update sample files in DASystem

ufs-community · Dec 7, 2023 · fd741f7 · fd741f7
1 parent d8f11d0
commit fd741f7
Showing 1 changed file with 43 additions and 41 deletions.
diff --git a/docs/source/CustomizingTheWorkflow/DASystem.rst b/docs/source/CustomizingTheWorkflow/DASystem.rst
@@ -41,38 +41,38 @@ Users may find the following example ``GHCN.yaml`` configuration file to be a he
      fms initialization:
        namelist filename: Data/fv3files/fmsmpp.nml
        field table filename: Data/fv3files/field_table
-     akbk: Data/fv3files/akbk127.nc4
-     npx: 97
-     npy: 97
-     npz: 127
+     akbk: Data/fv3files/akbk64.nc4
+     npx: 49
+     npy: 49
+     npz: 64
      field metadata override: Data/fieldmetadata/gfs-land.yaml
      time invariant fields:
        state fields:
-         datetime: 2016-01-02T18:00:00Z
+         datetime: 2019-12-21T00:00:00Z
          filetype: fms restart
          skip coupler file: true
          state variables: [orog_filt]
-         datapath: /mnt/lfs4/HFIP/hfv3gfs/role.epic/landda/inputs/forcing/gdas/orog_files
+         datapath: /scratch2/NAGAPE/epic/UFS_Land-DA/inputs/forcing/era5/orog_files
          filename_orog: oro_C96.mx100.nc
 
-   window begin: 2016-01-02T12:00:00Z
-   window length: PT6H
+   window begin: 2019-12-21T00:00:00Z
+   window length: PT24H
 
    background:
-     date: &date 2016-01-02T18:00:00Z
+     date: &date 2019-12-21T00:00:00Z
      members:
-       - datetime: 2016-01-02T18:00:00Z
+       - datetime: 2019-12-21T00:00:00Z
          filetype: fms restart
          state variables: [snwdph,vtype,slmsk]
          datapath: mem_pos/
-         filename_sfcd: 20160102.180000.sfc_data.nc
-         filename_cplr: 20160102.180000.coupler.res
-       - datetime: 2016-01-02T18:00:00Z
+         filename_sfcd: 20191221.000000.sfc_data.nc
+         filename_cplr: 20191221.000000.coupler.res
+       - datetime: 2019-12-21T00:00:00Z
          filetype: fms restart
          state variables: [snwdph,vtype,slmsk]
          datapath: mem_neg/
-         filename_sfcd: 20160102.180000.sfc_data.nc
-         filename_cplr: 20160102.180000.coupler.res
+         filename_sfcd: 20191221.000000.sfc_data.nc
+         filename_cplr: 20191221.000000.coupler.res
 
    driver:
      save posterior mean: false
@@ -94,19 +94,19 @@ Users may find the following example ``GHCN.yaml`` configuration file to be a he
    observations:
      observers:
      - obs space:
-         name: Simulate
+         name: SnowDepthGHCN
          distribution:
            name: Halo
            halo size: 250e3
          simulated variables: [totalSnowDepth]
          obsdatain:
            engine:
              type: H5File
-             obsfile: GHCN_2016010218.nc
+             obsfile: GHCN_2019122100.nc
          obsdataout:
            engine:
              type: H5File
-             obsfile: output/DA/hofx/letkf_hofx_ghcn_2016010218.nc
+             obsfile: output/DA/hofx/letkf_hofx_ghcn_2019122100.nc
        obs operator:
          name: Identity
        obs error:
@@ -126,12 +126,12 @@ Users may find the following example ``GHCN.yaml`` configuration file to be a he
        - filter: Domain Check # missing station elevation (-999.9)
          where:
          - variable:
-             name: height@MetaData
+             name: MetaData/height
            minvalue: -999.0
        - filter: Domain Check # land only
          where:
          - variable:
-             name: slmsk@GeoVaLs
+             name: GeoVaLs/slmsk
            minvalue: 0.5
            maxvalue: 1.5
        # GFSv17 only.
@@ -143,7 +143,7 @@ Users may find the following example ``GHCN.yaml`` configuration file to be a he
        - filter: RejectList  # no land-ice
          where:
          - variable:
-             name: vtype@GeoVaLs
+             name: GeoVaLs/vtype
            minvalue: 14.5
            maxvalue: 15.5
        - filter: Background Check # gross error check
@@ -232,7 +232,7 @@ Background
 The ``background:`` section includes information on the analysis file(s) (also known as "members") generated by the previous cycle. 
 
    ``date``
-      Specifies the background date. The format is ``&date YYYY-MM-DDTHH:00:00Z``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour. For example: ``&date 2016-01-02T18:00:00Z``
+      Specifies the background date. The format is ``&date YYYY-MM-DDTHH:00:00Z``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour. For example: ``&date 2019-12-21T00:00:00Z``
 
    ``members``
       Specifies information on analysis file(s) generated by a previous cycle. 
@@ -250,10 +250,10 @@ The ``background:`` section includes information on the analysis file(s) (also k
          Specifies the path for state variables data. Valid values: ``mem_pos/`` | ``mem_neg/``. (With default experiment values, the full path will be ``workdir/mem000/jedi/$datapath``.)
 
