GDASApp companion to Global Workflow marine refactoring

parm/marine/jcb-base.yaml.j2

@@ -18,8 +18,8 @@ final_increment_file: marine_final_increment
 # Assimilation standard things (not prepended with model choice)
 # ----------------------------
 pslot: '{{ PSLOT }}'
-window_begin: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-window_length: '{{MARINE_WINDOW_LENGTH}}'
+window_begin: '{{ WINDOW_BEGIN | to_isotime }}'
+window_length: '{{ WINDOW_LENGTH }}'
 bound_to_include: begin
 minimizer: RPCG
 final_diagnostics_departures: oman
@@ -37,18 +37,18 @@ analysis_variables:
 
 # Model things
 # ------------
-marine_window_begin: '{{MARINE_WINDOW_BEGIN}}'
-marine_window_middle: '{{MARINE_WINDOW_MIDDLE}}'
-marine_window_begin_iso: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
-marine_window_middle_iso: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
-marine_window_end_iso: '{{ MARINE_WINDOW_END | to_isotime }}'
-enspert_relpath: '{{ ENSPERT_RELPATH }}'
+marine_window_begin: '{{ WINDOW_BEGIN }}'
+marine_window_middle: '{{ WINDOW_MIDDLE }}'
+marine_window_begin_iso: '{{ WINDOW_BEGIN | to_isotime }}'
+marine_window_middle_iso: '{{ WINDOW_MIDDLE | to_isotime }}'
+marine_window_end_iso: '{{ WINDOW_END | to_isotime }}'
+marine_enspert_relpath: '{{ ENSPERT_RELPATH }}'
 {% if DOIAU %}
-marine_cice_date_fms: '{{ MARINE_WINDOW_BEGIN | to_fv3time }}'
-marine_cice_date_iso: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
+marine_cice_date_fms: '{{ WINDOW_BEGIN | to_fv3time }}'
+marine_cice_date_iso: '{{ WINDOW_BEGIN | to_isotime }}'
 {% else %}
-marine_cice_date_fms: '{{ MARINE_WINDOW_MIDDLE | to_fv3time }}'
-marine_cice_date_iso: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
+marine_cice_date_fms: '{{ WINDOW_MIDDLE | to_fv3time }}'
+marine_cice_date_iso: '{{ WINDOW_MIDDLE | to_isotime }}'
 {% endif %}
 
 # Geometry
@@ -57,7 +57,7 @@ marine_vt_levels: '{{MOM6_LEVS}}'
 
 # Initial conditions
 marine_background_path: ./INPUT/
-marine_background_time: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
+marine_background_time: '{{ WINDOW_BEGIN | to_isotime }}'
 
 # Pseudo model
 marine_forecast_timestep: PT3H
@@ -66,7 +66,7 @@ marine_forecast_timestep: PT3H
 background_error_file: '{{berror_model}}'
 marine_number_ensemble_members: '{{NMEM_ENS}}'
 marine_number_ensemble_members_per_mpi: '{{NMEM_ENS_PER_MPI}}'
-marine_stddev_time: '{{ MARINE_WINDOW_MIDDLE  | to_isotime }}'
+marine_stddev_time: '{{ WINDOW_MIDDLE  | to_isotime }}'
 
 # Observations
 observations: all_observations
@@ -105,3 +105,31 @@ obs_variables: {{ obs_variables | default({}) }}
 
 # COM path for configuration files
 marine_config_path: '{{COMOUT_CONF}}'
+
+# Local Ensemble DA (LETKF)
+# -------------------------
+
+# Solver
+local_ensemble_da_solver: Deterministic LETKF
+
+# Increment variables
+increment_variables: [sea_water_salinity, sea_water_potential_temperature, sea_surface_height_above_geoid, sea_water_cell_thickness, eastward_sea_water_velocity, northward_sea_water_velocity, sea_ice_area_fraction]
+
+# Driver
+driver_save_posterior_mean: true
+driver_save_prior_mean: true
+driver_save_posterior_mean_increment: true
+driver_save_prior_variance: true
+driver_save_posterior_variance: true
+driver_do_posterior_observer: true
+
+# Inflation
+inflation_rtps: 0.5
+inflation_rtpp: 0.6
+inflation_mult: 1.1
+
+# Using LETKF app? (used in obs YAMLs)
+marine_letkf_app: {{ letkf_app | default(false) }}
+marine_letkf_dist_halo_size: '{{ DIST_HALO_SIZE }}'
+
+

parm/marine/jcb-prototype_letkf.yaml.j2

@@ -0,0 +1,5 @@
+# JEDI algorithm being invoked
+algorithm: local_ensemble_da
+
+# Observations
+{% include OBS_LIST_YAML %}

