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The COSMIC project provides data from a series of satellites. There are two forms of the data that are used by DART: GPS Radio Occultation data and Electron Density. The programs in this directory extract the data from the distribution files and put them into DART observation sequence (obs_seq) file format.
The COSMIC satellites measure the phase delay caused by deviation of the straight-line path of the GPS satellite signal as it passes through the Earth's atmosphere when the GPS and COSMIC satellites rise and set relative to each other. This deviation results from changes in the angle of refraction of light as it passes through regions of varying density of atmosphere. These changes are a result of variations in the temperature, pressure, and moisture content. Vertical profiles of temperature and moisture can be derived as the signal passes through more and more atmosphere until it is obscured by the earth's horizon. There are thousands of observations each day distributed around the globe, including in areas which previously were poorly observed. These data are converted with the convert_cosmic_gps_cdf.f90 program and create DART observations of GPSRO_REFRACTIVITY.
The COSMIC satellites also provide ionospheric profiles of electron density. The accuracy is generally about 10-4 ∼ 10-5 cm-3. These data are converted with the convert_cosmic_ionosphere.f90 program and create DART observations tagged as COSMIC_ELECTRON_DENSITY.
Data from the COSMIC Program are available by signing up on the data access web page. We prefer delivery in netCDF file format.
The files we use as input to these conversion programs are
the Level 2 data, Atmospheric Profiles (filenames include
the string 'atmPrf').
Each vertical profile is stored in a separate netCDF file, and there are between 1000-3000 profiles/day, so converting a day's worth of observations used to involve downloading many individual files. There are now daily tar files available which makes it simpler to download the raw data all in a single file and then untar it to get the individual profiles.
The scripts in the shell_scripts directory can now download profiles from any of the available satellites that return GPS RO data to the CDAAC web site. See the gpsro_to_obsseq.csh or convert_many_gpsro.csh script for where to specify the satellites to be included.
The files we have used as input to these conversion programs are from
the COSMIC 2013 Mission and have a data type of 'ionPrf'.
The file naming convention and file format are described by COSMIC here and there can be more than 1000 profiles/day. Like the GPS radio occultation data, the profiles are now available in a single daily tar file which can be downloaded then be unpacked into the individual files. COSMIC has instructions on ways to download the data at
The data are distributed in
file format. DART requires all observations to be in a proprietary
format often called DART "obs_seq" format.
The files in this directory (a combination
of C shell scripts and a Fortran source executable)
do this data conversion.
The shell_scripts directory contains several example scripts, including one which downloads the raw data files a day at a time (download_script.csh), and one which executes the conversion program (convert_script.csh). These scripts make 6 hour files by default, but have options for other times. Each profile is stored in a separate netcdf file and there are usually between 1000-3000 files/day, so the download process can be lengthy. You probably want to download as a separate preprocess step and do not use the script options to automatically delete the input files. Keep the files around until you are sure you are satisified with the output files and then delete them by hand.
The conversion executable convert_cosmic_gps_cdf, reads the namelist &convert_cosmic_gps_nml from the file input.nml.
The namelist lets you select from one of two different forward operators. The 'local' forward operator computes the expected observation value at a single point: the requested height at the tangent point of the ray between satellites. The 'non-local' operator computes values along the ray-path and does an integration to get the expected value. The length of the integration segments and height at which to end the integration are given in the namelist. In some experiments the difference between the two types of operators was negligible. This choice is made at the time of the conversion, and the type of operator is stored in the observation, so at runtime the corresponding forward operator will be used to compute the expected observation value.
The namelist also lets you specify at what heights you want observations to be extracted. The raw data is very dense in the vertical; using all values would not results in a set of independent observations. The current source code no longer does an intermediate interpolation; the original profiles appear to be smooth enough that this is not needed. The requested vertical output heights are interpolated directly from the full profile.
Each profile is interpolated to a set of desired levels that are specified at run time.
During the conversion process, each profile is checked for negative values of
electron density above the minimum desired level. If negative values are found,
the entire profile is discarded. If an observation sequence file already exists,
the converter will simply add the new observations to it. Multiple profiles may
be converted in a single execution, so it is easy to consolidate all the profiles
for a single day into a single observation sequence file, for example.
convert_cosmic_ionosphere reads the namelist &convert_cosmic_ionosphere_nml from the file input.nml.
