Update submodules (#891)

NOAA-EMC · Feb 1, 2024 · dd714cc · dd714cc
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Showing 9 changed files with 9 additions and 9 deletions.
diff --git a/sorc/fv3-jedi b/sorc/fv3-jedi
diff --git a/sorc/gsibec b/sorc/gsibec
diff --git a/sorc/ioda b/sorc/ioda
diff --git a/sorc/iodaconv b/sorc/iodaconv
diff --git a/sorc/land-imsproc b/sorc/land-imsproc
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
+50 −16		CMakeLists.txt
+55 −9		src/fv3jedi/CMakeLists.txt
+0 −4		src/fv3jedi/Geometry/fv_init_control_mod.F90
+0 −4		src/fv3jedi/IO/AuxGrid/IOAuxGrid.h
+0 −4		src/fv3jedi/IO/CubeSphereHistory/IOCubeSphereHistory.h
+0 −4		src/fv3jedi/IO/FV3Restart/IOFms.h
+22 −29		src/fv3jedi/Model/ufs/ModelUFS.cc
+4 −1		src/fv3jedi/Model/ufs/ModelUFS.h
+2 −1		src/fv3jedi/Model/ufs/ModelUFS.interface.h
+10 −7		src/fv3jedi/Model/ufs/fv3jedi_ufs_interface_mod.F90
+404 −107		src/fv3jedi/Model/ufs/fv3jedi_ufs_mod.F90
+1 −2		src/fv3jedi/VariableChange/VertRemap/fv3jedi_vc_vertremap_mod.f90
+19 −19		src/mains/CMakeLists.txt
+103 −90		test/CMakeLists.txt
+1 −0		test/Data/fieldmetadata/ufs.yaml
+1 −0		test/Data/forecast/.gitignore
+37 −0		test/fv3jedi_setup_ufs_rundir.py
+95 −0		test/setup-c48.sh
+1 −1		test/testinput/3dvar_gfs_0obs.yaml
+1 −2		test/testinput/3dvar_gfs_aero.yaml
+1 −1		test/testinput/eda_4dvar_fv3lm_1.yaml
+1 −1		test/testinput/eda_4dvar_fv3lm_2.yaml
+26 −0		test/testinput/ensfc_ufs.yaml
+1 −1		test/testinput/forecast_geos.yaml
+15 −12		test/testinput/forecast_ufs_1.yaml
+39 −0		test/testinput/forecast_ufs_2.yaml
+40 −0		test/testinput/forecast_ufs_c48_warmstart.yaml
+3 −3		test/testinput/hyb-3dvar.yaml
+1 −1		test/testinput/hyb-3dvar_geos.yaml
+1 −1		test/testinput/hyb-3dvar_gfs.yaml
+1 −1		test/testinput/hyb-4denvar_geos_sondes_c12.yaml
+0 −1		test/testinput/letkf.yaml
+0 −1		test/testinput/letkf3d.yaml
+0 −1		test/testinput/letkf_observer_soil_moisture.yaml
+0 −1		test/testinput/letkf_snow.yaml
+0 −1		test/testinput/lgetkf.yaml
+0 −34		test/testinput/model_ufs.yaml
+39 −0		test/testinput/model_ufs_c48_warmstart.yaml
+0 −142		test/testinput/staticb_cor_gfs.yaml
+150 −4		test/testinput/staticb_estimate_gfs.yaml
+0 −62		test/testinput/staticb_vbal_gfs.yaml
+0 −6		test/testoutput/staticb_cor_gfs.ref
+7 −0		test/testoutput/staticb_estimate_gfs.ref
+0 −0		test/testoutput/staticb_vbal_gfs.ref
+1 −1		CMakeLists.txt
+80 −3		src/gsibec/gsi/guess_grids.f90
+3 −3		src/gsibec/gsi/jfunc.f90
+21 −14		src/gsibec/gsi/prewgt.F90
+2 −3		src/gsibec/gsi/write_bkgvars_grid.F90
+34 −4		src/engines/ioda/CMakeLists.txt
+58 −0		src/engines/ioda/include/ioda/Engines/ReadScriptFile.h
+49 −0		src/engines/ioda/include/ioda/Engines/Script.h
+3 −1		src/engines/ioda/python/py_engines.cpp
+73 −0		src/engines/ioda/src/ioda/Engines/ReadScriptFile.cpp
+277 −0		src/engines/ioda/src/ioda/Engines/Script/Script.cpp
