GEOS-Chem restart files
This page contains information about files produced by GEOS-Chem simulations, including diagnostic data and restart files used for initial conditions. For information the input files that ship with the GEOS-Chem run directories, please see our GEOS-Chem Input Files wiki page.
Contents
- 1 File Formats
- 2 GEOS-Chem 12
- 3 GEOS-Chem v11-01
- 4 Previous issues that are now resolved
- 5 Obsolete information
File Formats
Binary Punch File Format
In GEOS-Chem v10-01 and earlier versions, the GEOS-Chem diagnostic output and restart files are in "binary punch" format. These binary punch files may be viewed and manipulated with the IDL-based data visualization package GAMAP which is maintained and supported by the GEOS-Chem Support Team. Several users have also developed Python software packages for reading, visualizing, and processing GEOS-Chem binary punch files.
Binary punch file format will be phased out beginning with GEOS-Chem v11-01. Default reading and writing NetCDF restart files for all simulations except mercury will be introduced in v11-01f, as described in the next section. Temporarily, users may choose to use a binary punch input restart file by specifying BPCH_RST_IN=y at compile time. Similarly, users may opt to output restart files in binary punch format by specifying compile option BPCH_RST_OUT=y. Diagnostic output will remain in binary punch format in v11-01f, automatically setting BPCH_DIAG=y at compile time.
NetCDF File Format
The HEMCO emissions component contains utility functions and linked-list objects to save diagnostic output (time-averaged or instantaneous) as well as end-of-run restart information to netCDF files. In v10-01, this feature is used only for emissions-related data. The GEOS-Chem Support Team is currently leveraging HEMCO’s I/O capabilities to replace all binary punch input/output with netCDF within GEOS-Chem v11-01. This work has started in v11-01f and will continue into future internal versions.
Migrating to netCDF format will bring the following benefits:
- Using HEMCO’s diagnostic archival functions will ensure that all quantities will be archived consistently throughout GEOS-Chem.
- Use of netCDF output will facilitate further GEOS-Chem High Performance development since binary files cannot be written efficiently in high-performance computing (HPC) environments.
- GEOS-Chem users will have more options for visualizing GEOS-Chem output since many free and open-source software packages (e.g. Python tools) are compatible with netCDF format.
Viewing and manipulating netCDF files
There are many free and open-source software packages readily available for visualizing and manipulating netCDF files. These tools will reduce the need for the GEOS-Chem user community to rely on IDL (and GAMAP), which can be prohibitively expensive for some user groups. Some recommend tools are listed below.
- 1. ncdump: This command-line tool generates a text representation of netCDF data and can be used to quickly view the variables contained in a netCDF file. For example:
# Display header information (dimensions, variables, attributes) only
ncdump -h GEOSChem_restart.201308010000 | less
# Display header information followed by data values for variable(s) specified
ncdump -v SPC_NO GEOSChem_restart.201308010000 | less
- 2. ncview: Visualization package for netCDF files, recommended for a quick and easy look at netCDF files.
- 3. Panoply: Data viewer for netCDF files. This package offers an alternative to ncview. From our experience, Panoply works nicely when installed on the desktop, but is slow to respond in the Linux environment.
- 5. Other programming languages may be used for viewing or manipulating netCDF files, including but not limited to:
Some of the tools listed above, such as ncdump and ncview, may come pre-installed on your system. Others like NCO, CDO, and Panoply may need to be installed or loaded (e.g. via the module load command). Check with your system administrator or IT staff to see what is available on your system.
--Melissa Sulprizio (talk) 15:58, 17 January 2017 (UTC)
Regridding netCDF restart files
The same netCDF tools listed above can also be used to regrid netCDF restart files produced by GEOS-Chem.
- 1. CDO: The Climate Data Operators include tools for regridding netCDF files. For example, the following command will apply distance-weighted regridding:
cdo remapdis,gridfile infile.nc outfile.nc
- For gridfile, you can use the files in ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/grids/. See the Interpolation section in the CDO Guide for more information.
