Difference between revisions of "Bugs and fixes"

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(Issues resolved in GEOS-Chem v9-02)
(Issues resolved in GEOS-Chem v10-01)
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##[[Development_of_Fast-JX_in_GEOS-Chem#Reactivation_of_bromine_species_photolysis_for_tropospheric_simulation|Reactivation of Br species photolysis in Fast-JX for tropospheric chemistry simulation]]
 
##[[Development_of_Fast-JX_in_GEOS-Chem#Reactivation_of_bromine_species_photolysis_for_tropospheric_simulation|Reactivation of Br species photolysis in Fast-JX for tropospheric chemistry simulation]]
 
##[[Development_of_Fast-JX_in_GEOS-Chem#Error_in_reducing_wavelength_bins_for_tropospheric_simulation|Fixed wavelength bin interpolation error in Fast-JX for tropospheric-only simulation]]
 
##[[Development_of_Fast-JX_in_GEOS-Chem#Error_in_reducing_wavelength_bins_for_tropospheric_simulation|Fixed wavelength bin interpolation error in Fast-JX for tropospheric-only simulation]]
#Fixes for chemistry simulations:
+
#Fixes for chemistry (both specialty and full-chem simulations):
 
##[[UCX_chemistry_mechanism#Modify_treatment_of_N2O5_.2B_H2O_reaction_in_calcrate.F|Modify treatment of N2O5+H2O reaction in calcrate.F]]
 
##[[UCX_chemistry_mechanism#Modify_treatment_of_N2O5_.2B_H2O_reaction_in_calcrate.F|Modify treatment of N2O5+H2O reaction in calcrate.F]]
 
##[[TOMAS_aerosol_microphysics#Prevent_sea_salt_from_being_emitted_over_ice_in_TOMAS|Prevent sea salt from being emitted over ice in TOMAS]]
 
##[[TOMAS_aerosol_microphysics#Prevent_sea_salt_from_being_emitted_over_ice_in_TOMAS|Prevent sea salt from being emitted over ice in TOMAS]]

Revision as of 18:58, 14 May 2014

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.

Issues resolved in GEOS-Chem v10-01

  1. Fixes for the stratospheric chemistry module:
    1. Reduce memory footprint of the stratospheric chemistry module
    2. Bug fix in GET_RATES_INTERP
  2. 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
  3. Fixes for chemistry (both specialty and full-chem simulations):
    1. Modify treatment of N2O5+H2O reaction in calcrate.F
    2. Prevent sea salt from being emitted over ice in TOMAS
    3. Fixed library linking issue when building GTMM into GEOS-Chem
    4. Minor fixes to CH4 simulation for MERRA meteorology
    5. Avoid div-by-zero errors in POPs simulation
  4. 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
  5. Other miscellaneous fixes:
    1. Now use correct value of molecular weight for PROPNN tracer

--Bob Y. 14:34, 14 May 2014 (EDT)

Issues resolved in GEOS-Chem v9-02

  1. 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. [GEOS-Chem_v9-02#Bug_fixes_in_day-of-week_computation|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
  2. Fixes for dry deposition and wet deposition modules:
    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. Bug fix for biofuels when using RCP scenarios
    6. Fix for parallelization bug in subroutine METERO (in drydep module)
    7. Fixed parallelization error in routine DRYFLX (in dry deposition module)
    8. Prevent bad drydep flux values from being passed to the soil NOx module
    9. Fixed minor bug in AD44 diagnostic in routine DRY DEPOSITION (sea salt aerosols)
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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

--Bob Y. 14:53, 14 May 2014 (EDT)

Issues resolved in GEOS-Chem v9-01-03

  1. Bug fix for GLCO3 and GLPAN in standard mechanism
  2. Structural changes to clarify science behind washout
  3. Correct out-of-bounds error in offline aerosol simulation
  4. Bug fix for mass transport flux diagnostics
  5. Bug fix in ND67 sea level pressure diagnostic
  6. Bug fixes for nested-grid simulation
  7. Bug fix in streets_anthro_mod.F for offline simulations
  8. Bug fixes for dicarbonyls simulation
  9. Bug fixes for regional emission masks

--Bob Y. 10:19, 13 November 2012 (EST)

Issues resolved in GEOS-Chem v9-01-02

  1. Corrected mis-indexing error in partition.f caused by the dynamic tropopause
  2. Corrected out-of-bounds error in readchem.f
  3. Fix for mis-indexing issue in CSPEC restart file
  4. Various bug fixes for the offline Hg simulation
  5. Bug fixes for leap years when using GCAP met fields
  6. Minor bug fixes for emissions routines affecting offline simulations
  7. Minor bug fixes for emissions routines affecting offline simulations
  8. Fixes for better compatibility with the PGI compiler
  9. Washout fix for non-aerosol species
  10. Fix for GEIA emissions scaling factor over Botswana
  11. Fixed minor issues in MERRA cloud convection routine
  12. Fix for vertical regridding of offline OH for offline simulations
  13. Further bug fixes for the offline Hg simulation
  14. Further fixes for nested-grid simulations
  15. Fix for partitioning chemical species
  16. Bug fixes for biofuel emissions
  17. Fix bug in EDGAR ship emissions code
  18. Bug fix for ship NOx emissions
  19. Prevent out-of-bounds errors in ND01 and ND02 diagnostics (Rn-Pb-Be simulation)
  20. Do not use erroneous MEGAN AEF data for nested-grid simulations

--Melissa Payer 12:08, 21 November 2011 (EST)
--Bob Y. 12:05, 28 November 2011 (EST)

Issues resolved in GEOS-Chem v9-01-01

  1. Standardization of patches from v8-03-02
  2. Bug fix for biofuels in EPA/NEI05
  3. Important bug fixes for ship emissions
  4. Duplicate diagnostics
  5. Starting runs at times other than 00 GMT
  6. Fix ND15 for non-local PBL scheme
  7. Fix to prevent div-by-zero in sulfate_mod.f
  8. PEDGE-$ in timeseries diagnostics
  9. Running offline simulations on the GEOS-5 72L grid
  10. Fixes to improve efficiency in vdiff_mod.f90
  11. Typos in megan_mod.f
  12. Typos in edgar_mod.f

--Bob Y. 11:25, 18 February 2011 (EST)

Issues resolved in GEOS-Chem v8-03-02

  1. Fix for EPA/NEI 2005 emissions
  2. Minor fixes in gamap_mod.f
  3. Bug fix for ND42 diagnostic and ISORROPIA II
  4. Minor fix for AOD calculation
  5. Avoid using unallocated arrays in edgar_mod.f
  6. Transport fix for GEOS-5 nested grid simulations

--Bob Y. 16:53, 7 September 2010 (EDT)

Issues resolved in GEOS-Chem v8-03-01

  1. Patch to enable call to SOA PARA INIT
  2. Patch to fix declaration of IONIC in ISORROPIA_II
  3. Patch to fix bug in Aromatic SOA
  4. Patch to scale AOD diagnostic output to other wavelengths
  5. Photolysis now computed at midpoint of chemistry timestep
  6. Bug fix in ISORROPIA for offline aerosol
  7. Minor bug fix in SRCSO2
  8. Bug in GET_EMMONOT_MEGAN
  9. Bug in READ_ANTHRO_NH3
  10. Fix for initialization of EMEP ship emissions
  11. Bug fix in AVGPOLE
  12. Bug fix in EMITHIGH (carbon_mod.f)
  13. Fix to prevent numerical overflow in EXP function

--Bob Y. 15:05, 30 June 2010 (EDT)

Issues resolved in GEOS-Chem v8-02-04

  1. Memory issue with KPP
  2. Updated reactions in sulfate_mod.f
  3. Bug fix for EMEP ship emissions
  4. Minor fix for molecular weights in drydep_mod.f
  5. Bug fix in biomass_mod.f
  6. Minor bug fix in gamap_mod.f
  7. Fixes and updates in seasalt_mod.f
  8. Bug fix in emfossil.f for 0.5 x 0.666 nested grid tagged-CO option
  9. Bug fix in DIAG20 (diag_pl_mod.f)
  10. Div-by-zero error encountered in arsl1k.f
  11. Fix for diagnostic arrays in TPCORE
  12. MEGAN now uses MODIS LAI by default

--Bob Y. 16:29, 23 February 2010 (EST)

Issues resolved in GEOS-Chem v8-02-03

  1. Patch for KPP solver for v8-02-03
  2. Corrected Bond et al BC/OC emissions
  3. Several bug fixes in sulfate_mod.f
  4. Missing NOx data in S.E.-Asia
  5. Mis-calculation of Courant numbers in tpcore_fvdas_mod.f90
  6. Format problem in planeflight_mod.f

--Bob Y. 16:55, 4 February 2010 (EST)

Issues resolved in GEOS-Chem v8-02-02

  1. EPA/NEI inventory: reset other species to zero
  2. Scale factor for oceanic acetone for GEOS5 2x2.5 was fixed in GEOS-Chem v8-02-02.
  3. Bug with PRIVATE declaration in sulfate_mod.f
  4. Bug with online 2ndary aerosol
  5. Typo in HO2 uptake

--Bob Y. 16:40, 11 January 2010 (EST)

Issues resolved in GEOS-Chem v8-02-01

  1. Output selected tracers only for dry and wet deposition, convection and rain diagnotics
  2. On-the-fly regridding for 0.5x0.667 nested grids
  3. Bug with EMEP ship emissions for nested grids
  4. Bug in sulfate_mod.f to turn off biomass emissions
  5. Minor error in gamap_mod.f
  6. Bug fix for Streets emissions on 0.5x0.666 nested grid

--Bob Y. 09:55, 12 January 2010 (EST)

Issues resolved in GEOS-Chem v8-01-04

  1. Seg fault in GEOS-5 China nested grid simulation
  2. Error message in partition.f
  3. Erroneous O3 diagnostic (ND45)
  4. Post-Release Patches

--Bob Y. 09:58, 12 January 2010 (EST)

Issues resolved in GEOS-Chem v8-01-03

  1. TPCORE replaced with version based on GMI model
  2. Output of ND51 does not match output in the ctm.bpch file
  3. ND22 (J-value) diagnostic
  4. ND34 (biofuel emissions) diagnostic
  5. Change of location of calls to diagnostics in main.f

--Bob Y. 10:29, 12 January 2010 (EST)

Issues resolved in GEOS-Chem v8-01-02

  1. Quick fix for GEOS-5 optical depth
  2. Corrected labeling of SOA quantities in carbon_mod.f
  3. Double-substitution error in GET_ALK
  4. Robustness fix for reading anthropogenic SO2 and NH3
  5. Minor bug in gasconc.f & calcrate.f
  6. Minor bug in emfossil.f
  7. Fix for mass balance of HNO3 and NIT
  8. Bug in ND43
  9. Problem w/ ND65 diagnostic and dynamic tropopause
  10. Albedo diagnostic in GEOS-4
  11. Pressure diagnostic : PS-PTOP vs. PEDGE
  12. Minor bug in log file output

--Bob Y. 10:29, 12 January 2010 (EST)

Issues resolved in GEOS-Chem v8-01-01

  1. Post-release patches
  2. Fixes for offline simulations
  3. Bugs in ND47/ND65/ND45 in v8-01-01

--Bob Y. 10:35, 12 January 2010 (EST)

Issues resolved in GEOS-Chem v7-04-13

  1. Error in regrid_1x1_mod.f
  2. Error in smvgear.f

--Bob Y. 10:49, 12 January 2010 (EST)

Issues resolved in GEOS-Chem v7-04-10

  1. NaN's in smvgear.f

--Bob Y. 10:53, 12 January 2010 (EST)