Merge branch 'develop' into feature/update_soil

algorithm/marine/soca_diagb.yaml.j2

@@ -39,7 +39,7 @@ number of halo points: 4
 number of neighbors: 16
 
 simple smoothing:
-  horizontal iterations: 10
+  horizontal iterations: 100
   vertical iterations: 1
 
 # TODO(G): Too slow for the below scale

algorithm/marine/soca_parameters_diffusion_hz.yaml.j2

@@ -18,7 +18,7 @@ background error:
     calibration:
       normalization:
         method: randomization
-        iterations: 10000
+        iterations: 1000
 
       groups:
       - horizontal:

algorithm/marine/soca_setcorscales.yaml.j2

@@ -9,8 +9,8 @@ corr variables: [sea_surface_height_above_geoid]
 scales:
   vert layers: 5 # in units of layer
   sea_surface_height_above_geoid:
-    rossby mult: 1.00
-    min grid mult: 2.0
+    rossby mult: 2.00
+    min grid mult: 6.0
 
 rh output:
   datadir: ./

algorithm/marine/socaincr2mom6.yaml.j2

@@ -6,7 +6,16 @@ date: '{{ marine_window_begin }}'
 
 layers variable: [sea_water_cell_thickness]
 
-increment variables: [sea_water_potential_temperature, sea_water_salinity, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
+increment variables:
+- sea_water_potential_temperature
+- sea_water_salinity
+#- eastward_sea_water_velocity
+#- northward_sea_water_velocity
+- sea_surface_height_above_geoid  # Not used in MOM6 iau
+
+set increment variables to zero:
+- eastward_sea_water_velocity
+- northward_sea_water_velocity
 
 vertical geometry:
   date: '{{ marine_window_begin }}'

algorithm/obstats/aero/viirs_n20_template.yaml.j2

@@ -0,0 +1,50 @@
+- obs space:
+    name: aod
+    obsdatain:
+      engine:
+        type: H5File
+        obsfile: {{ aero_obsdatain_path }}/diag_{{ obspace }}_{{ stat_current_cycle_YMDH }}.nc4
+    simulated variables: {{ aero_obsdatatin_simulated_variables }}
+    observed variables: {{ aero_obsdatain_observed_variables }}
+  variables: {{ aero_variables }}
+  groups to process: {{ aero_file_groups }}
+  qc groups: {{ aero_file_qc_groups }}
+  statistics to compute: ['mean', 'count', 'RMS']
+  output file: "{{ obspace }}_{{ stat_current_cycle_YMDH }}_output_aod.nc"
+  domains to process:
+  - domain:
+      name: "nowhere"
+      first mask variable: latitude
+      first mask range: [-180,-100]
+  - domain:
+      name: "SH"
+      first mask variable: latitude
+      first mask range: [-90,0]
+  - domain:
+      name: "NH"
+      first mask variable: latitude
+      first mask range: [0,90]
+  - domain:
+      name: "CONUS"
+      first mask variable: latitude
+      first mask range: [25,49]
+      second mask variable: longitude
+      second mask range: [-125,-66]
+  - domain:
+      name: "Europe"
+      first mask variable: latitude
+      first mask range: [35,70]
+      second mask variable: longitude
+      second mask range: [-11,38]
+  - domain:
+      name: "Africa"
+      first mask variable: latitude
+      first mask range: [-35,37]
+      second mask variable: longitude
+      second mask range: [-17,52]
+  - domain:
+      name: "Asia"
+      first mask variable: latitude
+      first mask range: [0,70]
+      second mask variable: longitude
+      second mask range: [38, 180]

algorithm/obstats/aero/viirs_npp_template.yaml.j2

@@ -0,0 +1,50 @@
+- obs space:
+    name: aod
+    obsdatain:
+      engine:
+        type: H5File
+        obsfile: {{ aero_obsdatain_path }}/diag_{{ obspace }}_{{ stat_current_cycle_YMDH }}.nc4
+    simulated variables: {{ aero_obsdatatin_simulated_variables }}
+    observed variables: {{ aero_obsdatain_observed_variables }}
+  variables: {{ aero_variables }}
+  groups to process: {{ aero_file_groups }}
+  qc groups: {{ aero_file_qc_groups }}
+  statistics to compute: ['mean', 'count', 'RMS']
+  output file: "{{ obspace }}_{{ stat_current_cycle_YMDH }}_output_aod.nc"
+  domains to process:
+  - domain:
+      name: "nowhere"
+      first mask variable: latitude
+      first mask range: [-180,-100]
+  - domain:
+      name: "SH"
+      first mask variable: latitude
+      first mask range: [-90,0]
+  - domain:
+      name: "NH"
+      first mask variable: latitude
+      first mask range: [0,90]
+  - domain:
+      name: "CONUS"
+      first mask variable: latitude
+      first mask range: [25,49]
+      second mask variable: longitude
+      second mask range: [-125,-66]
+  - domain:
+      name: "Europe"
+      first mask variable: latitude
+      first mask range: [35,70]
+      second mask variable: longitude
+      second mask range: [-11,38]
+  - domain:
+      name: "Africa"
+      first mask variable: latitude
+      first mask range: [-35,37]
+      second mask variable: longitude
+      second mask range: [-17,52]
+  - domain:
+      name: "Asia"
+      first mask variable: latitude
+      first mask range: [0,70]
+      second mask variable: longitude
+      second mask range: [38, 180]  