parm/marine/marine_bmat_config.yaml.j2

@@ -0,0 +1,124 @@
+jedi_config:
+    gridgen:
+        rundir: '{{ DATA }}'
+        exe_src: '{{ EXECgfs }}/gdas_soca_gridgen.x'
+        mpi_cmd: '{{ APRUN_MARINEBMAT }}'
+        jcb_base_yaml: '{{ PARMgfs }}/gdas/marine/jcb-base.yaml.j2'
+        jcb_algo: soca_gridgen
+    soca_diagb:
+        rundir: '{{ DATA }}'
+        exe_src: '{{ EXECgfs }}/gdas_soca_diagb.x'
+        mpi_cmd: '{{ APRUN_MARINEBMAT }}'
+        jcb_base_yaml: '{{ PARMgfs }}/gdas/marine/jcb-base.yaml.j2'
+        jcb_algo: soca_diagb
+    soca_chgres:
+        rundir: '{{ DATA }}'
+        exe_src: '{{ EXECgfs }}/gdas.x'
+        mpi_cmd: '{{ APRUN_MARINEBMAT }}'
+        jedi_args: ['soca', 'convertstate']
+        jcb_base_yaml: '{{ PARMgfs }}/gdas/marine/jcb-base.yaml.j2'
+        jcb_algo: soca_chgres
+    soca_parameters_diffusion_vt:
+        rundir: '{{ DATA }}'
+        exe_src: '{{ EXECgfs }}/gdas_soca_error_covariance_toolbox.x'
+        mpi_cmd: '{{ APRUN_MARINEBMAT }}'
+        jcb_base_yaml: '{{ PARMgfs }}/gdas/marine/jcb-base.yaml.j2'
+        jcb_algo: soca_parameters_diffusion_vt
+    soca_setcorscales:
+        rundir: '{{ DATA }}'
+        exe_src: '{{ EXECgfs }}/gdas_soca_setcorscales.x'
+        mpi_cmd: '{{ APRUN_MARINEBMAT }}'
+        jcb_base_yaml: '{{ PARMgfs }}/gdas/marine/jcb-base.yaml.j2'
+        jcb_algo: soca_setcorscales
+    soca_parameters_diffusion_hz:
+        rundir: '{{ DATA }}'
+        exe_src: '{{ EXECgfs }}/gdas_soca_error_covariance_toolbox.x'
+        mpi_cmd: '{{ APRUN_MARINEBMAT }}'
+        jcb_base_yaml: '{{ PARMgfs }}/gdas/marine/jcb-base.yaml.j2'
+        jcb_algo: soca_parameters_diffusion_hz
+    soca_ensb:
+        rundir: '{{ DATA }}'
+        exe_src: '{{ EXECgfs }}/gdas_soca_ens_handler.x'
+        mpi_cmd: '{{ APRUN_MARINEBMAT }}'
+        jcb_base_yaml: '{{ PARMgfs }}/gdas/marine/jcb-base.yaml.j2'
+        jcb_algo: soca_ensb
+    soca_ensweights:
+        rundir: '{{ DATA }}'
+        exe_src: '{{ EXECgfs }}/gdas_soca_hybridweights.x'
+        mpi_cmd: '{{ APRUN_MARINEBMAT }}'
+        jcb_base_yaml: '{{ PARMgfs }}/gdas/marine/jcb-base.yaml.j2'
+        jcb_algo: soca_ensweights
+
+data_in:
+    mkdir:
+    - '{{ DATA }}/bkg'
+    - '{{ DATA }}/INPUT'
+    - '{{ DATA }}/anl_geom'
+    - '{{ DATAens }}/ens'
+
+    copy:
+{% filter indent(width=4) %}
+{% include 'marine_det_stage_bkg.yaml.j2' %}
+{% include 'marine_stage_fix_' ~ OCNRES ~ '.yaml.j2' %}
+{% include 'marine_stage_utilities.yaml.j2' %}
+{% if DOHYBVAR_OCN == "YES" or NMEM_ENS >= 2 %}
+{% include 'marine_ens_stage_bkg.yaml.j2' %}
+{% endif %}
+{% endfilter %}
+
+    link:
+    - [ "{{ DATA }}/../staticb", "{{ DATA }}/staticb" ]
+
+data_out:
+    copy:
+    # soca grid
+    - ['{{ DATA }}/soca_gridspec.nc', '{{ COMOUT_OCEAN_BMATRIX }}']
+
+    # Copy the diffusion coefficient files to the ROTDIR
+    - ['{{ DATAstaticb }}/hz_ocean.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}hz.nc']
+    - ['{{ DATAstaticb }}/vt_ocean.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}vt.nc']
+
+    # diag B rename (do we really need this?)
+    - ['{{ DATAstaticb }}/ocn.bkgerr_parametric_stddev.incr.{{ WINDOW_END | to_isotime }}.nc', '{{ DATAstaticb }}/ocn.bkgerr_parametric_stddev.nc']
+    - ['{{ DATAstaticb }}/ice.bkgerr_parametric_stddev.incr.{{ WINDOW_END | to_isotime }}.nc', '{{ DATAstaticb }}/ice.bkgerr_parametric_stddev.nc']
+{% if DOHYBVAR_OCN == "YES" or NMEM_ENS >= 2 %}
