Companion PR to NOAA-EMC/jcb/pull/7

model/atmosphere/atmosphere_3dvar_outer_loop_1.yaml.j2

@@ -0,0 +1,17 @@
+- ninner: 2
+  gradient norm reduction: 1e-10
+  test: on
+  geometry:
+    fms initialization:
+      namelist filename: {{atmosphere_fv3jedi_files_path}}/fmsmpp.nml
+      field table filename: {{atmosphere_fv3jedi_files_path}}/field_table
+    akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+    layout:
+    - {{atmosphere_layout_x}}
+    - {{atmosphere_layout_y}}
+    npx: {{atmosphere_npx_anl}}
+    npy: {{atmosphere_npy_anl}}
+    npz: {{atmosphere_npz_anl}}
+    field metadata override: {{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml
+  diagnostics:
+    departures: bkgmob

model/atmosphere/atmosphere_3dvar_outer_loop_2.yaml.j2

@@ -0,0 +1,17 @@
+- ninner: 4
+  gradient norm reduction: 1e-10
+  test: on
+  geometry:
+    fms initialization:
+      namelist filename: {{atmosphere_fv3jedi_files_path}}/fmsmpp.nml
+      field table filename: {{atmosphere_fv3jedi_files_path}}/field_table
+    akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+    layout:
+    - {{atmosphere_layout_x}}
+    - {{atmosphere_layout_y}}
+    npx: {{atmosphere_npx_anl}}
+    npy: {{atmosphere_npy_anl}}
+    npz: {{atmosphere_npz_anl}}
+    field metadata override: {{atmosphere_fv3jedi_files_path}}/fv3jedi_fieldmetadata_restart.yaml
+  diagnostics:
+    departures: bkgmob1

model/atmosphere/background.yaml.j2 → model/atmosphere/atmosphere_background.yaml.j2

@@ -1,6 +1,6 @@
-datapath: {{ background_path}}
+datapath: {{ atmosphere_background_path}}
 filetype: fms restart
-datetime: "{{ atm_background_time_iso }}"
+datetime: "{{ atmosphere_background_time_iso }}"
 filename is datetime templated: true
 filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
 filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"

model/atmosphere/background_ensemble.yaml.j2 → model/atmosphere/atmosphere_background_ensemble.yaml.j2

@@ -1,18 +1,18 @@
-datetime: '{{ atm_background_time_iso }}'
+datetime: '{{ atmosphere_background_time_iso }}'
 members from template:
   template:
-    datetime: '{{ atm_background_time_iso }}'
+    datetime: '{{ atmosphere_background_time_iso }}'
     filetype: fms restart
     state variables: [ua,va,t,DZ,delp,ps,sphum,ice_wat,liq_wat,o3mr,phis,
                      slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,
                      u_srf,v_srf,f10m]
-    datapath: {{ background_ensemble_path}}
+    datapath: {{ atmosphere_background_ensemble_path}}
     filename is datetime templated: true
     filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
     filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
     filename_sfcd: "%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
     filename_sfcw: "%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
     filename_cplr: "%yyyy%mm%dd.%hh%MM%ss.coupler.res"
-  pattern: "{{ ensemble_pattern | default("%mem%", true) }}"
-  nmembers: {{ number_ensemble_members }}
+  pattern: "{{ atmosphere_ensemble_pattern | default("%mem%", true) }}"
+  nmembers: {{ atmosphere_number_ensemble_members }}
   zero padding: 3

model/atmosphere/background_error_hybrid_bump_bump.yaml.j2 → model/atmosphere/atmosphere_background_error_hybrid_bump_bump.yaml.j2

