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Merge branch 'develop' into feature/b2i
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@guillaumevernieres
guillaumevernieres committed Sep 26, 2024
2 parents 9efeaa4 + c797d33 commit eab6ca1
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Showing 13 changed files with 329 additions and 5 deletions.
2 changes: 1 addition & 1 deletion parm/io/fv3jedi_fieldmetadata_fv3inc.yaml
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Expand Up @@ -24,6 +24,6 @@ field metadata:
- long name: air_pressure_thickness
io name: delp_inc

- long name: hydrostatic_layer_thickness
- long name: layer_thickness
io name: delz_inc

2 changes: 1 addition & 1 deletion parm/jcb-gdas
Submodule jcb-gdas updated 2 files
+1 −1 algorithm/atmosphere/fv3jedi_fv3inc_lgetkf.yaml.j2
+1 −1 algorithm/atmosphere/fv3jedi_fv3inc_variational.yaml.j2
45 changes: 45 additions & 0 deletions parm/soca/obs/config/icec_amsu_mb_l2.yaml
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obs space:
name: icec_amsu_mb_l2
obsdatain:
engine:
type: H5File
obsfile: !ENV ${DATA}/obs/${OPREFIX}icec_amsu_mb_l2.${PDY}${cyc}.nc4
obsdataout:
engine:
type: H5File
obsfile: !ENV ${DATA}/diags/icec_amsu_mb_l2.${PDY}${cyc}.nc4
simulated variables: [seaIceFraction]
io pool:
max pool size: 1
get values:
time interpolation: linear
obs operator:
name: Identity
observation alias file: obsop_name_map.yaml
obs error:
covariance model: diagonal
obs filters:
- filter: Domain Check
where:
- variable: {name: GeoVaLs/sea_area_fraction}
minvalue: 0.9
- filter: Bounds Check
minvalue: 0.0
maxvalue: 1.0
#- filter: Background Check
# threshold: 5.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 2.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 0.0
action:
name: inflate error
inflation factor: 2.0
- filter: Domain Check
where:
- variable: {name: GeoVaLs/distance_from_coast}
minvalue: 100e3
45 changes: 45 additions & 0 deletions parm/soca/obs/config/icec_atms_n20_l2.yaml
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obs space:
name: icec_atms_n20_l2
obsdatain:
engine:
type: H5File
obsfile: !ENV ${DATA}/obs/${OPREFIX}icec_atms_n20_l2.{PDY}${cyc}.nc4
obsdataout:
engine:
type: H5File
obsfile: !ENV ${DATA}/diags/icec_atms_n20_l2.${PDY}${cyc}.nc4
simulated variables: [seaIceFraction]
io pool:
max pool size: 1
get values:
time interpolation: linear
obs operator:
name: Identity
observation alias file: obsop_name_map.yaml
obs error:
covariance model: diagonal
obs filters:
- filter: Domain Check
where:
- variable: {name: GeoVaLs/sea_area_fraction}
minvalue: 0.9
- filter: Bounds Check
minvalue: 0.0
maxvalue: 1.0
#- filter: Background Check
# threshold: 5.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 2.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 0.0
action:
name: inflate error
inflation factor: 2.0
- filter: Domain Check
where:
- variable: {name: GeoVaLs/distance_from_coast}
minvalue: 100e3
45 changes: 45 additions & 0 deletions parm/soca/obs/config/icec_atms_n21_l2.yaml
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obs space:
name: icec_atms_n21_l2
obsdatain:
engine:
type: H5File
obsfile: !ENV ${DATA}/obs/${OPREFIX}icec_atms_n21_l2.{PDY}${cyc}.nc4
obsdataout:
engine:
type: H5File
obsfile: !ENV ${DATA}/diags/icec_atms_n21_l2.${PDY}${cyc}.nc4
simulated variables: [seaIceFraction]
io pool:
max pool size: 1
get values:
time interpolation: linear
obs operator:
name: Identity
observation alias file: obsop_name_map.yaml
obs error:
covariance model: diagonal
obs filters:
- filter: Domain Check
where:
- variable: {name: GeoVaLs/sea_area_fraction}
minvalue: 0.9
- filter: Bounds Check
minvalue: 0.0
maxvalue: 1.0
#- filter: Background Check
# threshold: 5.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 2.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 0.0
action:
name: inflate error
