Difference between revisions of "GEOS-Chem v8-02-04"
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(→Bug fix in DIAG20 (diag_pl_mod.f)) |
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! Zero counter | ! Zero counter | ||
COUNT(I,J,L) = 0 <=== ERROR: (I,J,L) indices used outside loop! | COUNT(I,J,L) = 0 <=== ERROR: (I,J,L) indices used outside loop! | ||
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! Zero PL24H array | ! Zero PL24H array | ||
!$OMP PARALLEL DO | !$OMP PARALLEL DO | ||
Revision as of 15:05, 1 December 2009
Contents
- 1 Overview
- 2 Previous issues now resolved in v8-02-04
- 2.1 Updated reactions in sulfate_mod.f
- 2.2 Bug fix for EMEP ship emissions
- 2.3 Minor fix for molecular weights in drydep_mod.f
- 2.4 Bug fix in biomass_mod.f
- 2.5 Minor bug fix in gamap_mod.f
- 2.6 Fixes and updates in seasalt_mod.f
- 2.7 Bug fix in emfossil.f for 0.5 x 0.666 nested grid tagged-CO option
- 2.8 Bug fix in DIAG20 (diag_pl_mod.f)
- 3 Outstanding issues not yet resolved in v8-02-04
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:
- In CHEM_DMS, definition of RK2.
- 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)
Fixes and updates in seasalt_mod.f
Updates to the sea-salt emissions scheme
Lyatt Jaeglé (jaegle@atmos.washington.edu) wrote:
- I recommend 3 fixes to the Monahan sea-salt emissions scheme in GEOS-Chem:
- 1. The source function is for wet aerosol radius (RH=80%, with a radius twice the size of dry aerosols) so in function SRCSALT in seasalt_mod.f, BETHA should be set to 2 instead of 1. Change the line:
REAL*8, PARAMETER :: BETHA = 1.d0
- to:
REAL*8, PARAMETER :: BETHA = 2.d0
- 2. It turns out that the LOG in the Monahan source function is a log base 10. Therefore these lines:
! Sea salt base source [kg/m2]
SRC(R,N) = CONST * SS_DEN( N )
& * ( 1.d0 + 0.057d0*( BETHA * RMID(R,N) )**1.05d0 )
& * 10d0**( 1.19d0*
& EXP(-((0.38d0-LOG(BETHA*RMID(R,N)))/0.65d0)**2))
& / BETHA**2
! Sea salt base source [#/m2] (bec, bmy, 4/13/05)
SRC_N(R,N) = CONST_N * (1.d0/RMID(R,N)**3)
& * (1.d0+0.057d0*(BETHA*RMID(R,N))**1.05d0)
& * 10d0**(1.19d0*EXP(-((0.38d0-LOG(BETHA*RMID(R,N)))
& /0.65d0)**2))/ BETHA**2
- should be replaced with
!-----------------------------------------------------------
! IMPORTANT NOTE!
!
! In mathematics, "LOG" means "log10".
! In Fortran, "LOG" means "ln" (and LOG10 is "log10").
!
! The following equations require log to the base 10, so
! we need to use the Fortran function LOG10 instead of LOG.
! (jaegle, bmy, 11/23/09)
!-----------------------------------------------------------
! Sea salt base source [kg/m2]
SRC(R,N) = CONST * SS_DEN( N )
& * ( 1.d0 + 0.057d0*( BETHA * RMID(R,N) )**1.05d0 )
& * 10d0**( 1.19d0*
& EXP(-((0.38d0-LOG10(BETHA*RMID(R,N)))/0.65d0)**2))
& / BETHA**2
! Sea salt base source [#/m2] (bec, bmy, 4/13/05)
SRC_N(R,N) = CONST_N * (1.d0/RMID(R,N)**3)
& * (1.d0+0.057d0*(BETHA*RMID(R,N))**1.05d0)
& * 10d0**(1.19d0*EXP(-((0.38d0-LOG10(BETHA*RMID(R,N)))
& /0.65d0)**2))/ BETHA**2
3. Finally I think that we should change the dry size bins for the coarse mode aerosols in input.geos. Please see the discussion on our Sea salt aerosols wiki page for more information.
--Bob Y. 10:44, 23 November 2009 (EST)
Updated hygroscopic growth factors
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)
Bug fix in emfossil.f for 0.5 x 0.666 nested grid tagged-CO option
Yuxuan Wang (zjiang@atmosp.physics.utoronto.ca) wrote:
- Zhe Jiang at University of Toronto found a bug in emfossil.f for the nested_CH tagged-CO option in code version v8-02-01 and higher. In emfossil.f, we need to make the following fix:
IF ( ITS_A_TAGCO_SIM() ) THEN
!----------------------------------------------------------------
! Prior to 11/23/09:
! The reason for this change is because LNEI99 is set as .FALSE.
! for the NESTED_CH option so GET_USA_MASK doesn't have a
! definition which causes the run to crash. So we need to
! add an ELSE to the IF ( LICARTT ) block to cover for this.
! (zie, yxw, bmy, 11/23/09)
!IF ( LICARTT ) THEN
! IF ( GET_USA_MASK(I,J) > 0.d0 ) THEN
! IF ( NN == IDTCO ) EMX(1) = EMX(1) * 1.39d0
! ELSE
! IF ( NN == IDTCO ) EMX(1) = EMX(1) * 1.19d0
! ENDIF
!ENDIF
!----------------------------------------------------------------
IF ( LICARTT ) THEN
IF ( GET_USA_MASK(I,J) > 0.d0 ) THEN
IF ( NN == IDTCO ) EMX(1) = EMX(1) * 1.39d0
ELSE
IF ( NN == IDTCO ) EMX(1) = EMX(1) * 1.19d0
ENDIF
ELSE
IF ( NN == IDTCO ) EMX(1) = EMX(1) * 1.19d0
ENDIF
ELSE
IF ( NN == IDTCO ) EMX(1) = EMX(1) * 1.02d0
ENDIF
This bug is now fixed in GEOS-Chem v8-02-04.
--Bob Y. 16:40, 23 November 2009 (EST)
Bug fix in DIAG20 (diag_pl_mod.f)
Both Dylan Jones and Yuxuan Wang found a bug in the ND20 diagnostic (production and loss rate of Ox for tagged Ox simulation) in code version 8-02-01 and higher. In routine DIAG20 of diag_pl_mod.f, the COUNT variable for ND20 is not zeroed correctly at the beginning of each new day.
The following lines of code:
! Zero counter
COUNT(I,J,L) = 0 <=== ERROR: (I,J,L) indices used outside loop!
! Zero PL24H array
!$OMP PARALLEL DO !$OMP+DEFAULT( SHARED ) !$OMP+PRIVATE( I, J, L, N )
DO N = 1, 2
DO L = 1, LD65
DO J = 1, JJPAR
DO I = 1, IIPAR
PL24H(I,J,L,N) = 0d0
ENDDO
ENDDO
ENDDO
ENDDO
!$OMP END PARALLEL DO
can now be replaced by the F90 array assignment statements:
! Zero arrays
COUNT = 0
PL24H = 0d0
and then there will be no chance of an out-of-bounds error.
--Bob Y. 10:05, 1 December 2009 (EST)
