Merge branch 'develop' into feature/add_marine_j2

algorithm/marine/soca_2cice_global.yaml.j2

@@ -29,10 +29,20 @@ variable change:
     sno_lev: 1
   cice output:
     restart: {{ ice_rst }}
+  increment output:
+    datadir: Data
+    exp: soca2cice
+    type: incr
+    date: '{{ fcst_begin }}'
+  soca increment:
+    read_from_file: 1
+    basename: ./
+    ocn_filename: {{ ocn_inc }}
+    ice_filename: {{ ice_inc }}
+    date: '{{ fcst_begin }}'
   output variables:
   - sea_water_potential_temperature
   - sea_water_salinity
-  - sea_water_cell_thickness
   - sea_ice_area_fraction
   - sea_ice_thickness
   - sea_ice_snow_thickness
@@ -47,7 +57,6 @@ states:
      state variables:
      - sea_water_potential_temperature
      - sea_water_salinity
-     - sea_water_cell_thickness
      - sea_ice_area_fraction
      - sea_ice_thickness
      - sea_ice_snow_thickness

algorithm/marine/soca_chgres.yaml.j2

@@ -0,0 +1,33 @@
+input geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+output geometry:
+  geom_grid_file: ./anl_geom/soca_gridspec.nc
+  mom6_input_nml: ./anl_geom/mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+states:
+- input:
+    date: '{{ marine_window_end_iso }}'
+    basename: ./bkg/
+    ocn_filename: 'ocean.bkg.f009.nc'
+    ice_filename: 'ice.bkg.f009.nc'
+    read_from_file: 1
+
+    state variables:
+    - sea_surface_height_above_geoid
+    - sea_water_potential_temperature
+    - sea_water_salinity
+    - sea_water_cell_thickness
+    - sea_water_depth
+    - mom6_mld
+    - sea_ice_area_fraction
+    - sea_ice_thickness
+    - sea_ice_snow_thickness
+
+  output:
+     datadir: anl_geom/
+     exp: f009_anl_geom
+     type: fc
+     date: '{{ marine_window_end_iso }}'

algorithm/marine/soca_diagb.yaml.j2

@@ -2,6 +2,11 @@ geometry:
   mom6_input_nml: mom_input.nml
   fields metadata: ./fields_metadata.yaml
 
+output geometry:
+  geom_grid_file: ./anl_geom/soca_gridspec.nc
+  mom6_input_nml: ./anl_geom/mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
 date: '{{ marine_window_end_iso }}'
 
 background:
@@ -31,10 +36,11 @@ variables:
   - mom6_mld
 
 vertical e-folding scale: 500.0
+min efold depth ratio: 3.0  # keep the e-folding scale at most
+                            # 1/(min efold depth ratio) of the local depth
 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
+min depth: 50.0 # zero out the bkg. error. at less than min depth
 number of halo points: 4
 number of neighbors: 16
 

algorithm/marine/soca_ensb.yaml.j2

@@ -3,6 +3,11 @@ geometry:
   mom6_input_nml: mom_input.nml
   fields metadata: ./fields_metadata.yaml
 
+output geometry:
+  geom_grid_file: ./anl_geom/soca_gridspec.nc
+  mom6_input_nml: ./anl_geom/mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
 date: '{{ marine_window_begin_iso }}'
 
 layers variable: [sea_water_cell_thickness]
@@ -113,5 +118,5 @@ output increment:
   date: '{{ marine_window_begin_iso }}'
   exp: trash
   type: incr
-  output file: 'ocn.pert.steric.%mem%.nc'
+  output file: 'pert.%mem%.nc'
   pattern: '%mem%'

algorithm/marine/soca_ensweights.yaml.j2

@@ -2,6 +2,11 @@ geometry:
   mom6_input_nml: mom_input.nml
   fields metadata: ./fields_metadata.yaml
 
