Adds recentering task script and methods, with ctests (#968)

Resolves #912

---------

Co-authored-by: Guillaume Vernieres <guillaume.vernieres@noaa.gov>

parm/soca/berror/soca_ensrecenter.yaml

@@ -0,0 +1,102 @@
+# This yaml is for applying deterministic recentering increments to the ensemble members
+
+geometry:
+  mom6_input_nml: mom_input.nml
+  fields metadata: ./fields_metadata.yaml
+
+date: '{{ ATM_WINDOW_BEGIN }}'
+
+layers variable: [hocn]
+
+increment variables: [tocn, socn, uocn, vocn, ssh, hocn, cicen, hicen, hsnon]
+
+set increment variables to zero: [ssh]
+
+vertical geometry:
+  date: '{{ ATM_WINDOW_BEGIN }}'
+  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: {{ NMEM_ENS }}
+  pattern: '%mem%'
+  template:
+    date: '{{ ATM_WINDOW_BEGIN }}'
+    basename: ./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: ./static_ens
+#  date: '{{ ATM_WINDOW_BEGIN }}'
+#  exp: ens_mean
+#  type: incr
+
+ssh output:
+  unbalanced:
+    datadir: ./
+    date: '{{ ATM_WINDOW_BEGIN }}'
+    exp: ssh_unbal_stddev
+    type: incr
+
+  steric:
+    datadir: ./
+    date: '{{ ATM_WINDOW_BEGIN }}'
+    exp: ssh_steric_stddev
+    type: incr
+
+  total:
+    datadir: ./
+    date: '{{ ATM_WINDOW_BEGIN }}'
+    exp: ssh_total_stddev
+    type: incr
+
+  explained variance:
+    datadir: ./
+    date: '{{ ATM_WINDOW_BEGIN }}'
+    exp: steric_explained_variance
+    type: incr
+
+  recentering error:
+    datadir: ./
+    date: '{{ ATM_WINDOW_BEGIN }}'
+    exp: ssh_recentering_error
+    type: incr
+
+background error output:
+  datadir: ./
+  date: '{{ ATM_WINDOW_BEGIN }}'
+  exp: bkgerr_stddev
+  type: incr
+
+#linear variable change:
+#  linear variable changes:
+#  - linear variable change name: BkgErrFILT
+#    ocean_depth_min: 500  # zero where ocean is shallower than 500m
+#    rescale_bkgerr: 1.0   # rescale perturbation
+#    efold_z: 1500.0       # Apply exponential decay
+#  - linear variable change name: BalanceSOCA
+
+trajectory:
+  state variables: [tocn, socn, uocn, vocn, ssh, hocn, layer_depth, mld, cicen, hicen, hsnon]
+  date: '{{ ATM_WINDOW_BEGIN }}'
+  basename: ./INPUT/
+  ocn_filename: MOM.res.nc
+  ice_filename: cice.res.nc
+  read_from_file: 1
+
+output increment:
+  datadir: ./
+  date: '{{ ATM_WINDOW_BEGIN }}'
+  exp: trash
+  type: incr
+  output file: 'ocn.recenter.incr.%mem%.nc'
+  pattern: '%mem%'

parm/soca/obsprep/obsprep_config.yaml

@@ -22,6 +22,7 @@ observations:
     window:
        back: 8         # look back 8 six-hourly obs dumps
        forward: 1    #  look forward 1 six-hourly bin
+    error ratio: 0.4  # meters per day
 
 # Ice concentration
 - obs space:

scripts/exgdas_global_marine_analysis_ecen.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+# exgdas_global_marine_analysis_ecen.py
+# This script creates an MarineRecenter class
+# and runs the initialize, run, and finalize  methods
+# which currently are stubs
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+# TODO (AFE): change to from pygfs.task.marine_recenter import MarineRecenter
+from soca.marine_recenter import MarineRecenter
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Instantiate the aerosol analysis task
+    MarineRecen = MarineRecenter(config)
+    MarineRecen.initialize()
+    MarineRecen.run()
+    MarineRecen.finalize()

test/soca/gw/CMakeLists.txt

@@ -45,6 +45,7 @@ set(jjob_list "JGLOBAL_PREP_OCEAN_OBS"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN"
+              "JGDAS_GLOBAL_OCEAN_ANALYSIS_ECEN"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_POST"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY")

test/soca/gw/run_jjobs.yaml.test

@@ -35,6 +35,7 @@ gw environement:
 
   run scripts:
     GDASPREPOCNOBSPY: @HOMEgfs@/sorc/gdas.cd/scripts/exglobal_prep_ocean_obs.py
+    GDASOCNCENPY: @HOMEgfs@/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_ecen.py
 
 setup_expt config:
   base:

ush/soca/bkg_utils.py

@@ -101,13 +101,13 @@ def gen_bkg_list(bkg_path, out_path, window_begin=' ', yaml_name='bkg.yaml', ice
     bkg_date = window_begin
 
     # Construct list of background file names
-    GDUMP = os.getenv('GDUMP')
+    RUN = os.getenv('RUN')
     cyc = str(os.getenv('cyc')).zfill(2)
     gcyc = str((int(cyc) - 6) % 24).zfill(2)  # previous cycle
     fcst_hrs = list(range(3, 10, dt_pseudo))
     files = []
     for fcst_hr in fcst_hrs:
-        files.append(os.path.join(bkg_path, f'{GDUMP}.ocean.t'+gcyc+'z.inst.f'+str(fcst_hr).zfill(3)+'.nc'))
+        files.append(os.path.join(bkg_path, f'{RUN}.ocean.t'+gcyc+'z.inst.f'+str(fcst_hr).zfill(3)+'.nc'))
 
     # Identify the ocean background that will be used for the  vertical coordinate remapping
     ocn_filename_ic = os.path.splitext(os.path.basename(files[0]))[0]+'.nc'