Create JCB templates for marine B-matrix (#36)

This PR is a companion to Global Workflow PR
[#2992](NOAA-EMC/global-workflow#2992) and
GDASApp PR [#1346](NOAA-EMC/GDASApp#1346).

It adds JCB templates for the input YAMLS of JEDI applications used in
the marine B-matrix task in the Global Workflow.

---------

Co-authored-by: Dan Holdaway <[email protected]>
Co-authored-by: Guillaume Vernieres <[email protected]>

algorithm/marine/soca_diagb.yaml.j2

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+geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+date: '{{ marine_window_end_iso }}'
+
+background:
+  date: '{{ marine_window_end_iso }}'
+  basename: ./bkg/
+  ocn_filename: 'ocean.bkg.f009.nc'
+  ice_filename: 'ice.bkg.f009.nc'
+  read_from_file: 1
+
+background error:
+  datadir: ./staticb/
+  date: '{{ marine_window_middle_iso }}'
+  exp: bkgerr_stddev
+  type: incr
+
+variables:
+  name: [tocn, socn, uocn, vocn, hocn, ssh, cicen, hicen, hsnon, mom6_mld]
+
+rescale: 2.0    # rescales the filtered std. dev. by "rescale"
+min sst: 0.0    # Added to sst bkg. err.
+max ssh: 0.0    # Limits the amplitude of the unbalanced bkg err
+min depth: 500.0 # zero out the bkg. error. at less than min depth
+number of halo points: 4
+number of neighbors: 16
+
+simple smoothing:
+  horizontal iterations: 10
+  vertical iterations: 1
+
+# TODO(G): Too slow for the below scale
+#diffusion:
+#  horizontal: 500.0e3
+#  vertical: 3.0

algorithm/marine/soca_ensb.yaml.j2

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+# Configuration for the recentering and re-balancing of the ensemble members
+geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+date: '{{ marine_window_begin_iso }}'
+
+layers variable: [hocn]
+
+increment variables: [tocn, socn, uocn, vocn, ssh, hocn, cicen, hicen, hsnon]
+
+set increment variables to zero: [ssh]
+
+vertical geometry:
+  date: '{{ marine_window_begin_iso }}'
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  read_from_file: 3
+
+add recentering increment: false
+
+soca increments:  # Could also be states, but they are read as increments
+  number of increments: '{{ marine_number_ensemble_members }}'
+  pattern: '%mem%'
+  template:
+    date: '{{ marine_window_begin_iso }}'
+    basename: '{{ enspert_relpath }}/ens/'
+    ocn_filename: 'ocean.%mem%.nc'
+    ice_filename: 'ice.%mem%.nc'
+    read_from_file: 3
+
+steric height:
+  linear variable changes:
+  - linear variable change name: BalanceSOCA  # Only the steric balance is applied
+
+ensemble mean output:
+  datadir: ./staticb/
+  date: '{{ marine_window_begin_iso }}'
+  exp: ens_mean
+  type: incr
+
+ssh output:
+  unbalanced:
+    datadir: ./staticb/
+    date: '{{ marine_window_begin_iso }}'
+    exp: ssh_unbal_stddev
+    type: incr
+
+  steric:
+    datadir: ./staticb/
+    date: '{{ marine_window_begin_iso }}'
+    exp: ssh_steric_stddev
+    type: incr
+
+  total:
+    datadir: ./staticb/
+    date: '{{ marine_window_begin_iso }}'
+    exp: ssh_total_stddev
+    type: incr
+
+  explained variance:
+    datadir: ./staticb/
+    date: '{{ marine_window_begin_iso }}'
+    exp: steric_explained_variance
+    type: incr
+
+  recentering error:
+    datadir: ./staticb/
+    date: '{{ marine_window_begin_iso }}'
+    exp: ssh_recentering_error
+    type: incr
+
+background error output:
+  datadir: ./staticb/
+  date: '{{ marine_window_begin_iso }}'
+  exp: bkgerr_stddev
+  type: incr
+
+linear variable change:
+  linear variable changes:
+  - linear variable change name: BalanceSOCA
+
+trajectory:
+  state variables: [tocn, socn, uocn, vocn, ssh, hocn, layer_depth, mld, cicen, hicen, hsnon]
+  date: '{{ marine_window_begin_iso }}'
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  ice_filename: cice.res.nc
+  read_from_file: 1
+
+output increment:
+  # TODO: Revert this when fms can take more than 128 charactres file names
+  datadir: '{{ enspert_relpath }}/enspert/'
+  date: '{{ marine_window_begin_iso }}'
+  exp: trash
+  type: incr
+  output file: 'ocn.pert.steric.%mem%.nc'
+  pattern: '%mem%'

