From 2833e0506f4a6795855887fbf5f8456d57be7e10 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Sun, 8 Sep 2024 17:16:46 +0000
Subject: [PATCH 01/25] Initial commit

---
 algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 | 67 ++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 algorithm/atmosphere/fv3jedi_calcanl.yaml.j2

diff --git a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
new file mode 100644
index 0000000..987b352
--- /dev/null
+++ b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
@@ -0,0 +1,67 @@
+datetime: '{{ current_cycle | to_isotime }}'
+forecast hours: ['06']
+increment variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz]
+analysis variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz,
+                     w,graupel,surface_geopotential_height,ice_nc,rain_nc,ps,rainwat,snowwat]
+geometries:
+  increment:
+    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 }}
+    field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
+  full resolution state:
+    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 }}
+    field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+  ensemble resolution state:
+    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 }}
+    field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
+io from template: 
+  pattern: '%hr%'
+  template:
+    increment:
+        filetype: cube sphere history
+        filename: ./calcanl_%hr%/siginc.nc.%hr%
+        provider: ufs
+    full resolution states:
+      background:
+        filetype: cube sphere history
+        filename: ./calcanl_%hr%/ges.%hr%
+        provider: ufs
+      analysis: 
+        filetype: auxgrid
+        gridtype: gaussian
+        filename: ./calcanl_%hr%/anl.%hr%.
+    ensemble resolution states:
+      background:
+        filetype: cube sphere history
+        filename: ./calcanl_ensres_%hr%/ges.ensres.%hr%
+        provider: ufs
+      analysis:
+        filetype: auxgrid
+        gridtype: gaussian
+        filename: ./calcanl_ensres_%hr%/anl.ensres.%hr%.

From 77ed7cef9205d9f8019b6b973b9dc88bd95113f0 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 11 Sep 2024 13:31:43 +0000
Subject: [PATCH 02/25] Redo YAML config for calcanl

---
 algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 | 105 ++++++++-----------
 1 file changed, 41 insertions(+), 64 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
index 987b352..3ee6d7e 100644
--- a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
@@ -1,67 +1,44 @@
-datetime: '{{ current_cycle | to_isotime }}'
-forecast hours: ['06']
-increment variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz]
-analysis variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz,
-                     w,graupel,surface_geopotential_height,ice_nc,rain_nc,ps,rainwat,snowwat]
-geometries:
-  increment:
-    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 }}
-    field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
-  full resolution state:
-    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 }}
-    field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
-  ensemble resolution state:
-    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 }}
-    field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_history.yaml
-io from template: 
+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_restart.yaml    
+additions from template: 
   pattern: '%hr%'
+  forecast hours: ['06']
   template:
+    state:
+      datetime: {{ atmosphere_background_time_iso }}
+      filetype: cube sphere history
+      filename: ./calcanl_%hr%/ges.%hr%
+      provider: ufs
+      state variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz,
+                        w,graupel,surface_geopotential_height,ice_nc,rain_nc,ps,rainwat,snowwat]
     increment:
-        filetype: cube sphere history
-        filename: ./calcanl_%hr%/siginc.nc.%hr%
-        provider: ufs
-    full resolution states:
-      background:
-        filetype: cube sphere history
-        filename: ./calcanl_%hr%/ges.%hr%
-        provider: ufs
-      analysis: 
-        filetype: auxgrid
-        gridtype: gaussian
-        filename: ./calcanl_%hr%/anl.%hr%.
-    ensemble resolution states:
-      background:
-        filetype: cube sphere history
-        filename: ./calcanl_ensres_%hr%/ges.ensres.%hr%
-        provider: ufs
-      analysis:
-        filetype: auxgrid
-        gridtype: gaussian
-        filename: ./calcanl_ensres_%hr%/anl.ensres.%hr%.
+      filetype: cube sphere history
+      filename: ./calcanl_%hr%/siginc.nc.%hr%
+      provider: ufs
+      added variable: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz]
+    output:
+      filetype: auxgrid
+      gridtype: gaussian
+      filename: ./calcanl_%hr%/anl.%hr%.
\ No newline at end of file

