From 48273dec91a14210b3a6f97a9f7400e394bd1ece Mon Sep 17 00:00:00 2001
From: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Thu, 14 Nov 2024 14:02:28 -0500
Subject: [PATCH 1/7] Make do_testing an optional parameter (#44)

Does the same thing as jcb-algorithms PR
[#8](https://github.com/NOAA-EMC/jcb-algorithms/pull/8)
---
 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2      | 2 +-
 algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index bb53866..723abc6 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
@@ -64,7 +64,7 @@ members from template:
   zero padding: 3
 
 # Optionally test the application
-{% if do_testing %}
+{% if do_testing | default(false) %}
 test:
   reference filename: {{test_reference_filename}}
 {% if test_output_filename is defined %}
diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
index f0d06a6..b795b06 100644
--- a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
+++ b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
@@ -60,7 +60,7 @@ members:
     filename: ./anl/atminc.
 
 # Optionally test the application
-{% if do_testing %}
+{% if do_testing | default(false) %}
 test:
   reference filename: {{test_reference_filename}}
 {% if test_output_filename is defined %}

From c41e7d7aca3f4053b177709adaa66488f3643980 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Fri, 15 Nov 2024 14:45:30 -0500
Subject: [PATCH 2/7] Update variables to be consistent with updated jedi
 hashes (#45)

This PR updates variables to be consistent with the updated jedi hashes
in GDASApp branch
[`feature/resume_nightly`](https://github.com/NOAA-EMC/GDASApp/tree/feature/resume_nightly)

Resolves #43
---
 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2   |  2 +-
 .../atmosphere/fv3jedi_fv3inc_variational.yaml.j2    |  2 +-
 algorithm/marine/soca_2cice_antarctic.yaml.j2        |  4 ++--
 algorithm/marine/soca_2cice_arctic.yaml.j2           |  4 ++--
 algorithm/marine/soca_diagb.yaml.j2                  |  2 +-
 .../marine/soca_parameters_diffusion_hz.yaml.j2      |  4 ++--
 .../marine/soca_parameters_diffusion_vt.yaml.j2      |  4 ++--
 algorithm/marine/soca_setcorscales.yaml.j2           |  4 ++--
 algorithm/marine/socaincr2mom6.yaml.j2               |  4 ++--
 model/atmosphere/atmosphere_background.yaml.j2       |  4 ++--
 .../atmosphere_background_ensemble.yaml.j2           |  4 ++--
 ...phere_background_error_hybrid_gsibec_bump.yaml.j2 | 12 ++++++------
 ...atmosphere_background_error_static_gsibec.yaml.j2 |  4 ++--
 model/marine/marine_background.yaml.j2               |  2 +-
 .../marine_background_error_static_diffusion.yaml.j2 |  8 ++++----
 .../atmosphere-lgetkf/ascatw.ascat_metop-b.yaml.j2   |  2 +-
 .../atmosphere-lgetkf/conventional_ps.yaml.j2        |  4 ++--
 .../atmosphere-lgetkf/satwnd.abi_goes-16.yaml.j2     |  2 +-
 observations/atmosphere/ascatw.ascat_metop-b.yaml.j2 |  2 +-
 observations/atmosphere/conventional_ps.yaml.j2      |  4 ++--
 observations/atmosphere/satwnd.abi_goes-16.yaml.j2   |  2 +-
 .../atmosphere/scatwind_ascat_metop-a.yaml.j2        |  2 +-
 observations/atmosphere/sondes.yaml.j2               |  4 ++--
 23 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
index 723abc6..576a133 100644
--- 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,surface_geopotential_height]
+  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc]
   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
diff --git a/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2 b/algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
index b795b06..dd60ebb 100644
--- 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,surface_geopotential_height]
+  input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc]
   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
diff --git a/algorithm/marine/soca_2cice_antarctic.yaml.j2 b/algorithm/marine/soca_2cice_antarctic.yaml.j2
index 73fa367..c740c53 100644
--- a/algorithm/marine/soca_2cice_antarctic.yaml.j2
+++ b/algorithm/marine/soca_2cice_antarctic.yaml.j2
@@ -26,7 +26,7 @@ variable change:
     tstep: PT1H
   cice output:
     restart: {{ ice_rst }}
-  output variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+  output variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
 
 states:
 - input:
@@ -35,7 +35,7 @@ states:
      ocn_filename: {{ ocn_ana }}
      ice_filename: {{ ice_ana }}
      date: '{{ fcst_begin }}'
-     state variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+     state variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
   output:
      datadir: Data
      exp: soca2cice
diff --git a/algorithm/marine/soca_2cice_arctic.yaml.j2 b/algorithm/marine/soca_2cice_arctic.yaml.j2
index e686eea..178b8fa 100644
--- a/algorithm/marine/soca_2cice_arctic.yaml.j2
+++ b/algorithm/marine/soca_2cice_arctic.yaml.j2
@@ -23,7 +23,7 @@ variable change:
     tstep: PT1H
   cice output:
     restart: {{ ice_rst }}
-  output variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+  output variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
 
 states:
 - input:
@@ -32,7 +32,7 @@ states:
      ocn_filename: {{ ocn_ana }}
      ice_filename: {{ ice_ana }}
      date: '{{ fcst_begin }}'
-     state variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+     state variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
   output:
      datadir: Data
      exp: soca2cice
diff --git a/algorithm/marine/soca_diagb.yaml.j2 b/algorithm/marine/soca_diagb.yaml.j2
index 7d8e0d6..02633ac 100644
--- a/algorithm/marine/soca_diagb.yaml.j2
+++ b/algorithm/marine/soca_diagb.yaml.j2
@@ -18,7 +18,7 @@ background error:
   type: incr
 
 variables:
-  name: [tocn, socn, uocn, vocn, hocn, ssh, cicen, hicen, hsnon, mom6_mld]
+  name: [sea_water_potential_temperature, sea_water_salinity, eastward_sea_water_velocity, northward_sea_water_velocity, sea_water_cell_thickness, sea_surface_height_above_geoid, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, mom6_mld]
 
 rescale: 2.0    # rescales the filtered std. dev. by "rescale"
 min sst: 0.0    # Added to sst bkg. err.
diff --git a/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2 b/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
index d313e46..c79d469 100644
--- a/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
+++ b/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
@@ -8,7 +8,7 @@ background:
   ocn_filename: MOM.res.nc
   ice_filename: cice.res.nc
   date: '{{ marine_window_end_iso }}'
-  state variables: [ssh]
+  state variables: [sea_surface_height_above_geoid]
 
 background error:
   covariance model: SABER
@@ -26,7 +26,7 @@ background error:
             date: '{{ marine_window_end_iso }}'
             basename: ./
             ocn_filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
-          model variable: ssh
+          model variable: sea_surface_height_above_geoid
         write:
           filepath: ./staticb/hz_ocean
 
diff --git a/algorithm/marine/soca_parameters_diffusion_vt.yaml.j2 b/algorithm/marine/soca_parameters_diffusion_vt.yaml.j2
index 07f56de..8e23f2d 100644
--- a/algorithm/marine/soca_parameters_diffusion_vt.yaml.j2
+++ b/algorithm/marine/soca_parameters_diffusion_vt.yaml.j2
@@ -8,7 +8,7 @@ background:
   ocn_filename: MOM.res.nc
   ice_filename: cice.res.nc
   date: '{{ marine_window_middle_iso }}'
-  state variables: [tocn]
+  state variables: [sea_water_potential_temperature]
 
 background error:
   covariance model: SABER
@@ -29,6 +29,6 @@ background error:
             date: '{{ marine_window_middle_iso }}'
             basename: ./
             ocn_filename: vt_scales.nc
-          model variable: tocn
+          model variable: sea_water_potential_temperature
         write:
           filepath: ./staticb/vt_ocean
diff --git a/algorithm/marine/soca_setcorscales.yaml.j2 b/algorithm/marine/soca_setcorscales.yaml.j2
index b7b80a7..c1a1ec8 100644
--- a/algorithm/marine/soca_setcorscales.yaml.j2
+++ b/algorithm/marine/soca_setcorscales.yaml.j2
@@ -4,11 +4,11 @@ resolution:
 
 date: "0001-01-01T00:00:00Z"
 
