Difference between revisions of "Bugs and fixes"

Revision as of 17:06, 28 November 2011

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

Issues resolved in GEOS-Chem v9-01-02

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

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

Issues resolved in GEOS-Chem v9-01-01

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

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

Issues resolved in GEOS-Chem v8-03-02

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

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

Issues resolved in GEOS-Chem v8-03-01

NOTE: GEOS-Chem v8-03-01 refers to the version that was previously noted as GEOS-Chem v8-02-05.

• Patch to enable call to SOA PARA INIT
• Patch to fix declaration of IONIC in ISORROPIA_II
• Patch to fix bug in Aromatic SOA
• Patch to scale AOD diagnostic output to other wavelengths
• Photolysis now computed at midpoint of chemistry timestep
• Bug fix in ISORROPIA for offline aerosol
• Minor bug fix in SRCSO2
• Bug in GET_EMMONOT_MEGAN
• Bug in READ_ANTHRO_NH3
• Fix for initialization of EMEP ship emissions
• Bug fix in AVGPOLE
• Bug fix in EMITHIGH (carbon_mod.f)
• Fix to prevent numerical overflow in EXP function

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

Issues resolved in GEOS-Chem v8-02-04

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

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

Issues resolved in GEOS-Chem v8-02-03

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

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

Issues resolved in GEOS-Chem v8-02-02

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

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

Issues resolved in GEOS-Chem v8-02-01

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

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

Issues resolved in GEOS-Chem v8-01-04

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

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

Issues resolved in GEOS-Chem v8-01-03

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

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

Issues resolved in GEOS-Chem v8-01-02

• Quick fix for GEOS-5 optical depth
  • Please see the discussion about this quick fix for the GEOS-5 optical depths.
  • NOTE: if you are using GEOS-Chem v8-01-04 or higher with the reprocessed GEOS-5 met fields, then you do not need to use this quick fix.
• Corrected labeling of SOA quantities in carbon_mod.f
• Double-substitution error in GET_ALK
• Robustness fix for reading anthropogenic SO2 and NH3
• Minor bug in gasconc.f & calcrate.f
• Minor bug in emfossil.f
• Fix for mass balance of HNO3 and NIT
• Bug in ND43
• Problem w/ ND65 diagnostic and dynamic tropopause
• Albedo diagnostic in GEOS-4
• Pressure diagnostic : PS-PTOP vs. PEDGE
• Minor bug in log file output

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

Issues resolved in GEOS-Chem v8-01-01

• Post-release patches
• Fixes for offline simulations
• Bugs in ND47/ND65/ND45 in v8-01-01

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

Issues resolved in GEOS-Chem v7-04-13

• Error in regrid_1x1_mod.f
• Error in smvgear.f

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

Issues resolved in GEOS-Chem v7-04-10

• NaN's in smvgear.f

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

Other issues

ND05 diagnostic quantities zeroed unexpectedly

Helen McIntyre wrote:

I'm running the new and old versions of GEOS-Chem, and both seem to not output all the ND05 diagnostics correctly. There are 10 prod/loss diagnostics in this category, but only the 5th, 6th and 7th work. All the rest come out as zero.

I've had a brief look though the code, and it seems that the ones that work are calculated in one part of the routine (sulfate_mod.f), and the zero ones in another (I don't know if this has anything to do with it).

I've just done a 1 day run, with GEOS-Chem v8-01-01 at 4x5 resolution using GEOS-5 met fields. The old version I'm using is v7-02-04 and I get the same result.

The 'ctm.bpch', 'geos.log' and 'input.geos' files from the v8-01-01 run can be found here: http://homepages.see.leeds.ac.uk/~lechlm/files/

Claire Carouge replied:

There are some problems in the calculations. For the 5th element of AD05 (in Fortran notations and not IDL), the diagnostic come from the value of L1 which is calculated line 1529 (v8-01-04):

   L1     = ( SO20 - SO2_cd + PSO2_DMS(I,J,L) ) * RK1/RK

But on line 1508, we have:

   RK1 = 0.d0

with the previous comment:

  ! For online runs, SMVGEAR deals w/ this computation,
  ! so we can simply set RK1 = 0 (rjp, bmy, 3/23/03)

So L1 is always 0. I have no idea what RK1 is for, you may have to go into the physics/chemistry behind the code and we are not qualified to help you with it.

The other values for AD05 are calculated in the routine CHEM_DMS and this routine is only called in an offline aerosol simulation (l. 545 in sulfate_mod.f).

So my guess is that the ND05 diagnostic was designed for offline simulations and if you want it for online chemistry, you need to implement it.

Bad GEOS-4 A6 met data causing segmentation fault

Please see this post about bad GEOS-4 A6 met data causing a segmentation fault in GEOS-Chem simulations.

--Bob Y. 15:19, 16 February 2010 (EST)

Too many levels in photolysis code

Please see this discussion about the "Too many levels in photolysis code" error that can sometimes happen in the FAST-J photolysis code.

--Bob Y. 11:05, 12 January 2010 (EST)

Negative tracer in routine WETDEP

See this post: Small negative RH value in in 20060206.a6.2x25 file. This has been corrected in GEOS-Chem v8-01-02 and higher versions.

Also see this post for more information.

--Bob Y. 14:48, 31 March 2011 (EDT)

ISORROPIA and RPMARES

Please see the discussion about the bugs & fixes for ISORROPIA and RPMARES on the Code Developer's Forum for Aerosol thermodynamical equilibrium.

Also, if you are trying to run an aerosol-only simulation, then please see this discussion about a bug that manifested itself only after switching from ISORROPIA to RPMARES.

NOTE: We have switched from RPMARES to ISORROPIA II in GEOS-Chem v8-03-01 and higher versions. This eliminates the problems that ISORROPIA I exhibited at low RH values.

--Bob Y. 14:48, 31 March 2011 (EDT)