From 2a70595d80b80c73c24171280952d795a8c3363a Mon Sep 17 00:00:00 2001
From: CoryMartin-NOAA <cory.r.martin@noaa.gov>
Date: Fri, 11 Oct 2024 16:47:50 +0000
Subject: [PATCH] commit before trying in workflow

---
 parm/jcb-gdas                            |   2 +-
 parm/snow/jcb-base.yaml.j2               |  56 ++++++------
 parm/snow/jcb-prototype_2dvar.yaml.j2    |  12 +++
 parm/snow/obs/config/adpsfc_snow.yaml.j2 | 109 ----------------------
 parm/snow/obs/config/ghcn_snow.yaml.j2   |  53 -----------
 parm/snow/obs/config/ims_snow.yaml.j2    |  46 ----------
 parm/snow/obs/config/sfcsno_snow.yaml.j2 | 110 -----------------------
 parm/snow/obs/config/snocvr_snow.yaml.j2 | 103 ---------------------
 8 files changed, 41 insertions(+), 450 deletions(-)
 create mode 100644 parm/snow/jcb-prototype_2dvar.yaml.j2
 delete mode 100644 parm/snow/obs/config/adpsfc_snow.yaml.j2
 delete mode 100644 parm/snow/obs/config/ghcn_snow.yaml.j2
 delete mode 100644 parm/snow/obs/config/ims_snow.yaml.j2
 delete mode 100644 parm/snow/obs/config/sfcsno_snow.yaml.j2
 delete mode 100644 parm/snow/obs/config/snocvr_snow.yaml.j2

diff --git a/parm/jcb-gdas b/parm/jcb-gdas
index 2b46aa19b..b9c7b92ba 160000
--- a/parm/jcb-gdas
+++ b/parm/jcb-gdas
@@ -1 +1 @@
-Subproject commit 2b46aa19b22df22f33ef0be5030fb719a8fa6298
+Subproject commit b9c7b92bada9db0e08fdff291e08f48cd382029a
diff --git a/parm/snow/jcb-base.yaml.j2 b/parm/snow/jcb-base.yaml.j2
index 672b1bf8f..283c2761e 100644
--- a/parm/snow/jcb-base.yaml.j2
+++ b/parm/snow/jcb-base.yaml.j2
@@ -3,8 +3,8 @@
 algorithm_path: "{{PARMgfs}}/gdas/jcb-algorithms"
 app_path_algorithm: "{{PARMgfs}}/gdas/jcb-gdas/algorithm/snow"
 app_path_model: "{{PARMgfs}}/gdas/jcb-gdas/model/snow"
-app_path_observations: "{{PARMgfs}}/gdas/jcb-gdas/observations/atmosphere"
-app_path_observation_chronicle: "{{PARMgfs}}/gdas/jcb-gdas/observation_chronicle/atmosphere"
+app_path_observations: "{{PARMgfs}}/gdas/jcb-gdas/observations/snow"
+app_path_observation_chronicle: "{{PARMgfs}}/gdas/jcb-gdas/observation_chronicle/snow"
 
 
 # Places where we deviate from the generic file name of a yaml
@@ -37,12 +37,12 @@ snow_increment_time_fv3: "{{ bkg_time_fv3 }}"
 
 # Analysis standard things
 # ------------------------
-analysis_variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+analysis_variables: [totalSnowDepth]
 minimizer: DRPCG
 final_diagnostics_departures: anlmob
 final_prints_frequency: PT3H
 cost_type: 3D-Var
-number_of_outer_loops: 2
+number_of_outer_loops: 1
 
 # Model things
 # ------------
@@ -52,9 +52,9 @@ layout_y: {{ layout_y | default(1, true) }}
 npx_ges: {{ npx_ges | default(49, true) }}
 npy_ges: {{ npy_ges | default(49, true) }}
 npz_ges: {{ npz_ges | default(127, true) }}
-npx_anl: {{ npx_anl | default(49, true) }}
-npy_anl: {{ npy_anl | default(49, true) }}
-npz_anl: {{ npz_anl | default(127, true) }}
+npx_anl: {{ npz_ges | default(49, true) }}
+npy_anl: {{ npz_ges | default(49, true) }}
+npz_anl: {{ npz_ges | default(127, true) }}
 
 fv3jedi_files_path: ./fv3jedi  # Ideally this would be {{DATA}}/fv3jedi but FMS
 
@@ -72,7 +72,7 @@ layout_gsib_y: {{ layout_gsib_y | default(1, true) }}
 background_error_file: "{{BERROR_YAML}}"
 
