Merge branch 'develop' into feature/move_jcb

* develop:
  Changes name of rossrad file for letkf (#1151)
  Adds staging jinja/yaml file for letkf task (#1137)

parm/soca/letkf/letkf.yaml.j2

@@ -4,15 +4,15 @@ geometry:
   fields metadata: fields_metadata.yaml
 
 time window:
-  begin: &date '{{ ATM_WINDOW_BEGIN }}'
+  begin: &date '{{ WINDOW_BEGIN | to_isotime }}'
   length: PT6H 
 
 background:
   members from template:
     template:
-      date: '{{ ATM_WINDOW_MIDDLE }}'
-      ocn_filename: enkfgdas.ocean.t06z.inst.f009.nc
-      ice_filename: enkfgdas.ice.t06z.inst.f009.nc
+      date: '{{ WINDOW_MIDDLE | to_isotime }}'
+      ocn_filename: "{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc"
+      ice_filename: "{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc"
       read_from_file: 1
       basename: ./ens/mem%mem%
       state variables: [socn, tocn, ssh, uocn, vocn, cicen]

parm/soca/letkf/letkf_stage.yaml.j2

@@ -0,0 +1,49 @@
+######################################
+# set some variables
+######################################
+{% set gPDY = previous_cycle | to_YMD %}
+{% set gcyc = previous_cycle | strftime("%H") %}
+{% set PDY = current_cycle | to_YMD %}
+{% set cyc = current_cycle | strftime("%H") %}
+######################################
+# create working directories
+######################################
+mkdir:
+- "{{ DATA }}/Data"
+- "{{ DATA }}/obs"
+- "{{ DATA }}/INPUT"
+{% for mem in range(1, NMEM_ENS + 1) %}
+- "{{ DATA }}/ens/mem{{ '%03d' % mem }}"
+{% endfor %}
+copy:
+######################################
+# copy mom input template 
+######################################
+- ["{{ PARMgfs }}/gdas/soca/fms/input.nml", "{{ DATA }}/mom_input.nml.tmpl"]
+######################################
+# copy ensemble background files
+######################################
+{% for mem in range(1, NMEM_ENS + 1) %}
+# define variables
+# Declare a dict of search and replace terms to GDUMP on each template
+{% set tmpl_dict = {'ROTDIR':ROTDIR,
+                    'RUN': GDUMP_ENS,
+                    'YMD':gPDY,
+                    'HH':gcyc,
+                    'MEMDIR':"mem" + '%03d' % mem} %}
+
+# Replace template variables with tmpl_dict, one key at a time
+# This must be done in a namespace to overcome jinja scoping
+#  Variables set inside of a for loop are lost at the end of the loop
+#  unless they are part of a namespace
+{% set com_prev_ocn = namespace(COM_OCEAN_HISTORY_MEM = COM_OCEAN_HISTORY_TMPL) %}
+{% set com_prev_ice = namespace(COM_ICE_HISTORY_MEM = COM_ICE_HISTORY_TMPL) %}
+{% for key in tmpl_dict.keys() %}
+{% set search_term = '${' + key + '}' %}
+{% set replace_term = tmpl_dict[key] %}
+{% set com_prev_ocn.COM_OCEAN_HISTORY_MEM = com_prev_ocn.COM_OCEAN_HISTORY_MEM.replace(search_term, replace_term) %}
+{% set com_prev_ice.COM_ICE_HISTORY_MEM = com_prev_ice.COM_ICE_HISTORY_MEM.replace(search_term, replace_term) %}
+{% endfor %}
+- ["{{ com_prev_ocn.COM_OCEAN_HISTORY_MEM }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc", "{{ DATA }}/ens/mem{{ '%03d' % mem }}/{{ GDUMP_ENS }}.ocean.t{{ gcyc }}z.inst.f006.nc"]
+- ["{{ com_prev_ice.COM_ICE_HISTORY_MEM }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc", "{{ DATA }}/ens/mem{{ '%03d' % mem }}/{{ GDUMP_ENS }}.ice.t{{ gcyc }}z.inst.f006.nc"]
+{% endfor %}

parm/soca/letkf/soca_fix_stage.yaml.j2

@@ -0,0 +1,16 @@
+######################################
+# fix files to copy
+######################################
+copy:
+- ["{{ SOCA_INPUT_FIX_DIR }}/rossrad.nc", "{{ DATA }}/rossrad.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/field_table", "{{ DATA }}/field_table"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/diag_table", "{{ DATA }}/diag_table"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/MOM_input", "{{ DATA }}/MOM_input"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/fields_metadata.yaml", "{{ DATA }}/fields_metadata.yaml"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/obsop_name_map.yaml", "{{ DATA }}/obsop_name_map.yaml"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/grid_spec.nc", "{{ DATA }}/INPUT/grid_spec.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/hycom1_25.nc", "{{ DATA }}/INPUT/hycom1_25.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/layer_coord25.nc", "{{ DATA }}/INPUT/layer_coord25.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/ocean_hgrid.nc", "{{ DATA }}/INPUT/ocean_hgrid.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/ocean_mosaic.nc", "{{ DATA }}/INPUT/ocean_mosaic.nc"]
+- ["{{ SOCA_INPUT_FIX_DIR }}/INPUT/ocean_topog.nc", "{{ DATA }}/INPUT/ocean_topog.nc"]

test/soca/gw/CMakeLists.txt

@@ -50,7 +50,7 @@ set(jjob_list "JGLOBAL_PREP_OCEAN_OBS"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_ECEN"
-#	            "JGDAS_GLOBAL_OCEAN_ANALYSIS_LETKF"
+#	      "JGDAS_GLOBAL_OCEAN_ANALYSIS_LETKF"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_POST"
               "JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY")

test/soca/gw/prep.sh

@@ -68,9 +68,11 @@ do
     oceandir=${COMENS}/06/mem00${mem}/model_data/ocean/history
     mkdir -p $oceandir
     cp ${clim_ens_dir}/ocean.${mem}.nc $oceandir/enkfgdas.ocean.t06z.inst.f009.nc
+    cp ${clim_ens_dir}/ocean.${mem}.nc $oceandir/enkfgdas.ocean.t06z.inst.f006.nc
 
     # ice member
     icedir=${COMENS}/06/mem00${mem}/model_data/ice/history
     mkdir -p $icedir
     cp ${clim_ens_dir}/ice.${mem}.nc $icedir/enkfgdas.ice.t06z.inst.f009.nc
+    cp ${clim_ens_dir}/ice.${mem}.nc $icedir/enkfgdas.ice.t06z.inst.f006.nc
 done