GEOS-Chem output files

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This page contains information about files produced by GEOS-Chem simulations, including diagnostic data and restart files used for initial conditions. For information about the input files that ship with the GEOS-Chem run directories, please see our GEOS-Chem Input Files wiki page.

List of files created by GEOS-Chem

Each time you compile and run GEOS-Chem, several files are written in the GEOS-Chem run directory. The table below provides a comprehensive list of all GEOS-Chem output files:

NOTE: Several of the files listed in the tables below (e.g. log files and diagnostic output files) contain the .mp or .sp suffix:
  • .mp ("multi-processor") denotes GEOS-Chem was compiled with OpenMP parallelization.
  • .sp ("single-processor") denotes that GEOS-Chem was compiled without OpenMP parallelization.
  • The .mp or .sp suffixes are typically applied upon successful completion of a GEOS-Chem simulation. If a GEOS-Chem simulation dies prematurely, certain files might lack the .mp or .sp suffix.

Log files

File(s) Format Description Notes
lastbuild.mp or
lastbuild.sp 		Text The lastbuild file. Contains a summary of all of the options that were used to build the GEOS-Chem executable. This file is created each time you compile GEOS-Chem. Please include this file when submitting a GEOS-Chem support request.
GC_*.log or
GC_*.log.mp or
GC_*.log.sp 		Text The GEOS-Chem log file. Contains an "echo-back" of all input options that were specified in input.geos, the list of diagnostic quantities that are being archived, the list of files that are being read, and information about the operations that are being done at each GEOS-Chem timestep. If you run dies with an error, a detailed error message should be printed here. Please include this file when submitting a GEOS-Chem support request.
HEMCO.log or
HEMCO.log.mp or
HEMCO.log.sp 		Text The HEMCO log file. Contains information about how emissions, met fields, and other relevant data are read from disk and processed by HEMCO for input into GEOS-Chem. Please include this file when submitting a GEOS-Chem support request.
slurm-JOBID.out Text The job output file. If you used a batch scheduler such as SLURM, PBS, LSF, etc. to submit your GEOS-Chem simulation, then output from the Unix stdout and/or stderr streams may be printed to this file. This file may contain important error messages. Please include this file when submitting a GEOS-Chem support request.

--Bob Yantosca (talk) 16:19, 30 November 2018 (UTC)

Restart files

File(s) Format Description Notes
GEOSChem.Restart.YYYYMMDD_hhmmz.nc4 netCDF The GEOS-Chem restart file. Contains species concentrations that are read in at simulation startup.

GEOS-Chem writes a restart file at the end of each simulation. This allows a long simulation to be split into several individal run stages..

For example, the restart file that was created at 00:00 UTC on August 1, 2016 is named: GEOSChem.Restart.20160801_0000z.nc4. The z indicates "Zulu" or "Z" time, which is another name for UTC.

For more information, please see our GEOS-Chem restart files wiki page.

HEMCO_restart.YYYYMMDDhhmm.nc netCDF The HEMCO restart file. The HEMCO emissions component will save out certain quantities (mostly pertaining to soil NOx and biogenic emissions) in order to facilitate long GEOS-Chem simulations with several run stages.

Diagnostic output files

File(s) Format Description Notes
GEOSChem.*.YYYYMMDD_hhmmz.nc4 netCDF GEOS-Chem netCDF diagnostic (aka "History") output. NetCDF files containing diagnostic output from GEOS-Chem, for each of the various diagnostic collections. The data may be either time-averaged or instantaneous. You can specify which collections to archive in the HISTORY.rc input file. Available in GEOS-Chem 12
HEMCO_diagnostics.YYYYMMDDhhmm NetCDF HEMCO diagnostic files. Files containing diagnostic quantities that are archived directly by the HEMCO emissions component.
GEOSChem.ObsPack.YYYYMMDD_hhmmz.nc4 NetCDF ObsPack diagnostic files. Files containing diagnostic quantities that are archived directly by the optional ObsPack diagnostic. Available in GEOS-Chem 12.2.0 and later versions
trac_avg.{met}_{grid}_{sim}.YYYYMMDDhh BPCH GEOS-Chem "binary punch" (aka "bpch") diagnostic data. For several years, this was the standard file format for GEOS-Chem diagnostics. We will soon retire the bpch file format in favor of netCDF diagnostics.
plane.log.YYYYMMDD Text File containing from the GEOS-Chem plane-flight diagnostic output.
stations.YYYYMMDDhh BPCH Diagnostic output file that contains ND48 station timeseries output as specified in input.geos. We will soon retire the bpch file format in favor of netCDF diagnostics.
tsYYYYMMDDhh.bpch BPCH Diagnostic output file that contains ND49 instantaneous timeseries output as specified in input.geos. We will soon retire the bpch file format in favor of netCDF diagnostics.
ts_24hr_avg.YYYYMMDDhh.bpch BPCH Diagnostic output file that contains ND50 24-hour average timeseries output as specified in input.geos. We will soon retire the bpch file format in favor of netCDF diagnostics.
ts_satellite.YYYYMMDDhh.bpch BPCH Diagnostic output file that contains ND51 local-time-average (satellite) timeseries output as specified in input.geos. We will soon retire the bpch file format in favor of netCDF diagnostics.
paranox_ts.YYYYMMDDhh.bpch BPCH Diagnostic output file that contains ND63 ship timeseries output as specified in input.geos. We will soon retire the bpch file format in favor of netCDF diagnostics.
diaginfo.dat and tracerinfo.dat Text Contains metadata used by GAMAP to read data in binary punch format.ostic output file that contains We will soon retire the bpch file format in favor of netCDF diagnostics.

