Companion PR to NOAA-EMC/jcb/pull/7 (#15)

- Rename the atmosphere YAML files to be `atmosphere_<class>.yaml.j2` - Change all the keys associated with the atmosphere to be `{{atmosphere_<key>}}` - Add the marine YAML files. --------- Co-authored-by: danholdaway <[email protected]> Co-authored-by: RussTreadon-NOAA <[email protected]>
NOAA-EMC · Jun 20, 2024 · 41ee2a2 · 41ee2a2
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diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -10,49 +10,49 @@ background geometry:
     field table filename: ./fv3jedi/field_table
   akbk: ./fv3jedi/akbk.nc4
   layout:
-  - {{ layout_x }}
-  - {{ layout_y }}
-  npx: {{ npx_ges }}
-  npy: {{ npy_ges }}
-  npz: {{ npz_ges }}
+  - {{ atmosphere_layout_x }}
+  - {{ atmosphere_layout_y }}
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
   field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
 jedi increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
     field table filename: ./fv3jedi/field_table
   akbk: ./fv3jedi/akbk.nc4
   layout:
-  - {{ layout_x }}
-  - {{ layout_y }}
-  npx: {{ npx_ges }}
-  npy: {{ npy_ges }}
-  npz: {{ npz_ges }}
+  - {{ atmosphere_layout_x }}
+  - {{ atmosphere_layout_y }}
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
   field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
 fv3 increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
     field table filename: ./fv3jedi/field_table
   akbk: ./fv3jedi/akbk.nc4
   layout:
-  - {{ layout_x }}
-  - {{ layout_y }}
-  npx: {{ npx_ges }}
-  npy: {{ npy_ges }}
-  npz: {{ npz_ges }}
+  - {{ atmosphere_layout_x }}
+  - {{ atmosphere_layout_y }}
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
   field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
 members from template:
   template:
     background input:
       datapath: ./bkg/mem%mem%
       filetype: fms restart
-      datetime: '{{ atm_background_time_iso }}'
+      datetime: '{{ atmosphere_background_time_iso }}'
       filename is datetime templated: true
       filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
       filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
       filename_sfcd: "%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
       filename_sfcw: "%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
       filename_cplr: "%yyyy%mm%dd.%hh%MM%ss.coupler.res"
-      state variables: *bkgvars    
+      state variables: *bkgvars
     jedi increment input:
       filetype: cube sphere history
       filename: ./anl/mem%mem%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
@@ -62,5 +62,5 @@ members from template:
       gridtype: gaussian
       filename: ./anl/mem%mem%/atminc.
   pattern: '%mem%'
-  nmembers: {{ number_ensemble_members }}
+  nmembers: {{ atmosphere_number_ensemble_members }}
   zero padding: 3
diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -10,41 +10,41 @@ background geometry:
     field table filename: ./fv3jedi/field_table
   akbk: ./fv3jedi/akbk.nc4
   layout:
-  - {{ layout_x }}
-  - {{ layout_y }}
-  npx: {{ npx_ges }}
-  npy: {{ npy_ges }}
-  npz: {{ npz_ges }}
+  - {{ atmosphere_layout_x }}
+  - {{ atmosphere_layout_y }}
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
   field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
 jedi increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
     field table filename: ./fv3jedi/field_table
   akbk: ./fv3jedi/akbk.nc4
   layout:
-  - {{ layout_x }}
-  - {{ layout_y }}
-  npx: {{ npx_anl }}
-  npy: {{ npy_anl }}
-  npz: {{ npz_anl }}
+  - {{ atmosphere_layout_x }}
+  - {{ atmosphere_layout_y }}
+  npx: {{ atmosphere_npx_anl }}
+  npy: {{ atmosphere_npy_anl }}
+  npz: {{ atmosphere_npz_anl }}
   field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
 fv3 increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
     field table filename: ./fv3jedi/field_table
   akbk: ./fv3jedi/akbk.nc4
   layout:
-  - {{ layout_x }}
-  - {{ layout_y }}
-  npx: {{ npx_anl }}
-  npy: {{ npy_anl }}
-  npz: {{ npz_anl }}
+  - {{ atmosphere_layout_x }}
+  - {{ atmosphere_layout_y }}
+  npx: {{ atmosphere_npx_anl }}
+  npy: {{ atmosphere_npy_anl }}
+  npz: {{ atmosphere_npz_anl }}
   field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
 members:
 - background input:
     datapath: ./bkg
     filetype: fms restart
-    datetime: "{{ atm_background_time_iso }}"
+    datetime: "{{ atmosphere_background_time_iso }}"
     filename is datetime templated: true
     filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
     filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"