The original observation times are preserved in the conversion process. If it is desired to subset the observation sequence file such that observations too far away from desired assimilation times are rejected, a separate post-processing step using the obs_sequence_tool is required. A script will be necessary to take a start date, an end date, an assimilation time step, and a desired time 'window' - and strip out the unwanted observations from a series of observation sequence files.
There are multiple ways of specifying the observation error variance at run time. They are implemented in a routine named electron_density_error() and are selected by the namelist variable observation_error_method.
|'constant'||a scalar value for all observations|
|'scaled'||the electron density is multiplied by a scalar value|
|'lookup'||a lookup table is read|
|'scaled_lookup'||the lookup table value is multiplied by a scalar value and the electron density value|
I-Te Lee: " ... the original idea for error of ionospheric observation is 1%. Thus, I put the code as "oerr = 0.01_r8 * obsval". Liu et. al and Yue et al investigated the Abel inversion error of COSMIC ionosphere profile, both of them figure out the large error would appear at the lower altitude and push model toward wrong direction at the lower ionosphere while assimilating these profiles. On the other hand, the Abel inversion error depends on the ionospheric electron density structure, which is a function of local time, altitude and geomagnetic latitude. To simplify the procedure to define observation error of profiles, Xinan Yue help me to estimate an error matrix and saved in the file which named 'f3coerr.nc'. ... The number in the matrix is error percentage (%), which calculated by OSSE. Here are two reference papers. In the end, the observation error consists of instrumentation error (10%) and Abel error."
- X. Yue, W.S. Schreiner, J. Lei, S.V. Sokolovskiy, C. Rocken, D.C. Hunt, and Y.-H. Kuo (2010),
Error analysis of Abel retrieved electron density profiles from radio occultation measurements.
Annales Geophysicae: Atmospheres, Hydrospheres and Space Sciences. 28 No. 1, pp 217-222, doi:10.5194/angeo-28-217-2010
- J.Y. Liu, C.Y. Lin, C.H. Lin, H.F. Tsai, S.C. Solomon, Y.Y. Sun, I.T. Lee, W.S. Schreiner, and Y.H. Kuo (2010),
Artificial plasma cave in the low-latitude ionosphere results from the radio occultation inversion of the FORMOSAT-3/COSMIC}, Journal of Geophysical Research: Space Physics. 115 No. A7, pp 2156-2202, doi:10.1029/2009JA015079
It is possible to create observation sequence files for perfect model experiments that have realistic observation sampling patterns and observation error variances that do not have any actual electron densities. The COSMIC data files are read, but the electron density information is not written. Keep in mind that some methods of specifying the observation error variance require knowledge of the observation value. If the observation value is bad or the entire profile is bad, no observation locations are created for the profile.
This namelist is read from the file input.nml. Namelists start with an ampersand '&' and terminate with a slash '/'. Character strings that contain a '/' must be enclosed in quotes to prevent them from prematurely terminating the namelist.
&convert_cosmic_gps_nml obs_levels = -1.0 use_original_kuo_error = .false. local_operator = .true. ray_ds = 5000.0 ray_htop = 15000.0 gpsro_netcdf_file = 'cosmic_gps_input.nc' gpsro_netcdf_filelist = '' gpsro_out_file = 'obs_seq.gpsro' /
|obs_levels||integer(200)||A series of heights, in kilometers, where observations from this profile should be interpolated. (Note that the other distances and heights in the namelist are specified in meters.) The values should be listed in increasing height order.|
|use_original_kuo_error||logical||If .true. use the observation error variances for a refractivity observation that come from a Kuo paper and were implied to be used for the CONUS domain. If .false. use observation error variances similar to what is used in GSI.|
|local_operator||logical||If .true. compute the observation using a method which assumes all effects occur at the tangent point. If .false. integrate along the tangent line and do ray-path reconstruction.|
|ray_ds||real(r8)||For the non-local operator only, the delta stepsize, in meters, to use for the along-path integration in each direction out from the tangent point.|
|ray_htop||real(r8)||For the non-local operator only, stop the integration when one of the endpoints of the next integration step goes above this height. Specify in meters.|
|gpsro_netcdf_file||character(len=128)||The input filename when converting a single profile. Only one of the file or filelist items can have a valid value, so to use the single filename set the list name 'gpsro_netcdf_filelist' to the empty string (' ').|