inflation factor: 2.0
- filter: Domain Check
where:
- variable: {name: GeoVaLs/distance_from_coast}
minvalue: 100e3
45 changes: 45 additions & 0 deletions parm/soca/obs/config/icec_atms_npp_l2.yaml
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obs space:
name: icec_atms_npp_l2
obsdatain:
engine:
type: H5File
obsfile: !ENV ${DATA}/obs/${OPREFIX}icec_atms_npp_l2.{PDY}${cyc}.nc4
obsdataout:
engine:
type: H5File
obsfile: !ENV ${DATA}/diags/icec_atms_npp_l2.${PDY}${cyc}.nc4
simulated variables: [seaIceFraction]
io pool:
max pool size: 1
get values:
time interpolation: linear
obs operator:
name: Identity
observation alias file: obsop_name_map.yaml
obs error:
covariance model: diagonal
obs filters:
- filter: Domain Check
where:
- variable: {name: GeoVaLs/sea_area_fraction}
minvalue: 0.9
- filter: Bounds Check
minvalue: 0.0
maxvalue: 1.0
#- filter: Background Check
# threshold: 5.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 2.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 0.0
action:
name: inflate error
inflation factor: 2.0
- filter: Domain Check
where:
- variable: {name: GeoVaLs/distance_from_coast}
minvalue: 100e3
45 changes: 45 additions & 0 deletions parm/soca/obs/config/icec_gmi_gpm_l2.yaml
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obs space:
name: icec_gmi_gpm_l2
obsdatain:
engine:
type: H5File
obsfile: !ENV ${DATA}/obs/${OPREFIX}icec_gmi_gpm_l2.${PDY}${cyc}.nc4
obsdataout:
engine:
type: H5File
obsfile: !ENV ${DATA}/diags/icec_gmi_gpm_l2.${PDY}${cyc}.nc4
simulated variables: [seaIceFraction]
io pool:
max pool size: 1
get values:
time interpolation: linear
obs operator:
name: Identity
observation alias file: obsop_name_map.yaml
obs error:
covariance model: diagonal
obs filters:
- filter: Domain Check
where:
- variable: {name: GeoVaLs/sea_area_fraction}
minvalue: 0.9
- filter: Bounds Check
minvalue: 0.0
maxvalue: 1.0
#- filter: Background Check
# threshold: 5.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 2.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 0.0
action:
name: inflate error
inflation factor: 2.0
- filter: Domain Check
where:
- variable: {name: GeoVaLs/distance_from_coast}
minvalue: 100e3
45 changes: 45 additions & 0 deletions parm/soca/obs/config/icec_ssmis_f17_l2.yaml
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obs space:
name: icec_ssmis_f17_l2
obsdatain:
engine:
type: H5File
obsfile: !ENV ${DATA}/obs/${OPREFIX}icec_ssmis_f17_l2.${PDY}${cyc}.nc4
obsdataout:
engine:
type: H5File
obsfile: !ENV ${DATA}/diags/icec_ssmis_f17_l2.${PDY}${cyc}.nc4
simulated variables: [seaIceFraction]
io pool:
max pool size: 1
get values:
time interpolation: linear
obs operator:
name: Identity
observation alias file: obsop_name_map.yaml
obs error:
covariance model: diagonal
obs filters:
- filter: Domain Check
where:
- variable: {name: GeoVaLs/sea_area_fraction}
minvalue: 0.9
- filter: Bounds Check
minvalue: 0.0
maxvalue: 1.0
#- filter: Background Check
# threshold: 5.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 2.0
- filter: Domain Check
where:
- variable: { name: GeoVaLs/sea_surface_temperature}
maxvalue: 0.0
action:
name: inflate error
inflation factor: 2.0
- filter: Domain Check
where:
- variable: {name: GeoVaLs/distance_from_coast}
minvalue: 100e3
6 changes: 6 additions & 0 deletions parm/soca/obs/obs_list.yaml
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Expand Up @@ -15,6 +15,12 @@ observers:
# Ice concentration
- !INC ${MARINE_OBS_YAML_DIR}/icec_amsr2_north.yaml
- !INC ${MARINE_OBS_YAML_DIR}/icec_amsr2_south.yaml
#- !INC ${MARINE_OBS_YAML_DIR}/icec_amsu_mb_l2.yaml
#- !INC ${MARINE_OBS_YAML_DIR}/icec_atms_n20_l2.yaml
#- !INC ${MARINE_OBS_YAML_DIR}/icec_atms_n21_l2.yaml
#- !INC ${MARINE_OBS_YAML_DIR}/icec_atms_npp_l2.yaml
#- !INC ${MARINE_OBS_YAML_DIR}/icec_gmi_gpm_l2.yaml
#- !INC ${MARINE_OBS_YAML_DIR}/icec_ssmis_f17_l2.yaml

