Difference between revisions of "Bugs and fixes"

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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.   
 
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).
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== Bugs and fixes lists have now been migrated to Github ==
  
== Issues resolved in GEOS-Chem v11-02 ==
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We have been migrating bug reports to our GEOS-Chem issue tracker, which is located on our Github repository: https://github.com/geoschem/geos-chem/issues/.  We recommend that you also look through both the open and closed issues on this page, as your issue might be listed there.
  
----
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=== GEOS-Chem 13 ===
----
+
<big><strong>GEOS-Chem v11-02-final</strong> '''will also carry the designation''' <strong>GEOS-Chem 12.0.0</strong>'''.'''  We are migrating to a purely numeric versioning system in order to adhere more closely to software development best practices. For a complete description of the new versioning system, please see [[GEOS-Chem version numbering system|our ''GEOS-Chem version numbering system'' wiki page]].</big>
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----
+
----
+
  
 
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{| border=1 cellspacing=0 cellpadding=5  
The bugs and technical issues listed below were resolved in [[GEOS-Chem v11-02]] (aka 12.0.0).  Also be sure to visit [[Known issues caused by compiler bugs|our ''Known issues caused by compiler bugs'' wiki page]] for a list of compiler-related issues and workarounds.
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250px"|Module or area
+
!Version
!width="750px"|Issue that was resolved
+
!Released
 +
!colspan="2"|List of bugs and issues (now posted on the listed Github repository)
  
 
|-valign="top"
 
|-valign="top"
|Chemistry
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|[[GEOS-Chem_model_development_priorities#13.3.0|13.3.0]]
|
+
|TBD
*[[FlexChem#Add_simplified_P.2FL_families_to_KPP|(v11-02a) Add simplified prod/loss families to KPP to gain computational speedup]]
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[Chemistry_Issues#Fixes_to_correct_ALK4_lumping_issue|(v11-02a) Fixes to correct ALK4 lumping issue]]
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|[https://github.com/geoschem/geos-chem/milestone/19 '''Milestone 13.3.0''']
*[[Sulfate_aerosols#Fix_bug_in_CHEM_NIT_routine|(v11-02a) Fix bug in CHEM_NIT routine]]
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*[[Sulfate_aerosols#Fix_error_in_production_of_SO4s.2C_NITs_in_SEASALT_CHEM_routine|(v11-02a) Fix error in production of SO4s and NITs in SEASALT_CHEM routine]]
+
*[[Sulfate_aerosols#Fix_for_sulfate_production_in_HET_DROP_CHEM|(v11-02a) Fix for sulfate production in HET_DROP_CHEM]]
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*[[Sulfate_aerosols#Fix_bugs_in_sulfate_chemistry_routines|(v11-02a) Fix bugs in sulfate chemistry routines]]
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*[[Chemistry_Issues#Fixes_for_carbon_creating_reactions|(v11-02c) Add fixes to chemical mechanism to preserve total carbon]]
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*[[PAN#Bug_fixes_for_EOH_and_MGLY|(v11-02c) Fix bugs for EOH and MGLY following implementation of PAN updates in v11-02a]]
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*[[UCX_chemistry_mechanism#Fix_bug_impacting_dust_radius_obtained_in_RDUST_ONLINE|(v11-02d) Fix bug impacting dust radii obtained in RDUST_ONLINE]]
+
*[[GEOS-Chem_v11-02#Add_fix_for_IPMN_reactions_contributing_to_high_P.28Ox.29_and_L.28NOx.29|(v11-02d) Fixed IMPN reactions that contributed to high P(Ox) and L(Ox)]]
+
*[[GEOS-Chem_v11-02#Add_bug_fixes_for_GLYX.2C_MGLY.2C_IEPOX.2C_and_IMAE_heterogeneous_chemistry_added_in_v11-02c|(v11-02d) Fixed bugs in GLYX, MGLY, IEPOX, and IMAE heterogeneous chemistry]]
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*[[ISORROPIA_II#Bug_fixes_for_ISORROPIA_II_stable_mode|(v11-02e) Bug fixes for ISORROPIA II stable mode]]
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*[[GEOS-Chem_v11-02#Remove_MONX_from_chemical_mechanisms|(v11-02e) Remove MONX from chemical mechanisms]]
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*[[Secondary_organic_aerosols#Add_MTPO_as_an_advected_and_chemical_species_to_all_full-chemistry_simulations|(v11-02e) Add MTPO to all full-chemistry simulations]]
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*[[Secondary_organic_aerosols#SOA_formation_from_aqueous_isoprene_uptake|(v11-02e) Always use SOA formation from aqueous isoprene uptake (remove input switch)]]
+
*[[Halogen_chemistry_mechanism#Fixes_in_gckpp_HetRates.F90_following_implementation_in_v11-02d|(v11-02e) Fixes for KPP heterogenous chemistry module for halogen chemistry mechanism]]
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*[[Secondary_organic_aerosols#Fixes_for_isoprene_SOA_for_consistency_with_Marais_et_al._.282016.29|(v11-02e) Fixes for isoprene SOA for consistency with Marais et al  (2016)]]
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*[[UCX_chemistry_mechanism#v11-02|(v11-02e) Remove UCX 2-D initial boundary conditions option]]
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*[[UCX_chemistry_mechanism#Fix_for_UCX_mesospheric_NOy_routine|(v11-02f) Fix for UCX mesospheric NOy routine]]
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*[[Halogen_chemistry_mechanism#Fix_for_N2O5_uptake|(v11-02f) Fix for N2O5 update]]
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*[[GEOS-Chem_v11-02#Fix_for_organic_nitrate_chemistry|(v11-02f) Fix for organic nitrate chemistry]]
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*[[GEOS-Chem_v11-02#KPP_errors_with_halogen_chemistry_and_tropchem-based_mechanisms|(v11-02f) Change tolerance value as a temporary fix for convergence errors in 2x2.5 tropchem simulation]]
+
 
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*[[Secondary_organic_aerosols#Only add ISOAAQ species to OCPISOA when using the complex SOA option|(v11-02-rc) Only add ISOAAQ species to OCPISOA when using the complex SOA option]]
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*[[Secondary_organic_aerosols#Only_add_ISOAAQ_species_to_PM2.5_diagnostics_for_simulations_using_the_complex_SOA_option|(v11-02-rc) Only add ISOAAQ species to the PM2.5 diagnostics when using the Complex SOA option]]
+
  
 
|-valign="top"
 
|-valign="top"
|[[Cloud convection]]
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|[[GEOS-Chem_model_development_priorities#13.2.0|13.2.0]]
|
+
|TBD
*[[Cloud_convection#Computational_bottleneck_in_the_v11-01_convection_module|(v11-02a) Remove computational bottleneck in the convection module]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/18 '''Milestone 13.2.0''']
  
 
|-valign="top"
 
|-valign="top"
|[[CO2 simulation]]
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|[[GEOS-Chem 13.1.0|13.1.0]]
|
+
|TBD
*[[CO2 simulation#CO2_emissions_unit_conversion_not_consistent_with_new_advection_pressure|(v11-02b) CO2 emissions unit conversion was not consistent with the new advection pressure]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/17 '''Milestone 13.1.0''']
  
 
|-valign="top"
 
