Difference between revisions of "GEOS-Chem v8-02-04"

Revision as of 15:23, 23 November 2009

Overview

BETA RELEASE -- Date TBA

Will contain everything in GEOS-Chem v8-02-03, plus:

• LINOZ stratospheric ozone chemistry (Dylan Jones group @ U. Toronto)
• Updated inventory of volcanic SO2 emissions from AeroCom (J. Fisher)
• Update to near-IR photolysis of HNO4 (J. Mao)
• Updated MEGAN biogenic emissions (M. Barkley)
• Updates and fixes for sea salt aerosols (L. Jaeglé, B. Alexander)

Note about Linoz validation

Dylan Jones (dbj@atmosp.physics.utoronto.ca) wrote:

Testing [the Linoz code in v8-02-04] was more difficult that I thought. I began by trying to compare the output of v8-02-04 with our previous runs with v8-02-01. I accounted for the changes in the transport_mod.f and I tried to undo the changes in when the diagnostics are archived in v8-02-04, but I was still getting large differences between v8-02-04 and v8-02-01. I finally gave up on this since I may have made a mistake in reverting to the old way of doing the diagnostics in v8-02-04. In the end I took the new linoz code from v8-02-04 and used it in v8-02-01. I ran two GEOS-5 full chemistry simulations for 2007 and the output were consistent over the full year.

I think that it is safe to release [Linoz in v8-02-04]. However, we should acknowledge that it was [only] tested in v8-02-01, since I was not able to assess the quality of the output in v8-02-04.

--Bob Y. 16:52, 18 November 2009 (EST)

Previous issues now resolved in v8-02-04

Updated reactions in sulfate_mod.f

Jenny Fisher (jafisher@fas.harvard.edu) wrote:

I made two very small changes to sulfate_mod.f that should be included in the standard code. The change updates the reaction rates used for the offline aerosol simulation so that they match the rates Jingqiu implemented in the full chemistry simulation.

The changes are:

1. In CHEM_DMS, definition of RK2.
2. In CHEM_SO2, definitions of K0 and Ki. Note that I also removed the definition of Ki earlier in the subroutine (line 1497) and moved it to this section so it can be easily updated for future rate constant revisions.

--Bob Y. 09:50, 15 October 2009 (EDT)

Bug fix for EMEP ship emissions

Monika Kopacz (mkopacz@princeton.edu) wrote:

I noticed that the code crashes when EMEP is set to false but ship emissions from EMEP are true in the input file. Sure, it makes sense, but I would suggest the following addition to the input_mod.f, around say around line 1550 to prevent the code from crashing.

   ! Make sure we're not using EMEP ship emissions, if EMEP is off
   IF (.not. LEMEP ) THEN
      LEMEPSHIP = .FALSE.
   ENDIF 

Bob Yantosca (yantosca@seas.harvard.edu) replied:

Good catch. We've put this code into READ_EMISSIONS_MENU in input_mod.f:

    !%%% Bug fix!  If LEMEPSHIP is turned on but LEMEP is turned %%%
    !%%% off, this will cause an error (because arrays are not   %%%
    !%%% allocated, etc.).  For now, just turn off LEMEPSHIP     %%%
    !%%% and print a warning message.  Whoever wants to fix this %%%
    !%%% in a more robust way is welcome to do so.               %%%
    !%%% (mak, bmy, 10/19/09)                                    %%%
    IF ( LEMEPSHIP .and. ( .not. LEMEP ) ) THEN
       LEMEPSHIP = .FALSE.
       WRITE( 6, '(a)' ) REPEAT( '=', 79 )
       WRITE( 6, '(a)' ) 'WARNING! EMEP emissions are turned off,'
       WRITE( 6, '(a)' ) 'so also turn off EMEP ship emissions'
       WRITE( 6, '(a)' ) 'in order to avoid crashing GEOS-Chem!'
       WRITE( 6, '(a)' ) REPEAT( '=', 79 )
    ENDIF

As you pointed out the simple solution is to just turn off LEMEPSHIP if LEMEP=F. However, it may still be possible to keep LEMEPSHIP turned on...one would have to go thru emep_mod.f to make sure that the ship emissions arrays get allocated even if the other arrays don't. Whoever wants to can feel free to do that...

--Bob Y. 10:57, 19 October 2009 (EDT)

Minor fix for molecular weights in drydep_mod.f

Bob Yantosca (yantosca@seas.harvard.edu) replied:

I found a minor inconsistency in INIT_DRYDEP (in drydep_mod.f) which only affects the SOA tracers. In the big loop where we initialize everything, the following updates were made:

       ! ALPH (Alpha-pinene)
       ELSE IF ( N == IDTALPH ) THEN
          ...

