Land update

parm/jcb-gdas/model/snow/snow_background_ensemble.yaml.j2

@@ -0,0 +1,16 @@
+members from template:
+  template:
+    datetime: '{{ snow_background_time_iso }}'
+    filetype: fms restart
+    skip coupler file: true
+    state variables: {{ snow_det_state_variables }}
+    field io names: {{ snow_field_io_names }}
+    datapath: {{ snow_background_ensemble_path }}
+    filename is datetime templated: true
+    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'
+    max allowable geometry difference: 1e-4
+  pattern: "{{ snow_ensemble_pattern | default("%mem%", true) }}"
+  nmembers: {{ snow_number_ensemble_members }}
+  zero padding: 3

parm/jcb-gdas/model/snow/snow_ensemble_increments_fms.yaml.j2

@@ -0,0 +1,2 @@
+prefix: snowinc
+{% include 'snow_ensemble_output_fms_common.yaml.j2' %}

parm/jcb-gdas/model/snow/snow_ensemble_output_fms_common.yaml.j2

@@ -0,0 +1,10 @@
+datapath: ./anl/mem%{member}%
+filetype: fms restart
+filename_sfcd: '{{ snow_background_time_fv3 }}.sfc_data.nc'
+filename_cplr: '{{ snow_background_time_fv3 }}.coupler.res'
+state variables:
+- totalSnowDepth
+- vtype
+- slmsk
+field io names:
+  totalSnowDepth: snodl

parm/jcb-gdas/model/snow/snow_output_increment_fms.yaml.j2

@@ -0,0 +1,2 @@
+prefix: snowinc_ensmean
+{% include 'snow_ensemble_output_fms_common.yaml.j2' %}

parm/jcb-gdas/model/snow/snow_output_mean_prior_fms.yaml.j2

@@ -0,0 +1,2 @@
+prefix: snow_ensmean_prior
+{% include 'snow_ensemble_output_fms_common.yaml.j2' %}

parm/jcb-gdas/model/snow/snow_output_variance_posterior_fms.yaml.j2

@@ -0,0 +1,2 @@
+prefix: snow_ensvariance_posterior
+{% include 'snow_ensemble_output_fms_common.yaml.j2' %}

parm/jcb-gdas/model/snow/snow_output_variance_prior_fms.yaml.j2

@@ -0,0 +1,2 @@
+prefix: snow_ensvariance_prior
+{% include 'snow_ensemble_output_fms_common.yaml.j2' %}

parm/jcb-gdas/model/snow/snow_posterior_output_fms.yaml.j2

@@ -0,0 +1,2 @@
+prefix: snow_ens_anl
+{% include 'snow_ensemble_output_fms_common.yaml.j2' %}

parm/jcb-gdas/model/soil/soil_3dvar_outer_loop_1.yaml.j2

@@ -12,16 +12,5 @@
     npx: {{ soil_npx_anl }}
     npy: {{ soil_npy_anl }}
     npz: {{ soil_npz_anl }}
-    time invariant fields:
-      state fields:
-        datetime: '{{ soil_background_time_iso }}'
-        filetype: fms restart
-        skip coupler file: true
-        state variables:
-        - filtered_orography
-        - fraction_of_land
-        field io names: {{ soil_field_io_names }}
-        datapath: {{ soil_orog_files_path }}/
-        filename_orog: {{ soil_orog_prefix }}_oro_data.nc
   diagnostics:
     departures: bkgmob

parm/jcb-gdas/model/soil/soil_background_csg.yaml.j2

@@ -0,0 +1,10 @@
+datapath: {{ soil_background_path }}
+filetype: cube sphere history
+provider: ufs
+datetime: '{{ soil_background_time_iso }}'
+filenames:
+- {{ soil_variational_history_prefix }}csg_atm.f006.nc
+- {{ soil_variational_history_prefix }}csg_sfc.f006.nc    
+max allowable geometry difference: 1e-4
+state variables: {{ soil_state_variables }}
+field io names: {{ soil_field_io_names }}

parm/jcb-gdas/model/soil/soil_background_ensemble_csg.yaml.j2

@@ -0,0 +1,15 @@
+members from template:
+  template:
+    datetime: '{{ soil_background_time_iso }}'
+    datapath: {{ soil_background_ensemble_path }}
+    filetype: cube sphere history
+    provider: ufs
+    filenames:
+    - {{ soil_ensemble_history_prefix }}csg_atm.f006.nc
+    - {{ soil_ensemble_history_prefix }}csg_sfc.f006.nc    
+    max allowable geometry difference: 1e-4
+    state variables: {{ soil_state_variables }}
+    field io names: {{ soil_field_io_names }}
+  pattern: "{{ soil_ensemble_pattern | default("%mem%", true) }}"
+  nmembers: {{ soil_number_ensemble_members }}
+  zero padding: 3

parm/jcb-gdas/model/soil/soil_background_error.yaml.j2 → parm/jcb-gdas/model/soil/soil_background_error_static_csg.yaml.j2

