Add 3DEnVar

3denvar/files/3denvar.yaml

@@ -0,0 +1,151 @@
+cost function:
+  cost type: 3D-Var
+  time window:
+    begin: 2021-08-01T00:00:00Z
+    length: PT24H
+  geometry: &geom
+    geom_grid_file: ./soca_gridspec.nc
+    mom6_input_nml: ./mom_input.nml
+    fields metadata: ./fields_metadata.yml
+  analysis variables: &soca_vars [socn, tocn, uocn, vocn, ssh, hocn, mld, layer_depth]
+
+  background:
+    read_from_file: 1
+    basename: ./bkg/
+    ocn_filename: ocn.bkg.2019080112.nc
+    date: &date 2021-08-01T12:00:00Z
+    state variables: [socn, tocn, uocn, vocn, ssh, hocn, mld, layer_depth]
+
+  background error:
+    covariance model: ensemble
+    _ens_file: &ens_file
+      # common parameters for each of the states listed below
+      read_from_file: 1
+      basename: ./bkg_ens/
+      #remap_filename: data_static/72x35x25/restarts/MOM.res.nc
+      state variables: *soca_vars
+      date: 2021-08-01T12:00:00Z
+    members:
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2017070112.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2017071512.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2017080112.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2017081512.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2017090112.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2018070112.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2018071512.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2018080112.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2018081512.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2018090112.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2019070112.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2019071512.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2019080112.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2019081512.nc
+    - <<: *ens_file
+      ocn_filename: ocn.bkg.2019083012.nc        
+    localization:
+      localization method: SABER
+      saber central block:
+        saber block name: BUMP_NICAS
+        read:
+          io:
+            data directory: ./
+            files prefix: nicas_loc
+          drivers:
+            multivariate strategy: duplicated
+            read local nicas: true
+
+  observations:
+    observers:
+    - obs space:
+        name: sst_avhrr_metop-b
+        obsdatain:
+          engine:
+            type: H5File
+            obsfile: ./obs/20210801/obs.sst_avhrr_metop-c.20210801T120000Z.nc4
+        obsdataout:
+          engine:
+            type: H5File
+            obsfile: ./obs_out/3denvar.sst_avhrr_metop-b.20210801T120000Z.nc4
+        simulated variables: [seaSurfaceTemperature]
+      obs operator:
+        name: Identity
+        observation alias file: ./obsop_name_map.yml
+      obs error:
+        covariance model: diagonal
+      obs filters:
+      - filter: Bounds Check
+        minvalue: -1.8
+        maxvalue: 40.0
+      - filter: Background Check
+        threshold: 4.0
+      - filter: Domain Check
+        where:
+        - variable: {name: ObsError/seaSurfaceTemperature}
+          minvalue: 0.001
+
+    - obs space:
+        name: adt_c2
+        obsdatain:
+          engine:
+            type: H5File
+            obsfile: ./obs/20210801/obs.adt_c2.20210801T120000Z.nc4
+        obsdataout:
+          engine:
+            type: H5File
+            obsfile: ./obs_out/3denvar.adt_c2.20210801T120000Z.nc4
+        simulated variables: [absoluteDynamicTopography]
+      obs operator:
+        name: ADT
+      obs error:
+        covariance model: diagonal
+      obs filters:
+      - filter: Bounds Check
+        minvalue: -2.0
+        maxvalue: 2.0
+      - filter: Domain Check
+        where:
+        - variable: {name: GeoVaLs/sea_floor_depth_below_sea_surface}
+          minvalue: 2000     
+      - filter: Background Check
+        threshold: 4.0             
+
+variational:
+  minimizer:
+    algorithm: RPCG
+  iterations:
+  - geometry: *geom
+    ninner: 20
+    gradient norm reduction: 1e-3
+    diagnostics:
+      departures: ombg
+    online diagnostics:
+      write increment: true
+      increment:
+        state component:      
+          datadir: ./
+          date: 2021-08-01T12:00:00Z
+          exp: 3denvar
+          type: incr  
+
+output:
+  datadir: ./
+  exp: 3denvar
+  type: an
+
+final:
+  diagnostics:
+    departures: oman

