Difference between revisions of "Bugs and fixes"
(→Issues resolved in GEOS-Chem v10-01) |
(→Issues resolved in GEOS-Chem v10-01) |
||
Line 8: | Line 8: | ||
##[[Stratospheric_chemistry#Reduce_memory_footprint_of_the_stratospheric_chemistry_module|Reduce memory footprint of the stratospheric chemistry module]] | ##[[Stratospheric_chemistry#Reduce_memory_footprint_of_the_stratospheric_chemistry_module|Reduce memory footprint of the stratospheric chemistry module]] | ||
##[[Stratospheric_chemistry#Bug_fix_in_routine_GET_RATES_INTERP|Bug fix in GET_RATES_INTERP]] | ##[[Stratospheric_chemistry#Bug_fix_in_routine_GET_RATES_INTERP|Bug fix in GET_RATES_INTERP]] | ||
+ | ##[[Bromine_chemistry_mechanism#Bugs_in_data_files_used_to_prescribe_stratospheric_Bry|Now read corrected stratospheric Bry data via HEMCO]] | ||
#Fixes for the photolysis mechanism: | #Fixes for the photolysis mechanism: | ||
##[[FAST-J photolysis mechanism#Now_use_MAP_A2A_to_regrid_1x1_TOMS_O3_to_model_resolution|Now use MAP_A2A to regrid 1x1 TOMS O3 to model resolution]] | ##[[FAST-J photolysis mechanism#Now_use_MAP_A2A_to_regrid_1x1_TOMS_O3_to_model_resolution|Now use MAP_A2A to regrid 1x1 TOMS O3 to model resolution]] | ||
Line 13: | Line 14: | ||
##[[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 full-chemistry | + | #Fixes for the full-chemistry simulations and nested-grid 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]] | ||
+ | ##[[Setting_up_GEOS-Chem_nested_grid_simulations#Parallelization_error_in_nested_grid_simulations|Fixed parallelization error in nested grid simulations]] | ||
+ | ##[[Ship_emissions#Fix_for_high_values_of_O3_dry_deposition|Fix for high values of O3 dry deposition]] | ||
+ | ##[[New_isoprene_scheme#Remove_duplicate_GLYX_product_from_RIO2_reaction|Remove duplicate GLYX product from RIO2 reaction]] | ||
+ | ##[[Sea_salt_aerosols#Bug_in_ND44_drydep_diagnostic_for_sea_salt_aerosols|Bug fix in ND44 drydep diagnostic for sea salt aerosols]] | ||
+ | ##[[FAST-JX_v7.0_photolysis_mechanism#Final_recommendation_for_J.28HAC.29_and_J.28PAN.29|Implement final recommendation for J(HAC) and J(PAN)]] | ||
+ | ##[[FAST-JX_v7.0_photolysis_mechanism#Acetaldehyde_photolysis|Now use updated cross-sections for computing J(ALD2)]] | ||
+ | ##[[Nested_Model_Working_Group#Bug_fixes_for_the_0.25x0.3125_nested_CH_simulation|Resolved technical issues for 0.25° x 0.3125° CH nested simulation]] | ||
+ | ##[[GEOS-Chem_v10-01#Bug_fixes_and_and_updates_for_v10-01g|Bug fix for planeflight diagnostic when using chemistry timesteps < 15 min]] | ||
+ | ##[[Wet_deposition#Bug_fixes_for_scavenging_by_co-condensation|Bug fixes for wet scavenging by co-condensation]] | ||
+ | #Fixes for specialty simulations (including aerosol microphysics) | ||
+ | ##[[TOMAS_aerosol_microphysics#Reactivating_dust_tracers_in_TOMAS_simulations|Reactivating dust tracers in TOMAS simulations]] | ||
##[[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]] | ||
+ | ##[[TOMAS_aerosol_microphysics#Fix_for_ND61_diagnostic|Fix for ND61 diagnostic in TOMAS simulations]] | ||
##[[Global_Terrestrial_Mercury_Model#Fixed_library_linking_issue_when_building_GTMM_into_GEOS-Chem|Fixed library linking issue when building GTMM into GEOS-Chem]] | ##[[Global_Terrestrial_Mercury_Model#Fixed_library_linking_issue_when_building_GTMM_into_GEOS-Chem|Fixed library linking issue when building GTMM into GEOS-Chem]] | ||
##[[CH4_simulation#Minor_fixes_to_CH4_simulation_for_MERRA_meteorology|Minor fixes to CH4 simulation for MERRA meteorology]] | ##[[CH4_simulation#Minor_fixes_to_CH4_simulation_for_MERRA_meteorology|Minor fixes to CH4 simulation for MERRA meteorology]] | ||
##[[POPs_simulation#Avoid_div-by-zero_errors_in_POPs_simulation|Avoid div-by-zero errors in POPs simulation]] | ##[[POPs_simulation#Avoid_div-by-zero_errors_in_POPs_simulation|Avoid div-by-zero errors in POPs simulation]] | ||
− | |||
##[[Tagged_CO_simulation#Bug_fixes_and_updates_for_tagged_CO_in_v9-02|Bug fixes and updates for tagged CO simulation in v9-02]] | ##[[Tagged_CO_simulation#Bug_fixes_and_updates_for_tagged_CO_in_v9-02|Bug fixes and updates for tagged CO simulation in v9-02]] | ||
− | |||
##[[Mercury#Bug_in_tagged_Hg_emissions_in_v9-02|Fixed bug in tagged Hg emissions]] | ##[[Mercury#Bug_in_tagged_Hg_emissions_in_v9-02|Fixed bug in tagged Hg emissions]] | ||
− | ##[[ | + | #Fixes for the [[HEMCO|HEMCO emissions component]] |
− | ##[[ | + | ##[[Implementation_of_HEMCO_in_GEOS-Chem#Fix_for_segmentation_fault_when_emissions_are_turned_off|Prevent segmentation fault errors in HEMCO when emissions are turned off]] |
+ | ##[[Implementation_of_HEMCO_in_GEOS-Chem#Features_added_in_v10-01f|Add new functionality into HEMCO]] | ||
#Fixes to remove computational bottlenecks: | #Fixes to remove computational bottlenecks: | ||
##[[Cloud convection#Removed array temporaries in call to FVDAS_CONVECT|Removed array temporaries in the call to the GEOS-4 convection routine]] | ##[[Cloud convection#Removed array temporaries in call to FVDAS_CONVECT|Removed array temporaries in the call to the GEOS-4 convection routine]] | ||
Line 32: | Line 44: | ||
#Other miscellaneous fixes: | #Other miscellaneous fixes: | ||
##[[GEOS-Chem_v9-02#Incorrect_value_of_molecular_weight_for_the_PROPNN_tracer_in_input.geos|Now use correct value of molecular weight for PROPNN tracer]] | ##[[GEOS-Chem_v9-02#Incorrect_value_of_molecular_weight_for_the_PROPNN_tracer_in_input.geos|Now use correct value of molecular weight for PROPNN tracer]] | ||
+ | ##[[Installing_libraries_for_GEOS-Chem#How_GEOS-Chem_uses_nc-config_and_nf-config|Make the netCDF library linking process more portable]] | ||
− | --[[User:Bmy|Bob Y.]] | + | --[[User:Bmy|Bob Y.]] 18:38, 14 January 2015 (EST) |
− | + | ||
== Issues resolved in GEOS-Chem v9-02 == | == Issues resolved in GEOS-Chem v9-02 == |
Revision as of 23:38, 14 January 2015
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).
Contents
- 1 Issues resolved in GEOS-Chem v10-01
- 2 Issues resolved in GEOS-Chem v9-02
- 3 Issues resolved in GEOS-Chem v9-01-03
- 4 Issues resolved in GEOS-Chem v9-01-02
- 5 Issues resolved in GEOS-Chem v9-01-01
- 6 Issues resolved in GEOS-Chem v8-03-02
- 7 Issues resolved in GEOS-Chem v8-03-01
- 8 Issues resolved in GEOS-Chem v8-02-04
- 9 Issues resolved in GEOS-Chem v8-02-03
- 10 Issues resolved in GEOS-Chem v8-02-02
- 11 Issues resolved in GEOS-Chem v8-02-01
- 12 Issues resolved in GEOS-Chem v8-01-04
- 13 Issues resolved in GEOS-Chem v8-01-03
- 14 Issues resolved in GEOS-Chem v8-01-02
- 15 Issues resolved in GEOS-Chem v8-01-01
- 16 Issues resolved in GEOS-Chem v7-04-13
- 17 Issues resolved in GEOS-Chem v7-04-10
Issues resolved in GEOS-Chem v10-01
- Fixes for the stratospheric chemistry module:
- Fixes for the photolysis mechanism:
- Fixes for the full-chemistry simulations 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
- Bug fixes for wet scavenging by co-condensation
- Fixes for specialty simulations (including aerosol microphysics)
- 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
- Fixes for the HEMCO emissions component
- Fixes to remove computational bottlenecks:
- Other miscellaneous fixes:
--Bob Y. 18:38, 14 January 2015 (EST)
Issues resolved in GEOS-Chem v9-02
- Fixes for emissions modules:
- Bug fix for updated CAC emissions
- Bug fix for Br2 emissions
- Bug fix in regridding of anthro emissions
- Bug in MEGAN emissions when using MERRA or GEOS-FP
- Bug fix in nei2005_anthro_mod.F
- Bug fix in EMIS_STREETS_ANTHRO_05x0666
- Bug fixes in biofuel_mod.F and emfossil.F
- Bug fix for 3-hourly GFED3 emissions
- Fixed typo in Aerocom volcanic SO2 emissions routine
- Bug fixes in day-of-week computation
- Prevent negative emissions over Canada
- Minor bug fix in TOMAS sulfate emissions
- Bug fix for NEI2005 SO4 emissions in sulfate_mod.F
- Prevent LOG(0) error from occurring in soil NOx module
- Bug fix for biofuels when using RCP scenarios
- Fixes for dry deposition and wet deposition modules:
- Add missing DRYACET to globchem.dat mechanism file
- Bug fix in Henry's law constant
- Bug fix in definition of RIP, IEPOX drydep species
- Bug fix: Do not call PARANOX plume model for offline simulations
- Fix for parallelization bug in subroutine METERO (in drydep module)
- Fixed parallelization error in routine DRYFLX (in dry deposition module)
- Prevent bad drydep flux values from being passed to the soil NOx module
- Fixed minor bug in AD44 diagnostic in routine DRY DEPOSITION (sea salt aerosols)
- Fixes for met fields:
- Fixes for computational efficiency:
- Fixes for diagnostics:
- Fixes for specialty and microphysics simulations:
- Bug fixes for tagged CO simulation
- Bug fixes for nested Hg simulation
- Bug fix for reading OH file in offline simulations
- Now include emissions in the aerosol-only simulation when using non-local PBL mixing
- Avoid error in ISOROPIAII when using offline aerosol simulation
- Modifications for v9-02 tagged O3 simulation
- Fixes for wetland emissions in CH4 simulation
- Reactivate stratospheric P(Ox) in tagged Ox simulation
- Replace LD65 with LLTROP in tagged_ox_mod.F
- Several fixes for TOMAS aerosol microphysics
- Prevent error in POPs simulation when reading global OC
- Fixes for the photolysis mechanism:
- Other fixes:
--Bob Y. 14:11, 20 May 2014 (EDT)
Issues resolved in GEOS-Chem v9-01-03
- Bug fix for GLCO3 and GLPAN in standard mechanism
- Structural changes to clarify science behind washout
- Correct out-of-bounds error in offline aerosol simulation
- Bug fix for mass transport flux diagnostics
- Bug fix in ND67 sea level pressure diagnostic
- Bug fixes for nested-grid simulation
- Bug fix in streets_anthro_mod.F for offline simulations
- Bug fixes for dicarbonyls simulation
- Bug fixes for regional emission masks
--Bob Y. 10:19, 13 November 2012 (EST)
Issues resolved in GEOS-Chem v9-01-02
- Corrected mis-indexing error in partition.f caused by the dynamic tropopause
- Corrected out-of-bounds error in readchem.f
- Fix for mis-indexing issue in CSPEC restart file
- Various bug fixes for the offline Hg simulation
- Bug fixes for leap years when using GCAP met fields
- Minor bug fixes for emissions routines affecting offline simulations
- Minor bug fixes for emissions routines affecting offline simulations
- Fixes for better compatibility with the PGI compiler
- Washout fix for non-aerosol species
- Fix for GEIA emissions scaling factor over Botswana
- Fixed minor issues in MERRA cloud convection routine
- Fix for vertical regridding of offline OH for offline simulations
- Further bug fixes for the offline Hg simulation
- Further fixes for nested-grid simulations
- Fix for partitioning chemical species
- Bug fixes for biofuel emissions
- Fix bug in EDGAR ship emissions code
- Bug fix for ship NOx emissions
- Prevent out-of-bounds errors in ND01 and ND02 diagnostics (Rn-Pb-Be simulation)
- 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
- Standardization of patches from v8-03-02
- Bug fix for biofuels in EPA/NEI05
- Important bug fixes for ship emissions
- Duplicate diagnostics
- Starting runs at times other than 00 GMT
- Fix ND15 for non-local PBL scheme
- Fix to prevent div-by-zero in sulfate_mod.f
- PEDGE-$ in timeseries diagnostics
- Running offline simulations on the GEOS-5 72L grid
- Fixes to improve efficiency in vdiff_mod.f90
- Typos in megan_mod.f
- Typos in edgar_mod.f
--Bob Y. 11:25, 18 February 2011 (EST)
Issues resolved in GEOS-Chem v8-03-02