 # Forecasting
-forecast_length: "{{ ATM_WINDOW_LENGTH }}"
+forecast_length: "{{ SNOW_WINDOW_LENGTH }}"
 forecast_timestep: "{{ BKG_TSTEP }}"
 
 # Write final increment on Guassian grid in variational
@@ -86,28 +86,28 @@ observations: all_observations
 crtm_coefficient_path: "{{ DATA }}/crtm/"
 
 # Naming conventions for observational files
-atm_obsdatain_path: "{{atm_obsdatain_path}}"
-atm_obsdatain_prefix: "{{OPREFIX}}"
-atm_obsdatain_suffix: ".tm00.nc"
+snow_obsdatain_path: "{{snow_obsdatain_path}}"
+snow_obsdatain_prefix: "{{OPREFIX}}"
+snow_obsdatain_suffix: ".tm00.nc"
 
-atm_obsdataout_path: "{{atm_obsdataout_path}}"
-atm_obsdataout_prefix: diag_
-atm_obsdataout_suffix: "_{{ current_cycle | to_YMDH }}.nc"
+snow_obsdataout_path: "{{snow_obsdataout_path}}"
+snow_obsdataout_prefix: diag_
+snow_obsdataout_suffix: "_{{ current_cycle | to_YMDH }}.nc"
 
 # Naming conventions for bias correction files
-atm_obsbiasin_path: "{{DATA}}/obs/"
-atm_obsbiasin_prefix: "{{GPREFIX}}"
-atm_obsbiasin_suffix: ".satbias.nc"
-atm_obstlapsein_prefix: "{{GPREFIX}}"
-atm_obstlapsein_suffix: ".tlapse.txt"
-atm_obsbiascovin_prefix: "{{GPREFIX}}"
-atm_obsbiascovin_suffix: ".satbias_cov.nc"
+snow_obsbiasin_path: "{{DATA}}/obs/"
+snow_obsbiasin_prefix: "{{GPREFIX}}"
+snow_obsbiasin_suffix: ".satbias.nc"
+snow_obstlapsein_prefix: "{{GPREFIX}}"
+snow_obstlapsein_suffix: ".tlapse.txt"
+snow_obsbiascovin_prefix: "{{GPREFIX}}"
+snow_obsbiascovin_suffix: ".satbias_cov.nc"
 
-atm_obsbiasout_path: "{{DATA}}/bc/"
-atm_obsbiasout_prefix: "{{APREFIX}}"
-atm_obsbiasout_suffix: ".satbias.nc"
-atm_obsbiascovout_prefix: "{{APREFIX}}"
-atm_obsbiascovout_suffix: ".satbias_cov.nc"
+snow_obsbiasout_path: "{{DATA}}/bc/"
+snow_obsbiasout_prefix: "{{APREFIX}}"
+snow_obsbiasout_suffix: ".satbias.nc"
+snow_obsbiascovout_prefix: "{{APREFIX}}"
+snow_obsbiascovout_suffix: ".satbias_cov.nc"
 
 
 # Local Ensemble DA (LETKF)
@@ -133,5 +133,5 @@ driver_save_posterior_mean_increment: false
 driver_save_posterior_ensemble_increments: true
 
