Merge branch 'develop' into feature/aero_qc

NOAA-EMC · Jun 6, 2024 · 9f87a01 · 9f87a01
2 parents 448ac8a + 5071c52
commit 9f87a01
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diff --git a/parm/jcb-gdas b/parm/jcb-gdas
diff --git a/parm/soca/gridgen/gridgen.yaml b/parm/soca/gridgen/gridgen.yaml
@@ -1,5 +1,5 @@
 geometry:
   geom_grid_file: soca_gridspec.nc
-  full_init: true
   mom6_input_nml: mom_input.nml
-  fields metadata: fields_metadata.yaml
+  fields metadata: fields_metadata.yaml
+  rossby file: rossrad.nc
diff --git a/parm/soca/letkf/letkf.yaml.j2 b/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]

diff --git a/parm/soca/letkf/letkf_stage.yaml.j2 b/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 %}
diff --git a/parm/soca/letkf/soca_fix_stage.yaml.j2 b/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"]
diff --git a/sorc/fv3-jedi b/sorc/fv3-jedi
diff --git a/sorc/ioda b/sorc/ioda
diff --git a/sorc/iodaconv b/sorc/iodaconv
diff --git a/sorc/oops b/sorc/oops
diff --git a/sorc/saber b/sorc/saber
diff --git a/sorc/soca b/sorc/soca
diff --git a/sorc/ufo b/sorc/ufo
diff --git a/sorc/vader b/sorc/vader
diff --git a/test/atm/global-workflow/3dvar.ref b/test/atm/global-workflow/3dvar.ref
@@ -1,17 +1,17 @@
 CostJb   : Nonlinear Jb = 0.0000000000000000e+00
-CostJo   : Nonlinear Jo(AMSUA N19) = 3.8984270736441467e+04, nobs = 74275, Jo/n = 5.2486396144653613e-01, err = 6.3650648936327991e+00
+CostJo   : Nonlinear Jo(AMSUA N19) = 3.9490015258330794e+04, nobs = 73667, Jo/n = 5.3606112992697941e-01, err = 6.2697697603629345e+00
 CostJo   : Nonlinear Jo(sondes) = 1.0738490911289638e+04, nobs = 4255, Jo/n = 2.5237346442513839e+00, err = 1.0981085630539836e+01
-CostFunction: Nonlinear J = 4.9722761647731109e+04
-DRPCGMinimizer: reduction in residual norm = 9.6484392730339263e-01
+CostFunction: Nonlinear J = 5.0228506169620436e+04
+DRPCGMinimizer: reduction in residual norm = 9.6305250910882700e-01
 CostFunction::addIncrement: Analysis: 
 ----------------------------------------------------------------------------------------------------
 State print | number of fields = 22 | cube sphere face size: C48
-eastward_wind                                | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288534099e+01
-northward_wind                               | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891570887e+00
-air_temperature                              | Min:+1.7482158077318462e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883089124e+02
+eastward_wind                                | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288534095e+01
+northward_wind                               | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891570869e+00
+air_temperature                              | Min:+1.7482158077318448e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883092669e+02
 air_pressure_thickness                       | Min:+6.0599999874109178e-01 Max:+1.7760098554198755e+03 RMS:+9.5680601590204810e+02
 surface_pressure                             | Min:+5.3297486514404744e+04 Max:+1.0397927292902800e+05 RMS:+9.8896232762674656e+04
-specific_humidity                            | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792636981582193e-03
+specific_humidity                            | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792636816418408e-03
 cloud_liquid_ice                             | Min:+0.0000000000000000e+00 Max:+1.2024392024662985e-03 RMS:+1.4396968866569995e-05
 cloud_liquid_water                           | Min:+0.0000000000000000e+00 Max:+1.5935686618789048e-03 RMS:+4.1931345590543333e-05
 ozone_mass_mixing_ratio                      | Min:+1.1998327271379204e-08 Max:+1.7808431790670831e-05 RMS:+4.4947917149861064e-06
@@ -32,31 +32,31 @@ f10m                                         | Min:+9.4613586695410434e-01 Max:+
 
