ObsPack diagnostic¶
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:
Turning ObsPack or off
Specifying which GEOS-Chem species you would like to archive.
At present, you can archive individual species, or all advected species.
Specifying the names of input files
These are the files from which coordinate data will be read)
Specifying the names of output files
These are the files that will contain GEOS-Chem data sampled by the ObsPack diagnostic.
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/).
Attention
Starting in ObsPack v6, time_components indicates the
start-time of the sampling interval, not the center time. For the
center time, we need to read the time variable. The
time variable represents the center of the averaging window
in all ObsPack data versions.
Obspack file metadata¶
Here is the metadata from an ObsPack data file. We have only displayed the variables that the ObsPack module needs to read.
netcdf obspack_co2_1_GLOBALVIEWplus_v6.0_2020-09-11.20190408 {
dimensions:
obs = UNLIMITED ; // (3111 currently)
calendar_components = 6 ;
string_of_200chars = 200 ;
string_of_500chars = 500 ;
variables:
int obs(obs) ;
obs:long_name = "obs" ;
obs:_Storage = "chunked" ;
obs:_ChunkSizes = 1024 ;
obs:_Endianness = "little" ;
int time(obs) ;
time:units = "Seconds since 1970-01-01 00:00:00 UTC" ;
time:_FillValue = -999999999 ;
time:long_name = "Seconds since 1970-01-01 00:00:00 UTC" ;
time:_Storage = "chunked" ;
time:_ChunkSizes = 778 ;
time:_DeflateLevel = 5 ;
time:_Endianness = "little" ;
...
float latitude(obs) ;
latitude:units = "degrees_north" ;
latitude:_FillValue = -1.e+34f ;
latitude:long_name = "Sample latitude" ;
latitude:_Storage = "chunked" ;
latitude:_ChunkSizes = 778 ;
latitude:_DeflateLevel = 5 ;
latitude:_Endianness = "little" ;
float longitude(obs) ;
longitude:units = "degrees_east" ;
longitude:_FillValue = -1.e+34f ;
longitude:long_name = "Sample longitude" ;
longitude:_Storage = "chunked" ;
longitude:_ChunkSizes = 778 ;
longitude:_DeflateLevel = 5 ;
longitude:_Endianness = "little" ;
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 surface elevation plus sample intake height in meters above sea level." ;
altitude:_Storage = "chunked" ;
altitude:_ChunkSizes = 778 ;
altitude:_DeflateLevel = 5 ;
...
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." ;
obspack_id:_Storage = "chunked" ;
obspack_id:_ChunkSizes = 1, 200 ;
obspack_id:_DeflateLevel = 5 ;
...
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" ;
CT_sampling_strategy:_Storage = "chunked" ;
CT_sampling_strategy:_ChunkSizes = 778 ;
CT_sampling_strategy:_DeflateLevel = 5 ;
CT_sampling_strategy:_Endianness = "little"
... omitting global attributes etc. ...
Notes¶
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.
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 in 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.
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.=
... 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, &
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 hose 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.