          !----------------------------------------------------------
          ! Prior to 10/19/09:
          ! Molwt should be 136.23 not 136 even (bmy, 10/19/09)
          !XMW(NUMDEP)     = 136d-3
          !----------------------------------------------------------
          XMW(NUMDEP)     = 136.23d-3

          ...            

       ! LIMO (Limonene)
       ELSE IF ( N == IDTLIMO ) THEN
          ...

          !----------------------------------------------------------
          ! Prior to 10/19/09:
          ! Molwt should be 136.23 not 136 even (bmy, 10/19/09)
          !XMW(NUMDEP)     = 136d-3
          !----------------------------------------------------------
          XMW(NUMDEP)     = 136.23d-3
  

So in other words, the mol wt of ALPH and LIMO was listed as 136d-3 but it should be 136.23d-3. It doesn't change things drastically, just in the last few decimal places of the surface resistance array RSURFC.

--Bob Y. 14:46, 19 October 2009 (EDT)

Bug fix in biomass_mod.f

Monika Kopacz (mkopacz@princeton.edu) and Jenny Fisher (jafisher@fas.harvard.edu) wrote:

We have a bug fix for biomass_mod.f. This is based on the GEOS-Chem v8-02-03 code, though we believe the problem has been there since at least GEOS-Chem v8-02-01. The corrected file is located via anonymous FTP at:

   ftp://ftp.gfdl.noaa.gov/home/m1k/biomass_mod.f.corrected

This fix required moving the co-emitted VOC scaling of emissions (in routine COMPUTE_BIOMASS_EMISSIONS) to places where the BIOMASS array is being reset or recalculated to prevent rescaling at every time step and thus blowing up. It might not have been a problem when using GFED2 emissions, but it was definitely a problem for other inventories that do not update the BIOMASS array at every time step.

This fix will be included in GEOS-Chem v8-02-04.

--Bob Y. 16:36, 6 November 2009 (EST)

Minor bug fix in gamap_mod.f

Daven Henze (Daven.Henze@Colorado.EDU) wrote:

The wiki says that MOLC was switched from 3 to 2 for ALD2 in gamap_mod.f, but the v8-02-03 code looks like the switch was accidentally applied to PRPE instead,

                 CASE( 6  )
                    NAME (T,28) = 'ALD2'
                    INDEX(T,28) = 11 + ( SPACING * 45 )
                    MWT  (T,28) = 12e-3
                    MOLC (T,28) = 3
                    UNIT (T,28) = 'atoms C/cm2/s'
                 CASE( 7  )
                    NAME (T,28) = 'PRPE'
                    INDEX(T,28) = 18 + ( SPACING * 45 )
                    MWT  (T,28) = 12e-3
                    !-------------------------------------------------
                    ! Prior to 10/9/09:
                    ! ALD2 has 2 carbons, not 3 (dbm, bmy, 10/9/09)
                    !MOLC (T,28) = 3
                    !-------------------------------------------------
                    MOLC (T,28) = 2
                    UNIT (T,28) = 'atoms C/cm2/s'

Bob Yantosca (yantosca@seas.harvard.edu) replied:

Yes it was a typo. I've since fixed it, it'll go into GEOS-Chem v8-02-04. Indeed, ALD2 should have 2 carbons and PRPE should have 3 carbons.

--Bob Y. 12:36, 19 November 2009 (EST)

Updated hygroscopic growth factors for sea-salt

Becky Alexander (beckya@u.washington.edu) wrote:

The hygroscopic growth factors in routine GET_ALK (seasalt_mod.f) are incorrect. These:

       ! hygroscopic growth factor for sea-salt from Chin et al. (2002)
       IF ( IRH < 100 ) HGF = 2.2d0
       IF ( IRH < 99  ) HGF = 1.9d0
       IF ( IRH < 95  ) HGF = 1.8d0
       IF ( IRH < 90  ) HGF = 1.6d0
       IF ( IRH < 80  ) HGF = 1.5d0
       IF ( IRH < 70  ) HGF = 1.4d0
       IF ( IRH < 50  ) HGF = 1.0d0

should be replaced with:

       ! hygroscopic growth factor for sea-salt from Chin et al. (2002)
       IF ( IRH < 100 ) HGF = 4.8d0
       IF ( IRH < 99  ) HGF = 2.9d0
       IF ( IRH < 95  ) HGF = 2.4d0
       IF ( IRH < 90  ) HGF = 2.0d0
       IF ( IRH < 80  ) HGF = 1.8d0
       IF ( IRH < 70  ) HGF = 1.6d0
       IF ( IRH < 50  ) HGF = 1.0d0

This has now been done in GEOS-Chem v8-02-04.

--Bob Y. 09:48, 23 November 2009 (EST)

Outstanding issues not yet resolved in v8-02-04