|-valign="top"
|Diagnostics
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|[[GEOS-Chem 13.0.2|13.0.2]]
|
+
|12 Apr 2021
*[[Particulate_matter_in_GEOS-Chem#Save_out_PM2.5_diagnostic_at_STP_conditions|(v11-02a) Save out PM2.5 diagnostic at STP conditions]]
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[GEOS-Chem_v11-01#Bugs_in_convective_flux_diagnostics_.28ND14.29|(v11-02a) Bug fixes in convective flux diagnostics (ND14)]]
+
|[https://github.com/geoschem/geos-chem/milestone/21?closed=1 '''Milestone 13.0.2''']
*[[GEOS-Chem_v11-01#P.28OH.29_not_saved_out_in_ND22_diagnostic|(v11-02a) Restore P(OH) in ND22 diagnostic]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Make_anthropogenic_emissions_diagnostics_3D|(v11-02a) Make anthropogenic emissions diagnostics 3D]]
+
*[[Tagged_CO_simulation#Fix_ND65_bugs_in_tagged_CO_simulation|(v11-02a) Fix ND65 bugs in tagged CO simulation]]
+
*[[Mineral_dust_aerosols#Bug_in_ND21_diagnostic_indexing_for_size-resolved_dust_species|(v11-02a) Fix bug in ND21 diagnostic indexing for dust species]]
+
*[[GEOS-Chem_v11-02#ND40_planeflight_diagnostic_not_always_written_out_when_turned_on|(v11-02b) Always write out ND40 planeflight diagnostic when enabled]]
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*[[GEOS-Chem v11-02#Bug fixes for the ND50 timeseries diagnostic|(v11-02c) Bug fixes for the ND50 timeseries diagnostic]]
+
*[[Stratospheric_chemistry#STE_fluxes|(v11-02c) Fix the STE diagnostics and use them in the standard benchmarking procedure]]
+
*[[Secondary_organic_aerosols#Fix_diagnostics_bugs_in_the_SOA-SVPOA_simulation|(v11-02c) Fix diagnostic bugs in the SOA-SVPOA simulation]]
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*[[GEOS-Chem_v11-02#Fixes_for_two_new_ND21_binary_diagnostics_introduced_in_v11-02|(v11-02e) Fixes for two new ND21 binary diagnostics introduced in v11-02]]
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*[[Secondary_organic_aerosols#Calculation_of_PM2.5.2C_AOD.2C_and_aerosol_mass|(v11-02e} Always use simple SOA in computation of PM2.5 and AOD]]
+
  
 
|-valign="top"
 
|-valign="top"
|Date and time (and related quantities)
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|[[GEOS-Chem 13.0.1|13.0.1]]
|
+
|23 Mar 2021
*[[GEOS-Chem_v11-01#Bug_in_cos.28SZA.29_for_start_of_timestep|(v11-02a) Fixed bug in computation of cosine of solar zenith angle]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/20?closed=1 '''Milestone 13.0.1''']
  
 
|-valign="top"
 
|-valign="top"
|[[Dry deposition|Dry]] and [[Wet deposition|wet deposition]]
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|width="80px"|[[GEOS-Chem 13.0.0|13.0.0]]
|
+
|width="100px"|18 Mar 2021
*[[Dry_deposition#Bug_in_computation_of_aerodynamic_resistance_RA|(v11-02a) Fix bug in computation of dry deposition aerodynamic resistance Ra]]
+
|width="200px"|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[Aerosol_emissions#Bug_fix_for_MOPO_and_MOPI_definitions_in_species_database|(v11-02c) Fix bug in species definitions for marine POA simulation]]
+
|width="400px"|[https://github.com/geoschem/geos-chem/milestone/8?closed=1 '''Milestone 13.0.0''']
*[[GEOS-Chem_v11-02#Fix_dust_rainout_settings_to_match_BCPO|(v11-02e) Fix dust rainout settings to match that of hydrophobic BC (aka BCPO)]]
+
*[[Physical_properties_of_GEOS-Chem_species#Fix_Henry.27s_law_parameters_for_HCl|(v11-02f) Fix Henry's law parameters for HCl]]
+
 
+
|-valign="top"
+
|[[HEMCO|Emissions (via HEMCO)]]
+
|
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Features_added_in_v11-02a|(v11-02a) Update to HEMCO v2.0.004]]
+
*[[EPA/NEI11_North_American_emissions#Default_US_emissions_to_NEI2011_after_2013|(v11-02a) Default US emissions to NEI2011 after 2013]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Fixed_bug_in_computation_of_local_time_in_HCO_GetSuncos|(v11-02a) Fixed bug in computation of local time in the HEMCO routine <tt>HCO_GetSuncos</tt>]]
+
*[[Acetone#Fix_acetone_parameterization_in_hcox_seaflux_mod.F90|(v11-02a) Fix acetone parameterization in hcox_seaflux_mod.F90]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Read_default_DEP_RESERVOIR_fields_from_file_when_not_found_in_HEMCO_restart_file|(v11-02a) Change DEP_RESERVOIR time cycling option to C]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Now_use_YYYYMMDDhhmm_format_for_time_stamp_values|(v11-02c) Now use <tt>YYYYMMDDhhmm</tt> for time stamp values]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Avoid_segmentation_fault_in_DustGinoux_extension|(v11-02c) Add error trap in to avoid a segmentation fault when the DustGinoux extension is turned off]]
+
*[[Mercury#Bug_fixes_for_Hg_emissions|(v11-02c) Bug fixes for Hg emissions]]
+
*[[Secondary_organic_aerosols#Update_simple_SOA_entries_in_HEMCO_to_follow_MTPA.2BLIMO.2BMTPO|(v11-02e) Update simple SOA entries in HEMCO_Config.rc to follow MTPA+LIMO+MTPO]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Features_added_in_v11-02e|(v11-02e) Fix bug in HEMCO reference time algorithm]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Features_added_in_v11-02f|(v11-02f) Update from HEMCO v2.1.001 to 2.1.005]]
+
*[[Biomass_burning_emissions#Fix_bug_in_biomass_burning_emissions_when_GFED_is_turned_off|(v11-02f) Fix bug in biomass burning when GFED is turned off]]
+
*[[RCP_future_emissions_scenarios#Fix_missing_HCOOH_factors_for_RCP_in_HEMCO_Config.rc|(v11-02f) Fix missing HCOOH factors for RCP scenarios in HEMCO_Config.rc file]]
+
*(v11-02-rc) Turn off XIAO inventory to avoid double-counting anthropogenic propane emissions]]
+
 
+
|-valign="top"
+
|Fixes to facilitate running GEOS-Chem in HPC environments
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|
+
*[[UCX_chemistry_mechanism#Bug_fixes_for_running_UCX_in_ESMF_environment|(v11-02a) Bug fixes for using UCX chemistry in the ESMF environment]]
+
 
+
|-valign="top"
+
|[[Nested Model Working Group|Nested-grid simulations]]
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|
+
*[[Mercury#Fixed_typo_in_nested_grid_transport_routine_INIT_WINDOW|(v11-02a) Fixed typo in nested-grid transport routine <tt>INIT_WINDOW</tt>]]
+
 
+
|-valign="top"
+
|[[Mercury|Mercury simulation]]
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|
+
*(v11-02-rc) Minor fixes (including updated parameters) for the [[Mercury]] simulation.
+
 
+
|-valign="top"
+
|[[Overview_of_GMAO_met_data_products|Meteorological fields]]
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|
+
*[[GEOS-Chem v11-02#Add MERRA2 to #if and #elif statements where it had been omitted|(v11-02c) Add MERRA2 to <tt>#if</tt> and <tt>#elif</tt> statements where it had been omitted]]
+
*[[Downloading_GEOS-Chem_source_code_and_data#Inconsistency_in_GEOS-FP_files_at_Harvard_and_Dalhousie_for_July_2013|(v11-02e) Sync GEOS-FP met field files on Harvard FTP with those at Dalhousie]]
+
 
+
|-valign="top"
+
|[[The NcdfUtilities package|netCDF]] and file I/O issues
+
|
+
*[[The NcdfUtilities package#Routine DO_ERR_OUT now returns a non-zero error code|(v11-02a) Routine <tt>DO_ERR_OUT</tt> now returns a non-zero error code]]
+
*[[The NcdfUtilities package#Enable_compression_in_netCDF-4_output_files|(v11-02a) Enable data compression in netCDF-4 output files]]
+
*[[Implementation of HEMCO in GEOS-Chem#HEMCO diagnostic and restart files now have an unlimited time dimension|(v11-02a) HEMCO diagnostic and restart files now have an unlimited time dimension]]
+
 
