JEDI-based ensemble recentering and analysis calculation and native grid increments

algorithm/aero/aero_addincrement.yaml.j2

@@ -0,0 +1,43 @@
+state geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ aero_layout_x }}
+  - {{ aero_layout_y }}
+  npx: {{ aero_npx_ges }}
+  npy: {{ aero_npy_ges }}
+  npz: {{ aero_npz_ges }}
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+increment geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ aero_layout_x }}
+  - {{ aero_layout_y }}
+  npx: {{ aero_npx_ges }}
+  npy: {{ aero_npy_ges }}
+  npz: {{ aero_npz_ges }}
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+state:
+  datetime: {{ atmosphere_background_time_iso }}
+  state variables: {{ analysis_variables }}
+  filetype: cube sphere history
+  provider: ufs
+  datapath: ./
+  filename: {{ aero_variational_history_prefix }}cubed_sphere_grid_atmf006.nc
+increment:
+  added variables: {{ analysis_variables }}
+  filetype: fms restart
+  datapath: ./
+  filename is datetime templated: true
+  filename_trcr: '%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc'
+  prefix: aeroinc
+output:
+  filetype: auxgrid
+  gridtype: gaussian
+  datapath: ./
+  filename: aeroanl.

algorithm/atmosphere/atm_addincrement.yaml.j2

@@ -0,0 +1,41 @@
+state geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ atmosphere_layout_x }}
+  - {{ atmosphere_layout_y }}
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+increment geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ 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
+state:
+  datetime: {{ atmosphere_background_time_iso }}
+  state variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
+  filetype: cube sphere history
+  provider: ufs
+  filename: {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf006.nc
+  datapath: ./
+increment:
+  added variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
+  filetype: fms restart
+  is restart: false
+  filename_nonrestart: {{ atmosphere_variational_analysis_prefix }}cubed_sphere_grid_atminc.nc
+  datapath: ./
+output:
+  filetype: auxgrid
+  gridtype: gaussian
+  filename: atmanl.

algorithm/atmosphere/fv3jedi_correction_increment.yaml.j2

@@ -0,0 +1,73 @@
+increment variables: [liq_wat,delz,delp,ice_wat,o3mr,sphum,t,ua,va]
+deterministic background geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ atmosphere_layout_x }}
+  - {{ atmosphere_layout_y }}
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+variational increment geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ 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
+ensemble mean analysis geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ 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
+correction increment geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ 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
+forecast hours:
+{% for ihour in range( atmosphere_iau_hours | length ) %}
+- datetime: {{ atmosphere_iau_times_iso[ihour] }}
+  deterministic background:
+    filetype: cube sphere history
+    provider: ufs
+    datapath: ./
+    filename: {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+  variational increment:
+    filetype: fms restart
+    is restart: false
+    datapath: ./
+    filename_nonrestart: {{ atmosphere_variational_analysis_prefix }}cubed_sphere_grid_atmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+  ensemble mean analysis:
+    filetype: cube sphere history
+    provider: ufs
+    datapath: ./
+    filename: enkf{{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_atma{{ '%03d' % atmosphere_iau_hours[ihour] }}.ensmean.nc
+  correction increment:
+    filetype: cube sphere history
+    provider: ufs
+    datapath: ./
+    filename: enkf{{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_catmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+{% endfor %}