-corr variables: [ssh]
+corr variables: [sea_surface_height_above_geoid]
 
 scales:
   vert layers: 5 # in units of layer
-  ssh:
+  sea_surface_height_above_geoid:
     rossby mult: 1.00
     min grid mult: 2.0
 
diff --git a/algorithm/marine/socaincr2mom6.yaml.j2 b/algorithm/marine/socaincr2mom6.yaml.j2
index ececb6b..deaec76 100644
--- a/algorithm/marine/socaincr2mom6.yaml.j2
+++ b/algorithm/marine/socaincr2mom6.yaml.j2
@@ -4,9 +4,9 @@ geometry:
 
 date: '{{ marine_window_begin }}'
 
-layers variable: [hocn]
+layers variable: [sea_water_cell_thickness]
 
-increment variables: [tocn, socn, uocn, vocn, ssh]
+increment variables: [sea_water_potential_temperature, sea_water_salinity, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
 
 vertical geometry:
   date: '{{ marine_window_begin }}'
diff --git a/model/atmosphere/atmosphere_background.yaml.j2 b/model/atmosphere/atmosphere_background.yaml.j2
index 580fc68..24a45f4 100644
--- a/model/atmosphere/atmosphere_background.yaml.j2
+++ b/model/atmosphere/atmosphere_background.yaml.j2
@@ -5,6 +5,6 @@ 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 ]
-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,
+state variables: [ua,va,t,delp,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc,
+                  slmsk,sheleg,tmpsfc,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
index 16b980e..2167885 100644
--- a/model/atmosphere/atmosphere_background_ensemble.yaml.j2
+++ b/model/atmosphere/atmosphere_background_ensemble.yaml.j2
@@ -6,8 +6,8 @@ members from template:
     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,
+    state variables: [ua,va,t,delz,delp,ps,sphum,ice_wat,liq_wat,o3mr,hgtsfc,
+                     slmsk,sheleg,tmpsfc,vtype,stype,vfrac,stc,smc,snwdphMeters,
                      u_srf,v_srf,f10m]
     datapath: {{ atmosphere_background_ensemble_path }}
     filename is datetime templated: true
diff --git a/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2 b/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2
index e5b06aa..5880917 100644
--- a/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2
+++ b/model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2
@@ -21,8 +21,8 @@ components:
       debugging mode: false
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
-                                      specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+      input variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+                                      water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
                                       mole_fraction_of_ozone_in_air]
       output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
@@ -45,8 +45,8 @@ components:
       localization method: SABER
       saber central block:
         saber block name: BUMP_NICAS
-        active variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
-                                             specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+        active variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+                                             water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
                                              ozone_mass_mixing_ratio ]
         read:
           general:
@@ -198,8 +198,8 @@ components:
               value: 0.3
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
-                                             specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+      input variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+                                             water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
                                              ozone_mass_mixing_ratio ]
       output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
diff --git a/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2 b/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2
index 242ce4f..1133aaf 100644
--- a/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2
+++ b/model/atmosphere/atmosphere_background_error_static_gsibec.yaml.j2
@@ -19,7 +19,7 @@ saber outer blocks:
   debugging mode: false
 linear variable change:
   linear variable change name: Control2Analysis
-  input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
-                           specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+  input variables: [eastward_wind,northward_wind,air_temperature,air_pressure_at_surface,
+                           water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,
                            mole_fraction_of_ozone_in_air]
   output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
diff --git a/model/marine/marine_background.yaml.j2 b/model/marine/marine_background.yaml.j2
index d0047e8..205f583 100644
--- a/model/marine/marine_background.yaml.j2
+++ b/model/marine/marine_background.yaml.j2
@@ -3,4 +3,4 @@ basename: {{ marine_background_path}}
 ocn_filename: MOM.res.nc
 ice_filename: cice.res.nc
 date: "{{ marine_background_time }}"
-state variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh, hocn, mld, layer_depth]
+state variables: [sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, sea_water_salinity, sea_water_potential_temperature, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid, sea_water_cell_thickness, ocean_mixed_layer_thickness, sea_water_depth]
diff --git a/model/marine/marine_background_error_static_diffusion.yaml.j2 b/model/marine/marine_background_error_static_diffusion.yaml.j2
index bb5de61..0c57790 100644
--- a/model/marine/marine_background_error_static_diffusion.yaml.j2
+++ b/model/marine/marine_background_error_static_diffusion.yaml.j2
@@ -3,13 +3,13 @@ saber central block:
   saber block name: diffusion
   read:
     groups:
-    - variables: [tocn, socn, ssh]
+    - variables: [sea_water_potential_temperature, sea_water_salinity, sea_surface_height_above_geoid]
       horizontal:
         filepath: ./staticb/hz_ocean
       vertical:
         levels: {{marine_vt_levels}}
         filepath: ./staticb/vt_ocean
-    - variables: [cicen]
+    - variables: [sea_ice_area_fraction]
       horizontal:
         filepath: ./staticb/hz_ice
 
@@ -24,7 +24,7 @@ saber outer blocks:
       read_from_file: 3
 
 linear variable change:
-  input variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
-  output variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
+  input variables: [sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, sea_water_salinity, sea_water_potential_temperature, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
+  output variables: [sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, sea_water_salinity, sea_water_potential_temperature, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
   linear variable changes:
   - linear variable change name: BalanceSOCA
diff --git a/observations/atmosphere-lgetkf/ascatw.ascat_metop-b.yaml.j2 b/observations/atmosphere-lgetkf/ascatw.ascat_metop-b.yaml.j2
index 35a8a06..831fb80 100644
--- a/observations/atmosphere-lgetkf/ascatw.ascat_metop-b.yaml.j2
+++ b/observations/atmosphere-lgetkf/ascatw.ascat_metop-b.yaml.j2
@@ -110,7 +110,7 @@
     - variable: ObsType/windEastward
       is_in: 290
   #   - variable: GeoVaLs/surface_temperature
-    - variable: GeoVaLs/surface_temperature_where_land
+    - variable: GeoVaLs/skin_temperature_at_surface_where_land
       maxvalue: 273.
     action:
       name: reject
diff --git a/observations/atmosphere-lgetkf/conventional_ps.yaml.j2 b/observations/atmosphere-lgetkf/conventional_ps.yaml.j2
index f094ca9..49f99a5 100644
--- a/observations/atmosphere-lgetkf/conventional_ps.yaml.j2
+++ b/observations/atmosphere-lgetkf/conventional_ps.yaml.j2
@@ -27,7 +27,7 @@
     - name: stationPressure
     da_psfc_scheme: GSI
     station_altitude: height
-    geovar_sfc_geomz: surface_altitude
+    geovar_sfc_geomz: height_above_mean_sea_level_at_surface
     geovar_geomz: geopotential_height
 
   # Linear Observation Operator
@@ -264,7 +264,7 @@
       function:
         name: ObsFunction/ObsErrorFactorSfcPressure
         options:
-          geovar_sfc_geomz: surface_altitude
+          geovar_sfc_geomz: height_above_mean_sea_level_at_surface
           geovar_geomz: geopotential_height
           station_altitude: height
 
diff --git a/observations/atmosphere-lgetkf/satwnd.abi_goes-16.yaml.j2 b/observations/atmosphere-lgetkf/satwnd.abi_goes-16.yaml.j2
index e5543ba..d3b214c 100644
--- a/observations/atmosphere-lgetkf/satwnd.abi_goes-16.yaml.j2
+++ b/observations/atmosphere-lgetkf/satwnd.abi_goes-16.yaml.j2
@@ -448,7 +448,7 @@
     - variable:
         name: ObsType/windEastward
       is_in: 247
-    reference: GeoVaLs/surface_pressure
+    reference: GeoVaLs/air_pressure_at_surface
     value: MetaData/pressure
     maxvalue: -11000.                   # within 110 hPa above surface pressure, negative p-diff
     action:
diff --git a/observations/atmosphere/ascatw.ascat_metop-b.yaml.j2 b/observations/atmosphere/ascatw.ascat_metop-b.yaml.j2
index bb3d5de..88ee802 100644
--- a/observations/atmosphere/ascatw.ascat_metop-b.yaml.j2
+++ b/observations/atmosphere/ascatw.ascat_metop-b.yaml.j2
@@ -107,7 +107,7 @@
     - variable: ObsType/windEastward
       is_in: 290
   #   - variable: GeoVaLs/surface_temperature
-    - variable: GeoVaLs/surface_temperature_where_land
+    - variable: GeoVaLs/skin_temperature_at_surface_where_land
       maxvalue: 273.
     action:
       name: reject
diff --git a/observations/atmosphere/conventional_ps.yaml.j2 b/observations/atmosphere/conventional_ps.yaml.j2
index d8d90f9..1ecd386 100644
--- a/observations/atmosphere/conventional_ps.yaml.j2
+++ b/observations/atmosphere/conventional_ps.yaml.j2
@@ -24,7 +24,7 @@
     - name: stationPressure
     da_psfc_scheme: GSI
     station_altitude: height
-    geovar_sfc_geomz: surface_altitude
+    geovar_sfc_geomz: height_above_mean_sea_level_at_surface
     geovar_geomz: geopotential_height
 