+
|-valign="top"
+
|[[Rn-Pb-Be simulation|Rn-Pb-Be simulation]]
+
|
+
*[[Rn-Pb-Be_simulation#Vertical_Grid|(v11-02e) The Rn-Pb-Be simulation now uses 72 vertical levels by default]]
+
 
+
|-valign="top"
+
|Structural issues
+
|
+
*[[ISORROPIA_II#Implement_ISORROPIA_v2.0_as_a_Fortran_module|(v11-02a) Implement ISORROPIA v2.0 as a Fortran module (eliminating <code>COMMON</code> blocks)]]
+
*[[GEOS-Chem_Makefile_Structure#Bug_fix:_Specifying_NO_REDUCED.3Dno_now_compiles_GEOS-Chem_for_reduced_grids|(v11-02a) Bug fix: Specifing <tt>NO_REDUCED=no</tt> now compiles GEOS-Chem for reduced grids]]
+
*[[GEOS-Chem_Makefile_Structure#Removed_the_COMPILER_variable_from_Makefile_header.mk_for_a_cleaner_build_sequence|(v11-02a) Removed the <tt>COMPILER</tt> variable from <tt>Makefile_header.mk</tt> for a cleaner build sequence]]
+
*[[GEOS-Chem v11-02#Print the version number to the log file|(v11-02a) Print the version number to the log file]]
+
*[[#Removed_the_NNPAR_parameter_from_CMN_SIZE_mod.F|(v11-02a) Removed the <tt>NNPAR</tt> parameter from <tt>CMN_SIZE_mod.F</tt>]]
+
*[[Wet_deposition#Removal_of_obsolete_variables_NSOL_and_IDWETD|(v11-02a) Removed obsolete variables <tt>NSOL</tt> and <tt>IDWETD</tt> in the wetdep module]]
+
*[[Derived type objects used by GEOS-Chem#Summary of fields removed from Input_Opt|(v11-02a) Removed obsolete fields of the <tt>Input_Opt</tt> object]]
+
*[[GEOS-Chem_v11-02#Fixed_an_incorrect_format_statement_in_input_mod.F|(v11-02c) Fixed an incorrect format statement in <tt>input_mod.F</tt>]]
+
*[[Sulfate_aerosols#Add_bug_fix_in_sulfate_mod.F_involving_reorder_IF_statements_for_Fahey_and_Seinfeld_decision_algorithm|(v11-02e) Reordered IF statement in <tt>sulfate_mod.F</tt> for Fahey & Seinfeld decision algorithm]]
+
*[[GEOS-Chem_v11-02#Change_timestep_units_from_minutes_to_seconds|(v11-02e) Change timestep units from minutes to seconds]]
+
*[[UCX_chemistry_mechanism#Remove_UCX_.23ifdefs_and_replace_with_Input_Opt.25LUCX|(v11-02e) Remove #ifdefs for UCX and replace with <tt>Input_Opt%LUCX</tt> logical switch]]
+
*[[GEOS-Chem_v11-02#Fix_bug_in_units_of_UCX_P.2FL_rates|(v11-02f) Fix bug in units of UCX prod/loss rates]]
+
*[[MERRA-2_implementation_details#Default_timestep_for_MERRA-2_nested_grid_simulations|(v11-02f) Change default timesteps for MERRA-2 nested-grid simulations]]
+
 
+
|-valign="top"
+
|[[Tagged O3 simulation]]
+
|
+
*[[Tagged_O3_simulation#Write_initial_and_final_Ox_mass_to_file|(v11-02b) Write initial and final O3 mass to file, to facilitate budget computations]]
+
*[[Tagged_O3_simulation#Fix_bug_in_calculation_of_L.28Ox.29|(v11-02f) Fix bug in calculation of L(Ox) for tagged O3 simulations]]
+
 
+
|-valign="top"
+
|[[TOMAS aerosol microphysics]]
+
|
+
*[[TOMAS_aerosol_microphysics#Typo_in_wetscav_mod.F_for_TOMAS30_simulation|(v11-02c) Fixed typo in <tt>wetscav_mod.F</tt> for the TOMAS30 simulation]]
+
  
 
|}
 
|}
  
== Issues resolved in GEOS-Chem v11-01 ==
+
=== GEOS-Chem 12 ===
 
+
The bugs and technical issues listed below were resolved in [[GEOS-Chem v11-01]].  Also be sure to visit [[Known issues caused by compiler bugs|our ''Known issues caused by compiler bugs'' wiki page]] for a list of compiler-related issues and workarounds.
+
  
{| border=1 cellspacing=0 cellpadding=5
+
{| border=1 cellspacing=0 cellpadding=5  
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250px"|Module or area
+
!Version
!width="750px"|Issue that was resolved
+
!Released
 +
!colspan="2"|List of bugs and issues (now posted on the listed Github repository)
  
 
|-valign="top"
 
|-valign="top"
|[[Aerosol-only simulation]]
+
|[[GEOS-Chem 12#12.9.3|12.9.3]]
|
+
|06 Aug 2020
*[[Aerosol-only_simulation#Fixed_undefined_molecular_weight_of_HNO3_in_routine_SEASALT_CHEM|Fixed undefined molecular weight of HNO3 in routine SEASALT_CHEM]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/16?closed=1 '''Milestone 12.9.3''']
  
 
|-valign="top"
 
|-valign="top"
|[[CH4 simulation]]
+
|[[GEOS-Chem 12#12.9.2|12.9.2]]
|
+
|24 Jul 2020
*[[CH4_simulation#Fix_bug_in_CH4_emissions|Fix bug in CH4 emissions unit]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/15?closed=1 '''Milestone 12.9.2''']
  
 
|-valign="top"
 
|-valign="top"
|[[GEOS-Chem chemistry mechanisms|Chemistry]]
+
|[[GEOS-Chem 12#12.9.1|12.9.1]]
|
+
|17 Jul 2020
*[[Centralized_chemistry_time_step#Optimal_Configuration|Adopt the optimal timestep recommendations of Philip et al 2015]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[GEOS-Chem_v11-01#Update_of_PMN_.2B_O3_reaction_products_in_globchem.dat_file|Update of PMN + O3 reaction products in globchem.dat file]]
+
|[https://github.com/geoschem/geos-chem/milestone/14?closed=1 '''Milestone 12.9.1''']
*[[UCX_chemistry_mechanism#Fix_for_black_carbon_in_ucx_mod.F|Fix for black carbon in <tt>ucx_mod.F</tt>]]
+
*[[GEOS-Chem_v11-01#Modifications_to_ND20_to_archive_afternoon_P.28O3.29_and_L.28O3.29|Modifications to ND20 to archive afternoon P(O3) and L(O3)]]
+
*[[Sulfate_aerosols#Bug_fix_for_sea_salt_alkalinity_in_sulfate_mod.F|Bug fix for sea salt alkalinity in <tt>sulfate_mod.F</tt>]]
+
*[[GEOS-Chem_v10-01#Bug_fix_for_offline_dust_aerosols_when_UCX_is_on|Bug fix for offline dust aerosols when UCX is on]]
+
*[[Mineral_dust_aerosols#Bug_fixes_for_hydrophobic_aerosol_properties|Bug fixes for hydrophobic aerosol properties]]
+
*[[New_isoprene_scheme#Syntax_error_in_globchem.dat_file_for_MOBA_reaction_rate|Fix syntax error in <tt>globchem.dat</tt> for the MOBA + OH —> MOBAOO reaction rate]]
+
*[[New_isoprene_scheme#Bug_in_reaction_ISNOOA_.2B_NO2_in_globchem.dat|Fixed typo in the ISNOOA + NO2 -> PMN reaction rate in <tt>globchem.dat</tt>]]
+
*[[Stratospheric_chemistry#Fix_for_monthly_stratospheric_P.2FL_rates_in_HEMCO|Fix for monthly stratospheric P/L rates in HEMCO]]
+
*[[Stratospheric_chemistry#Bug_in_the_GMI_stratospheric_production_rates_for_HCOOH|Fix bug in the GMI stratospheric production rates for HCOOH]]
+
**[[Stratospheric_chemistry#Fixed_incorrect_timestamps_in_the_newest_HCOOH_prod.2Floss_file|Fixed incorrect timestamps in the updated GMI HCOOH strat P/L file]]
+
*[[FlexChem#Incorrect_species_units_used_in_routines_UCX_NOX_and_UCX_H2SO4PHOT|Fix incorrect species units in routines UCX_NOX and UCX_H2SO4PHOT]]
+
*[[GEOS-Chem_v11-01#Fix_molecular_weight_of_N2O5|Fix molecular weight of N2O5]]
+
*[[Aerosol_optical_properties#Fix_for_TITLEAAt_out-of-bounds_error|Fix for out-of-bounds error when using the brown carbon option]]
+
  
