NOAA-EMC · JingCheng-NOAA · Dec 20, 2024 · Nov 13, 2024 · Nov 14, 2024
diff --git a/bundle/CMakeLists.txt b/bundle/CMakeLists.txt
@@ -35,6 +35,19 @@ set( ENABLE_MPI ON CACHE BOOL "Compile with MPI" )
 option(BUILD_HDASBUNDLE "Build HDAS Bundle" ON)
 option(CLONE_JCSDADATA "Clone JCSDA test data repositories" OFF)
 
+# Depend path for non-ecbuild packages
+set(DEPEND_LIB_ROOT ${CMAKE_CURRENT_BINARY_DIR}/Depends)
+list(APPEND CMAKE_PREFIX_PATH ${DEPEND_LIB_ROOT})
+
+# Library path for non-ecbuild packages
+link_directories(${CMAKE_CURRENT_BINARY_DIR}/lib)
+
+include( GNUInstallDirs )
+if(APPLE)
+  list( APPEND CMAKE_INSTALL_RPATH $ENV{llvm_openmp_ROOT}/lib )
+endif()
+list( APPEND CMAKE_INSTALL_RPATH ${CMAKE_CURRENT_BINARY_DIR}/fv3 )
+
 # Initialize bundle
 # -----------------
 ecbuild_bundle_initialize()
@@ -75,7 +88,7 @@ if(BUILD_HDASBUNDLE)
   ecbuild_bundle( PROJECT ufo SOURCE "../sorc/ufo" )
 
 # FMS and FV3 dynamical core
-  ecbuild_bundle( PROJECT fms SOURCE "../sorc/fms" )
+  include(fv3-interface.cmake)
   ecbuild_bundle( PROJECT fv3 SOURCE "../sorc/fv3" )
 
 # fv3-jedi and associated repositories

diff --git a/hafs-test/scripts/setup_experiment.sh b/hafs-test/scripts/setup_experiment.sh
@@ -102,6 +102,7 @@ fi
 mkdir -p testinput
 mkdir -p Data/obs
 cp -rp $YOUR_PATH_TO_HDASAPP/hafs-test/validated_yamls/* testinput
+cp -rp $YOUR_PATH_TO_HDASAPP/hafs-test/testinput/* testinput
 cp -p ${DATA_STAGE}/obs/* Data/obs/.
 
 

diff --git a/hafs-test/testinput/SFCSHP_singleob_airTemperature_fv3jedi.yaml b/hafs-test/testinput/SFCSHP_singleob_airTemperature_fv3jedi.yaml
@@ -26,15 +26,15 @@ cost function:
       namelist filename: DataFix/fmsmpp.nml
       field table filename: DataFix/field_table
     <<: *geometry_configs
-  analysis variables: &ana_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,specific_humidity,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio]
+  analysis variables: &ana_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio]
 
 
   background:
     datetime: &AnaDate '2020-08-25T12:00:00Z'
     filetype: fms restart
     datapath: Data/bkg
     <<: *fv3file_names
-    state variables: &state_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,specific_humidity,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio,phis,slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,u_srf,v_srf,f10m]
+    state variables: &state_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio,phis,slmsk,sheleg,vtype,stype,vfrac,stc,smc,snwdph,u_srf,v_srf,f10m]
   background error:
     covariance model: ensemble
     members from template:

diff --git a/hafs-test/testinput/hafs_fv3jedi_3DEnVar_2024063012.yaml b/hafs-test/testinput/hafs_fv3jedi_3DEnVar_2024063012.yaml
@@ -26,14 +26,14 @@ cost function:
       namelist filename: DataFix/fmsmpp.nml
       field table filename: DataFix/field_table
     <<: *geometry_configs
-  analysis variables: &ana_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,specific_humidity,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio]
+  analysis variables: &ana_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio]
 
   background:
     datetime: &AnaDate '2024-06-30T12:00:00Z'
     filetype: fms restart
     datapath: Data/bkg
     <<: *fv3file_names
-    state variables: &state_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,specific_humidity,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio,phis,slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,u_srf,v_srf,f10m]
+    state variables: &state_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio,phis,slmsk,sheleg,vtype,stype,vfrac,stc,smc,snwdph,u_srf,v_srf,f10m]
   background error:
     covariance model: ensemble
     members from template:

diff --git a/hafs-test/testinput/sfcship_singleob_airTemperature_fv3jedi_3DEnVar.yaml b/hafs-test/testinput/sfcship_singleob_airTemperature_fv3jedi_3DEnVar.yaml
@@ -0,0 +1,177 @@
+_filenames: &fv3file_names
+  filename_core: '20200825.120000.fv_core.res.tile1.nc'
+  filename_trcr: '20200825.120000.fv_tracer.res.tile1.nc'
+  filename_sfcd: '20200825.120000.sfc_data.nc'
+  filename_sfcw: '20200825.120000.fv_srf_wnd.res.tile1.nc'
+  filename_cplr: '20200825.120000.coupler.res'
+
+_geometry: &geometry_configs
+  namelist filename: DataFix/input_hafs.nml
+  field metadata override: Data/fieldmetadata/gfs-restart.yaml
+  akbk: DataFix/fix/akbk65.nc
+  npx: 721
+  npy: 541
+  npz: 65
+  layout: [10,6]
+  io_layout: [1,1]
+  ntiles: 1
+  fms initialization:
+    namelist filename: DataFix/fmsmpp.nml
+    field table filename: DataFix/field_table
+  fieldsets:
+    fieldset: DataFix/dynamics_lam_cmaq.yaml
+
+cost function:
+  cost type: 3D-Var
+  time window:
+      begin: &InitialDate '2020-08-25T09:00:00Z'
+      length: PT6H
+
+  geometry:
+    <<: *geometry_configs
+  analysis variables: &ana_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio]
+  background:
+    datetime: &AnaDate '2020-08-25T12:00:00Z'
+    filetype: fms restart
+    datapath: Data/bkg
+    <<: *fv3file_names
+    state variables: &state_vars [eastward_wind,northward_wind,air_temperature,air_pressure_thickness,water_vapor_mixing_ratio_wrt_moist_air,cloud_liquid_ice,cloud_liquid_water,ozone_mass_mixing_ratio,phis,slmsk,sheleg,vtype,stype,vfrac,stc,smc,snwdph,u_srf,v_srf,f10m] 
+  background error:
+    covariance model: ensemble
+    members from template:
+      template:
+        datetime: *AnaDate
+        filetype: fms restart
+        state variables: *state_vars  
+        datapath: ens/mem%mem%/
+        <<: *fv3file_names
+      pattern: '%mem%'
+      nmembers: 5 
+      zero padding: 3
+    localization:
+      localization method: SABER
+      saber central block:
+        saber block name: BUMP_NICAS
+        active variables: *ana_vars
+        read:
+          io:
+            data directory: Data/bump
+            files prefix: fv3jedi_bumpparameters_nicas_lam_atm
+            alias:
+            - in code: common
+              in file: t_250km
+          drivers:
+             multivariate strategy: duplicated
+             read local nicas: true
+
+#------------------------------------------------------------------------------
+  observations:
+     observers:
+     - obs space:
+         name: sfcshp
+         obsdatain:
+           engine:
+             type: H5File
+             obsfile: Data/obs/sfcshp.tm00.singleob.nc
+         obsdataout:
+           engine:
+             type: H5File
+             obsfile: diag_SFCSHP.prepbufr_singleobs.nc
+             allow overwrite: true
+         io pool:
+           max pool size: 1
+         observed variables: [airTemperature]
+         simulated variables: [airTemperature]
+
+       obs operator:
+         name: Composite
+         components:
+         - name: VertInterp
+           vertical coordinate: air_pressure
+           observation vertical coordinate: pressure
+           observation vertical coordinate group: MetaData
+           interpolation method: log-linear
+           variables:
+           - name: airTemperature
+
+       obs post filters:
+         - filter: Perform Action
+           filter variables:
+           - name: airTemperature
+           where:
+           - variable: ObsType/airTemperature
+             is_in: 180
+           action:
+             name: assign error
+             error parameter: 0.92823
+           defer to post: true
+      # Adjusted error after initial assignment (qcmod.f90)
+         - filter: Perform Action
+           filter variables:
+           - name: airTemperature
+           where:
+           - variable: ObsType/airTemperature
+             is_in: 180
+           action:
+             name: inflate error
+             inflation variable:
+               name: ObsFunction/ObsErrorFactorConventional
+               options:
+                 test QCflag: PreQC
+                 test QCthreshold: 3
+                 inflate variables: [airTemperature]
+                 pressure: MetaData/pressure
+                 distance threshold: -1.
+           defer to post: true
+      # error inflation based on pressure check
+         - filter: Perform Action
+           filter variables:
+           - name: airTemperature
+           where:
+           - variable: ObsType/airTemperature
+             is_in: 180
+           action:
+             name: inflate error
+             inflation variable:
+               name: ObsFunction/ObsErrorFactorPressureCheck
+               options:
+                 variable: airTemperature
+                 inflation factor: 8.0
+                 geovar_sfc_geomz: surface_geometric_height
+           defer to post: true
+        #- filter: Bounds Check
+      #  filter variables:
+      #  - name: airTemperature
+      #  minvalue: 195.0
+      #  maxvalue: 327.0
+      #  action:
+      #    name: reject
+      #- filter: Background Check
+      #  filter variables:
+      #  - name: airTemperature
+      #  threshold: 7.0
+      #  absolute threshold: 9.0
+      #  action:
+      #    name: reject
+      #  defer to post: true
+
+variational:
+  minimizer:
+    algorithm: DRPCG    # Derber-Rosati Conjugate Gradients
+  iterations:
+  - ninner: 50
+    gradient norm reduction: 1e-60
+    geometry:
+      <<: *geometry_configs
+    diagnostics:
+      departures: bkgmob
+final:
+  diagnostics:
+    departures: oman
+
+output:
+  filetype: fms restart
+  datapath: Data/analysis/
+  prefix: envar-fv3_hafs_singleOBS_sfcshp #Ens3dvar-fv3_lam-C775
+  frequency: PT3H
+