algorithm/atmosphere/fv3jedi_ensemble_recenter.yaml.j2

@@ -0,0 +1,47 @@
+members:
+{% for imember in range(atmosphere_number_ensemble_members) %}
+{% for ihour in range( atmosphere_iau_hours | length ) %}
+- state geometry:
+    fms initialization:
+      namelist filename: ./fv3jedi/fmsmpp.nml
+      field table filename: ./fv3jedi/field_table
+    akbk: ./fv3jedi/akbk.nc4
+    layout:
+    - {{ 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
+  increment geometry:
+    fms initialization:
+      namelist filename: ./fv3jedi/fmsmpp.nml
+      field table filename: ./fv3jedi/field_table
+    akbk: ./fv3jedi/akbk.nc4
+    layout:
+    - {{ 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
+  state:
+    datetime: {{ atmosphere_iau_times_iso[ihour] }}
+    state variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
+    filetype: cube sphere history
+    provider: ufs
+    datapath: ./
+    filename: enkf{{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_catmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+  increment:
+    added variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
+    filetype: cube sphere history
+    provider: ufs
+    datapath: ./mem{{ '%0{}d'.format(3)|format(imember+1) }}
+    filename: enkf{{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_atmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+  output:
+    filetype: fms restart
+    is restart: false
+    datapath: ./mem{{ '%0{}d'.format(3)|format(imember+1) }}
+    filename_nonrestart: enkf{{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_ratmi{{ '%03d' % atmosphere_iau_hours[ihour] }}.nc
+{% endfor %}
+{% endfor %}

algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2

@@ -39,7 +39,7 @@ fv3 increment geometry:
   npx: {{ atmosphere_npx_ges }}
   npy: {{ atmosphere_npy_ges }}
   npz: {{ atmosphere_npz_ges }}
-  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
 members from template:
   template:
     background input:
@@ -53,12 +53,14 @@ members from template:
       state variables: *bkgvars
     jedi increment input:
       filetype: cube sphere history
-      filename: ./anl/mem%mem%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
       provider: ufs
+      datapath: ./anl/mem%mem%
+      filename: cubed_sphere_grid_atminc.jedi.nc
     fv3 increment output:
-      filetype: auxgrid
-      gridtype: gaussian
-      filename: ./anl/mem%mem%/atminc.
+      filetype: cube sphere history
+      provider: ufs
+      datapath: ./anl/mem%mem%
+      filename: {{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_atminc.nc
   pattern: '%mem%'
   nmembers: {{ atmosphere_number_ensemble_members }}
   zero padding: 3

algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2

@@ -24,9 +24,9 @@ jedi increment geometry:
   layout:
   - {{ atmosphere_layout_x }}
   - {{ atmosphere_layout_y }}
-  npx: {{ atmosphere_npx_anl }}
-  npy: {{ atmosphere_npy_anl }}
-  npz: {{ atmosphere_npz_anl }}
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
   field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
 fv3 increment geometry:
   fms initialization:
@@ -36,9 +36,9 @@ fv3 increment geometry:
   layout:
   - {{ atmosphere_layout_x }}
   - {{ atmosphere_layout_y }}
-  npx: {{ atmosphere_npx_anl }}
-  npy: {{ atmosphere_npy_anl }}
-  npz: {{ atmosphere_npz_anl }}
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
   field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
 members:
 - background input:
@@ -48,16 +48,20 @@ members:
     ufs soil nlev: 4
     ufs fields split by level: [smc,stc]
     datetime: "{{ atmosphere_background_time_iso }}"
-    filenames: [ {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf006.nc, {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_sfcf006.nc ]
+    filenames:
+    - {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf006.nc
+    - {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_sfcf006.nc
     state variables: *bkgvars
   jedi increment input:
     filetype: cube sphere history
-    filename: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
     provider: ufs
+    datapath: ./anl
+    filename: cubed_sphere_grid_atminc.jedi.nc
   fv3 increment output:
-    filetype: auxgrid
-    gridtype: gaussian
-    filename: ./anl/atminc.
+    filetype: fms restart
+    is restart: false
+    datapath: ./anl
+    filename_nonrestart: {{ atmosphere_variational_analysis_prefix }}cubed_sphere_grid_atminc.nc
 