 
|-valign="top"
 
|-valign="top"
|[[CO2 simulation]]
+
|[[GEOS-Chem 12#12.9.0|12.9.0]]
|
+
|17 Jul 2020
*[[CO2_simulation#Additional_Update_and_Bug_Fix|Update CO2 emission files]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[CO2_simulation#Bug_fix:_Make_sure_nAdvect_is_initialized_in_EMISSCO2|Bug fix: Make sure <tt>nAdvect</tt> is initialized in EMISSCO2]]
+
|[https://github.com/geoschem/geos-chem/milestone/10?closed=1 '''Milestone 12.9.0''']
  
 
|-valign="top"
 
|-valign="top"
|[[Cloud convection]]
+
|[[GEOS-Chem 12#12.8.2|12.8.2]]
|
+
|27 May 2020
*[[Cloud_convection#Fixed bug in DO_MERRA_CONVECTION affecting mass conservation|Correct bug in below cloud average mixing ratio calculation in DO_MERRA_CONVECTION to improve mass balance]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[Cloud_convection#Resolve_very_high_tracer_concentrations_in_MERRA_and_GEOS-FP_convective_scavenging|Resolve very high tracer concentrations in GEOS-FP and MERRA convective scavenging]]
+
|[https://github.com/geoschem/geos-chem/milestone/13?closed=1 '''Milestone 12.8.2''']
  
 
|-valign="top"
 
|-valign="top"
|Compiler / Fortran issues
+
|[[GEOS-Chem 12#12.8.1|12.8.1]]
|Compiler issues:
+
|21 May 2020
*[[GNU Fortran compiler|Add support for GNU Fortran compiler]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[PGI Fortran compiler#File_Linking_Error|Fix linker error when using the PGI compiler]]
+
|[https://github.com/geoschem/geos-chem/milestone/12?closed=1 '''Milestone 12.8.1''']
*[[PGI Fortran compiler#Updates_for_GEOS-Chem_v11-01|Additional updates compiling GEOS-Chem with the PGI Fortran compiler]]
+
*[[PGI Fortran compiler#Updates_for_GEOS-Chem_v11-01|Add further fixes for compiling GEOS-Chem with PGI Fortran]]
+
*[[GEOS-Chem_Makefile_Structure#TRACEBACK.3Dy_is_now_the_default_setting|<tt>TRACEBACK=y</tt> is now the default setting for all simulations]]
+
*[[Intel_Fortran_Compiler#Cannot_compile_GEOS-Chem_v10-01_with_Intel_Fortran_Compiler_v17|Remove offending code that was preventing GEOS-Chem from compiling with Intel Fortran v17]]
+
 
+
Fortran language issues:
+
*[[GEOS-Chem_v11-01#Do_not_nullify_local_pointers_in_the_same_line_where_they_are_declared|Do not nullify local pointers in the same line where they are declared]]
+
*[[Flexible_precision_in_GEOS-Chem#Update_KIND_parameters_to_facilitate_interface_with_the_Beijing_Climate_Center_model|Update flexible precision parameters so that GEOS-Chem can interface with the Beijing Climate Center model]]
+
*[[GEOS-Chem v11-01#Prevent errors caused by uninitialized fields of the State_Met object|Prevent errors caused by uninitialized fields of the <tt>State_Met</tt> object]]
+
*[[UCX_chemistry_mechanism#Only_allocate_certain_fields_of_State_Chm_for_UCX-based_simulations|Only allocate certain fields of <tt>State_Chm</tt> for UCX-based simulations]]
+
*[[GEOS-Chem v11-01#Allocate aerosol fields of State_Chm only for full-chemistry or aerosol-only simulations|Allocate aerosol fields of <tt>State_Chm</tt> only for full-chemistry or aerosol-only simulations]]
+
*[[Aerosol_emissions#Online_emission_of_marine_primary_organic_aerosol_.28POA.29|Parallelization bug fix for marine POA]]
+
  
 
|-valign="top"
 
|-valign="top"
|[[List of diagnostics for v11-01|Diagnostics]]
+
|[[GEOS-Chem 12#12.8.0|12.8.0]]
|
+
|04 Mar 2020
*[[GEOS-Chem_v11-01#Bug_fixes_for_the_ND21_diagnostic|Bug fix for the ND21 diagnostic]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Bug_fix_for_monoterpenes_in_ND46_diagnostic|Bug fix for monoterpenes in ND46 diagnostic]]
+
|[https://github.com/geoschem/geos-chem/milestone/7?closed=1 '''Milestone 12.8.0''']
*[[GEOS-Chem_v11-01#Fix_units_of_O1D_and_O3P_in_ND43_diagnostic|Fix units of O1D and O3P in ND43 diagnostic]]
+
*[[GEOS-Chem_v11-01#Fix_incorrect_unit_strings_for_ND65_diagnostic_in_diag3.F|Fix incorrect unit strings for ND65 diagnostic in <tt>diag3.F</tt>]]
+
  
 
|-valign="top"
 
|-valign="top"
|[[HEMCO data directories|Emissions (via HEMCO)]]
+
|[[GEOS-Chem 12#12.7.2|12.7.2]]
|
+
|09 Mar 2020
*[[Lightning_NOx_emissions#Correct_problem_in_OTD-LIS_local_redistribution_files|Fix problem in OTD/LIS lighning redistribution files]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[GEOS-Chem_v10-01#Fix_for_reading_hourly_NEI2011_emissions|Fix for reading hourly NEI2011 emissions]]
+
|[https://github.com/geoschem/geos-chem/milestone/11?closed=1 '''Milestone 12.7.2''']
*[[EMEP_European_anthropogenic_emissions#Zero_EMEP_emissions_at_30N_for_2x25_and_higher_resolutions|Use an updated EMEP mask file to prevent zero emissions at 30 N for 2&deg; x 2.5&deg; or higher resolutions]]
+
*[[Secondary_organic_aerosols#Incorrect_concentrations_in_SOA-SVPOA_simulation|Fix an emissions error in the SOA-SVPOA simulation]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Fixed_missing_pointer_in_call_to_HCO_CalcVertGrid|Fixed missing pointer in call to HEMCO routine Hco_CalcVertGrid]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Enable_emissions_in_the_stratosphere_for_specialty_simulations|Correct bug introduced in v11-01e where emissions were disabled in the stratosphere for specialty simulations]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Fix_bug_preventing_HEMCO_from_writing_restart_files_more_than_once_per_run|Fixed bug preventing HEMCO from writing restart files more than once per run]]
+
*[[EDGAR_v4.2_anthropogenic_emissions#Correct_bug_in_units_of_EDGAR_v4.2_SO2_emissions|Correct bug in units of EDGAR v4.2 SO2 emissions]]
+
*[[EDGAR_v4.2_anthropogenic_emissions#Prevent_biofuel_emissions_from_being_double_counted|Prevent biofuel emissions from being double counted in EDGAR v4.2]]
+
*[[Scale_factors_for_anthropogenic_emissions#Bug_fix_for_NOx_diurnal_scale_factors|Fix bug in NOx diurnal scale factors]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem|Update HEMCO from version 1.1.016 to latest version available]]
+
*[[Implementation_of_RETRO_Anthropogenic_Emissions#RETRO_anthropogenic_propane_emissions_are_too_low|Replace RETRO C3H8 emissions with emissions from Xiao et al.]]
+
*[[QFED_biomass_burning_emissions#Biomass_burning_emissions_diagnostic_is_zero_when_QFED_is_used|Fix for biomass burning diagnostic when QFED emissions are used]]
+
*[[HEMCO#Update:_Preventing_seg_fault_in_HEMCO_v2.0_caused_by_compiler_bug|Prevent seg fault in HEMCO v2.0 caused by Intel Fortran compiler bug]]
+
  