- Fix for EPA/NEI 2005 emissions
- Minor fixes in gamap_mod.f
- Bug fix for ND42 diagnostic and ISORROPIA II
- Minor fix for AOD calculation
- Avoid using unallocated arrays in edgar_mod.f
- Transport fix for GEOS-5 nested grid simulations
--Bob Y. 16:53, 7 September 2010 (EDT)
Issues resolved in GEOS-Chem v8-03-01
- Patch to enable call to SOA PARA INIT
- Patch to fix declaration of IONIC in ISORROPIA_II
- Patch to fix bug in Aromatic SOA
- Patch to scale AOD diagnostic output to other wavelengths
- Photolysis now computed at midpoint of chemistry timestep
- Bug fix in ISORROPIA for offline aerosol
- Minor bug fix in SRCSO2
- Bug in GET_EMMONOT_MEGAN
- Bug in READ_ANTHRO_NH3
- Fix for initialization of EMEP ship emissions
- Bug fix in AVGPOLE
- Bug fix in EMITHIGH (carbon_mod.f)
- Fix to prevent numerical overflow in EXP function
--Bob Y. 15:05, 30 June 2010 (EDT)
Issues resolved in GEOS-Chem v8-02-04
- Memory issue with KPP
- Updated reactions in sulfate_mod.f
- Bug fix for EMEP ship emissions
- Minor fix for molecular weights in drydep_mod.f
- Bug fix in biomass_mod.f
- Minor bug fix in gamap_mod.f
- Fixes and updates in seasalt_mod.f
- Bug fix in emfossil.f for 0.5 x 0.666 nested grid tagged-CO option
- Bug fix in DIAG20 (diag_pl_mod.f)
- Div-by-zero error encountered in arsl1k.f
- Fix for diagnostic arrays in TPCORE
- MEGAN now uses MODIS LAI by default
--Bob Y. 16:29, 23 February 2010 (EST)
Issues resolved in GEOS-Chem v8-02-03
- Patch for KPP solver for v8-02-03
- Corrected Bond et al BC/OC emissions
- Several bug fixes in sulfate_mod.f
- Missing NOx data in S.E.-Asia
- Mis-calculation of Courant numbers in tpcore_fvdas_mod.f90
- Format problem in planeflight_mod.f
--Bob Y. 16:55, 4 February 2010 (EST)
Issues resolved in GEOS-Chem v8-02-02
- EPA/NEI inventory: reset other species to zero
- Scale factor for oceanic acetone for GEOS5 2x2.5 was fixed in GEOS-Chem v8-02-02.
- Bug with PRIVATE declaration in sulfate_mod.f
- Bug with online 2ndary aerosol
- Typo in HO2 uptake
--Bob Y. 16:40, 11 January 2010 (EST)
Issues resolved in GEOS-Chem v8-02-01
- Output selected tracers only for dry and wet deposition, convection and rain diagnotics
- On-the-fly regridding for 0.5x0.667 nested grids
- Bug with EMEP ship emissions for nested grids
- Bug in sulfate_mod.f to turn off biomass emissions
- Minor error in gamap_mod.f
- 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
- Seg fault in GEOS-5 China nested grid simulation
- Error message in partition.f
- Erroneous O3 diagnostic (ND45)
- Post-Release Patches
--Bob Y. 09:58, 12 January 2010 (EST)
Issues resolved in GEOS-Chem v8-01-03
- TPCORE replaced with version based on GMI model
- Output of ND51 does not match output in the ctm.bpch file
- ND22 (J-value) diagnostic
- ND34 (biofuel emissions) diagnostic
- 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
- Quick fix for GEOS-5 optical depth
- Please see the discussion about this quick fix for the GEOS-5 optical depths.
- NOTE: if you are using GEOS-Chem v8-01-04 or higher with the reprocessed GEOS-5 met fields, then you do not need to use this quick fix.
- Corrected labeling of SOA quantities in carbon_mod.f
- Double-substitution error in GET_ALK
- Robustness fix for reading anthropogenic SO2 and NH3
- Minor bug in gasconc.f & calcrate.f
- Minor bug in emfossil.f
- Fix for mass balance of HNO3 and NIT
- Bug in ND43
- Problem w/ ND65 diagnostic and dynamic tropopause
- Albedo diagnostic in GEOS-4
- Pressure diagnostic : PS-PTOP vs. PEDGE
- Minor bug in log file output
--Bob Y. 10:29, 12 January 2010 (EST)
Issues resolved in GEOS-Chem v8-01-01
--Bob Y. 10:35, 12 January 2010 (EST)
Issues resolved in GEOS-Chem v7-04-13
--Bob Y. 10:49, 12 January 2010 (EST)
Issues resolved in GEOS-Chem v7-04-10
--Bob Y. 10:53, 12 January 2010 (EST)