|gpsro_netcdf_filelist||character(len=128)||To convert a series of profiles in a single execution create a text file which contains each input file, in ascii, one filename per line. Set this item to the name of that file, and set 'gpsro_netcdf_file' to the empty string (' ').|
|gpsro_out_file||character(len=128)||The output file to be created. To be compatible with earlier versions of this program, if this file already exists it will be read in and the new data will be appended to that file.|
A more useful example follows:
&convert_cosmic_gps_nml gpsro_netcdf_file = '' gpsro_netcdf_filelist = 'flist' gpsro_out_file = 'obs_seq.gpsro' local_operator = .true. use_original_kuo_error = .false. ray_ds = 5000.0 ray_htop = 13000.1 obs_levels = 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, 3.6, 3.8, 4.0, 4.2, 4.4, 4.6, 4.8, 5.0, 5.2, 5.4, 5.6, 5.8, 6.0, 6.2, 6.4, 6.6, 6.8, 7.0, 7.2, 7.4, 7.6, 7.8, 8.0, 8.2, 8.4, 8.6, 8.8, 9.0, 9.2, 9.4, 9.6, 9.8, 10.0, 10.2, 10.4, 10.6, 10.8, 11.0, 11.2, 11.4, 11.6, 11.8, 12.0, 12.2, 12.4, 12.6, 12.8, 13.0, 13.2, 13.4, 13.6, 13.8, 14.0, 14.2, 14.4, 14.6, 14.8, 15.0, 15.2, 15.4, 15.6, 15.8, 16.0, 16.2, 16.4, 16.6, 16.8, 17.0, 17.2, 17.4, 17.6, 17.8, 18.0, 19.0, 20.0, 21.0, 22.0, 23.0, 24.0, 25.0, 26.0, 27.0, 28.0, 29.0, 30.0, 31.0, 32.0, 33.0, 34.0, 35.0, 36.0, 37.0, 38.0, 39.0, 40.0, 41.0, 42.0, 43.0, 44.0, 45.0, 46.0, 47.0, 48.0, 49.0, 50.0, 51.0, 52.0, 53.0, 54.0, 55.0, 56.0, 57.0, 58.0, 59.0, 60.0, /
&convert_cosmic_ionosphere_nml input_file = '' input_file_list = 'input_file_list.txt' output_file = 'obs_seq.out' observation_error_file = 'none' observation_error_method = 'scaled_lookup' locations_only = .false. obs_error_factor = 1.0 verbose = 0 obs_levels = -1.0 /
|input_file||character(len=256)||The input filename when converting a single profile. Only one of the input_file or input_file_list items can have a valid value, so to use a single filename set input_file_list = ''|
|input_file_list||character(len=256)||To convert a series of profiles in a single execution create a text file which contains one filename per line. Set this item to the name of that file, and set input_file = ''|
|output_file||character(len=256)||The output file to be created. If this file already exists the new data will be added to that file. DART observation sequences are linked lists. When the list is traversed, the observations are in ascending time order. The order they appear in the file is completely irrelevant.|
|observation_error_file||character(len=256)||This specifies a lookup table. The table created by I-Te Lee and Xinan Yue is called f3coerr.nc.|
|observation_error_method||character(len=128)||There are multiple ways of specifying the observation error variance. This character string allows you to select the method. The selection is not case-sensitive. Allowable values are: 'constant', 'scaled', 'lookup', or 'scaled_lookup'. Anything else will result in an error. Look in the electron_density_error() routine for specifics.|
|locations_only||logical||If locations_only = .true. then the actual observation values are not written to the output observation sequence file. This is useful for designing an OSSE that has a realistic observation sampling pattern. Keep in mind that some methods of specifying the observation error variance require knowledge of the observation value. If the observation value is bad or the entire profile is bad, this profile is rejected - even if locations_only = .true.|
|obs_error_factor||real(r8)||This is the scalar that is used in several of the methods specifying the observation error variance.|
|verbose||integer||controls the amount of run-time output echoed to the screen. 0 is nearly silent, higher values write out more. The filenames of the profiles that are skipped are ALWAYS printed.|
|obs_levels||integer(200)||A series of heights, in kilometers, where observations from this profile should be interpolated. (Note that the other distances and heights in the namelist are specified in meters.) The values must be listed in increasing height order.|
A more useful example follows:
&convert_cosmic_ionosphere_nml input_file = '' input_file_list = 'file_list.txt' output_file = 'obs_seq.out' observation_error_file = 'f3coeff.dat' observation_error_method = 'scaled' locations_only = .false. obs_error_factor = 0.01 verbose = 1 obs_levels = 160.0, 170.0, 180.0, 190.0, 200.0, 210.0, 220.0, 230.0, 240.0, 250.0, 260.0, 270.0, 280.0, 290.0, 300.0, 310.0, 320.0, 330.0, 340.0, 350.0, 360.0, 370.0, 380.0, 390.0, 400.0, 410.0, 420.0, 430.0, 440.0, 450.0 /
If you are converting only a day or two of observations you can download the files by hand and call the converter programs from the command line. However if you are going convert many days/months/years of data you need an automated script, possibly submitted to a batch queue on a large machine. The following instructions describe shell scripts we provide as a guide in the shell_scripts directory. You will have to adapt them for your own system unless you are running on an NCAR superscomputer.
