Difference between revisions of "Bugs and fixes"

Revision as of 16:06, 6 October 2016

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

Please also be sure to visit our Common GEOS-Chem error messages wiki page for more general information about some frequently encountered errors. Also visit our Currently unresolved issues in GEOS-Chem wiki page to see a list of unresolved issues by GEOS-Chem version (and if they have been fixed in subsequent releases).

Issues resolved in GEOS-Chem v11-01

The following bugs and/or technical issues were resolved in GEOS-Chem v11-01:

Module or area	Issue that was resolved
Chemistry	Update of PMN + O3 reaction products in globchem.dat file Fix for black carbon in `ucx_mod.F` Modifications to ND20 to archive afternoon P(O3) and L(O3) Bug fix for sea salt alkalinity in `sulfate_mod.F` Bug fix for offline dust aerosols when UCX is on Bug fixes for hydrophobic aerosol properties Fix syntax error in `globchem.dat` for the MOBA + OH —> MOBAOO reaction rate Fixed typo in the ISNOOA + NO2 -> PMN reaction rate in `globchem.dat` Fix for monthly stratospheric P/L rates in HEMCO Fix bug in the GMI stratospheric production rates for HCOOH
Cloud convection	Correct bug in below cloud average mixing ratio calculation in DO_MERRA_CONVECTION to improve mass balance Resolve very high tracer concentrations in GEOS-FP and MERRA convective scavenging
Emissions (via HEMCO)	Fix problem in OTD/LIS lighning redistribution files Fix for reading hourly NEI2011 emissions Use an updated EMEP mask file to prevent zero emissions at 30 N for 2° x 2.5° or higher resolutions Fix an emissions error in the SOA-SVPOA simulation Fixed missing pointer in call to HEMCO routine Hco_CalcVertGrid Fixed bug preventing HEMCO from writing restart files more than once per run Correct bug in units of EDGAR v4.2 SO2 emissions Prevent biofuel emissions from being double counted in EDGAR v4.2 Fix bug in NOx diurnal scale factors Update HEMCO from version 1.1.016 to latest version available Replace RETRO C3H8 emissions with emissions from Xiao et al.
Met fields and derived quantities	Incorporate moisture into air quantities, tracer units, and tracer unit conversions Bug fix to update air quantities after specific humidity is updated in non-local PBL mixing Now correctly incorporate moisture into GEOS-Chem air quantities
RRTMG radiative transfer model	Fix bug that prevents storage of O3 and CH4 RF's Bug fix in RRTMG array sizes Further bug fixes in `rrtmg_transfer_mod.F`
Photolysis	Fix for TOMS/HEMCO to address strange cycle in OH output
Specialty simulations	CO2 Update CO2 emission files CH4 Fix bug in CH4 emissions unit Mercury Bug fixes for computing MLD in `ocean_mercury_mod.F` Fix parallelization errors that prevented Hg simulations from passing unit tests Avoid floating-point exception in OCEAN_MERCURY_READ Bug fixes for Arctic Hg updates in v11-01c Correct too-high emissions of Hg2 over China and EU POPs Avoid floating-point error in routine CHEM_POPGP Radon-Lead-Beryllium Fix typo in HEMCO extension module `hcox_gc_RnPbBe_mod.F90` Tagged O3 Bug fix in European grid range for tagged O3 simulation Bug fix for PBLTOP and MTTOP values in tagged O3 simulation TOMAS Microphysics Updates to TOMAS Jeagle sea salt extension
Structural updates	Fix linker error when using the PGI compiler Bug fix for the ND21 diagnostic Bug fix for custom nested grid in `tpcore_bc_mod.F` Bug fix for monoterpenes in ND46 diagnostic Parallelization bug fix for marine POA Remove inconsistencies in the definitions of physical properties of GEOS-Chem species; Use proper molecular weights for sea salt aerosols in the dry deposition module; Give SO4s and NITs the same molecular weight as SALC; Define molecular weight fields of the `Input_Opt` object from the species database Now use consistent physical parameter values throughout GEOS-Chem Add further fixes for compiling GEOS-Chem with PGI Fortran Adopt the optimal timestep recommendations of Philip et al 2015 Do not nullify local pointers in the same line where they are declared Additional updates compiling GEOS-Chem with the PGI Fortran compiler Now use consistent physical constant declarations Migration from bpch to netCDF output file format Add support for GNU Fortran compiler
Wet deposition	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 Quick fix for low tropospheric 210Pb lifetime against wet deposition Fix bug in GEOS-FP re-evaporation calculation