   # Linear Observation Operator
@@ -261,7 +261,7 @@
       function:
         name: ObsFunction/ObsErrorFactorSfcPressure
         options:
-          geovar_sfc_geomz: surface_altitude
+          geovar_sfc_geomz: height_above_mean_sea_level_at_surface
           geovar_geomz: geopotential_height
           station_altitude: height
 
diff --git a/observations/atmosphere/satwnd.abi_goes-16.yaml.j2 b/observations/atmosphere/satwnd.abi_goes-16.yaml.j2
index e01f17c..94b0458 100644
--- a/observations/atmosphere/satwnd.abi_goes-16.yaml.j2
+++ b/observations/atmosphere/satwnd.abi_goes-16.yaml.j2
@@ -445,7 +445,7 @@
     - variable:
         name: ObsType/windEastward
       is_in: 247
-    reference: GeoVaLs/surface_pressure
+    reference: GeoVaLs/air_pressure_at_surface
     value: MetaData/pressure
     maxvalue: -11000.                   # within 110 hPa above surface pressure, negative p-diff
     action:
diff --git a/observations/atmosphere/scatwind_ascat_metop-a.yaml.j2 b/observations/atmosphere/scatwind_ascat_metop-a.yaml.j2
index 0c1a745..774fef9 100644
--- a/observations/atmosphere/scatwind_ascat_metop-a.yaml.j2
+++ b/observations/atmosphere/scatwind_ascat_metop-a.yaml.j2
@@ -107,7 +107,7 @@
     - variable: ObsType/windEastward
       is_in: 290
   #   - variable: GeoVaLs/surface_temperature
-    - variable: GeoVaLs/surface_temperature_where_land
+    - variable: GeoVaLs/skin_temperature_at_surface_where_land
       maxvalue: 273.
     action:
       name: reject
diff --git a/observations/atmosphere/sondes.yaml.j2 b/observations/atmosphere/sondes.yaml.j2
index aff438b..224c814 100644
--- a/observations/atmosphere/sondes.yaml.j2
+++ b/observations/atmosphere/sondes.yaml.j2
@@ -34,7 +34,7 @@
       - name: specificHumidity
     - name: SfcPCorrected
       da_psfc_scheme: GSI
-      geovar_sfc_geomz: surface_geopotential_height
+      geovar_sfc_geomz: geopotential_height_at_surface
       geovar_geomz: geopotential_height
       variables:
       - name: stationPressure
@@ -106,7 +106,7 @@
           error_min: 100.0           # 1 mb
           error_max: 300.0           # 3 mb
           geovar_geomz: geopotential_height
-          geovar_sfc_geomz: surface_geopotential_height
+          geovar_sfc_geomz: geopotential_height_at_surface
     #
     # Gross error check with (O - B) / ObsError greater than threshold
   - filter: Background Check

From 77fdc329d45b54529499f4033851e50e1dee0697 Mon Sep 17 00:00:00 2001
From: Anna Shlyaeva <annash@ucar.edu>
Date: Thu, 21 Nov 2024 12:06:39 -0700
Subject: [PATCH 3/7] Add soca->cice global file (#47)

---
 algorithm/marine/soca_2cice_arctic.yaml.j2    | 40 -------------------
 ...ctic.yaml.j2 => soca_2cice_global.yaml.j2} | 25 +++++++-----
 2 files changed, 14 insertions(+), 51 deletions(-)
 delete mode 100644 algorithm/marine/soca_2cice_arctic.yaml.j2
 rename algorithm/marine/{soca_2cice_antarctic.yaml.j2 => soca_2cice_global.yaml.j2} (76%)

diff --git a/algorithm/marine/soca_2cice_arctic.yaml.j2 b/algorithm/marine/soca_2cice_arctic.yaml.j2
deleted file mode 100644
index 178b8fa..0000000
--- a/algorithm/marine/soca_2cice_arctic.yaml.j2
+++ /dev/null
@@ -1,40 +0,0 @@
-input geometry:
-  mom6_input_nml: mom_input.nml
-  fields metadata: ./fields_metadata.yaml
-
-output geometry:
-  mom6_input_nml: mom_input.nml
-  fields metadata: ./fields_metadata.yaml
-
-variable change:
-  variable change name: Soca2Cice
-  do inverse: false
-  seaice edge: 0.8
-  shuffle: false
-  rescale prior:
-    min hice: 0.5
-    min hsno: 0.1
-  domain: arctic
-  cice background state:
-    restart: {{ ice_rst }}
-    ncat: 5
-    ice_lev: 7
-    sno_lev: 1
-    tstep: PT1H
-  cice output:
-    restart: {{ ice_rst }}
-  output variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
-
-states:
-- input:
-     read_from_file: 1
-     basename: ./
-     ocn_filename: {{ ocn_ana }}
-     ice_filename: {{ ice_ana }}
-     date: '{{ fcst_begin }}'
-     state variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
-  output:
-     datadir: Data
-     exp: soca2cice
-     type: fc
-     date: '{{ fcst_begin }}'
diff --git a/algorithm/marine/soca_2cice_antarctic.yaml.j2 b/algorithm/marine/soca_2cice_global.yaml.j2
similarity index 76%
rename from algorithm/marine/soca_2cice_antarctic.yaml.j2
rename to algorithm/marine/soca_2cice_global.yaml.j2
index c740c53..0798d02 100644
--- a/algorithm/marine/soca_2cice_antarctic.yaml.j2
+++ b/algorithm/marine/soca_2cice_global.yaml.j2
@@ -1,29 +1,32 @@
 input geometry:
   mom6_input_nml: mom_input.nml
   fields metadata: fields_metadata.yaml
-  geom_grid_file: soca_gridspec.nc
 
 output geometry:
   mom6_input_nml: mom_input.nml
   fields metadata: fields_metadata.yaml
-  geom_grid_file: soca_gridspec.nc
 
 variable change:
   variable change name: Soca2Cice
-  do inverse: false
-  seaice edge: 0.9
-  shuffle: false  # seg. fault when true
-  rescale prior:
-    min hice: 0.5
-    min hsno: 0.1
-  domain: antarctic
+  arctic:
+    seaice edge: 0.8
+    shuffle: false
+    rescale prior:
+      rescale: true
+      min hice: 0.5
+      min hsno: 0.1
+  antarctic:
+    seaice edge: 0.9
+    shuffle: false  # seg. fault when true
+    rescale prior:
+      rescale: true
+      min hice: 0.5
+      min hsno: 0.1
   cice background state:
     restart: {{ ice_rst }}
-    grid: ' '
     ncat: 5
     ice_lev: 7
     sno_lev: 1
-    tstep: PT1H
   cice output:
     restart: {{ ice_rst }}
   output variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]

From 7d406643316163faf27d5b269a3313cdb08a50ce Mon Sep 17 00:00:00 2001
From: Cory Martin <cory.r.martin@noaa.gov>
Date: Tue, 26 Nov 2024 14:37:02 -0500
Subject: [PATCH 4/7] more changes for switching aerosol DA to JCB (#48)