3denvar/files/dirac.yaml

@@ -0,0 +1,77 @@
+geometry: &geom
+  geom_grid_file: ./soca_gridspec.nc
+  mom6_input_nml: ./mom_input.nml
+  fields metadata: ./fields_metadata.yml
+
+background:
+  read_from_file: 1
+  basename: ./bkg/
+  date: &date 2022-02-15T12:00:00Z
+  ocn_filename: ocn.bkg.2019080112.nc
+
+  state variables: &soca_vars [tocn, socn, ssh, hocn, uocn, vocn, mld, layer_depth]
+
+background error:
+  covariance model: ensemble
+  _ens_file: &ens_file
+    # common parameters for each of the states listed below
+    read_from_file: 1
+    basename: ./bkg_ens/
+    #remap_filename: data_static/72x35x25/restarts/MOM.res.nc
+    state variables: *soca_vars
+    date: 2021-08-01T12:00:00Z  
+  members:
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2017070112.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2017071512.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2017080112.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2017081512.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2017090112.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2018070112.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2018071512.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2018080112.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2018081512.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2018090112.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2019070112.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2019071512.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2019080112.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2019081512.nc
+  - <<: *ens_file
+    ocn_filename: ocn.bkg.2019083012.nc        
+  localization:
+    localization method: SABER
+    saber central block:
+      saber block name: BUMP_NICAS
+      read:
+        io:
+          data directory: ./
+          files prefix: nicas_loc
+        drivers:
+          multivariate strategy: duplicated
+          read local nicas: true
+
+dirac:
+  # unit increments to use for the dirac test
+  ixdir: [131, 214, 172]  # the x coordinate
+  iydir: [151, 177, 148]  # the y coordinate
+  izdir: [  1,   1,   1 ] # the vertical level
+  ifdir: [  1,   1,   3]  # the variable (1=T, 2=S, 3=SSH, ...)
+
+output dirac:
+  datadir: ./
+  date: *date
+  exp: dirac_ens_%id%
+  type: an

3denvar/files/nicas_parameters.yaml

@@ -0,0 +1,43 @@
+geometry: &geom
+  geom_grid_file: ./soca_gridspec.nc
+  mom6_input_nml: ./mom_input.nml
+  fields metadata: ./fields_metadata.yml
+
+background:
+  read_from_file: 1
+  basename: ./bkg/
+  date: &date 2022-02-15T12:00:00Z
+  ocn_filename: ocn.bkg.2019080112.nc
+  state variables: [tocn]
+
+background error:
+  covariance model: SABER
+  saber central block:
+    saber block name: BUMP_NICAS
+    calibration:
+      io:
+        data directory: ./
+        files prefix: nicas_loc
+      drivers:
+        multivariate strategy: duplicated
+        compute nicas: true
+        write local nicas: true
+      nicas:
+        #> Check the log, and make sure this is larger than nc1max!
+        max horizontal grid size: 150000 
+        resolution: 8.0
+        explicit length-scales: true
+        horizontal length-scale:
+        - groups:
+          - common
+          value: 750e3 # meters
+        vertical length-scale:
+        # set the vertical length scale very large, (basically turning off
+        # vertical localization)
+        - groups:
+          - common
+          value: 5000 # number of levels
+      grids:
+      - model:
+          variables:
+          - tocn

3denvar/files/obsop_name_map.yml

@@ -0,0 +1,23 @@
+variable maps:
+  - name: depthBelowWaterSurface
+    alias: ocean_depth
+  - name: waterTemperature
+    alias: sea_water_temperature
+  - name: seaSurfaceTemperature
+    alias: sea_surface_temperature
+  - name: salinity
+    alias: sea_water_salinity
+  - name: seaSurfaceSalinity
+    alias: sea_surface_salinity
+  - name: seaIceFraction
+    alias: sea_ice_area_fraction
+  - name: waterSurfaceZonalVelocity
+    alias: surface_eastward_sea_water_velocity
+  - name: waterSurfaceMeridionalVelocity
+    alias: surface_northward_sea_water_velocity
+  - name: seaSurfaceChlorophyllMassConcentration
+    alias: sea_surface_chlorophyll
+  - name: oceanSurfaceBiomassContent
+    alias: sea_surface_biomass_in_p_units
+  - name: waveHeightSignificant
+    alias: sea_surface_wave_significant_height