Merge branch 'develop' into feature/anlstat-workflow

algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2

@@ -73,7 +73,26 @@ variables:
   - mass_fraction_of_sea_salt003_in_air
   - mass_fraction_of_sea_salt004_in_air
 
-rescale: {{ aero_diagb_rescale_factor }}    # rescales the filtered std. dev. by "rescale"
+global rescale:
+  geometry:
+    fms initialization:
+        namelist filename: "{{aero_fv3jedi_files_path}}/fmsmpp.nml"
+        field table filename: "{{aero_fv3jedi_files_path}}/field_table"
+    akbk: "{{aero_fv3jedi_files_path}}/akbk.nc4"
+    layout:
+    - {{ aero_layout_x }}
+    - {{ aero_layout_y }}
+    npx: {{ aero_npx_clim_b }}
+    npy: {{ aero_npy_clim_b }}
+    npz: {{ aero_npz_clim_b }}
+    field metadata override: "{{aero_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml"
+  rescale stddev:
+    filetype: fms restart
+    skip coupler file: true
+    datapath: {{ aero_rescale_b_path }}
+    filename_trcr: rescale.fv_tracer.res.nc
+    filename_cplr: rescale.coupler.res
+
 number of halo points: {{ aero_diagb_n_halo }}
 number of neighbors: {{ aero_diagb_n_neighbors }}
 simple smoothing:

algorithm/aero/aero_obs_staging.yaml.j2

@@ -0,0 +1,8 @@
+mkdir:
+    - '{{aero_obsdatain_path}}'
+copy:
+    {% for observation_from_jcb in observations %}
+    {% if use_observer(observation_from_jcb) %}
+    - ['{{aero_obsdataroot_path}}/{{aero_obsdatain_prefix}}{{observation_from_jcb}}{{aero_obsdatain_suffix}}', '{{aero_obsdatain_path}}']
+    {% endif %}
+    {% endfor %}

algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2

@@ -1,6 +1,6 @@
 variable change:
   variable change name: Model2GeoVaLs
-  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height]
+  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc]
   output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
 jedi increment variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 fv3 increment variables: *fv3incrvars
@@ -64,7 +64,7 @@ members from template:
   zero padding: 3
 
 # Optionally test the application
-{% if do_testing %}
+{% if do_testing | default(false) %}
 test:
   reference filename: {{test_reference_filename}}
 {% if test_output_filename is defined %}

algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2

@@ -1,6 +1,6 @@
 variable change:
   variable change name: Model2GeoVaLs
-  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height]
+  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc]
   output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
 jedi increment variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 fv3 increment variables: *fv3incrvars
@@ -60,7 +60,7 @@ members:
     filename: ./anl/atminc.
 
 # Optionally test the application
-{% if do_testing %}
+{% if do_testing | default(false) %}
 test:
   reference filename: {{test_reference_filename}}
 {% if test_output_filename is defined %}

algorithm/marine/soca_2cice_global.yaml.j2

@@ -0,0 +1,59 @@
+input geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: fields_metadata.yaml
+
+output geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: fields_metadata.yaml
+
+variable change:
+  variable change name: Soca2Cice
+  arctic:
+    seaice edge: 0.8
+    shuffle: false
+    rescale prior:
+      rescale: true
+      min hice: 0.5
+      min hsno: 0.1
+  antarctic:
+    seaice edge: 0.9
+    shuffle: false  # seg. fault when true
+    rescale prior:
+      rescale: true
+      min hice: 0.5
+      min hsno: 0.1
+  cice background state:
+    restart: {{ ice_rst }}
+    ncat: 5
+    ice_lev: 7
+    sno_lev: 1
+  cice output:
+    restart: {{ ice_rst }}
+  output variables:
+  - sea_water_potential_temperature
+  - sea_water_salinity
+  - sea_water_cell_thickness
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
+
+states:
+- input:
+     read_from_file: 1
+     basename: ./
+     ocn_filename: {{ ocn_ana }}
+     ice_filename: {{ ice_ana }}
+     date: '{{ fcst_begin }}'
+     state variables:
+     - sea_water_potential_temperature
+     - sea_water_salinity
+     - sea_water_cell_thickness
+     - sea_ice_area_fraction
+     - sea_ice_thickness
+     - sea_ice_snow_thickness
+
+  output:
+     datadir: Data
+     exp: soca2cice
+     type: fc
+     date: '{{ fcst_begin }}'

algorithm/marine/soca_diagb.yaml.j2

@@ -18,9 +18,20 @@ background error:
   type: incr
 
 variables:
-  name: [tocn, socn, uocn, vocn, hocn, ssh, cicen, hicen, hsnon, mom6_mld]
+  name:
+  - sea_water_potential_temperature
+  - sea_water_salinity
+  - eastward_sea_water_velocity
+  - northward_sea_water_velocity
+  - sea_water_cell_thickness
+  - sea_surface_height_above_geoid
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
+  - mom6_mld
 