From 6ea2a9714a483d9b344d827835f2e007282a06a3 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 11 Sep 2024 18:17:58 +0000
Subject: [PATCH 03/25] Initial commit

---
 .../atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2  | 14 +++++-----
 .../fv3jedi_fv3inc_variational.yaml.j2        | 26 +++++++++----------
 ...ere_final_increment_fms_nonrestart.yaml.j2 | 18 +++++++++++++
 ...ensemble_increments_fms_nonrestart.yaml.j2 |  3 +++
 4 files changed, 41 insertions(+), 20 deletions(-)
 create mode 100644 model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
 create mode 100644 model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index f69bca2..556d7c9 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -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_history.yaml
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
 fv3 increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
@@ -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_restart.yaml
 members from template:
   template:
     background input:
@@ -52,13 +52,13 @@ members from template:
       datetime: '{{ atmosphere_background_time_iso }}'
       state variables: *bkgvars
     jedi increment input:
-      filetype: cube sphere history
+      filetype: fms restart
+      is restart: false
       filename: ./anl/mem%mem%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
-      provider: ufs
     fv3 increment output:
-      filetype: auxgrid
-      gridtype: gaussian
-      filename: ./anl/mem%mem%/atminc.
+      filetype: fms restart
+      is restart: false
+      filename: ./anl/mem%mem%/atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
   pattern: '%mem%'
   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
index d5277f1..809ad0d 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
+++ b/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_restart.yaml
 fv3 increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
@@ -36,10 +36,10 @@ fv3 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_fv3inc.yaml
+  npx: {{ atmosphere_npx_ges }}
+  npy: {{ atmosphere_npy_ges }}
+  npz: {{ atmosphere_npz_ges }}
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
 members:
 - background input:
     datapath: ./bkg
@@ -51,10 +51,10 @@ 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
+    filetype: fms restart
+    is restart: false
     filename: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
-    provider: ufs
   fv3 increment output:
-    filetype: auxgrid
-    gridtype: gaussian
-    filename: ./anl/atminc.
+    filetype: fms restart	
+    is restart: false
+    filename: ./anl/atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
diff --git a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
new file mode 100644
index 0000000..1596416
--- /dev/null
+++ b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
@@ -0,0 +1,18 @@
+output:
+  state component:
+    filetype: fms restart
+    is restart: false
+    filename: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+    fields to write: [ugrd,vgrd,tmp,pressfc,spfh,icmr,clwmr,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_restart.yaml"
diff --git a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
new file mode 100644
index 0000000..1228c54
--- /dev/null
+++ b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
@@ -0,0 +1,3 @@
+filetype: fms restart
+is restart: false
+filename: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4

From 1f19dff879fb4235aa1400a660cce9a79c7aefa3 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 11 Sep 2024 19:10:12 +0000
Subject: [PATCH 04/25] Update to reflect changes to FMS nonrestart

---
 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2            | 4 ++--
 algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2       | 4 ++--
 .../atmosphere_final_increment_fms_nonrestart.yaml.j2         | 2 +-
 ...mosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index 556d7c9..e64a059 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -54,11 +54,11 @@ members from template:
     jedi increment input:
       filetype: fms restart
       is restart: false
-      filename: ./anl/mem%mem%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+      filename_nonrestart: ./anl/mem%mem%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
     fv3 increment output:
       filetype: fms restart
       is restart: false
-      filename: ./anl/mem%mem%/atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
+      filename_nonrestart: ./anl/mem%mem%/atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
   pattern: '%mem%'
   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
index 809ad0d..3189ab3 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -53,8 +53,8 @@ members:
   jedi increment input:
     filetype: fms restart
     is restart: false
-    filename: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+    filename_nonrestart: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
   fv3 increment output:
     filetype: fms restart	
     is restart: false
-    filename: ./anl/atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
+    filename_nonrestart: ./anl/atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
diff --git a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
index 1596416..e549107 100644
--- a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
@@ -2,7 +2,7 @@ output:
   state component:
     filetype: fms restart
     is restart: false
-    filename: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+    filename_nonrestart: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
     fields to write: [ugrd,vgrd,tmp,pressfc,spfh,icmr,clwmr,o3mr]
 geometry:
   fms initialization:
diff --git a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
index 1228c54..c1bb9ed 100644
--- a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
@@ -1,3 +1,3 @@
 filetype: fms restart
 is restart: false
-filename: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+filename_nonrestart: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4