--Bob Yantosca (talk) 17:23, 11 January 2019 (UTC)

Output files created by GCHP

Please see the GCHP Output Data wiki page for information about GCHP output.

--Lizzie Lundgren (talk) 18:38, 10 May 2019 (UTC)

In-depth descriptions of GEOS-Chem output files

diaginfo.dat and tracerinfo.dat files

NOTE: For the time being, you can still archive diagnostics to binary punch (aka bpch) file format in GEOS-Chem 12. But note that the bpch output will be removed in a future GEOS-Chem version.

The metadata for GEOS-Chem diagnostics in binary punch format is stored in two different text files: diaginfo.dat and tracerinfo.dat. Please see Chapter 7 of The GAMAP User's Guide for more information about these files.

--Bob Yantosca (talk) 17:22, 30 November 2018 (UTC)

GEOS-Chem binary punch diagnostic files

NOTE: For the time being, you can still archive diagnostics to binary punch (aka bpch) file format in GEOS-Chem 12. But note that the bpch output will be removed in a future GEOS-Chem version.

For a complete description of all available GEOS-Chem diagnostics in binary punch format, please see our List of diagnostics archived to bpch format wiki page.

--Bob Yantosca (talk) 17:08, 30 November 2018 (UTC)

GEOS-Chem netCDF diagnostic files

For a complete description of netCDF diagnostic collections that are available via the GEOS-Chem History Component, please see our List of diagnostics archived to netCDF format wiki page.

--Bob Yantosca (talk) 17:40, 11 January 2019 (UTC)

GEOS-Chem log file

The GEOS-Chem log file contains an "echo-back" of all input options, as well as a list of files that are being read in, and operations that are being done at each timestep. Here is an example log file from a recent 1-month benchmark simulation: 

*************   S T A R T I N G   4 x 5   G E O S - C H E M   *************

===> Mode of operation         : GEOS-Chem "Classic"
===> GEOS-Chem version         : 12.1.0
===> Compiler                  : Intel Fortran Compiler (aka ifort)
===> Driven by meteorology     : GMAO GEOS-FP (on native 72-layer vertical grid)
===> ISORROPIA ATE package     : ON
===> Parallelization w/ OpenMP : ON
===> Binary punch diagnostics  : ON
===> netCDF diagnostics        : ON
===> netCDF file compression   : SUPPORTED

===> SIMULATION START TIME: 2018/11/21 10:38 <=== 

===============================================================================
G E O S - C H E M   U S E R   I N P U T 

READ_INPUT_FILE: Reading input.geos

SIMULATION MENU
---------------
Start time of run           : 20160701 000000
End time of run             : 20160801 000000
Run directory               : ./
Data Directory              : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/
CHEM_INPUTS directory       : /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/CHEM_INPUTS/
Resolution-specific dir     : GEOS_4x5/
Is this a nested-grid sim?  :     F
Global offsets I0, J0       :     0    0

TIMESTEP MENU
---------------
Transport/Convection [sec]  :   600
Chemistry/Emissions  [sec]  :  1200 

... etc ...

If your simulation stopped with an error, a detailed error message should also appear in the GEOS-Chem log file.

--Bob Yantosca (talk) 17:13, 30 November 2018 (UTC)

GEOS-Chem plane-flight diagnostic output

Please see our Planeflight diagnostic wiki page for more information about the input and output file formats used by the GEOS-Chem plane-flight diagnostic.

--Bob Yantosca (talk) 17:38, 30 November 2018 (UTC)

ObsPack diagnostic output

In GEOS-Chem 12.2.0 and later, you can use the optional ObsPack diagnostic to archive GEOS-Chem quantities at specified coordinates (e.g. lon/lat/alt) to netCDF files. You might find ObsPack useful if you need to get GEOS-Chem output for locations where you have either station data or flight track data.

For more information about the ObsPack file structure, please follow this link.

--Bob Yantosca (talk) 17:46, 11 January 2019 (UTC)

GEOS-Chem restart files

Please see our GEOS-Chem restart files wiki page for more information.

--Bob Yantosca (talk) 17:08, 30 November 2018 (UTC)

HEMCO diagnostic output files

Pease see the Diagnostics section of The HEMCO User's Guide for more information.

--Bob Yantosca (talk) 17:08, 30 November 2018 (UTC)

HEMCO log file

The HEMCO emissions component also produces a log file, which is named HEMCO.log. The HEMCO log file contains information about how emissions, met fields, and other relevant data are read from disk and processed for input into GEOS-Chem.

(NOTE: When your simulation finishes successfully, the HEMCO.log file is automatically renamed to either HEMCO.log.mp (if OpenMP parallelization is turned on) or HEMCO.log.sp (if OpenMP parallelization is turned off). But if your run dies with an error, the HEMCO log file will not have been renamed.)

Here is a sample HEMCO.log file from a recent 1-month benchmark simulation (edited for brevity): 

-------------------------------------------------------------------------------
Using HEMCO v2.1.010    
-------------------------------------------------------------------------------
Registering HEMCO species:
Species NO
Species O3
Species PAN
Species CO
... etc ...

-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Use air-sea flux emissions (extension module)
   - Use species:
    - DMS          25
    - ACET           9
    - ALD2          11
-------------------------------------------------------------------------------
Use ParaNOx ship emissions (extension module)
    - Use the following species: (MW, emitted as HEMCO ID)
     NO  : 30.00    1
     NO2 : 46.00   64
     O3  : 48.00    2
     HNO3: 63.00    7
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_02ms.nc
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_06ms.nc
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_10ms.nc
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_14ms.nc
READ_LUT_NCFILE: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/PARANOX/v2015-02/ship_plume_lut_18ms.nc
-------------------------------------------------------------------------------
Use lightning NOx emissions (extension module)
  - Use species NO->           1
  - Use OTD-LIS factors from file?  T
  - Use GEOS-5 flash rates:  F
  - Use scalar scale factor:    1.000000
  - Use gridded scale field: none
     - INIT_LIGHTNOX: Reading /n/holylfs/EXTERNAL_REPOS/GEOS-CHEM/gcgrid/data/ExtData/HEMCO/LIGHTNOX/v2014-07/light_dist.ott2010.dat
-------------------------------------------------------------------------------
Use soil NOx emissions (extension module)
    - NOx species            : NO           1
    - NOx scale factor       :    1.000000
    - NOx scale field        : none
    - Use fertilizer NOx     :  T
    - Fertilizer scale factor:   6.800000090152025E-003
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Use DEAD dust emissions (extension module)
Use the following species (Name: HcoID):
 DST1:          38
 DST2:          39
 DST3:          40
 DST4:          41
 Global mass flux tuning factor:   8.328599999999999E-004
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Use sea salt aerosol emissions (extension module)
 Accumulation aerosol: SALA:          42
  - size range       :   1.000000000000000E-002  0.500000000000000
  Coarse aerosol      : SALC:          43
  - size range       :   1.000000000000000E-002  0.500000000000000
  - wind scale factor:    1.00000000000000
-------------------------------------------------------------------------------
Use MEGAN biogenic emissions (extension module)
-------------------------------------------------------------------------------
  - This is instance            1
 - Use the following species:
    Isoprene   = ISOP           6
    Acetone    = ACET           9
    C3 Alkenes = PRPE          18
    Ethene     = C2H4          -1
    ALD2       = ALD2          11
    EOH        = EOH          96
  SOA-Precursor = SOAP          94
  SOA-Simple  = SOAS          95
  --> Isoprene scale factor is    1.00000000000000
  --> Use CO2 inhibition on isoprene option  T
  --> Global atmospheric CO2 concentration :    390.000000000000       ppmv
  --> Normalize LAI by PFT:  T
 - MEGAN monoterpene option enabled
    CO         = CO           4
      a-,b-pinene    = MTPA          70
      Other monoterp.= MTPO          72
      Limonene       = LIMO          71
      Sesquiterpenes = SESQ         184
-------------------------------------------------------------------------------
Use GFED extension
    - Use GFED-4              :  T
    - Use daily scale factors :  F
    - Use hourly scale factors:  F
    - Hydrophilic OC fraction :   0.5000000
    - Hydrophilic BC fraction :   0.2000000
    - POG1 fraction           :   0.4900000
    - SOAP fraction           :   1.3000000E-02
   - Emit GFED species NO     as model species NO
      --> Will use scale factor:    1.000000
      --> Will use scale field : none
   - Emit GFED species CO     as model species CO
      --> Will use scale factor:    1.050000
     --> Will use scale field : none
   ... etc...
 
-------------------------------------------------------------------------------
HEMCO v2.1.010 FINISHED.
Warnings (level 1 or lower):  25386
-------------------------------------------------------------------------------

For more information, please see The HEMCO User's Guide.

--Bob Yantosca (talk) 17:24, 30 November 2018 (UTC)

HEMCO restart files

Pease see the Restart variables section of The HEMCO User's Guide for more information.

--Bob Yantosca (talk) 17:08, 30 November 2018 (UTC)

The lastbuild file

The GEOS-Chem "Classic" compilation sequence generates a file that contains all of the options that were used to build the executable file. This file is named either lastbuild.mp (if OpenMP parallelization is turned on) or lastbuild.sp (if OpenMp parallelization is turned off).

Here is a sample lastbuild.mp file from a recent 1-month benchmark simulation: 

LAST BUILD INFORMATION:
  CODE_DIR     : /n/home05/msulprizio/GC/Code.Dev
  CODE_BRANCH  : dev/12.1.0 
  LAST_COMMIT  : Revert to reading I3 met fields each hour instead of once per day 
  COMMIT_DATE  : Wed Nov 21 09:07:51 2018 -0500 
  VERSION      : 12.1.0
  VERSION_TAG  : GC_12.1.0
  MET          : geosfp
  GRID         : 4x5
  SIM          : benchmark
  NEST         : n
  TRACEBACK    : y
  BOUNDS       : n
  DEBUG        : n
  FPE          : n
  NO_ISO       : n
  NO_REDUCED   : y
  CHEM         : Standard
  TOMAS12      : n
  TOMAS15      : n
  TOMAS30      : n
  TOMAS40      : n
  RRTMG        : n
  MASSCONS     : n
  TIMERS       : 1
  TAU_PROF     : n
  BPCH_DIAG    : y
  NC_DIAG      : y
  COMPILER     : ifort 17.0.4
  Datetime     : 2018/11/21 10:33

The GEOS-Chem Support Team will need to see the following fields of the lastbuild file in order to assist you in resolving bugs or technical issues that you might encounter.

Item Description
LAST_COMMIT The location (aka "commit") of your source code in the Git version history. (You can use the gitk browser to view the Git version history.)
VERSION The GEOS-Chem version number.
MET The meteorology that is driving GEOS-Chem (e.g. geosfp, merra2).
GRID The horizontal grid (e.g. 4° x 5° , 2° x 2.5°, 0.25° x 0.3125°, 0.5° x 0.625°) that your simulation uses.
SIM The name of your GEOS-Chem simulation (e.g. Standard, Benchmark, CH4, Rn-Pb-Be, Hg, etc.).
NEST The nested region that your simulation uses (e.g. as, af, ch, na, eu, etc.). This only applies to nested-grid simulations.
COMPILER The compiler version that you used to build the GEOS-Chem executable file.

--Bob Yantosca (talk) 17:09, 30 November 2018 (UTC)

Previous issues that are now resolved

Enable compression in netCDF-4 output files

This update was included in v11-02a (approved 12 May 2017).

For more information about this issue, please see this post on our The NcdfUtilities package wiki page.

--Bob Yantosca (talk) 17:50, 24 May 2018 (UTC)

Improve write speed of netCDF output files

This update was included in GEOS-Chem v11-01 public release

For more information about this issue, please see this post on our The NcdfUtilities package wiki page.

--Bob Yantosca (talk) 19:05, 8 March 2017 (UTC)

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