Stage atmospheric backgrounds and UFS cubed-sphere history files (#19)

This PR changes the G-W so that backgrounds for the atmospheric analyses are staged as UFS cubed-sphere history files rather than FMS restarts. The motivation being that FMS restarts include many data we don't need for the analyses and thus take up too much disk space/bandwidth. This is a companion PR to Global Workflow [#2791](NOAA-EMC/global-workflow#2792) and GDASApp [#1236](NOAA-EMC/GDASApp#1236).
NOAA-EMC · Aug 6, 2024 · c340ad9 · c340ad9
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diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -1,6 +1,6 @@
 variable change:
   variable change name: Model2GeoVaLs
-  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,phis]
+  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height]
   output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz]
 jedi increment variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 fv3 increment variables: *fv3incrvars
@@ -15,7 +15,7 @@ background geometry:
   npx: {{ atmosphere_npx_ges }}
   npy: {{ atmosphere_npy_ges }}
   npz: {{ atmosphere_npz_ges }}
-  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
 jedi increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
@@ -27,7 +27,7 @@ jedi increment geometry:
   npx: {{ atmosphere_npx_ges }}
   npy: {{ atmosphere_npy_ges }}
   npz: {{ atmosphere_npz_ges }}
-  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
 fv3 increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
@@ -44,14 +44,12 @@ members from template:
   template:
     background input:
       datapath: ./bkg/mem%mem%
-      filetype: fms restart
+      filetype: cube sphere history
+      provider: ufs
+      ufs soil nlev: 4
+      ufs fields split by level: [smc,stc]
+      filenames: [ {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_atmf006.nc, {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_sfcf006.nc ]
       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
     jedi increment input:
       filetype: cube sphere history

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -1,6 +1,6 @@
 variable change:
   variable change name: Model2GeoVaLs
-  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,phis]
+  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height]
   output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz]
 jedi increment variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 fv3 increment variables: *fv3incrvars
@@ -15,7 +15,7 @@ background geometry:
   npx: {{ atmosphere_npx_ges }}
   npy: {{ atmosphere_npy_ges }}
   npz: {{ atmosphere_npz_ges }}
-  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
 jedi increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
@@ -43,14 +43,12 @@ fv3 increment geometry:
 members:
 - background input:
     datapath: ./bkg
-    filetype: fms restart
+    filetype: cube sphere history
+    provider: ufs
+    ufs soil nlev: 4
+    ufs fields split by level: [smc,stc]
     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"
+    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

diff --git a/model/atmosphere/atmosphere_3dvar_outer_loop_1.yaml.j2 b/model/atmosphere/atmosphere_3dvar_outer_loop_1.yaml.j2
@@ -12,6 +12,6 @@
     npx: {{atmosphere_npx_anl}}
     npy: {{atmosphere_npy_anl}}
     npz: {{atmosphere_npz_anl}}
-    field metadata override: {{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml
+    field metadata override: {{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_history.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
@@ -12,6 +12,6 @@
     npx: {{atmosphere_npx_anl}}
     npy: {{atmosphere_npy_anl}}
     npz: {{atmosphere_npz_anl}}
-    field metadata override: {{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml
+    field metadata override: {{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_history.yaml
   diagnostics:
     departures: bkgmob1
diff --git a/model/atmosphere/atmosphere_background.yaml.j2 b/model/atmosphere/atmosphere_background.yaml.j2
@@ -1,12 +1,10 @@
-datapath: {{ atmosphere_background_path}}
-filetype: fms restart
+datapath: {{ atmosphere_background_path }}
+filetype: cube sphere history
+provider: ufs
+ufs soil nlev: 4
+ufs fields split by level: [smc,stc]
 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: [ua,va,t,delp,ps,sphum,ice_wat,liq_wat,o3mr,phis,
-                  slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,
+filenames: [ {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_atmf006.nc, {{ atmosphere_variational_history_prefix }}cubed_sphere_grid_sfcf006.nc ]
+state variables: [ua,va,t,delp,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height,
+                  slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdphMeters,
                   u_srf,v_srf,f10m]
diff --git a/model/atmosphere/atmosphere_background_ensemble.yaml.j2 b/model/atmosphere/atmosphere_background_ensemble.yaml.j2
@@ -2,17 +2,16 @@ datetime: '{{ atmosphere_background_time_iso }}'
 members from template:
   template:
     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,
+    filetype: cube sphere history
+    provider: ufs
+    ufs soil nlev: 4
+    ufs fields split by level: [smc,stc]
+    state variables: [ua,va,t,delz,delp,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height,
+                     slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdphMeters,
                      u_srf,v_srf,f10m]
-    datapath: {{ atmosphere_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"
+    filenames: [ {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_atmf006.nc, {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_sfcf006.nc ]
   pattern: "{{ atmosphere_ensemble_pattern | default("%mem%", true) }}"
   nmembers: {{ atmosphere_number_ensemble_members }}
   zero padding: 3
diff --git a/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2 b/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2
@@ -32,15 +32,12 @@ components:
     members from template:
       template:
         datetime: "{{ atmosphere_background_time_iso }}"
-        filetype: fms restart
+        filetype: cube sphere history
+        provider: ufs
         state variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
-        datapath: {{ atmosphere_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"
+        filenames: [ {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_atmf006.nc, {{ atmosphere_ensemble_history_prefix }}cubed_sphere_grid_sfcf006.nc ]
       pattern: "{{ atmosphere_ensemble_pattern | default("%mem%", true) }}"
       nmembers: {{atmosphere_number_ensemble_members}}
       zero padding: 3

diff --git a/model/atmosphere/atmosphere_geometry_background.yaml.j2 b/model/atmosphere/atmosphere_geometry_background.yaml.j2
@@ -8,4 +8,4 @@ layout:
 npx: {{atmosphere_npx_ges}}
 npy: {{atmosphere_npy_ges}}
 npz: {{atmosphere_npz_ges}}
-field metadata override: "{{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml"
+field metadata override: "{{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_history.yaml"