From fd741f7d3261ea338297d4901922f33fb37392ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cgspetro-NOAA=E2=80=9D?= Date: Thu, 7 Dec 2023 15:46:59 -0500 Subject: [PATCH] update sample files in DASystem --- .../CustomizingTheWorkflow/DASystem.rst | 84 ++++++++++--------- 1 file changed, 43 insertions(+), 41 deletions(-) diff --git a/docs/source/CustomizingTheWorkflow/DASystem.rst b/docs/source/CustomizingTheWorkflow/DASystem.rst index 7d7881ab..3157a65d 100644 --- 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 @@ -94,7 +94,7 @@ 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 @@ -102,11 +102,11 @@ Users may find the following example ``GHCN.yaml`` configuration file to be a he 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/$datapath``.) ``filename_sfcd`` - Specifies the name of the surface data file. This usually takes the form ``YYYYMMDD.HHmmss.sfc_data.nc``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour, mm is a valid 2-digit minute and ss is a valid 2-digit second. For example: ``20160102.180000.sfc_data.nc`` + Specifies the name of the surface data file. This usually takes the form ``YYYYMMDD.HHmmss.sfc_data.nc``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour, mm is a valid 2-digit minute and ss is a valid 2-digit second. For example: ``20191221.000000.sfc_data.nc`` ``filename_cprl`` - Specifies the name of file that contains metadata for the restart. This usually takes the form ``YYYYMMDD.HHmmss.coupler.res``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour, mm is a valid 2-digit minute and ss is a valid 2-digit second. For example: ``20160102.180000.coupler.res`` + Specifies the name of file that contains metadata for the restart. This usually takes the form ``YYYYMMDD.HHmmss.coupler.res``, where YYYY is a 4-digit year, MM is a valid 2-digit month, DD is a valid 2-digit day, and HH is a valid 2-digit hour, mm is a valid 2-digit minute and ss is a valid 2-digit second. For example: ``20191221.000000.coupler.res`` Driver ^^^^^^^^^ @@ -557,44 +557,46 @@ where ``${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" ; @@ -602,7 +604,7 @@ The IODA-formatted GHCN files are structured as follows (using 20160102 as an ex group: ObsValue { variables: - float totalSnowDepth(nlocs) ; + float totalSnowDepth(Location) ; totalSnowDepth:_FillValue = 9.96921e+36f ; string totalSnowDepth:coordinates = "longitude latitude" ; string totalSnowDepth:units = "mm" ; @@ -610,7 +612,7 @@ The IODA-formatted GHCN files are structured as follows (using 20160102 as an ex group: PreQC { variables: - int totalSnowDepth(nlocs) ; + int totalSnowDepth(Location) ; totalSnowDepth:_FillValue = -2147483647 ; string totalSnowDepth:coordinates = "longitude latitude" ; } // group PreQC