+13 −0		test/CMakeLists.txt
+52 −0		test/testinput/iodatest_time_io_script.py
+20 −0		test/testinput/iodatest_time_io_script.yaml
+8 −3		src/bufr/BufrParser/Exports/Variables/RemappedBrightnessTemperatureVariable.cpp
+84 −41		src/compo/tempo_nc2ioda.py
+51 −22		src/gnssro/gnssro_bufr2ioda.py
+4 −9		src/hdf5/muon_2ioda.py
+23 −29		test/CMakeLists.txt
+3 −0		test/testinput/TEMPO_no2_L2_V01_20231101T210157Z_S011G07.nc
+3 −0		test/testinput/TEMPO_no2_L2_V01_20231101T210834Z_S011G08.nc
+3 −0		test/testinput/TEMPO_no2_L2_V01_20231101T211511Z_S011G09.nc
+0 −366		test/testinput/adpupa_prepbufr.yaml
+123 −291		test/testinput/bufr_ncep_prepbufr_adpupa.yaml
+168 −0		test/testinput/bufr_ncep_rtma_aircar.yaml
+3 −0		test/testinput/rtma_ru.t0000z.aircar_NC004004.tm00.bufr_d
+0 −3		test/testinput/tempo_hcho_proxy_20130801T100000Z_S002G01.nc
+0 −3		test/testinput/tempo_hcho_proxy_20130801T100600Z_S002G02.nc
+0 −3		test/testinput/tempo_hcho_proxy_20130801T101200Z_S002G03.nc
+0 −3		test/testinput/tempo_no2_proxy_20130801T100000Z_S002G01.nc
+0 −3		test/testinput/tempo_no2_proxy_20130801T100600Z_S002G02.nc
+0 −3		test/testinput/tempo_no2_proxy_20130801T101200Z_S002G03.nc
+0 −3		test/testoutput/adpupa_prepbufr.nc
+0 −3		test/testoutput/bufr_ncep_prepbufr_adpupa.nc
+3 −0		test/testoutput/gdas.t12z.adpupa.prepbufr.nc
+3 −0		test/testoutput/rtma_ru.t0000z.aircar_NC004004.tm00.nc
+2 −2		test/testoutput/tempo_no2_stratosphere.nc
+2 −2		test/testoutput/tempo_no2_total.nc
+2 −2		test/testoutput/tempo_no2_troposphere.nc
+30 −13		.github/workflows/ci.yml
+2 −3		CI/meto/build-and-test
+4 −4		coupled/test/testinput/coupledstateparallel.yaml
+3 −9		qg/mains/CMakeLists.txt
+4 −4		qg/mains/qgEnsembleInflation.cc
+11 −11		qg/test/CMakeLists.txt
+44 −0		qg/test/testinput/ens_infl_inc.yaml
+13 −5		qg/test/testinput/ens_infl_states.yaml
+4 −3		qg/test/testinput/gen_hybrid_linear_model_coeffs_with_subtimestep.yaml
+3 −3		qg/test/testinput/hybrid_linear_model.yaml
+0 −26		qg/test/testinput/rtpp.yaml
+17 −17		qg/test/testoutput/4dvar_hybrid_linear_model.test
+42 −0		qg/test/testoutput/ens_infl_inc.test
+48 −0		qg/test/testoutput/ens_infl_states.test
+8 −4		qg/test/testoutput/gen_hybrid_linear_model_coeffs_with_subtimestep.test
+0 −24		qg/test/testoutput/rtpp.test
+0 −24		qg/test/testoutput/rtps.test
+20 −2		src/CMakeLists.txt
+59 −0		src/oops/base/IncrementSet.h
+101 −0		src/oops/base/Inflation.h
+138 −0		src/oops/base/InflationBase.h
+14 −11		src/oops/base/ModelSpaceCovarianceBase.h
+288 −0		src/oops/base/MultiplicativeInflation.h
+144 −0		src/oops/base/RTPP.h
+146 −0		src/oops/base/RTPS.h
+0 −10		src/oops/base/State4D.h
+3 −2		src/oops/base/StateEnsemble.h
+40 −2		src/oops/base/StateSet.h
+25 −0		src/oops/base/instantiateInflationFactory.h
+2 −0		src/oops/coupled/IncrementCoupled.h
+48 −31		src/oops/generic/HtlmCalculator.h
