Bugs and fixes

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Revision as of 16:53, 29 April 2015 by Bmy (Talk | contribs) (Fixes for the HEMCO emissions component)

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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 v10-01

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

Fixes for the stratospheric chemistry module

  1. Reduce memory footprint of the stratospheric chemistry module
  2. Bug fix in GET_RATES_INTERP
  3. Now read corrected stratospheric Bry data via HEMCO

Fixes for the photolysis mechanism

  1. Now use MAP_A2A to regrid 1x1 TOMS O3 to model resolution
  2. Bug fix for determining when to use TOMS O3 columns
  3. Reactivation of Br species photolysis in Fast-JX for tropospheric chemistry simulation
  4. Fixed wavelength bin interpolation error in Fast-JX for tropospheric-only simulation

Fixes for fullchem and nested-grid simulations

  1. Modify treatment of N2O5+H2O reaction in calcrate.F
  2. Fixed parallelization error in nested grid simulations
  3. Fix for high values of O3 dry deposition
  4. Remove duplicate GLYX product from RIO2 reaction
  5. Bug fix in ND44 drydep diagnostic for sea salt aerosols
  6. Implement final recommendation for J(HAC) and J(PAN)
  7. Now use updated cross-sections for computing J(ALD2)
  8. Resolved technical issues for 0.25° x 0.3125° CH nested simulation
  9. Bug fix for planeflight diagnostic when using chemistry timesteps < 15 min
  10. Now call the planeflight diagnostic after chemistry, not after emissions
  11. Bug fixes for wet scavenging by co-condensation
  12. Fixes for bugs in wet deposition when using MERRA meteorology
  13. Remove obsolete ISN2 drydep species

Fixes for specialty simulations

  1. Reactivating dust tracers in TOMAS simulations
  2. Prevent sea salt from being emitted over ice in TOMAS
  3. Fix for ND61 diagnostic in TOMAS simulations
  4. Fixed library linking issue when building GTMM into GEOS-Chem
  5. Minor fixes to CH4 simulation for MERRA meteorology
  6. Avoid div-by-zero errors in POPs simulation
  7. Bug fixes and updates for tagged CO simulation in v9-02
  8. Fixed bug in tagged Hg emissions

Fixes for the HEMCO emissions component

  1. Prevent segmentation fault errors in HEMCO when emissions are turned off
  2. Add new functionality into HEMCO
  3. Bug fixes for the PARANOX extension in HEMCO
  4. Bug fix for regridding of regional data files by HEMCO
  5. Prevent array out-of-bounds error if MEGAN_mono extension is turned off
  6. Restore missing diagnostic: "Biogenic CO from monoterpenes"

Fixes to remove computational bottlenecks

  1. Removed array temporaries in the call to the GEOS-4 convection routine
  2. Removed array temporaries in the call to the GCAP convection routine
  3. Removed array temporaries in subroutine READ_HG2_PARTITIONING
  4. Reduce time spent in advection driver routine TPCORE_FVDAS

Other miscellaneous fixes

  1. Now use correct value of molecular weight for PROPNN tracer
  2. Make the netCDF library linking process more portable
  3. Fix for optimization error discovered in v10-01h

--Bob Y. 17:28, 16 April 2015 (EDT)

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. [Tagged_Ox_simulation#Reactivate_stratospheric_P.28Ox.29_in_tagged_Ox_simulation|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)