Making DART Observations from Radio Occultation atmPrf Profiles:
Description of the scripts provided to process the COSMIC and CHAMP GPS radio occultation data. Summary of workflow: 1) cd to the ../work directory and run ./quickbuild.csh to compile everything. 2) Edit ./gpsro_to_obsseq.csh once to set the directory where the DART code is installed, and your CDAAC web site user name and password. 3) Edit ./convert_many_gpsro.csh to set the days of data to download/convert/remove. 4) Run ./convert_many_gpsro.csh either on the command line or submit to a batch system. More details: 1) quickbuild.csh: Make sure your $DART/mkmf/mkmf.template is one that matches the platform and compiler for your system. It should be the same as how you have it set to build the other DART executables. Run quickbuild.csh and it should compile all the executables needed to do the GPS conversion into DART obs_sequence files. 2) gpsro_to_obsseq.csh: Edit gpsro_to_obsseq.csh once to set the DART_DIR to where you have downloaded the DART distribution. (There are a few additional options in this script, but the distribution version should be good for most users.) If you are downloading data from the CDAAC web site, set your web site user name and password. After this you should be able to ignore this script. 3) convert_many_gpsro.csh: A wrapper script that calls the converter script a day at a time. Set the days of data you want to download/convert/remove. See the comments at the top of this script for the various options to set. Rerun this script for all data you need. This script depends on the advance_time executable, which should automatically be built in the ../work directory, but you may have to copy or link to a version from this dir. you also need a minimal input.nml here: &utilities_nml / is all the contents it needs. It can be risky to use the automatic delete/cleanup option - if there are any errors in the script or conversion (file system full, bad file format, etc) and the script doesn't exit, it can delete the input files before the conversion has succeeded. But if you have file quota concerns this allows you to keep the total disk usage lower.
Making DART Observations from Ionospheric ionPrf Profiles:
0) run quickbuild.csh as described above 1) iono_to_obsseq.csh set the start and stop days. downloads from the CDAAC and untars into 100s of files per day. runs the converter to create a single obs_seq.ion.YYYYMMDD file per day. 2) split_obs_seq.csh split the daily files into X minute/hour files - set the window times at the top of the file before running.
