3dvar_lowres.yml

# common filters used later on
_: &land_mask
  filter: Domain Check
  where:
  - variable: {name: GeoVaLs/sea_area_fraction}
    minvalue: 0.5

cost function:
  cost type: 3D-Var
  time window:
    begin: 2018-04-14T00:00:00Z
    length: P2D
  analysis variables: &soca_an_vars
  - sea_ice_area_fraction
  - sea_ice_thickness
  - sea_ice_snow_thickness
  - sea_water_salinity
  - sea_water_potential_temperature
  - sea_surface_height_above_geoid
  - net_downwelling_shortwave_radiation
  - upward_latent_heat_flux_in_air
  - upward_sensible_heat_flux_in_air
  - net_downwelling_longwave_radiation
  - friction_velocity_over_water

  geometry:
    geom_grid_file: data_generated/gridgen/soca_gridspec.72x35x25.nc
    mom6_input_nml: data_static/72x35x25/input.nml
    fields metadata: data_static/fields_metadata.yml

  background:
    read_from_file: 1
    basename: data_static/72x35x25/restarts/
    ocn_filename: MOM.res.nc
    ice_filename: cice.res.nc
    sfc_filename: sfc.res.nc
    date: &bkg_date 2018-04-15T00:00:00Z
    state variables:
    - sea_ice_area_fraction
    - sea_ice_thickness
    - sea_ice_snow_thickness
    - sea_water_salinity
    - sea_water_potential_temperature
    - sea_surface_height_above_geoid
    - sea_water_cell_thickness
    - net_downwelling_shortwave_radiation
    - upward_latent_heat_flux_in_air
    - upward_sensible_heat_flux_in_air
    - net_downwelling_longwave_radiation
    - friction_velocity_over_water
    - ocean_mixed_layer_thickness
    - sea_water_depth

  background error:
    covariance model: SABER
    change background resolution: true

    saber central block:
      saber block name: diffusion
      read:
        groups:
        # NOTE, the lower resolution files are used here
        - variables:
          - sea_water_potential_temperature
          - sea_water_salinity
          horizontal:
            filepath: data_generated/parameters_diffusion_lowres/hz_smaller
          vertical:
            levels: 25
            filepath: data_generated/parameters_diffusion_lowres/vt_5lvls
        - variables: [sea_surface_height_above_geoid]
          horizontal:
            filepath: data_generated/parameters_diffusion_lowres/hz_smaller

    saber outer blocks:
    - saber block name: SOCABkgErrFilt
      ocean_depth_min: 1000 # [m]
      rescale_bkgerr: 1.0
      efold_z: 2500.0       # [m]

    - saber block name: SOCAParametricOceanStdDev
      temperature:
        sst:
          filepath: data_static/godas_sst_bgerr.nc
          variable: sst_bgerr
      unbalanced salinity: {} # use default values
      unbalanced ssh: {} # use default values
      other variables:
      - variable: sea_ice_area_fraction
        min: 0.1
      - variable: sea_ice_thickness
        min: 10.0
      - variable: eastward_sea_water_velocity
        fraction of background: 0.2
      - variable: northward_sea_water_velocity
        fraction of background: 0.2
      - variable: net_downwelling_shortwave_radiation
        fraction of background: 0.1
      - variable: upward_latent_heat_flux_in_air
        fraction of background: 0.1
      - variable: upward_sensible_heat_flux_in_air
        fraction of background: 0.1
      - variable: net_downwelling_longwave_radiation
        fraction of background: 0.1
      - variable: friction_velocity_over_water
        fraction of background: 0.1

    linear variable change:
      input variables: *soca_an_vars
      output variables: *soca_an_vars
      linear variable changes:

      - linear variable change name: BalanceSOCA
        kst:
          dsdtmax: 0.1
          dsdzmin: 3.0e-6
          dtdzmin: 1.0e-6
          nlayers: 999
        ksshts:
          nlayers: 10
        # NOTE not using dcdt, because i was too lazy to convert the file to low res
        # dcdt:
        #   filename: data_static/36x17x25/dcdt.nc
        #   name: dcdt

  observations:
    observers:
    - obs space:
        name: CoolSkin
        obsdataout:
          engine:
            type: H5File
            obsfile: data_output/sst_coolskin.nc
        obsdatain:
          engine:
            type: H5File
            obsfile: data_static/obs/sst.nc
        simulated variables: [seaSurfaceTemperature]
      obs operator:
        name: CoolSkin
      obs error:
        covariance model: diagonal