Bram Maasakkers wrote:
- I have noticed a problem regridding a 4x5 restart file to 2x2.5 using cdo 1.9.4. When I use:
cdo remapdis,geos.2x25.grid GEOSChem_restart.200901010000.nc GEOSChem_restart.2009_2x25.nc
- The last latitudinal band (-89.5) remains empty and gets filled with the standard missing value of cdo, which is really large. This leads to immediate problems in the methane simulation as enormous concentrations enter the domain from the South Pole. For now I’ve solved this problem by just using bicubic interpolation:
cdo remapbic,geos.2x25.grid GEOSChem_restart.200901010000.nc GEOSChem_restart.2009_2x25_bicub.nc
- 2. NCO: The netCDF Operators also include tools for regridding. See the Regridding section of the NCO User Guide for more information.
- 3. Jenny Fisher provided an IDL script regridh_restart_nc.pro which is now included with GAMAP. Jenny wrote:
The one caveat that I cannot figure out is something weird with the units. I have done this in such a way that it reads in whatever attributes (including units) are in the original file and writes the same units back to the regridded file. But when GEOS-Chem reads the new file it gives an “incompatible units” error — although printing them in the code shows something identical to what the case statement is searching for, as far as I can tell. If I use ncatted to overwrite the units (with identical name) they are fine. So it must be something to do with the way IDL encodes the units string, but I have no idea what. The relevant nco command is ncatted -O -a units,,m,c,"mol mol-1" INFILENAME.nc
- 4. Regridding routines written in NCL are also available in the NCL4GC package available on Bitbucket.
--Melissa Sulprizio (talk) 22:06, 19 January 2017 (UTC)
Creating a netCDF restart file or adding new species to a netCDF restart file
You have a few options for adding new species to a netCDF restart file:
- 1. In GEOS-Chem v11-01, if the model cannot find a species in the netCDF restart file, it should set the initial concentration to the background concentration. The default background concentration is 1e-20 v/v. If you want to change that to a different value, you can add BackgroundVV = {VALUE}_fp to the call to Spc_Create for that species in Headers/species_database_mod.F90. To confirm your species is getting set to the background value you can turn on ND70 debug output, which will print the initial species concentrations (min/max) read from the restart file to the log file. At the end of your simulation, a new restart file will be saved out with the new species included. We recommend spinning up GEOS-Chem for an appropriate duration to achieve reasonable concentrations for the new species.
- 2. You can use CDO and NCO to copy the restart field for one species to a new species. For example:
module load nco module load cdo # Extract field SPC_PMN from the original restart file cdo selvar,SPC_PMN initial_GEOSChem_rst.4x5_standard.nc GEOSChem_restart.PMN.nc # Rename selected field to SPC_NPMN ncrename -h -v SPC_PMN,SPC_NPMN GEOSChem_restart.PMN.nc GEOSChem_restart.NPMN.nc # Append new species to existing restart file ncks -h -A -M GEOSChem_restart.NPMN.nc initial_GEOSChem_rst.4x5_standard.nc
- 3. Sal Farina wrote a simple Python script for adding a new species to the netCDF restart file:
#!/usr/bin/env python
import netCDF4 as nc
import sys
import os
for nam in sys.argv[1:]:
f = nc.Dataset(nam,mode='a')
try:
o = f['SPC_OCPI']
except:
print "SPC_OCPI not defined"
f.createVariable('SPC_SOAP',o.datatype,dimensions=o.dimensions,fill_value=o._FillValue)
soap = f['SPC_SOAP']
soap[:] = 0.0
soap.long_name= 'SOAP tracer'
soap.units = o.units
soap.add_offset = 0.0
soap.scale_factor = 1.0
soap.missing_value = 1.0e30
f.close()
--Melissa Sulprizio (talk) 23:33, 7 November 2017 (UTC)
Cropping netCDF restart files to nested domains
If needed, regrid a coarse netCDF restart file to the nested grid resolution using GAMAP routine regridh_restart_nc.pro.
Cropping netCDF files can be easily achieved with tools such as CDO or NCO. For example, CDO has a SELBOX operator for selecting a box by specifying the lat/lon bounds:
cdo sellonlatbox,lon1,lon2,lat1,lat2 infile outfile
See page 44 of the CDO guide for more information.