---
 algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2 | 21 ++++++++++++++++++-
 algorithm/aero/aero_obs_staging.yaml.j2       |  8 +++++++
 2 files changed, 28 insertions(+), 1 deletion(-)
 create mode 100644 algorithm/aero/aero_obs_staging.yaml.j2

diff --git a/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2 b/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2
index d1f3eda..d90756e 100644
--- a/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2
+++ b/algorithm/aero/aero_gen_bmatrix_diagb.yaml.j2
@@ -73,7 +73,26 @@ variables:
   - mass_fraction_of_sea_salt003_in_air
   - mass_fraction_of_sea_salt004_in_air
 
-rescale: {{ aero_diagb_rescale_factor }}    # rescales the filtered std. dev. by "rescale"
+global rescale:
+  geometry:
+    fms initialization:
+        namelist filename: "{{aero_fv3jedi_files_path}}/fmsmpp.nml"
+        field table filename: "{{aero_fv3jedi_files_path}}/field_table"
+    akbk: "{{aero_fv3jedi_files_path}}/akbk.nc4"
+    layout:
+    - {{ aero_layout_x }}
+    - {{ aero_layout_y }}
+    npx: {{ aero_npx_clim_b }}
+    npy: {{ aero_npy_clim_b }}
+    npz: {{ aero_npz_clim_b }}
+    field metadata override: "{{aero_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml"
+  rescale stddev:
+    filetype: fms restart
+    skip coupler file: true
+    datapath: {{ aero_rescale_b_path }}
+    filename_trcr: rescale.fv_tracer.res.nc
+    filename_cplr: rescale.coupler.res
+
 number of halo points: {{ aero_diagb_n_halo }}
 number of neighbors: {{ aero_diagb_n_neighbors }}
 simple smoothing:
diff --git a/algorithm/aero/aero_obs_staging.yaml.j2 b/algorithm/aero/aero_obs_staging.yaml.j2
new file mode 100644
index 0000000..0e5c992
--- /dev/null
+++ b/algorithm/aero/aero_obs_staging.yaml.j2
@@ -0,0 +1,8 @@
+mkdir:
+    - '{{aero_obsdatain_path}}'
+copy:
+    {% for observation_from_jcb in observations %}
+    {% if use_observer(observation_from_jcb) %}
+    - ['{{aero_obsdataroot_path}}/{{aero_obsdatain_prefix}}{{observation_from_jcb}}{{aero_obsdatain_suffix}}', '{{aero_obsdatain_path}}']
+    {% endif %}
+    {% endfor %}

From c9f2d79833de83f342055140cac679e6e7ec9ff7 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Mon, 2 Dec 2024 13:19:10 -0500
Subject: [PATCH 5/7] Bug fixes and changes necessary to run the Ens. var (#46)

---
 algorithm/marine/soca_2cice_global.yaml.j2    | 17 +++++++--
 algorithm/marine/soca_diagb.yaml.j2           | 15 ++++++--
 algorithm/marine/soca_ensb.yaml.j2            | 31 ++++++++++++----
 algorithm/marine/soca_ensweights.yaml.j2      | 13 +++++--
 .../soca_parameters_diffusion_hz.yaml.j2      | 13 ++++---
 ..._background_error_static_diffusion.yaml.j2 | 35 +++++++++++++++----
 6 files changed, 101 insertions(+), 23 deletions(-)

diff --git a/algorithm/marine/soca_2cice_global.yaml.j2 b/algorithm/marine/soca_2cice_global.yaml.j2
index 0798d02..8d13d46 100644
--- a/algorithm/marine/soca_2cice_global.yaml.j2
+++ b/algorithm/marine/soca_2cice_global.yaml.j2
@@ -29,7 +29,13 @@ variable change:
     sno_lev: 1
   cice output:
     restart: {{ ice_rst }}
-  output variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
+  output variables:
+  - sea_water_potential_temperature
+  - sea_water_salinity
+  - sea_water_cell_thickness
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
 
 states:
 - input:
@@ -38,7 +44,14 @@ states:
      ocn_filename: {{ ocn_ana }}
      ice_filename: {{ ice_ana }}
      date: '{{ fcst_begin }}'
-     state variables: [sea_water_potential_temperature, sea_water_salinity, sea_water_cell_thickness, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness]
+     state variables:
+     - sea_water_potential_temperature
+     - sea_water_salinity
+     - sea_water_cell_thickness
+     - sea_ice_area_fraction
+     - sea_ice_thickness
+     - sea_ice_snow_thickness
+
   output:
      datadir: Data
      exp: soca2cice
diff --git a/algorithm/marine/soca_diagb.yaml.j2 b/algorithm/marine/soca_diagb.yaml.j2
index 02633ac..30e9c68 100644
--- a/algorithm/marine/soca_diagb.yaml.j2
+++ b/algorithm/marine/soca_diagb.yaml.j2
@@ -18,9 +18,20 @@ background error:
   type: incr
 
 variables:
-  name: [sea_water_potential_temperature, sea_water_salinity, eastward_sea_water_velocity, northward_sea_water_velocity, sea_water_cell_thickness, sea_surface_height_above_geoid, sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, mom6_mld]
+  name:
+  - sea_water_potential_temperature
+  - sea_water_salinity
+  - eastward_sea_water_velocity
+  - northward_sea_water_velocity
+  - sea_water_cell_thickness
+  - sea_surface_height_above_geoid
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
+  - mom6_mld
 
-rescale: 2.0    # rescales the filtered std. dev. by "rescale"
+vertical e-folding scale: 500.0
+rescale: 1.0    # rescales the filtered std. dev. by "rescale"
 min sst: 0.0    # Added to sst bkg. err.
 max ssh: 0.0    # Limits the amplitude of the unbalanced bkg err
 min depth: 500.0 # zero out the bkg. error. at less than min depth
diff --git a/algorithm/marine/soca_ensb.yaml.j2 b/algorithm/marine/soca_ensb.yaml.j2
index 01c9777..852850f 100644
--- a/algorithm/marine/soca_ensb.yaml.j2
+++ b/algorithm/marine/soca_ensb.yaml.j2
@@ -5,11 +5,20 @@ geometry:
 
 date: '{{ marine_window_begin_iso }}'
 
-layers variable: [hocn]
+layers variable: [sea_water_cell_thickness]
 
-increment variables: [tocn, socn, uocn, vocn, ssh, hocn, cicen, hicen, hsnon]
+increment variables:
+- sea_water_potential_temperature
+- sea_water_salinity
+- eastward_sea_water_velocity
+- northward_sea_water_velocity
+- sea_surface_height_above_geoid
+- sea_water_cell_thickness
+- sea_ice_area_fraction
+- sea_ice_thickness
+- sea_ice_snow_thickness
 
-set increment variables to zero: [ssh]
+set increment variables to zero: [sea_surface_height_above_geoid]
 
 vertical geometry:
   date: '{{ marine_window_begin_iso }}'
@@ -81,7 +90,18 @@ linear variable change:
   - linear variable change name: BalanceSOCA
 
 trajectory:
-  state variables: [tocn, socn, uocn, vocn, ssh, hocn, layer_depth, mld, cicen, hicen, hsnon]
+  state variables:
+  - sea_water_potential_temperature
+  - sea_water_salinity
+  - eastward_sea_water_velocity
+  - northward_sea_water_velocity
+  - sea_surface_height_above_geoid
+  - sea_water_cell_thickness
+  - sea_water_depth
+  - ocean_mixed_layer_thickness
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
   date: '{{ marine_window_begin_iso }}'
   basename: ./INPUT/
   ocn_filename: MOM.res.nc
@@ -89,8 +109,7 @@ trajectory:
   read_from_file: 1
 
 output increment:
-  # TODO: Revert this when fms can take more than 128 charactres file names
-  datadir: '{{ enspert_relpath }}/enspert/'
+  datadir: '{{ enspert_relpath }}/'
   date: '{{ marine_window_begin_iso }}'
   exp: trash
   type: incr
diff --git a/algorithm/marine/soca_ensweights.yaml.j2 b/algorithm/marine/soca_ensweights.yaml.j2
index 792bbdc..9f818b3 100644
--- a/algorithm/marine/soca_ensweights.yaml.j2
+++ b/algorithm/marine/soca_ensweights.yaml.j2
@@ -5,8 +5,17 @@ geometry:
 date: '{{ marine_window_middle_iso }}'
 
 variables:
-  ice: [cicen, hicen, hsnon]
-  ocean: [tocn, socn, uocn, vocn, ssh]
+  ice:
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
+
+  ocean:
+  - sea_water_potential_temperature
+  - sea_water_salinity
+  - eastward_sea_water_velocity
+  - northward_sea_water_velocity
+  - sea_surface_height_above_geoid
 
 background:
   date: '{{ marine_window_begin_iso }}'
diff --git a/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2 b/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
index c79d469..a0fc0e1 100644
--- a/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
+++ b/algorithm/marine/soca_parameters_diffusion_hz.yaml.j2
@@ -30,8 +30,11 @@ background error:
         write:
           filepath: ./staticb/hz_ocean
 