 Obs bias coefficients: 
 ---------------------------------------------------------------
-            constant:  Min= -1.2490630149841309,  Max= 1.6242779492736057,  Norm= 3.1216962856027304
-  lapse_rate_order_2:  Min= -6.0771207806339094,  Max= 52.3767318715110477,  Norm= 52.7793275314599910
-          lapse_rate:  Min= -6.1173920629465659,  Max= 0.4750269950800435,  Norm= 6.1658157312728985
-          emissivity:  Min= -0.2395000010728836,  Max= 10.5581263135712575,  Norm= 10.5655898122368264
-  scan_angle_order_4:  Min= -7.9506011008096911,  Max= 2.3034050466999081,  Norm= 13.1727465012547444
-  scan_angle_order_3:  Min= -1.1903680560584049,  Max= 2.3802189822803275,  Norm= 3.1970135720803450
-  scan_angle_order_2:  Min= -5.1212630271747548,  Max= 2.9977130889532191,  Norm= 7.3569496454063597
-          scan_angle:  Min= -0.6766870022405442,  Max= 0.0732169970537269,  Norm= 1.1485053152110289
+            constant:  Min= -1.2424509525299072,  Max= 1.6504349708035770,  Norm= 3.1030146353133463
+   lapseRate_order_2:  Min= -7.0903420445872838,  Max= 46.3166084284223771,  Norm= 47.0185597979528609
+           lapseRate:  Min= -5.5814771650607220,  Max= 1.2464430332789806,  Norm= 5.7524772942406086
+  emissivityJacobian:  Min= -1.0039629936218262,  Max= 10.5191706304246591,  Norm= 10.5711704384468028
+sensorScanAngle_order_4:  Min= -8.0552864073222832,  Max= 2.4945130349138593,  Norm= 13.5132453944315909
+sensorScanAngle_order_3:  Min= -1.1528069971066446,  Max= 2.1735479829142181,  Norm= 3.0673534349517819
+sensorScanAngle_order_2:  Min= -5.1097259521664853,  Max= 2.8632600308292808,  Norm= 7.2817410561999560
+     sensorScanAngle:  Min= -0.6898530126095289,  Max= 0.0655509978252007,  Norm= 1.1442823316972326
 ---------------------------------------------------------------
 
 
-CostJb   : Nonlinear Jb = 0.0000003263133461
-CostJo   : Nonlinear Jo(AMSUA N19) = 38981.7238460305161425, nobs = 74275, Jo/n = 0.5248296714376374, err = 6.3650648936327991
-CostJo   : Nonlinear Jo(sondes) = 10687.2756506645455374, nobs = 4255, Jo/n = 2.5116981552678133, err = 10.9810856305398357
-CostFunction: Nonlinear J = 49668.9994970213738270
-DRPCGMinimizer: reduction in residual norm = 1.0147575953754833
+CostJb   : Nonlinear Jb = 0.0000003247124839
+CostJo   : Nonlinear Jo(AMSUA N19) = 39487.6033905208023498, nobs = 73667, Jo/n = 0.5360283897881114, err = 6.2697697603629345
+CostJo   : Nonlinear Jo(sondes) = 10687.3021478507725988, nobs = 4255, Jo/n = 2.5117043825736247, err = 10.9810856305398357
+CostFunction: Nonlinear J = 50174.9055386962863849
+DRPCGMinimizer: reduction in residual norm = 1.0067413227955442
 CostFunction::addIncrement: Analysis: 
 ----------------------------------------------------------------------------------------------------
 State print | number of fields = 22 | cube sphere face size: C48
-eastward_wind                                | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288542711e+01
-northward_wind                               | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891586359e+00
-air_temperature                              | Min:+1.7482158077318311e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883200961e+02
+eastward_wind                                | Min:-5.5495644220059390e+01 Max:+8.4934651204487366e+01 RMS:+1.6388250288542654e+01
+northward_wind                               | Min:-7.3712421229093422e+01 Max:+7.6984825502186652e+01 RMS:+8.1424144891586234e+00
+air_temperature                              | Min:+1.7482158077318232e+02 Max:+3.1467235233685437e+02 RMS:+2.4978424883219918e+02
 air_pressure_thickness                       | Min:+6.0599999874109178e-01 Max:+1.7760098554198755e+03 RMS:+9.5680601590204810e+02
 surface_pressure                             | Min:+5.3297486514404744e+04 Max:+1.0397927292902800e+05 RMS:+9.8896232762674656e+04
-specific_humidity                            | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792638362681448e-03
+specific_humidity                            | Min:+0.0000000000000000e+00 Max:+2.0041369334954085e-02 RMS:+4.7792637405692116e-03
 cloud_liquid_ice                             | Min:+0.0000000000000000e+00 Max:+1.2024392024662985e-03 RMS:+1.4396968866569995e-05
 cloud_liquid_water                           | Min:+0.0000000000000000e+00 Max:+1.5935686618789048e-03 RMS:+4.1931345590543333e-05
 ozone_mass_mixing_ratio                      | Min:+1.1998327271379204e-08 Max:+1.7808431790670831e-05 RMS:+4.4947917149861064e-06
@@ -77,18 +77,18 @@ f10m                                         | Min:+9.4613586695410434e-01 Max:+
 
