Photolysis mechanism

This page describes some of the updates to the FAST-J photolysis mechanism, as is currently implemented in GEOS-Chem.

Input files for FAST-J

The following input files are required for the FAST-J photolysis mechanism:

ratj.d

This file is where you specify each of the FAST-J photolysis species. Each species is mapped to a corresponding entry of the GEOS-Chem chemical mechanism.

jv_atms.dat

This file specifies the reference O3 climatology for FAST-J. NOTE: GEOS-Chem will overwrite this reference climatology with TOMS/SBUV data for those months and locations where such data exists.

jv_spec.dat

This file is where the various quantum yields and aerosol cross-sections are specified.

Overhead TOMS O3 columns for 2006 and 2007

Bob Yantosca has updated the TOMS overhead O3 columns to account for years 2006 and 2007. The data files are available at:

ftp ftp.as.harvard.edu
cd pub/geos-chem/data/GEOS_2x2.5/TOMS_200701/
get README
get TOMS_O3col_2006.geos.2x25
get TOMS_O3col_2007.geos.2x25
cd pub/geos-chem/data/GEOS_4x5/TOMS_200701/
get README
get TOMS_O3col_2006.geos.4x5
get TOMS_O3col_2007.geos.4x5

Also you will have to make a modification in the subroutine READ_TOMS in toms_mod.f. Replace the following lines:

     ! Use 2005 data after 2005
     IF ( YEAR > 2005 ) THEN
        WRITE( 6, 105 ) YEAR
        YEAR = 2005
     ENDIF
    

with these lines:

     ! Use 2007 data after 2007
     IF ( YEAR > 2007 ) THEN
        WRITE( 6, 105 ) YEAR
        YEAR = 2007
     ENDIF

This will make sure the code uses the files for 2006 and 2007. This fix is slated to go into the next standard GEOS-Chem code release (v8-01-04).

--Bob Y. 14:49, 14 January 2009 (EST)

O1D reaction updated to JPL 2006

The rate constants in the "FAST-J" jv_atms.dat file have been updated by Lin Zhang.

These were the old values:

O3_1d  180 9.500E-01 9.330E-01 4.270E-01 6.930E-02 6.060E-02       0.0       0.0
O3_1d  260 9.500E-01 9.420E-01 4.890E-01 1.360E-01 7.110E-02       0.0       0.0
O3_1d  300 9.500E-01 9.550E-01 5.870E-01 2.370E-01 8.570E-02       0.0       0.0

which are now replaced by the new values from JPL 2006:

O3_1d  180 9.000E-01 9.000E-01 3.824E-01 8.092E-02 7.650E-02       0.0       0.0
O3_1d  260 9.000E-01 9.000E-01 4.531E-01 1.438E-01 7.654E-02       0.0       0.0
O3_1d  300 9.000E-01 9.000E-01 5.273E-01 2.395E-01 7.659E-02       0.0       0.0

Also the new file has the following header line (the O1D update is noted there):

jv_spec.dat:  FAST-J, std JPL 00 (mje 4/02) -- aer/dust (rvm, 3/02) -- O1D (lzh 5/06)

For more information, please contact Lin Zhang (linzhang@fas.harvard.edu).

This update is slated to go into our "Chemistry" release of GEOS-Chem, probably to be denoted v8-01-05.

--Bob Y. 14:49, 14 January 2009 (EST)

Cloud overlap options in FAST-J

GEOS-Chem now has 3 cloud overlap options in the FAST-J photolysis mechanism:

Linear cloud overlap assumption

The linear cloud overlap option is the default in GEOS-Chem versions v8-01-01 and prior. The option is:

    Grid Box Optical depth = In-cloud optical depth * Cloud fraction.  

Approximate random overlap assumption

This approximate random overlap option was introduced into the standard code in GEOS-Chem v8-01-02:

    Grid Box Optical Depth = In-Cloud Optical Depth * ( Cloud Fraction )^1.5 

Maximum random overlap assumption

This maximum random overlap option is much more computationally intensive, and therefore is not used as the default option. However, if you wish to use this option, then manually edit the fast_j.f source code file such that OVERLAP = 3.

The Maximum-Random Overlap (MRAN) scheme assumes that clouds in adjacent layers are maximally overlapped to form a cloud block and that blocks of clouds separated by clear layers are randomly overlapped. A vertical profile of fractional cloudiness is converted into a series of column configurations with corresponding fractions see Liu et al., JGR 2006; hyl,3/3/04).

For more details about cloud overlap assumptions and their effect on photolysis frequencies and key oxidants in the troposphere, refer to the following articles:

1. Liu, H., et al., Radiative effect of clouds on tropospheric chemistry in a global three-dimensional chemical transport model, J. Geophys. Res., 111, D20303, doi:10.1029/2005JD006403, 2006.
2. Tie, X., et al., Effect of clouds on photolysis and oxidants in the troposphere, J. Geophys. Res., 108(D20), 4642, doi:10.1029/2003JD003659, 2003.
3. Feng, Y., et al., Effects of cloud overlap in photochemical models, J. Geophys. Res., 109, D04310, doi:10.1029/2003JD004040, 2004.
4. Stubenrauch, C.J., et al., Implementation of subgrid cloud vertical structure inside a GCM and its effect on the radiation budget, J. Clim., 10, 273-287, 1997.

Discussion

Hongyu Liu (hyl@nianet.org) wrote:

I have a comment about how the effect of cloud overlap in the vertical may be included in GEOS-Chem. The standard GEOS-Chem assumes linear scaling of cloud optical depth with cloud fraction in a grid box, i.e., the grid average cloud optical depth TAU' = TAU * f, where TAU is the COD in the cloudy portion of the grid and f is cloud fraction in the layer. This linear assumption (LIN) not only introduces a significant bias because of the nonlinear relationship between J-values and COD, but also is not consistent with the cloud-radiation interactions taking place in the original GEOS-DAS. Current GCMs or DAS usually use random overlap (RAN) or maximum-random overlap (MRAN) in their cloud-radiation packages.

Ideally, GEOS-Chem should use the same cloud overlap assumption as the one used in GEOS-DAS where TOA radiative fluxes have been validated against e.g. satellite observations. But the ("exact") random overlap and MRAN approaches are computationally expensive. Fortunately, the so-called "approximate" random overlap scheme [TAU' = TAU * f^(3/2) which is computationally cheap] has been demonstrated to be a good approximation to both the "exact" random overlap and MRAN calculations. For details, see my GEOS-Chem cloud paper (section 2.3 & Figures 8d,9d: http://research.nianet.org/~hyl/publications/liu2006_cloud1.abs.html

So, if we don't want to use any cloud overlap assumptions because of computational cost, the "approximate" random overlap seems a good option - it makes more sense physically and is more consistent with the mother GCM or DAS. Actually it has been used in the MOZART model for years [see Brasseur et al., 1998].

Hongyu Liu

For more information, please contact Hongyu Liu (hyl@nianet.org).

--Bob Y. 12:44, 23 May 2008 (EDT)