# in situ: monthly
#- !INC ${MARINE_OBS_YAML_DIR}/insitu_profile_bathy.yaml
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48 changes: 48 additions & 0 deletions parm/soca/obsprep/obsprep_config.yaml
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Expand Up @@ -46,6 +46,54 @@ observations:
dmpdir regex: 'AMSR2-SEAICE-SH_v2r2_GW1_s*.nc'
ocean basin: RECCAP2_region_masks_all_v20221025.nc

- obs space:
name: icec_amsu_mb_l2
provider: MIRS
dmpdir subdir: ocean/icec
type: nc
dmpdir regex: 'NPR-MIRS-IMG_v11r9_ma1_s*.nc'
ocean basin: RECCAP2_region_masks_all_v20221025.nc

- obs space:
name: icec_atms_n20_l2
provider: MIRS
dmpdir subdir: ocean/icec
type: nc
dmpdir regex: 'NPR-MIRS-IMG_v11r9_n20_s*.nc'
ocean basin: RECCAP2_region_masks_all_v20221025.nc

- obs space:
name: icec_atms_n21_l2
provider: MIRS
dmpdir subdir: ocean/icec
type: nc
dmpdir regex: 'NPR-MIRS-IMG_v11r9_n21_s*.nc'
ocean basin: RECCAP2_region_masks_all_v20221025.nc

- obs space:
name: icec_atms_npp_l2
provider: MIRS
dmpdir subdir: ocean/icec
type: nc
dmpdir regex: 'NPR-MIRS-IMG_v11r4_npp_s*.nc'
ocean basin: RECCAP2_region_masks_all_v20221025.nc

- obs space:
name: icec_gmi_gpm_l2
provider: MIRS
dmpdir subdir: ocean/icec
type: nc
dmpdir regex: 'NPR-MIRS-IMG_v11r9_gpm_s*.nc'
ocean basin: RECCAP2_region_masks_all_v20221025.nc

- obs space:
name: icec_ssmis_f17_l2
provider: MIRS
dmpdir subdir: ocean/icec
type: nc
dmpdir regex: 'NPR-MIRS-IMG_v11r4_f17_s*.nc'
ocean basin: RECCAP2_region_masks_all_v20221025.nc

# SST
- obs space:
name: sst_avhrr_ma_l3u
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2 changes: 1 addition & 1 deletion sorc/fv3-jedi
Submodule fv3-jedi updated 26 files
+0 −10 src/fv3jedi/FieldMetadata/FieldsMetadataDefault.h
+16 −5 src/fv3jedi/Geometry/Geometry.cc
+2 −0 src/fv3jedi/Geometry/GeometryParameters.h
+4 −3 src/fv3jedi/IO/FV3Restart/IOFms.cc
+1 −0 src/fv3jedi/IO/FV3Restart/IOFms.h
+10 −4 src/fv3jedi/IO/FV3Restart/IOFms.interface.F90
+2 −2 src/fv3jedi/IO/FV3Restart/IOFms.interface.h
+7 −4 src/fv3jedi/IO/FV3Restart/fv3jedi_io_fms_mod.f90
+2 −0 src/fv3jedi/LinearVariableChange/LinearVariableChange.cc
+2 −1 src/fv3jedi/ModelData/ModelData.cc
+15 −15 src/fv3jedi/VariableChange/Model2GeoVaLs/fv3jedi_vc_model2geovals_mod.f90
+10 −5 test/CMakeLists.txt
+13 −6 test/setup-c48.sh
+152 −0 test/testinput/4dvar_append_obs.yaml
+0 −1 test/testinput/4dvar_hybrid_linear_model.yaml
+19 −9 test/testinput/linearization_error.yaml
+1 −1 test/testinput/state_gfs.yaml
+8 −8 test/testoutput/3dvar_lam_cmaq.ref
+47 −0 test/testoutput/4dvar_append_obs.ref
+10 −10 test/testoutput/convertstate_gfs_ana2bvars.ref
+2 −2 test/testoutput/diffstates_lam_cmaq.ref
+23 −23 test/testoutput/eda_4dvar_fv3lm.ref
+17 −17 test/testoutput/ensembleb_dirac_local_gfs_12pe.ref
+1 −1 test/testoutput/ensembleb_nicas_gfs.ref
+12 −11 test/testoutput/hofx_nomodel_lam_cmaq.ref
+16 −16 test/testoutput/letkf3d.ref
2 changes: 1 addition & 1 deletion test/fv3jedi/testinput/gdasapp_fv3jedi_fv3inc.yaml
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@@ -1,7 +1,7 @@
variable change:
variable change name: Model2GeoVaLs
input variables: &bkgvars [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr,surface_geopotential_height]
output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,hydrostatic_delz]
output variables: &fv3incrvars [ua,va,t,sphum,ice_wat,liq_wat,o3mr,delp,delz]
jedi increment variables: [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]
fv3 increment variables: *fv3incrvars
background geometry:
Expand Down
2 changes: 1 addition & 1 deletion test/fv3jedi/testoutput/gdasapp_fv3jedi_fv3inc.ref
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Expand Up @@ -37,5 +37,5 @@ cloud_liquid_ice | Min:+0.0000000000000000e+00 Max:+
cloud_liquid_water | Min:+0.0000000000000000e+00 Max:+0.0000000000000000e+00 RMS:+0.0000000000000000e+00
ozone_mass_mixing_ratio | Min:+0.0000000000000000e+00 Max:+0.0000000000000000e+00 RMS:+0.0000000000000000e+00
air_pressure_thickness | Min:-2.9992886080290191e+00 Max:+1.5291703492039233e+00 RMS:+1.7535872214547940e-01
hydrostatic_layer_thickness | Min:-4.6699236754648155e-01 Max:+7.4693987323735200e-01 RMS:+3.1162055487823255e-02
layer_thickness | Min:-4.6699236754648155e-01 Max:+7.4693987323735200e-01 RMS:+3.1162055487823255e-02
----------------------------------------------------------------------------------------------------

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