+15 −31		src/oops/generic/HybridLinearModelCoeffs.h
+1 −0		src/oops/runs/EnsMeanAndVariance.h
+152 −0		src/oops/runs/EnsembleInflation.h
+0 −163		src/oops/runs/RTPP.h
+0 −186		src/oops/runs/RTPS.h
+183 −0		src/oops/util/FieldSetHelpers.cc
+12 −0		src/oops/util/FieldSetHelpers.h
+134 −0		src/oops/util/FunctionSpaceHelpers.cc
+38 −0		src/oops/util/FunctionSpaceHelpers.h
+39 −39		src/test/util/FieldSetHelpersAndOperations.h
+4 −5		src/test/util/FunctionSpaceHelpers.cc
+184 −0		src/test/util/FunctionSpaceHelpers.h
+14 −139		quench/src/Geometry.cc
+0 −1		quench/src/Geometry.h
+12 −0		src/saber/blocks/SaberBlockParametersBase.h
+6 −4		src/saber/fastlam/CMakeLists.txt
+639 −271		src/saber/fastlam/FastLAM.cc
+22 −6		src/saber/fastlam/FastLAM.h
+4 −1		src/saber/fastlam/FastLAMParametersBase.h
+0 −2,237		src/saber/fastlam/Layer.cc
+0 −198		src/saber/fastlam/Layer.h
+1,056 −0		src/saber/fastlam/LayerBase.cc
+229 −0		src/saber/fastlam/LayerBase.h
+1,008 −0		src/saber/fastlam/LayerHalo.cc
+101 −0		src/saber/fastlam/LayerHalo.h
+1,220 −0		src/saber/fastlam/LayerRC.cc
+116 −0		src/saber/fastlam/LayerRC.h
+0 −38		src/saber/fastlam/Layers.cc
+0 −50		src/saber/fastlam/Layers.h
+10 −86		src/saber/interpolation/Geometry.cc
+11 −27		src/saber/interpolation/Geometry.h
+3 −1		src/saber/interpolation/Interpolation.cc
+1 −1		src/saber/interpolation/Interpolation.h
+28 −0		src/saber/oops/ErrorCovarianceToolbox.h
+42 −8		src/saber/oops/Utilities.cc
+22 −7		src/saber/oops/Utilities.h
+18 −41		src/saber/spectralb/GaussUVToGP.cc
+4 −2		src/saber/spectralb/GaussUVToGP.h
+21 −22		src/saber/spectralb/HydrostaticPressure.cc
+2 −2		src/saber/spectralb/HydrostaticPressure.h
+15 −6		src/saber/vader/AirTemperature.cc
+3 −1		src/saber/vader/AirTemperature.h
+15 −6		src/saber/vader/DryAirDensity.cc
+19 −0		src/saber/vader/DryAirDensity.h
+34 −14		src/saber/vader/GpToHp.cc
+3 −2		src/saber/vader/GpToHp.h
+16 −8		src/saber/vader/HpHexnerToPExner.cc
+22 −2		src/saber/vader/HpHexnerToPExner.h
+4 −4		src/saber/vader/HpToHexner.cc
+20 −6		src/saber/vader/HydroBal.cc
+27 −5		src/saber/vader/HydroBal.h
+20 −11		src/saber/vader/HydrostaticExner.cc
+32 −2		src/saber/vader/HydrostaticExner.h
+29 −8		src/saber/vader/MoistIncrOp.cc
+3 −1		src/saber/vader/MoistIncrOp.h
+72 −4		src/saber/vader/MoistIncrOpParameters.h
+20 −7		src/saber/vader/MoistureControl.cc
+29 −6		src/saber/vader/MoistureControl.h
+67 −0		src/saber/vader/PressureParameters.h
+15 −11		src/saber/vader/SuperMoistIncrOp.cc
+3 −3		src/saber/vader/SuperMoistIncrOp.h
+7 −0		test/CMakeLists.txt
+0 −0		test/testdeps/dirac_fastlam_7.txt
+3 −0		test/testdeps/dirac_fastlam_8.txt
+1 −0		test/testdeps/dirac_fastlam_9.txt
+0 −0		test/testdeps/dirac_spectralb_gauss_vader_4.txt
+0 −0		test/testdeps/randomization_fastlam.txt
+4 −0		test/testinput/compare_diagnostics_outer_vars.yaml
+0 −5		test/testinput/dirac_bump_3.yaml