-      - horizontal:
-          as gaussian: true
-          fixed value: 50000.0
-        write:
-          filepath: ./staticb/hz_ice
+# TODO(G): OK to not use what's below but it will need
+#          to be fixed when we add ice thickness and
+#          snow depth
+#      - horizontal:
+#          as gaussian: true
+#          fixed value: 50000.0
+#        write:
+#          filepath: ./staticb/hz_ice
diff --git a/model/marine/marine_background_error_static_diffusion.yaml.j2 b/model/marine/marine_background_error_static_diffusion.yaml.j2
index 0c57790..4b31572 100644
--- a/model/marine/marine_background_error_static_diffusion.yaml.j2
+++ b/model/marine/marine_background_error_static_diffusion.yaml.j2
@@ -3,15 +3,22 @@ saber central block:
   saber block name: diffusion
   read:
     groups:
-    - variables: [sea_water_potential_temperature, sea_water_salinity, sea_surface_height_above_geoid]
+    - variables:
+      - sea_water_potential_temperature
+      - sea_water_salinity
+      - sea_surface_height_above_geoid
+      - sea_ice_area_fraction
       horizontal:
         filepath: ./staticb/hz_ocean
       vertical:
         levels: {{marine_vt_levels}}
         filepath: ./staticb/vt_ocean
-    - variables: [sea_ice_area_fraction]
-      horizontal:
-        filepath: ./staticb/hz_ice
+# TODO(G): OK to not use what's below but it will need
+#          to be fixed when we add ice thickness and
+#          snow depth
+#    - variables: [sea_ice_area_fraction]
+#      horizontal:
+#        filepath: ./staticb/hz_ice
 
 saber outer blocks:
 - saber block name: StdDev
@@ -24,7 +31,23 @@ saber outer blocks:
       read_from_file: 3
 
 linear variable change:
-  input variables: [sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, sea_water_salinity, sea_water_potential_temperature, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
-  output variables: [sea_ice_area_fraction, sea_ice_thickness, sea_ice_snow_thickness, sea_water_salinity, sea_water_potential_temperature, eastward_sea_water_velocity, northward_sea_water_velocity, sea_surface_height_above_geoid]
+  input variables:
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
+  - sea_water_salinity
+  - sea_water_potential_temperature
+  - eastward_sea_water_velocity
+  - northward_sea_water_velocity
+  - sea_surface_height_above_geoid
+  output variables:
+  - sea_ice_area_fraction
+  - sea_ice_thickness
+  - sea_ice_snow_thickness
+  - sea_water_salinity
+  - sea_water_potential_temperature
+  - eastward_sea_water_velocity
+  - northward_sea_water_velocity
+  - sea_surface_height_above_geoid
   linear variable changes:
   - linear variable change name: BalanceSOCA

From 5a468be9996dd44cb45f05bb4445da1b3a340a5b Mon Sep 17 00:00:00 2001
From: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu, 12 Dec 2024 14:28:59 -0500
Subject: [PATCH 6/7] Changes to get snow 2DVar for deterministic and ensemble
 mean working (#52)

Changes to JCB templates to allow for 2DVar snow analyses for the
deterministic and the ensemble mean for GDAS.

---------

Co-authored-by: Jiarui Dong <Jiarui.Dong@noaa.gov>
Co-authored-by: yuanxue2870 <136842224+yuanxue2870@users.noreply.github.com>
---
 algorithm/snow/fv3jedi_snow_ensmean.yaml.j2 |  26 +++++
 algorithm/snow/snow_obs_staging.yaml.j2     |  16 +++
 model/snow/snow_3dvar_outer_loop_1.yaml.j2  |  25 +++++
 model/snow/snow_background.yaml.j2          |   8 ++
 model/snow/snow_background_error.yaml.j2    |  47 ++++++++
 model/snow/snow_final_increment_fms.yaml.j2 |  20 ++++
 model/snow/snow_geometry.yaml.j2            |   0
 model/snow/snow_geometry_background.yaml.j2 |  11 ++
 observations/snow/adpsfc_snow.yaml.j2       | 114 +++++++++++++++++++
 observations/snow/ghcn_snow.yaml.j2         |  57 ++++++++++
 observations/snow/ims_snow.yaml.j2          |  68 ++++++++++++
 observations/snow/sfcsno.yaml.j2            | 116 ++++++++++++++++++++
 observations/snow/snocvr_snow.yaml.j2       | 109 ++++++++++++++++++
 13 files changed, 617 insertions(+)
 create mode 100644 algorithm/snow/fv3jedi_snow_ensmean.yaml.j2
 create mode 100644 algorithm/snow/snow_obs_staging.yaml.j2
 create mode 100644 model/snow/snow_3dvar_outer_loop_1.yaml.j2
 create mode 100644 model/snow/snow_background.yaml.j2
 create mode 100644 model/snow/snow_background_error.yaml.j2
 create mode 100644 model/snow/snow_final_increment_fms.yaml.j2
 delete mode 100644 model/snow/snow_geometry.yaml.j2
 create mode 100644 model/snow/snow_geometry_background.yaml.j2
 create mode 100644 observations/snow/adpsfc_snow.yaml.j2
 create mode 100644 observations/snow/ghcn_snow.yaml.j2
 create mode 100644 observations/snow/ims_snow.yaml.j2
 create mode 100644 observations/snow/sfcsno.yaml.j2
 create mode 100644 observations/snow/snocvr_snow.yaml.j2

