Difference between revisions of "Bugs and fixes"

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(Issues resolved in GEOS-Chem v11-01)
(Bugs and fixes lists have now been migrated to Github)
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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).
+
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]] and [[Known issues caused by compiler bugs]] wiki pages for more information about unresolved issues.
  
== Issues resolved in GEOS-Chem v11-02 ==
+
== Bugs and fixes lists have now been migrated to Github ==
  
TBD
+
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.
  
== Issues resolved in GEOS-Chem v11-01 ==
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!Version
 +
!Released
 +
!colspan="2"|List of bugs and issues (now posted on the listed Github repository)
  
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.
+
|-valign="top"
 +
|13.0.0
 +
|TBD
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|
 +
*[https://github.com/geoschem/geos-chem/milestone/8 '''Milestone 13.0.0''' (open issues)]
 +
*[https://github.com/geoschem/geos-chem/milestone/8?closed=1 '''Milestone 13.0.0''' (closed issues)]
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.9.0|12.9.0]]
 +
|TBD
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|
 +
*[https://github.com/geoschem/geos-chem/milestone/10 '''Milestone 12.9.0''' (open issues)]
 +
*[https://github.com/geoschem/geos-chem/milestone/10?closed=1 '''Milestone 12.9.0''' (closed issues)]
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.8.1|12.8.1]]
 +
|TBD
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|
 +
*[https://github.com/geoschem/geos-chem/milestone/12 '''Milestone 12.8.1''' (open issues)]
 +
*[https://github.com/geoschem/geos-chem/milestone/12?closed=1 '''Milestone 12.8.1''' (closed issues)]
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.8.0|12.8.0]]
 +
|pending
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/7?closed=1 '''Milestone 12.8.0''']
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.7.2|12.7.2]]
 +
|09 Mar 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/11?closed=1 '''Milestone 12.7.2''']
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.7.1|12.7.1]]
 +
|19 Feb 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/9?closed=1 '''Milestone 12.7.1''']
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.7.0|12.7.0]]
 +
|03 Feb 2020
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/4?closed=1 '''Milestone 12.7.0''']
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.6.3|12.6.3]]
 +
|25 Nov 2019
 +
|[https://github.com/geoschem/gchp geoschem/gchp]
 +
|[https://github.com/geoschem/gchp/milestone/2?closed=1 '''Milestone 12.6.3''']
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.6.2|12.6.2]]
 +
|15 Nov 2019
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/6?closed=1 '''Milestone 12.6.2''']
 +
 
 +
|-valign="top"
 +
|[[GEOS-Chem 12#12.6.1|12.6.1]]
 +
|28 Oct 2019
 +
|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|[https://github.com/geoschem/geos-chem/milestone/5?closed=1 '''Milestone 12.6.1''']
 +
 
 +
|-valign="top"
 +
|width="80px"|[[GEOS-Chem 12#12.6.0|12.6.0]]
 +
|width="100px"|18 Oct 2019
 +
|width="200px"|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 +
|width="400px"|[https://github.com/geoschem/geos-chem/milestone/2?closed=1 '''Milestone 12.6.0''']
 +
 
 +
|}
 +
 
 +
== Issues resolved in GEOS-Chem 12.5.0 ==
 +
 
 +
The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.5.0|GEOS-Chem 12.5.0]], release date TBD.
  
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250px"|Module or area
+
!width="200px"|Module or area
!width="750px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
|[[GEOS-Chem chemistry mechanisms|Chemistry]]
+
|Chemistry
 
|
 
|
*[[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]]
+
#[[Stratospheric_chemistry#Bug_fix:_make_sure_stratospheric_BrY_concentrations_are_read_properly_each_month|Bug fix: Make sure stratospheric BrY concentrations are properly read each month]]
*[[UCX_chemistry_mechanism#Fix_for_black_carbon_in_ucx_mod.F|Fix for black carbon in <tt>ucx_mod.F</tt>]]
+
#[[FAST-JX_v7.0_photolysis_mechanism#FAST-JX_directory|Add photolysis menu to input.geos for specifying FAST-JX directory]]
*[[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)]]
+
#[[GEOS-Chem_12#Corrections_for_CFCs_in_the_chemistry_mechanism|Correction for CFCs in the chemistry mechanism]]
*[[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_12#Fix_typo_in_CLD_PARAMS_routine_in_gckpp_HetRates.F90|Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90]]
*[[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]]
+
#[https://github.com/geoschem/geos-chem-unittest/commit/0588a269376e0f1d8c7acd04f4b954402e31a76a 0588a269]
*[[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]]
+
#[https://github.com/geoschem/geos-chem/commit/03e94fed99cf2bb538dfc59ec514690a122b01a9 03e94fed]
*[[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>]]
+
#[https://github.com/geoschem/geos-chem/commit/1b9f69f048243cfb59226a69885ef152bfd33441 1b9f69f0]
*[[Stratospheric_chemistry#Fix_for_monthly_stratospheric_P.2FL_rates_in_HEMCO|Fix for monthly stratospheric P/L rates in HEMCO]]
+
#[https://github.com/geoschem/geos-chem/commit/95d124e0302d46d64f51ac4ff8db57febb81dda9 95d124e0]
*[[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"
|[[Cloud convection]]
+
|Diagnostics
 
|
 
|
*[[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]]
+
#[[List_of_diagnostics_archived_to_netCDF_format#Sample_HISTORY.rc_diagnostic_input_file|Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally]]
*[[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]]
+
#[[GEOS-Chem 12#Enable accurate cloud pH diagnostic calculation|Enable accurate cloud pH diagnostic calculation via post-processing ]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/6acd4ce393d9fdc4be8e8a70a532e6391f54b218 6acd4ce3]
 +
#[https://github.com/geoschem/geos-chem/pull/37/commits/1c15e54ad1c4f34ecdbb03266716c992001c8cc5 1c15e54a]
  
 
|-valign="top"
 
|-valign="top"
|[[HEMCO data directories|Emissions (via HEMCO)]]
+
|Structural updates
 
|
 
|
*[[Lightning_NOx_emissions#Correct_problem_in_OTD-LIS_local_redistribution_files|Fix problem in OTD/LIS lighning redistribution files]]
+
#Add optional capability to compile GEOS-Chem Classic and GCHP using CMake
*[[GEOS-Chem_v10-01#Fix_for_reading_hourly_NEI2011_emissions|Fix for reading hourly NEI2011 emissions]]
+
|
*[[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]]
+
#[https://github.com/geoschem/gchp/pull/27/commits pull/27]
*[[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"
|Met fields and derived quantities
+
|Emissions
 
|
 
|
*[[Air_Quantity_Updates_for_v11-01|Incorporate moisture into air quantities, tracer units, and tracer unit conversions]]
+
#Fixes for GFED4 biomass burning emissions, including:
*[[GEOS-Chem_species_units#Updating_Air_Quantities|Bug fix to update air quantities after specific humidity is updated in non-local PBL mixing]]
+
#*Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year
*[[GEOS-Chem_v11-01#Incorrect_incorporation_of_moisture_in_GEOS-Chem_air_quantities|Fix to remove moisture signature in dry mixing ratio]]
+
#*Remove the 27% scaling of POG to POA and emit 1:1 instead
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/3813a6fbd8a016842b16d7daa81f623d3d4edeb6 381386fb]
  
 
|-valign="top"
 
|-valign="top"
|[[Coupling_GEOS-Chem_with_RRTMG|RRTMG radiative transfer model]]
+
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
 +
 
 +
|-valign="top"
 +
|Structural updates
 
|
 
|
*[[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]]
+
#Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28
*[[Coupling_GEOS-Chem_with_RRTMG#Bug_in_RRTMG_array_sizes|Bug fix in RRTMG array sizes]]
+
#*Will introuduce faster parallel I/O
*[[Coupling_GEOS-Chem_with_RRTMG#Bug_fixes_in_rrtmg_rad_transfer_mod.F|Further bug fixes in <tt>rrtmg_transfer_mod.F</tt>]]
+
#*Will enable full use of gfortran compiler
 +
|
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:03, 15 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.4.0 ==
 +
 
