NOAA-EMC · RussTreadon-NOAA · Oct 4, 2024 · Oct 1, 2024 · Oct 1, 2024 · Oct 1, 2024
diff --git a/parm/jcb-gdas b/parm/jcb-gdas
diff --git a/parm/soca/berror/obsolete/soca_parameters_diffusion_hz.yaml b/parm/soca/berror/obsolete/soca_parameters_diffusion_hz.yaml
@@ -13,7 +13,7 @@ background:
 background error:
   covariance model: SABER
   saber central block:
-    saber block name: EXPLICIT_DIFFUSION
+    saber block name: diffusion
     geometry: *geom
     calibration:
       normalization:

diff --git a/parm/soca/berror/obsolete/soca_parameters_diffusion_vt.yaml b/parm/soca/berror/obsolete/soca_parameters_diffusion_vt.yaml
@@ -13,7 +13,7 @@ background:
 background error:
   covariance model: SABER
   saber central block:
-    saber block name: EXPLICIT_DIFFUSION
+    saber block name: diffusion
     geometry: *geom
     calibration:
       normalization:

diff --git a/parm/soca/berror/soca_hybrid_bmat.yaml b/parm/soca/berror/soca_hybrid_bmat.yaml
@@ -3,7 +3,7 @@ components:
 - covariance:
     covariance model: SABER
     saber central block:
-      saber block name: EXPLICIT_DIFFUSION
+      saber block name: diffusion
       active variables: [tocn, socn, ssh, cicen]
       geometry:
         mom6_input_nml: mom_input.nml
@@ -62,7 +62,7 @@ components:
     localization:
       localization method: SABER
       saber central block:
-        saber block name: EXPLICIT_DIFFUSION
+        saber block name: diffusion
         active variables: [tocn, socn, ssh]
         geometry:
           mom6_input_nml: mom_input.nml

diff --git a/parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2 b/parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2
@@ -8,30 +8,30 @@ background:
   ocn_filename: MOM.res.nc
   ice_filename: cice.res.nc
   date: '{{ MARINE_WINDOW_END  | to_isotime }}'
-  state variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
+  state variables: [ssh]
 
 background error:
   covariance model: SABER
   saber central block:
-    saber block name: EXPLICIT_DIFFUSION
+    saber block name: diffusion
     geometry: *geom
     calibration:
       normalization:
         method: randomization
         iterations: 10000
 
       groups:
-      - name: ocean
-        horizontal:
-          from file:
-            filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
-            variable name: ave_ssh
+      - horizontal:
+          model file:
+            date: '{{ MARINE_WINDOW_END  | to_isotime }}'
+            basename: ./
+            ocn_filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
+          model variable: ssh
         write:
-          filename: ./staticb/hz_ocean.nc
+          filepath: ./staticb/hz_ocean
 
-      - name: ice
-        horizontal:
+      - horizontal:
           as gaussian: true
           fixed value: 50000.0
         write:
-          filename: ./staticb/hz_ice.nc
+          filepath: ./staticb/hz_ice
diff --git a/parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2 b/parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2
@@ -8,12 +8,12 @@ background:
   ocn_filename: MOM.res.nc
   ice_filename: cice.res.nc
   date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
-  state variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
+  state variables: [tocn]
 
 background error:
   covariance model: SABER
   saber central block:
-    saber block name: EXPLICIT_DIFFUSION
+    saber block name: diffusion
     geometry: *geom
     calibration:
       normalization:
@@ -22,11 +22,12 @@ background error:
         iterations: 1000       #< in the real world you'll want to use 1e4 or so
 
       groups:
-      - name: vt_ocean
-        vertical:
+      - vertical:
           as gaussian: true
-          from file:
-            filename: vt_scales.nc
-            variable name: vt
+          model file:
+            date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
+            basename: ./
+            ocn_filename: vt_scales.nc
+          model variable: tocn
         write:
-          filename: ./staticb/vt_ocean.nc
+          filepath: ./staticb/vt_ocean
diff --git a/parm/soca/berror/soca_static_bmat.yaml b/parm/soca/berror/soca_static_bmat.yaml
diff --git a/parm/soca/berror/soca_vtscales.yaml.j2 b/parm/soca/berror/soca_vtscales.yaml.j2
@@ -2,8 +2,8 @@ gridspec_filename: soca_gridspec.nc
 restart_filename: ./INPUT/MOM.res.nc
 mld_filename: './staticb/ocn.bkgerr_stddev.incr.{{ MARINE_WINDOW_END | to_isotime }}.nc'
 output_filename: ./vt_scales.nc
-output_variable_vt: vt
-output_variable_hz: hz
+output_variable_vt: Temp
+output_variable_hz: ave_ssh
 