--Bob Yantosca (talk) 16:06, 6 October 2016 (UTC)

Issues resolved in GEOS-Chem v10-01

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

Module or area	Issue that was resolved
Stratospheric chemistry module	Reduce memory footprint of the stratospheric chemistry module Bug fix in GET_RATES_INTERP Now read corrected stratospheric Bry data via HEMCO
Photolysis	Now use MAP_A2A to regrid 1x1 TOMS O3 to model resolution Bug fix for determining when to use TOMS O3 columns Reactivation of Br species photolysis in Fast-JX for tropospheric chemistry simulation Fixed wavelength bin interpolation error in Fast-JX for tropospheric-only simulation Now use proper photolysis input file `org.dat`
NOx-Ox chemistry and nested grid simulations	Modify treatment of N2O5+H2O reaction in calcrate.F Fixed parallelization error in nested grid simulations Fix for high values of O3 dry deposition Remove duplicate GLYX product from RIO2 reaction Bug fix in ND44 drydep diagnostic for sea salt aerosols Implement final recommendation for J(HAC) and J(PAN) Now use updated cross-sections for computing J(ALD2) Resolved technical issues for 0.25° x 0.3125° CH nested simulation Bug fix for planeflight diagnostic when using chemistry timesteps < 15 min Now call the planeflight diagnostic after chemistry, not after emissions Bug fixes for wet scavenging by co-condensation Fixes for bugs in wet deposition when using MERRA meteorology Remove obsolete ISN2 drydep species Fixed typo for BROMOCARB_SEASON in HEMCO configuration files Bug fixes for GEOS-FP nested EU simulation Fixes for wet deposition when using MERRA met fields Fix MEGAN AEF's for sesquiterpenes in the SOA simulation
Specialty simulations	Reactivating dust tracers in TOMAS simulations Prevent sea salt from being emitted over ice in TOMAS Fix for ND61 diagnostic in TOMAS simulations Fixed library linking issue when building GTMM into GEOS-Chem Minor fixes to CH4 simulation for MERRA meteorology Avoid div-by-zero errors in POPs simulation Bug fixes and updates for tagged CO simulation in v9-02 Fixed bug in tagged Hg emissions
HEMCO emissions component	Prevent segmentation fault errors in HEMCO when emissions are turned off Add new functionality into HEMCO Bug fixes for the PARANOX extension in HEMCO Bug fix for regridding of regional data files by HEMCO Prevent array out-of-bounds error if `MEGAN_mono` extension is turned off Restore missing diagnostic: "Biogenic CO from monoterpenes" Additional HEMCO updates made during the v10-01 period of public comment Fixed filename for ICOADS_SHIP in HEMCO configuration files Fix for error in PARANOX caused by improper timestamps of SUNCOS Minor fixes for FINNv1 biomass burning emissions Removing leftover code that was orphaned by HEMCO
Removing computational bottlenecks	Removed array temporaries in the call to the GEOS-4 convection routine Removed array temporaries in the call to the GCAP convection routine Removed array temporaries in subroutine `READ_HG2_PARTITIONING` Reduce time spent in advection driver routine TPCORE_FVDAS
Miscellaneous	Now use correct value of molecular weight for PROPNN tracer Make the netCDF library linking process more portable Fix for optimization error discovered in v10-01h Bug fix for I3 field interpolation Bug fix in gamap_mod.F Bug fixes for the PGI compiler Now use "percent" instead of "%" in data files

--Bob Y. (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.