+    - ['{{ DATAstaticb }}/ocn.bkgerr_ens_stddev.incr.{{ WINDOW_BEGIN | to_isotime }}.nc','{{ DATAstaticb }}/ocn.bkgerr_ens_stddev.nc']
+    - ['{{ DATAstaticb }}/ice.bkgerr_ens_stddev.incr.{{ WINDOW_BEGIN | to_isotime }}.nc','{{ DATAstaticb }}/ice.bkgerr_ens_stddev.nc']
+{% endif %}
+
+    # diag B
+    - ['{{ DATAstaticb }}/ocn.bkgerr_parametric_stddev.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}bkgerr_parametric_stddev.nc']
+    - ['{{ DATAstaticb }}/ice.bkgerr_parametric_stddev.nc', '{{ COMOUT_ICE_BMATRIX }}/{{ APREFIX }}bkgerr_parametric_stddev.nc']
+{% if DOHYBVAR_OCN == "YES" or NMEM_ENS >= 2 %}
+    - ['{{ DATAstaticb }}/ocn.bkgerr_ens_stddev.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}bkgerr_ens_stddev.nc']
+    - ['{{ DATAstaticb }}/ice.bkgerr_ens_stddev.nc', '{{ COMOUT_ICE_BMATRIX }}/{{ APREFIX }}bkgerr_ens_stddev.nc']
+    - ['{{ DATAstaticb }}/ocn.ssh_recentering_error.incr.{{ WINDOW_BEGIN | to_isotime }}.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}recentering_error.nc']
+    - ['{{ DATAstaticb }}/ice.ssh_recentering_error.incr.{{ WINDOW_BEGIN | to_isotime }}.nc', '{{ COMOUT_ICE_BMATRIX }}/{{ APREFIX }}recentering_error.nc']
+{% endif %}
+
+{% if DOHYBVAR_OCN == "YES" or NMEM_ENS >= 2 %}
+    # ensemble perturbation diagnostics
+    - ['{{ DATA }}/ocn.ens_weights.incr.{{ WINDOW_MIDDLE | to_isotime }}.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}ens_weights.nc']
+    - ['{{ DATA }}/ice.ens_weights.incr.{{ WINDOW_MIDDLE | to_isotime }}.nc', '{{ COMOUT_ICE_BMATRIX }}/{{ APREFIX }}ens_weights.nc']
+
+    # ssh diagnostics
+    - ['{{ DATA }}/staticb/ocn.ssh_steric_stddev.incr.{{ WINDOW_BEGIN | to_isotime }}.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}ssh_steric_stddev.nc']
+    - ['{{ DATA }}/staticb/ocn.ssh_unbal_stddev.incr.{{ WINDOW_BEGIN | to_isotime }}.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}ssh_unbal_stddev.nc']
+    - ['{{ DATA }}/staticb/ocn.ssh_total_stddev.incr.{{ WINDOW_BEGIN | to_isotime }}.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}ssh_total_stddev.nc']
+    - ['{{ DATA }}/staticb/ocn.steric_explained_variance.incr.{{ WINDOW_BEGIN | to_isotime }}.nc', '{{ COMOUT_OCEAN_BMATRIX }}/{{ APREFIX }}steric_explained_variance.nc']
+{% endif %}
+
+    # yaml files
+    - ['{{ DATA }}/fields_metadata.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}bmat_fields_metadata.yaml']
+    - ['{{ DATA }}/gridgen.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}gridgen.yaml']
+    - ['{{ DATA }}/obsop_name_map.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}obsop_name_map.yaml']
+    - ['{{ DATA }}/soca_chgres.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}soca_chgres.yaml']
+    - ['{{ DATA }}/soca_diagb.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}soca_diagb.yaml']
+    - ['{{ DATA }}/soca_parameters_diffusion_hz.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}soca_parameters_diffusion_hz.yaml']
+    - ['{{ DATA }}/soca_parameters_diffusion_vt.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}soca_parameters_diffusion_vt.yaml']
+    - ['{{ DATA }}/soca_setcorscales.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}soca_setcorscales.yaml']
+    - ['{{ DATA }}/soca_vtscales.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}soca_vtscales.yaml']
+{% if DOHYBVAR_OCN == "YES" or NMEM_ENS >= 2 %}
+    - ['{{ DATA }}/soca_ensb.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}soca_ensb.yaml']
+    - ['{{ DATA }}/soca_ensweights.yaml', '{{ COMOUT_CONF }}/{{ APREFIX }}soca_ensweights.yaml']
+{% endif %}