Merge branch 'develop' into feature/update_soil

parm/aero/berror/aero_diagb.yaml.j2

@@ -76,25 +76,25 @@ variables:
   - mass_fraction_of_sea_salt003_in_air
   - mass_fraction_of_sea_salt004_in_air
 
-#global rescale:
-#  geometry:
-#    fms initialization:
-#      namelist filename: ./fv3jedi/fmsmpp.nml
-#      field table filename: ./fv3jedi/field_table
-#    akbk: ./fv3jedi/akbk.nc4
-#    layout:
-#    - {{ layout_x }}
-#    - {{ layout_y }}
-#    npx: {{ npx_rescale }}
-#    npy: {{ npy_rescale }}
-#    npz: {{ npz_ges }}
-#    field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
-#  rescale stddev:
-#    filetype: fms restart
-#    skip coupler file: true
-#    dateapath: ./stddev
-#    filename_trcr: rescale.fv_tracer.res.nc
-#    filename_cplr: rescale.coupler.res
+global rescale:
+  geometry:
+    fms initialization:
+      namelist filename: ./fv3jedi/fmsmpp.nml
+      field table filename: ./fv3jedi/field_table
+    akbk: ./fv3jedi/akbk.nc4
+    layout:
+    - {{ layout_x }}
+    - {{ layout_y }}
+    npx: {{ npx_rescale }}
+    npy: {{ npy_rescale }}
+    npz: {{ npz_ges }}
+    field metadata override: ./fv3jedi/fv3jedi_fieldmetadata_restart.yaml
+  rescale stddev:
+    filetype: fms restart
+    skip coupler file: true
+    dateapath: ./stddev
+    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 }}

parm/aero/jcb-base.yaml.j2

@@ -74,19 +74,22 @@ aero_background_error_time_fv3: "{{ background_time | to_fv3time }}"
 # Background error
 aero_berror_data_directory: "{{ DATA }}/berror"
 aero_berror_diffusion_directory: "{{ DATA }}/diffusion"
-aero_standard_devation_path: ./stddev
+aero_standard_deviation_path: ./stddev
 aero_climatological_b_path: ./clm_stddev
+aero_rescale_b_path: ./rescale
 aero_diagb_weight: {{ aero_diagb_weight | default(1.0, true) }}
 aero_diagb_static_rescale_factor: {{aero_staticb_rescaling_factor | default(1.0, true) }}
-aero_diagb_rescale_factor: {{aero_diagb_rescale | default(1.0, true) }}
-aero_diagb_n_halo: {{ aero_diagb_n_halo  | default(1, true)  }}
-aero_diagb_n_neighbors: {{ aero_diagb_n_neighbors | default(1, true) }}
-aero_diagb_smooth_horiz_iter: {{ aero_diagb_smooth_horiz_iter | default(1, true) }}
-aero_diagb_smooth_vert_iter: {{ aero_diagb_smooth_vert_iter | default(1, true) }}
-aero_diffusion_iter: {{ aero_diffusion_iter | default(1, true) }}
+aero_diagb_n_halo: {{ aero_diagb_n_halo  | default(0)  }}
+aero_diagb_n_neighbors: {{ aero_diagb_n_neighbors | default(0) }}
+aero_diagb_smooth_horiz_iter: {{ aero_diagb_smooth_horiz_iters | default(0) }}
+aero_diagb_smooth_vert_iter: {{ aero_diagb_smooth_vert_iters | default(0) }}
+aero_diffusion_iter: {{ aero_diffusion_iter | default(0) }}
 aero_diffusion_horiz_len: {{ aero_diffusion_horiz_len  | default(1.0, true)}}
 aero_diffusion_fixed_val: {{ aero_diffusion_fixed_val  | default(1.0, true)}}
 
+# Analysis
+aero_analysis_path: ./anl
+
 # Forecasting
 aero_forecast_timestep: "{{ BKG_TSTEP }}"
 

parm/snow/letkfoi/ens_apply_incr_nml.j2 → parm/snow/ens_apply_incr_nml.j2

@@ -3,8 +3,8 @@
   hour_str = "{{ current_cycle | strftime('%H') }}",
   res = {{ CASE_ENS[1:] }},
   frac_grid = .true.,
-  rst_path = "{{ DATAROOT }}/anl/mem{{ MYMEM }}",
-  inc_path = "{{ DATAROOT }}/inc/ensmean",
+  rst_path = "{{ DATA }}/anl/mem{{ MYMEM }}",
+  inc_path = "{{ DATA }}/anl",
   orog_path = "{{ HOMEgfs }}/fix/orog/{{ CASE_ENS }}",
   otype = "{{ CASE_ENS }}.mx{{ OCNRES }}_oro_data"
 /

parm/snow/jcb-base.yaml.j2

@@ -3,15 +3,13 @@
 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
 # ------------------------------------------------------------
-#final_increment_file: final_increment_gaussian
-final_increment_file: final_increment_cubed_sphere
-output_ensemble_increments_file: output_ensemble_increments_gaussian
+final_increment_file: snow_final_increment_fms
 model_file: model_pseudo
 initial_condition_file: background  # Initial conditions for 4D apps is background
 