algorithm/marine/soca_ensweights.yaml.j2

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+geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+date: '{{ marine_window_middle_iso }}'
+
+variables:
+  ice: [cicen, hicen, hsnon]
+  ocean: [tocn, socn, uocn, vocn, ssh]
+
+background:
+  date: '{{ marine_window_begin_iso }}'
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  ice_filename: cice.res.nc
+  read_from_file: 1
+
+weights:
+  # Need to provide weights^2 when reading from file
+  ice: 0.0025   #  5% of original variance
+  ocean: 0.0625   # 25%      "       "
+  # Apply localized weights to the ocean ens. B
+  ocean local weights:
+  - lon: -172.0
+    lat: 11.0
+    amplitude: -1.0
+    length scale: 700.0
+  - lon: -160.0
+    lat: 12.0
+    amplitude: -1.0
+    length scale: 700.0
+
+output:
+  datadir: ./
+  date: '{{ marine_window_middle_iso }}'
+  exp: ens_weights
+  type: incr

algorithm/marine/soca_gridgen.yaml.j2

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+geometry:
+  geom_grid_file: soca_gridspec.nc
+  mom6_input_nml: mom_input.nml
+  fields metadata: fields_metadata.yaml
+  rossby file: rossrad.nc

algorithm/marine/soca_parameters_diffusion_hz.yaml.j2

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+geometry: &geom
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+background:
+  read_from_file: 1
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  ice_filename: cice.res.nc
+  date: '{{ marine_window_end_iso }}'
+  state variables: [ssh]
+
+background error:
+  covariance model: SABER
+  saber central block:
+    saber block name: diffusion
+    geometry: *geom
+    calibration:
+      normalization:
+        method: randomization
+        iterations: 10000
+
+      groups:
+      - horizontal:
+          model file:
+            date: '{{ marine_window_end_iso }}'
+            basename: ./
+            ocn_filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
+          model variable: ssh
+        write:
+          filepath: ./staticb/hz_ocean
+
+      - horizontal:
+          as gaussian: true
+          fixed value: 50000.0
+        write:
+          filepath: ./staticb/hz_ice

algorithm/marine/soca_parameters_diffusion_vt.yaml.j2

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+geometry: &geom
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+background:
+  read_from_file: 1
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  ice_filename: cice.res.nc
+  date: '{{ marine_window_middle_iso }}'
+  state variables: [tocn]
+
+background error:
+  covariance model: SABER
+  saber central block:
+    saber block name: diffusion
+    geometry: *geom
+    calibration:
+      normalization:
+        # NOTE, not actually used here, since the normalization spec is only used for hz
+        method: randomization  #< other option is "brute force"
+        iterations: 1000       #< in the real world you'll want to use 1e4 or so
+
+      groups:
+      - vertical:
+          as gaussian: true
+          levels: '{{ marine_vt_levels }}'
+          model file:
+            date: '{{ marine_window_middle_iso }}'
+            basename: ./
+            ocn_filename: vt_scales.nc
+          model variable: tocn
+        write:
+          filepath: ./staticb/vt_ocean

algorithm/marine/soca_setcorscales.yaml.j2

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+resolution:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+date: "0001-01-01T00:00:00Z"
+
+corr variables: [ssh]
+
+scales:
+  vert layers: 5 # in units of layer
+  ssh:
+    rossby mult: 1.00
+    min grid mult: 2.0
+
+rh output:
+  datadir: ./
+  exp: cor_rh
+  type: incr
+
+rv output:
+  datadir: ./
+  exp: cor_rv
+  type: incr

algorithm/marine/soca_vtscales.yaml.j2

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+gridspec_filename: soca_gridspec.nc
+restart_filename: ./INPUT/MOM.res.nc
+mld_filename: './staticb/ocn.bkgerr_stddev.incr.{{ marine_window_end_iso }}.nc'
+output_filename: ./vt_scales.nc
+output_variable_vt: Temp
+output_variable_hz: ave_ssh
+
+VT_MIN: 5
+VT_MAX: 15
+
+HZ_ROSSBY_MULT: 1.0
+HZ_MAX: 200e3
+HZ_MIN_GRID_MULT: 2.0