Merge branch 'develop' into feature/phase3_validation

NOAA-EMC · Feb 26, 2025 · 4c1fa5f · 4c1fa5f
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diff --git a/sorc/fv3-jedi b/sorc/fv3-jedi
diff --git a/sorc/fv3-jedi-lm b/sorc/fv3-jedi-lm
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
+1 −1		CMakeLists.txt
+276 −2		src/dynamics/fv3jedi_lm_dynamics_mod.F90
+115 −32		src/fv3jedi_lm_mod.F90
+6 −6		src/physics/moist/fv3jedi_lm_moist_mod.F90
+1 −1		src/physics/turbulence/fv3jedi_lm_turbulence_mod.F90
+10 −2		src/utils/fv3jedi_lm_utils_mod.F90
+11 −2		CMakeLists.txt
+2 −0		share/CMakeLists.txt
+20 −0		share/ioda/yaml/iodatest_odb_fciasr.yaml
+22 −0		share/ioda/yaml/iodatest_odb_fciclr.yaml
+16 −0		share/ioda/yaml/validation/ObsSpace.yaml
+378 −58		src/ObsSpace.cc
+30 −7		src/ObsSpace.h
+2 −0		src/ObsSpaceParameters.h
+110 −16		src/ObsVector.cc
+10 −5		src/ObsVector.h
+5 −0		src/engines/ioda/include/ioda/Engines/ReadBufrFile.h
+57 −23		src/engines/ioda/src/ioda/Engines/ReadBufrFile.cpp
+2 −2		src/mains/buildInputFileSet.h
+1 −1		src/mains/filterObs/filterObs.hpp
+2 −2		src/mains/timeIodaIO.h
+50 −7		test/CMakeLists.txt
+10 −12		test/ioda/ObsVectorPackEigen.h
+67 −7		test/testinput/iodatest_obsspace.yaml
+18 −0		test/testinput/iodatest_obsspace_missing_obs_file_error_bufr.yaml
+105 −0		test/testinput/iodatest_obsspace_missing_obs_file_warn_bufr.yaml
+279 −100		src/compo/viirs_aod2ioda.py
+1 −0		src/hdf5/CMakeLists.txt
+14 −29		src/hdf5/cowvr_hdf5_2ioda.py
+52 −2		test/CMakeLists.txt
+3 −0		test/testinput/COWVR_TSDR.020421.20240430T215845.20240430T230345.V1001.sample.h5
+2 −2		test/testinput/bufr_tables/bufrtab.CodeFlag_STD_0_29
+3 −0		test/testinput/nasa_viirs_db_aod.nc
+3 −0		test/testinput/nasa_viirs_dt_aod.nc
+3 −0		test/testoutput/obs.20240430T220600Z_PT2M_cowvr_iss.nc4
+2 −2		test/testoutput/viirs_aod.nc
+3 −0		test/testoutput/viirs_db_aod.nc
+3 −0		test/testoutput/viirs_dt_aod.nc
+1 −1		l95/src/lorenz95/ModelBias.cc
+1 −1		l95/src/lorenz95/ObsBias.cc
+21 −15		l95/src/lorenz95/ObsVec1D.cc
+5 −3		l95/src/lorenz95/ObsVec1D.h
+5 −0		l95/src/lorenz95/StateL95.h
+14 −0		l95/test/CMakeLists.txt
+66 −0		l95/test/testinput/getkf_perturbed_linearobserver.yaml
+90 −0		l95/test/testinput/letkf_perturbed_linearobserver.yaml
+65 −0		l95/test/testoutput/getkf_perturbed_linearobserver.test
+74 −0		l95/test/testoutput/letkf_perturbed_linearobserver.test
+1 −1		qg/model/ObsBias.cc
+7 −0		qg/model/ObsSpaceQG.cc
+2 −1		qg/model/ObsSpaceQG.h
+31 −12		qg/model/ObsVecQG.cc
+6 −3		qg/model/ObsVecQG.h
+1 −0		qg/model/QgFortran.h
+5 −0		qg/model/StateQG.h
+23 −0		qg/model/qg_obsdb_interface.F90
+26 −1		qg/model/qg_obsdb_mod.F90
+3 −0		src/CMakeLists.txt
+2 −2		src/oops/assimilation/ControlVariable.h
+4 −12		src/oops/assimilation/CostJo.h
+18 −19		src/oops/assimilation/GETKFSolver.h
+229 −0		src/oops/assimilation/GETKFSolverPert.h
+16 −16		src/oops/assimilation/LETKFSolver.h
+7 −6		src/oops/assimilation/LETKFSolverGSI.h
+216 −0		src/oops/assimilation/LETKFSolverPert.h
+19 −15		src/oops/assimilation/LocalEnsembleSolver.h
