Bugs and fixes

On this page we list the GEOS-Chem specific bugs and issues that users have recently encountered, and how to fix them.

Please also be sure to visit our Common GEOS-Chem error messages wiki page for more general information about some frequently encountered errors. Also visit our Currently unresolved issues in GEOS-Chem wiki page to see a list of unresolved issues by GEOS-Chem version (and if they have been fixed in subsequent releases).

Issues resolved in GEOS-Chem v11-01

The following bugs and/or technical issues were resolved in GEOS-Chem v11-01:

Module	Issue that was resolved
Chemistry	Update of PMN + O3 reaction products in globchem.dat file Fix for black carbon in ucx_mod.F Modifications to ND20 to archive afternoon P(O3) and L(O3) Bug fix for sea salt alkalinity in sulfate_mod.F Bug fix for offline dust aerosols when UCX is on
Cloud convection	Correct bug in below cloud average mixing ratio calculation in DO_MERRA_CONVECTION to improve mass balance
Emissions (via HEMCO)	Fix problem in OTD/LIS lighning redistribution files Fix for reading hourly NEI2011 emissions
Met fields and derived quantities	Incorporate moisture into air quantities, tracer units, and tracer unit conversions
RRTMG radiative transfer model	Fix bug that prevents storage of O3 and CH4 RF's Bug fix in RRTMG array sizes Further bug fixes in rrtmg_transfer_mod.F
Specialty simulations	Bug fixes for computing MLD in ocean_mercury_mod.F Update CO2 emission files Bug fix in European grid range for tagged O3 simulation Bug fix for PBLTOP and MTTOP values in tagged O3 simulation
Structural updates	Fix linker error when using the PGI compiler Bug fix for the ND21 diagnostic Bug fix for custom nested grid in tpcore_bc_mod.F Bug fix for monoterpenes in ND46 diagnostic Parallelization bug fix for marine POA
Wet deposition	Now treat DST2-DST4 as coarse mode in wet scavenging NOTE: This also will apply to dust uptake tracers DSTAL2-4, NITD2-4, SO4D2-4 Resolve very high tracer concentrations in MERRA wet deposition Quick fix for low tropospheric 210Pb lifetime against wet deposition

--Bob Y. (talk) 17:05, 26 October 2015 (UTC)

Issues resolved in GEOS-Chem v10-01

The following bugs and/or technical issues were resolved in GEOS-Chem v10-01:

Module or area	Issue that was resolved
Stratospheric chemistry module	Reduce memory footprint of the stratospheric chemistry module Bug fix in GET_RATES_INTERP Now read corrected stratospheric Bry data via HEMCO
Photolysis	Now use MAP_A2A to regrid 1x1 TOMS O3 to model resolution Bug fix for determining when to use TOMS O3 columns Reactivation of Br species photolysis in Fast-JX for tropospheric chemistry simulation Fixed wavelength bin interpolation error in Fast-JX for tropospheric-only simulation Now use proper photolysis input file org.dat
NOx-Ox chemistry and nested grid simulations	Modify treatment of N2O5+H2O reaction in calcrate.F Fixed parallelization error in nested grid simulations Fix for high values of O3 dry deposition Remove duplicate GLYX product from RIO2 reaction Bug fix in ND44 drydep diagnostic for sea salt aerosols Implement final recommendation for J(HAC) and J(PAN) Now use updated cross-sections for computing J(ALD2) Resolved technical issues for 0.25° x 0.3125° CH nested simulation Bug fix for planeflight diagnostic when using chemistry timesteps < 15 min Now call the planeflight diagnostic after chemistry, not after emissions Bug fixes for wet scavenging by co-condensation Fixes for bugs in wet deposition when using MERRA meteorology Remove obsolete ISN2 drydep species Fixed typo for BROMOCARB_SEASON in HEMCO configuration files Bug fixes for GEOS-FP nested EU simulation Fixes for wet deposition when using MERRA met fields Fix MEGAN AEF's for sesquiterpenes in the SOA simulation
Specialty simulations	Reactivating dust tracers in TOMAS simulations Prevent sea salt from being emitted over ice in TOMAS Fix for ND61 diagnostic in TOMAS simulations Fixed library linking issue when building GTMM into GEOS-Chem Minor fixes to CH4 simulation for MERRA meteorology Avoid div-by-zero errors in POPs simulation Bug fixes and updates for tagged CO simulation in v9-02 Fixed bug in tagged Hg emissions
HEMCO emissions component	Prevent segmentation fault errors in HEMCO when emissions are turned off Add new functionality into HEMCO Bug fixes for the PARANOX extension in HEMCO Bug fix for regridding of regional data files by HEMCO Prevent array out-of-bounds error if MEGAN_mono extension is turned off Restore missing diagnostic: "Biogenic CO from monoterpenes" Additional HEMCO updates made during the v10-01 period of public comment Fixed filename for ICOADS_SHIP in HEMCO configuration files Fix for error in PARANOX caused by improper timestamps of SUNCOS Minor fixes for FINNv1 biomass burning emissions Removing leftover code that was orphaned by HEMCO
Removing computational bottlenecks	Removed array temporaries in the call to the GEOS-4 convection routine Removed array temporaries in the call to the GCAP convection routine Removed array temporaries in subroutine READ_HG2_PARTITIONING Reduce time spent in advection driver routine TPCORE_FVDAS
Miscellaneous	Now use correct value of molecular weight for PROPNN tracer Make the netCDF library linking process more portable Fix for optimization error discovered in v10-01h Bug fix for I3 field interpolation Bug fix in gamap_mod.F Bug fixes for the PGI compiler Now use "percent" instead of "%" in data files

--Bob Y. (talk) 20:56, 26 October 2015 (UTC)

Issues resolved in GEOS-Chem v9-02

The following bugs and/or technical issues were resolved in GEOS-Chem v9-02.

Fixes for emissions modules

1. Bug fix for updated CAC emissions
2. Bug fix for Br2 emissions
3. Bug fix in regridding of anthro emissions
4. Bug in MEGAN emissions when using MERRA or GEOS-FP
5. Bug fix in nei2005_anthro_mod.F
6. Bug fix in EMIS_STREETS_ANTHRO_05x0666
7. Bug fixes in biofuel_mod.F and emfossil.F
8. Bug fix for 3-hourly GFED3 emissions
9. Fixed typo in Aerocom volcanic SO2 emissions routine
10. Bug fixes in day-of-week computation
11. Prevent negative emissions over Canada
12. Minor bug fix in TOMAS sulfate emissions
13. Bug fix for NEI2005 SO4 emissions in sulfate_mod.F
14. Prevent LOG(0) error from occurring in soil NOx module
15. Bug fix for biofuels when using RCP scenarios

Fixes for drydep and wetdep

1. Add missing DRYACET to globchem.dat mechanism file
2. Bug fix in Henry's law constant
3. Bug fix in definition of RIP, IEPOX drydep species
4. Bug fix: Do not call PARANOX plume model for offline simulations
5. Fix for parallelization bug in subroutine METERO (in drydep module)
6. Fixed parallelization error in routine DRYFLX (in dry deposition module)
7. Prevent bad drydep flux values from being passed to the soil NOx module
8. Fixed minor bug in AD44 diagnostic in routine DRY DEPOSITION (sea salt aerosols)

Fixes for met fields

1. Correction for GEOS-5 PBL heights
2. Reset NaNs in MOISTQ to zero
3. Convert MERRA and GEOS-FP relative humidity fields to percent after reading from disk
4. Bug fix for declaration of certain GEOS-FP met fields

Fixes for computational efficiency

1. Eliminate inefficient subroutine calls
2. Corrected several floating-point errors
3. Eliminate array temporaries in pjc_pfix_mod.F and pressure_mod.F
4. Eliminate array temporaries in GCAP convection module

Fixes for diagnostics

1. Bug fix in hdf_mod.F
2. Bug fixes in diag48_mod.F
3. Bug fix in ND36 diagnostic when ship emissions are turned off

Fixes for specialty and microphysics simulations

1. Bug fixes for tagged CO simulation
2. Bug fixes for nested Hg simulation
3. Bug fix for reading OH file in offline simulations
4. Now include emissions in the aerosol-only simulation when using non-local PBL mixing
5. Avoid error in ISOROPIAII when using offline aerosol simulation
6. Modifications for v9-02 tagged O3 simulation
7. Fixes for wetland emissions in CH4 simulation
8. Reactivate stratospheric P(Ox) in tagged Ox simulation
9. Replace LD65 with LLTROP in tagged_ox_mod.F
10. Several fixes for TOMAS aerosol microphysics
11. Prevent error in POPs simulation when reading global OC

Fixes for the photolysis mechanism

1. Prevent 0.5 x 0.667 nested grid simulations from crashing when reading TOMS data
2. Add fix to jv_spec_aod.dat file
3. Post-release patch to fix bug in acetone photolysis pressure dependency

Other fixes

1. Additional bug fixes for MAP_A2A regridding
2. Bug fix in grid_mod.F90
3. Fixed typos in GCAP code
4. Reactivate parallel DO loop in LINOZ_CHEMO3 routine
5. Corrected unit conversion bug when TURBDAY PBL mixing is used
6. Fixes for minor technical issues

Bugs and fixes in older GEOS-Chem versions

For a complete list of bugs and fixes in older GEOS-Chem versions, please see our Bugs and fixes prior to v9-02 wiki page.

--Bob Y. 17:40, 16 April 2015 (EDT) --Bob Y. 14:11, 20 May 2014 (EDT)