Add workflow and tasks for performing 3DVar (tested with SOCA) (#152)

* Add shell for the new tasks (#133)

* add shell for all the new tasaks

* rename b clim task

* update registry

Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>

* Feature/3dvar generateb (#136)

* fetch bump or execution with seg fault

* Feature/3dvar standalone godas (#138)

* Add the basis for running standalone 3DVar

* add bclim to flow

* changes in executable

* 3dvar is executing now, seg fault is fixed

* hofx fix

* changes in eva

* GODAS observations and golden period

* SPECIAL case in executable and modifications for 3dvar EVA

* changes in flow

* changes in flow and codestyle fixes

* trailing spaces

Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>

* write logs in the executable tasks

* update YAML files to ioda v3

* Feature/3dvar bump eva (#140)

* Add the basis for running standalone 3DVar

* add bclim to flow

* changes in executable

* 3dvar is executing now, seg fault is fixed

* hofx fix

* changes in eva

* GODAS observations and golden period

* SPECIAL case in executable and modifications for 3dvar EVA

* changes in flow

* changes in flow and codestyle fixes

* trailing spaces

* bump SABER update works

* ioda_v3 changes

* changes in eva

* yaml fixes

* yaml fixes

---------

Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>

* refactor eva to allow plotting jedi log things

* fixes to workflow files

* add new task for generating static b by linking (#147)

* add new task for generating static b by linking.

* remove prints

* correct py norms

* yaml norms

---------

Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>

* Feature/3dvar lowres (#151)

* fixing workflow

* linking changes

* lowres works

* hofx working

* 3dvar workflow running

* DA recommended changes

---------

Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>
Co-authored-by: Doruk Ardağ <38666458+Dooruk@users.noreply.github.com>

Author: danholdaway

src/swell/__init__.py

@@ -9,4 +9,4 @@
 repo_directory = os.path.dirname(__file__)
 
 # Set the version for swell
-__version__ = '1.1.3'
+__version__ = '1.2.0'

src/swell/configuration/jedi/interfaces/geos_atmosphere/model/stage.yaml

@@ -1,5 +1,5 @@
 - link_files:
     directories:
-      - ['{{swell_static_files}}/jedi/fv3-jedi/geos_atmosphere/GEOS_CRTM_Surface/geos.crtmsrf.{{horizontal_resolution}}.nc4', '{{experiment_dir}}/stage/fv3-jedi/geos_atmosphere/bkg/']
+      - ['{{swell_static_files}}/jedi/interfaces/geos_atmosphere/GEOS_CRTM_Surface/geos.crtmsrf.{{horizontal_resolution}}.nc4', '{{experiment_dir}}/stage/fv3-jedi/geos_atmosphere/bkg/']
       - ['{{experiment_dir}}/jedi_bundle/source/fv3-jedi/test/Data/fieldmetadata/*', '{{experiment_dir}}/stage/fv3-jedi/geos_atmosphere/fieldmetadata/']
       - ['{{experiment_dir}}/jedi_bundle/source/fv3-jedi/test/Data/fv3files/*', '{{experiment_dir}}/stage/fv3-jedi/geos_atmosphere/fv3files/']

src/swell/configuration/jedi/interfaces/geos_ocean/geos_ocean.yaml

@@ -3,3 +3,4 @@ executables:
   hofx3d: soca_hofx3d.x
   hofx: soca_hofx.x
   var: soca_var.x
+  bump: soca_staticbinit.x

src/swell/configuration/jedi/interfaces/geos_ocean/model/analysis.yaml

@@ -0,0 +1,3 @@
+datadir: ./
+exp: {{experiment_id}}
+type: an

src/swell/configuration/jedi/interfaces/geos_ocean/model/background.yaml

@@ -1,5 +1,5 @@
 date: '{{local_background_time_iso}}'
 read_from_file: 1
-basename: '{{cycle_dir}}/'
+basename: './'
 ocn_filename: 'MOM6.res.{{local_background_time}}.nc'
-state variables: [socn, tocn, ssh, hocn, uocn, vocn]
+state variables: [socn, tocn, ssh, hocn, mld, layer_depth]

src/swell/configuration/jedi/interfaces/geos_ocean/model/background_error.yaml

@@ -0,0 +1,44 @@
+covariance model: 'SocaError'
+analysis variables: {{analysis_variables}}
+date: '{{local_background_time_iso}}'
+bump:
+  io:
+    data directory: '{{cycle_dir}}/background_error_model/'
+  drivers:
+    multivariate strategy: 'univariate'
+    read local nicas: true
+
+correlation:
+- name: 'ocn'
+  variables: {{analysis_variables}}
+
+linear variable change:
+  input variables: {{analysis_variables}}
+  output variables: {{analysis_variables}}
+  linear variable changes:
+  - linear variable change name: BkgErrFILT
+    ocean_depth_min: 1000 # [m]
+    rescale_bkgerr: 1.0
+    efold_z: 2500.0       # [m]
+
+  - linear variable change name: BkgErrGODAS
+    sst_bgerr_file: '{{cycle_dir}}/soca/godas_sst_bgerr.nc'
+    t_min: 0.1
+    t_max: 2.0
+    t_dz:  20.0
+    t_efold: 500.0
+    s_min: 0.0
+    s_max: 0.25
+    ssh_min: 0.0   # value at EQ
+    ssh_max: 0.1   # value in Extratropics
+    ssh_phi_ex: 20 # lat of transition from extratropics
+    cicen_min: 0.1
+    cicen_max: 0.5
+    hicen_min: 10.0
+    hicen_max: 100.0
+
+  - linear variable change name: VertConvSOCA
+    Lz_min: 2.0
+    Lz_mld: 1
+    Lz_mld_max: 500.0
+    scale_layer_thick: 1.5

src/swell/configuration/jedi/interfaces/geos_ocean/model/background_error_init.yaml

@@ -0,0 +1,19 @@
+covariance model: 'SocaError'
+analysis variables: {{analysis_variables}}
+date: '{{local_background_time_iso}}'
+bump:
+  io:
+    data directory: '{{cycle_dir}}/background_error_model'
+  drivers:
+    multivariate strategy: 'univariate'
+    compute nicas: true
+    write local nicas: true
+  model:
+    do not cross mask boundaries: true
+  nicas:
+    resolution: 6.0
+correlation:
+- name: 'ocn'
+  base value: 840336.134453782
+  rossby mult: 0.280112045
+  variables: {{analysis_variables}}

src/swell/configuration/jedi/interfaces/geos_ocean/model/geometry.yaml

@@ -1,3 +1,3 @@
-mom6_input_nml: '{{experiment_dir}}/stage/soca/geos_ocean/socafiles/input.nml'
-fields metadata: '{{experiment_dir}}/stage/soca/geos_ocean/fieldmetadata/fields_metadata.yaml'
-geom_grid_file: '{{experiment_dir}}/stage/soca/geos_ocean/gridfiles/soca_gridspec.nc'
+mom6_input_nml: 'soca/input.nml'
+fields metadata: 'soca/fields_metadata.yaml'
+geom_grid_file: 'INPUT/soca_gridspec.nc'

src/swell/configuration/jedi/interfaces/geos_ocean/model/geometry_inner.yaml

@@ -0,0 +1,3 @@
+mom6_input_nml: 'soca/input.nml'
+fields metadata: 'soca/fields_metadata.yaml'
+geom_grid_file: 'INPUT/soca_gridspec.nc'