 # Optionally test the application
 {% if do_testing | default(false) %}

algorithm/snow/snow_addincrement.yaml.j2

@@ -0,0 +1,43 @@
+state geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ snow_layout_x }}
+  - {{ snow_layout_y }}
+  npx: {{ snow_npx_ges }}
+  npy: {{ snow_npy_ges }}
+  npz: {{ snow_npz_ges }}
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+increment geometry:
+  fms initialization:
+    namelist filename: ./fv3jedi/fmsmpp.nml
+    field table filename: ./fv3jedi/field_table
+  akbk: ./fv3jedi/akbk.nc4
+  layout:
+  - {{ snow_layout_x }}
+  - {{ snow_layout_y }}
+  npx: {{ snow_npx_ges }}
+  npy: {{ snow_npy_ges }}
+  npz: {{ snow_npz_ges }}
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+state:
+  datetime: {{ atmosphere_background_time_iso }}
+  state variables: {{ analysis_variables }}
+  filetype: cube sphere history
+  provider: ufs
+  datapath: ./
+  filename: {{ snow_variational_history_prefix }}cubed_sphere_grid_sfcf006.nc
+increment:
+  added variables: {{ analysis_variables }}
+  filetype: fms restart
+  datapath: ./
+  filename is datetime templated: true
+  filename_sfcd: '%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc'
+  prefix: snowinc
+output:
+  filetype: auxgrid
+  gridtype: gaussian
+  datapath: ./
+  filename: snowanl.

model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2

@@ -1,7 +1,7 @@
 output:
   state component:
     filetype: cube sphere history
-    filename: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+    filename: ./anl/cubed_sphere_grid_atminc.jedi.nc
     provider: ufs
     fields to write: [ugrd,vgrd,tmp,pressfc,spfh,icmr,clwmr,o3mr]
 geometry:
@@ -12,7 +12,7 @@ geometry:
   layout:
   - {{atmosphere_layout_x}}
   - {{atmosphere_layout_y}}
-  npx: {{atmosphere_npx_anl}}
-  npy: {{atmosphere_npy_anl}}
-  npz: {{atmosphere_npz_anl}}
+  npx: {{atmosphere_npx_ges}}
+  npy: {{atmosphere_npy_ges}}
+  npz: {{atmosphere_npz_ges}}
   field metadata override: "{{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_history.yaml"

model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2

@@ -0,0 +1,18 @@
+output:
+  state component:
+    filetype: fms restart
+    is restart: false
+    filename_nonrestart: ./anl/cubed_sphere_grid_atminc.jedi.nc
+    fields to write: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+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_ges}}
+  npy: {{atmosphere_npy_ges}}
+  npz: {{atmosphere_npz_ges}}
+  field metadata override: "{{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_fv3inc.yaml"

model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2

@@ -1,3 +1,3 @@
 filetype: cube sphere history
 provider: ufs
-filename: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+filename: ./anl/mem%{member}%/cubed_sphere_grid_atminc.jedi.nc

model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2

@@ -0,0 +1,4 @@
+filetype: fms restart
+is restart: false
+datapath: ./anl/mem%{member}%
+filename_nonrestart: cubed_sphere_grid_atminc.jedi.nc

model/atmosphere/atmosphere_posterior_output_cubed_sphere.yaml.j2

@@ -0,0 +1,5 @@
+filetype: cube sphere history
+provider: ufs
+ufs soil nlev: 4
+ufs fields split by level: [smc,stc]
+filename: ./anl/{{ atmosphere_ensemble_analysis_prefix }}cubed_sphere_grid_atmanl.ensmean.nc

test/client_integration/gdas-atmosphere-templates.yaml

@@ -63,6 +63,9 @@ atmosphere_background_ensemble_path: "DATA/ens/mem%mem%"
 atmosphere_variational_history_prefix: "bkg_"
 atmosphere_ensemble_history_prefix: "ens_"
 
+atmosphere_variational_analysis_prefix: "anl_"
+atmosphere_ensemble_analysis_prefix: "anl_"
+
 atmosphere_background_time_iso: '2024-02-02T00:00:00Z'
 
 # Background error