 VT_MIN: 5
 VT_MAX: 15

diff --git a/parm/soca/marine-jcb-base.yaml b/parm/soca/marine-jcb-base.yaml
@@ -34,6 +34,7 @@ marine_window_middle: '{{MARINE_WINDOW_MIDDLE}}'
 
 # Geometry
 marine_soca_files_path: .
+marine_vt_levels: '{{MOM6_LEVS}}'
 
 # Initial conditions
 marine_background_path: ./INPUT/

diff --git a/sorc/fv3-jedi b/sorc/fv3-jedi
diff --git a/sorc/ioda b/sorc/ioda
diff --git a/sorc/iodaconv b/sorc/iodaconv
diff --git a/sorc/oops b/sorc/oops
diff --git a/sorc/saber b/sorc/saber
diff --git a/sorc/soca b/sorc/soca
diff --git a/sorc/ufo b/sorc/ufo
diff --git a/sorc/vader b/sorc/vader
diff --git a/test/atm/global-workflow/3dvar.ref b/test/atm/global-workflow/3dvar.ref
@@ -1,19 +1,19 @@
 CostJb   : Nonlinear Jb = 0.0000000000000000e+00
-CostJo   : Nonlinear Jo(AMSUA N19) = 3.9490015258335385e+04, nobs = 73667, Jo/n = 5.3606112992704180e-01, err = 6.2697697603632934e+00
+CostJo   : Nonlinear Jo(AMSUA N19) = 3.9490015258335392e+04, nobs = 73667, Jo/n = 5.3606112992704180e-01, err = 6.2697697603632934e+00
 CostJo   : Nonlinear Jo(sondes) = 1.0738590249678713e+04, nobs = 4255, Jo/n = 2.5237579905237868e+00, err = 1.0981123140127320e+01
-CostFunction: Nonlinear J = 5.0228605508014094e+04
-DRPCGMinimizer: reduction in residual norm = 9.6305250910880724e-01
+CostFunction: Nonlinear J = 5.0228605508014109e+04
+DRPCGMinimizer: reduction in residual norm = 1.2654930990384508e+00
 CostFunction::addIncrement: Analysis: 
 ----------------------------------------------------------------------------------------------------
 State print | number of fields = 22 | cube sphere face size: C48
-eastward_wind                                | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288534095e+01
-northward_wind                               | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891570869e+00
-air_temperature                              | Min:+1.7482158077318448e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883092669e+02
+eastward_wind                                | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288535051e+01
+northward_wind                               | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891572610e+00
+air_temperature                              | Min:+1.7482158077318425e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883106894e+02
 air_pressure_thickness                       | Min:+6.0599999874109178e-01 Max:+1.7760098554198755e+03 RMS:+9.5680601590204810e+02
 surface_pressure                             | Min:+5.3298485514404747e+04 Max:+1.0398027192902798e+05 RMS:+9.8897229693652524e+04
-specific_humidity                            | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792636816418417e-03
-cloud_liquid_ice                             | Min:+0.0000000000000000e+00 Max:+1.2024392024662985e-03 RMS:+1.4396968866569995e-05
-cloud_liquid_water                           | Min:+0.0000000000000000e+00 Max:+1.5935686618789048e-03 RMS:+4.1931345590543333e-05
+specific_humidity                            | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792637035328151e-03
+cloud_liquid_ice                             | Min:+0.0000000000000000e+00 Max:+1.2024285059501723e-03 RMS:+1.4396343608618137e-05
+cloud_liquid_water                           | Min:+0.0000000000000000e+00 Max:+1.5935686450466631e-03 RMS:+4.1864377574483124e-05
 ozone_mass_mixing_ratio                      | Min:+1.1998327271379204e-08 Max:+1.7808431790670831e-05 RMS:+4.4947917149861064e-06
 surface_geopotential_height                  | Min:-2.7018394470214844e+01 Max:+5.2697460937500000e+03 RMS:+6.3032575784066080e+02
 slmsk                                        | Min:+0.0000000000000000e+00 Max:+2.0000000000000000e+00 RMS:+7.3450427349184144e-01
@@ -32,33 +32,33 @@ f10m                                         | Min:+9.4613586695410434e-01 Max:+
 