diff --git a/algorithm/marine/socaincr2mom6.yaml b/algorithm/marine/socaincr2mom6.yaml
@@ -0,0 +1,28 @@
+geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+date: '{{marine_window_begin}}'
+
+layers variable: [hocn]
+
+increment variables: [tocn, socn, uocn, vocn, ssh]
+
+vertical geometry:
+  date: '{{marine_window_begin}}'
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  read_from_file: 1
+
+soca increment:
+  date: '{{marine_window_begin}}'
+  basename: ./Data/
+  ocn_filename: 'ocn.3dvarfgat_pseudo.incr.{{ATM_WINDOW_MIDDLE}}.nc'
+  read_from_file: 1
+
+output increment:
+  datadir: ./
+  date: '{{marine_window_begin}}'
+  exp: mom6_iau
+  type: incr
+  output file: inc.nc
diff --git a/model/aero/geometry.yaml.j2 → model/aero/aero_geometry.yaml.j2 b/model/aero/geometry.yaml.j2 → model/aero/aero_geometry.yaml.j2
diff --git a/model/atmosphere/3dvar_outer_loop_1.yaml.j2 b/model/atmosphere/3dvar_outer_loop_1.yaml.j2
diff --git a/model/atmosphere/3dvar_outer_loop_2.yaml.j2 b/model/atmosphere/3dvar_outer_loop_2.yaml.j2
diff --git a/model/atmosphere/atmosphere_3dvar_outer_loop_1.yaml.j2 b/model/atmosphere/atmosphere_3dvar_outer_loop_1.yaml.j2
@@ -0,0 +1,17 @@
+- ninner: 2
+  gradient norm reduction: 1e-10
+  test: on
+  geometry:
+    fms initialization:
+      namelist filename: {{atmosphere_fv3jedi_files_path}}/fmsmpp.nml
+      field table filename: {{atmosphere_fv3jedi_files_path}}/field_table
+    akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+    layout:
+    - {{atmosphere_layout_x}}
+    - {{atmosphere_layout_y}}
+    npx: {{atmosphere_npx_anl}}
+    npy: {{atmosphere_npy_anl}}
+    npz: {{atmosphere_npz_anl}}
+    field metadata override: {{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml
+  diagnostics:
+    departures: bkgmob
diff --git a/model/atmosphere/atmosphere_3dvar_outer_loop_2.yaml.j2 b/model/atmosphere/atmosphere_3dvar_outer_loop_2.yaml.j2
@@ -0,0 +1,17 @@
+- ninner: 4
+  gradient norm reduction: 1e-10
+  test: on
+  geometry:
+    fms initialization:
+      namelist filename: {{atmosphere_fv3jedi_files_path}}/fmsmpp.nml
+      field table filename: {{atmosphere_fv3jedi_files_path}}/field_table
+    akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+    layout:
+    - {{atmosphere_layout_x}}
+    - {{atmosphere_layout_y}}
+    npx: {{atmosphere_npx_anl}}
+    npy: {{atmosphere_npy_anl}}
+    npz: {{atmosphere_npz_anl}}
+    field metadata override: {{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml
+  diagnostics:
+    departures: bkgmob1
diff --git a/model/atmosphere/background.yaml.j2 → .../atmosphere/atmosphere_background.yaml.j2 b/model/atmosphere/background.yaml.j2 → .../atmosphere/atmosphere_background.yaml.j2
@@ -1,6 +1,6 @@
-datapath: {{ background_path}}
+datapath: {{ atmosphere_background_path}}
 filetype: fms restart
-datetime: "{{ atm_background_time_iso }}"
+datetime: "{{ atmosphere_background_time_iso }}"
 filename is datetime templated: true
 filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
 filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"

diff --git a/model/atmosphere/background_ensemble.yaml.j2 → ...re/atmosphere_background_ensemble.yaml.j2 b/model/atmosphere/background_ensemble.yaml.j2 → ...re/atmosphere_background_ensemble.yaml.j2
@@ -1,18 +1,18 @@
-datetime: '{{ atm_background_time_iso }}'
+datetime: '{{ atmosphere_background_time_iso }}'
 members from template:
   template:
-    datetime: '{{ atm_background_time_iso }}'
+    datetime: '{{ atmosphere_background_time_iso }}'
     filetype: fms restart
     state variables: [ua,va,t,DZ,delp,ps,sphum,ice_wat,liq_wat,o3mr,phis,
                      slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,
                      u_srf,v_srf,f10m]
-    datapath: {{ background_ensemble_path}}
+    datapath: {{ atmosphere_background_ensemble_path}}
     filename is datetime templated: true
     filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
     filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
     filename_sfcd: "%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
     filename_sfcw: "%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
     filename_cplr: "%yyyy%mm%dd.%hh%MM%ss.coupler.res"
-  pattern: "{{ ensemble_pattern | default("%mem%", true) }}"
-  nmembers: {{ number_ensemble_members }}
+  pattern: "{{ atmosphere_ensemble_pattern | default("%mem%", true) }}"
+  nmembers: {{ atmosphere_number_ensemble_members }}
   zero padding: 3
diff --git a/...background_error_hybrid_bump_bump.yaml.j2 → ...background_error_hybrid_bump_bump.yaml.j2 b/...background_error_hybrid_bump_bump.yaml.j2 → ...background_error_hybrid_bump_bump.yaml.j2
