Jcb land letkf

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

@@ -0,0 +1,4 @@
+filetype: fms restart
+is restart: false
+datapath: ./anl/mem%{member}%
+filename_nonrestart: cubed_sphere_grid_sfcinc.jedi.nc

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

@@ -0,0 +1,30 @@
+#datetime: '{{ snow_background_time_iso }}'
+members from template:
+  template:
+    datetime: '{{ snow_background_time_iso }}'
+    filetype: fms restart
+    skip coupler file: true
+#    provider: ufs
+    state variables:
+    - totalSnowDepth
+    - vtype
+    - slmsk
+    - sheleg
+    - filtered_orography
+    - fraction_of_ice
+    - fraction_of_land
+    - stc
+    field io names:
+      totalSnowDepth: snodl
+      filtered_orography: orog_filt
+      fraction_of_ice: fice
+      fraction_of_land: land_frac
+    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/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)
   # ------------------------

parm/snow/jcb-base.yaml.j2

@@ -9,10 +9,16 @@ app_path_observation_chronicle: "{{PARMgfs}}/gdas/jcb-gdas/observation_chronicle
 
 # Places where we deviate from the generic file name of a yaml
 # ------------------------------------------------------------
-final_increment_file: snow_final_increment_fms
 model_file: model_pseudo
 initial_condition_file: background  # Initial conditions for 4D apps is background
-
+final_increment_file: snow_final_increment_fms
+output_mean_prior_file: snow_output_mean_prior_fms
+posterior_output_file: snow_posterior_output_fms
+output_ensemble_increments_file: snow_ensemble_increments_fms
+output_increment_file: snow_output_increment_fms  #snow_ensemblemean_increment_fms.yaml.j2 
+output_variance_prior_file: snow_output_variance_prior_fms
+output_variance_posterior_file: snow_output_variance_posterior_fms
+#jedi_increment_output: gaussian
 
 # Assimilation window
 # -------------------
@@ -30,7 +36,6 @@ snow_background_time_julian: "{{ bkg_time_julian }}"
 snow_increment_time_iso: "{{ bkg_time_iso }}"
 snow_increment_time_fv3: "{{ bkg_time_fv3 }}"
 
-
 # Analysis standard things
 # ------------------------
 analysis_variables: [totalSnowDepth]
@@ -60,12 +65,11 @@ snow_orog_prefix: "{{ CASE }}.mx{{ OCNRES }}"
 
 # Background
 snow_background_path: {{snow_bkg_path}}
-background_ensemble_path: ./ens/mem%mem%
+#background_ensemble_path: ./ens/mem%mem%   #TODO: this may not be ncessary
+snow_background_ensemble_path: ./bkg/mem%mem%
 
 # Background error
 snow_bump_data_directory: "{{ DATA }}/berror"
-number_ensemble_members: {{ NMEM_ENS | default(1, true) }}
-
 snow_background_error_file: "{{BERROR_YAML}}"
 
 # Forecasting
@@ -105,13 +109,14 @@ snow_obsbiascovout_prefix: "{{APREFIX}}"
 snow_obsbiascovout_suffix: ".satbias_cov.nc"
 
 # Ensemble mean things
-snow_number_ensemble_members: {{NMEM_ENS}}
+snow_number_ensemble_members: {{NMEM_ENS | default(1, true) }}   #do we need the one below?
+#number_ensemble_members: {{ NMEM_ENS | default(1, true) }}
 
 # Local Ensemble DA (LETKF)
 # -------------------------
 local_ensemble_da_solver: Deterministic GETKF
 
-increment_variables: [ua,va,DZ,delp,t,ps,sphum,ice_wat,liq_wat,o3mr]
+increment_variables: [totalSnowDepth,vtype,slmsk] #[ua,va,DZ,delp,t,ps,sphum,ice_wat,liq_wat,o3mr]
 
 # Veritcal localization for GETKF
 vl_fraction_of_retained_variance: 0.750
@@ -123,12 +128,17 @@ inflation_mult: 1.0
 
 # Driver
 driver_update_obs_config_with_geometry_info: true
-driver_save_posterior_mean: false
-driver_save_posterior_ensemble: false
-driver_save_prior_mean: false
-driver_save_posterior_mean_increment: false
+driver_save_posterior_mean: true
+driver_save_posterior_ensemble: true
+driver_save_posterior_mean_increment: true
 driver_save_posterior_ensemble_increments: true
+driver_save_prior_variance: true
+driver_save_posterior_variance: true
+driver_save_prior_mean: true  #(default false)
+#driver_do_test_prints: false (default true)
+#default driver_do_posterior_observer: true
+#default driver_use_control_member: false
 
 # Diagnostics
-ensemble_increment_prefix: "./anl/mem%{member}%/snowinc."
+#ensemble_increment_prefix: "./anl/mem%{member}%/snowinc."
 #posterior_output_gaussian: "./mem%{member}%/snowanl."