 Obs bias coefficients: 
 ---------------------------------------------------------------
-            constant:  Min= -1.2424509525299072,  Max= 1.6504349708035770,  Norm= 3.1030146353133463
-   lapseRate_order_2:  Min= -7.0903420445872838,  Max= 46.3166084284223771,  Norm= 47.0185597979528609
-           lapseRate:  Min= -5.5814771650607220,  Max= 1.2464430332789806,  Norm= 5.7524772942406086
-  emissivityJacobian:  Min= -1.0039629936218262,  Max= 10.5191706304246591,  Norm= 10.5711704384468028
-sensorScanAngle_order_4:  Min= -8.0552864073222832,  Max= 2.4945130349138593,  Norm= 13.5132453944315909
-sensorScanAngle_order_3:  Min= -1.1528069971066446,  Max= 2.1735479829142181,  Norm= 3.0673534349517819
-sensorScanAngle_order_2:  Min= -5.1097259521664853,  Max= 2.8632600308292808,  Norm= 7.2817410561999560
-     sensorScanAngle:  Min= -0.6898530126095289,  Max= 0.0655509978252007,  Norm= 1.1442823316972326
+            constant:  Min= -1.2424509525299072,  Max= 1.6504349707778374,  Norm= 3.1030146350620180
+   lapseRate_order_2:  Min= -7.0903420444281888,  Max= 46.3166084283797588,  Norm= 47.0185597978996128
+           lapseRate:  Min= -5.5814771649382546,  Max= 1.2464430333259036,  Norm= 5.7524772941123183
+  emissivityJacobian:  Min= -1.0039629936218262,  Max= 10.5191705643602678,  Norm= 10.5711703727068684
+sensorScanAngle_order_4:  Min= -8.0552864072427965,  Max= 2.4945130349633651,  Norm= 13.5132453941396253
+sensorScanAngle_order_3:  Min= -1.1528069970056642,  Max= 2.1735479827935875,  Norm= 3.0673534348153715
+sensorScanAngle_order_2:  Min= -5.1097259521743421,  Max= 2.8632600308748679,  Norm= 7.2817410561387739
+     sensorScanAngle:  Min= -0.6898530126324298,  Max= 0.0655509978110177,  Norm= 1.1442823317381461
 ---------------------------------------------------------------
 