From fb54e307bf731ee141b47557bfed34f132de1bd3 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Thu, 12 Sep 2024 14:23:54 +0000
Subject: [PATCH 05/25] Add datetime templating flag for FMS increments

---
 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2      | 1 +
 algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 | 3 ++-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index e64a059..f05d10e 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -54,6 +54,7 @@ members from template:
     jedi increment input:
       filetype: fms restart
       is restart: false
+      filename is datetime templated: true
       filename_nonrestart: ./anl/mem%mem%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
     fv3 increment output:
       filetype: fms restart
diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
index 3189ab3..af6caa6 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -53,8 +53,9 @@ members:
   jedi increment input:
     filetype: fms restart
     is restart: false
+    filename is datetime templated: true
     filename_nonrestart: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
   fv3 increment output:
-    filetype: fms restart	
+    filetype: fms restart
     is restart: false
     filename_nonrestart: ./anl/atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4

From f3fbc9ff85f0149be6a2be1db3ca61272fd77442 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Fri, 13 Sep 2024 01:19:15 +0000
Subject: [PATCH 06/25] Use JCB template variables for 'fields to write'
 parameter

---
 .../atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2  | 2 +-
 .../atmosphere_final_increment_fms_nonrestart.yaml.j2           | 2 +-
 .../atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2  | 1 +
 ...atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 | 1 +
 4 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2 b/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
index 7d9f7e7..61e35d7 100644
--- a/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
+++ b/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
@@ -3,7 +3,7 @@ output:
     filetype: cube sphere history
     filename: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
     provider: ufs
-    fields to write: [ugrd,vgrd,tmp,pressfc,spfh,icmr,clwmr,o3mr]
+    fields to write: {{analysis_variables}}
 geometry:
   fms initialization:
     namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"
diff --git a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
index e549107..d7aae52 100644
--- a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
@@ -3,7 +3,7 @@ output:
     filetype: fms restart
     is restart: false
     filename_nonrestart: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
-    fields to write: [ugrd,vgrd,tmp,pressfc,spfh,icmr,clwmr,o3mr]
+    fields to write: {{analysis_variables}}
 geometry:
   fms initialization:
     namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"
diff --git a/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2 b/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
index cf655f1..f72ab59 100644
--- a/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
+++ b/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
@@ -1,3 +1,4 @@
 filetype: cube sphere history
 provider: ufs
 filename: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+fields to write: {{increment_variables}}
\ No newline at end of file
diff --git a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
index c1bb9ed..573d5f2 100644
--- a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
@@ -1,3 +1,4 @@
 filetype: fms restart
 is restart: false
 filename_nonrestart: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+fields to write: {{increment_variables}}
\ No newline at end of file

From e82d17978da10d69f8752aa095761bd483d42fe7 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Fri, 13 Sep 2024 01:43:28 +0000
Subject: [PATCH 07/25] Use fv3inc fields metadata for JEDI increment output

---
 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2    | 11 +++++------
 .../atmosphere/fv3jedi_fv3inc_variational.yaml.j2     |  4 ++--
 .../atmosphere_final_increment_fms_nonrestart.yaml.j2 |  2 +-
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index f05d10e..56cb7ad 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -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
@@ -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_restart.yaml
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
 members from template:
   template:
     background input:
@@ -52,10 +52,9 @@ members from template:
       datetime: '{{ atmosphere_background_time_iso }}'
       state variables: *bkgvars
     jedi increment input:
-      filetype: fms restart
-      is restart: false
-      filename is datetime templated: true
-      filename_nonrestart: ./anl/mem%mem%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+      filetype: cube sphere history
+      filename: ./anl/mem%mem%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+      provider: ufs
     fv3 increment output:
       filetype: fms restart
       is restart: false
diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
index af6caa6..a2fc3ee 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -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_fv3inc.yaml
 fv3 increment geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
@@ -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_restart.yaml
+  field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_fv3inc.yaml
 members:
 - background input:
     datapath: ./bkg
diff --git a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
index d7aae52..c992db7 100644
--- a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
@@ -15,4 +15,4 @@ geometry:
   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_fv3inc.yaml"