parm/snow/jcb-prototype_lgetkf.yaml.j2

@@ -0,0 +1,29 @@
+# Use observations for lgetkf
+# ---------------------------
+app_path_observations: {{PARMgfs}}/gdas/jcb-gdas/observations/snow
+app_path_observation_chronicle: {{PARMgfs}}/gdas/jcb-gdas/observation_chronicle/snow/{{cycle}}
+# Algorithm
+# ---------
+algorithm: local_ensemble_da
+
+# Model things
+# ------------
+snow_background_ensemble_path: ./bkg/mem%mem%
+
+# Observation things
+# ------------------
+{% include OBS_LIST_YAML %}
+
+# Observation distribution and localization
+# TODO: 
+distribution_type: "Halo"
+localization_method: "Horizontal Box car"
+halo_size: 250e3
+loc_length_scale: 250e3
+max_nobs: 50
+
+# Testing things
+# --------------
+{% if DO_TEST_MODE %}
+{% include LETKF_JEDI_TEST_YAML %}
+{% endif %}

parm/snow/jcb-prototype_lgetkf_observer.yaml.j2

@@ -0,0 +1,28 @@
+# Use observations for lgetkf
+# ---------------------------
+app_path_observations: {{PARMgfs}}/gdas/jcb-gdas/observations/snow
+app_path_observation_chronicle: {{PARMgfs}}/gdas/jcb-gdas/observation_chronicle/snow/{{cycle}}
+
+# Algorithm
+# ---------
+algorithm: local_ensemble_da_observer
+
+# Model things
+# ------------
+atmosphere_background_ensemble_path: ./bkg/mem%mem%
+
+# Naming conventions for observation files
+atmosphere_obsdataout_prefix: diag_lobs_
+
+# Distribution type
+distribution_type: RoundRobin
+
+# Observation things
+# ------------------
+{% include OBS_LIST_YAML %}
+
+# Testing things
+# --------------
+{% if DO_TEST_MODE %}
+{% include OBS_JEDI_TEST_YAML %}
+{% endif %}

parm/snow/jcb-prototype_lgetkf_solver.yaml.j2

@@ -0,0 +1,31 @@
+# Use observations for lgetkf
+# ---------------------------
+app_path_observations: {{PARMgfs}}/gdas/jcb-gdas/observations/snow
+app_path_observation_chronicle: {{PARMgfs}}/gdas/jcb-gdas/observation_chronicle/snow/{{cycle}}
+
+# Algorithm
+# ---------
+algorithm: local_ensemble_da_solver
+
+# Model things
+# ------------
+atmosphere_background_ensemble_path: ./bkg/mem%mem%
+
+# Naming conventions for observation files
+snow_obsdatain_path: "{{DATA}}/diags"
+snow_obsdatain_prefix: diag_lobs_
+snow_obsdatain_suffix: "_{{ current_cycle | to_YMDH }}.nc"
+snow_obsdataout_prefix: diag_solv_
+
+# Distribution type
+distribution_type: Halo
+
+# Observation things
+# ------------------
+{% include OBS_LIST_YAML %}
+
+# Testing things
+# --------------
+{% if DO_TEST_MODE %}
+{% include SOL_JEDI_TEST_YAML %}
+{% endif %}

parm/snow/letkf_apply_incr_nml.j2

@@ -0,0 +1,16 @@
+&noahmp_snow
+  date_str = "{{ current_cycle | to_YMD }}",
+  hour_str = "{{ current_cycle | strftime('%H') }}",
+  res = {{ CASE_ENS[1:] }},
+  frac_grid = .true.,
+  rst_path = "{{ DATA }}/anl", 
+  inc_path = "{{ DATA }}/anl",
+  orog_path = "{{ HOMEgfs }}/fix/orog/{{ CASE_ENS }}",
+  otype = "{{ CASE_ENS }}.mx{{ OCNRES }}_oro_data", 
+  ntiles={{ ntiles }},
+  ens_size={{ ens_size }},
+  noincr_threshold={{ noincr_threshold }},
+  print_summary=.true.,
+  print_debug={{ print_debug }} ,
+  truncate={{ truncate_incr }}
+/

parm/snow/snow_ens_obs_dist_localizations.yaml.j2

@@ -0,0 +1,21 @@
+obs_distribution_localizations:
+  obs_distribution:
+    name: {{ distribution_type }}
+    halo size: 250e3
+  obs_localizations:
+  - localization method: Horizontal Box car
+    lengthscale: 250e3
+    max nobs: 50
+
+#override_obs_distribution_localizations:
+#  override: false
+#  ims_snow:
+#    obs_distribution:
+#      name: {{ distribution_type }}
+#      halo size: 250e3
+#    obs_localizations:
+#    - localization method: Horizontal SOAR
+#      lengthscale: 250e3
+#      soar horizontal decay: 0.000021
+##assuming one obs every 40 Km
+#      max nobs: 6