Notes on already converted observations on the NCAR supercomputers
GPS Radio Occultation Data:
See /glade/p/image/Observations/GPS These are DART observation sequence files that contain radio-occultation measurements from the COSMIC (and other) satellites. Uses temperature/moisture bending of the signals as they pass through the atmosphere between GPS source satellites and low-earth-orbit receiving satellites to compute the delay in the arrival of data. the files also contain the bending angle data, but we are not using that currently. the subdirectories include: local -- original processed files, single obs at nadir local-cosmic2013 -- reprocessed by CDAAC in 2013 local-test2013 -- 2013 data, denser in vertical, diff errors local-complete2013 - all satellites available for that time, new errors (from lydia c), 2013 cosmic reprocessed data nonlocal -- original processed files, ray-path integrated rawdata -- netcdf data files downloaded from the CDAAC local: the ob is at a single location (the tangent point of the ray and earth) and the entire effect is assumed to be impacting the state at that point. non-local: computes the ob value by doing a line integral along the ray path to accumulate the total effect. (in our experiments we have compared both and did not see a large difference between the two methods, and so have mistly used the local version because it's faster to run.) some directories contain only the gps obs and must be merged (with the obs_sequence_tool) with the rest of the conventional obs before assimilation. some directories contain both the gps-only files and the obs merged with NCEP and ACARS data. if a directory exists but is empty, the files are likely archived on the HPSS. see the README files in the next level directory down for more info on where they might be. nsc jan 2016
See /glade/p/image/Observation/ionosphere These are COSMIC 'ionPrf' ionospheric profile observations. They are downloaded from the CDAAC website as daily tar files and unpacked into the 'raw' directory. They distribute these observations with one profile per netcdf file. Each profile has data at ~500-1000 different levels. Our converter has a fixed number of levels in the namelist and we interpolate between the two closest levels to get the data for that level. If you give the converter a list of input netcdf files it will convert all of them into a single output file. The 'daily' directory is a collection of all the profiles for that day. The 'convert' directory has the executables and scripting for breaking up the daily files into 10 minute files which are put in the '10min' directory. Change the 'split_obs_seq.csh' script to change the width of this window, or the names of the output files. The 'verify.csh' script prints out any missing files, which happens if there are no profiles in the given window. Our convention is to make a 0 length file for missing intervals and we expect the filter run script to look at the file size and loop if there is a file but with no contents. This will allow us to distinguish between a time where we haven't converted the observations and a time where there are no observations. In that case the script should add time to the next model advance request and loop to the next interval.
convert_cosmic_gps_cdf and convert_cosmic_ionosphere use the same set of modules.
assimilation_code/location/threed_sphere/location_mod.f90 assimilation_code/modules/assimilation/adaptive_inflate_mod.f90 assimilation_code/modules/assimilation/assim_model_mod.f90 assimilation_code/modules/io/dart_time_io_mod.f90 assimilation_code/modules/io/direct_netcdf_mod.f90 assimilation_code/modules/io/io_filenames_mod.f90 assimilation_code/modules/io/state_structure_mod.f90 assimilation_code/modules/io/state_vector_io_mod.f90 assimilation_code/modules/observations/obs_kind_mod.f90 assimilation_code/modules/observations/obs_sequence_mod.f90 assimilation_code/modules/utilities/distributed_state_mod.f90 assimilation_code/modules/utilities/ensemble_manager_mod.f90 assimilation_code/modules/utilities/netcdf_utilities_mod.f90 assimilation_code/modules/utilities/null_mpi_utilities_mod.f90 assimilation_code/modules/utilities/null_win_mod.f90 assimilation_code/modules/utilities/options_mod.f90 assimilation_code/modules/utilities/random_seq_mod.f90 assimilation_code/modules/utilities/sort_mod.f90 assimilation_code/modules/utilities/time_manager_mod.f90 assimilation_code/modules/utilities/types_mod.f90 assimilation_code/modules/utilities/utilities_mod.f90 models/template/model_mod.f90 models/utilities/default_model_mod.f90 observations/forward_operators/obs_def_mod.f90 observations/forward_operators/obs_def_utilities_mod.f90 observations/obs_converters/utilities/obs_utilities_mod.f90
Some COSMIC files seem to have internal times which differ from the times encoded in the filenames by as much as 2-3 minutes. If it is important to get all the observations within a particular time window files with filenames from a few minutes before and after the window should be converted. Times really outside the window can be excluded in a separate step using the obs_sequence_tool.
The converters have a parameter declaring the maximum number of desired levels as 200. If more than 200 levels are entered as input (to obs_levels), a rather uninformative run-time error is generated:
ERROR FROM: routine: check_namelist_read message: INVALID NAMELIST ENTRY: / in namelist convert_cosmic_ionosphere_nml
Your error may be different if obs_levels is not the last namelist item before the slash '/'
|Revision:||$Revision: 12591 $|
|Source:||$URL: https://svn-dares-dart.cgd.ucar.edu/DART/releases/Manhattan/observations/obs_converters/gps/gps.html $|
|Change Date:||$Date: 2018-05-21 14:49:26 -0600 (Mon, 21 May 2018) $|
|Change history:||try "svn log" or "svn diff"|