From c0f1fef272c9ac1aa36da2ac60ccf9cb6afd82cd Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Fri, 13 Sep 2024 12:49:59 +0000
Subject: [PATCH 08/25] Revert some stuff

---
 .../atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2 | 1 -
 ...tmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 | 3 +--
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2 b/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
index f72ab59..cf655f1 100644
--- a/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
+++ b/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
@@ -1,4 +1,3 @@
 filetype: cube sphere history
 provider: ufs
 filename: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
-fields to write: {{increment_variables}}
\ No newline at end of file
diff --git a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
index 573d5f2..dcc54af 100644
--- a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
@@ -1,4 +1,3 @@
 filetype: fms restart
 is restart: false
-filename_nonrestart: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
-fields to write: {{increment_variables}}
\ No newline at end of file
+filename_nonrestart: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
\ No newline at end of file

From 597c0f9dc34c32f9499d7498ceeed32231518bfb Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Fri, 13 Sep 2024 08:50:46 -0400
Subject: [PATCH 09/25] Update
 atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2

---
 ...atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
index dcc54af..c1bb9ed 100644
--- a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
@@ -1,3 +1,3 @@
 filetype: fms restart
 is restart: false
-filename_nonrestart: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
\ No newline at end of file
+filename_nonrestart: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4

From 641c7959654dbad5558ed112b2dd7191bb63a501 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Fri, 13 Sep 2024 13:17:24 +0000
Subject: [PATCH 10/25] read FMS non-restart increment

---
 algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
index 3ee6d7e..9432d23 100644
--- a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
@@ -21,7 +21,7 @@ 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_fv3inc.yaml    
 additions from template: 
   pattern: '%hr%'
   forecast hours: ['06']
@@ -29,14 +29,14 @@ additions from template:
     state:
       datetime: {{ atmosphere_background_time_iso }}
       filetype: cube sphere history
-      filename: ./calcanl_%hr%/ges.%hr%
+      filename: ./calcanl_%hr%/ges.%hr%.nc
       provider: ufs
       state variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz,
                         w,graupel,surface_geopotential_height,ice_nc,rain_nc,ps,rainwat,snowwat]
     increment:
-      filetype: cube sphere history
-      filename: ./calcanl_%hr%/siginc.nc.%hr%
-      provider: ufs
+      filetype: fms restart
+      is restart: false
+      filename_nonrestart: ./calcanl_%hr%/siginc.%hr%.nc
       added variable: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz]
     output:
       filetype: auxgrid

From e102bb0983f576bec8bf636f1815bca8623c273c Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Fri, 13 Sep 2024 11:58:05 -0400
Subject: [PATCH 11/25] Update fv3jedi_calcanl.yaml.j2

---
 algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
index 9432d23..af6233d 100644
--- a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
@@ -41,4 +41,4 @@ additions from template:
     output:
       filetype: auxgrid
       gridtype: gaussian
-      filename: ./calcanl_%hr%/anl.%hr%.
\ No newline at end of file
+      filename: ./calcanl_%hr%/anl.%hr%.