+2 −0		test/testinput/dirac_fastlam_1.yaml
+2 −0		test/testinput/dirac_fastlam_2.yaml
+2 −0		test/testinput/dirac_fastlam_3.yaml
+2 −0		test/testinput/dirac_fastlam_4.yaml
+2 −0		test/testinput/dirac_fastlam_5.yaml
+2 −0		test/testinput/dirac_fastlam_6.yaml
+121 −0		test/testinput/dirac_fastlam_7.yaml
+160 −0		test/testinput/dirac_fastlam_8.yaml
+143 −0		test/testinput/dirac_fastlam_9.yaml
+3 −13		test/testinput/dirac_spectralb_gauss_vader_1.yaml
+0 −10		test/testinput/dirac_spectralb_gauss_vader_2.yaml
+0 −10		test/testinput/dirac_spectralb_gauss_vader_3.yaml
+230 −0		test/testinput/dirac_spectralb_gauss_vader_4.yaml
+42 −0		test/testinput/randomization_fastlam.yaml
+0 −11		test/testinput/randomization_sqrtspectralb_2.yaml
+4 −0		test/testlist/saber_test_tier1-fastlam.txt
+2 −0		test/testlist/saber_test_tier1-spectralb-vader.txt
+115 −8		test/testref/dirac_bump_3.ref
+2 −0		test/testref/dirac_fastlam_1.ref
+2 −0		test/testref/dirac_fastlam_2.ref
+7 −5		test/testref/dirac_fastlam_3.ref
+7 −5		test/testref/dirac_fastlam_4.ref
+7 −5		test/testref/dirac_fastlam_5.ref
+7 −5		test/testref/dirac_fastlam_6.ref
+75 −0		test/testref/dirac_fastlam_7.ref
+77 −0		test/testref/dirac_fastlam_8.ref
+72 −0		test/testref/dirac_fastlam_9.ref
+12 −31		test/testref/dirac_spectralb_gauss_vader_1.ref
+11 −27		test/testref/dirac_spectralb_gauss_vader_2.ref
+0 −24		test/testref/dirac_spectralb_gauss_vader_3.ref
+106 −0		test/testref/dirac_spectralb_gauss_vader_4.ref
+42 −0		test/testref/randomization_fastlam.ref
+8 −28		test/testref/randomization_sqrtspectralb_2.ref
+244 −85		src/soca/ExplicitDiffusion/soca_diffusion.F90
+7 −0		src/soca/LinearVariableChange/BkgErrGodas/soca_bkgerrgodas_mod.F90
+10 −3		test/CMakeLists.txt
+0 −8		test/Data/fields_metadata.yml
+179 −0		test/testinput/3dhyb_diffusion.yml
+7 −7		test/testinput/3dhyb_nicas.yml
+3 −0		test/testinput/3dvar_godas.yml
+2 −0		test/testinput/dirac_diffusion.yml
+2 −2		test/testinput/hofx_oasim_3d.yml
+28 −0		test/testref/3dhyb_diffusion.test
+0 −0		test/testref/3dhyb_nicas.test
+0 −2		test/testref/hofx_oasim_3d.test
+123 −110		tools/calc_scales.py
+13 −0		tools/calc_scales.yaml
+2 −39		src/ufo/ObsBias.cc
+91 −2		src/ufo/ObsBiasIncrement.cc
+22 −2		src/ufo/ObsBiasIncrement.h
+4 −1		src/ufo/ObsBiasParameters.h
+2 −0		src/ufo/filters/CMakeLists.txt
+1 −1		src/ufo/filters/ProfileAverageObsToModLevels.cc
+262 −0		src/ufo/filters/SuperRefractionCheckNBAM.cc
+87 −0		src/ufo/filters/SuperRefractionCheckNBAM.h
+12 −4		src/ufo/filters/processWhere.cc
+24 −11		src/ufo/filters/processWhere.h
+6 −0		src/ufo/filters/rttovonedvarcheck/RTTOVOneDVarCheckParameters.h
+10 −4		src/ufo/filters/rttovonedvarcheck/ufo_rttovonedvarcheck_mod.f90
+16 −0		src/ufo/filters/rttovonedvarcheck/ufo_rttovonedvarcheck_obs_mod.f90
+6 −0		src/ufo/filters/rttovonedvarcheck/ufo_rttovonedvarcheck_setup_mod.f90