    - obs space:
        name: SeaSurfaceTemp
        obsdataout:
          engine:
            type: H5File
            obsfile: data_output/sst.nc
        obsdatain:
          engine:
            type: H5File
            obsfile: data_static/obs/sst.nc
        simulated variables: [seaSurfaceTemperature]
      obs operator:
        name: Identity
        observation alias file: testinput/obsop_name_map.yml
      obs error:
        covariance model: diagonal
      obs filters:
      - *land_mask
      - filter: Thinning
        amount: 0.1
        random seed: 0

    - obs space:
        name: SeaSurfaceSalinity
        obsdataout:
          engine:
            type: H5File
            obsfile: data_output/sss.nc
        obsdatain:
          engine:
            type: H5File
            obsfile: data_static/obs/sss.nc
        simulated variables: [seaSurfaceSalinity]
      obs operator:
        name: Identity
        observation alias file: testinput/obsop_name_map.yml
      obs error:
        covariance model: diagonal
      obs filters:
      - filter: Domain Check
        where:
        - variable: {name: GeoVaLs/distance_from_coast}
          minvalue: 1500e3
      - filter: Domain Check
        where:
        - variable: {name: GeoVaLs/sea_surface_temperature}
          minvalue: 15

    - obs space:
        name: ADT
        obsdataout:
          engine:
            type: H5File
            obsfile: data_output/adt.nc
        obsdatain:
          engine:
            type: H5File
            obsfile: data_static/obs/adt.nc
        simulated variables: [absoluteDynamicTopography]
      obs operator:
        name: ADT
      obs error:
        covariance model: diagonal
      obs filters:
      - *land_mask
      - filter: Bounds Check
        minvalue: -2.0
        maxvalue: 2.0
      - filter: Perform Action
        action:
          name: assign error
          error function:
            name: ObsFunction/LinearCombination
            options:
              variables: [GeoVaLs/mesoscale_representation_error,
                          ObsError/absoluteDynamicTopography]
              coefs: [1.0,
                      1.0]

    - obs space:
        name: InsituTemperature
        obsdataout:
          engine:
            type: H5File
            obsfile: data_output/prof_T.nc
        obsdatain:
          engine:
            type: H5File
            obsfile: data_static/obs/prof.nc
        simulated variables: [waterTemperature]
      obs operator:
        name: InsituTemperature
      obs error:
        covariance model: diagonal
      obs filters:
      - *land_mask
      - filter: Background Check
        threshold: 5

    - obs space:
        name: InsituSalinity
        obsdataout:
          engine:
            type: H5File
            obsfile: data_output/prof_S.nc
        obsdatain:
          engine:
            type: H5File
            obsfile: data_static/obs/prof.nc
        simulated variables: [salinity]
      obs operator:
        name: VertInterp
        observation alias file: testinput/obsop_name_map.yml
        vertical coordinate: sea_water_depth
        observation vertical coordinate: depth
        interpolation method: linear
      obs error:
        covariance model: diagonal
      obs filters:
      - *land_mask

    - obs space:
        name: SeaIceFraction
        obsdataout:
          engine:
            type: H5File
            obsfile: data_output/icec.nc
        obsdatain:
          engine:
            type: H5File
            obsfile: data_static/obs/icec.nc
        simulated variables: [seaIceFraction]
      obs operator:
        name: Identity
        observation alias file: testinput/obsop_name_map.yml
      obs error:
        covariance model: diagonal
      obs filters:
      - *land_mask

variational:
  minimizer:
    algorithm: RPCG
  iterations:
  # NOTE, the lower resolution files are used here
  - geometry:
      geom_grid_file: data_static/36x17x25/soca_gridspec.nc
      mom6_input_nml: data_static/36x17x25/input.nml
      fields metadata: data_static/fields_metadata.yml
    ninner: 5
    gradient norm reduction: 1e-15
    test: on
    online diagnostics:
      write increment: true
      increment:
        state component:
          datadir: data_output
          date: *bkg_date
          exp: 3dvar_lowres.iter1
          type: incr

output:
  datadir: data_output
  exp: 3dvar_lowres
  type: an

test:
  reference filename: testref/3dvar_lowres.test
  test output filename: testoutput/3dvar_lowres.test
  float relative tolerance: 2e-4