Difference between revisions of "Bugs and fixes"

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(Bad GEOS-4 A6 met data causing segmentation fault)
(Issues resolved in GEOS-Chem v8-02-04)
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* [[GEOS-Chem v8-02-04#Div-by-zero error encountered in arsl1k.f|Div-by-zero error encountered in arsl1k.f]]
 
* [[GEOS-Chem v8-02-04#Div-by-zero error encountered in arsl1k.f|Div-by-zero error encountered in arsl1k.f]]
 
* [[GEOS-Chem v8-02-04#Fix for diagnostic arrays in TPCORE|Fix for diagnostic arrays in TPCORE]]
 
* [[GEOS-Chem v8-02-04#Fix for diagnostic arrays in TPCORE|Fix for diagnostic arrays in TPCORE]]
 +
* [[GEOS-Chem v8-02-04#MEGAN now uses MODIS LAI by default|MEGAN now uses MODIS LAI by default]]
  
--[[User:Bmy|Bob Y.]] 10:11, 12 January 2010 (EST)
+
--[[User:Bmy|Bob Y.]] 16:29, 23 February 2010 (EST)
  
 
== Issues resolved in GEOS-Chem v8-02-03 ==
 
== Issues resolved in GEOS-Chem v8-02-03 ==

Revision as of 21:29, 23 February 2010

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

Issues resolved in GEOS-Chem v8-02-05

--Ccarouge 12:55, 26 January 2010 (EST)

Issues resolved in GEOS-Chem v8-02-04

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

Issues resolved in GEOS-Chem v8-02-03

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

Issues resolved in GEOS-Chem v8-02-02

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

Issues resolved in GEOS-Chem v8-02-01

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

Issues resolved in GEOS-Chem v8-01-04

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

Issues resolved in GEOS-Chem v8-01-03

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

Issues resolved in GEOS-Chem v8-01-02

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

Issues resolved in GEOS-Chem v8-01-01

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

Issues resolved in GEOS-Chem v7-04-13

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

Issues resolved in GEOS-Chem v7-04-10

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

ND05 diagnostic quantities zeroed unexpectedly

Helen McIntyre (h.macintyre@see.leeds.ac.uk) 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 (ccarouge@seas.harvard.edu) 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 because of negative RH

See this post: GEOS-5 issues#Small negative RH value in 20060206.a6.2x25 file

Fixes are available at ftp://ftp.as.harvard.edu/pub/geos-chem/patches/v8-01-01.

--phs 16:31, 6 June 2008 (EDT)

Negative tracer in routine WETDEP

Please see this post for more information.

--Bob Y. 14:25, 16 February 2010 (EST)

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 will upgrade to ISORROPIA II in GEOS-Chem v8-02-05. This will eliminate the problems that ISORROPIA I exhibited at low RH values.

--Bob Y. 14:25, 16 February 2010 (EST)