Update to the marine yamls (#1309)

I have yet to update the # for `jcb-gdas`. This will be done when
[/NOAA-EMC/jcb-gdas/pull/30](NOAA-EMC/jcb-gdas#30)
is merged.

This branch requires changes in the `global-worflow` as well, see here:
[https://github.com/guillaumevernieres/global-workflow/tree/feature/update_hashes](https://github.com/guillaumevernieres/global-workflow/tree/feature/update_hashes)
. We'll need to update the # and coordinate the merge ...

parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2

@@ -8,7 +8,7 @@ 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
@@ -21,17 +21,17 @@ background error:
         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

parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2

@@ -8,7 +8,7 @@ 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
@@ -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

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

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/