 
|-valign="top"
 
|-valign="top"
|[[Mercury]] and [[POPs simulation|POPs]] simulations
+
|[[GEOS-Chem 12#12.7.1|12.7.1]]
|
+
|19 Feb 2020
*[[Mercury#Hg_ocean_MLD_bug_fixes|Bug fixes for computing MLD in <tt>ocean_mercury_mod.F</tt>]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[Mercury#Parallelization_bug_fixes_for_GEOS-5_Hg_simulations|Fix parallelization errors that prevented Hg simulations from passing unit tests]]
+
|[https://github.com/geoschem/geos-chem/milestone/9?closed=1 '''Milestone 12.7.1''']
*[[Mercury#Avoid_floating-point_exception_in_OCEAN_MERCURY_READ|Avoid floating-point exception in OCEAN_MERCURY_READ]]
+
*[[Mercury#Bug_Fixes_to_v11-01c_Hg_Updates|Bug fixes for Arctic Hg updates in v11-01c]]
+
*[[Mercury#Correct_too-high_emissions_of_Hg2_over_China_and_EU|Correct too-high emissions of Hg2 over China and EU]]
+
*[[Mercury#Now_call_DO_RED_INPLUME_after_the_HEMCO_configuration_file_is_read|Now call subrouine DO_RED_INPLUME after the HEMCO configuration file is read]]
+
*[[POPs_simulation#Avoid_floating-point_exception_in_routine_CHEM_POPGP|Avoid floating-point error in routine CHEM_POPGP]]
+
  
 
|-valign="top"
 
|-valign="top"
|Met fields and derived quantities
+
|[[GEOS-Chem 12#12.7.0|12.7.0]]
|
+
|03 Feb 2020
*[[Air_Quantity_Updates_for_v11-01|Incorporate moisture into air quantities, tracer units, and tracer unit conversions]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[GEOS-Chem_species_units#Updating_Air_Quantities|Bug fix to update air quantities after specific humidity is updated in non-local PBL mixing]]  
+
|[https://github.com/geoschem/geos-chem/milestone/4?closed=1 '''Milestone 12.7.0''']
*[[GEOS-Chem_v11-01#Incorrect_incorporation_of_moisture_in_GEOS-Chem_air_quantities|Fix to remove moisture signature in dry mixing ratio]]
+
  
 
|-valign="top"
 
|-valign="top"
|[[Preparing data files for use with HEMCO#The COARDS netCDF standard|netCDF I/O]]
+
|[[GEOS-Chem 12#12.6.3|12.6.3]]
|
+
|25 Nov 2019
*[[GEOS-Chem_Output_Files#NetCDF_File_Format|Migration from bpch to netCDF output file format]]
+
|[https://github.com/geoschem/gchp geoschem/gchp]
*[[GEOS-Chem_Output_Files#Improve_write_speed_of_netCDF_output_files|Improve write speed of netCDF output files]]
+
|[https://github.com/geoschem/gchp/milestone/2?closed=1 '''Milestone 12.6.3''']
*[[GEOS-Chem_Output_Files#GAMAP_can_now_read_GEOS-Chem_restart_files_in_netCDF_format|GAMAP can now read GEOS-Chem restart files in netCDF format]]
+
  
 
|-valign="top"
 
|-valign="top"
|[[FAST-JX_v7.0_photolysis_mechanism|Photolysis]]
+
|[[GEOS-Chem 12#12.6.2|12.6.2]]
|
+
|15 Nov 2019
*[[FAST-JX_v7.0_photolysis_mechanism#Fix_for_TOMS_to_address_strange_cycle_in_OH_output|Fix for TOMS/HEMCO to address strange cycle in OH output]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[FAST-JX_v7.0_photolysis_mechanism#Use_TOMS_ozone_for_all_years_when_running_simulations_with_GEOS-5|Use TOMS ozone for all years when running simulations with GEOS-5 meteorology]]
+
|[https://github.com/geoschem/geos-chem/milestone/6?closed=1 '''Milestone 12.6.2''']
  
 
|-valign="top"
 
|-valign="top"
|[[Regridding in GEOS-Chem|Regridding]]
+
|[[GEOS-Chem 12#12.6.1|12.6.1]]
|
+
|28 Oct 2019
*[[Regridding_in_GEOS-Chem#Bug_fix:_MAP_A2A_now_only_uses_periodic_BCs_for_global_data|Bug fix: MAP_A2A now applies periodic boundary conditions only to global data sets during regridding]]
+
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[Implementation_of_HEMCO_in_GEOS-Chem#Fixed_bug_in_time_interpolation_in_ncdf_mod.F90|Bug fix for time interpolation in netCDF utility module <tt>ncdf_mod.F90</tt>]]
+
|[https://github.com/geoschem/geos-chem/milestone/5?closed=1 '''Milestone 12.6.1''']
  
 
|-valign="top"
 
|-valign="top"
|[[Coupling_GEOS-Chem_with_RRTMG|RRTMG radiative transfer model]]
+
|width="80px"|[[GEOS-Chem 12#12.6.0|12.6.0]]
|
+
|width="100px"|18 Oct 2019
*[[Coupling_GEOS-Chem_with_RRTMG#Fix_bug_that_prevents_storage_of_O3_and_CH4_RFs|Fix bug that prevents storage of O3 and CH4 RF's]]
+
|width="200px"|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
*[[Coupling_GEOS-Chem_with_RRTMG#Bug_in_RRTMG_array_sizes|Bug fix in RRTMG array sizes]]
+
|width="400px"|[https://github.com/geoschem/geos-chem/milestone/2?closed=1 '''Milestone 12.6.0''']
*[[Coupling_GEOS-Chem_with_RRTMG#Bug_fixes_in_rrtmg_rad_transfer_mod.F|Further bug fixes in <tt>rrtmg_transfer_mod.F</tt>]]
+
*[[Coupling_GEOS-Chem_with_RRTMG#Replace_nonstandard_DLOG_function_with_LOG|Replace nonstandard DLOG function with LOG]]
+
 
+
|-valign="top"
+
|Marine POA simulations
+
|
+
*[[Aerosol_emissions#Bug_fix:_Allocate_the_OCCONV_array_for_marine_POA_simulations|Allocate the OCCONV array for marine POA simulations]]
+
 
+
|-valign="top"
+
|[[Rn-Pb-Be simulation|Radon-Lead-Beryllium simulation]]
+
|
+
*[[Rn-Pb-Be_simulation#Typo_in_HEMCO_extension_module_hcox_gc_RnPbBe_mod.F90|Fix typo in HEMCO extension module <tt>hcox_gc_RnPbBe_mod.F90</tt>]]
+
 