From 3cbfa5c2258a5b3416a8708c3ce0f072747f8215 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Tue, 17 Sep 2024 14:59:45 +0000
Subject: [PATCH 12/25] Make hydrostatic_delz just delz

---
 algorithm/atmosphere/fv3jedi_calcanl.yaml.j2            | 6 +++---
 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2      | 2 +-
 algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
index af6233d..5214ad5 100644
--- a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
@@ -27,17 +27,17 @@ additions from template:
   forecast hours: ['06']
   template:
     state:
-      datetime: {{ atmosphere_background_time_iso }}
+      datetime: "{{ atmosphere_background_time_iso }}"
       filetype: cube sphere history
       filename: ./calcanl_%hr%/ges.%hr%.nc
       provider: ufs
-      state variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz,
+      state variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz,
                         w,graupel,surface_geopotential_height,ice_nc,rain_nc,ps,rainwat,snowwat]
     increment:
       filetype: fms restart
       is restart: false
       filename_nonrestart: ./calcanl_%hr%/siginc.%hr%.nc
-      added variable: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz]
+      added variable: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
     output:
       filetype: auxgrid
       gridtype: gaussian
diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index 56cb7ad..580c9bd 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -1,7 +1,7 @@
 variable change:
   variable change name: Model2GeoVaLs
   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]
+  output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
 jedi increment variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 fv3 increment variables: *fv3incrvars
 background geometry:
diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
index a2fc3ee..ab59198 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -1,7 +1,7 @@
 variable change:
   variable change name: Model2GeoVaLs
   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]
+  output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
 jedi increment variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 fv3 increment variables: *fv3incrvars
 background geometry:

From 3817d08c8a0aecbac06302a8c88c1f45355c35dd Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Tue, 17 Sep 2024 20:19:19 +0000
Subject: [PATCH 13/25] Add surface background file

---
 algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
index 5214ad5..9e27cc9 100644
--- a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
@@ -29,7 +29,8 @@ additions from template:
     state:
       datetime: "{{ atmosphere_background_time_iso }}"
       filetype: cube sphere history
-      filename: ./calcanl_%hr%/ges.%hr%.nc
+      datapath: ./calcanl_%hr%
+      filenames: [ges.atm.%hr%.nc, ges.sfc.%hr%.nc]
       provider: ufs
       state variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz,
                         w,graupel,surface_geopotential_height,ice_nc,rain_nc,ps,rainwat,snowwat]
@@ -37,7 +38,7 @@ additions from template:
       filetype: fms restart
       is restart: false
       filename_nonrestart: ./calcanl_%hr%/siginc.%hr%.nc
-      added variable: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
+      added variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
     output:
       filetype: auxgrid
       gridtype: gaussian

From df8b2e81a72daf53b909707d15bf21bf0f1628da Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Mon, 23 Sep 2024 15:21:46 +0000
Subject: [PATCH 14/25] Update YAML for analysis calc

---
 algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 | 36 +++++++++++++++++---
 1 file changed, 32 insertions(+), 4 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
index 9e27cc9..4029c1b 100644
--- a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
@@ -1,4 +1,4 @@
-state geometry:
+background geometry:
   fms initialization:
     namelist filename: ./fv3jedi/fmsmpp.nml
     field table filename: ./fv3jedi/field_table
@@ -21,12 +21,36 @@ 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_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:
-    state:
+    background:
       datetime: "{{ atmosphere_background_time_iso }}"
       filetype: cube sphere history
       datapath: ./calcanl_%hr%
@@ -39,7 +63,11 @@ additions from template:
       is restart: false
       filename_nonrestart: ./calcanl_%hr%/siginc.%hr%.nc
       added variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
-    output:
+    full resolution analysis:
       filetype: auxgrid
       gridtype: gaussian
       filename: ./calcanl_%hr%/anl.%hr%.
+    ensemble resolution analysis:
+      filetype: auxgrid
+      gridtype: gaussian
+      filename: ./calcanl_%hr%/anl.ensres.%hr%.

