicas: true
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write local nicas: true
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model:
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do not cross mask boundaries: true
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nicas:
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resolution: 6.0
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correlation:
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- name: 'ocn'
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base value: 840336.134453782
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rossby mult: 0.280112045
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variables: {{analysis_variables}}

‎src/swell/configuration/jedi/interfaces/geos_ocean/model/geometry.yaml

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mom6_input_nml: '{{experiment_dir}}/stage/soca/geos_ocean/socafiles/input.nml'
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fields metadata: '{{experiment_dir}}/stage/soca/geos_ocean/fieldmetadata/fields_metadata.yaml'
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geom_grid_file: '{{experiment_dir}}/stage/soca/geos_ocean/gridfiles/soca_gridspec.nc'
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mom6_input_nml: 'soca/input.nml'
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fields metadata: 'soca/fields_metadata.yaml'
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geom_grid_file: 'INPUT/soca_gridspec.nc'

‎src/swell/configuration/jedi/interfaces/geos_ocean/model/geometry_inner.yaml

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mom6_input_nml: 'soca/input.nml'
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fields metadata: 'soca/fields_metadata.yaml'
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geom_grid_file: 'INPUT/soca_gridspec.nc'

‎src/swell/configuration/jedi/interfaces/geos_ocean/model/stage.yaml

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‎src/swell/configuration/jedi/interfaces/geos_ocean/model/stage_cycle.yaml

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- copy_files:
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directories:
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- ['{{swell_static_files}}/jedi/interfaces/geos_ocean/model/geometry/common/*', '{{cycle_dir}}/soca/']
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- ['{{swell_static_files}}/jedi/interfaces/geos_ocean/model/geometry/{{horizontal_resolution}}x{{vertical_resolution}}/socafiles/*', '{{cycle_dir}}/soca/']
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link_files:
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directories:
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- ['{{swell_static_files}}/jedi/interfaces/geos_ocean/model/geometry/{{horizontal_resolution}}x{{vertical_resolution}}/INPUT/*', '{{cycle_dir}}/INPUT']

‎src/swell/configuration/jedi/interfaces/geos_ocean/observations/adt_3a_egm2008.yaml

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obs space:
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name: adt_3a_egm2008
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obsdatain:
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engine:
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type: H5File
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obsfile: '{{cycle_dir}}/adt_3a_egm2008.{{window_begin}}.nc4'
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obsdataout:
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engine:
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type: H5File
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obsfile: '{{cycle_dir}}/{{experiment_id}}.adt_3a_egm2008.{{window_begin}}.nc4'
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simulated variables: [absoluteDynamicTopography]
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obs operator:
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name: ADT
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obs error:
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covariance model: diagonal
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obs filters:
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- filter: Domain Check
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where:
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- variable: {name: GeoVaLs/sea_area_fraction}
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minvalue: 0.9
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- filter: Domain Check
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where:
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- variable: { name: GeoVaLs/sea_surface_temperature}
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minvalue: 15.0
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- filter: Background Check
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absolute threshold: 0.2
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- filter: Domain Check
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where:
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- variable: {name: GeoVaLs/sea_floor_depth_below_sea_surface}
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minvalue: 500
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# - filter: Perform Action
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# action:
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# name: assign error
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# error function:
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# name: ObsFunction/LinearCombination
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# options:
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# variables: [{name: GeoVaLs/mesoscale_representation_error},
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# {name: ObsError/absolute_dynamic_topography}]
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# # variables: [mesoscale_representation_error@GeoVaLs,
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# # absolute_dynamic_topography@ObsError]
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# coefs: [0.1,
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# 0.5]
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- filter: BlackList
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where:
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- variable:
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name: MetaData/latitude
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minvalue: -65
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maxvalue: -30
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- variable:
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name: MetaData/longitude
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minvalue: -125
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maxvalue: -90
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- filter: BlackList
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where:
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- variable:
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name: MetaData/latitude
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minvalue: -65
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maxvalue: -30
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- variable:
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name: MetaData/longitude
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minvalue: 60
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maxvalue: 110
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# - filter: Domain Check
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# where:
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# - variable: { name: GeoVaLs/sea_ice_area_fraction}
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# maxvalue: 0.00001
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- filter: Domain Check
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where:
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- variable: { name: GeoVaLs/distance_from_coast}
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minvalue: 100e3

‎src/swell/configuration/jedi/interfaces/geos_ocean/observations/adt_3b_egm2008.yaml