+
|-valign="top"
+
|[[GEOS-Chem species database|Species database]] and [[Physical_constants|definitions of physical constants]]
+
|
+
*[[Physical_properties_of_GEOS-Chem_species#Discrepancies_found_in_the_dry_deposition_module|Remove inconsistencies in the definitions of physical properties of GEOS-Chem species]]
+
*[[Sea_salt_aerosols#Molecular_weight_discrepancy_in_drydep_mod.F|Use proper molecular weights for sea salt aerosols in the dry deposition module]]
+
*[[Sulfate_aerosols#Give_SO4s_and_NITs_the_same_molecular_weight_as_SALC|Give SO4s and NITs the same molecular weight as SALC]]
+
*[[Mineral_dust_aerosols#Now_treat_DST2-DST4_as_coarse_mode_in_wet_scavenging|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
+
*[[GEOS-Chem_species_database#Defining_molecular_weight_fields_of_the_Input_Opt_object_from_the_species_database|Define molecular weight fields of the <tt>Input_Opt</tt> object from the species database]]
+
*[[Physical_constants|Now use consistent physical parameter values throughout GEOS-Chem]]
+
*[[Physical_constants|Now use consistent physical constant declarations]]
+
 
+
|-valign="top"
+
|[[Tagged CO simulation]]
+
|
+
*[[Tagged_CO_simulation#OH_is_now_converted_to_the_proper_units_after_being_read_from_HEMCO|Now convert OH to the proper units in the tagged CO simulation]]
+
 
+
|-valign="top"
+
|[[Tagged O3 simulation]]
+
|
+
*[[GEOS-Chem_v10-01#Bug_in_European_grid_range_for_tagged_Ox_simulation|Bug fix in European grid range for tagged O3 simulation]]
+
*[[GEOS-Chem_v10-01#Bug_fix_for_PBLTOP_and_MTTOP_values_in_tagged_ozone_simulation|Bug fix for PBLTOP and MTTOP values in tagged O3 simulation]]
+
 
+
|-valign="top"
+
|[[TOMAS aerosol microphysics]]
+
|
+
*[[TOMAS_aerosol_microphysics#Updates_to_TOMAS_Jeagle_sea_salt_extension|Updates to TOMAS Jeagle sea salt extension]]
+
*[[TOMAS_aerosol_microphysics#Add_temporary_fix_to_get_TOMAS_dry_deposition_to_pass_unit_tests|Add temporary fix to get TOMAS dry deposition to pass unit tests]]
+
 
+
|-valign="top"
+
|Various structural updates
+
|
+
*[[GEOS-Chem_v11-01#Bug_fix_for_custom_grid_in_tpcore_bc_mod.F|Bug fix for custom nested grid in <tt>tpcore_bc_mod.F</tt>]]
+
*[[GEOS-Chem v11-01#Rename_grid_mod.F90_to_gc_grid_mod.F90|Rename <tt>grid_mod.F90</tt> to <tt>gc_grid_mod.F90</tt>]]
+
*[[GEOS-Chem v11-01#Error message output now advises users to check the HEMCO log file|GEOS-Chem error messages now advise the user to check the HEMCO log file]]
+
*[[GEOS-Chem_v11-01#Print_message_to_log_file_if_OpenMP_parallelization_is_turned_off|Print message to log file if OpenMP parallelization is turned off]]
+
 
+
|-valign="top"
+
|[[Wet deposition]]
+
|
+
*[[Wet_deposition#Low_tropospheric_210Pb_lifetime_against_deposition_in_v11-01b|Quick fix for low tropospheric 210Pb lifetime against wet deposition]]
+
*[[Wet_deposition#Fix_bug_in_GEOS-FP_re-evaporation_calculation|Fix bug in GEOS-FP re-evaporation calculation]]
+
  
 
|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:57, 23 January 2017 (UTC)
+
== Bugs and fixes in older GEOS-Chem versions ==
  
== Issues resolved in GEOS-Chem v10-01 ==
+
For a complete list of bugs and fixes in older GEOS-Chem versions, please see:
 
+
The following bugs and/or technical issues were resolved in [[GEOS-Chem v10-01]].  Also be sure to visit [[Known issues caused by compiler bugs|our ''Known issues caused by compiler bugs'' wiki page]] for a list of compiler-related issues and workarounds.
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-bgcolor="#CCCCCC"
+
!width="250px"|Module or area
+
!width="750px"|Issue that was resolved
+
 
+
|-valign="top"
+
|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]]
+
*[[Bromine_chemistry_mechanism#Bugs_in_data_files_used_to_prescribe_stratospheric_Bry|Now read corrected stratospheric Bry data via HEMCO]]
+
 
+
|-valign="top"
+
|Photolysis
+
|
+
*[[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#Bug_fix_for_determining_when_to_use_TOMS_O3_columns|Bug fix for determining when to use TOMS O3 columns]]
+
*[[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]]
+
*[[FAST-JX_v7.0_photolysis_mechanism#Now_use_proper_org.dat_file_with_data_for_multiple_wavelengths|Now use proper photolysis input file <tt>org.dat</tt>]]
+
 
+
|-valign="top"
+
|NOx-Ox chemistry 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]]
+
*[[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&deg; x 0.3125&deg; 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]]
+
*[[GEOS-Chem_v10-01#Bug_fixes_and_updates_for_v10-01i|Now call the planeflight diagnostic after chemistry, not after emissions]]
+
*[[Wet_deposition#Bug_fixes_for_scavenging_by_co-condensation|Bug fixes for wet scavenging by co-condensation]]
+
*[[Wet_deposition#Bugs_in_MERRA_wet_deposition|Fixes for bugs in wet deposition when using MERRA meteorology]]
+
*[[Dry_deposition#Remove_obsolete_ISN2_drydep_species|Remove obsolete ISN2 drydep species]]
+
*[[GEOS-Chem_v10-01#Fixed_typo_for_BROMOCARB_SEASON_in_HEMCO_configuration_files|Fixed typo for BROMOCARB_SEASON in HEMCO configuration files]]
+
*[[GEOS-Chem_v10-01#Fixes_for_the_0.25_x_0.3125_nested_EU_simulation_using_GEOS-FP_meteorology|Bug fixes for GEOS-FP nested EU simulation]]
+
*[[GEOS-Chem_v10-01#Additional_fixes_for_MERRA_wet_deposition|Fixes for wet deposition when using MERRA met fields]]
+
*[[GEOS-Chem_v10-01#Fix_AEFs_for_sesquiterpenes_in_the_SOA_simulation|Fix MEGAN AEF's for sesquiterpenes in the SOA simulation]]
+
 
+
|-valign="top"
+
|Specialty simulations
+
|
+
*[[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#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]]
+
*[[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]]
+
*[[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]]
+
 
+
|-valign="top"
+
|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]]
+
*[[Ship_emissions#Bug_fixes_for_the_PARANOX_HEMCO_extension|Bug fixes for the PARANOX extension in HEMCO]]
+
*[[Regridding_in_GEOS-Chem#Error_in_regridding_regional_data_files|Bug fix for regridding of regional data files by HEMCO]]
+
*[[MEGAN v2.1 plus Guenther 2012 biogenic_emissions#Minor_bug_fix_in_MEGAN_Mono_extension|Prevent array out-of-bounds error if <tt>MEGAN_mono</tt> extension is turned off]]
+
*[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Restore_missing_BIOGENIC_CO_diagnostics|Restore missing diagnostic: "Biogenic CO from monoterpenes"]]
+
*[[Implementation_of_HEMCO_in_GEOS-Chem#Features_added_during_the_public_comment_period_prior_to_v10-01_release|Additional HEMCO updates made during the v10-01 period of public comment]]
+
*[[GEOS-Chem_v10-01#Updated_name_of_ICOADS_SHIP_files_in_HEMCO_configuration_files|Fixed filename for ICOADS_SHIP in HEMCO configuration files]]
+
*[[GEOS-Chem v10-01#Avoid PARANOX SUNCOS error by using the proper timestamps|Fix for error in PARANOX caused by improper timestamps of SUNCOS]]
+
*[[GEOS-Chem_v10-01#Minor_fixes_for_FINNv1_biomass_burning|Minor fixes for FINNv1 biomass burning emissions]]
+
*[[GEOS-Chem_v10-01#Removing_additional_code_made_obsolete_by_HEMCO|Removing leftover code that was orphaned by HEMCO]]
+
 