 
-CostJb   : Nonlinear Jb = 0.0000003247124839
-CostJo   : Nonlinear Jo(AMSUA N19) = 39487.6033905210933881, nobs = 73667, Jo/n = 0.5360283897881154, err = 6.2697697603632934
-CostJo   : Nonlinear Jo(sondes) = 10687.4014846169593511, nobs = 4255, Jo/n = 2.5117277284646202, err = 10.9811231401273197
-CostFunction: Nonlinear J = 50175.0048754627641756
-DRPCGMinimizer: reduction in residual norm = 1.0067413227974593
+CostJb   : Nonlinear Jb = 0.0000014612994971
+CostJo   : Nonlinear Jo(AMSUA N19) = 39390.2547489576390944, nobs = 73667, Jo/n = 0.5347069209952575, err = 6.2697697603632934
+CostJo   : Nonlinear Jo(sondes) = 10684.1056534407689469, nobs = 4255, Jo/n = 2.5109531500448341, err = 10.9811231401273197
+CostFunction: Nonlinear J = 50074.3604038597040926
+DRPCGMinimizer: reduction in residual norm = 1.3784563235297740
 CostFunction::addIncrement: Analysis: 
 ----------------------------------------------------------------------------------------------------
 State print | number of fields = 22 | cube sphere face size: C48
-eastward_wind                                | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288542654e+01
-northward_wind                               | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891586234e+00
-air_temperature                              | Min:+1.7482158077318232e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883219918e+02
+eastward_wind                                | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288545034e+01
+northward_wind                               | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891590498e+00
+air_temperature                              | Min:+1.7482158077318175e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883255175e+02
 air_pressure_thickness                       | Min:+6.0599999874109178e-01 Max:+1.7760098554198755e+03 RMS:+9.5680601590204810e+02
 surface_pressure                             | Min:+5.3298485514404747e+04 Max:+1.0398027192902798e+05 RMS:+9.8897229693652524e+04
-specific_humidity                            | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792637405692090e-03
-cloud_liquid_ice                             | Min:+0.0000000000000000e+00 Max:+1.2024392024662985e-03 RMS:+1.4396968866569995e-05
-cloud_liquid_water                           | Min:+0.0000000000000000e+00 Max:+1.5935686618789048e-03 RMS:+4.1931345590543333e-05
+specific_humidity                            | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792636598075200e-03
+cloud_liquid_ice                             | Min:+0.0000000000000000e+00 Max:+1.2023914586805969e-03 RMS:+1.4394270245713929e-05
+cloud_liquid_water                           | Min:+0.0000000000000000e+00 Max:+1.5935685862194550e-03 RMS:+4.1737200829311335e-05
 ozone_mass_mixing_ratio                      | Min:+1.1998327271379204e-08 Max:+1.7808431790670831e-05 RMS:+4.4947917149861064e-06
 surface_geopotential_height                  | Min:-2.7018394470214844e+01 Max:+5.2697460937500000e+03 RMS:+6.3032575784066080e+02
 slmsk                                        | Min:+0.0000000000000000e+00 Max:+2.0000000000000000e+00 RMS:+7.3450427349184144e-01
@@ -77,18 +77,18 @@ f10m                                         | Min:+9.4613586695410434e-01 Max:+
 
 Obs bias coefficients: 
 ---------------------------------------------------------------
-            constant:  Min= -1.2424509525299072,  Max= 1.6504349705701049,  Norm= 3.1030146330531774
-   lapseRate_order_2:  Min= -7.0903420434846316,  Max= 46.3166084260648887,  Norm= 47.0185597955718677
-           lapseRate:  Min= -5.5814771643207211,  Max= 1.2464430335558840,  Norm= 5.7524772934110207
-  emissivityJacobian:  Min= -1.0039629936218262,  Max= 10.5191700403026349,  Norm= 10.5711698512230932
-sensorScanAngle_order_4:  Min= -8.0552864066518524,  Max= 2.4945130353434313,  Norm= 13.5132453918536388
-sensorScanAngle_order_3:  Min= -1.1528069962369289,  Max= 2.1735479817619940,  Norm= 3.0673534336938850
-sensorScanAngle_order_2:  Min= -5.1097259522434877,  Max= 2.8632600312042698,  Norm= 7.2817410556587614
-     sensorScanAngle:  Min= -0.6898530128249588,  Max= 0.0655509976984332,  Norm= 1.1442823320888615
+            constant:  Min= -1.2424509525299072,  Max= 1.6504349705176715,  Norm= 3.1030146324339514
+   lapseRate_order_2:  Min= -7.0903420430554904,  Max= 46.3166084270832954,  Norm= 47.0185597965343405
+           lapseRate:  Min= -5.5814771637081586,  Max= 1.2464430337450372,  Norm= 5.7524772928124595
+  emissivityJacobian:  Min= -1.0039629936218262,  Max= 10.5191698767122261,  Norm= 10.5711696884361785
+sensorScanAngle_order_4:  Min= -8.0552864064916889,  Max= 2.4945130355171092,  Norm= 13.5132453912586890
+sensorScanAngle_order_3:  Min= -1.1528069959771197,  Max= 2.1735479816041132,  Norm= 3.0673534334487149
+sensorScanAngle_order_2:  Min= -5.1097259522379295,  Max= 2.8632600311870164,  Norm= 7.2817410554387321
+     sensorScanAngle:  Min= -0.6898530128687219,  Max= 0.0655509976643010,  Norm= 1.1442823321434776
 ---------------------------------------------------------------
 
