Add JEDI-based analysis calculation

algorithm/atmosphere/fv3jedi_analcalc.yaml.j2

@@ -0,0 +1,73 @@
+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
+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
+full resolution 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_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+ensemble resolution 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_restart.yaml
+additions from template: 
+  pattern: '%hr%'
+  forecast hours: ['06']
+  template:
+    background:
+      datetime: "{{ atmosphere_background_time_iso }}"
+      filetype: cube sphere history
+      datapath: ./analcalc_%hr%
+      filename: ges.%hr%.nc
+      provider: ufs
+      state variables: [liq_wat,delz,delp,w,graupel,surface_geopotential_height,
+                        ice_wat,ice_nc,rain_nc,o3mr,rainwat,snowwat,sphum,t,ua,va]
+    increment:
+      filetype: fms restart
+      is restart: false
+      filename_nonrestart: ./analcalc_%hr%/siginc.%hr%.nc
+      added variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
+    full resolution analysis:
+      filetype: auxgrid
+      gridtype: gaussian
+      filename: ./analcalc_%hr%/anl.%hr%.
+    ensemble resolution analysis:
+      filetype: auxgrid
+      gridtype: gaussian
+      filename: ./analcalc_%hr%/anl.ensres.%hr%.

algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2

@@ -53,7 +53,7 @@ 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
+      filename: ./anl/mem%mem%/cubed_sphere_grid_atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
       provider: ufs
     fv3 increment output:
       filetype: auxgrid

algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2

@@ -24,10 +24,10 @@ jedi increment geometry:
   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
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
 fv3 increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
@@ -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:
@@ -51,10 +51,11 @@ members:
     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
+    filetype: fms restart
+    is restart: false
+    filename is datetime templated: true
+    filename_nonrestart: ./anl/cubed_sphere_grid_atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
   fv3 increment output:
-    filetype: auxgrid
-    gridtype: gaussian
-    filename: ./anl/atminc.
+    filetype: fms restart
+    is restart: false
+    filename_nonrestart: ./anl/cubed_sphere_grid_atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4

model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2

@@ -1,9 +1,9 @@
 output:
   state component:
     filetype: cube sphere history
-    filename: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+    filename: ./anl/cubed_sphere_grid_atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
     provider: ufs
-    fields to write: [ugrd,vgrd,tmp,pressfc,spfh,icmr,clwmr,o3mr]
+    fields to write: {{atmosphere_analysis_variables}}
 geometry:
   fms initialization:
     namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"

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.%yyyy%mm%dd.%hh%MM%ssz.nc4
+    fields to write: {{atmosphere_analysis_variables}}
+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.%yyyy%mm%dd.%hh%MM%ssz.nc4

model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2

@@ -0,0 +1,3 @@
+filetype: fms restart
+is restart: false
+filename_nonrestart: ./anl/mem%{member}%/cubed_sphere_grid_atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4