+
|-valign="top"
+
|Removing computational bottlenecks
+
|
+
*[[Cloud convection#Removed array temporaries in call to FVDAS_CONVECT|Removed array temporaries in the call to the GEOS-4 convection routine]]
+
*[[GCAP#Removed_array_temporaries_in_call_to_GCAP_CONVECT|Removed array temporaries in the call to the GCAP convection routine]]
+
*[[Mercury#Remove_array_temporaries_in_routine_READ_HG2_PARTITIONING|Removed array temporaries in subroutine <tt>READ_HG2_PARTITIONING</tt>]]
+
*[[Advection_scheme_TPCORE#Reduce_time_spent_in_routine_TPCORE_FVDAS|Reduce time spent in advection driver routine TPCORE_FVDAS]]
+
 
+
|-valign="top"
+
|Miscellaneous
+
|
+
*[[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]]
+
*[[Regridding_in_GEOS-Chem#Fix_for_optimization_error_discovered_in_v10-01h|Fix for optimization error discovered in v10-01h]]
+
*[[GEOS-Chem_v10-01#Bug_fix_in_I3_field_interpolation|Bug fix for I3 field interpolation]]
+
*[[GEOS-Chem_v10-01#Minor_bug_fix_in_gamap_mod.F|Bug fix in gamap_mod.F]]
+
*[[GEOS-Chem_v10-01#Bug_fixes_for_the_PGI_compiler|Bug fixes for the PGI compiler]]
+
*[[GEOS-Chem_v10-01#Other miscellaneous updates|Now use "percent" instead of "%" in data files]]
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|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.  Also be sure to visit [[Known issues caused by compiler bugs|our ''Known issues caused by compiler bugs'' wiki page]] for a list of compiler-related issues and workarounds.
+
 
+
{| border=1 cellspacing=0 cellpadding=5
+
|-bgcolor="#CCCCCC"
+
!width="250px"|Module or area
+
!width="750px"|Issue that was resolved
+
 
+
|-valign="top"
+
|Emissions
+
|
+
*[[GEOS-Chem_v9-02#Bug_fix_for_updated_CAC_emissions|Bug fix for updated CAC emissions]]
+
*[[GEOS-Chem_v9-02#Bug_fix_for_Br2_emissions|Bug fix for Br2 emissions]]
+
*[[GEOS-Chem_v9-02#Bug_in_regridding_of_anthropogenic_emissions|Bug fix in regridding of anthro emissions]]
+
*[[GEOS-Chem_v9-02#Bug_in_MEGAN_emissions_when_running_with_MERRA_or_GEOS-FP|Bug in MEGAN emissions when using MERRA or GEOS-FP]]
+
*[[GEOS-Chem_v9-02#Bug_fix_in_nei2005_anthro_mod.F|Bug fix in nei2005_anthro_mod.F]]
+
*[[David_Streets_regional_emissions_for_China_and_SE_Asia#Bug_in_EMIS_STREETS_ANTHRO_05x0666|Bug fix in EMIS_STREETS_ANTHRO_05x0666]]
+
*[[GEOS-Chem_v9-02#Bug_fixes_in_biofuel_mod.F_and_emfossil.F|Bug fixes in biofuel_mod.F and emfossil.F]]
+
*[[GFED3_biomass_burning_emissions#Bug_fix_for_3-hourly_GFED3_emissions|Bug fix for 3-hourly GFED3 emissions]]
+
*[[Volcanic_SO2_emissions_from_Aerocom#Typo_in_VOLCPRESS_definition|Fixed typo in Aerocom volcanic SO2 emissions routine]]
+
*[[GEOS-Chem_v9-02#Bug_fixes_in_day-of-week_computation|Bug fixes in day-of-week computation]]
+
*[[Anthropogenic_emissions#Prevent_negative_emissions_over_Canada|Prevent negative emissions over Canada]]
+
*[[TOMAS_aerosol_microphysics#Minor_bug_in_TOMAS_sulfate_emissions|Minor bug fix in TOMAS sulfate emissions]]
+
*[[EPA/NEI05 North American emissions#Bug fix for NEI2005 SO4 emissions in sulfate_mod.F|Bug fix for NEI2005 SO4 emissions in sulfate_mod.F]]
+
*[[Hudman_et_al_2012_soil_NOx_emissions_algorithm#Prevent_LOG.280.29_error_from_occurring_in_soil_NOx_module|Prevent LOG(0) error from occurring in soil NOx module]]
+
*[[Historical_and_Future_Emissions#Bug_fix_for_BC.2FOC_biofuels_when_using_RCP_scenarios|Bug fix for biofuels when using RCP scenarios]]
+
 
+
|-valign="top"
+
|Dry deposition and wet deposition
+
|
+
*[[Acetone#DRYACET_is_missing_from_globchem.dat|Add missing DRYACET to globchem.dat mechanism file]]
+
*[[Wet_deposition#Bug_in_Henry.27s_constant|Bug fix in Henry's law constant]]
+
*[[Dry_deposition#Error_in_definition_of_RIP_and_IEPOX_drydep_species|Bug fix in definition of RIP, IEPOX drydep species]]
+
*[[Ship_emissions#Only_call_PARANOX_with_the_full-chemistry_simulations|Bug fix: Do not call PARANOX plume model for offline simulations]]
+
*[[Dry_deposition#Parallelization_error_in_routine_METERO|Fix for parallelization bug in subroutine METERO (in drydep module)]]
+
*[[Dry_deposition#Parallelization_error_in_routine_DRYFLX|Fixed parallelization error in routine DRYFLX (in dry deposition module)]]
+
*[[GEOS-Chem_v9-02#Prevent_bad_drydep_flux_values_from_being_passed_to_the_soil_NOx_emissions_module|Prevent bad drydep flux values from being passed to the soil NOx module]]
+
*[[Sea_salt_aerosols#Minor_bug_in_AD44_diagnostic_in_routine_DRY_DEPOSITION|Fixed minor bug in AD44 diagnostic in routine DRY DEPOSITION (sea salt aerosols)]]
+
 
+
|-valign="top"
+
|Met fields
+
|
+
*[[GEOS-Chem_v9-02#Correction_for_GEOS-5_PBL_heights|Correction for GEOS-5 PBL heights]]
+
*[[GEOS-5 issues#Reset NaNs in MOISTQ to zero|Reset NaNs in MOISTQ to zero]]
+
*[[GEOS-Chem_v9-02#Convert_MERRA_and_GEOS-FP_relative_humidity_fields_to_percent_after_reading_from_disk|Convert MERRA and GEOS-FP relative humidity fields to percent after reading from disk]]
+
*[[GEOS-Chem_v9-02#Bug_fix_for_declaration_of_GEOS-FP_PFICU.2C_PFLCU.2C_PFILSAN.2C_PFLLSAN_fields|Bug fix for declaration of certain GEOS-FP met fields]]
+
 