 +
The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.4.0|GEOS-Chem 12.4.0]], release date TBD.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
|[[FAST-JX_v7.0_photolysis_mechanism|Photolysis]]
+
|Photolysis
 
|
 
|
*[[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]]
+
#[[FAST-JX_v7.0_photolysis_mechanism#Further_fix_added_in_12.4.0|Bug fix: Rebuild chemical mechanisms for FAST-JX fix added in 12.3.2]]
*[[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]]
+
#[[FAST-JX_v7.0_photolysis_mechanism#FAST-JX_directory|Add photolysis menu to input.geos for specifying FAST-JX directory]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/fcd0cfba13d63ee0b94c8fd06d29f6e49156aff6 fcd0cfba]
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/d34a9cd29f1272d85cd1355183ca02373f0b2ee8 d34a9cd2]
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:04, 15 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.3.2 ==
 +
 
 +
The bugs and technical issues listed below will be resolved [[GEOS-Chem 12#12.3.2|GEOS-Chem 12.3.2]].
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
|Specialty simulations
+
|Chemistry
|Aerosol-only
+
|
*[[Aerosol-only_simulation#Fixed_undefined_molecular_weight_of_HNO3_in_routine_SEASALT_CHEM|Fixed undefined molecular weight of HNO3 in routine SEASALT_CHEM]]
+
#[[GEOS-Chem 12#Inconsistency in H2402 concentrations in GCHP vs GEOS-Chem Classic|Fix inconsistency for species H2402 between GCHP and GEOS-Chem "Classic"]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/releases/tag/12.3.2 rel/12.3.2]
  
CO2
+
|-valign="top"
*[[CO2_simulation#Additional_Update_and_Bug_Fix|Update CO2 emission files]]
+
|Photolysis
 +
|
 +
#[[FAST-JX_v7.0_photolysis_mechanism#Duplicate_entries_for_species_ClNO2_in_FJX_j2j.dat_file|Remove duplicate entry for species ClNO2 in the FJX_j2j.dat file]]
 +
#[[FAST-JX_v7.0_photolysis_mechanism#Species_DHDC_was_not_listed_as_photolyzing_in_the_species_database|Species DHDC was not listed as photolyzing in the GEOS-Chem species database]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/releases/tag/12.3.2 rel/12.3.2]
 +
#[https://github.com/geoschem/gchp/commit/d7c48d144707aa25ac65bb7270466864e0559a0f d7c48d14]
  
CH4
+
|-
*[[CH4_simulation#Fix_bug_in_CH4_emissions|Fix bug in CH4 emissions unit]]
+
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
Marine POA
+
|-valign="top"
*[[Aerosol_emissions#Bug_fix:_Allocate_the_OCCONV_array_for_marine_POA_simulations|Allocate the OCCONV array for marine POA simulations]]
+
|Emissions
 +
|
 +
#Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default
 +
#Fix HEMCO diagnostics settings for lightning NO and seasalt emissions
 +
|
 +
#[https://github.com/geoschem/gchp/commit/f6ac477ad7637d7cfc4a6f2d479fd2509ecca9ef f6ac477a]
 +
#[https://github.com/geoschem/gchp/commit/cda5044e9c8430954fc6a0d550553f9f9a80bb33 cda5044e]
  
Mercury
+
|}
*[[Mercury#Hg_ocean_MLD_bug_fixes|Bug fixes for computing MLD in <tt>ocean_mercury_mod.F</tt>]]
+
*[[Mercury#Parallelization_bug_fixes_for_GEOS-5_Hg_simulations|Fix parallelization errors that prevented Hg simulations from passing unit tests]]
+
*[[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
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:37, 15 July 2019 (UTC)
*[[POPs_simulation#Avoid_floating-point_exception_in_routine_CHEM_POPGP|Avoid floating-point error in routine CHEM_POPGP]]
+
  
Radon-Lead-Beryllium
+
== Issues resolved in GEOS-Chem 12.3.1 ==
*[[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>]]
+
  
RRTMG
+
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.3.1|GEOS-Chem 12.3.1]] (release 08 Apr 2019).
*[[Coupling_GEOS-Chem_with_RRTMG#Replace_nonstandard_DLOG_function_with_LOG|Replace nonstandard DLOG function with LOG]]
+
  
Tagged CO
+
{| border=1 cellspacing=0 cellpadding=5
*[[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]]
+
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
Tagged O3
+
|-valign="top"
*[[GEOS-Chem_v10-01#Bug_in_European_grid_range_for_tagged_Ox_simulation|Bug fix in European grid range for tagged O3 simulation]]
+
|Diagnostics
*[[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]]
+
|
 +
#[[Planeflight_diagnostic#Planeflight_diagnostic_now_writes_out_data_for_the_last_timestep_of_the_day|Planeflight diagnostic now writes out data for the last timestep of the day]]
 +
#[[List_of_diagnostics_archived_to_netCDF_format#The_JValuesLocalNoon_collection|Fix the netCDF diagnostic for noontime J-values]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/04da94cdbe01c9032904a9f7d14ec3a5aded5aee 04da94cd]
 +
#[https://github.com/geoschem/gchp/commit/f4d43b7ace1d74adc2b8aed1bcd7b4d33a594878 f4d43b7a]
  
TOMAS Microphysics
+
|-valign="top"
*[[TOMAS_aerosol_microphysics#Updates_to_TOMAS_Jeagle_sea_salt_extension|Updates to TOMAS Jeagle sea salt extension]]
+
|Structural
*[[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]]
+
|
 +
#[[Stratospheric_chemistry#Do not allocate memory to array MINIT in strat_chem_mod.F90|Do not allocate memory to array MINIT in <tt>strat_chem_mod.F90</tt>]]
 +
#[[GEOS-Chem_12#Declare_State_Met.25AREA_M2_as_2-dimensional.2C_not_3-dimensional|Declare <tt>State_Met%Area_M2</tt> as 2-dimensional, not 3-dimensional]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/729fd2a7ed79b8a6a4a7fd6231097fbb1c4baf21 729fd2a7]
 +
#[https://github.com/geoschem/gchp/commit/e4af25f3b893263d1236c3a35c64e2e46f2e78cb e4af25f3b]
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:06, 16 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.3.0 ==
 +
 
 +
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.3.0|GEOS-Chem 12.3.0]] (release date TBD).
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
|Structural updates
+
|Diagnostics / Restart files
 
|
 
|
*[[PGI Fortran compiler#File_Linking_Error|Fix linker error when using the PGI compiler]]
+
#[[#Further_bug_fix_to_prevent_incorrect_restart_file_output_when_spanning_leap_year_days|Further bug fix for netCDF diagnostics spanning leap years]]
*[[GEOS-Chem_v11-01#Bug_fixes_for_the_ND21_diagnostic|Bug fix for the ND21 diagnostic]]
+
|
*[[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>]]
+
#[https://github.com/geoschem/geos-chem/commit/fb093d61b8321834d5f1d9565760e2828138b321 fb093d61]  
*[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Bug_fix_for_monoterpenes_in_ND46_diagnostic|Bug fix for monoterpenes in ND46 diagnostic]]
+
*[[Aerosol_emissions#Online_emission_of_marine_primary_organic_aerosol_.28POA.29|Parallelization bug fix for marine POA]]
+
*[[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]];
+
*[[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]]
+
*[[PGI Fortran compiler#Updates_for_GEOS-Chem_v11-01|Add further fixes for compiling GEOS-Chem with PGI Fortran]]
+
*[[Centralized_chemistry_time_step#Optimal_Configuration|Adopt the optimal timestep recommendations of Philip et al 2015]]
+
*[[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]]
+
*[[PGI Fortran compiler#Updates_for_GEOS-Chem_v11-01|Additional updates compiling GEOS-Chem with the PGI Fortran compiler]]
+
*[[Physical_constants|Now use consistent physical constant declarations]]
+
*[[GEOS-Chem_Output_Files#NetCDF_File_Format|Migration from bpch to netCDF output file format]]
+
*[[GNU Fortran compiler|Add support for GNU Fortran compiler]]
+
*[[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]]
+
*[[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_Makefile_Structure#TRACEBACK.3Dy_is_now_the_default_setting|<tt>TRACEBACK=y</tt> is now the default setting for all simulations]]
+
*[[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]]
+
*[[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]]
+
  