diff --git a/algorithm/snow/fv3jedi_snow_ensmean.yaml.j2 b/algorithm/snow/fv3jedi_snow_ensmean.yaml.j2
new file mode 100644
index 0000000..bf13c15
--- /dev/null
+++ b/algorithm/snow/fv3jedi_snow_ensmean.yaml.j2
@@ -0,0 +1,26 @@
+geometry:
+{% filter indent(width=2) %}
+{% set geometry_background_file = geometry_background_file|default(model_component ~ 'geometry_background', true) ~ '.yaml.j2' %}
+{% include geometry_background_file %}
+{% endfilter %}
+mean output:
+  filetype: fms restart
+  datapath: ./bkg/ensmean
+  filename_core: fv_core.res.nc
+  filename_trcr: fv_tracer.res.nc
+  filename_sfcd: sfc_data.nc
+  filename_sfcw: fv_srf_wnd.res.nc
+  filename_cplr: coupler.res
+ensemble:
+  members from template:
+    template:
+      datetime: '{{ snow_background_time_iso }}'
+      filetype: fms restart
+      state variables: [snodl,vtype,slmsk,orog_filt,stc,sheleg]
+      datapath: ./bkg/mem%mem%/
+      filename_sfcd: '{{ snow_background_time_fv3 }}.sfc_data.nc'
+      filename_cplr: '{{ snow_background_time_fv3 }}.coupler.res'
+      filename_orog: '{{ snow_orog_prefix }}_oro_data.nc'
+    pattern: '%mem%'
+    nmembers: {{ snow_number_ensemble_members }}
+    zero padding: 3
diff --git a/algorithm/snow/snow_obs_staging.yaml.j2 b/algorithm/snow/snow_obs_staging.yaml.j2
new file mode 100644
index 0000000..a8d3dc8
--- /dev/null
+++ b/algorithm/snow/snow_obs_staging.yaml.j2
@@ -0,0 +1,16 @@
+mkdir:
+    - '{{snow_obsdatain_path}}'
+copy:
+    {% for observation_from_jcb in observations %}
+      {% if use_observer(observation_from_jcb) %}
+        {% if not observation_from_jcb == 'ims_snow' %}
+        # skip if ims_snow since it is special
+          {% if observation_from_jcb == 'snocvr_snow' %}
+          # snocvr_snow is a .nc file, TODO rename this eventually?
+    - ['{{snow_obsdataroot_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}.nc4', '{{snow_obsdatain_path}}']
+          {% else %}
+    - ['{{snow_obsdataroot_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}{{snow_obsdatain_suffix}}', '{{snow_obsdatain_path}}']
+          {% endif %}
+        {% endif %}
+      {% endif %}
+    {% endfor %}
diff --git a/model/snow/snow_3dvar_outer_loop_1.yaml.j2 b/model/snow/snow_3dvar_outer_loop_1.yaml.j2
new file mode 100644
index 0000000..48de31e
--- /dev/null
+++ b/model/snow/snow_3dvar_outer_loop_1.yaml.j2
@@ -0,0 +1,25 @@
+- ninner: 50
+  gradient norm reduction: 1e-10
+  test: on
+  geometry:
+    fms initialization:
+      namelist filename: {{ snow_fv3jedi_files_path }}/fmsmpp.nml
+      field table filename: {{ snow_fv3jedi_files_path }}/field_table
+    akbk: {{ snow_fv3jedi_files_path }}/akbk.nc4
+    layout:
+    - {{ snow_layout_x }}
+    - {{ snow_layout_y }}
+    npx: {{ snow_npx_anl }}
+    npy: {{ snow_npy_anl }}
+    npz: {{ snow_npz_anl }}
+    field metadata override: {{ snow_fv3jedi_files_path }}/fv3jedi_fieldmetadata_restart.yaml
+    time invariant fields:
+      state fields:
+        datetime: '{{ snow_background_time_iso }}'
+        filetype: fms restart
+        skip coupler file: true
+        state variables: [orog_filt]
+        datapath: {{ snow_orog_files_path }}/
+        filename_orog: {{ snow_orog_prefix }}_oro_data.nc
+  diagnostics:
+    departures: bkgmob
diff --git a/model/snow/snow_background.yaml.j2 b/model/snow/snow_background.yaml.j2
new file mode 100644
index 0000000..737d5e3
--- /dev/null
+++ b/model/snow/snow_background.yaml.j2
@@ -0,0 +1,8 @@
+datapath: {{ snow_background_path }}
+filetype: fms restart
+skip coupler file: true
+datetime: '{{ snow_background_time_iso }}'
+state variables: [snodl,vtype,slmsk,sheleg,orog_filt]
+filename_sfcd: '{{ snow_background_time_fv3 }}.sfc_data.nc'
+filename_cplr: '{{ snow_background_time_fv3 }}.coupler.res'
+filename_orog: '{{ snow_orog_prefix }}_oro_data.nc'
diff --git a/model/snow/snow_background_error.yaml.j2 b/model/snow/snow_background_error.yaml.j2
new file mode 100644
index 0000000..3d85303
--- /dev/null
+++ b/model/snow/snow_background_error.yaml.j2
@@ -0,0 +1,47 @@
+covariance model: SABER
+saber central block:
+  saber block name: BUMP_NICAS
+  read:
+    general:
+      universe length-scale: 300000.0
+    drivers:
+      multivariate strategy: univariate
+      read global nicas: true
+    nicas:
+      explicit length-scales: true
+      horizontal length-scale:
+      - groups:
+        - totalSnowDepth_shadowLevels
+        value: 250000.0
+      vertical length-scale:
+      - groups:
+        - totalSnowDepth_shadowLevels
+        value: 0.0
+      interpolation type:
+      - groups:
+        - totalSnowDepth_shadowLevels
+        type: c0
+      same horizontal convolution: true
+    io:
+      data directory: {{snow_bump_data_directory}}
+      files prefix: snow_bump_nicas_250km_shadowlevels
+saber outer blocks:
+- saber block name: ShadowLevels
+  fields metadata:
+    totalSnowDepth:
+      vert_coord: filtered_orography
+  calibration:
+    number of shadow levels: 50
+    lowest shadow level: -450.0
+    highest shadow level: 8850.0
+    vertical length-scale: 2000.0
+- saber block name: BUMP_StdDev
+  read:
+    drivers:
+      compute variance: true
+    variance:
+      explicit stddev: true
+      stddev:
+      - variables:
+        - totalSnowDepth
+        value: 30.0
diff --git a/model/snow/snow_final_increment_fms.yaml.j2 b/model/snow/snow_final_increment_fms.yaml.j2
new file mode 100644
index 0000000..3bd182f
--- /dev/null
+++ b/model/snow/snow_final_increment_fms.yaml.j2
@@ -0,0 +1,20 @@
+output:
+  state component:
+    datapath: ./anl
+    prefix: snowinc
+    filetype: fms restart
+    filename_sfcd: '{{ snow_background_time_fv3 }}.sfc_data.nc'
+    filename_cplr: '{{ snow_background_time_fv3 }}.coupler.res'
+    state variables: [snodl,vtype,slmsk]
+geometry:
+  fms initialization:
+    namelist filename: "{{ snow_fv3jedi_files_path }}/fmsmpp.nml"
+    field table filename: "{{ snow_fv3jedi_files_path }}/field_table"
+  akbk: "{{ snow_fv3jedi_files_path }}/akbk.nc4"
+  layout:
+  - {{ snow_layout_x }}
+  - {{ snow_layout_y }}
+  npx: {{ snow_npx_ges }}
+  npy: {{ snow_npy_ges }}
+  npz: {{ snow_npz_ges }}
+  field metadata override: "{{ snow_fv3jedi_files_path }}/fv3jedi_fieldmetadata_restart.yaml"
diff --git a/model/snow/snow_geometry.yaml.j2 b/model/snow/snow_geometry.yaml.j2
deleted file mode 100644
index e69de29..0000000
diff --git a/model/snow/snow_geometry_background.yaml.j2 b/model/snow/snow_geometry_background.yaml.j2
new file mode 100644
index 0000000..e53d5ae
--- /dev/null
+++ b/model/snow/snow_geometry_background.yaml.j2
@@ -0,0 +1,11 @@
+fms initialization:
+  namelist filename: "{{snow_fv3jedi_files_path}}/fmsmpp.nml"
+  field table filename: "{{snow_fv3jedi_files_path}}/field_table"
+akbk: "{{snow_fv3jedi_files_path}}/akbk.nc4"
+layout:
+- {{snow_layout_x}}
+- {{snow_layout_y}}
+npx: {{snow_npx_ges}}
+npy: {{snow_npy_ges}}
+npz: {{snow_npz_ges}}
+field metadata override: "{{snow_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml"
diff --git a/observations/snow/adpsfc_snow.yaml.j2 b/observations/snow/adpsfc_snow.yaml.j2
new file mode 100644
index 0000000..2f7726b
--- /dev/null
+++ b/observations/snow/adpsfc_snow.yaml.j2
@@ -0,0 +1,114 @@
+-
+
+  # Observation Space (I/O)
+  # -----------------------
+  obs space:
+    name: adpsfc_snow
+    obsdatain:
+      engine:
+        type: H5File
+        obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}{{snow_obsdatain_suffix}}"
+    obsdataout:
+      engine:
+        type: H5File
+        obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+    simulated variables: [totalSnowDepth]
+  #
+
+  # Observation Operator
+  # --------------------
+  obs operator:
+    name: Composite
+    components:
+    - name: Identity
+    - name: BackgroundErrorIdentity
+  obs error:
+    covariance model: diagonal
+
+  # Observation Filters (QC)
+  # ------------------------
+  obs pre filters:
+    - filter: Perform Action
+      filter variables:
+      - name: totalSnowDepth
+      action:
+        name: assign error
+        error parameter: 40.0
+    - filter: Variable Assignment
+      assignments:
+      - name: GrossErrorProbability/totalSnowDepth
+        type: float
+        value: 0.02
+      - name: BkgError/totalSnowDepth_background_error
+        type: float
+        value: 30.0
+  obs prior filters:
+    - filter: Bounds Check
+      filter variables:
+      - name: totalSnowDepth
+      minvalue: 0.0
+      maxvalue: 20000.0
+      action:
+        name: reject
+    - filter: Domain Check
+      where:
+      - variable:
+          name: MetaData/stationElevation
+        value: is_valid
+    - filter: Domain Check # land only
+      where:
+      - variable:
+          name: GeoVaLs/slmsk
+        minvalue: 0.5
+        maxvalue: 1.5
+    - filter: RejectList  # no land-ice
+      where:
+      - variable:
+          name: GeoVaLs/vtype
+        minvalue: 14.5
+        maxvalue: 15.5
+    - filter: Difference Check # elevation check
+        reference: MetaData/stationElevation
+        value: GeoVaLs/filtered_orography
+        threshold: 200.
+    - filter: BlackList
+      where:
+      - variable:
+          name: MetaData/stationIdentification
+        is_in: [71120,71397,71621,71727,71816]
+        size where true: 5
+  obs post filters:
+    - filter: Background Check # gross error check
+      filter variables:
+      - name: totalSnowDepth
+      threshold: 6.25
+      action:
+        name: reject
+    - filter: Temporal Thinning
+      min_spacing: '{{ window_length }}'
+      seed_time: '{{ snow_background_time_iso }}'
+      category_variable:
+        name: MetaData/stationIdentification
+    - filter: Met Office Buddy Check
+      filter variables:
+      - name: totalSnowDepth
+        rejection_threshold: 0.5
+        traced_boxes: # trace all observations
+          min_latitude: -90
+          max_latitude:  90
+          min_longitude: -180
+          max_longitude:  180
+        search_radius: 150 # km
+        station_id_variable:
+          name: MetaData/stationIdentification
+        num_zonal_bands: 24
+        sort_by_pressure: false
+        max_total_num_buddies: 15
+        max_num_buddies_from_single_band: 10
+        max_num_buddies_with_same_station_id: 5
+        use_legacy_buddy_collector: false
+        horizontal_correlation_scale: { "-90": 150, "90": 150 }
+        temporal_correlation_scale: PT6H
+        damping_factor_1: 1.0