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obs space:
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name: adt_3b_egm2008
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obsdatain:
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engine:
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type: H5File
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obsfile: '{{cycle_dir}}/adt_3b_egm2008.{{window_begin}}.nc4'
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obsdataout:
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engine:
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type: H5File
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obsfile: '{{cycle_dir}}/{{experiment_id}}.adt_3b_egm2008.{{window_begin}}.nc4'
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simulated variables: [absoluteDynamicTopography]
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obs operator:
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name: ADT
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obs error:
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covariance model: diagonal
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obs filters:
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- filter: Domain Check
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where:
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- variable: {name: GeoVaLs/sea_area_fraction}
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minvalue: 0.9
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- filter: Domain Check
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where:
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- variable: { name: GeoVaLs/sea_surface_temperature}
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minvalue: 15.0
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- filter: Background Check
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absolute threshold: 0.2
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- filter: Domain Check
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where:
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- variable: {name: GeoVaLs/sea_floor_depth_below_sea_surface}
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minvalue: 500
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# - filter: Perform Action
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# action:
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# name: assign error
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# error function:
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# name: ObsFunction/LinearCombination
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# options:
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# variables: [mesoscale_representation_error@GeoVaLs,
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# absolute_dynamic_topography@ObsError]
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# coefs: [0.1,
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# 0.5]
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- filter: BlackList
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where:
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- variable:
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name: MetaData/latitude
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minvalue: -65
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maxvalue: -30
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- variable:
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name: MetaData/longitude
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minvalue: -125
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maxvalue: -90
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- filter: BlackList
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where:
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- variable:
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name: MetaData/latitude
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minvalue: -65
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maxvalue: -30
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- variable:
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name: MetaData/longitude
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minvalue: 60
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maxvalue: 110
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# - filter: Domain Check
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# where:
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# - variable: { name: GeoVaLs/sea_ice_area_fraction}
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# maxvalue: 0.00001
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- filter: Domain Check
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where:
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- variable: {name: GeoVaLs/distance_from_coast}
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minvalue: 100e3

‎src/swell/configuration/jedi/interfaces/geos_ocean/observations/adt_c2_egm2008.yaml

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obs space:
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name: adt_c2_egm2008
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obsdatain:
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engine:
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type: H5File
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obsfile: '{{cycle_dir}}/adt_c2_egm2008.{{window_begin}}.nc4'
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obsdataout:
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engine:
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type: H5File
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obsfile: '{{cycle_dir}}/{{experiment_id}}.adt_c2_egm2008.{{window_begin}}.nc4'
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simulated variables: [absoluteDynamicTopography]
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obs operator:
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name: ADT
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obs error:
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covariance model: diagonal
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obs filters:
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- filter: Domain Check
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where:
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- variable: {name: GeoVaLs/sea_area_fraction}
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minvalue: 0.9
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- filter: Domain Check
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where:
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- variable: { name: GeoVaLs/sea_surface_temperature}
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minvalue: 15.0
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- filter: Background Check
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absolute threshold: 0.2
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- filter: Domain Check
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where:
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- variable: {name: GeoVaLs/sea_floor_depth_below_sea_surface}
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minvalue: 500
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# - filter: Perform Action
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# action:
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# name: assign error
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# error function:
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# name: ObsFunction/LinearCombination
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# options:
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# variables: [mesoscale_representation_error@GeoVaLs,
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# absolute_dynamic_topography@ObsError]
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# coefs: [0.1,
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# 0.5]
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- filter: BlackList
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where:
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- variable:
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name: MetaData/latitude
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minvalue: -65
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maxvalue: -30
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- variable:
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name: MetaData/longitude
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minvalue: -125
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maxvalue: -90
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- filter: BlackList
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where:
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- variable:
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name: MetaData/latitude
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minvalue: -65
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maxvalue: -30
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- variable:
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name: MetaData/longitude
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minvalue: 60
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maxvalue: 110
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# - filter: Domain Check
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# where:
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# - variable: { name: GeoVaLs/sea_ice_area_fraction}
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# maxvalue: 0.00001

‎src/swell/configuration/jedi/interfaces/geos_ocean/observations/adt_coperl4.yaml

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obs space:
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name: adt_coperl4
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obsdatain:
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engine:
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type: H5File
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obsfile: '{{cycle_dir}}/adt_coperl4.{{window_begin}}.nc4'
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obsdataout:
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engine:
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type: H5File
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obsfile: '{{cycle_dir}}/{{experiment_id}}.adt_coperl4.{{window_begin}}.nc4'
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simulated variables: [absoluteDynamicTopography]
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obs operator:
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name: ADT
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obs error:
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covariance model: diagonal
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obs filters:
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# - filter: Domain Check
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# where:
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# - variable: {name: GeoVaLs/sea_area_fraction}
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# minvalue: 0.9
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# Reject obs where ocean fraction is < 90%
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- filter: Domain Check
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action:
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name: reject
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where:
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- variable: {name: GeoVaLs/sea_area_fraction}
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minvalue: 0.9
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# Passivate obs where ocean fraction is > 90%
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- filter: Domain Check
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action:
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name: passivate
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where:
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- variable: {name: GeoVaLs/sea_area_fraction}
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maxvalue: 0.9
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# Reject obs outside of [-4.0m,4.0m]
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- filter: Bounds Check
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action:
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name: reject
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minvalue: -4.0
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maxvalue: 4.0
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- filter: Domain Check
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where:
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- variable: {name: GeoVaLs/distance_from_coast}
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minvalue: 100e3

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