Module or area	Issue that was resolved
Emissions	Bug fix for updated CAC emissions Bug fix for Br2 emissions Bug fix in regridding of anthro emissions Bug in MEGAN emissions when using MERRA or GEOS-FP Bug fix in nei2005_anthro_mod.F Bug fix in EMIS_STREETS_ANTHRO_05x0666 Bug fixes in biofuel_mod.F and emfossil.F Bug fix for 3-hourly GFED3 emissions Fixed typo in Aerocom volcanic SO2 emissions routine Bug fixes in day-of-week computation Prevent negative emissions over Canada Minor bug fix in TOMAS sulfate emissions Bug fix for NEI2005 SO4 emissions in sulfate_mod.F Prevent LOG(0) error from occurring in soil NOx module Bug fix for biofuels when using RCP scenarios
Dry deposition and wet deposition	Add missing DRYACET to globchem.dat mechanism file Bug fix in Henry's law constant Bug fix in definition of RIP, IEPOX drydep species Bug fix: Do not call PARANOX plume model for offline simulations Fix for parallelization bug in subroutine METERO (in drydep module) Fixed parallelization error in routine DRYFLX (in dry deposition module) Prevent bad drydep flux values from being passed to the soil NOx module Fixed minor bug in AD44 diagnostic in routine DRY DEPOSITION (sea salt aerosols)
Met fields	Correction for GEOS-5 PBL heights Reset NaNs in MOISTQ to zero Convert MERRA and GEOS-FP relative humidity fields to percent after reading from disk Bug fix for declaration of certain GEOS-FP met fields
Computational efficiency	Eliminate inefficient subroutine calls Corrected several floating-point errors Eliminate array temporaries in pjc_pfix_mod.F and pressure_mod.F Eliminate array temporaries in GCAP convection module
Diagnostics	Bug fix in hdf_mod.F Bug fixes in diag48_mod.F Bug fix in ND36 diagnostic when ship emissions are turned off
Specialty simulations (including microphysics)	Bug fixes for tagged CO simulation Bug fixes for nested Hg simulation Bug fix for reading OH file in offline simulations Now include emissions in the aerosol-only simulation when using non-local PBL mixing Avoid error in ISOROPIAII when using offline aerosol simulation Modifications for v9-02 tagged O3 simulation Fixes for wetland emissions in CH4 simulation Reactivate stratospheric P(Ox) in tagged Ox simulation Replace LD65 with LLTROP in tagged_ox_mod.F Several fixes for TOMAS aerosol microphysics Prevent error in POPs simulation when reading global OC
Photolysis	Prevent 0.5 x 0.667 nested grid simulations from crashing when reading TOMS data Add fix to jv_spec_aod.dat file Post-release patch to fix bug in acetone photolysis pressure dependency
Miscellaneous	Additional bug fixes for MAP_A2A regridding Bug fix in grid_mod.F90 Fixed typos in GCAP code Reactivate parallel DO loop in LINOZ_CHEMO3 routine Corrected unit conversion bug when TURBDAY PBL mixing is used Fixes for minor technical issues

--Bob Y. (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 our Bugs and fixes prior to v9-02 wiki page.

--Bob Y. 17:40, 16 April 2015 (EDT) --Bob Y. 14:11, 20 May 2014 (EDT)

@@ Line 23: / Line 23: @@
 *[[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]]
 |-valign="top"
@@ Line 39: / Line 41: @@
 *[[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#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.]]
 |-valign="top"
@@ Line 53: / Line 60: @@
 *[[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>]]
+|-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]]
 |-valign="top"
@@ Line 58: / Line 70: @@
 |CO2
 *[[CO2_simulation#Additional_Update_and_Bug_Fix|Update CO2 emission files]]
+CH4
+*[[CH4_simulation#Fix_bug_in_CH4_emissions|Fix bug in CH4 emissions unit]]
 Mercury
@@ Line 75: / Line 90: @@
 *[[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]]
+TOMAS Microphysics
+*[[TOMAS_aerosol_microphysics#Updates_to_TOMAS_Jeagle_sea_salt_extension|Updates to TOMAS Jeagle sea salt extension]]
 |-valign="top"
@@ Line 107: / Line 125: @@
 |}
---[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:31, 6 October 2016 (UTC)
+--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:06, 6 October 2016 (UTC)
 == Issues resolved in GEOS-Chem v10-01 ==

Difference between revisions of "Bugs and fixes"

Revision as of 16:06, 6 October 2016

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Issues resolved in GEOS-Chem v11-01

Issues resolved in GEOS-Chem v10-01

Issues resolved in GEOS-Chem v9-02

Bugs and fixes in older GEOS-Chem versions

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