From afa5b6ccd4fc7c4d35db4f2cdb8af0aaf78f3999 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Mon, 23 Sep 2024 20:40:33 +0000
Subject: [PATCH 15/25] Rename some stuff per Rahul's comment

---
 algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
index 4029c1b..3555aab 100644
--- a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
@@ -53,7 +53,7 @@ additions from template:
     background:
       datetime: "{{ atmosphere_background_time_iso }}"
       filetype: cube sphere history
-      datapath: ./calcanl_%hr%
+      datapath: ./analcalc_%hr%
       filenames: [ges.atm.%hr%.nc, ges.sfc.%hr%.nc]
       provider: ufs
       state variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz,
@@ -61,13 +61,13 @@ additions from template:
     increment:
       filetype: fms restart
       is restart: false
-      filename_nonrestart: ./calcanl_%hr%/siginc.%hr%.nc
+      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: ./calcanl_%hr%/anl.%hr%.
+      filename: ./analcalc_%hr%/anl.%hr%.
     ensemble resolution analysis:
       filetype: auxgrid
       gridtype: gaussian
-      filename: ./calcanl_%hr%/anl.ensres.%hr%.
+      filename: ./analcalc_%hr%/anl.ensres.%hr%.

From c6dd00ff1f6aaa023331e535479b379e80ced519 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Mon, 23 Sep 2024 20:40:59 +0000
Subject: [PATCH 16/25] Final renaming

---
 .../{fv3jedi_calcanl.yaml.j2 => fv3jedi_analcalc.yaml.j2}         | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename algorithm/atmosphere/{fv3jedi_calcanl.yaml.j2 => fv3jedi_analcalc.yaml.j2} (100%)

diff --git a/algorithm/atmosphere/fv3jedi_calcanl.yaml.j2 b/algorithm/atmosphere/fv3jedi_analcalc.yaml.j2
similarity index 100%
rename from algorithm/atmosphere/fv3jedi_calcanl.yaml.j2
rename to algorithm/atmosphere/fv3jedi_analcalc.yaml.j2

From ba1379aa84b24536aafa554da9ee50440794eea7 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Wed, 25 Sep 2024 21:07:10 +0000
Subject: [PATCH 17/25] Add cubed_sphere_grid_ to prefixes

---
 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2      | 6 +++++-
 algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index 580c9bd..1ac6ae5 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -58,7 +58,11 @@ members from template:
     fv3 increment output:
       filetype: fms restart
       is restart: false
-      filename_nonrestart: ./anl/mem%mem%/atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
+      filename_nonrestart: ./anl/mem%mem%/cubed_sphere_grid_atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
+    temporary fv3 increment output:
+      filetype: auxgrid
+      gridtype: gaussian
+      filename: ./anl/mem%mem%/atminc.
   pattern: '%mem%'
   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
index ab59198..cb9ca59 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -58,4 +58,4 @@ members:
   fv3 increment output:
     filetype: fms restart
     is restart: false
-    filename_nonrestart: ./anl/atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
+    filename_nonrestart: ./anl/cubed_sphere_grid_atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4

From 607b74c4d73f00af540355715a549507762e92fd Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Thu, 26 Sep 2024 14:55:48 +0000
Subject: [PATCH 18/25] Revert some stuff

---
 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index 1ac6ae5..4e64060 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -56,10 +56,6 @@ members from template:
       filename: ./anl/mem%mem%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
       provider: ufs
     fv3 increment output:
-      filetype: fms restart
-      is restart: false
-      filename_nonrestart: ./anl/mem%mem%/cubed_sphere_grid_atminc.%yyyy%mm%dd_%hh%MM%ssz.nc4
-    temporary fv3 increment output:
       filetype: auxgrid
       gridtype: gaussian
       filename: ./anl/mem%mem%/atminc.

From 85ccdb433638ee8f1a83ada79e5fd4a8d4d2601b Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Thu, 26 Sep 2024 15:10:03 +0000
Subject: [PATCH 19/25] Add "cubed_sphere_grid_" prefix where appropriate