+
|-valign="top"
+
|Computational efficiency
+
|
+
*[[Passing_array_arguments_efficiently_in_GEOS-Chem|Eliminate inefficient subroutine calls]]
+
*[[Numerical issues discovered in GEOS-Chem|Corrected several floating-point errors]]
+
*Eliminate array temporaries in [[Passing_array_arguments_efficiently_in_GEOS-Chem#pjc_pfix_mod.F|pjc_pfix_mod.F]] and [[Passing_array_arguments_efficiently_in_GEOS-Chem#pressure_mod.F|pressure_mod.F]]
+
*[[Passing_array_arguments_efficiently_in_GEOS-Chem#gcap_convect_mod.F|Eliminate array temporaries in GCAP convection module]]
+
 
+
|-valign="top"
+
|Diagnostics
+
|
+
*[[GEOS-Chem_v9-01-03#Bug_fix_in_hdf_mod.F|Bug fix in hdf_mod.F]]
+
*[[GEOS-Chem_v9-02#Bug_fixes_in_diag48_mod.F|Bug fixes in diag48_mod.F]]
+
*[[Ship_emissions#Bug_in_ND36_diagnostic_when_ship_emissions_are_turned_off|Bug fix in ND36 diagnostic when ship emissions are turned off]]
+
 
+
|-valign="top"
+
|Specialty simulations (including microphysics)
+
|
+
*[[GEOS-Chem_v9-02#Bug_fixes_for_tagged_CO_simulation|Bug fixes for tagged CO simulation]]
+
*[[Mercury#Bug_fixes_for_nested_Hg_simulation|Bug fixes for nested Hg simulation]]
+
*[[GEOS-Chem_v9-02#Bug_fix_for_reading_OH_file_in_offline_simulations|Bug fix for reading OH file in offline simulations]]
+
*[[Aerosol-only_simulation#Emissions_not_included_when_using_non-local_PBL_mixing_scheme|Now include emissions in the aerosol-only simulation when using non-local PBL mixing]]
+
*[[Aerosol-only_simulation#Error_in_ISOROPIAII_when_sulfate_aerosols_are_turned_off|Avoid error in ISOROPIAII when using offline aerosol simulation]]
+
*[[Tagged_O3_simulation#Modifications_for_v9-02_tagged_O3_simulation|Modifications for v9-02 tagged O3 simulation]]
+
*[[CH4_simulation#Fixes_for_wetland_emissions|Fixes for wetland emissions in CH4 simulation]]
+
*[[Tagged_O3_simulation#Reactivate_stratospheric_P.28Ox.29_in_tagged_Ox_simulation|Reactivate stratospheric P(Ox) in tagged Ox simulation]]
+
*[[Tagged_O3_simulation#Replace_LD65_with_LLTROP_in_tagged_ox_mod.F|Replace LD65 with LLTROP in tagged_ox_mod.F]]
+
*[[TOMAS_aerosol_microphysics#Updates_for_GEOS-Chem_v9-02_public_release|Several fixes for TOMAS aerosol microphysics]]
+
*[[POPs_simulation#Prevent_error_when_reading_global_OC|Prevent error in POPs simulation when reading global OC]]
+
 
+
|-valign="top"
+
|Photolysis
+
|
+
*[[FAST-J photolysis mechanism#Prevent 0.5 x 0.667 nested grid simulations from crashing when reading TOMS data|Prevent 0.5 x 0.667 nested grid simulations from crashing when reading TOMS data]]
+
*[[Aerosol_optical_properties#Fix_to_jv_spec_aod.dat|Add fix to jv_spec_aod.dat file]]
+
*[[FAST-J photolysis mechanism#v9-02 post-release patch to fix bug in acetone photolysis pressure dependency|Post-release patch to fix bug in acetone photolysis pressure dependency]]
+
 
+
|-valign="top"
+
|Miscellaneous
+
|
+
*[[GEOS-Chem_v9-02#Additional_bug_fixes_for_MAP_A2A_regridding_algorithm|Additional bug fixes for MAP_A2A regridding]]
+
*[[Regridding_in_GEOS-Chem#Bug_in_grid_mod.F90|Bug fix in grid_mod.F90]]
+
*[[GCAP#Fixed_bugs_caused_by_GIGC_edits|Fixed typos in GCAP code]]
+
*[[Linoz stratospheric ozone chemistry#Reactivate parallel DO loop in LINOZ_CHEMO3|Reactivate parallel DO loop in LINOZ_CHEMO3 routine]]
+
*[[Boundary_layer_mixing#Corrected_unit_conversion_bug_in_calls_to_SET_CH3Br.2C_SET_BrO_for_TURBDAY_PBL_mixing|Corrected unit conversion bug when TURBDAY PBL mixing is used]]
+
*[[GEOS-Chem_v9-02#Fixes_for_minor_technical_issues|Fixes for minor technical issues]]
+
 
+
|}
+
 
+
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 21:00, 26 October 2015 (UTC)
+
 
+
== Bugs and fixes in older GEOS-Chem versions ==
+
  
For a complete list of bugs and fixes in older GEOS-Chem versions, please see [[Bugs and fixes prior to v9-02|our ''Bugs and fixes prior to v9-02'' wiki page]].
+
*[[Bugs and fixes in GEOS-Chem 12.0.0 to 12.5.0]]
 +
*[[Bugs and fixes in GEOS-Chem v9, v10, and v11]]
 +
*[[Bugs and fixes in GEOS-Chem v7 and v8]]
  
--[[User:Bmy|Bob Y.]] 17:40, 16 April 2015 (EDT)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:23, 22 March 2021 (UTC)
--[[User:Bmy|Bob Y.]] 14:11, 20 May 2014 (EDT)
+

Latest revision as of 13:56, 14 April 2021

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

Bugs and fixes lists have now been migrated to Github

We have been migrating bug reports to our GEOS-Chem issue tracker, which is located on our Github repository: https://github.com/geoschem/geos-chem/issues/. We recommend that you also look through both the open and closed issues on this page, as your issue might be listed there.

GEOS-Chem 13

Version Released List of bugs and issues (now posted on the listed Github repository)
13.3.0 TBD geoschem/geos-chem Milestone 13.3.0
13.2.0 TBD geoschem/geos-chem Milestone 13.2.0
13.1.0 TBD geoschem/geos-chem Milestone 13.1.0
13.0.2 12 Apr 2021 geoschem/geos-chem Milestone 13.0.2
13.0.1 23 Mar 2021 geoschem/geos-chem Milestone 13.0.1
13.0.0 18 Mar 2021 geoschem/geos-chem Milestone 13.0.0

GEOS-Chem 12

Version Released List of bugs and issues (now posted on the listed Github repository)
12.9.3 06 Aug 2020 geoschem/geos-chem Milestone 12.9.3
12.9.2 24 Jul 2020 geoschem/geos-chem Milestone 12.9.2
12.9.1 17 Jul 2020 geoschem/geos-chem Milestone 12.9.1
12.9.0 17 Jul 2020 geoschem/geos-chem Milestone 12.9.0
12.8.2 27 May 2020 geoschem/geos-chem Milestone 12.8.2
12.8.1 21 May 2020 geoschem/geos-chem Milestone 12.8.1
12.8.0 04 Mar 2020 geoschem/geos-chem Milestone 12.8.0
12.7.2 09 Mar 2020 geoschem/geos-chem Milestone 12.7.2
12.7.1 19 Feb 2020 geoschem/geos-chem Milestone 12.7.1
12.7.0 03 Feb 2020 geoschem/geos-chem Milestone 12.7.0
12.6.3 25 Nov 2019 geoschem/gchp Milestone 12.6.3
12.6.2 15 Nov 2019 geoschem/geos-chem Milestone 12.6.2
12.6.1 28 Oct 2019 geoschem/geos-chem Milestone 12.6.1
12.6.0 18 Oct 2019 geoschem/geos-chem Milestone 12.6.0

Bugs and fixes in older GEOS-Chem versions

For a complete list of bugs and fixes in older GEOS-Chem versions, please see:

--Bob Yantosca (talk) 14:23, 22 March 2021 (UTC)