+6 −0		src/oops/assimilation/instantiateLocalEnsembleSolverFactory.h
+39 −23		src/oops/base/Departures.h
+5 −4		src/oops/base/DeparturesEnsemble.h
+59 −3		src/oops/base/FieldSet3D.cc
+6 −6		src/oops/base/IncrementEnsemble4D.h
+1 −1		src/oops/base/Model.h
+1 −1		src/oops/base/ObsAuxControls.h
+20 −6		src/oops/base/ObsSpaces.h
+26 −1		src/oops/base/Observations.h
+0 −1		src/oops/base/State.h
+102 −34		src/oops/base/StateEnsemble4D.h
+76 −5		src/oops/base/StateSet.h
+14 −12		src/oops/base/StateSetSaver.h
+5 −5		src/oops/generic/PseudoModelState4D.h
+1 −0		src/oops/interface/ObsSpace.h
+34 −23		src/oops/interface/ObsVector.h
+16 −1		src/oops/interface/State.h
+1 −1		src/oops/runs/EnsembleGETKFApplication.h
+20 −9		src/oops/runs/HofX3D.h
+19 −9		src/oops/runs/HofX4D.h
+181 −13		src/oops/runs/LocalEnsembleDA.h
+61 −0		src/oops/util/DateTime.cc
+7 −0		src/oops/util/DateTime.h
+5 −1		src/oops/util/LibOOPS.cc
+2 −0		src/oops/util/LibOOPS.h
+9 −0		src/oops/util/datetime.intfb.h
+12 −0		src/oops/util/datetime_f.cc
+2 −0		src/oops/util/datetime_f.h
+26 −1		src/oops/util/datetime_mod.F90
+24 −19		src/oops/util/parameters/Parameters.cc
+3 −2		src/test/base/ObsErrorCovariance.h
+5 −11		src/test/interface/ObsVector.h
+13 −3		src/test/util/DateTime.cc
+22 −2		src/test/util/datetime.F90
+1 −1		external/icepack/Icepack
+21 −13		src/soca/AnalyticInit/soca_analytic_mod.F90
+27 −19		src/soca/Fields/Fields.cc
+1 −2		src/soca/Fields/Fields.h
+390 −752		src/soca/Fields/soca_fields_mod.F90
+17 −2		src/soca/Geometry/soca_geom_mod.F90
+59 −34		src/soca/Increment/Increment.cc
+1 −0		src/soca/Increment/Increment.h
+0 −1		src/soca/Increment/IncrementFortran.h
+0 −28		src/soca/Increment/soca_increment.interface.F90
+124 −87		src/soca/Increment/soca_increment_mod.F90
+8 −20		src/soca/LinearVariableChange/Balance/soca_balance_mod.F90
+4 −0		src/soca/LinearVariableChange/LinearModel2GeoVaLs/LinearModel2GeoVaLs.cc
+6 −3		src/soca/SaberBlocks/BkgErrFilt/BkgErrFilt.cc
+120 −16		src/soca/State/State.cc
+4 −0		src/soca/State/State.h
+0 −9		src/soca/State/StateFortran.h
+0 −103		src/soca/State/soca_state.interface.F90
+0 −137		src/soca/State/soca_state_mod.F90
+9 −4		src/soca/VariableChange/Model2GeoVaLs/Model2GeoVaLs.F90
+0 −2		src/soca/VariableChange/Soca2Cice/Soca2Cice.F90
+3 −1		src/soca/VariableChange/Soca2Cice/Soca2Cice.cc
+2 −3		src/soca/VariableChange/Soca2Cice/soca_ciceutils_mod.F90
+120 −86		src/soca/VariableChange/Soca2Cice/soca_soca2cice_mod.F90
+2 −1		src/soca/VariableChange/VariableChange.cc
+1 −9		test/CMakeLists.txt
+7 −4		test/testinput/3dhybfgat_pseudo.yml
+7 −4		test/testinput/4dvar_htlm.yml
+7 −4		test/testinput/4dvar_identity.yml
+0 −60		test/testinput/hofx_oasim_3d.yml
+7 −4		test/testinput/varchange_balance.yml
+7 −4		test/testinput/varchange_balance_TSSSH.yml
+12 −12		test/testref/3dhybfgat_pseudo.test
+7 −7		test/testref/4dvar_htlm.test
+2 −2		test/testref/4dvar_identity.test
+0 −26		test/testref/hofx_oasim_3d.test
+12 −0		src/ufo/GeoVaLs.cc
+1 −1		src/ufo/ObsBias.cc