+output geometry:
+  geom_grid_file: ./anl_geom/soca_gridspec.nc
+  mom6_input_nml: ./anl_geom/mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
 date: '{{ marine_window_middle_iso }}'
 
 variables:
@@ -29,15 +34,16 @@ weights:
   ice: 0.0025   #  5% of original variance
   ocean: 0.0625   # 25%      "       "
   # Apply localized weights to the ocean ens. B
-  ocean local weights:
-  - lon: -172.0
-    lat: 11.0
-    amplitude: -1.0
-    length scale: 700.0
-  - lon: -160.0
-    lat: 12.0
-    amplitude: -1.0
-    length scale: 700.0
+  # Example below was for old ens. from Xiao
+  #  ocean local weights:
+  #  - lon: -172.0
+  #    lat: 11.0
+  #    amplitude: -1.0
+  #    length scale: 700.0
+  #  - lon: -160.0
+  #    lat: 12.0
+  #    amplitude: -1.0
+  #    length scale: 700.0
 
 output:
   datadir: ./

algorithm/marine/soca_parameters_diffusion_hz.yaml.j2

@@ -1,12 +1,15 @@
+# Analysis/B-mat resolution
 geometry: &geom
-  mom6_input_nml: mom_input.nml
+  geom_grid_file: ./anl_geom/soca_gridspec.nc
+  mom6_input_nml: ./anl_geom/mom_input.nml
   fields metadata: ./fields_metadata.yaml
 
+# Background interpolated at the analysis resolution
 background:
   read_from_file: 1
-  basename: ./INPUT/
-  ocn_filename: MOM.res.nc
-  ice_filename: cice.res.nc
+  basename: ./anl_geom/
+  ocn_filename: 'ocn.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.nc'
+  ice_filename: 'ice.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.nc'
   date: '{{ marine_window_end_iso }}'
   state variables: [sea_surface_height_above_geoid]
 

algorithm/marine/soca_parameters_diffusion_vt.yaml.j2

@@ -1,13 +1,15 @@
+# Analysis/B-mat resolution
 geometry: &geom
-  mom6_input_nml: mom_input.nml
+  geom_grid_file: ./anl_geom/soca_gridspec.nc
+  mom6_input_nml: ./anl_geom/mom_input.nml
   fields metadata: ./fields_metadata.yaml
 
+# Background interpolated at the analysis resolution
 background:
   read_from_file: 1
-  basename: ./INPUT/
-  ocn_filename: MOM.res.nc
-  ice_filename: cice.res.nc
-  date: '{{ marine_window_middle_iso }}'
+  basename: ./anl_geom/
+  ocn_filename: 'ocn.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.nc'
+  date: '{{ marine_window_end_iso }}'
   state variables: [sea_water_potential_temperature]
 
 background error:

algorithm/marine/soca_setcorscales.yaml.j2

@@ -1,5 +1,6 @@
 resolution:
-  mom6_input_nml: mom_input.nml
+  geom_grid_file: ./anl_geom/soca_gridspec.nc
+  mom6_input_nml: ./anl_geom/mom_input.nml
   fields metadata: ./fields_metadata.yaml
 
 date: "0001-01-01T00:00:00Z"
@@ -9,8 +10,8 @@ corr variables: [sea_surface_height_above_geoid]
 scales:
   vert layers: 5 # in units of layer
   sea_surface_height_above_geoid:
-    rossby mult: 2.00
-    min grid mult: 6.0
+    rossby mult: 1.50
+    min grid mult: 2.0
 
 rh output:
   datadir: ./

algorithm/marine/soca_vtscales.yaml.j2

@@ -1,6 +1,6 @@
-gridspec_filename: soca_gridspec.nc
-restart_filename: ./INPUT/MOM.res.nc
-mld_filename: './staticb/ocn.bkgerr_stddev.incr.{{ marine_window_end_iso }}.nc'
+gridspec_filename: ./anl_geom/soca_gridspec.nc
+restart_filename: './anl_geom/ocn.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.nc'
+mld_filename: './anl_geom/ocn.f009_anl_geom.fc.{{ marine_window_end_iso }}.PT0S.nc'
 output_filename: ./vt_scales.nc
 output_variable_vt: Temp
 output_variable_hz: ave_ssh

algorithm/marine/socaincr2mom6.yaml.j2

@@ -6,6 +6,8 @@ date: '{{ marine_window_begin }}'
 
 layers variable: [sea_water_cell_thickness]
 