 Obs bias coefficients: 
 ---------------------------------------------------------------
-            constant:  Min= -1.2490630149841309,  Max= 1.6242779490057870,  Norm= 3.1216962826704004
-  lapse_rate_order_2:  Min= -6.0771207792168234,  Max= 52.3767318668067006,  Norm= 52.7793275266354911
-          lapse_rate:  Min= -6.1173920620497713,  Max= 0.4750269957036114,  Norm= 6.1658157301802641
-          emissivity:  Min= -0.2395000010728836,  Max= 10.5581256964462273,  Norm= 10.5655891955375107
-  scan_angle_order_4:  Min= -7.9506011003013111,  Max= 2.3034050477855654,  Norm= 13.1727464989080296
-  scan_angle_order_3:  Min= -1.1903680549739593,  Max= 2.3802189803928178,  Norm= 3.1970135704212637
-  scan_angle_order_2:  Min= -5.1212630270944297,  Max= 2.9977130887912211,  Norm= 7.3569496444930564
-          scan_angle:  Min= -0.6766870025059790,  Max= 0.0732169969027750,  Norm= 1.1485053159201970
+            constant:  Min= -1.2424509525299072,  Max= 1.6504349705701049,  Norm= 3.1030146330531774
+   lapseRate_order_2:  Min= -7.0903420434846316,  Max= 46.3166084260648887,  Norm= 47.0185597955718677
+           lapseRate:  Min= -5.5814771643207211,  Max= 1.2464430335558840,  Norm= 5.7524772934110207
+  emissivityJacobian:  Min= -1.0039629936218262,  Max= 10.5191700403026349,  Norm= 10.5711698512230932
+sensorScanAngle_order_4:  Min= -8.0552864066518524,  Max= 2.4945130353434313,  Norm= 13.5132453918536388
+sensorScanAngle_order_3:  Min= -1.1528069962369289,  Max= 2.1735479817619940,  Norm= 3.0673534336938850
+sensorScanAngle_order_2:  Min= -5.1097259522434877,  Max= 2.8632600312042698,  Norm= 7.2817410556587614
+     sensorScanAngle:  Min= -0.6898530128249588,  Max= 0.0655509976984332,  Norm= 1.1442823320888615
 ---------------------------------------------------------------
 
 
-CostJb   : Nonlinear Jb = 0.0000033688688972
-CostJo   : Nonlinear Jo(AMSUA N19) = 38970.3026556682743831, nobs = 74275, Jo/n = 0.5246759024660824, err = 6.3650648936327991
-CostJo   : Nonlinear Jo(sondes) = 10639.1209516101644112, nobs = 4255, Jo/n = 2.5003809521998037, err = 10.9810856305398357
-CostFunction: Nonlinear J = 49609.4236106473108521
+CostJb   : Nonlinear Jb = 0.0000033199535370
+CostJo   : Nonlinear Jo(AMSUA N19) = 39476.8510820809169672, nobs = 73667, Jo/n = 0.5358824315104581, err = 6.2697697603629345
+CostJo   : Nonlinear Jo(sondes) = 10639.1482810630404856, nobs = 4255, Jo/n = 2.5003873751029473, err = 10.9810856305398357
+CostFunction: Nonlinear J = 50115.9993664639114286