algorithm/snow/fv3jedi_snow_ensmean.yaml.j2

@@ -0,0 +1,26 @@
+geometry:
+{% filter indent(width=2) %}
+{% set geometry_background_file = geometry_background_file|default(model_component ~ 'geometry_background', true) ~ '.yaml.j2' %}
+{% include geometry_background_file %}
+{% endfilter %}
+mean output:
+  filetype: fms restart
+  datapath: ./bkg/ensmean
+  filename_core: fv_core.res.nc
+  filename_trcr: fv_tracer.res.nc
+  filename_sfcd: sfc_data.nc
+  filename_sfcw: fv_srf_wnd.res.nc
+  filename_cplr: coupler.res
+ensemble:
+  members from template:
+    template:
+      datetime: '{{ snow_background_time_iso }}'
+      filetype: fms restart
+      state variables: [snodl,vtype,slmsk,orog_filt,stc,sheleg]
+      datapath: ./bkg/mem%mem%/
+      filename_sfcd: '{{ snow_background_time_fv3 }}.sfc_data.nc'
+      filename_cplr: '{{ snow_background_time_fv3 }}.coupler.res'
+      filename_orog: '{{ snow_orog_prefix }}_oro_data.nc'
+    pattern: '%mem%'
+    nmembers: {{ snow_number_ensemble_members }}
+    zero padding: 3

algorithm/snow/snow_obs_staging.yaml.j2

@@ -0,0 +1,16 @@
+mkdir:
+    - '{{snow_obsdatain_path}}'
+copy:
+    {% for observation_from_jcb in observations %}
+      {% if use_observer(observation_from_jcb) %}
+        {% if not observation_from_jcb == 'ims_snow' %}
+        # skip if ims_snow since it is special
+          {% if observation_from_jcb == 'snocvr_snow' %}
+          # snocvr_snow is a .nc file, TODO rename this eventually?
+    - ['{{snow_obsdataroot_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}.nc4', '{{snow_obsdatain_path}}']
+          {% else %}
+    - ['{{snow_obsdataroot_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}{{snow_obsdatain_suffix}}', '{{snow_obsdatain_path}}']
+          {% endif %}
+        {% endif %}
+      {% endif %}
+    {% endfor %}

model/aero/aero_final_increment_cubed_sphere.yaml.j2

@@ -6,9 +6,9 @@ geometry:
   layout:
   - {{aero_layout_x}}
   - {{aero_layout_y}}
-  npx: {{aero_npx_anl}}
-  npy: {{aero_npy_anl}}
-  npz: {{aero_npz_anl}}
+  npx: {{aero_npx_ges}}
+  npy: {{aero_npy_ges}}
+  npz: {{aero_npz_ges}}
   field metadata override: "{{aero_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml"
 output:
   state component:

model/marine/marine_background.yaml.j2

@@ -3,4 +3,18 @@ basename: {{ marine_background_path}}
 ocn_filename: MOM.res.nc
 ice_filename: cice.res.nc
 date: "{{ marine_background_time }}"
-state variables: [sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, sea_water_salinity, sea_water_potential_temperature, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid, sea_water_cell_thickness, ocean_mixed_layer_thickness, sea_water_depth]
+state variables:
+- sea_ice_area_fraction
+- sea_ice_thickness
+- sea_ice_snow_thickness
+- snow_ice_surface_temperature
+- air_temperature
+- bulk_ice_salinity
+- sea_water_salinity
+- sea_water_potential_temperature
+#- eastward_sea_water_velocity
+#- northward_sea_water_velocity
+- sea_surface_height_above_geoid
+- sea_water_cell_thickness
+- ocean_mixed_layer_thickness
+- sea_water_depth

model/marine/marine_background_error_hybrid_diffusion_diffusion.yaml.j2

@@ -6,15 +6,22 @@ components:
       saber block name: diffusion
       read:
         groups:
-        - variables: [tocn, socn, ssh]
+        - variables:
+          - sea_water_potential_temperature
+          - sea_water_salinity
+          - sea_surface_height_above_geoid
+          - sea_ice_area_fraction
           horizontal:
             filepath: ./staticb/hz_ocean
           vertical:
             levels: {{marine_vt_levels}}
             filepath: ./staticb/vt_ocean
-        - variables: [cicen]
-          horizontal:
-            filepath: ./staticb/hz_ice
+    # TODO(G): OK to not use what's below but it will need
+    #          to be fixed when we add ice thickness and
+    #          snow depth
+    #    - variables: [sea_ice_area_fraction]
+    #      horizontal:
+    #        filepath: ./staticb/hz_ice
 