 # Diagnostics
-ensemble_increment_prefix: "./anl/mem%{member}%/atminc."
-#posterior_output_gaussian: "./mem%{member}%/atmanl."
+ensemble_increment_prefix: "./anl/mem%{member}%/snowinc."
+#posterior_output_gaussian: "./mem%{member}%/snowanl."
diff --git a/parm/snow/jcb-prototype_2dvar.yaml.j2 b/parm/snow/jcb-prototype_2dvar.yaml.j2
new file mode 100644
index 000000000..77926c69b
--- /dev/null
+++ b/parm/snow/jcb-prototype_2dvar.yaml.j2
@@ -0,0 +1,12 @@
+# Algorithm
+# ---------
+algorithm: 3dvar
+
+# Observation things
+# ------------------
+observations:
+  - adpsfc_snow
+  - ims_snow
+#  - ghcn_snow
+#  - sfcsno_snow
+#  - snocvr_snow
diff --git a/parm/snow/obs/config/adpsfc_snow.yaml.j2 b/parm/snow/obs/config/adpsfc_snow.yaml.j2
deleted file mode 100644
index 1ddcb7e21..000000000
--- a/parm/snow/obs/config/adpsfc_snow.yaml.j2
+++ /dev/null
@@ -1,109 +0,0 @@
-- obs space:
-    name: adpsfc_snow
-    distribution:
-      name: Halo
-      halo size: 250e3
-    obsdatain:
-      engine:
-        type: H5File
-        obsfile: './obs/{{ OPREFIX }}adpsfc_snow.nc4'
-    obsdataout:
-      engine:
-        type: H5File
-        obsfile: './diags/diag_adpsfc_snow.nc4'
-    simulated variables: [totalSnowDepth]
-  obs operator:
-    name: Composite
-    components:
-    - name: Identity
-    - name: BackgroundErrorIdentity
-  obs error:
-    covariance model: diagonal
-  obs localizations:
-    - localization method: Horizontal SOAR
-      lengthscale: 250e3
-      soar horizontal decay: 0.000021
-      max nobs: 50
-    - localization method: Vertical Brasnett
-      vertical lengthscale: 700
-  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: 2000.0
-      action:
-        name: reject
-    - filter: Domain Check
-      where:
-      - variable:
-          name: MetaData/stationElevation
-        minvalue: -999.0
-    - 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: 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: '{{ SNOW_WINDOW_LENGTH }}'
-      seed_time: '{{ current_cycle | to_isotime }}'
-      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/parm/snow/obs/config/ghcn_snow.yaml.j2 b/parm/snow/obs/config/ghcn_snow.yaml.j2
deleted file mode 100644
index b2a037cf1..000000000
--- a/parm/snow/obs/config/ghcn_snow.yaml.j2
+++ /dev/null
@@ -1,53 +0,0 @@
-- obs space:
-    name: ghcn_snow
-    distribution:
-      name: Halo
-      simulated variables: [totalSnowDepth]
-    obsdatain:
-      engine:
-        type: H5File
-        obsfile: './obs/{{ OPREFIX }}ghcn_snow_{{ current_cycle | to_YMDH }}.nc4'
-    obsdataout:
-      engine:
-        type: H5File
-        obsfile: './diags/diag_ghcn_snow_{{ current_cycle | to_YMDH }}.nc4'
-
-  obs operator:
-    name: Identity
-  obs error:
-    covariance model: diagonal
-  obs localizations:
-    - localization method: Horizontal SOAR
-      lengthscale: 250e3
-      soar horizontal decay: 0.000021
-      max nobs: 50
-    - localization method: Vertical Brasnett
-      vertical lengthscale: 700
-  obs filters:
-    - filter: Bounds Check
-      filter variables:
-      - name: totalSnowDepth
-      minvalue: 0.0
-    - filter: Domain Check
-      where:
-      - variable:
-          name: MetaData/height
-        minvalue: -999.0
-    - 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: Background Check
-      filter variables:
-      - name: totalSnowDepth
-      threshold: 6.25
-      action:
-        name: reject
diff --git a/parm/snow/obs/config/ims_snow.yaml.j2 b/parm/snow/obs/config/ims_snow.yaml.j2
deleted file mode 100644
index c222d0dfe..000000000
--- a/parm/snow/obs/config/ims_snow.yaml.j2
+++ /dev/null
@@ -1,46 +0,0 @@
-- obs space:
-    name: ims_snow
-    distribution:
-      name: Halo
-      halo size: 250e3
-    obsdatain:
-      engine:
-        type: H5File
-        obsfile: './obs/{{ OPREFIX }}ims_snow.nc4'
