Revive the marine jcb implementation (#26)

Some updates/fixes to the marine yaml templates.

algorithm/marine/soca_2cice_antarctic.yaml.j2

@@ -0,0 +1,43 @@
+input geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: fields_metadata.yaml
+  geom_grid_file: soca_gridspec.nc
+
+output geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: fields_metadata.yaml
+  geom_grid_file: soca_gridspec.nc
+
+variable change:
+  variable change name: Soca2Cice
+  do inverse: false
+  seaice edge: 0.9
+  shuffle: false  # seg. fault when true
+  rescale prior:
+    min hice: 0.5
+    min hsno: 0.1
+  domain: antarctic
+  cice background state:
+    restart: {{ ice_rst }}
+    grid: ' '
+    ncat: 5
+    ice_lev: 7
+    sno_lev: 1
+    tstep: PT1H
+  cice output:
+    restart: {{ ice_rst }}
+  output variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+
+states:
+- input:
+     read_from_file: 1
+     basename: ./
+     ocn_filename: {{ ocn_ana }}
+     ice_filename: {{ ice_ana }}
+     date: '{{ fcst_begin }}'
+     state variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+  output:
+     datadir: Data
+     exp: soca2cice
+     type: fc
+     date: '{{ fcst_begin }}'

algorithm/marine/soca_2cice_arctic.yaml.j2

@@ -0,0 +1,40 @@
+input geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+output geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+variable change:
+  variable change name: Soca2Cice
+  do inverse: false
+  seaice edge: 0.8
+  shuffle: false
+  rescale prior:
+    min hice: 0.5
+    min hsno: 0.1
+  domain: arctic
+  cice background state:
+    restart: {{ ice_rst }}
+    ncat: 5
+    ice_lev: 7
+    sno_lev: 1
+    tstep: PT1H
+  cice output:
+    restart: {{ ice_rst }}
+  output variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+
+states:
+- input:
+     read_from_file: 1
+     basename: ./
+     ocn_filename: {{ ocn_ana }}
+     ice_filename: {{ ice_ana }}
+     date: '{{ fcst_begin }}'
+     state variables: [tocn, socn, hocn, cicen, hicen, hsnon]
+  output:
+     datadir: Data
+     exp: soca2cice
+     type: fc
+     date: '{{ fcst_begin }}'

algorithm/marine/socaincr2mom6.yaml → algorithm/marine/socaincr2mom6.yaml.j2

@@ -2,27 +2,27 @@ geometry:
   mom6_input_nml: mom_input.nml
   fields metadata: ./fields_metadata.yaml
 
-date: '{{marine_window_begin}}'
+date: '{{ marine_window_begin }}'
 
 layers variable: [hocn]
 
 increment variables: [tocn, socn, uocn, vocn, ssh]
 
 vertical geometry:
-  date: '{{marine_window_begin}}'
+  date: '{{ marine_window_begin }}'
   basename: ./INPUT/
   ocn_filename: MOM.res.nc
   read_from_file: 1
 
 soca increment:
-  date: '{{marine_window_begin}}'
+  date: '{{ marine_window_begin }}'
   basename: ./Data/
-  ocn_filename: 'ocn.3dvarfgat_pseudo.incr.{{ATM_WINDOW_MIDDLE}}.nc'
+  ocn_filename: 'ocn.3dvarfgat_pseudo.incr.{{marine_window_middle}}.nc'
   read_from_file: 1
 
 output increment:
   datadir: ./
-  date: '{{marine_window_begin}}'
+  date: '{{ marine_window_begin }}'
   exp: mom6_iau
   type: incr
   output file: inc.nc

model/marine/marine_background_error_static_diffusion.yaml.j2

@@ -18,21 +18,21 @@ saber central block:
     groups:
     - name: ocean
       horizontal:
-        filename: hz_ocean.nc
+        filename: ./staticb/hz_ocean.nc
       vertical:
-        filename: vt_ocean.nc
+        filename: ./staticb/vt_ocean.nc
     - name: ice
       horizontal:
-        filename: hz_ice.nc
+        filename: ./staticb/hz_ice.nc
 
 saber outer blocks:
 - saber block name: StdDev
   read:
     model file:
       date: '{{marine_stddev_time}}'
-      basename: ./
-      ocn_filename: 'ocn.bkgerr_stddev.incr.{{marine_stddev_time}}.nc'
-      ice_filename: 'ice.bkgerr_stddev.incr.{{marine_stddev_time}}.nc'
+      basename: ./staticb/
+      ocn_filename: 'ocn.bkgerr_stddev.nc'
+      ice_filename: 'ice.bkgerr_stddev.nc'
       read_from_file: 3
 
 linear variable change: