ObsPack diagnostic

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On this page we provide information about the ObsPack diagnostic in GEOS-Chem, which is intended to sample GEOS-Chem data at specified coordinates and times (e.g. corresponding to surface or flight track measurements). This feature was written by Andy Jacobson of NOAA and Andrew Schuh of Colorado State University and implemented in GEOS-Chem 12.2.0.

Specifying ObsPack diagnostic options

The ObsPack Menu section of input.geos is where you define the following settings:

  1. Turning ObsPack or off
  2. Specifying which GEOS-Chem species you would like to archive.
    • At present, you can archive individual species, or all advected species.
  3. Specifying the names of input files.
    • These are the files from which coordinate data will be read)
  4. Specifying the names of output files.
    • These are the files that will contain GEOS-Chem data sampled by the ObsPack diagnostic.

--Bob Yantosca (talk) 21:06, 11 January 2019 (UTC)

Input file format

The ObsPack diagnostic reads input information (such as coordinates, sampling method, and observation ID's) from netCDF files having the format shown below. You will need to prepare an input file for each YYYY/MM/DD date on which you would like to obtain ObsPack diagnostic output from GEOS-Chem. (The ObsPack diagnostic will skip over days on which it cannot find an input file.)

ObsPack input files can be downloaded from NOAA (see https://www.esrl.noaa.gov/gmd/ccgg/obspack/). Only the following variables are used as input by the GEOS-Chem ObsPack diagnostic:

netcdf obspack_co2_1_OCO2MIP_2018-11-28.20180926 {
dimensions:
        obs = UNLIMITED ; // (662 currently)
        calendar_components = 6 ;
        string_of_200chars = 200 ;
variables:         
        float latitude(obs) ;
                latitude:units = "degrees_north" ;
                latitude:_FillValue = -1.e+34f ;
                latitude:long_name = "Sample latitude" ;
        float longitude(obs) ;
                longitude:units = "degrees_east" ;
                longitude:_FillValue = -1.e+34f ;
                longitude:long_name = "Sample longitude" ;
        float altitude(obs) ;
                altitude:units = "meters" ;
                altitude:_FillValue = -1.e+34f ;
                altitude:long_name = "sample altitude in meters above sea level" ;
                altitude:comment = "Altitude is elevation plus sample intake height in meters above sea level." ;
        int time_components(obs, calendar_components) ;
                time_components:_FillValue = -9 ;
                time_components:long_name = "Calendar time components as integers.  Times and dates are UTC." ;
                time_components:order = "year, month, day, hour, minute, second" ;
                time_components:comment = "Calendar time components as integers.  Times and dates are UTC." ;            
        char obspack_id(obs, string_of_200chars) ;
                obspack_id:long_name = "Unique ObsPack observation id" ;
                obspack_id:comment = "Unique observation id string that includes obs_id, dataset_id and obspack_num." ;
        int CT_sampling_strategy(obs) ;
                CT_sampling_strategy:_FillValue = -9 ;
                CT_sampling_strategy:long_name = "model sampling strategy" ;
                CT_sampling_strategy:values = "How to sample model. 1=4-hour avg; 2=1-hour avg; 3=90-min avg; 4=instantaneous" ;

  ... omitting global attributes etc ...
}

The ObsPack ID string should be 200 characters long.

If you have coordinate data in another format (e.g. a text-based Planeflight.dat file) then you'll need to create a netCDF file using the format shown above, or else ObsPack will not be able to read it.

--Bob Yantosca (talk) 20:04, 11 January 2019 (UTC)

Output file format

The ObsPack diagnostic will produce a file called GEOSChem.ObsPack.YYYYMMDD_hhmmz.nc4 for each day where an input file has been specified. (You can change the output file name in the ObsPack Menu of input.geos.)

Below is shown an ObsPack output file for the GEOS-Chem methane simulation. If you are using the ObsPack diagnostic with other GEOS-Chem simulations, your output files will look similar to this, except for the species names.

netcdf GEOSChem.ObsPack.20180926_0000z.nc4 {
dimensions:
        obs = UNLIMITED ; // (662 currently)
        species = 1 ;
        char_len_obs = 200 ;
variables:
        char obspack_id(obs, char_len_obs) ;
                obspack_id:long_name = "obspack_id" ;
                obspack_id:units = "1" ;
        int nsamples(obs) ;
                nsamples:long_name = "no. of model samples" ;
                nsamples:units = "1" ;
                nsamples:comment = "Number of discrete model samples in average" ;
        int averaging_interval(obs) ;
                averaging_interval:long_name = "Amount of model time over which this observation is averaged" ;
                averaging_interval:units = "seconds" ;
        int averaging_interval_start(obs) ;
                averaging_interval_start:long_name = "Start of averaging interval" ;
                averaging_interval_start:units = "seconds since 1970-01-01 00:00:00 UTC" ;
                averaging_interval_start:calendar = "standard" ;
        int averaging_interval_end(obs) ;
                averaging_interval_end:long_name = "End of averaging interval" ;
                averaging_interval_end:units = "seconds since 1970-01-01 00:00:00 UTC" ;
                averaging_interval_end:calendar = "standard" ;
        float lon(obs) ;
                lon:long_name = "longitude" ;
                lon:units = "degrees_east" ;
        float lat(obs) ;
                lat:long_name = "latitude" ;
                lat:units = "degrees_north" ;
        float u(obs) ;
                u:long_name = "Zonal component of wind" ;
                u:units = "m s^-1" ;
        float v(obs) ;
                v:long_name = "Meridional component of wind" ;
                v:units = "m s^-1" ;
        float blh(obs) ;
                blh:long_name = "Boundary layer height" ;
                blh:units = "m" ;
        float q(obs) ;
                q:long_name = "mass_fraction_of_water_inair" ;
                q:units = "kg water (kg air)^-1" ;
        float pressure(obs) ;
                pressure:long_name = "pressure" ;
                pressure:units = "Pa" ;
        float temperature(obs) ;
                temperature:long_name = "temperature" ;
                temperature:units = "K" ;
        float CH4(obs) ;
                CH4:long_name = "Methane" ;
                CH4:units = "mol mol-1" ;
                CH4:_FillValue = -1.e+34f ;

// global attributes:
                :history = "GEOS-Chem simulation at 2019/01/11 14:54" ;
                :conventions = "CF-1.4" ;
                :references = "www.geos-chem.org; wiki.geos-chem.org" ;
                :model_start_date = "2018/09/26 00:00:00 UTC" ;
                :model_end_date = "2018/09/27 00:00:00 UTC" ;
}

You can several different types of netCDF-reading software to read and plot data from Obspack diagnostic output files. We recommend using either Python scripts or Jupyter notebooks.

--Bob Yantosca (talk) 20:31, 11 January 2019 (UTC)

Known issues

Unit conversions are currently done for all species

In routine ObsPack_Sample (located in module ObsPack/obspack_mod.F90), the following algorithm is used:

    ! Ensure that units of species are "v/v dry", which is dry
    ! air mole fraction.  Capture the InUnit value, this is
    ! what the units are prior to this call.  After we sample
    ! the species, we'll call this again requesting that the
    ! species are converted back to the InUnit values.
    CALL Convert_Spc_Units( am_I_root, Input_Opt, State_Met,                 &
                            State_Chm, "v/v dry", RC,       PriorUnit       )

    ... THEN DO THE DATA SAMPLING ...............................................
    ... i.e. determine which GEOS-Chem grid boxes to include in the averaging ...

    ! Return State_Chm%SPECIES to whatever units they had
    ! coming into this routine
    call Convert_Spc_Units( am_I_root, Input_Opt, State_Met,                 &
                            State_Chm, PriorUnit, RC                        )

The routine Convert_Spc_Units performs unit conversions for all of the species in the State_Chm%Species array, regardless of whether they are being archived with ObsPack or not. This can lead to a bottleneck in performance, as ObsPack_Sample is called on every GEOS-Chem "heartbeat" timestep.

What would be more efficient would be to do the unit conversion only for those species that are being archived by ObsPack. A typical full-chemistry simulation includes about 200 species. But if we are only using ObsPack to archive 10 of these species, GEOS-Chem would execute much faster if we were doing unit conversions for only the 10 archived species instead of all 200 species.

This issue is currently unresolved.

--Bob Yantosca (talk) 21:24, 11 January 2019 (UTC)

Previous issues that are now resolved

None at this time.