@@ -23,60 +21,52 @@ window_length: "{{ SNOW_WINDOW_LENGTH }}"
 bound_to_include: begin
 
 # Default background time is for 3D applications
-{% if DOIAU %}
-{% set bkg_time_iso = SNOW_WINDOW_BEGIN | to_isotime %}
-{% set bkg_time_fv3 = SNOW_WINDOW_BEGIN | to_fv3time %}
-{% else %}
 {% set bkg_time_iso = current_cycle | to_isotime %}
 {% set bkg_time_fv3 = current_cycle | to_fv3time %}
-{% endif %}
 snow_background_time_iso: "{{ bkg_time_iso }}"
+snow_background_time_fv3: "{{ bkg_time_fv3 }}"
 snow_increment_time_iso: "{{ bkg_time_iso }}"
 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
 # ------------
 # Geometry
-layout_x: {{ layout_x | default(1, true) }}
-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) }}
-
-fv3jedi_files_path: ./fv3jedi  # Ideally this would be {{DATA}}/fv3jedi but FMS
+snow_layout_x: {{ layout_x | default(1, true) }}
+snow_layout_y: {{ layout_y | default(1, true) }}
+snow_npx_ges: {{ npx_ges | default(49, true) }}
+snow_npy_ges: {{ npy_ges | default(49, true) }}
+snow_npz_ges: {{ npz_ges | default(127, true) }}
+snow_npx_anl: {{ npx_ges | default(49, true) }}
+snow_npy_anl: {{ npy_ges | default(49, true) }}
+snow_npz_anl: {{ npz_ges | default(127, true) }}
+
+snow_fv3jedi_files_path: ./fv3jedi  # Ideally this would be {{DATA}}/fv3jedi but FMS
+snow_orog_files_path: "{{ FIXgfs }}/orog/{{ CASE }}"
+snow_orog_prefix: "{{ CASE }}.mx{{ OCNRES }}"
 
 # Background
-background_path: ./bkg
+snow_background_path: {{snow_bkg_path}}
 background_ensemble_path: ./ens/mem%mem%
 
 # Background error
-bump_data_directory: "{{ DATA }}/berror"
-gsibec_path: "{{ DATA }}/berror"
+snow_bump_data_directory: "{{ DATA }}/berror"
 number_ensemble_members: {{ NMEM_ENS | default(1, true) }}
-layout_gsib_x: {{ layout_gsib_x | default(1, true) }}
-layout_gsib_y: {{ layout_gsib_y | default(1, true) }}
 
-background_error_file: "{{BERROR_YAML}}"
+snow_background_error_file: "{{BERROR_YAML}}"
 
 # Forecasting
-forecast_length: "{{ ATM_WINDOW_LENGTH }}"
-forecast_timestep: "{{ BKG_TSTEP }}"
-
-# Write final increment on Guassian grid in variational
-final_increment_prefix: "./anl/atminc."
+snow_forecast_length: "{{ SNOW_WINDOW_LENGTH }}"
+snow_forecast_timestep: "{{ BKG_TSTEP }}"
 
 
 # Observation things
@@ -86,29 +76,32 @@ 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_obsdataroot_path: "{{COMIN_OBS}}"
+snow_obsdatain_path: "{{snow_obsdatain_path}}"
+snow_obsdatain_prefix: "{{OPREFIX}}"
+snow_obsdatain_suffix: ".tm00.bufr_d"
 
-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"
-
-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_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"
+
+snow_obsbiasout_path: "{{DATA}}/bc/"
+snow_obsbiasout_prefix: "{{APREFIX}}"
+snow_obsbiasout_suffix: ".satbias.nc"
+snow_obsbiascovout_prefix: "{{APREFIX}}"
+snow_obsbiascovout_suffix: ".satbias_cov.nc"
+
+# Ensemble mean things
+snow_number_ensemble_members: {{NMEM_ENS}}
 
 # Local Ensemble DA (LETKF)
 # -------------------------
@@ -133,5 +126,5 @@ 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."

parm/snow/jcb-prototype_2dvar.yaml.j2

@@ -0,0 +1,12 @@
+# Algorithm
+# ---------
+algorithm: 3dvar
+
+# Observation things
+# ------------------
+observations:
+#  - adpsfc_snow
+  - ims_snow
+#  - ghcn_snow
+  - sfcsno
+  - snocvr_snow