 
|-valign="top"
 
|-valign="top"
|[[Wet deposition]]
+
|Emissions
 
|
 
|
*[[Mineral_dust_aerosols#Now_treat_DST2-DST4_as_coarse_mode_in_wet_scavenging|Now treat DST2-DST4 as coarse mode in wet scavenging]]
+
#[[HEMCO_versions#Bug_fixes_for_HEMCO_interpolation_algorithm|Bug fixes for the HEMCO interpolation algorithm]]
**NOTE: This also will apply to dust uptake tracers DSTAL2-4, NITD2-4, SO4D2-4
+
#[[HEMCO_versions#Updates from the NASA GEOS development branch|Updates from the NASA GEOS development branch]]
*[[Wet_deposition#Low_tropospheric_210Pb_lifetime_against_deposition_in_v11-01b|Quick fix for low tropospheric 210Pb lifetime against wet deposition]]
+
#[[HEMCO_versions#Add_option_to_always_use_simulation_year_for_specified_fields|Add option to always use simulation year for specified fields]]
*[[Wet_deposition#Fix_bug_in_GEOS-FP_re-evaporation_calculation|Fix bug in GEOS-FP re-evaporation calculation]]
+
#[[HEMCO_versions#Prevent zero emissions for MEGAN_Mono extension species|Prevent zero emissions for MEGAN_Mono extension species]]
 +
#[[HEMCO_versions#Updates to the volcanic emissions extension|Updates to the volcanic emissions extension]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/e947fc8027b75eaa4ff5e22b65f046728b5ee7fb e947fc80]
 +
#[https://github.com/geoschem/geos-chem/commit/7df3fc8eefd47b8835335bd5c48f469d5c7e4385 7df3fc8e]
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/23189032720058b34d7b8140aac52989cfe4c1ee 23189032]
 +
#[https://github.com/geoschem/geos-chem/commit/af86c4ddc10e240662a572d8542292b2d30f5cc7 af86c4dd]
 +
#[https://github.com/geoschem/geos-chem/commit/07c103190221e1d77feaa97dfdd71749767c248a 07c10319]
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:53, 21 March 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.2.1 ==
 +
 
 +
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.2.1|GEOS-Chem 12.2.1]] (release date 28 Feb 2019).
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
 +
 
 +
|-valign="top"
 +
|Diagnostics / Restart files
 +
|
 +
#[[GEOS-Chem 12#Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days|Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/ca68f508b956a24663cf49722b437c638e9e9c6f ca68f508]
 +
 
 +
|-valign="top"
 +
|CO2 simulation
 +
|
 +
#[[CO2_simulation#Prevent_double-counting_in_CO2_chemical_source|Fix for CO2 simulation chemical source]]
 +
|
 +
#N/A
 +
 
 +
|-valign="top"
 +
|TOMAS simulations
 +
|
 +
#[[TOMAS_aerosol_microphysics#Restore_DST1.2C_DST2.2C_DST3.2C_and_DST4_in_TOMAS_simulations|Restore DST1, DST2, DST3, and DST4 in TOMAS simulations]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/5ed3e9cf3bdccfd7b144b5d768e64d0059357a7b 5ed3e9cf]
 +
 
 +
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
 +
 
 +
|-valign="top"
 +
|Emissions etc.
 +
|
 +
#[[GEOS-Chem_12#Use_online_sea_flux_emissions_by_default_in_GCHP|Use online sea flux emissions by default in GCHP]]
 +
#[[GEOS-Chem_12#GCHP_uses_outdated_MODIS_files_missing_projection_error_fix|Update MODIS LAI source directory to match GEOS-Chem Classic]]
 +
|
 +
#[https://github.com/geoschem/gchp/commit/9759d26bcbbb593f6e845a0dc67e1b7bde4b6410 9759d26b]
 +
#N/A
 +
 
 +
|-valign="top"
 +
|Met fields
 +
|
 +
#[[GEOS-Chem_12#Missing_scaling_factors_for_MERRA-2_simulations_with_GCHP|Missing scaling factors for MERRA-2 simulations with GCHP]]
 +
|
 +
#?
  
 
|}
 
|}
  
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:49, 4 January 2017 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 17:03, 15 July 2019 (UTC)
  
== Issues resolved in GEOS-Chem v10-01 ==
+
== Issues resolved in GEOS-Chem 12.2.0 ==
  
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.
+
The bugs and technical issues listed below were resolved [[GEOS-Chem 12#12.2.0|GEOS-Chem 12.2.0]] (release date 19 Feb 2019).
  
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250px"|Module or area
+
!width="200px"|Module or area
!width="750px"|Issue that was resolved
+
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
|Stratospheric chemistry module
+
|Diagnostics
 +
|
 +
#[[GEOS-Chem_12#Fix_bug_in_stratosperic_aerosol_surface_area_netcdf_diagnostics|Fix bug in stratospheric aerosol surface area in netCDF diagnostics]]
 
|
 
|
*[[Stratospheric_chemistry#Reduce_memory_footprint_of_the_stratospheric_chemistry_module|Reduce memory footprint of the stratospheric chemistry module]]
+
#[https://github.com/geoschem/geos-chem/commit/e4fecf01c87aa76169751c6e0a515ee717573121 e4fecf01]
*[[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]]
+
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
  
 
|-valign="top"
 
|-valign="top"
|Photolysis
+
|Restart files
 
|
 
|
*[[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]]
+
#[[GEOS-Chem_12#GCHP_Bug_fix:_use_checkpoint_output_file_as_subsequent_run_restart|GCHP bug fix: Use checkpoint output as the subsequent restart file]]
*[[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>]]
+
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:02, 14 March 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.1.1 ==
 +
 
 +
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.1.1|GEOS-Chem 12.1.1]], which was released on 13 Dec 2018.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
|NOx-Ox chemistry and nested grid simulations
+
|Compilation issues
 +
|
 +
#[[GEOS-Chem_12#Always_enable_BCPH_TPBC_to_allow_saving_out_BC_files_in_global_simulations|Always enable BPCH_TPBC to allow saving out BC files in global simulations]]
 +
#[https://github.com/geoschem/geos-chem/commit/096ad29d02afbdba64a5dd138df0c976ddee3140 Add hco_interface_mod.o to list of dependencies for get_met_mod.o and only compile get_met_mod.F90 and flexgrid_mod.F90 for GEOS-Chem "Classic"]
 +
#[https://github.com/geoschem/geos-chem/commit/f9b2f19593afeaa396ff3ee3d315148d5a6f8600 Add flexgrid_read_mod.o to list of dependencies for hcoi_gc_main_mod.o]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/072ec9d61580105bcfa755081bc5d238e1b3f60d 072ec9d6]
 +
#[https://github.com/geoschem/geos-chem/commit/096ad29d02afbdba64a5dd138df0c976ddee3140 096ad29d]
 +
#[https://github.com/geoschem/geos-chem/commit/f9b2f19593afeaa396ff3ee3d315148d5a6f8600 f9b2f195]
 +
 
 +
|-valign="top"
 +
|Diagnostics
 +
|
 +
#[[GEOS-Chem_12#Skip_planeflight_observations_outside_a_nested_domain|Skip planeflight observations outside a nested domain]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/f6f90fd404cae1f911277f27f7a4fcb15b3bb039 f6f90fd4]
 +
 
 +
|-valign="top"
 +
|Tagged CO simulation
 +
|
 +
#[[Tagged CO simulation#Do not multiply emission timestep by 60|Bug fix for tagged CO: don't multiply emissions timestep by 60]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/8a1b078e337edfa5fdfb0a5d9ca636b6d0c0634a 8a1b078e]
 +
 
 +
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
 +
 
 +
|-valign="top"
 +
|Transport (FvDycore)
 +
|
 +
#[[GEOS-Chem_12#GCHP_transport_fix_to_prevent_instant_propagation_from_troposphere_to_stratosphere|GCHP transport fix to prevent instant propagation from troposphere to stratosphere]]
 +
|
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:12, 16 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.1.0 ==
 +
 
