program obs_seq_verify

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$Id: obs_seq_verify.html 11427 2017-03-31 21:24:30Z nancy@ucar.edu $

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Overview

verify schematic

obs_seq_verify reorders the observations from a forecast run of DART into a structure that is amenable for the evaluation of the forecast. The big picture is that the verification locations and times identified in the obsdef_mask.nc and the observations from the forecast run (whose files must have an extension as in the following: obs_seq.forecast.YYYYMMDDHH) are put into a netCDF variable that looks like this:

verify variable

obs_seq_verify can read in a series of observation sequence files - each of the files must contain the entire forecast from a single analysis time. The extension of each filename is required to reflect the analysis time. Use obs_sequence_tool to concatenate multiple files into a single observation sequence file if necessary. Only the individual ensemble members forecast values are used - the ensemble mean and spread (as individual copies) are completely ignored. The individual "prior ensemble member NNNN" copies are used. As a special case, the "prior ensemble mean" copy is used if and only if there are no individual ensemble members present (i.e. input.nml &filter_nml:num_output_obs_members == 0).

Dimension Explanation
analysisT This is the netCDF UNLIMITED dimension, so it is easy to 'grow' this dimension. This corresponds to the number of forecasts one would like to compare.
stations The unique horizontal locations in the verification network.
levels The vertical level at each location. Observations with a pressure vertical coordinate are selected based on their proximity to the mandatory levels as defined in obs_seq_coverage. Surface observations or observations with undefined vertical coordinates are simply put into level 1.
copy This dimension designates the quantity of interest; the observation, the forecast value, or the observation error variance. These quantities are the ones required to calculate the evaluation statistics.
nmembers Each ensemble member contributes a forecast value.
forecast_lead   This dimension relates to the amount of time between the start of the forecast and the verification.

The USAGE section has more on the actual use of obs_seq_verify.

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NAMELIST

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.

&obs_seq_verify_nml
   obs_sequences     = ''
   obs_sequence_list = ''
   station_template  = 'obsdef_mask.nc'
   netcdf_out        = 'forecast.nc'
   obtype_string     = 'RADIOSONDE_TEMPERATURE'
   print_every       = 10000
   verbose           = .true.
   debug             = .false.
   /


You can specify either obs_sequences or obs_sequence_list -- not both. One of them has to be an empty string ... i.e. ' '.

Item Type Description
obs_sequences character(len=256), dimension(500) Names of the observation sequence files - each of which MUST have an extension that defines the start of the forecast (the analysis time). The observation sequence filenames must be something like obs_seq.forecast.YYYYMMDDHH . If obs_sequences is specified, obs_sequence_list must be empty.
obs_sequence_list character(len=256) Name of an ascii text file which contains a list of one or more observation sequence files, one per line. The observation sequence filenames MUST have an extension that defines the start of the forecast (the analysis time). The observation sequence filenames must be something like obs_seq.forecast.YYYYMMDDHH. obs_sequence_list can be created by any method, including sending the output of the 'ls' command to a file, a text editor, or another program. If obs_sequence_list is specified, obs_sequences must be empty.
station_template character(len=256) The name of the netCDF file created by obs_seq_coverage that contains the verification network description.
netcdf_out character(len=256) The base portion of the filename of the file that will contain the forecast quantities. Since each observation type of interest is processed with a separate run of obs_seq_verify, the observation type string is used to create a unique output filename.
calendar character(len=129) The type of the calendar used to interpret the dates.
obtype_string character(len=32) The observation type string that will be verified. The character string must match one of the standard DART observation types. This will be the name of the variable in the netCDF file, and will also be used to make a unique netCDF file name.
print_every integer Print run-time information for every "print_every" n-th observation.
verbose logical Print extra run-time information.
debug logical Print a frightening amount of run-time information.