@@ -1,29 +1,31 @@
 covariance model: SABER
 saber central block:
   saber block name: BUMP_NICAS
-  calibration:    #read:
+  read:
     general:
       universe length-scale: 5000000.0
     drivers:
       multivariate strategy: univariate
-      compute nicas: true     #read global nicas: true
-      write global nicas: true
+      read global nicas: true
     nicas:
       resolution: 4
       explicit length-scales: true
       horizontal length-scale:
-      - groups: {{ soil_det_increment_variables }}
+      - groups: 
+        - soill1
         value: 1000000.0
       vertical length-scale:
-      - groups: {{ soil_det_increment_variables }}
+      - groups: 
+        - soill1
         value: 1500.0
       interpolation type:
-      - groups: {{ soil_det_increment_variables }}
+      - groups: 
+        - soill1
         type: c0
       same horizontal convolution: true
     io:
       data directory: ./berror 
-      files prefix: smc_bump_nicas_1000km_{{ soil_background_time_fv3 }}
+      files prefix: smc_bump
 saber outer blocks:
 - saber block name: BUMP_StdDev
   read:
@@ -32,5 +34,6 @@ saber outer blocks:
     variance:
       explicit stddev: true
       stddev:
-      - variables: {{ soil_det_increment_variables }}
-        value: 0.2
+      - variables: 
+        - soill1
+        value: 0.05

parm/jcb-gdas/model/soil/soil_background_error_static_shadlev_csg.yaml.j2

@@ -0,0 +1,49 @@
+covariance model: SABER
+saber central block:
+  saber block name: BUMP_NICAS
+  read:
+    general:
+      universe length-scale: 250000.0
+    drivers:
+      multivariate strategy: univariate
+      read global nicas: true
+    nicas:
+      resolution: 6
+      max horizontal grid size: 250000
+      explicit length-scales: true
+      horizontal length-scale:
+      - groups:
+        - soill1_shadowLevels
+        value: 250000.
+      vertical length-scale:
+      - groups:
+        - soill1_shadowLevels
+        value: 0.0
+      interpolation type:
+      - groups:
+        - soill1_shadowLevels
+        type: c0
+      same horizontal convolution: true
+    io:
+      data directory: ./berror
+      files prefix: smc_bump
+saber outer blocks:
+- saber block name: ShadowLevels
+  fields metadata:
+    soill1:
+      vert_coord: filtered_orography
+  calibration:
+    number of shadow levels: 50
+    lowest shadow level: -450.0
+    highest shadow level: 8850.0
+    vertical length-scale: 700.0
+- saber block name: BUMP_StdDev
+  read:
+    drivers:
+      compute variance: true
+    variance:
+      explicit stddev: true
+      stddev:
+      - variables:
+        - soill1
+        value: 0.05

parm/jcb-gdas/model/soil/soil_ensemble_increments_csg.yaml.j2

@@ -0,0 +1,6 @@
+datapath: ./anl/mem%{member}%
+filetype: cube sphere history
+provider: ufs
+filename: soilinc_{{ soil_ensemble_history_prefix }}nc
+state variables: {{ soil_state_variables }}
+field io names: {{ soil_field_io_names }}

parm/jcb-gdas/model/soil/soil_ensemble_increments_gaussian.yaml.j2

@@ -0,0 +1,6 @@
+datapath: ./anl/mem%{member}%
+filetype: auxgrid
+gridtype: gaussian
+filename: ./anl/mem%{member}%/sfcinc.
+state variables: {{ soil_state_variables }}
+field io names: {{ soil_field_io_names }}

parm/jcb-gdas/model/soil/soil_final_increment_fms.yaml.j2 → parm/jcb-gdas/model/soil/soil_final_increment_csg.yaml.j2

@@ -1,12 +1,11 @@
 output:
   state component:
+    filetype: cube sphere history
+    provider: ufs
     datapath: ./anl
-    prefix: soilinc
-    filetype: fms restart
-    filename_sfcd: '{{ soil_background_time_fv3 }}.sfc_data.nc'
-    filename_cplr: '{{ soil_background_time_fv3 }}.coupler.res'
-    state variables: {{ soil_det_increment_variables_final }}
+    filename: soilinc_{{ soil_variational_history_prefix }}nc
     field io names: {{ soil_field_io_names }}
+
 geometry:
   fms initialization:
     namelist filename: "{{ soil_fv3jedi_files_path }}/fmsmpp.nml"
@@ -15,6 +14,6 @@ geometry:
   layout:
   - {{ soil_layout_x }}
   - {{ soil_layout_y }}
-  npx: {{ soil_npx_ges }}
-  npy: {{ soil_npy_ges }}
-  npz: {{ soil_npz_ges }}
+  npx: {{ soil_npx_anl }}
+  npy: {{ soil_npy_anl }}
+  npz: {{ soil_npz_anl }}