 +
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]], which was released on 26 Nov 2018.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
 +
 
 +
|-valign="top"
 +
|CH4 simulation
 +
|
 +
#[[CH4_simulation#Add_fixes_for_seasonal_scale_factors_in_CH4_simulations|Add fixes for seasonal scale factors in CH4 simulations]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/6f48d04570ea616a0c39f8dd02c2c902e6183393 6f48d045]
 +
 
 +
|-valign="top"
 +
|Chemistry and Photolysis
 +
|
 +
#[[FAST-JX_v7.0_photolysis_mechanism#Allow_for_SZA_to_98_degrees_when_getting_photolysis_rates|Allow for SZA to 98 degrees when getting photolysis rates]]
 +
#[[GEOS-Chem_v11-02#Code_cleanup_suggestions|Move Fast-JX .dat files from the <tt>geos-chem-unittest</tt> repository to <tt>gcgrid/ExtData</tt>]]
 +
|
 +
#[https://github.com/geoschem/geos-chem/commit/d06ae04ad44defd15854a9c4dadd36923dee0498 d06ae04a]
 +
#[https://github.com/geoschem/geos-chem/commit/03e94fed99cf2bb538dfc59ec514690a122b01a9 03e94fed]
 +
 
 +
|-valign="top"
 +
|Emissions
 +
|
 +
#[[CEDS_anthropogenic_emissions#Add_missing_RCO_sector_to_CEDS_emissions_entries|Add missing RCO sector to CEDS emissions entries]]
 +
#[[CEDS_anthropogenic_emissions#Include_CEDS_ship_emissions|Include CEDS ship emissions as default global ship emissions inventory]]
 +
#[[CEDS_anthropogenic_emissions#Reduce_file_size_for_CEDS_inventory|Reduce file size for CEDS inventory]]
 +
#[[Implementation_of_HEMCO_in_GEOS-Chem#Bug_fix:_Read_data_with_the_.22E.22_cycle_flag_just_once|HEMCO bug fix: prevent excessive attempts to read the HEMCO restart file when using GEOS-Chem "Classic"]]
 +
#[[Implementation_of_HEMCO_in_GEOS-Chem#Add_fix_for_collapsing_model_levels_to_reduced_grid|Add fix for collapsing model levels to reduced grid]]
 +
#[[Implementation_of_HEMCO_in_GEOS-Chem#Fix_unit_conversion_in_HCO_UNIT_GetAreaScal|Fix unit conversion in HCO_UNIT_GetAreaScal]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/642dd0af874e9ddfa87d096158a61f1d9f9c0fe6 642dd0af]
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/e71d0d6754faeed0adcfc9ed94846677551337f3 e71d0d67]
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/20451cb47bf8dace9b9fc7878bca6720b6fe3a56 20451cb4]
 +
#[https://github.com/geoschem/geos-chem/commit/3f62e74954136cbbabda166a453cbd3811689ac4 3f62e749]
 +
#[https://github.com/geoschem/geos-chem/commit/820b8d7d9b25a50f79cf6688a359c9dcc91d8c2b 820b8d7d]
 +
#[https://github.com/geoschem/geos-chem/commit/7dfd99da3d750046dc08478978b3f2cbd0a31018 7dfd99da]
 +
 
 +
|-valign="top"
 +
|PBL Mixing
 +
|
 +
#[[Boundary_layer_mixing#Mass_is_not_conserved_when_using_non-local_PBL_mixing|Fix mass conservation in non-local PBL mixing]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/57c75178c4f9b809c5abca5e3b236c3db7889669 57c75178]
 +
 
 +
|-valign="top"
 +
|Tagged CO simulation
 +
|
 +
#[[GEOS-Chem_12#Update_HEMCO_configuration_file_for_tagged_CO_simulation|Update HEMCO configuration file for the tagged CO simulation]]
 +
|
 +
#[https://github.com/geoschem/geos-chem-unittest/commit/02aaad73d32cbd54bba450b0a5b2abce6a5cad5e 02aaad73]
 +
 
 +
|-
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
 +
 
 +
|-valign="top"
 +
|Emissions (GCHP)
 +
|
 +
#[[GEOS-Chem_12#Fix_masked_anthropogenic_emissions_bug_in_GCHP|Fix masking bug to correctly apply anthropogenic emissions]]
 +
#[[GEOS-Chem_12#Fix_regional_tile_file_used_for_APEI_inventory_in_GCHP|Remove erroneous 180 degree longitude shift in APEI regridding]]
 +
|
 +
 
 +
|-valign="top"
 +
|Structural (GCHP)
 +
|
 +
*Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository
 +
|
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:12, 16 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.0.3 ==
 +
 
 +
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.0.3|GEOS-Chem 12.0.3]], which was released on 16 Oct 2018.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
 +
 
 +
|-valign="top"
 +
!colspan="3" bgcolor="#CCFFFF"|Fixes affecting GCHP only:
 +
 
 +
|-valign="top"
 +
|Emissions (GCHP)
 +
|
 +
#[[#Fix_incorrect_run_configuration_for_offline_sea_salt_emissions_in_GCHP|Fix incorrect run configuration for offline sea salt emissions in GCHP]]
 +
#[[#Fix_bug_in_application_of_CFC_surface_mixing_ratios_in_GCHP|Fix bug in application of CFC surface mixing ratios in GCHP]]
 +
|
 +
 
 +
|}
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:01, 21 December 2018 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.0.2 ==
 +
 
 +
The bugs and technical issues listed below were be resolved in [[GEOS-Chem 12#12.0.2|GEOS-Chem 12.0.2]], which was released on 10 Oct 2018.
 +
 
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
 +
 
 +
|-valign="top"
 +
|Diagnostics
 +
|
 +
#[[GEOS-Chem 12#Fixed_local-time_averaging_in_ND51_and_ND51b_satellite_timeseries_diagnostics|Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics]]
 
|
 
|
*[[UCX_chemistry_mechanism#Modify_treatment_of_N2O5_.2B_H2O_reaction_in_calcrate.F|Modify treatment of N2O5+H2O reaction in calcrate.F]]
+
#[https://github.com/geoschem/geos-chem/commit/14b29d3df84994a9251dd9b2fb0082b75c4affbc 14b29d3d]
*[[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"
 
|-valign="top"
 
|Specialty simulations
 
|Specialty simulations
 
|
 
|
*[[TOMAS_aerosol_microphysics#Reactivating_dust_tracers_in_TOMAS_simulations|Reactivating dust tracers in TOMAS simulations]]
+
#[[TOMAS_aerosol_microphysics#Fixes_for_missing_biomass_emissions_and_incorrect_aerosol_dry_deposition|Correct missing BC/OC biomass emissions and aerosol drydep 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]]
+
#[[CO2_simulation#CO2_emissions_are_double_counted|Avoid double-counting of emissions in the CO2 simulation]]
*[[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]]
+
#[https://github.com/geoschem/geos-chem/commit/6a944b929764b6e1e7d22f0fd396a3d1515f71dc 6a944b92]
*[[CH4_simulation#Minor_fixes_to_CH4_simulation_for_MERRA_meteorology|Minor fixes to CH4 simulation for MERRA meteorology]]
+
#[https://github.com/geoschem/geos-chem/commit/8320e73d06d94b3e39dd0440f6eb0b1cf3fa0e98 8320e73d]
*[[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]]
+
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:16, 16 July 2019 (UTC)
 +
 