---
 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2              | 2 +-
 algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2         | 2 +-
 .../atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2  | 2 +-
 .../atmosphere_final_increment_fms_nonrestart.yaml.j2           | 2 +-
 .../atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2  | 2 +-
 ...atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index 4e64060..543a413 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+++ b/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
diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
index cb9ca59..2424d3f 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -54,7 +54,7 @@ members:
     filetype: fms restart
     is restart: false
     filename is datetime templated: true
-    filename_nonrestart: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+    filename_nonrestart: ./anl/cubed_sphere_grid_atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
   fv3 increment output:
     filetype: fms restart
     is restart: false
diff --git a/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2 b/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
index 61e35d7..a325550 100644
--- a/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
+++ b/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.%yyyy%mm%dd.%hh%MM%ssz.nc4
     provider: ufs
     fields to write: {{analysis_variables}}
 geometry:
diff --git a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
index c992db7..67b7dec 100644
--- a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
@@ -2,7 +2,7 @@ output:
   state component:
     filetype: fms restart
     is restart: false
-    filename_nonrestart: ./anl/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+    filename_nonrestart: ./anl/cubed_sphere_grid_atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
     fields to write: {{analysis_variables}}
 geometry:
   fms initialization:
diff --git a/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2 b/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
index cf655f1..b7b9544 100644
--- a/model/atmosphere/atmosphere_output_ensemble_increments_cubed_sphere.yaml.j2
+++ b/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
diff --git a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
index c1bb9ed..e0afd5d 100644
--- a/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_output_ensemble_increments_fms_nonrestart.yaml.j2
@@ -1,3 +1,3 @@
 filetype: fms restart
 is restart: false
-filename_nonrestart: ./anl/mem%{member}%/atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
+filename_nonrestart: ./anl/mem%{member}%/cubed_sphere_grid_atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4

From ef5775a09d99c945f68dcfdddc933516d3537868 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Mon, 7 Oct 2024 14:00:32 +0000
Subject: [PATCH 20/25] Remove ges.sfc background file

---
 algorithm/atmosphere/fv3jedi_analcalc.yaml.j2 | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_analcalc.yaml.j2 b/algorithm/atmosphere/fv3jedi_analcalc.yaml.j2
index 3555aab..975fc4f 100644
--- a/algorithm/atmosphere/fv3jedi_analcalc.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_analcalc.yaml.j2
@@ -54,10 +54,11 @@ additions from template:
       datetime: "{{ atmosphere_background_time_iso }}"
       filetype: cube sphere history
       datapath: ./analcalc_%hr%
-      filenames: [ges.atm.%hr%.nc, ges.sfc.%hr%.nc]
+      filename: ges.%hr%.nc
       provider: ufs
-      state variables: [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz,
-                        w,graupel,surface_geopotential_height,ice_nc,rain_nc,ps,rainwat,snowwat]
+      state variables: [liq_wat,delz,delp,w,graupel,surface_geopotential_height
+                        surface_geopotential_height,ice_wat,ice_nc,rain_nc,o3mr,
+                        ps,rainwat,snowwat,sphum,t,ua,va]
     increment:
       filetype: fms restart
       is restart: false

From aa3b1109e13079428c89d88941976560c12e9578 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Tue, 8 Oct 2024 00:17:51 +0000
Subject: [PATCH 21/25] Finish update to list of analysis variables

---
 algorithm/atmosphere/fv3jedi_analcalc.yaml.j2 | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_analcalc.yaml.j2 b/algorithm/atmosphere/fv3jedi_analcalc.yaml.j2
index 975fc4f..317a127 100644
--- a/algorithm/atmosphere/fv3jedi_analcalc.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_analcalc.yaml.j2
@@ -56,9 +56,8 @@ additions from template:
       datapath: ./analcalc_%hr%
       filename: ges.%hr%.nc
       provider: ufs
-      state variables: [liq_wat,delz,delp,w,graupel,surface_geopotential_height
-                        surface_geopotential_height,ice_wat,ice_nc,rain_nc,o3mr,
-                        ps,rainwat,snowwat,sphum,t,ua,va]
+      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

From 96d9e8799a7cd707434f0284c39f199c8121a8bd Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Fri, 1 Nov 2024 15:08:14 +0000
Subject: [PATCH 22/25] add atmosphere_ prefix to analysis_variables