@@ -5,12 +5,12 @@ components:
     saber blocks:
     - saber block name: BUMP_NICAS
       saber central block: true
-      input variables: &control_vars [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
-      output variables: *control_vars
-      active variables: &active_vars [psi,chi,t,ps,rh,liq_wat,o3mr]
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
       bump:
         io:
-          data directory: &staticb_dir {{bump_data_directory}}
+          data directory: {{atmosphere_bump_data_directory}}
         drivers:
           multivariate strategy: specific_univariate
           read local nicas: true
@@ -36,30 +36,30 @@ components:
           io:
             files prefix: nicas/nicas_2D_gfs
     - saber block name: StdDev
-      input variables: *control_vars
-      output variables: *control_vars
-      active variables: *active_vars
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
       file:
         filetype: fms restart
         datetime: 2021-12-22T00:00:00Z
         set datetime on read: true
         psinfile: true
-        datapath: '*staticb_dir'
+        datapath: {{atmosphere_bump_data_directory}}
         prefix: stddev/20211222.000000
         filename_core: stddev.fv_core.res.nc
         filename_trcr: stddev.fv_tracer.res.nc
         filename_sfcd: stddev.sfc_data.nc
         filename_sfcw: stddev.fv_srf_wnd.res.nc
         filename_cplr: stddev.coupler.res
     - saber block name: BUMP_VerticalBalance
-      input variables: *control_vars
-      output variables: *control_vars
-      active variables: *active_vars
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
       bump:
         general:
           universe length-scale: 2000.0e3
         io:
-          data directory: *staticb_dir
+          data directory: {{atmosphere_bump_data_directory}}
           files prefix: vbal/vbal_gfs
           overriding sampling file: vbal/vbal_2021122200_gfs_sampling
         drivers:
@@ -74,49 +74,49 @@ components:
           - balanced variable: var4
             unbalanced variable: var1
     - saber block name: BUMP_PsiChiToUV
-      input variables: *control_vars
-      output variables: &3dvars_with_rh [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
+      input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
       active variables: [psi,chi,ua,va]
       bump:
         general:
           universe length-scale: 2000.0e3
         io:
-          data directory: *staticb_dir
+          data directory: {{atmosphere_bump_data_directory}}
           files prefix: psichitouv/psichitouv_gfs
         drivers:
           read local psichitouv: true
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: *3dvars_with_rh
-      output variables: &3dvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+      input variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
+      output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
     value: 0.1
 - covariance:
     covariance model: ensemble
     members from template:
       template:
-        datetime: "{{ atm_background_time_iso }}"
+        datetime: "{{ atmosphere_background_time_iso }}"
         filetype: fms restart
-        state variables: *3dvars
-        datapath: {{ background_ensemble_path}}
+        state variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+        datapath: {{ atmosphere_background_ensemble_path}}
         filename is datetime templated: true
         filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
         filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
         filename_sfcd: "%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
         filename_sfcw: "%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
         filename_cplr: "%yyyy%mm%dd.%hh%MM%ss.coupler.res"
-      pattern: "{{ ensemble_pattern | default("%mem%", true) }}"
-      nmembers: {{number_ensemble_members}}
+      pattern: "{{ atmosphere_ensemble_pattern | default("%mem%", true) }}"
+      nmembers: {{atmosphere_number_ensemble_members}}
       zero padding: 3
 #    localization:
 #      localization method: SABER
 #      saber block:
 #      - saber block name: BUMP_NICAS
-#        input variables: *control_vars
-#        output variables: *control_vars
-#        active variables: *active_vars
+#        input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+#        output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+#        active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
 #        bump:
-#          datadir: *staticb_dir
+#          datadir: {{atmosphere_bump_data_directory}}
 #          verbosity: main
 #          strategy: specific_univariate
 #          method: loc

model/atmosphere/background_error_hybrid_gsibec_bump.yaml.j2 → model/atmosphere/atmosphere_background_error_hybrid_gsibec_bump.yaml.j2

@@ -5,50 +5,50 @@ components:
     saber central block:
       saber block name: gsi covariance
       read:
-        gsi akbk: &akbk {{fv3jedi_files_path}}/akbk.nc4
-        gsi error covariance file: &gsiberr {{gsibec_path}}/gsi-coeffs-gfs-global.nc4
-        gsi berror namelist file: &gsibnml {{gsibec_path}}/gfs_gsi_global.nml
-        processor layout x direction: &layout_gsib_x {{layout_gsib_x}}
-        processor layout y direction: &layout_gsib_y {{layout_gsib_y}}
+        gsi akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+        gsi error covariance file: {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
+        gsi berror namelist file: {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
+        processor layout x direction: {{atmosphere_layout_gsib_x}}
+        processor layout y direction: {{atmosphere_layout_gsib_y}}
         debugging mode: false
     saber outer blocks:
     - saber block name: gsi interpolation to model grid
-      gsi akbk: *akbk
-      gsi error covariance file: *gsiberr
-      gsi berror namelist file: *gsibnml
-      processor layout x direction: *layout_gsib_x
-      processor layout y direction: *layout_gsib_y
+      gsi akbk: {{atmosphere_fv3jedi_files_path}}/akbk.nc4
+      gsi error covariance file: {{atmosphere_gsibec_path}}/gsi-coeffs-gfs-global.nc4
+      gsi berror namelist file: {{atmosphere_gsibec_path}}/gfs_gsi_global.nml
+      processor layout x direction: {{atmosphere_layout_gsib_x}}
+      processor layout y direction: {{atmosphere_layout_gsib_x}}
       debugging mode: false
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: &control_vars [eastward_wind,northward_wind,air_temperature,surface_pressure,
+      input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
                                       specific_humidity,cloud_liquid_ice,cloud_liquid_water,
                                       mole_fraction_of_ozone_in_air]
-      output variables: &3dvars_anal [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+      output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
     value: 0.125
 - covariance:
     covariance model: ensemble
     members from template:
       template:
-        datetime: "{{ atm_background_time_iso }}"
+        datetime: "{{ atmosphere_background_time_iso }}"
         filetype: fms restart
-        state variables: *3dvars_anal
-        datapath: {{ background_ensemble_path}}
+        state variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
+        datapath: {{ atmosphere_background_ensemble_path}}
         filename is datetime templated: true
         filename_core: "%yyyy%mm%dd.%hh%MM%ss.fv_core.res.nc"
         filename_trcr: "%yyyy%mm%dd.%hh%MM%ss.fv_tracer.res.nc"
         filename_sfcd: "%yyyy%mm%dd.%hh%MM%ss.sfc_data.nc"
         filename_sfcw: "%yyyy%mm%dd.%hh%MM%ss.fv_srf_wnd.res.nc"
         filename_cplr: "%yyyy%mm%dd.%hh%MM%ss.coupler.res"
-      pattern: "{{ ensemble_pattern | default("%mem%", true) }}"
-      nmembers: {{number_ensemble_members}}
+      pattern: "{{ atmosphere_ensemble_pattern | default("%mem%", true) }}"
+      nmembers: {{atmosphere_number_ensemble_members}}
       zero padding: 3
     localization:
       localization method: SABER
       saber central block:
         saber block name: BUMP_NICAS
-        active variables: &3dvars_anal_long [eastward_wind,northward_wind,air_temperature,surface_pressure,
+        active variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
                                              specific_humidity,cloud_liquid_ice,cloud_liquid_water,
                                              ozone_mass_mixing_ratio ]
         read:
@@ -201,7 +201,9 @@ components:
               value: 0.3
     linear variable change:
       linear variable change name: Control2Analysis
-      input variables: *3dvars_anal_long
-      output variables: *3dvars_anal
+      input variables: [eastward_wind,northward_wind,air_temperature,surface_pressure,
+                                             specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+                                             ozone_mass_mixing_ratio ]
+      output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
   weight:
     value: 0.875