 +
== Issues resolved in GEOS-Chem 12.0.1 ==
 +
 
 +
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.0.1|GEOS-Chem 12.0.1]], which was released on 24 Aug 2018.
 +
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="200px"|Module or area
 +
!width="650px"|Issue that was resolved
 +
!width="130px"|Git commit ID
  
 
|-valign="top"
 
|-valign="top"
|HEMCO emissions component
+
|Diagnostics
 +
|
 +
#[[GEOS-Chem 12#Fix typo when registering the State_Chm%SSAlk field|Fix typo when registering the <tt>State_Chm%SSAlk</tt> field]]
 +
#[[Sulfate aerosols#Fix mis-indexing in the ND05 diagnostic|Fix mis-indexing in the ND05 diagnostic]]
 
|
 
|
*[[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]]
+
#[https://github.com/geoschem/geos-chem/commit/55d1687384bcd1e0091cf96ad42fed4fa69cb450 55d16873]
*[[Implementation_of_HEMCO_in_GEOS-Chem#Features_added_in_v10-01f|Add new functionality into HEMCO]]
+
#[https://github.com/geoschem/geos-chem/commit/8e118c0e00403edac7f8d91a7c68c1144a0e64a6 8e118c0e]
*[[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"
 
|-valign="top"
|Removing computational bottlenecks
+
|Mercury
 
|
 
|
*[[Cloud convection#Removed array temporaries in call to FVDAS_CONVECT|Removed array temporaries in the call to the GEOS-4 convection routine]]
+
#[[Mercury#Restore_biomass_emissions_and_do_not_double_count_anthropogenic_emissions|Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions]]
*[[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>]]
+
#[https://github.com/geoschem/geos-chem/commit/e1e6668b901a49e82e78302bc83e03271af011b0 e1e6668b]
*[[Advection_scheme_TPCORE#Reduce_time_spent_in_routine_TPCORE_FVDAS|Reduce time spent in advection driver routine TPCORE_FVDAS]]
+
  
 
|-valign="top"
 
|-valign="top"
|Miscellaneous
+
|Structural updates
 +
|
 +
#Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP
 +
#[[GEOS-Chem_Makefile_Structure#Add a more robust test for netCDF-Fortran in Makefile_header.mk|Add a more robust test for netCDF-Fortran in Makefile_header.mk]]
 +
#[[GNU_Fortran_compiler#Compiliation_issues_with_GNU_Fortran_8.2.0|Fix compilation issues encountered with GNU Fortran 8.2.0]]
 +
#[[Intel_Fortran_Compiler#Compilation_issues_with_Intel_Fortran_18|Fix compilation issues encountered with Intel Fortran 18]]
 
|
 
|
*[[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]]
+
#[https://github.com/geoschem/geos-chem/commit/ff7b0c3c73faafa1fdbebaf163178d0a7d224af7 ff7b0c3c]
*[[Installing_libraries_for_GEOS-Chem#How_GEOS-Chem_uses_nc-config_and_nf-config|Make the netCDF library linking process more portable]]
+
#[https://github.com/geoschem/geos-chem/commit/a4d550552ecd3a4e2a9dc0b2b63f79500d7eae10 a4d55055]
*[[Regridding_in_GEOS-Chem#Fix_for_optimization_error_discovered_in_v10-01h|Fix for optimization error discovered in v10-01h]]
+
#[https://github.com/geoschem/geos-chem/commit/e0959563c23b9fe19d9a4e064be846b10cafbc63 e0959563]
*[[GEOS-Chem_v10-01#Bug_fix_in_I3_field_interpolation|Bug fix for I3 field interpolation]]
+
#[https://github.com/geoschem/geos-chem/commit/9833fff44cc1b12b41306140dbbd653004c71b54 9833fff4]
*[[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)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:20, 16 July 2019 (UTC)
  
== Issues resolved in GEOS-Chem v9-02 ==
+
== Issues resolved in GEOS-Chem 12.0.0 ==
  
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.
+
The bugs and technical issues listed below were resolved in [[GEOS-Chem 12#12.0.0|GEOS-Chem 12.0.0]], which was released on 10 Aug 2018.
  
 
{| border=1 cellspacing=0 cellpadding=5
 
{| border=1 cellspacing=0 cellpadding=5
Line 265: Line 593:
 
!width="250px"|Module or area
 
!width="250px"|Module or area
 
!width="750px"|Issue that was resolved
 
!width="750px"|Issue that was resolved
 +
 +
|-valign="top"
 +
|Aerosols
 +
|
 +
*[[GEOS-Chem_12#Fix_issues_in_complexSOA_and_complexSOA_SVPOA_restart_files|Fix issues in complexSOA and complexSOA_SVPOA restart files]]
 +
 +
|-valign="top"
 +
|Chemistry
 +
|
 +
*[[Stratospheric_chemistry#Disable_STE_calculation_printed_to_log_file|Disable STE calculation printed to log file]]
 +
*[[Linoz_stratospheric_ozone_chemistry#Turn_on_Synoz_when_Linoz_is_set_to_false_in_input.geos|Turn on Synoz when Linoz is set to false in input.geos]]
 +
*[[GEOS-Chem_12#Remove_duplicate_C3HI_spectrum_in_FJX_spec.dat_and_FJX_j2j.dat|Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat]]
 +
*[[GEOS-Chem 12#Add PH2O2 to the default list of prod/loss families in the KPP mechanisms|Add P(H2O2) to the default list of prod/loss families in the KPP mechanisms]]
 +
*[[GEOS-Chem_12#Bug_fix_for_liquid_water_content_in_gckpp_HetRates.F90|Bug fix for liquid water content in gckpp_Hetrates.F90]]
 +
*[[GEOS-Chem_12#Fixed_typo_in_call_to_GAMMA_HOBr_AER|Fixed typo in call to GAMMA_HOBr_AER (in KPP module gckpp_HetRates.F90)]]
 +
*[[Organics_Working_Group#Add_missing_Criegee_intermediate_reaction|Add missing Criegee intermediate reaction]]
 +
*[[GEOS-Chem_12#Bug_fix_for_CH4_boundary_conditions|Bug fix for CH4 boundary conditions]]
 +
*[[FlexChem#FlexChem bug fix: do not zero ACTA, EOH, HCOOH|Bug fix in FlexChem: do not zero out ACTA, EOH, HCOOH concentrations]]
 +
 +
|-valign="top"
 +
|Diagnostics
 +
|
 +
*[[GEOS-Chem 12#Fixed typo that prevented PM2.5 from being archived to netCDF output|Fixed typo that prevented PM2.5 from being archived to netCDF output]]
 +
*[[Planeflight_diagnostic#Stop_with_error_if_the_plane_type_is_not_specified_in_Planeflight.dat|Planeflight diagnostic fix: Stop with error if the plane type is not specified in Planeflight.dat]]
 +
*[[#Bug fix for reference time in netCDF diagnostic files|Bug fix for reference time in netCDF diagnostic files]]
  
 
|-valign="top"
 
|-valign="top"
 