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OTHER MODULES USED

assimilation_code/location/threed_sphere/location_mod.f90
assimilation_code/modules/assimilation/assim_model_mod.f90
models/your_model/model_mod.f90
assimilation_code/modules/observations/obs_kind_mod.f90
assimilation_code/modules/observations/obs_sequence_mod.f90
assimilation_code/modules/utilities/null_mpi_utilities_mod.f90
assimilation_code/modules/utilities/types_mod.f90
assimilation_code/modules/utilities/random_seq_mod.f90
assimilation_code/modules/utilities/time_manager_mod.f90
assimilation_code/modules/utilities/utilities_mod.f90
observations/forward_operators/obs_def_mod.f90
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FILES

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USAGE

obs_seq_verify is built in .../DART/models/your_model/work, in the same way as the other DART components.

Once the forecast has completed, each observation type may be extracted from the observation sequence file and stuffed into the appropriate verification structure. Each observation type must be processed serially at this time, and each results in a separate output netCDF file. Essentially, obs_seq_verify sorts an unstructured, unordered set of observations into a predetermined configuration.

Example: a single 48-hour forecast that is evaluated every 6 hours.

Example 1

In this example, the obsdef_mask.nc file was created by running obs_seq_coverage with the namelist specified in the single 48hour forecast evaluated every 6 hours example. The obsdef_mask.txt file was used to mask the input observation sequence files by obs_selection and the result was run through filter with the observations marked as evaluate_only - resulting in a file called obs_seq.forecast.2008060818. This filename could also be put in a file called verify_list.txt.

Just to reiterate the example, both namelists for obs_seq_coverage and obs_seq_verify are provided below.

&obs_seq_coverage_nml
   obs_sequences      = ''
   obs_sequence_list  = 'coverage_list.txt'
   obs_of_interest    = 'METAR_U_10_METER_WIND'
                        'METAR_V_10_METER_WIND'
   textfile_out       = 'obsdef_mask.txt'
   netcdf_out         = 'obsdef_mask.nc'
   calendar           = 'Gregorian'
   first_analysis     =  2008, 6, 8, 18, 0, 0 
   last_analysis      =  2008, 6, 8, 18, 0, 0 
   forecast_length_days          = 2
   forecast_length_seconds       = 0
   verification_interval_seconds = 21600
   temporal_coverage_percent     = 100.0
   lonlim1            =    0.0
   lonlim2            =  360.0
   latlim1            =  -90.0
   latlim2            =   90.0
   verbose            = .true.
   /

&obs_seq_verify_nml
   obs_sequences      = 'obs_seq.forecast.2008060818'
   obs_sequence_list  = ''
   station_template  = 'obsdef_mask.nc'
   netcdf_out        = 'forecast.nc'
   obtype_string     = 'METAR_U_10_METER_WIND'
   print_every       = 10000
   verbose           = .true.
   debug             = .false.
   /

The pertinent information from the obsdef_mask.nc file is summarized (from ncdump -v experiment_times,analysis,forecast_lead obsdef_mask.nc) as follows:

verification_times = 148812.75, 148813, 148813.25, 148813.5, 148813.75,
                                148814, 148814.25, 148814.5, 148814.75 ;

analysis           = 148812.75 ;

forecast_lead      = 0, 21600, 43200, 64800, 86400, 108000, 129600, 151200, 172800 ;

There is one analysis time, 9 forecast leads and 9 verification times. The analysis time is the same as the first verification time. The run-time output of obs_seq_verify and a dump of the resulting netCDF file follows:

[thoar@mirage2 work]$ ./obs_seq_verify |& tee my.verify.log
 Starting program obs_seq_verify
 Initializing the utilities module.
 Trying to log to unit           10
 Trying to open file dart_log.out

 --------------------------------------
 Starting ... at YYYY MM DD HH MM SS =
                 2011  3  1 10  2 54
 Program obs_seq_verify
 --------------------------------------

 set_nml_output Echo NML values to log file only
 Trying to open namelist log dart_log.nml
 ------------------------------------------------------