+3 −0		src/ufo/instantiateObsFilterFactory.h
+2 −0		src/ufo/operators/crtm/crtmParameters/ObsRadianceCRTMParameters.h
+52 −2		src/ufo/operators/crtm/ufo_crtm_utils_mod.F90
+0 −2		src/ufo/operators/oasim/ObsRadianceOASIM.cc
+8 −10		src/ufo/operators/oasim/ufo_oasim_mod.F90
+3 −3		src/ufo/operators/rttov/ufo_radiancerttov_mod.F90
+53 −20		src/ufo/operators/rttov/ufo_radiancerttov_tlad_mod.F90
+1 −1		src/ufo/operators/rttov/ufo_radiancerttov_utils_mod.F90
+3 −0		src/ufo/utils/CMakeLists.txt
+3 −0		src/ufo/utils/Constants.h
+52 −0		src/ufo/utils/SaveBiasCoeffs.cc
+28 −0		src/ufo/utils/SaveBiasCoeffs.h
+15 −0		test/mains/TestUfoObsBiasIncrement.cc
+6 −6		test/testinput/instrumentTests/Aircraft_obs/aircraft_geos_qc.yaml
+2 −2		test/testinput/instrumentTests/Pibal/pibal_geos_qc.yaml
+13 −13		test/testinput/instrumentTests/Sonde/sonde_geos_qc.yaml
+3 −3		test/testinput/instrumentTests/Surface_land_obs/sfcLand_geos_qc.yaml
+11 −11		test/testinput/instrumentTests/Surface_marine_obs/sfcMarine_geos_qc.yaml
+1 −1		test/testinput/unit_tests/filters/atms_rttov_ops_qc_rttovonedvarcheck.yaml
+18 −0		test/testinput/unit_tests/filters/gnssro_super_refraction_check.yaml
+3 −3		test/testinput/unit_tests/filters/gnssrobndnbam_qc_geos.yaml
+173 −3		test/testinput/unit_tests/filters/iasi_rttov_ops_qc_rttovonedvarcheck.yaml
+1 −1		test/testinput/unit_tests/filters/obsfunctions/function_selectstatistic.yaml
+24 −24		test/testinput/unit_tests/filters/processwhere.yaml
+1 −1		test/testinput/unit_tests/filters/qc_copy_flags_from_ext_to_orig_space.yaml
+6 −6		test/testinput/unit_tests/filters/qc_ocean_vertical_stability_check.yaml
+10 −5		test/testinput/unit_tests/filters/qc_profile_average_obs_to_mod_levels.yaml
+3 −3		test/testinput/unit_tests/filters/qc_profile_fewobs_check.yaml
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+5 −5		test/testinput/unit_tests/filters/qc_spike_and_step_check.yaml
+10 −0		test/testinput/unit_tests/operators/CMakeLists.txt
+9 −0		test/testinput/unit_tests/operators/atovs_rttov_scatt.yaml
+11 −0		test/testinput/unit_tests/predictors/CMakeLists.txt
+6 −0		test/testinput/unit_tests/predictors/bias_coeff.yaml
+3 −3		test/testinput/unit_tests/variabletransforms/observed_derived_and_simulated_variables.yaml
+4 −4		test/testinput/unit_tests/variabletransforms/variabletransforms_oceandensity.yaml
+2 −2		test/testinput/unit_tests/variabletransforms/variabletransforms_oceandepthtopressure.yaml
+2 −2		test/testinput/unit_tests/variabletransforms/variabletransforms_oceanpracticalsalinitytoabsolutesalinity.yaml
+2 −2		test/testinput/unit_tests/variabletransforms/variabletransforms_oceantemptoconservativetemp.yaml
+2 −2		test/testinput/unit_tests/variabletransforms/variabletransforms_oceantemptotheta.yaml
+3 −3		test/testinput/unit_tests/variabletransforms/variabletransforms_pstar.yaml
+102 −0		test/ufo/ObsBiasIncrement.h