+        damping_factor_2: 1.0
+        background_error_group: BkgError
diff --git a/observations/snow/ghcn_snow.yaml.j2 b/observations/snow/ghcn_snow.yaml.j2
new file mode 100644
index 0000000..37022cb
--- /dev/null
+++ b/observations/snow/ghcn_snow.yaml.j2
@@ -0,0 +1,57 @@
+ -
+
+  # Observation Space (I/O)
+  # -----------------------
+  obs space:
+    name: ghcn_snow
+    obsdatain:
+      engine:
+        type: H5File
+        obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}.nc"
+    obsdataout:
+      engine:
+        type: H5File
+        obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+    simulated variables: [totalSnowDepth]
+  #
+
+  # Observation Operator
+  # --------------------
+  obs operator:
+    name: Identity
+  #
+
+  # Observation Filters (QC)
+  # ------------------------
+  obs filters:
+    - filter: Bounds Check
+      filter variables:
+      - name: totalSnowDepth
+      minvalue: 0.0
+    - filter: Domain Check
+      where:
+      - variable:
+          name: MetaData/stationElevation
+        value: is_valid
+    - filter: Domain Check # land only
+      where:
+      - variable:
+          name: GeoVaLs/slmsk
+        minvalue: 0.5
+        maxvalue: 1.5
+    - filter: RejectList  # no land-ice
+      where:
+      - variable:
+          name: GeoVaLs/vtype
+        minvalue: 14.5
+        maxvalue: 15.5
+    - filter: Difference Check # elevation check
+        reference: MetaData/stationElevation
+        value: GeoVaLs/filtered_orography
+        threshold: 200.
+    - filter: Background Check
+      filter variables:
+      - name: totalSnowDepth
+      threshold: 6.25
+      action:
+        name: reject
diff --git a/observations/snow/ims_snow.yaml.j2 b/observations/snow/ims_snow.yaml.j2
new file mode 100644
index 0000000..612f2d7
--- /dev/null
+++ b/observations/snow/ims_snow.yaml.j2
@@ -0,0 +1,68 @@
+-
+
+  # Observation Space (I/O)
+  # -----------------------
+  obs space:
+    name: ims_snow
+    obsdatain:
+      engine:
+        type: H5File
+        obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}.tm00.nc"
+        missing file action: warn  
+    obsdataout:
+      engine:
+        type: H5File
+        obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+    simulated variables: [totalSnowDepth]
+  #
+
+  # Observation Operator
+  # --------------------
+  obs operator:
+    name: Identity
+  #
+
+  # Observation Filters (QC)
+  # ------------------------
+  obs pre filters:
+  # assign observation error
+  - filter: Perform Action
+    filter variables:
+    - name: totalSnowDepth
+    action:
+      name: assign error
+      error parameter: 80.0
+
+  obs prior filters:
+  # remove land-ice and sea points
+  - filter: Domain Check # land only
+    where:
+    - variable:
+        name: GeoVaLs/slmsk
+      minvalue: 0.5
+      maxvalue: 1.5
+  - filter: RejectList  # no land-ice
+    where:
+    - variable:
+        name: GeoVaLs/vtype
+      minvalue: 14.5
+      maxvalue: 15.5
+
+  obs post filters:
+  # gross error check
+  - filter: Background Check
+    filter variables:
+    - name: totalSnowDepth
+    threshold: 3.
+    action:
+      name: reject
+
+  # thinning of remaining obs
+  - filter: Gaussian Thinning
+    horizontal_mesh: 40.0 # km
+
+  # excludes where both obs & mod = 100% (set in IMS_proc)
+  - filter: Bounds Check
+    filter variables:
+    - name: totalSnowDepth
+    minvalue: 0.0
diff --git a/observations/snow/sfcsno.yaml.j2 b/observations/snow/sfcsno.yaml.j2
new file mode 100644
index 0000000..a8f340a
--- /dev/null
+++ b/observations/snow/sfcsno.yaml.j2
@@ -0,0 +1,116 @@
+-
+
+  # Observation Space (I/O)
+  # -----------------------
+  obs space:
+    name: sfcsno
+    obsdatain:
+      engine:
+        type: bufr
+        obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}sfcsno.tm00.bufr_d"
+        mapping file: "{{snow_obsdatain_path}}/bufr_sfcsno_mapping.yaml"
+    obsdataout:
+      engine:
+        type: H5File
+        obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}sfcsno{{snow_obsdataout_suffix}}"
+    simulated variables: [totalSnowDepth]
+  #
+
+  # Observation Operator
+  # --------------------
+  obs operator:
+    name: Composite
+    components:
+    - name: Identity
+    - name: BackgroundErrorIdentity
+  linear obs operator:
+    name: Identity
+  #
+
+  # Observation Filters (QC)
+  # ------------------------
+  obs pre filters:
+    - filter: Perform Action
+      filter variables:
+      - name: totalSnowDepth
+      action:
+        name: assign error
+        error parameter: 40.0
+    - filter: Variable Assignment
+      assignments:
+      - name: GrossErrorProbability/totalSnowDepth
+        type: float
+        value: 0.02
+      - name: BkgError/totalSnowDepth_background_error
+        type: float
+        value: 30.0
+  obs prior filters:
+    - filter: Bounds Check
+      filter variables:
+      - name: totalSnowDepth
+      minvalue: 0.0
+      maxvalue: 20000.0
+      action:
+        name: reject
+    - filter: Domain Check
+      where:
+      - variable:
+          name: MetaData/stationElevation
+        value: is_valid
+    - filter: Domain Check # land only
+      where:
+      - variable:
+          name: GeoVaLs/slmsk
+        minvalue: 0.5
+        maxvalue: 1.5
+    - filter: RejectList  # no land-ice
+      where:
+      - variable:
+          name: GeoVaLs/vtype
+        minvalue: 14.5
+        maxvalue: 15.5
+    - filter: Difference Check # elevation check
+        reference: MetaData/stationElevation
+        value: GeoVaLs/filtered_orography
+        threshold: 200.
+    - filter: BlackList
+      where:
+      - variable:
+          name: MetaData/stationIdentification
+        is_in: [71120,71397,71621,71727,71816]
+        size where true: 5
+  obs post filters:
+    - filter: Background Check # gross error check
+      filter variables:
+      - name: totalSnowDepth
+      threshold: 6.25
+      action:
+        name: reject
+    - filter: Temporal Thinning
+      min_spacing: '{{ window_length }}'
+      seed_time: '{{ snow_background_time_iso }}'
+      category_variable:
+        name: MetaData/stationIdentification
+    - filter: Met Office Buddy Check
+      filter variables:
+      - name: totalSnowDepth
+        rejection_threshold: 0.5
+        traced_boxes: # trace all observations
+          min_latitude: -90
+          max_latitude:  90
+          min_longitude: -180
+          max_longitude:  180
+        search_radius: 150 # km
+        station_id_variable:
+          name: MetaData/stationIdentification
+        num_zonal_bands: 24
+        sort_by_pressure: false
+        max_total_num_buddies: 15
+        max_num_buddies_from_single_band: 10
+        max_num_buddies_with_same_station_id: 5
+        use_legacy_buddy_collector: false
+        horizontal_correlation_scale: { "-90": 150, "90": 150 }
+        temporal_correlation_scale: PT6H
+        damping_factor_1: 1.0
+        damping_factor_2: 1.0
+        background_error_group: BkgError
diff --git a/observations/snow/snocvr_snow.yaml.j2 b/observations/snow/snocvr_snow.yaml.j2
new file mode 100644
index 0000000..b072f7f
--- /dev/null
+++ b/observations/snow/snocvr_snow.yaml.j2
@@ -0,0 +1,109 @@
+-
+
+  # Observation Space (I/O)
+  # -----------------------
+  obs space:
+    name: snocvr_snow
+    obsdatain:
+      engine:
+        type: H5File
+        obsfile: "{{snow_obsdatain_path}}/{{snow_obsdatain_prefix}}{{observation_from_jcb}}.nc4"
+    obsdataout:
+      engine:
+        type: H5File
+        obsfile: "{{snow_obsdataout_path}}/{{snow_obsdataout_prefix}}{{observation_from_jcb}}{{snow_obsdataout_suffix}}"
+    simulated variables: [totalSnowDepth]
+  #
+
+  # Observation Operator
+  # --------------------
+  obs operator:
+    name: Composite
+    components:
+    - name: Identity
+    - name: BackgroundErrorIdentity
+  linear obs operator:
+    name: Identity
+  #
+
+  # Observation Filters (QC)
+  # ------------------------
+  obs pre filters:
+    - filter: Perform Action
+      filter variables:
+      - name: totalSnowDepth
+      action:
+        name: assign error
+        error parameter: 40.0
+    - filter: Variable Assignment
+      assignments:
+      - name: GrossErrorProbability/totalSnowDepth
+        type: float
+        value: 0.02
+      - name: BkgError/totalSnowDepth_background_error
+        type: float
+        value: 30.0
+  obs prior filters:
+    - filter: Bounds Check
+      filter variables:
+      - name: totalSnowDepth
+      minvalue: 0.0
+      maxvalue: 20000.0
+      action:
+        name: reject
+    - filter: Domain Check
+      where:
+      - variable:
+          name: MetaData/stationElevation
+        value: is_valid
+    - filter: Domain Check # land only
+      where:
+      - variable:
+          name: GeoVaLs/slmsk
+        minvalue: 0.5
+        maxvalue: 1.5
+    - filter: RejectList  # no land-ice
+      where:
+      - variable:
+          name: GeoVaLs/vtype
+        minvalue: 14.5
+        maxvalue: 15.5
+    - filter: Difference Check # elevation check
+        reference: MetaData/stationElevation
+        value: GeoVaLs/filtered_orography
+        threshold: 200.
+  obs post filters:
+    - filter: Background Check # gross error check
+      filter variables:
+      - name: totalSnowDepth
+      threshold: 6.25
+      action:
+        name: reject
+    - filter: Temporal Thinning
+      min_spacing: '{{ window_length }}'
+      seed_time: '{{ snow_background_time_iso }}'
+      category_variable:
+        name: MetaData/stationIdentification
+    - filter: Met Office Buddy Check
+      filter variables:
+      - name: totalSnowDepth
+        rejection_threshold: 0.5
+        traced_boxes: # trace all observations
+          min_latitude: -90
+          max_latitude:  90
+          min_longitude: -180
+          max_longitude:  180
+        search_radius: 150 # km
+        station_id_variable:
+          name: MetaData/stationIdentification
+        num_zonal_bands: 24
+        sort_by_pressure: false
+        max_total_num_buddies: 15
+        max_num_buddies_from_single_band: 10
+        max_num_buddies_with_same_station_id: 5
+        use_legacy_buddy_collector: false
+        horizontal_correlation_scale: { "-90": 150, "90": 150 }
+        temporal_correlation_scale: PT6H
+        damping_factor_1: 1.0
+        damping_factor_2: 1.0
+        background_error_group: BkgError