 
-CostJb   : Nonlinear Jb = 0.0000033199535370
-CostJo   : Nonlinear Jo(AMSUA N19) = 39476.8510817764617968, nobs = 73667, Jo/n = 0.5358824315063252, err = 6.2697697603632934
-CostJo   : Nonlinear Jo(sondes) = 10639.2476170353256748, nobs = 4255, Jo/n = 2.5004107208073623, err = 10.9811231401273197
-CostFunction: Nonlinear J = 50116.0987021317414474
+CostJb   : Nonlinear Jb = 0.0000118072709876
+CostJo   : Nonlinear Jo(AMSUA N19) = 39219.8814513386896579, nobs = 73667, Jo/n = 0.5323941717640014, err = 6.2697697603632934
+CostJo   : Nonlinear Jo(sondes) = 10645.9197195859396743, nobs = 4255, Jo/n = 2.5019787825113844, err = 10.9811231401273197
+CostFunction: Nonlinear J = 49865.8011827318987343
diff --git a/test/atm/global-workflow/lgetkf_observer.ref b/test/atm/global-workflow/lgetkf_observer.ref
@@ -80,31 +80,31 @@ surface_northward_wind                       | Min:-1.4183550286832059e+01 Max:+
 f10m                                         | Min:+9.2995810057091766e-01 Max:+1.0787102983488339e+00 RMS:+9.9539268028154582e-01
 ----------------------------------------------------------------------------------------------------
 H(x) for member 1:
-AMSUA N19 nobs= 83277 Min=201.8068522798935, Max=282.1977771850452, RMS=233.8559407930978
+AMSUA N19 nobs= 83277 Min=201.8068522604288, Max=282.1977354171605, RMS=233.8559301511747
 
-sondes nobs= 8481 Min=-33.72958087992568, Max=309.9582199829497, RMS=141.2113994268562
+sondes nobs= 2812 Min=-33.46923510113491, Max=237.4511515234925, RMS=66.49450460686083
 
 
 H(x) for member 2:
-AMSUA N19 nobs= 83277 Min=201.6491455196041, Max=282.0442934777565, RMS=233.8549246604183
+AMSUA N19 nobs= 83277 Min=201.6491448573896, Max=282.0443032111758, RMS=233.8543791644241
 
-sondes nobs= 8481 Min=-30.53144491152982, Max=310.2016372514533, RMS=141.1993510066664
+sondes nobs= 2812 Min=-30.53144491152982, Max=237.5347783619015, RMS=66.47644691726953
 
 
 H(x) for member 3:
-AMSUA N19 nobs= 83277 Min=201.5822623660015, Max=282.1680720517217, RMS=233.8542062391686
+AMSUA N19 nobs= 83277 Min=201.5822623085232, Max=282.1681017005377, RMS=233.8547828542549
 
-sondes nobs= 8481 Min=-32.86095389873932, Max=310.3775309250524, RMS=141.1778363650817
+sondes nobs= 2812 Min=-32.86095389873932, Max=237.9311435831063, RMS=66.51314984035037
 
 
 H(x) ensemble background mean: 
-AMSUA N19 nobs= 83277 Min=201.7046771524233, Max=282.1363019533286, RMS=233.8550114850208
+AMSUA N19 nobs= 83277 Min=201.7046771524233, Max=282.1363019533287, RMS=233.8550114850208
 
 sondes nobs= 8481 Min=-32.28721130380135, Max=310.1791293864851, RMS=141.1946022453276
 
 
 background y - H(x): 
-AMSUA N19 nobs= 83254 Min=-40.1226250672521, Max=14.39438798864785, RMS=1.520218815029863
+AMSUA N19 nobs= 83254 Min=-40.1226250672521, Max=14.39438798864788, RMS=1.520218815029863
 
 sondes nobs= 3950 Min=-16.79891131775619, Max=16.07422994026274, RMS=4.060200040073279