+domains: [ocn]
+
 increment variables:
 - sea_water_potential_temperature
 - sea_water_salinity

algorithm/obstats/aero/viirs_n20_template.yaml.j2

@@ -3,17 +3,17 @@
     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 }}
+        obsfile: {{ aero_obsdatain_path }}/aero/diag_{{ obspace }}_aod_{{ stat_current_cycle_YMDH }}.nc
+    simulated variables: ['aerosolOpticalDepth']
+    observed variables: ['aerosolOpticalDepth']
+  variables: ['aerosolOpticalDepth']
+  groups to process: ['ombg', 'oman']
+  qc groups: ['EffectiveQC0', 'EffectiveQC1']
   statistics to compute: ['mean', 'count', 'RMS']
   output file: "{{ obspace }}_{{ stat_current_cycle_YMDH }}_output_aod.nc"
   domains to process:
   - domain:
-      name: "nowhere"
+      name: "Global"
       first mask variable: latitude
       first mask range: [-180,-100]
   - domain:

algorithm/obstats/aero/viirs_npp_template.yaml.j2

@@ -3,17 +3,17 @@
     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 }}
+        obsfile: {{ aero_obsdatain_path }}/aero/diag_{{ obspace }}_aod_{{ stat_current_cycle_YMDH }}.nc
+    simulated variables: ['aerosolOpticalDepth']
+    observed variables: ['aerosolOpticalDepth']
+  variables: ['aerosolOpticalDepth']
+  groups to process: ['ombg', 'oman']
+  qc groups: ['EffectiveQC0', 'EffectiveQC1']
   statistics to compute: ['mean', 'count', 'RMS']
   output file: "{{ obspace }}_{{ stat_current_cycle_YMDH }}_output_aod.nc"
   domains to process:
   - domain:
-      name: "nowhere"
+      name: "Global"
       first mask variable: latitude
       first mask range: [-180,-100]
   - domain:

algorithm/obstats/snow/ims_snow_template.yaml.j2

@@ -0,0 +1,47 @@
+- obs space:
+    name: ims_snow
+    obsdatain:
+      engine:
+        type: H5File
+        obsfile: {{ snow_obsdatain_path }}/snow/diag_{{ obspace }}_{{ stat_current_cycle_YMDH }}.nc
+    simulated variables: ['totalSnowDepth']
+    observed variables: ['totalSnowDepth']
+  statistics to compute: ['mean', 'count', 'RMS']
+  output file: "{{ obspace }}_{{ stat_current_cycle_YMDH }}_output_snow.nc"
+  domains to process:
+  - domain:
+      name: "Global"
+      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/snow_obs_staging.yaml.j2

@@ -1,6 +1,6 @@
 mkdir:
     - '{{snow_obsdatain_path}}'
-copy:
+copy_opt:
     {% for observation_from_jcb in observations %}
       {% if use_observer(observation_from_jcb) %}
         {% if not observation_from_jcb == 'ims_snow' %}

model/aero/aero_final_increment_gaussian.yaml.j2

@@ -2,7 +2,7 @@ grid type: regular gaussian
 local interpolator type: atlas interpolator
 interpolation method:
   type: finite-element
-number of latitude gridpoints: {{ aero_npy_ges - 1 }}
+number of latitude gridpoints: {{ aero_npy_anl - 1 }}
 variables to output: [mass_fraction_of_sulfate_in_air,
                        mass_fraction_of_hydrophobic_black_carbon_in_air,
                        mass_fraction_of_hydrophilic_black_carbon_in_air,

model/marine/marine_3dfgat_outer_loop_1.yaml.j2

@@ -1,7 +1,8 @@
 - ninner: {{marine_ninner_1}}
   gradient norm reduction: {{marine_grad_red_1}}
   geometry:
-    mom6_input_nml: mom_input.nml
+    geom_grid_file: ./anl_geom/soca_gridspec.nc
+    mom6_input_nml: ./anl_geom/mom_input.nml
     fields metadata: {{marine_soca_files_path}}/fields_metadata.yaml
   diagnostics:
     departures: ombg