     saber outer blocks:
     - saber block name: StdDev
@@ -25,10 +32,25 @@ components:
           ocn_filename: 'ocn.bkgerr_stddev.nc'
           ice_filename: 'ice.bkgerr_stddev.nc'
           read_from_file: 3
-
     linear variable change:
-      input variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
-      output variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
+      input variables:
+      - sea_ice_area_fraction
+      - sea_ice_thickness
+      - sea_ice_snow_thickness
+      - sea_water_salinity
+      - sea_water_potential_temperature
+      #- eastward_sea_water_velocity
+      #- northward_sea_water_velocity
+      - sea_surface_height_above_geoid
+      output variables:
+      - sea_ice_area_fraction
+      - sea_ice_thickness
+      - sea_ice_snow_thickness
+      - sea_water_salinity
+      - sea_water_potential_temperature
+      #- eastward_sea_water_velocity
+      #- northward_sea_water_velocity
+      - sea_surface_height_above_geoid
       linear variable changes:
       - linear variable change name: BalanceSOCA
   weight:
@@ -43,7 +65,15 @@ components:
         basename: ../ensdata/
         ocn_filename: 'ocn.pert.steric.%mem%.nc'
         ice_filename: 'ens/ice.%mem%.nc'
-        state variables: [tocn, socn, ssh, uocn, vocn, cicen, hicen, hsnon]
+        state variables:
+        - sea_ice_area_fraction
+        - sea_ice_thickness
+        - sea_ice_snow_thickness
+        - sea_water_salinity
+        - sea_water_potential_temperature
+        #- eastward_sea_water_velocity
+        #- northward_sea_water_velocity
+        - sea_surface_height_above_geoid
       pattern: '%mem%'
       nmembers: '{{marine_number_ensemble_members}}'
     localization:
@@ -52,15 +82,16 @@ components:
         saber block name: diffusion
         read:
           groups:
-          - variables: [tocn, socn, ssh]
-            multivariate strategy: duplicated
+          - variables:
+            - sea_water_potential_temperature
+            - sea_water_salinity
+            - sea_surface_height_above_geoid
+            - sea_ice_area_fraction
             horizontal:
               filepath: ./staticb/hz_ocean
             vertical:
-              strategy: duplicated
-          - variables: [cicen]
-            horizontal:
-              filepath: ./staticb/hz_ice
+              levels: {{marine_vt_levels}}
+              filepath: ./staticb/vt_ocean
   weight:
     read_from_file: 3
     basename: ./

model/marine/marine_background_error_static_diffusion.yaml.j2

@@ -30,24 +30,42 @@ saber outer blocks:
       ice_filename: 'ice.bkgerr_stddev.nc'
       read_from_file: 3
 
+#- saber block name: MLBalance
+#  geometry:
+#    mom6_input_nml: mom_input.nml
+#    fields metadata: ./fields_metadata.yaml
+#  ML Balances:
+#    arctic:
+#      ffnn:
+#        inputSize: 7
+#        outputSize: 1
+#        hiddenSize: 2
+#        load model: /work/noaa/da/gvernier/ai/runs/arctic.pt
+#    antarctic:
+#      ffnn:
+#        inputSize: 7
+#        outputSize: 1
+#        hiddenSize: 2
+#        load model: /work/noaa/da/gvernier/ai/runs/antarctic.pt
+
 linear variable change:
   input variables:
   - sea_ice_area_fraction
   - sea_ice_thickness
   - sea_ice_snow_thickness
   - sea_water_salinity
   - sea_water_potential_temperature
-  - eastward_sea_water_velocity
-  - northward_sea_water_velocity
+  #- eastward_sea_water_velocity
+  #- northward_sea_water_velocity
   - sea_surface_height_above_geoid
   output variables:
   - sea_ice_area_fraction
   - sea_ice_thickness
   - sea_ice_snow_thickness
   - sea_water_salinity
   - sea_water_potential_temperature
-  - eastward_sea_water_velocity
-  - northward_sea_water_velocity
+  #- eastward_sea_water_velocity
+  #- northward_sea_water_velocity
   - sea_surface_height_above_geoid
   linear variable changes:
   - linear variable change name: BalanceSOCA

model/snow/snow_3dvar_outer_loop_1.yaml.j2

@@ -0,0 +1,25 @@
+- ninner: 50
+  gradient norm reduction: 1e-10
+  test: on
+  geometry:
+    fms initialization:
+      namelist filename: {{ snow_fv3jedi_files_path }}/fmsmpp.nml
+      field table filename: {{ snow_fv3jedi_files_path }}/field_table
+    akbk: {{ snow_fv3jedi_files_path }}/akbk.nc4
+    layout:
+    - {{ snow_layout_x }}
+    - {{ snow_layout_y }}
+    npx: {{ snow_npx_anl }}
+    npy: {{ snow_npy_anl }}
+    npz: {{ snow_npz_anl }}
+    field metadata override: {{ snow_fv3jedi_files_path }}/fv3jedi_fieldmetadata_restart.yaml
+    time invariant fields:
+      state fields:
+        datetime: '{{ snow_background_time_iso }}'
+        filetype: fms restart
+        skip coupler file: true
+        state variables: [orog_filt]
+        datapath: {{ snow_orog_files_path }}/
+        filename_orog: {{ snow_orog_prefix }}_oro_data.nc
+  diagnostics:
+    departures: bkgmob