-    obsdataout:
-      engine:
-        type: H5File
-        obsfile: './diags/diag_ims_snow.nc4'
-    simulated variables: [totalSnowDepth]
-  obs operator:
-    name: Identity
-  obs error:
-    covariance model: diagonal
-  obs localizations:
-    - localization method: Horizontal SOAR
-      lengthscale: 250e3
-      soar horizontal decay: 0.000021
-      max nobs: 1
-  obs filters:
-    - filter: Bounds Check
-      filter variables:
-      - name: totalSnowDepth
-      minvalue: 0.0
-    - 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: Background Check # gross error check
-      filter variables:
-      - name: totalSnowDepth
-      threshold: 6.25
-      action:
-        name: reject
diff --git a/parm/snow/obs/config/sfcsno_snow.yaml.j2 b/parm/snow/obs/config/sfcsno_snow.yaml.j2
deleted file mode 100644
index 960ea8f64..000000000
--- a/parm/snow/obs/config/sfcsno_snow.yaml.j2
+++ /dev/null
@@ -1,110 +0,0 @@
-- obs space:
-    name: sfcsno_snow
-    distribution:
-      name: Halo
-      halo size: 250e3
-    obsdatain:
-      engine:
-        type: bufr
-        obsfile: '{{ DATA }}/obs/{{ OPREFIX }}sfcsno.tm00.bufr_d'
-        mapping file: '{{ DATA }}/obs/bufr_sfcsno_mapping.yaml'
-    obsdataout:
-      engine:
-        type: H5File
-        obsfile: '{{ DATA }}/diags/diag_sfcsno_snow.nc4'
-    simulated variables: [totalSnowDepth]
-  obs operator:
-    name: Composite
-    components:
-    - name: Identity
-    - name: BackgroundErrorIdentity
-  obs error:
-    covariance model: diagonal
-  obs localizations:
-    - localization method: Horizontal SOAR
-      lengthscale: 250e3
-      soar horizontal decay: 0.000021
-      max nobs: 50
-    - localization method: Vertical Brasnett
-      vertical lengthscale: 700
-  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: 2000.0
-      action:
-        name: reject
-    - filter: Domain Check
-      where:
-      - variable:
-          name: MetaData/stationElevation
-        minvalue: -999.0
-    - 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: 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: '{{ SNOW_WINDOW_LENGTH }}'
-      seed_time: '{{ current_cycle | to_isotime }}'
-      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/parm/snow/obs/config/snocvr_snow.yaml.j2 b/parm/snow/obs/config/snocvr_snow.yaml.j2
deleted file mode 100644
index 45a361f32..000000000
--- a/parm/snow/obs/config/snocvr_snow.yaml.j2
+++ /dev/null
@@ -1,103 +0,0 @@
-- obs space:
-    name: snocvr_snow
-    distribution:
-      name: Halo
-      halo size: 250e3
-    obsdatain:
-      engine:
-        type: H5File
-        obsfile: './obs/{{ OPREFIX }}snocvr_snow.nc4'
-    obsdataout:
-      engine:
-        type: H5File
-        obsfile: './diags/diag_snocvr_snow.nc4'
-    simulated variables: [totalSnowDepth]
-  obs operator:
-    name: Composite
-    components:
-    - name: Identity
-    - name: BackgroundErrorIdentity
-  obs error:
-    covariance model: diagonal
-  obs localizations:
-    - localization method: Horizontal SOAR
-      lengthscale: 250e3
-      soar horizontal decay: 0.000021
-      max nobs: 50
-    - localization method: Vertical Brasnett
-      vertical lengthscale: 700
-  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: 2000.0
-      action:
-        name: reject
-    - filter: Domain Check
-      where:
-      - variable:
-          name: MetaData/stationElevation
-        minvalue: -999.0
-    - 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:
-    - filter: Background Check # gross error check
-      filter variables:
-      - name: totalSnowDepth
-      threshold: 6.25
-      action:
-        name: reject
-    - filter: Temporal Thinning
-      min_spacing: '{{ SNOW_WINDOW_LENGTH }}'
-      seed_time: '{{ current_cycle | to_isotime }}'
-      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