---
 .../atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2  | 2 +-
 .../atmosphere_final_increment_fms_nonrestart.yaml.j2           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2 b/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
index a325550..43444f8 100644
--- a/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
+++ b/model/atmosphere/atmosphere_final_increment_cubed_sphere.yaml.j2
@@ -3,7 +3,7 @@ output:
     filetype: cube sphere history
     filename: ./anl/cubed_sphere_grid_atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
     provider: ufs
-    fields to write: {{analysis_variables}}
+    fields to write: {{atmosphere_analysis_variables}}
 geometry:
   fms initialization:
     namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"
diff --git a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2 b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
index 67b7dec..d2e15a4 100644
--- a/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
+++ b/model/atmosphere/atmosphere_final_increment_fms_nonrestart.yaml.j2
@@ -3,7 +3,7 @@ output:
     filetype: fms restart
     is restart: false
     filename_nonrestart: ./anl/cubed_sphere_grid_atminc.%yyyy%mm%dd.%hh%MM%ssz.nc4
-    fields to write: {{analysis_variables}}
+    fields to write: {{atmosphere_analysis_variables}}
 geometry:
   fms initialization:
     namelist filename: "{{atmosphere_fv3jedi_files_path}}/fmsmpp.nml"

From 62185624df3edca0a4c9d4b2c9c34c07f9a21ca2 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Fri, 1 Nov 2024 15:11:54 +0000
Subject: [PATCH 23/25] Update atmosphere test template

---
 test/client_integration/gdas-atmosphere-templates.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/client_integration/gdas-atmosphere-templates.yaml b/test/client_integration/gdas-atmosphere-templates.yaml
index bea2b27..9990b6e 100644
--- a/test/client_integration/gdas-atmosphere-templates.yaml
+++ b/test/client_integration/gdas-atmosphere-templates.yaml
@@ -36,12 +36,12 @@ window_length: PT6H
 bound_to_include: begin
 minimizer: DRPCG
 final_diagnostics_departures: anlmob
-analysis_variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 number_of_outer_loops: 2
 
 
 # Model things
 # ------------
+atmosphere_analysis_variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 atmosphere_layout_x: 2
 atmosphere_layout_y: 2
 atmosphere_npx_ges: 361

From de9264abc29392ba912e8ce99982ddfa71884769 Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Fri, 1 Nov 2024 11:20:20 -0400
Subject: [PATCH 24/25] Update
 test/client_integration/gdas-atmosphere-templates.yaml

Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
---
 test/client_integration/gdas-atmosphere-templates.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/client_integration/gdas-atmosphere-templates.yaml b/test/client_integration/gdas-atmosphere-templates.yaml
index 9990b6e..ea7657b 100644
--- a/test/client_integration/gdas-atmosphere-templates.yaml
+++ b/test/client_integration/gdas-atmosphere-templates.yaml
@@ -41,7 +41,8 @@ number_of_outer_loops: 2
 
 # Model things
 # ------------
-atmosphere_analysis_variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+analysis_variables: &anvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+atmosphere_analysis_variables: *anvars
 atmosphere_layout_x: 2
 atmosphere_layout_y: 2
 atmosphere_npx_ges: 361

From 9dfa810447c86fd3892f487c44f3c9a27aaced7f Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <david.new@noaa.gov>
Date: Fri, 1 Nov 2024 15:22:47 +0000
Subject: [PATCH 25/25] Slight asthetic change

---
 test/client_integration/gdas-atmosphere-templates.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/client_integration/gdas-atmosphere-templates.yaml b/test/client_integration/gdas-atmosphere-templates.yaml
index ea7657b..d187daa 100644
--- a/test/client_integration/gdas-atmosphere-templates.yaml
+++ b/test/client_integration/gdas-atmosphere-templates.yaml
@@ -36,12 +36,12 @@ window_length: PT6H
 bound_to_include: begin
 minimizer: DRPCG
 final_diagnostics_departures: anlmob
+analysis_variables: &anvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 number_of_outer_loops: 2
 
 
 # Model things
 # ------------
-analysis_variables: &anvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
 atmosphere_analysis_variables: *anvars
 atmosphere_layout_x: 2
 atmosphere_layout_y: 2