-rescale: 2.0    # rescales the filtered std. dev. by "rescale"
+vertical e-folding scale: 500.0
+rescale: 1.0    # rescales the filtered std. dev. by "rescale"
 min sst: 0.0    # Added to sst bkg. err.
 max ssh: 0.0    # Limits the amplitude of the unbalanced bkg err
 min depth: 500.0 # zero out the bkg. error. at less than min depth

algorithm/marine/soca_ensb.yaml.j2

@@ -5,11 +5,20 @@ geometry:
 
 date: '{{ marine_window_begin_iso }}'
 
-layers variable: [hocn]
+layers variable: [sea_water_cell_thickness]
 
-increment variables: [tocn, socn, uocn, vocn, ssh, hocn, cicen, hicen, hsnon]
+increment variables:
+- sea_water_potential_temperature
+- sea_water_salinity
+- eastward_sea_water_velocity
+- northward_sea_water_velocity
+- sea_surface_height_above_geoid
+- sea_water_cell_thickness
+- sea_ice_area_fraction
+- sea_ice_thickness
+- sea_ice_snow_thickness
 
-set increment variables to zero: [ssh]
+set increment variables to zero: [sea_surface_height_above_geoid]
 
 vertical geometry:
   date: '{{ marine_window_begin_iso }}'
@@ -81,16 +90,26 @@ linear variable change:
   - linear variable change name: BalanceSOCA
 
 trajectory:
-  state variables: [tocn, socn, uocn, vocn, ssh, hocn, layer_depth, mld, cicen, hicen, hsnon]
+  state variables:
+  - sea_water_potential_temperature
+  - sea_water_salinity
+  - eastward_sea_water_velocity
+  - northward_sea_water_velocity
+  - sea_surface_height_above_geoid
+  - sea_water_cell_thickness
+  - sea_water_depth
+  - ocean_mixed_layer_thickness
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
   date: '{{ marine_window_begin_iso }}'
   basename: ./INPUT/
   ocn_filename: MOM.res.nc
   ice_filename: cice.res.nc
   read_from_file: 1
 
 output increment:
-  # TODO: Revert this when fms can take more than 128 charactres file names
-  datadir: '{{ enspert_relpath }}/enspert/'
+  datadir: '{{ enspert_relpath }}/'
   date: '{{ marine_window_begin_iso }}'
   exp: trash
   type: incr

algorithm/marine/soca_ensweights.yaml.j2

@@ -5,8 +5,17 @@ geometry:
 date: '{{ marine_window_middle_iso }}'
 
 variables:
-  ice: [cicen, hicen, hsnon]
-  ocean: [tocn, socn, uocn, vocn, ssh]
+  ice:
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
+
+  ocean:
+  - sea_water_potential_temperature
+  - sea_water_salinity
+  - eastward_sea_water_velocity
+  - northward_sea_water_velocity
+  - sea_surface_height_above_geoid
 
 background:
   date: '{{ marine_window_begin_iso }}'

algorithm/marine/soca_parameters_diffusion_hz.yaml.j2

@@ -8,7 +8,7 @@ background:
   ocn_filename: MOM.res.nc
   ice_filename: cice.res.nc
   date: '{{ marine_window_end_iso }}'
-  state variables: [ssh]
+  state variables: [sea_surface_height_above_geoid]
 
 background error:
   covariance model: SABER
@@ -26,12 +26,15 @@ background error:
             date: '{{ marine_window_end_iso }}'
             basename: ./
             ocn_filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
-          model variable: ssh
+          model variable: sea_surface_height_above_geoid
         write:
           filepath: ./staticb/hz_ocean
 
-      - horizontal:
-          as gaussian: true
-          fixed value: 50000.0
-        write:
-          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
+#      - horizontal:
+#          as gaussian: true
+#          fixed value: 50000.0
+#        write:
+#          filepath: ./staticb/hz_ice

algorithm/marine/soca_parameters_diffusion_vt.yaml.j2

@@ -8,7 +8,7 @@ background:
   ocn_filename: MOM.res.nc
   ice_filename: cice.res.nc
   date: '{{ marine_window_middle_iso }}'
-  state variables: [tocn]
+  state variables: [sea_water_potential_temperature]
 
 background error:
   covariance model: SABER
@@ -29,6 +29,6 @@ background error:
             date: '{{ marine_window_middle_iso }}'
             basename: ./
             ocn_filename: vt_scales.nc
-          model variable: tocn
+          model variable: sea_water_potential_temperature
         write:
           filepath: ./staticb/vt_ocean

algorithm/marine/soca_setcorscales.yaml.j2

@@ -4,11 +4,11 @@ resolution:
 
 date: "0001-01-01T00:00:00Z"
 
-corr variables: [ssh]
+corr variables: [sea_surface_height_above_geoid]
 
 scales:
   vert layers: 5 # in units of layer
-  ssh:
+  sea_surface_height_above_geoid:
     rossby mult: 1.00
     min grid mult: 2.0
 

algorithm/marine/socaincr2mom6.yaml.j2

@@ -4,9 +4,9 @@ geometry:
 
 date: '{{ marine_window_begin }}'
 
-layers variable: [hocn]
+layers variable: [sea_water_cell_thickness]
 
-increment variables: [tocn, socn, uocn, vocn, ssh]
+increment variables: [sea_water_potential_temperature, sea_water_salinity, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
 
 vertical geometry:
   date: '{{ marine_window_begin }}'