--Melissa Sulprizio (talk) 19:04, 3 May 2017 (UTC)
Vertical coordinates in netCDF files produced by GEOS-Chem
All netCDF files produced by GEOS-Chem (i.e. diagnostic files and restart files) adhere to the the COARDS netCDF convention for the lon, lat, and time dimensions.
For the vertical dimension, we have chosen to use the following coordinate variables, emulating the file format of the NCAR Community Earth System Model (CESM):
variables:
double lev(lev) ;
lev:long_name = "hybrid level at midpoints (1000*(A+B))" ;
lev:units = "level" ;
lev:positive = "down" ;\
lev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
lev:formula_terms = "a: hyam b: hybm p0: P0 ps: PS" ;
double hyam(lev) ;
hyam:long_name = "hybrid A coefficient at layer midpoints" ;
double hybm(lev) ;
hybm:long_name = "hybrid B coefficient at layer midpoints" ;
double ilev(ilev) ;
ilev:long_name = "hybrid level at interfaces (1000*(A+B))" ;
ilev:units = "level" ;
ilev:positive = "down" ;
ilev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
ilev:formula_terms = "a: hyai b: hybi p0: P0 ps: PS" ;
double hyai(ilev) ;
hyai:long_name = "hybrid A coefficient at layer interfaces" ;
double hybi(ilev) ;
hybi:long_name = "hybrid B coefficient at layer interfaces" ;
double P0 ;
P0:long_name = "reference pressure" ;
The lev variable is used for data that is placed on the midpoints between vertical levels. This is an "approximate" eta coordinate, which is close to 1 at the surface and close to zero at the atmosphere top.
lev = 0.99250002413, 0.97749990013, 0.962499776, 0.947499955, 0.93250006,
0.91749991, 0.90249991, 0.88749996, 0.87249996, 0.85750006, 0.842500125,
0.82750016, 0.8100002, 0.78750002, 0.762499965, 0.737500105, 0.7125001,
0.6875001, 0.65625015, 0.6187502, 0.58125015, 0.5437501, 0.5062501,
0.4687501, 0.4312501, 0.3937501, 0.3562501, 0.31279158, 0.26647905,
0.2265135325, 0.192541016587707, 0.163661504087706, 0.139115, 0.11825,
0.10051436, 0.085439015, 0.07255786, 0.06149566, 0.05201591, 0.04390966,
0.03699271, 0.03108891, 0.02604911, 0.021761005, 0.01812435, 0.01505025,
0.01246015, 0.010284921, 0.008456392, 0.0069183215, 0.005631801,
0.004561686, 0.003676501, 0.002948321, 0.0023525905, 0.00186788,
0.00147565, 0.001159975, 0.00090728705, 0.0007059566, 0.0005462926,
0.0004204236, 0.0003217836, 0.00024493755, 0.000185422, 0.000139599,
0.00010452401, 7.7672515e-05, 5.679251e-05, 4.0142505e-05, 2.635e-05,
1.5e-05 ;
The lev variable may be used for quick plotting. To compute the actual pressure at the midpoint of the grid box (I,J,L), you will need to supply your own 2-D surface pressure field (e.g. saved from another diagnostic file):
Pmid = ( hyam(L) * PS(I,J) ) + hybm(L)
The ilev variable is used for data that is placed on vertical level edges or "interfaces" (hence the "i" in ilev). This is also an "approximate" eta coordinate.