       ``filename_sfcd``
-         Specifies the name of the surface data file. This usually takes the form ``YYYYMMDD.HHmmss.sfc_data.nc``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour, mm is a valid 2-digit minute and ss is a valid 2-digit second. For example: ``20160102.180000.sfc_data.nc``
+         Specifies the name of the surface data file. This usually takes the form ``YYYYMMDD.HHmmss.sfc_data.nc``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour, mm is a valid 2-digit minute and ss is a valid 2-digit second. For example: ``20191221.000000.sfc_data.nc``
 
       ``filename_cprl``
-         Specifies the name of file that contains metadata for the restart. This usually takes the form ``YYYYMMDD.HHmmss.coupler.res``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour, mm is a valid 2-digit minute and ss is a valid 2-digit second. For example: ``20160102.180000.coupler.res``
+         Specifies the name of file that contains metadata for the restart. This usually takes the form ``YYYYMMDD.HHmmss.coupler.res``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour, mm is a valid 2-digit minute and ss is a valid 2-digit second. For example: ``20191221.000000.coupler.res``
 
 Driver
 ^^^^^^^^^
@@ -557,60 +557,62 @@ where ``${YYYY}`` should be replaced with the year of interest. Note that these
 
 These raw snow depth observations need to be converted into IODA-formatted netCDF files for ingestion into the JEDI LETKF system. However, this process was preemptively handled outside of the Land DA workflow, and the 2019 GHCN IODA files were provided by NOAA PSL (Clara Draper).
 
-The IODA-formatted GHCN files are structured as follows (using 20160102 as an example):
+The IODA-formatted GHCN files are available in the ``inputs/DA/snow_depth/GHCN/data_proc/v3/`` directory and are structured as follows (using 20191221 as an example):
 
 .. code-block:: console
    
-   netcdf ghcn_snwd_ioda_20160102 {
+   netcdf ghcn_snwd_ioda_20191221 {
    dimensions:
-      nlocs = UNLIMITED ; // (9946 currently)
+      Location = 9379 ; 
    variables:
-      int nlocs(nlocs) ;
-		   nlocs:suggested_chunk_dim = 9946LL ;
+      int Location(Location) ;
+		   Location:suggested_chunk_dim = 9379LL ;
 
    // global attributes:
          string :_ioda_layout = "ObsGroup" ;
          :_ioda_layout_version = 0 ;
          string :converter = "ghcn_snod2ioda_newV2.py" ;
-         string :date_time_string = "2016-01-02T18:00:00Z" ;
-         :nlocs = 9946 ;
+         string :date_time_string = "2019-12-21T18:00:00Z" ;
+         :nlocs = 9379 ;
+         :history = "Fri Aug 12 20:27:37 2022: ncrename -O -v altitude,height ./data_proc_test/nc4_ghcn_snwd_ioda_20191221.nc ./data_proc_Update/ghcn_snwd_ioda_20191221.nc" ;
+         :NCO = "netCDF Operators version 4.9.1 (Homepage = http://nco.sf.net, Code = http://github.com/nco/nco)" ;
 
    group: MetaData {
       variables:
-         string datetime(nlocs) ;
-            string datetime:_FillValue = "" ;
-         float height(nlocs) ;
+         int64 dateTime(Location) ;
+            dateTime:_FillValue = -2208988800LL ;
+            string dateTime:units = "seconds since 1970-01-01T00:00:00Z" ;
+         float height(Location) ;
             height:_FillValue = 9.96921e+36f ;
-            string height:units = "m" ;
-         float latitude(nlocs) ;
+         float latitude(Location) ;
             latitude:_FillValue = 9.96921e+36f ;
             string latitude:units = "degrees_north" ;
-         float longitude(nlocs) ;
+         float longitude(Location) ;
             longitude:_FillValue = 9.96921e+36f ;
             string longitude:units = "degrees_east" ;
-         string stationIdentification(nlocs) ;
+         string stationIdentification(Location) ;
             string stationIdentification:_FillValue = "" ;
       } // group MetaData
 
    group: ObsError {
       variables:
-         float totalSnowDepth(nlocs) ;
+         float totalSnowDepth(Location) ;
             totalSnowDepth:_FillValue = 9.96921e+36f ;
             string totalSnowDepth:coordinates = "longitude latitude" ;
             string totalSnowDepth:units = "mm" ;
       } // group ObsError
 
    group: ObsValue {
       variables:
-         float totalSnowDepth(nlocs) ;
+         float totalSnowDepth(Location) ;
             totalSnowDepth:_FillValue = 9.96921e+36f ;
             string totalSnowDepth:coordinates = "longitude latitude" ;
             string totalSnowDepth:units = "mm" ;
       } // group ObsValue
 
    group: PreQC {
       variables:
-         int totalSnowDepth(nlocs) ;
+         int totalSnowDepth(Location) ;
             totalSnowDepth:_FillValue = -2147483647 ;
             string totalSnowDepth:coordinates = "longitude latitude" ;
       } // group PreQC