+3 −3		src/ufo/ObsFilters.cc
+1 −1		src/ufo/ObsFilters.h
+73 −1		src/ufo/filters/ConventionalProfileProcessing.cc
+27 −0		src/ufo/filters/ConventionalProfileProcessing.h
+22 −2		src/ufo/filters/ProcessAMVQI.cc
+13 −6		src/ufo/filters/obsfunctions/CloudFirstGuessMinimumResidual.cc
+1 −1		src/ufo/filters/obsfunctions/CloudFirstGuessMinimumResidual.h
+6 −0		src/ufo/operators/columnretrieval/ObsColumnRetrievalParameters.h
+5 −2		src/ufo/operators/columnretrieval/ufo_columnretrieval_mod.F90
+7 −3		src/ufo/operators/columnretrieval/ufo_columnretrieval_tlad_mod.F90
+34 −11		src/ufo/operators/columnretrieval/ufo_satcolumn_mod.F90
+4 −4		src/ufo/operators/crtm/ufo_crtm_active_mod.F90
+4 −4		src/ufo/operators/crtm/ufo_crtm_passive_mod.F90
+5 −5		src/ufo/operators/groundgnss/ZenithTotalDelayROPP/CMakeLists.txt
+15 −17		src/ufo/operators/rttov/ufo_radiancerttov_utils_mod.F90
+0 −5		src/ufo/operators/scatwind/NeutralMetOffice/ufo_scatwind_neutralmetoffice_mod.F90
+0 −6		src/ufo/operators/scatwind/NeutralMetOffice/ufo_scatwind_neutralmetoffice_tlad_mod.F90
+0 −3		src/ufo/profile/EntireSampleDataHandler.h
+24 −7		src/ufo/profile/ProfileAveragePressure.cc
+20 −4		src/ufo/profile/ProfileAverageRelativeHumidity.cc
+26 −11		src/ufo/profile/ProfileAverageTemperature.cc
+25 −10		src/ufo/profile/ProfileAverageWindSpeed.cc
+1 −1		src/ufo/profile/ProfileCheckBackgroundGeopotentialHeight.cc
+5 −2		src/ufo/profile/ProfileChecker.cc
+6 −2		src/ufo/profile/ProfileChecker.h
+2 −2		test/CMakeLists.txt
+2 −1		test/testinput/instrumentTests/tempo/tempo_no2.yaml
+1 −1		test/testinput/unit_tests/filters/CMakeLists.txt
+8 −0		test/testinput/unit_tests/filters/iasi_rttov_ops_qc_rttovonedvarcheck.yaml
+37 −0		test/testinput/unit_tests/filters/qc_processamvqi.yaml
+0 −14		test/testinput/unit_tests/operators/scatwind_neutral_metoffice.yaml
+20 −0		test/testinput/unit_tests/profile/CMakeLists.txt
+106 −0		.../testinput/unit_tests/profile/conventionalprofileprocessing_average_single_level_profile_MPI_obsfilter.yaml
+40 −0		test/testinput/unit_tests/profile/conventionalprofileprocessing_fewerobsthanranks.yaml
+2 −0		test/testinput/unit_tests/variabletransforms/CMakeLists.txt
+3 −2		test/ufo/Reconditioning.h
+0 −24		src/mo/control2analysis_varchange.cc
+0 −4		src/mo/control2analysis_varchange.h
+120 −9		src/mo/eval_air_pressure.cc
+4 −0		src/mo/eval_air_pressure.h
+101 −1		src/mo/eval_air_pressure_levels.cc
+10 −0		src/mo/eval_air_pressure_levels.h
+19 −12		src/mo/eval_air_temperature.cc
+25 −0		src/mo/eval_moisture_incrementing_operator.cc
+8 −2		src/mo/eval_moisture_incrementing_operator.h
+4 −3		src/mo/eval_ratio.cc
+97 −0		src/mo/eval_relative_humidity.cc
+16 −2		src/mo/eval_relative_humidity.h
+52 −1		src/mo/eval_surface_pressure.cc
+13 −2		src/mo/eval_surface_pressure.h
+90 −0		src/mo/eval_surface_temperature.cc
+21 −2		src/mo/eval_surface_temperature.h
+2 −0		src/mo/eval_total_mixing_ratio.h
+1 −1		src/mo/eval_water_vapor_mixing_ratio.cc
+1 −2		src/mo/eval_water_vapor_mixing_ratio.h
+5 −5		src/vader/recipes/HydrostaticExnerLevels_A.cc