@@ -5,12 +5,12 @@ components:
     saber blocks:
     - saber block name: BUMP_NICAS
       saber central block: true
-      input variables: &control_vars [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
-      output variables: *control_vars
-      active variables: &active_vars [psi,chi,t,ps,rh,liq_wat,o3mr]
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
       bump:
         io:
-          data directory: &staticb_dir {{bump_data_directory}}
+          data directory: {{atmosphere_bump_data_directory}}
         drivers:
           multivariate strategy: specific_univariate
           read local nicas: true
@@ -36,30 +36,30 @@ components:
           io:
             files prefix: nicas/nicas_2D_gfs
     - saber block name: StdDev
-      input variables: *control_vars
-      output variables: *control_vars
-      active variables: *active_vars
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
       file:
         filetype: fms restart
         datetime: 2021-12-22T00:00:00Z
         set datetime on read: true
         psinfile: true
-        datapath: '*staticb_dir'
+        datapath: {{atmosphere_bump_data_directory}}
         prefix: stddev/20211222.000000
         filename_core: stddev.fv_core.res.nc
         filename_trcr: stddev.fv_tracer.res.nc
         filename_sfcd: stddev.sfc_data.nc
         filename_sfcw: stddev.fv_srf_wnd.res.nc
         filename_cplr: stddev.coupler.res
     - saber block name: BUMP_VerticalBalance
-      input variables: *control_vars
-      output variables: *control_vars
-      active variables: *active_vars
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
       bump:
         general:
           universe length-scale: 2000.0e3
         io:
-          data directory: *staticb_dir
+          data directory: {{atmosphere_bump_data_directory}}
           files prefix: vbal/vbal_gfs
           overriding sampling file: vbal/vbal_2021122200_gfs_sampling
         drivers:
@@ -74,49 +74,49 @@ components:
           - balanced variable: var4
             unbalanced variable: var1
     - saber block name: BUMP_PsiChiToUV
-      input variables: *control_vars
-      output variables: &3dvars_with_rh [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
       active variables: [psi,chi,ua,va]
       bump:
         general:
           universe length-scale: 2000.0e3
         io:
-          data directory: *staticb_dir
+          data directory: {{atmosphere_bump_data_directory}}
           files prefix: psichitouv/psichitouv_gfs
         drivers:
           read local psichitouv: true
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: *3dvars_with_rh
-      output variables: &3dvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+      input variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
     value: 0.1
 - covariance:
     covariance model: ensemble
     members from template:
       template:
-        datetime: "{{ atm_background_time_iso }}"
+        datetime: "{{ atmosphere_background_time_iso }}"
         filetype: fms restart
-        state variables: *3dvars
-        datapath: {{ background_ensemble_path}}
+        state variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+        datapath: {{ atmosphere_background_ensemble_path}}
         filename is datetime templated: true
         filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
         filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
         filename_sfcd: "%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
         filename_sfcw: "%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
         filename_cplr: "%yyyy%mm%dd.%hh%MM%ss.coupler.res"
-      pattern: "{{ ensemble_pattern | default("%mem%", true) }}"
-      nmembers: {{number_ensemble_members}}
+      pattern: "{{ atmosphere_ensemble_pattern | default("%mem%", true) }}"
+      nmembers: {{atmosphere_number_ensemble_members}}
       zero padding: 3
 #    localization:
 #      localization method: SABER
 #      saber block:
 #      - saber block name: BUMP_NICAS
-#        input variables: *control_vars
-#        output variables: *control_vars
-#        active variables: *active_vars
+#        input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+#        output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+#        active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
 #        bump:
-#          datadir: *staticb_dir
+#          datadir: {{atmosphere_bump_data_directory}}
 #          verbosity: main
 #          strategy: specific_univariate
 #          method: loc