|Emissions
 
|Emissions
 
|
 
|
*[[GEOS-Chem_v9-02#Bug_fix_for_updated_CAC_emissions|Bug fix for updated CAC emissions]]
+
*[[Lightning_NOx_emissions#Limit_flash_rate_density_in_hcox_lightnox_mod.F90|Limit flash rate density in hcox_lightnox_mod.F90]]
*[[GEOS-Chem_v9-02#Bug_fix_for_Br2_emissions|Bug fix for Br2 emissions]]
+
*[[GEOS-Chem_12#Add_entries_to_HEMCO_Config.rc_for_SOAP_and_pFe_in_CEDS_inventory|Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory]]
*[[GEOS-Chem_v9-02#Bug_in_regridding_of_anthropogenic_emissions|Bug fix in regridding of anthro emissions]]
+
*[[Trash_burning_emissions#Avoid_double_counting_trash_emissions|Turn off TRASH emissions by default to avoid double counting]]
*[[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]]
+
*Update to HEMCO v2.1.007, which includes minor updates:
*[[GEOS-Chem_v9-02#Bug_fix_in_nei2005_anthro_mod.F|Bug fix in nei2005_anthro_mod.F]]
+
*#[[Implementation of HEMCO in GEOS-Chem#Fixed_error_in_HEMCO_.22exact.22_time_option|Fixed error in HEMCO "exact" cycling option]]
*[[David_Streets_regional_emissions_for_China_and_SE_Asia#Bug_in_EMIS_STREETS_ANTHRO_05x0666|Bug fix in EMIS_STREETS_ANTHRO_05x0666]]
+
*#[[Implementation of HEMCO in GEOS-Chem#Stop with error if multiple containers have the same name|Stop with error if multiple containers have the same name]]
*[[GEOS-Chem_v9-02#Bug_fixes_in_biofuel_mod.F_and_emfossil.F|Bug fixes in biofuel_mod.F and emfossil.F]]
+
*#[[Implementation of HEMCO in GEOS-Chem#Bug fix for distributing emissions in the vertical dimension|Bug fix for distributing emissions in the vertical dimension]]
*[[GFED3_biomass_burning_emissions#Bug_fix_for_3-hourly_GFED3_emissions|Bug fix for 3-hourly GFED3 emissions]]
+
*#[[Implementation of HEMCO in GEOS-Chem#Add extra error checks in HEMCO standalone module|Add extra error checks in HEMCO standalone module]]
*[[Volcanic_SO2_emissions_from_Aerocom#Typo_in_VOLCPRESS_definition|Fixed typo in Aerocom volcanic SO2 emissions routine]]
+
*#[[Implementation of HEMCO in GEOS-Chem#Remove null string character from netCDF unit string|Remove null string character from netCDF unit string for GEOS-Chem "Classic" simulations]]
*[[GEOS-Chem_v9-02#Bug_fixes_in_day-of-week_computation|Bug fixes in day-of-week computation]]
+
*#[[Implementation_of_HEMCO_in_GEOS-Chem#Bug fix for HEMCO soil NOx error with ifort 17|Bug fix for HEMCO soil NOx error with ifort 17]]
*[[Anthropogenic_emissions#Prevent_negative_emissions_over_Canada|Prevent negative emissions over Canada]]
+
*Correct issues when specifying [[DICE-Africa anthropogenic emissions inventory|DICE-Africa emissions]]:
*[[TOMAS_aerosol_microphysics#Minor_bug_in_TOMAS_sulfate_emissions|Minor bug fix in TOMAS sulfate emissions]]
+
*#[[DICE-Africa_anthropogenic_emissions_inventory#Avoid_double-counting_between_DICE-Africa_and_other_inventories|Avoid double-counting between DICE-Africa and other inventories]]
*[[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]]
+
*#[[DICE-Africa_anthropogenic_emissions_inventory#Use_unique_names_for_DICE-Africa_entries_in_HEMCO_Config.rc|Use unique names for DICE-Africa entries in the <tt>HEMCO_Config.rc</tt> file]]
*[[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]]
+
*Updates for [[QFED biomass burning emissions]]:
*[[Historical_and_Future_Emissions#Bug_fix_for_BC.2FOC_biofuels_when_using_RCP_scenarios|Bug fix for biofuels when using RCP scenarios]]
+
*#[[QFED biomass burning emissions#Update to QFED v2.5r1|Update to QFED v2.5r1]]
 +
*#[[QFED_biomass_burning_emissions#Fix_QFED_files_for_2016.2F10.2F13|Fix QFED v2.4r6 files for 2016/10/13]]
 +
*[[GEOS-Chem 12#Avoid double counting CEDS and GEIA NH3 biofuel emissions|Avoid double counting CEDS and GEIA NH3 biofuel emissions]]
 +
*[[Ship_emissions#Fix_bug_in_ARCTAS_SHIP_SO2_scale_factors|Bug fix for ARCTAS_SHIP in <tt>HEMCO_Config.rc</tt> files]]
  
 
|-valign="top"
 
|-valign="top"
|Dry deposition and wet deposition
+
|Specialty simulations
 
|
 
|
*[[Acetone#DRYACET_is_missing_from_globchem.dat|Add missing DRYACET to globchem.dat mechanism file]]
+
*[[Coupling_GEOS-Chem_with_RRTMG#Bug_fixes_for_RRTMG_in_v11-02|Bug fixes for v11-02 simulations using the RRTMG radiative transfer model]]
*[[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"
 
|-valign="top"
|Met fields
+
|Structural updates
 
|
 
|
*[[GEOS-Chem_v9-02#Correction_for_GEOS-5_PBL_heights|Correction for GEOS-5 PBL heights]]
+
*Initial structural updates to interface GEOS-Chem into WRF
*[[GEOS-5 issues#Reset NaNs in MOISTQ to zero|Reset NaNs in MOISTQ to zero]]
+
*Now always declare the netCDF time variable with an unlimited dimension
*[[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]]
+
|}
 +
 
 +
== Issues resolved in GEOS-Chem v11-01 ==
 +
 
 +
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
 +
|-bgcolor="#CCCCCC"
 +
!width="250px"|Module or area
 +
!width="750px"|Issue that was resolved
  
 
|-valign="top"
 
|-valign="top"
|Computational efficiency
+
|[[Aerosol-only simulation]]
 
|
 
|
*[[Passing_array_arguments_efficiently_in_GEOS-Chem|Eliminate inefficient subroutine calls]]
+
*[[Aerosol-only_simulation#Fixed_undefined_molecular_weight_of_HNO3_in_routine_SEASALT_CHEM|Fixed undefined molecular weight of HNO3 in routine SEASALT_CHEM]]
*[[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"
 
|-valign="top"
|Diagnostics
+
|[[CH4 simulation]]
 
|
 
|
*[[GEOS-Chem_v9-01-03#Bug_fix_in_hdf_mod.F|Bug fix in hdf_mod.F]]
+
*[[CH4_simulation#Fix_bug_in_CH4_emissions|Fix bug in CH4 emissions unit]]
*[[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"
 
|-valign="top"
|Specialty simulations (including microphysics)
+
|[[GEOS-Chem chemistry mechanisms|Chemistry]]
 
|
 
|
*[[GEOS-Chem_v9-02#Bug_fixes_for_tagged_CO_simulation|Bug fixes for tagged CO simulation]]
+
*[[Centralized_chemistry_time_step#Optimal_Configuration|Adopt the optimal timestep recommendations of Philip et al 2015]]
*[[Mercury#Bug_fixes_for_nested_Hg_simulation|Bug fixes for nested Hg simulation]]
+
*[[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]]
*[[GEOS-Chem_v9-02#Bug_fix_for_reading_OH_file_in_offline_simulations|Bug fix for reading OH file in offline simulations]]
+
*[[UCX_chemistry_mechanism#Fix_for_black_carbon_in_ucx_mod.F|Fix for black carbon in <tt>ucx_mod.F</tt>]]
*[[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]]
+
*[[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)]]
*[[Aerosol-only_simulation#Error_in_ISOROPIAII_when_sulfate_aerosols_are_turned_off|Avoid error in ISOROPIAII when using offline aerosol simulation]]
+
*[[Sulfate_aerosols#Bug_fix_for_sea_salt_alkalinity_in_sulfate_mod.F|Bug fix for sea salt alkalinity in <tt>sulfate_mod.F</tt>]]
*[[Tagged_O3_simulation#Modifications_for_v9-02_tagged_O3_simulation|Modifications for v9-02 tagged O3 simulation]]
+
*[[GEOS-Chem_v10-01#Bug_fix_for_offline_dust_aerosols_when_UCX_is_on|Bug fix for offline dust aerosols when UCX is on]]
*[[CH4_simulation#Fixes_for_wetland_emissions|Fixes for wetland emissions in CH4 simulation]]
+
*[[Mineral_dust_aerosols#Bug_fixes_for_hydrophobic_aerosol_properties|Bug fixes for hydrophobic aerosol properties]]
*[[Tagged_O3_simulation#Reactivate_stratospheric_P.28Ox.29_in_tagged_Ox_simulation|Reactivate stratospheric P(Ox) in tagged Ox simulation]]
+
*[[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]]
*[[Tagged_O3_simulation#Replace_LD65_with_LLTROP_in_tagged_ox_mod.F|Replace LD65 with LLTROP in tagged_ox_mod.F]]
+
*[[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>]]
*[[TOMAS_aerosol_microphysics#Updates_for_GEOS-Chem_v9-02_public_release|Several fixes for TOMAS aerosol microphysics]]
+
*[[Stratospheric_chemistry#Fix_for_monthly_stratospheric_P.2FL_rates_in_HEMCO|Fix for monthly stratospheric P/L rates in HEMCO]]
*[[POPs_simulation#Prevent_error_when_reading_global_OC|Prevent error in POPs simulation when reading global OC]]
+
*[[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"
|Photolysis
+
|[[CO2 simulation]]
 