 -------------- ASSIMILATE_THESE_OBS_TYPES --------------
 RADIOSONDE_TEMPERATURE
 RADIOSONDE_U_WIND_COMPONENT
 RADIOSONDE_V_WIND_COMPONENT
 SAT_U_WIND_COMPONENT
 SAT_V_WIND_COMPONENT
 -------------- EVALUATE_THESE_OBS_TYPES --------------
 RADIOSONDE_SPECIFIC_HUMIDITY
 ------------------------------------------------------

 find_ensemble_size:  opening obs_seq.forecast.2008060818
 location_mod: Ignoring vertical when computing distances; horizontal only
 find_ensemble_size: There are   50 ensemble members.

 fill_stations:  There are          221 stations of interest,
 fill_stations: ...  and              9 times    of interest.
 InitNetCDF:  METAR_U_10_METER_WIND_forecast.nc is fortran unit            5

 obs_seq_verify:  opening obs_seq.forecast.2008060818
 analysis            1 date is 2008 Jun 08 18:00:00

 index    6 is prior ensemble member      1
 index    8 is prior ensemble member      2
 index   10 is prior ensemble member      3
 ...
 index  100 is prior ensemble member     48
 index  102 is prior ensemble member     49
 index  104 is prior ensemble member     50

 QC index           1  NCEP QC index
 QC index           2  DART quality control

 Processing obs        10000  of        84691
 Processing obs        20000  of        84691
 Processing obs        30000  of        84691
 Processing obs        40000  of        84691
 Processing obs        50000  of        84691
 Processing obs        60000  of        84691
 Processing obs        70000  of        84691
 Processing obs        80000  of        84691

 METAR_U_10_METER_WIND dimlen            1  is            9
 METAR_U_10_METER_WIND dimlen            2  is           50
 METAR_U_10_METER_WIND dimlen            3  is            3
 METAR_U_10_METER_WIND dimlen            4  is            1
 METAR_U_10_METER_WIND dimlen            5  is          221
 METAR_U_10_METER_WIND dimlen            6  is            1
 obs_seq_verify:  Finished successfully.

 --------------------------------------
 Finished ... at YYYY MM DD HH MM SS =
                 2011  3  1 10  3  7
 --------------------------------------

[thoar@mirage2 work]$ ncdump -h METAR_U_10_METER_WIND_forecast.nc
netcdf METAR_U_10_METER_WIND_forecast {
dimensions:
        analysisT = UNLIMITED ; // (1 currently)
        copy = 3 ;
        station = 221 ;
        level = 14 ;
        ensemble = 50 ;
        forecast_lead = 9 ;
        linelen = 129 ;
        nlines = 446 ;
        stringlength = 64 ;
        location = 3 ;
variables:
        char namelist(nlines, linelen) ;
                namelist:long_name = "input.nml contents" ;
        char CopyMetaData(copy, stringlength) ;
                CopyMetaData:long_name = "copy quantity names" ;
        double analysisT(analysisT) ;
                analysisT:long_name = "time of analysis" ;
                analysisT:units = "days since 1601-1-1" ;
                analysisT:calendar = "Gregorian" ;
                analysisT:missing_value = 0. ;
                analysisT:_FillValue = 0. ;
        int copy(copy) ;
                copy:long_name = "observation copy" ;
                copy:note1 = "1 == observation" ;
                copy:note2 = "2 == prior" ;
                copy:note3 = "3 == observation error variance" ;
                copy:explanation = "see CopyMetaData variable" ;
        int station(station) ;
                station:long_name = "station index" ;
        double level(level) ;
                level:long_name = "vertical level of observation" ;
        int ensemble(ensemble) ;
                ensemble:long_name = "ensemble member" ;
        int forecast_lead(forecast_lead) ;
                forecast_lead:long_name = "forecast lead time" ;
                forecast_lead:units = "seconds" ;
        double location(station, location) ;
                location:description = "location coordinates" ;
                location:location_type = "loc3Dsphere" ;
                location:long_name = "threed sphere locations: lon, lat, vertical" ;
                location:storage_order = "Lon Lat Vertical" ;
                location:units = "degrees degrees which_vert" ;
        int which_vert(station) ;
                which_vert:long_name = "vertical coordinate system code" ;
                which_vert:VERTISUNDEF = -2 ;
                which_vert:VERTISSURFACE = -1 ;
                which_vert:VERTISLEVEL = 1 ;
                which_vert:VERTISPRESSURE = 2 ;
                which_vert:VERTISHEIGHT = 3 ;
                which_vert:VERTISSCALEHEIGHT = 4 ;
        double METAR_U_10_METER_WIND(analysisT, station, level, copy, ensemble, forecast_lead) ;
                METAR_U_10_METER_WIND:long_name = "forecast variable quantities" ;
                METAR_U_10_METER_WIND:missing_value = -888888. ;
                METAR_U_10_METER_WIND:_FillValue = -888888. ;
        int original_qc(analysisT, station, forecast_lead) ;
                original_qc:long_name = "original QC value" ;
                original_qc:missing_value = -888888 ;
                original_qc:_FillValue = -888888 ;
        int dart_qc(analysisT, station, forecast_lead) ;
                dart_qc:long_name = "DART QC value" ;
                dart_qc:explanation1 = "1 == prior evaluated only" ;
                dart_qc:explanation2 = "4 == forward operator failed" ;
                dart_qc:missing_value = -888888 ;
                dart_qc:_FillValue = -888888 ;
// global attributes:
                :creation_date = "YYYY MM DD HH MM SS = 2011 03 01 10 03 00" ;
                :source = "$URL: https://svn-dares-dart.cgd.ucar.edu/DART/releases/Manhattan/assimilation_code/programs/obs_seq_verify/obs_seq_verify.html $" ;
                :revision = "$Revision: 11427 $" ;
                :revdate = "$Date: 2017-03-31 15:24:30 -0600 (Fri, 31 Mar 2017) $" ;
                :obs_seq_file_001 = "obs_seq.forecast.2008060818" ;
}
[thoar@mirage2 work]$

