# GEOS-Chem restart files¶

## How are restart files read into GEOS-Chem?¶

GEOS-Chem restart files are read via HEMCO. The entries listed below have been added to HEMCO_Config.rc (and may vary slightly for different simulation types). These fields are obtained from HEMCO and copied to the appropriate State_Chm and State_Met fields in routine Get_GC_Restart (located in GeosCore/hcoi_gc_main_mod.F90).

#==============================================================================
# --- GEOS-Chem restart file ---
#==============================================================================
(((GC_RESTART
* SPC_           ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesRst_?ALL?$YYYY/$MM/$DD/$HH EFYO xyz 1 * - 1 1 * DELPDRY ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_DELPDRY         $YYYY/$MM/$DD/$HH EY   xyz 1 * - 1 1
* KPP_HVALUE     ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_KPPHvalue$YYYY/$MM/$DD/$HH EY xyz 1 * - 1 1 * WETDEP_N ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_WetDepNitrogen $YYYY/$MM/$DD/$HH EY   xy  1 * - 1 1
* DRYDEP_N       ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_DryDepNitrogen$YYYY/$MM/$DD/$HH EY xy 1 * - 1 1 * SO2_AFTERCHEM ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_SO2AfterChem   $YYYY/$MM/$DD/$HH EY   xyz 1 * - 1 1
* H2O2_AFTERCHEM ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_H2O2AfterChem$YYYY/$MM/$DD/$HH EY xyz 1 * - 1 1 * AEROH2O_SNA ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_AeroH2OSNA     $YYYY/$MM/$DD/$HH EY   xyz 1 * - 1 1
* ORVCSESQ       ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_ORVCSESQ$YYYY/$MM/$DD/$HH EY xyz 1 * - 1 1 * JOH ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_JOH            $YYYY/$MM/$DD/$HH EY   xy  1 * - 1 1
* JNO2           ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_JNO2$YYYY/$MM/$DD/$HH EY xy 1 * - 1 1 * STATE_PSC ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_StatePSC       $YYYY/$MM/$DD/$HH EY   xyz count * - 1 1
)))GC_RESTART


GEOS-Chem species (the SPC_ entry) use HEMCO time cycle flag EFYO by default. Other restart file fields use the time cycle flag EY. These are explained below.

E

Exact: Stops with an error if the date of the simulation is different than the file timestamp.

F

Forced: Stops with an error if the file isn’t found.

Y

Simulation Year: Only reads the data for the simulation year but not for other years.

O

Once: Does not keep cycling in time but only reads the file once.

When reading the species concentrations (time cycle flag: EFYO) from the restart file, HEMCO will cause your simulation to stop with an error if:

1. The restart file is missing, or;

3. The date in the restart file (which is usually 20190101 or 20190701, depending on your simulation) differs from the start date listed in geoschem_config.yml.

When reading other restart file fields (time cycle flag: EY). HEMCO will

1. The restart file is missing, or

2. The date in the restart file (which is usually 20190101 or 20190701, depending on your simulation) differs from the start date listed in geoschem_config.yml.

Attention

If you wish to spin up a GEOS-Chem simulation with a restart file that has (1) missing species or (2) a timestamp that does not match the start date in geoschem_config.yml, simply change the time cycle flag from

* SPC_ ... $YYYY/$MM/$DD/$HH EFYO xyz 1 * - 1 1


to

* SPC_ ... $YYYY/$MM/$DD/$HH CYS xyz 1 * - 1 1


This will direct HEMCO to read the closest date available (C), to use the simulation year (Y), and to skip any species (S) not found in the restart file.

Skipped species will be assigned the initial concentration (units: $$mol\ mol^{-1}$$ w/r/t dry air) specified by its BackgroundVV entry in species_database.yml. If the species does not have a BackgroundVV value specified, then its initial concentration will be set to $$1.0{\times}10^{-20}$$ instead.

## How can I determine the date of a restart file?¶

To determine the date of a netCDF restart file, you may use ncdump. For example:

ncdump -v time -t GEOSChem.Restart.YYYYMMDD_hhmmz.nc4


The -t option will return the time value in human-readable date-time strings rather than numerical values in unit such as "hours since 1985-1-1 00:00:0.0.