|
 
|
*[[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]]
+
*[[CO2_simulation#Additional_Update_and_Bug_Fix|Update CO2 emission files]]
*[[Aerosol_optical_properties#Fix_to_jv_spec_aod.dat|Add fix to jv_spec_aod.dat file]]
+
*[[CO2_simulation#Bug_fix:_Make_sure_nAdvect_is_initialized_in_EMISSCO2|Bug fix: Make sure <tt>nAdvect</tt> is initialized in EMISSCO2]]
*[[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"
 
|-valign="top"
|Miscellaneous
+
|[[Cloud convection]]
 
|
 
|
*[[GEOS-Chem_v9-02#Additional_bug_fixes_for_MAP_A2A_regridding_algorithm|Additional bug fixes for MAP_A2A regridding]]
+
*[[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]]
*[[Regridding_in_GEOS-Chem#Bug_in_grid_mod.F90|Bug fix in grid_mod.F90]]
+
*[[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]]
*[[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]]
+
|-valign="top"
*[[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]]
+
|Compiler / Fortran issues
*[[GEOS-Chem_v9-02#Fixes_for_minor_technical_issues|Fixes for minor technical issues]]
+
|Compiler issues:
 +
*[[GNU Fortran compiler|Add support for GNU Fortran compiler]]
 +
*[[PGI Fortran compiler#File_Linking_Error|Fix linker error when using the PGI compiler]]
 +
*[[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"
 +
|[[List of diagnostics for v11-01|Diagnostics]]
 +
|
 +
*[[GEOS-Chem_v11-01#Bug_fixes_for_the_ND21_diagnostic|Bug fix for the ND21 diagnostic]]
 +
*[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions#Bug_fix_for_monoterpenes_in_ND46_diagnostic|Bug fix for monoterpenes in ND46 diagnostic]]
 +
*[[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"
 +
|[[HEMCO data directories|Emissions (via HEMCO)]]
 +
|
 +
*[[Lightning_NOx_emissions#Correct_problem_in_OTD-LIS_local_redistribution_files|Fix problem in OTD/LIS lighning redistribution files]]
 +
*[[GEOS-Chem_v10-01#Fix_for_reading_hourly_NEI2011_emissions|Fix for reading hourly NEI2011 emissions]]
 +
*[[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"
 +
|[[Mercury]] and [[POPs simulation|POPs]] simulations
 +
|
 +
*[[Mercury#Hg_ocean_MLD_bug_fixes|Bug fixes for computing MLD in <tt>ocean_mercury_mod.F</tt>]]
 +
*[[Mercury#Parallelization_bug_fixes_for_GEOS-5_Hg_simulations|Fix parallelization errors that prevented Hg simulations from passing unit tests]]
 +
*[[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"
 +
|Met fields and derived quantities
 +
|
 +
*[[Air_Quantity_Updates_for_v11-01|Incorporate moisture into air quantities, tracer units, and tracer unit conversions]]
 +
*[[GEOS-Chem_species_units#Updating_Air_Quantities|Bug fix to update air quantities after specific humidity is updated in non-local PBL mixing]]
 +
*[[GEOS-Chem_v11-01#Incorrect_incorporation_of_moisture_in_GEOS-Chem_air_quantities|Fix to remove moisture signature in dry mixing ratio]]
 +
 
 +
|-valign="top"
 +
|[[Preparing data files for use with HEMCO#The COARDS netCDF standard|netCDF I/O]]
 +
|
 +
*[[GEOS-Chem_Output_Files#NetCDF_File_Format|Migration from bpch to netCDF output file format]]
 +
*[[GEOS-Chem_Output_Files#Improve_write_speed_of_netCDF_output_files|Improve write speed of netCDF output files]]
 +
*[[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"
 +
|[[FAST-JX_v7.0_photolysis_mechanism|Photolysis]]
 +
|
 +
*[[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]]
 +
*[[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]]
 +
 
 +
|-valign="top"
 +
|[[Regridding in GEOS-Chem|Regridding]]
 +
|
 +
*[[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]]
 +
*[[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>]]
 +
 
 +
|-valign="top"
 +
|[[Coupling_GEOS-Chem_with_RRTMG|RRTMG radiative transfer model]]
 +
|
 +
*[[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]]
 +
*[[Coupling_GEOS-Chem_with_RRTMG#Bug_in_RRTMG_array_sizes|Bug fix in RRTMG array sizes]]
 +
*[[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 Y.]] ([[User talk:Bmy|talk]]) 21:00, 26 October 2015 (UTC)
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:57, 23 January 2017 (UTC)
  
 
== Bugs and fixes in older GEOS-Chem versions ==
 
== 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]].
+
For a complete list of bugs and fixes in older GEOS-Chem versions, please see:
 +
 
 +
*[[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]]) 20:47, 2 January 2019 (UTC)
--[[User:Bmy|Bob Y.]] 14:11, 20 May 2014 (EDT)
+

Revision as of 15:25, 3 April 2020

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 and Known issues caused by compiler bugs wiki pages for more information about unresolved issues.

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.

Version Released List of bugs and issues (now posted on the listed Github repository)
13.0.0 TBD geoschem/geos-chem
12.9.0 TBD geoschem/geos-chem
12.8.1 TBD geoschem/geos-chem
12.8.0 pending 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

Issues resolved in GEOS-Chem 12.5.0

The bugs and technical issues listed below will be resolved GEOS-Chem 12.5.0, release date TBD.

Module or area Issue that was resolved Git commit ID
Chemistry
  1. Bug fix: Make sure stratospheric BrY concentrations are properly read each month
  2. Add photolysis menu to input.geos for specifying FAST-JX directory
  3. Correction for CFCs in the chemistry mechanism
  4. Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90
  1. 0588a269
  2. 03e94fed
  3. 1b9f69f0
  4. 95d124e0
Diagnostics
  1. Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally
  2. Enable accurate cloud pH diagnostic calculation via post-processing
  1. 6acd4ce3
  2. 1c15e54a
Structural updates
  1. Add optional capability to compile GEOS-Chem Classic and GCHP using CMake
  1. pull/27
Emissions
  1. Fixes for GFED4 biomass burning emissions, including:
    • Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year
    • Remove the 27% scaling of POG to POA and emit 1:1 instead
  1. 381386fb
Fixes affecting GCHP only:
Structural updates
  1. Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28
    • Will introuduce faster parallel I/O
    • Will enable full use of gfortran compiler

--Bob Yantosca (talk) 17:03, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.4.0

The bugs and technical issues listed below will be resolved GEOS-Chem 12.4.0, release date TBD.

Module or area Issue that was resolved Git commit ID
Photolysis
  1. Bug fix: Rebuild chemical mechanisms for FAST-JX fix added in 12.3.2
  2. Add photolysis menu to input.geos for specifying FAST-JX directory
  1. fcd0cfba
  2. d34a9cd2

--Bob Yantosca (talk) 17:04, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.3.2

The bugs and technical issues listed below will be resolved GEOS-Chem 12.3.2.

Module or area Issue that was resolved Git commit ID
Chemistry
  1. Fix inconsistency for species H2402 between GCHP and GEOS-Chem "Classic"
  1. rel/12.3.2
Photolysis
  1. Remove duplicate entry for species ClNO2 in the FJX_j2j.dat file
  2. Species DHDC was not listed as photolyzing in the GEOS-Chem species database
  1. rel/12.3.2
  2. d7c48d14
Fixes affecting GCHP only:
Emissions
  1. Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default
  2. Fix HEMCO diagnostics settings for lightning NO and seasalt emissions
  1. f6ac477a
  2. cda5044e

--Bob Yantosca (talk) 16:37, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.3.1

The bugs and technical issues listed below were resolved GEOS-Chem 12.3.1 (release 08 Apr 2019).