Discussion

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REFERENCES

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ERROR CODES and CONDITIONS

RoutineMessageComment
obs_seq_verify 'namelist: obtype_string (xxxx) is unknown. change input.nml' the requested observation type does not match any supported observation type. If it is spelled correctly, perhaps you need to rerun preprocess to build the appropriate obs_def_mod.modand obs_kind_mod.mod.
obs_seq_verify 'specify "obs_sequences" or "obs_sequence_list"' one of these namelist variables MUST be an empty string
obs_seq_verify 'xxxxxx ' is not a known observation type.' one of the obs_of_interest namelist entries specifies an observation type that is not supported. Perhaps you need to rerun preprocess with support for the observation, or perhaps it is spelled incorrectly. All DART observation types are strictly uppercase.
obs_seq_verify 'need at least 1 qc and 1 observation copy' an observation sequence does not have all the metadata necessary. Cannot use "obs_seq.in"-class sequences.
obs_seq_verify 'num_copies ##### does not match #####' ALL observation sequences must contain the same 'copy' information. At some point it may be possible to mix "obs_seq.out"-class sequences with "obs_seq.final"-class sequences, but this seems like it can wait.
obs_seq_verify 'No location had at least ### reporting times.' The input selection criteria did not result in any locations that had observations at all of the required verification times.
set_required_times 'namelist: forecast length is not a multiple of the verification interval' The namelist settings for forecast_length_[days,seconds] and verification_interval_seconds do not make sense. Refer to the forecast time diagram.
set_required_times 'namelist: last analysis time is not a multiple of the verification interval' The namelist settings for first_analysis and last_analysis are not separated by a multiple of verification_interval_seconds. Refer to the forecast time diagram.

KNOWN BUGS

none

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FUTURE PLANS

none

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Terms of Use

DART software - Copyright UCAR. This open source software is provided by UCAR, "as is", without charge, subject to all terms of use at http://www.image.ucar.edu/DAReS/DART/DART_download

Contact: Tim Hoar
Revision: $Revision: 11427 $
Source: $URL: https://svn-dares-dart.cgd.ucar.edu/DART/releases/Manhattan/assimilation_code/programs/obs_seq_verify/obs_seq_verify.html $
Change Date: $Date: 2017-03-31 15:24:30 -0600 (Fri, 31 Mar 2017) $
Change history:  try "svn log" or "svn diff"