parm/jcb-gdas/model/soil/soil_final_increment_gaussian.yaml.j2

@@ -0,0 +1,11 @@
+grid type: regular gaussian
+local interpolator type: oops unstructured grid interpolator
+number of latitude gridpoints: {{ (soil_npy_anl | int) - 1 }} 
+datapath: ./anl
+prefix: {{ soil_gaussian_increment_prefix }}
+all model levels: true
+date colons: false
+variables to output: 
+- soill1
+field io names: 
+  soill1: slc1_inc

parm/jcb-gdas/model/soil/soil_output_increment_csg.yaml.j2

@@ -0,0 +1,6 @@
+datapath: ./anl/mem%{member}%
+filetype: cube sphere history
+provider: ufs
+filename: soilinc_ensmean_{{ soil_ensemble_history_prefix }}nc
+state variables: {{ soil_state_variables }}
+field io names: {{ soil_field_io_names }}

parm/jcb-gdas/model/soil/soil_output_increment_gaussian.yaml.j2

@@ -0,0 +1,6 @@
+datapath: ./anl/mem000
+filetype: auxgrid
+gridtype: gaussian
+filename: ./anl/mem000/sfcinc_ensmean.
+state variables: {{ soil_state_variables }}
+field io names: {{ soil_field_io_names }}

parm/jcb-gdas/model/soil/soil_output_mean_prior_csg.yaml.j2

@@ -0,0 +1,7 @@
+prefix: soil_prior_ensmean
+datapath: ./anl/
+filetype: cube sphere history
+provider: ufs
+filename: {{ soil_ensemble_history_prefix }}.nc
+state variables: {{ soil_state_variables }}
+field io names: {{ soil_field_io_names }}

parm/jcb-gdas/model/soil/soil_output_variance_posterior_csg.yaml.j2

@@ -0,0 +1,7 @@
+prefix: soil_ensvariance_posterior
+datapath: ./anl/
+filetype: cube sphere history
+provider: ufs
+filename: soilinc_{{ soil_ensemble_history_prefix }}.nc
+state variables: {{ soil_state_variables }}
+field io names: {{ soil_field_io_names }}

parm/jcb-gdas/model/soil/soil_output_variance_prior_csg.yaml.j2

@@ -0,0 +1,7 @@
+prefix: soil_ensvariance_prior
+datapath: ./anl/
+filetype: cube sphere history
+provider: ufs
+filename: soilinc_{{ soil_ensemble_history_prefix }}.nc
+state variables: {{ soil_state_variables }}
+field io names: {{ soil_field_io_names }}

parm/jcb-gdas/model/soil/soil_posterior_output_csg.yaml.j2

@@ -0,0 +1,7 @@
+prefix: soil_ens_anl
+datapath: ./anl/
+filetype: cube sphere history
+provider: ufs
+filename: {{ soil_ensemble_history_prefix }}.nc
+state variables: {{ soil_state_variables }}
+field io names: {{ soil_field_io_names }}

parm/jcb-gdas/observation_chronicle/soil/smap_soil.yaml → parm/jcb-gdas/observation_chronicle/soil/smap_soilmoisture.yaml

@@ -4,7 +4,12 @@ commissioned: 2015-04-01T00:00:00
 
 observer_type: satellite # Type of chronicle to use
 
-window_option: max
+channel_variables:
+  simulated: min
+
+channel_values:
+  1: [true]
 
 # Chronicle of changes for this observation type
 # ----------------------------------------
+chronicles: []

parm/jcb-gdas/observations/snow/ghcn_snow.yaml.j2

@@ -4,6 +4,11 @@
   # -----------------------
   obs space:
     name: {{observation_from_jcb}}
+{% if algorithm == "local_ensemble_da" %}
+    distribution:
+      name: {{ distribution_type }}
+      halo size: {{ halo_size }}
+{% endif %}
     obsdatain:
       engine:
         type: H5File
@@ -21,6 +26,14 @@
   obs operator:
     name: Identity
   #
+  # localization TODO: generalize this condioned on da algo
+  # ------------
+{% if algorithm == "local_ensemble_da" %}
+  obs localizations:
+  - localization method: {{ localization_method }}
+    lengthscale: {{ loc_length_scale }}
+    max nobs: {{ max_nobs }}
+{% endif %}
 
   # Observation Filters (QC)
   # ------------------------