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Planeflight diagnostic now writes out data for the last timestep of the day
  2. Fix the netCDF diagnostic for noontime J-values
  1. 04da94cd
  2. f4d43b7a
Structural
  1. Do not allocate memory to array MINIT in strat_chem_mod.F90
  2. Declare State_Met%Area_M2 as 2-dimensional, not 3-dimensional
  1. 729fd2a7
  2. e4af25f3b

--Bob Yantosca (talk) 20:06, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.3.0

The bugs and technical issues listed below were resolved GEOS-Chem 12.3.0 (release date TBD).

Module or area Issue that was resolved Git commit ID
Diagnostics / Restart files
  1. Further bug fix for netCDF diagnostics spanning leap years
  1. fb093d61
Emissions
  1. Bug fixes for the HEMCO interpolation algorithm
  2. Updates from the NASA GEOS development branch
  3. Add option to always use simulation year for specified fields
  4. Prevent zero emissions for MEGAN_Mono extension species
  5. Updates to the volcanic emissions extension
  1. e947fc80
  2. 7df3fc8e
  3. 23189032
  4. af86c4dd
  5. 07c10319

--Bob Yantosca (talk) 15:53, 21 March 2019 (UTC)

Issues resolved in GEOS-Chem 12.2.1

The bugs and technical issues listed below were resolved GEOS-Chem 12.2.1 (release date 28 Feb 2019).

Module or area Issue that was resolved Git commit ID
Diagnostics / Restart files
  1. Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days
  1. ca68f508
CO2 simulation
  1. Fix for CO2 simulation chemical source
  1. N/A
TOMAS simulations
  1. Restore DST1, DST2, DST3, and DST4 in TOMAS simulations
  1. 5ed3e9cf
Fixes affecting GCHP only:
Emissions etc.
  1. Use online sea flux emissions by default in GCHP
  2. Update MODIS LAI source directory to match GEOS-Chem Classic
  1. 9759d26b
  2. N/A
Met fields
  1. Missing scaling factors for MERRA-2 simulations with GCHP
  1. ?

--Bob Yantosca (talk) 17:03, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.2.0

The bugs and technical issues listed below were resolved GEOS-Chem 12.2.0 (release date 19 Feb 2019).

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Fix bug in stratospheric aerosol surface area in netCDF diagnostics
  1. e4fecf01
Fixes affecting GCHP only:
Restart files
  1. GCHP bug fix: Use checkpoint output as the subsequent restart file

--Bob Yantosca (talk) 20:02, 14 March 2019 (UTC)

Issues resolved in GEOS-Chem 12.1.1

The bugs and technical issues listed below were resolved in GEOS-Chem 12.1.1, which was released on 13 Dec 2018.

Module or area Issue that was resolved Git commit ID
Compilation issues
  1. Always enable BPCH_TPBC to allow saving out BC files in global simulations
  2. Add hco_interface_mod.o to list of dependencies for get_met_mod.o and only compile get_met_mod.F90 and flexgrid_mod.F90 for GEOS-Chem "Classic"
  3. Add flexgrid_read_mod.o to list of dependencies for hcoi_gc_main_mod.o
  1. 072ec9d6
  2. 096ad29d
  3. f9b2f195
Diagnostics
  1. Skip planeflight observations outside a nested domain
  1. f6f90fd4
Tagged CO simulation
  1. Bug fix for tagged CO: don't multiply emissions timestep by 60
  1. 8a1b078e
Fixes affecting GCHP only:
Transport (FvDycore)
  1. GCHP transport fix to prevent instant propagation from troposphere to stratosphere

--Bob Yantosca (talk) 14:12, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.1.0

The bugs and technical issues listed below were resolved in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.

Module or area Issue that was resolved Git commit ID
CH4 simulation
  1. Add fixes for seasonal scale factors in CH4 simulations
  1. 6f48d045
Chemistry and Photolysis
  1. Allow for SZA to 98 degrees when getting photolysis rates
  2. Move Fast-JX .dat files from the geos-chem-unittest repository to gcgrid/ExtData
  1. d06ae04a
  2. 03e94fed
Emissions
  1. Add missing RCO sector to CEDS emissions entries
  2. Include CEDS ship emissions as default global ship emissions inventory
  3. Reduce file size for CEDS inventory
  4. HEMCO bug fix: prevent excessive attempts to read the HEMCO restart file when using GEOS-Chem "Classic"
  5. Add fix for collapsing model levels to reduced grid
  6. Fix unit conversion in HCO_UNIT_GetAreaScal
  1. 642dd0af
  2. e71d0d67
  3. 20451cb4
  4. 3f62e749
  5. 820b8d7d
  6. 7dfd99da
PBL Mixing
  1. Fix mass conservation in non-local PBL mixing
  1. 57c75178
Tagged CO simulation
  1. Update HEMCO configuration file for the tagged CO simulation
  1. 02aaad73
Fixes affecting GCHP only:
Emissions (GCHP)
  1. Fix masking bug to correctly apply anthropogenic emissions
  2. Remove erroneous 180 degree longitude shift in APEI regridding
Structural (GCHP)
  • Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository

--Bob Yantosca (talk) 15:12, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.0.3

The bugs and technical issues listed below were resolved in GEOS-Chem 12.0.3, which was released on 16 Oct 2018.

Module or area Issue that was resolved Git commit ID
Fixes affecting GCHP only:
Emissions (GCHP)
  1. Fix incorrect run configuration for offline sea salt emissions in GCHP
  2. Fix bug in application of CFC surface mixing ratios in GCHP

--Bob Yantosca (talk) 22:01, 21 December 2018 (UTC)

Issues resolved in GEOS-Chem 12.0.2

The bugs and technical issues listed below were be resolved in GEOS-Chem 12.0.2, which was released on 10 Oct 2018.

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics
  1. 14b29d3d
Specialty simulations
  1. Correct missing BC/OC biomass emissions and aerosol drydep in TOMAS simulations
  2. Avoid double-counting of emissions in the CO2 simulation
  1. 6a944b92
  2. 8320e73d

--Bob Yantosca (talk) 19:16, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.0.1

The bugs and technical issues listed below were resolved in GEOS-Chem 12.0.1, which was released on 24 Aug 2018.

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Fix typo when registering the State_Chm%SSAlk field
  2. Fix mis-indexing in the ND05 diagnostic
  1. 55d16873
  2. 8e118c0e
Mercury
  1. Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions
  1. e1e6668b
Structural updates
  1. Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP
  2. Add a more robust test for netCDF-Fortran in Makefile_header.mk
  3. Fix compilation issues encountered with GNU Fortran 8.2.0
  4. Fix compilation issues encountered with Intel Fortran 18
  1. ff7b0c3c
  2. a4d55055
  3. e0959563
  4. 9833fff4

--Bob Yantosca (talk) 19:20, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.0.0

The bugs and technical issues listed below were resolved in GEOS-Chem 12.0.0, which was released on 10 Aug 2018.

Module or area Issue that was resolved
Aerosols
Chemistry
Diagnostics
Emissions
Specialty simulations
Structural updates
  • Initial structural updates to interface GEOS-Chem into WRF
  • Now always declare the netCDF time variable with an unlimited dimension

Issues resolved in GEOS-Chem v11-01

The bugs and technical issues listed below were resolved in GEOS-Chem v11-01. Also be sure to visit our Known issues caused by compiler bugs wiki page for a list of compiler-related issues and workarounds.

Module or area Issue that was resolved
Aerosol-only simulation
CH4 simulation
Chemistry
CO2 simulation
Cloud convection
Compiler / Fortran issues Compiler issues:

Fortran language issues:

Diagnostics
Emissions (via HEMCO)
Mercury and POPs simulations
Met fields and derived quantities
netCDF I/O
Photolysis
Regridding
RRTMG radiative transfer model
Marine POA simulations
Radon-Lead-Beryllium simulation
Species database and definitions of physical constants
Tagged CO simulation
Tagged O3 simulation
TOMAS aerosol microphysics
Various structural updates
Wet deposition

--Bob Yantosca (talk) 19:57, 23 January 2017 (UTC)

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) 20:47, 2 January 2019 (UTC)