model/atmosphere/background_error_static_bump.yaml.j2 → model/atmosphere/atmosphere_background_error_static_bump.yaml.j2

@@ -3,12 +3,12 @@ full inverse: true
 saber blocks:
 - saber block name: BUMP_NICAS
   saber central block: true
-  input variables: &control_vars [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
-  output variables: *control_vars
-  active variables: &active_vars [psi,chi,t,ps,rh,liq_wat,o3mr]
+  input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
   bump:
     io:
-      data directory: &staticb_dir {{bump_data_directory}}
+      data directory: {{atmosphere_bump_data_directory}}
     drivers:
       multivariate strategy: specific_univariate
       read local nicas: true
@@ -34,30 +34,30 @@ saber blocks:
       io:
         files prefix: nicas/nicas_2D_gfs
 - saber block name: StdDev
-  input variables: *control_vars
-  output variables: *control_vars
-  active variables: *active_vars
+  input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
   file:
     filetype: fms restart
     datetime: 2021-12-22T00:00:00Z
     set datetime on read: true
     psinfile: true
-    datapath: *staticb_dir
+    datapath: {{atmosphere_bump_data_directory}}
     prefix: stddev/20211222.000000
     filename_core: stddev.fv_core.res.nc
     filename_trcr: stddev.fv_tracer.res.nc
     filename_sfcd: stddev.sfc_data.nc
     filename_sfcw: stddev.fv_srf_wnd.res.nc
     filename_cplr: stddev.coupler.res
 - saber block name: BUMP_VerticalBalance
-  input variables: *control_vars
-  output variables: *control_vars
-  active variables: *active_vars
+  input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  output variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  active variables: [psi,chi,t,ps,rh,liq_wat,o3mr]
   bump:
     general:
       universe length-scale: 2000.0e3
     io:
-      data directory: *staticb_dir
+      data directory: {{atmosphere_bump_data_directory}}
       files prefix: vbal/vbal_gfs
       overriding sampling file: vbal/vbal_2021122200_gfs_sampling
     drivers:
@@ -72,18 +72,18 @@ saber blocks:
       - balanced variable: var4
         unbalanced variable: var1
 - saber block name: BUMP_PsiChiToUV
-  input variables: *control_vars
-  output variables: &3dvars_with_rh [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
+  input variables: [psi,chi,t,ps,rh,ice_wat,liq_wat,o3mr]
+  output variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
   active variables: [psi,chi,ua,va]
   bump:
     general:
       universe length-scale: 2000.0e3
     io:
-      data directory: '*staticb_dir'
+      data directory: {{atmosphere_bump_data_directory}}
       files prefix: psichitouv/psichitouv_gfs
     drivers:
       read local psichitouv: true
 linear variable change:
   linear variable change name: Control2Analysis
-  input variables: *3dvars_with_rh
+  input variables: [ua,va,t,ps,rh,ice_wat,liq_wat,o3mr]
   output variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]