ilev = 1, 0.98500004826, 0.969999752, 0.9549998, 0.94000011, 0.92500001,
0.90999981, 0.89500001, 0.87999991, 0.86500001, 0.85000011, 0.83500014,
0.82000018, 0.80000022, 0.77499982, 0.75000011, 0.7250001, 0.7000001,
0.6750001, 0.6375002, 0.6000002, 0.5625001, 0.5250001, 0.4875001,
0.4500001, 0.4125001, 0.3750001, 0.3375001, 0.28808306, 0.24487504,
0.208152025, 0.176930008175413, 0.150393, 0.127837, 0.108663, 0.09236572,
0.07851231, 0.06660341, 0.05638791, 0.04764391, 0.04017541, 0.03381001,
0.02836781, 0.02373041, 0.0197916, 0.0164571, 0.0136434, 0.0112769,
0.009292942, 0.007619842, 0.006216801, 0.005046801, 0.004076571,
0.003276431, 0.002620211, 0.00208497, 0.00165079, 0.00130051, 0.00101944,
0.0007951341, 0.0006167791, 0.0004758061, 0.0003650411, 0.0002785261,
0.000211349, 0.000159495, 0.000119703, 8.934502e-05, 6.600001e-05,
4.758501e-05, 3.27e-05, 2e-05, 1e-05 ;
To compute the actual pressure at the bottom and top edges of the grid box (I,J,L), you will need to supply your own 2-D surface pressure field (e.g. saved from another diagnostic file):
Pbot = ( hyai(L ) * PS(I,J) ) + hybi(L ) Ptop = ( hyai(L+1) * PS(I,J) ) + hybi(L+1)
Seb Eastham wrote:
Daniel Rothenberg has been in touch regarding how vertical co-ordinates are set up in CESM. It's mostly the same (as COARDS), with the exception that EVERY file which includes a vertical co-ordinate also includes both lev and ilev dimensions. In this case, lev is the cell mid-points, and ilev is cell edges ("i"nterfaces). Both lev and ilev are set up just as we discussed before, although CESM doesn't include the formula_terms attribute, which I think we should use. In this case formula_terms would be ap: hyai b: hybi p0: P0 ps: ps for the ilev dimension and ap: hyam b: hybm p0: P0 ps: ps for the lev dimension.
- For lev and ilev, they should be set to A/1000 + B, where P0 = 1000.
- Both ilev and lev should be in all 3D files, even though only one of the two dimensions is used in a given file).
- I think we can leave PS out of the files. It will make them non-compliant but I think it's one of those "accepted" non-compliances. If it turns out to be a problem we can revisit it later, but for plotting the expectation is that it's up to the user to figure out where they're getting PS from, rather than automatically archiving it in every file.
--Bob Yantosca (talk) 19:27, 5 September 2018 (UTC)
GEOS-Chem 12
These updates were included in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.
In GEOS-Chem 12.1.0, several restart file updates were introduced. These include:
New fields in GEOS-Chem restart file
Several new fields have been added to the GEOS-Chem restart file in an attempt to remove differences between single and multi-segmented GEOS-Chem simulations.
- Module-level variables H2O2s and SO2s from wetscav_mod.F have been added to State_Chm (as State_Chm%H2O2AfterChem, StateChm%SO2AfterChem). These fields will be output to the GEOS-Chem restart file and then initialized to the values saved in the restart file at the start of the next simulation. Prior to this update, both H2O2s and SO2s were initialized to the H2O2 and SO2 tracer concentrations at the start of every simulation. This change will impact multi-segmented runs only.
- Module-level variables DRY_TOTN and WET_TOTN from get_ndep_mod.F have been added to State_Chm (as State_Chm%DryDepNitrogen, StateChm%WetDepNitrogen). These fields will be output to the GEOS-Chem restart file and then initialized to the values saved in the restart file at the start of the next simulation. Prior to this update, both variables were initialized to zero at the start of every simulation. Storing them in the restart file may improve accuracy of soil NOx emissions over multi-segmented runs. This change will impact multi-segmented runs only.
- Move State_PSC from the HEMCO restart file to the GEOS-Chem restart file.
- Save out instantaneous met fields TMPU1, SPHU1, PS1DRY, PS1WET, DELPDRY to the GEOS-Chem restart file. These will be used to initialize the met fields at the start of the timestep, otherwise they will be set to the values of those fields at the end of the timestep.
While this update was added to GEOS-Chem Classic in 12.1.0, it will be added to GCHP in 12.2.0.
Restart collection in History.rc
GEOS-Chem restart files are now saved out via the history component. A new Restart collection has been defined in HISTORY.rc and fields saved out to the restart file can be modified in that file.
Read restart file via HEMCO
GEOS-Chem restart files are now read in 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 the new routine Get_GC_Restart (found in GeosCore/hcoi_gc_main_mod.F90).
#============================================================================== # --- GEOS-Chem restart file --- # # PSC state only needed for UCX #============================================================================== (((GC_RESTART * SPC_ ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesRst_?ALL? $YYYY/$MM/$DD/$HH CS xyz 1 * - 1 1 * TMPU1 ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_TMPU1 $YYYY/$MM/$DD/$HH E xyz 1 * - 1 1 * SPHU1 ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_SPHU1 $YYYY/$MM/$DD/$HH E xyz 1 * - 1 1 * PS1DRY ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_PS1DRY $YYYY/$MM/$DD/$HH E xy 1 * - 1 1 * PS1WET ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_PS1WET $YYYY/$MM/$DD/$HH E xy 1 * - 1 1 * DELPDRY ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_DELPDRY $YYYY/$MM/$DD/$HH E xyz 1 * - 1 1 * KPP_HVALUE ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_KPPHvalue $YYYY/$MM/$DD/$HH E xyz 1 * - 1 1 * WETDEP_N ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_WetDepNitrogen $YYYY/$MM/$DD/$HH E xy 1 * - 1 1 * DRYDEP_N ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_DryDepNitrogen $YYYY/$MM/$DD/$HH E xy 1 * - 1 1 * SO2_AFTERCHEM ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_SO2AfterChem $YYYY/$MM/$DD/$HH E xyz 1 * - 1 1 * H2O2_AFTERCHEM ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_H2O2AfterChem $YYYY/$MM/$DD/$HH E xyz 1 * - 1 1 (((+STATE_PSC+ * STATE_PSC ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_StatePSC $YYYY/$MM/$DD/$HH E xyz count * - 1 1 )))+STATE_PSC+ )))GC_RESTART
The CS cycle flag was added as an option to HEMCO in GEOS-Chem 12.1.0 to tell HEMCO to skip fields that aren't found in the provided file. This is useful when certain species aren't found in the restart file and, in that case, GEOS-Chem will initialize that species to the background concentrations specified in the species database.
--Melissa Sulprizio (talk) 16:30, 7 November 2018 (UTC)
GEOS-Chem v11-01
Impact of Output File Format Change
While migrating from binary punch to netCDF file formats is a structural change, several changes are also being introduced which will result in output differences. These changes include the following:
- Starting in v11-01f, species will always be written to the GEOS-Chem netCDF restart file and will always be initialized to restart file values if present in the file. In contrast, when using binary punch format restart files, species are initialized to background values stored in globchem.dat by default unless the option to read/write the species restart file is turned on in input.geos. This change will only impact multi-segmented full chemistry runs where users previously did not enable the species restart file.
- Starting in v11-01f, species units will be [mol/mol] in the netCDF restart file while they are in [molec/cm3/box] in the binary punch restart file. This change will facilitate the future replacement of tracers with species. However, due to the meteorology state-dependency of the unit conversion from [molec/cm3] to [mol/mol], there will be small differences in [molec/mc3] species values between using binary punch and Netcdf in multi-segmented runs. This is because the meteorology used at restart write is the timestep before the simulation end time while the meteorology used at restart read is the simulation start time which is the same as previous end time. This change will only impact multi-segmented full chemistry runs where users previously enabled the species restart file.
Output files in v11-01
Output files in GEOS-Chem v11-01 are listed below.
| File | Data Format | Description | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| trac_avg.{met}_{grid}_{sim}.YYYYMMDDhh | BPCH | GEOS-Chem output diagnostic data | ||||||||||||||||||
| GEOSChem_restart.YYYYMMDDhhmm | NetCDF | GEOS-Chem output restart file containing advected tracer concentrations in units of [mol/mol]. If running a full chemistry simulation, then the restart file will also contain species concentrations, also in units of [mol/mol]. If running a mercury simulation, then the restart file will also contain ocean mercury data. | ||||||||||||||||||
| HEMCO_restart.YYYYMMDDhhmm | NetCDF | HEMCO output restart file | ||||||||||||||||||
| HEMCO_diagnostics.YYYYMMDDhhmm | NetCDF | HEMCO output diagnostics data | ||||||||||||||||||
| Optional output files: | ||||||||||||||||||||
| stations.YYYYMMDDhh | BPCH | Diagnostic output file that contains ND48 station timeseries output as specified in input.geos. | ||||||||||||||||||
| tsYYYYMMDDhh.bpch | BPCH | Diagnostic output file that contains ND49 instantaneous timeseries output as specified in input.geos. | ||||||||||||||||||
| ts_24hr_avg.YYYYMMDDhh.bpch | BPCH | Diagnostic output file that contains ND50 24-hour average timeseries output as specified in input.geos. | ||||||||||||||||||
| ts_satellite.YYYYMMDDhh.bpch | BPCH | Diagnostic output file that contains ND51 local-time-average (satellite) timeseries output as specified in input.geos. | ||||||||||||||||||
| paranox_ts.YYYYMMDDhh.bpch | BPCH | Diagnostic output file that contains ND63 ship timeseries output as specified in input.geos. | ||||||||||||||||||
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)
GAMAP can now read GEOS-Chem restart files in netCDF format
This update was included in GEOS-Chem v11-01 public release
Starting in GEOS-Chem v11-01, all restart files are now saved in COARDS-compliant netCDF format. We have had to make some minor modifications to both GEOS-Chem and GAMAP in order to allow GAMAP to read these files. The table below gives a summary of these modifications.
| GEOS-Chem or GAMAP? | File | Modification |
|---|---|---|
| GEOS-Chem | GeosCore/gamap_mod.F | In routine INIT_TRACERINFO, we now write metadata for all species (advected or not) to the tracerinfo.dat file under the ND45 tracer concentration diagnostic section. Because the netCDF restart file contains concentrations for both advected and non-advected species, we need to make sure that the tracerinfo.dat file created by GEOS-Chem contains metadata for all species. |
| GAMAP | internals/ctm_open_file.pro | The prior algorithm always assumed that a netCDF file would end in either .nc or .nc4. We now have removed this restriction. We now split the filename string on . and then examine the substrings for nc or nc4 (case-insensitive). |
| GAMAP | internals/ctm_read_coards.pro | Added some minor modifications to read netCDF restart files:
|
--Bob Yantosca (talk) 19:29, 23 January 2017 (UTC)
Obsolete information
These sections pertain to data that is no longer relevant in the latest GEOS-Chem versions. We shall preserve this information here for reference.
Legacy files made obsolete in v11-01
The following files were rendered obsolete starting in GEOS-Chem v11-01.
| File | Description | Reason for removal |
|---|---|---|
| smv2.log | SMVGEAR II log file containing information about reactions and species used by the ND65 prod-loss diagnostic. | This was removed when SMVGEAR was replaced by FlexChem. |
| trac_rst.geosfp_4x5_fullchem.YYYYMMDDhhmm.mp or trac_rst.geosfp_4x5_fullchem.YYYYMMDDhhmm.sp |
Tracer restart file that contains instantaneous tracer concentrations at simulation end time. | The new netCDF restart file format (prefix GEOSCHEM_restart_) contains concentrations for all species (whether advected or not). |
| spec_rst.geosfp_4x5_fullchem.YYYYMMDDhh | Species restart file that contains instantaneous species concentrations at simulation end time. This file saves instantaneous concentrations of all chemical species (listed in globchem.dat) on all levels and may be used to initialize another GEOS-Chem simulation. | The new netCDF restart file format (prefix GEOSCHEM_restart_) contains concentrations for all species (whether advected or not). |
| ocean_rst.YYYYMMDDhhmm.nc | Ocean mercury restart file containing several quantities pertaining to the ocean mercury module saved at the end of the GEOS-Chem simulation. Like the tracer restart file, this file may be used to initialize another GEOS-Chem mercury simulation. | The new netCDF restart file format (prefix GEOSCHEM_restart_) contains concentrations for all species (whether advected or not). |
GEOS-Chem v10-01 and earlier versions
After a GEOS-Chem simulation has completed successfully, you will see several new files in the run directory. Some of these are generated for all simulations while others may be simulation-dependent.
For full-chemistry simulations, the following files are saved out:
| File | Description |
|---|---|
| trac_avg.geosfp_4x5_fullchem.YYYYMMDDhh.mp or trac_avg.geosfp_4x5_fullchem.YYYYMMDDhh.sp |
Diagnostic output file that contains time-averaged output for diagnostics enabled in input.geos.
Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. |
| trac_rst.geosfp_4x5_fullchem.YYYYMMDDhhmm.mp or trac_rst.geosfp_4x5_fullchem.YYYYMMDDhhmm.sp |
Tracer restart file that contains instantaneous tracer concentrations at simulation end time. This file saves instantaneous concentrations of all transported tracers (listed in the Tracer Menu of input.geos) on all levels and may be used to initialize another GEOS-Chem simulation.
Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. |
| HEMCO_restart.YYYYMMDDhh.nc.mp or HEMCO_restart.YYYYMMDDhh.nc.sp |
HEMCO restart file containing several quantities tracked by HEMCO for use in initializing another GEOS-Chem simulation. This file includes data used to calculate soil NOx emissions, PARANOX ship plume chemistry, and MEGAN biogenic emissions.
Data in this file are in netcdf format. |
| v10-01.geosfp_4x5_fullchem.mp or v10-01.geosfp_4x5_fullchem.sp |
GEOS-Chem simulation log file.
Open this file in a text editor to diagnose compile and run errors. |
| HEMCO.log.mp or HEMCO.log.sp |
HEMCO log file containing detailed information about the emissions read from disk into HEMCO.
Open this file in a text editor to diagnose HEMCO errors. |
| smv2.log | SMVGEAR II log file containing information about reactions and species used by the ND65 prod-loss diagnostic. This file is only produced when SMVGEAR, and thus it will not be created for the specialty simulations.
Open this file in a text editor to see if SMVGEAR read the globchem.dat file properly. |
| diaginfo.dat | File generated by GEOS-Chem that contains diagnostic quantities for use with GAMAP. |
| tracerinfo.dat | File generated by GEOS-Chem that contains tracer name metadata for use with GAMAP. |
Additional files may be created by GEOS-Chem, depending on your simulation type and the options specified in the input.geos file. Other optional GEOS-Chem output files include:
| File | Description |
|---|---|
| spec_rst.geosfp_4x5_fullchem.YYYYMMDDhh | Species restart file that contains instantaneous species concentrations at simulation end time. This file saves instantaneous concentrations of all chemical species (listed in globchem.dat) on all levels and may be used to initialize another GEOS-Chem simulation.
NOTE: If you are going to be running a very long GEOS–Chem simulation and must split your simulation into several stages (i.e. in order to stay within the computational time limits of your system), then you should set LSVCSPEC to T in the Chemistry Menu of input.geos. That will make sure that the chemical species concentrations are preserved when the next run stage starts. Otherwise, GEOS-Chem use the default species concentrations specified in globchem.dat at the beginning of each run. Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. |
| stations.YYYYMMDDhh | Diagnostic output file that contains ND48 station timeseries output as specified in input.geos.
Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. For more information on working with ND48 timeseries output, see our timeseries tutorial. |
| tsYYYYMMDDhh.bpch | Diagnostic output file that contains ND49 instantaneous timeseries output as specified in input.geos.
Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. For more information on working with ND49 timeseries output, see our timeseries tutorial. |
| ts_24hr_avg.YYYYMMDDhh.bpch | Diagnostic output file that contains ND50 24-hour average timeseries output as specified in input.geos.
Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. |
| ts_satellite.YYYYMMDDhh.bpch | Diagnostic output file that contains ND51 local-time-average (satellite) timeseries output as specified in input.geos.
Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. |
| paranox_ts.YYYYMMDDhh.bpch | Diagnostic output file that contains ND63 ship timeseries output as specified in input.geos.
Data in this file are in "binary punch" format and may be viewed and manipulated using GAMAP. |
| ocean_rst.YYYYMMDDhhmm.nc | Ocean mercury restart file containing several quantities pertaining to the ocean mercury module saved at the end of the GEOS-Chem simulation. Like the tracer restart file, this file may be used to initialize another GEOS-Chem mercury simulation.
Data in this file are in the in netcdf format. |
| plane.log.YYYYMMDD | Diagnostic output file containing planeflight information scheduled via the Planeflight.dat file. This diagnostic is turned on in the Planeflight Menu of input.geos.
The data in this text file can be read and plotted using GAMAP routines CTM_READ_PLANEFLIGHT and PLANE_PLOT. |
--Melissa Sulprizio 15:42, 3 April 2015 (EDT)