## Where can I get a restart file for my simulation?¶

GEOS-Chem Classic run directories are configured to use sample GEOS-Chem restart files in netCDF format. These files are available for download at: http://geoschemdata.wustl.edu/ExtData/GEOSCHEM_RESTARTS/.

Tip

We recommend that you download restart files to your disk space with either a dry-run simulation or with the bashdatacatalog. This will ensure that the proper files will be downloaded.

If you have the ExtData/GEOSCHEM_RESTARTS folder in your GEOS-Chem data paths, then a sample restart file will be copied to your run directory when you generate a new GEOS-Chem classic run directory.

Monthly GEOS-Chem restart files from the GEOS-Chem 13.0.0 10-year benchmark may be found at http://ftp.as.harvard.edu/gcgrid/geos-chem/10yr_benchmarks/13.0.0/GCClassic/restarts. We will also add restart files from the 14.0.0 10-year benchmark simulation shortly.

Attention

The sample restart files do not reflect the actual atmospheric state and should only be used to “spin up” the model. In other words, they should be used as initial values in an initialization simulation to generate more accurate initial conditions for your production runs.

## For how long should I spin up before starting a production simulation?¶

Doing a 6-month year spin up is usually sufficient for full-chemistry simulations. We recommend ten years for ozone, carbon dioxide, and methane simulations, and four years for radon-lead-beryllium simulations. If you are in doubt about how long your spin up should be for your simulation, we recommend contacting the GEOS-Chem Working Group that specializes in your area of research.

You may spin up the model starting at any year for which there is met data, but you should always start your simulations at the month and day corresponding to the restart file to more accurately capture seasonal variation. If you want to start your production run at a specific date, we recommend doing a spin up for the appropriate number of years plus the number of days needed to reach your ultimate start date. For example, if you want to do a production simulation starting on 12/1/13, you could spin up the model for one year using the initial GEOS-FP restart file dated 7/1/13 and then use the new restart file to spin up the model for five additional months, from 7/1/13 to 12/1/13.

See also this discussion on our Github page for further guidance: https://github.com/geoschem/geos-chem/discussions/911.

## How do I check my initial conditions?¶

To ensure you are using the expected initial conditions for your simulation, please check the GEOS-Chem log file. You should see something like:

HEMCO: Opening ./GEOSChem.Restart.20190701_0000z.nc4
- Found all CN     met fields for 2011/01/01 00:00
- Found all A1     met fields for 2019/07/01 00:30
- Found all A3cld  met fields for 2019/07/01 01:30
- Found all A3dyn  met fields for 2019/07/01 01:30
- Found all A3mstC met fields for 2019/07/01 01:30
- Found all A3mstE met fields for 2019/07/01 01:30
- Found all I3     met fields for 2019/07/01 00:00
Initialize TMPU1    from restart file
Initialize SPHU1    from restart file
Initialize PS1_WET  from restart file
Initialize PS1_DRY  from restart file
Initialize DELP_DRY from restart file
- Found all I3     met fields for 2019/07/01 03:00
===============================================================================
R E S T A R T   F I L E   I N P U T
Min and Max of each species in restart file [mol/mol]:
Species   1,     ACET: Min = 1.000458833E-22  Max = 6.680149323E-09
Species   2,     ACTA: Min = 6.574137699E-23  Max = 6.108235029E-10
Species   3,     AERI: Min = 4.122849756E-16  Max = 1.213838925E-11
Species   4,     ALD2: Min = 4.186668786E-23  Max = 4.571487633E-09
...


If a species is not found in the restart file, you may see something like:

Species 178,       pFe: Use background = 9.999999683E-21


## How are GEOS-Chem restart files written?¶

GEOS-Chem restart files are now saved via the History component. A Restart collection has been defined in HISTORY.rc and fields saved out to the restart file can be modified in that file.

For more information, please see our documentation about the Restart collection in GEOS-Chem History diagnostics. This documentation is currently on the GEOS-Chem wiki, but will be ported to ReadTheDocs in the near future.