From accd7a5bf96524430d8d03a4b2d707eca4c48c13 Mon Sep 17 00:00:00 2001
From: Jiarui Dong <Jiarui.Dong@noaa.gov>
Date: Fri, 13 Dec 2024 09:29:40 -0500
Subject: [PATCH 7/7] Fix the ParserError due to the indent spaces. (#54)

This PR fixes the issues with yaml format for the `Difference Check`
filter.
---
 observations/snow/adpsfc_snow.yaml.j2 | 6 +++---
 observations/snow/ghcn_snow.yaml.j2   | 6 +++---
 observations/snow/sfcsno.yaml.j2      | 6 +++---
 observations/snow/snocvr_snow.yaml.j2 | 6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/observations/snow/adpsfc_snow.yaml.j2 b/observations/snow/adpsfc_snow.yaml.j2
index 2f7726b..f0fe2fd 100644
--- a/observations/snow/adpsfc_snow.yaml.j2
+++ b/observations/snow/adpsfc_snow.yaml.j2
@@ -68,9 +68,9 @@
         minvalue: 14.5
         maxvalue: 15.5
     - filter: Difference Check # elevation check
-        reference: MetaData/stationElevation
-        value: GeoVaLs/filtered_orography
-        threshold: 200.
+      reference: MetaData/stationElevation
+      value: GeoVaLs/filtered_orography
+      threshold: 200.
     - filter: BlackList
       where:
       - variable:
diff --git a/observations/snow/ghcn_snow.yaml.j2 b/observations/snow/ghcn_snow.yaml.j2
index 37022cb..ea7a956 100644
--- a/observations/snow/ghcn_snow.yaml.j2
+++ b/observations/snow/ghcn_snow.yaml.j2
@@ -46,9 +46,9 @@
         minvalue: 14.5
         maxvalue: 15.5
     - filter: Difference Check # elevation check
-        reference: MetaData/stationElevation
-        value: GeoVaLs/filtered_orography
-        threshold: 200.
+      reference: MetaData/stationElevation
+      value: GeoVaLs/filtered_orography
+      threshold: 200.
     - filter: Background Check
       filter variables:
       - name: totalSnowDepth
diff --git a/observations/snow/sfcsno.yaml.j2 b/observations/snow/sfcsno.yaml.j2
index a8f340a..f1ef5d4 100644
--- a/observations/snow/sfcsno.yaml.j2
+++ b/observations/snow/sfcsno.yaml.j2
@@ -70,9 +70,9 @@
         minvalue: 14.5
         maxvalue: 15.5
     - filter: Difference Check # elevation check
-        reference: MetaData/stationElevation
-        value: GeoVaLs/filtered_orography
-        threshold: 200.
+      reference: MetaData/stationElevation
+      value: GeoVaLs/filtered_orography
+      threshold: 200.
     - filter: BlackList
       where:
       - variable:
diff --git a/observations/snow/snocvr_snow.yaml.j2 b/observations/snow/snocvr_snow.yaml.j2
index b072f7f..29ba159 100644
--- a/observations/snow/snocvr_snow.yaml.j2
+++ b/observations/snow/snocvr_snow.yaml.j2
@@ -69,9 +69,9 @@
         minvalue: 14.5
         maxvalue: 15.5
     - filter: Difference Check # elevation check
-        reference: MetaData/stationElevation
-        value: GeoVaLs/filtered_orography
-        threshold: 200.
+      reference: MetaData/stationElevation
+      value: GeoVaLs/filtered_orography
+      threshold: 200.
   obs post filters:
     - filter: Background Check # gross error check
       filter variables: