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/SBUV merged 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.

Here is an excerpt from the README that describes the TOMS data set versions that we are currently using:

  Data source and version:
  -------------------------

  1985 - 2005 are taken from:

    http://code916.gsfc.nasa.gov/Data_services/merged/index.html

    TOMS/SBUV MERGED TOTAL OZONE DATA, Version 8, Revision 3.
    Resolution:  5 x 10 deg.

    Contact person for the merged data product:
    Stacey Hollandsworth Frith (smh@hyperion.gsfc.nasa.gov)

  2006 and 2007 are taken from:

     http://code916.gsfc.nasa.gov/Data_services/merged/index.html

     Version 8 Merged Ozone Data Sets
     Revision 04
     DATA THROUGH: SEP 2008
     LAST MODIFIED: 20 OCT 2008 

NOTE: This fix was introduced into version v8-01-04.

--Bob Y. 14:15, 24 March 2009 (EDT)

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)

Updated aerosol optical properties

This is slated for inclusion into GEOS-Chem v8-02-05.

Authors

Name	Affiliation	E-mail	Date
Randall Martin	Dalhousie University	randall.martin@dal.ca	19 November 2009
Colette Heald	Colorado State University	heald@atmos.colostate.edu	29 January 2010

Overview

The updated jv_spec.dat file was created to reflect current information about aerosol size distributions for sulfate, organic carbon, black carbon and sea salt. The method follows Martin et al., [2003]. Refractive indices are based on GADS. The Mie code is from ftp://ftp.giss.nasa.gov/pub/crmim/spher.f and described in Mischenko et al. [1999]. The current calculation uses an geometric standard deviation (sigma_g) of 1.6 for sulfate, BC and OC following Wang et al. [2003ab] and Drury et al. [submitted]. The sigma_g was also reduced to 1.5 and 1.8 for fine and coarse sea salt respectively following Jaegle et al. [2010]. Specific geometric mean radii (r_g) for each species and relative humidity are in the headers of jv_spec.dat. Consistent aerosol optical properties at 550nm were also created for the file jv_spec_aod.dat.

Some illustrative differences between the "old" jv_spec.dat and the "current" one are given below for 70% relative humidity. The most important change is that organic carbon aerosols are larger in the current version, and that sea salt are substantially smaller.

r_g (um)

Sulfate	Old Value	New Value
r_g (um)	0.07	0.11
sigma_g	2.0	1.6
r_eff (um)	0.24	0.19
Qext (at 300nm)	2.4	2.6
Qext (at 600nm)	1.3	0.93
Organic Carbon	Old Value	New Value
r_g (um)	0.03	0.09
sigma_g	2.0	1.6
r_eff (um)	0.095	0.15
Qext (at 300nm)	1.2	2.3
Qext (at 600nm)	0.34	0.75
Black Carbon	Old value	New value
0.01	0.02
sigma_g	2.0	1.6
r_eff (um)	0.039	0.035
Qext (at 300nm)	1.06	0.95
Qext (at 600nm)	0.43	0.33
Sea salt (accumulation mode)	Old value	New value
r_g (um)	0.38	0.15
sigma_g	2.0	1.5
r_eff (um)	1.32	0.23
Qext (at 300nm)	2.33	3.04
Qext (at 600nm)	2.60	1.37
Sea salt (coarse mode)	Old value	New value
r_g (um)	3.2	0.73
sigma_g	2.0	1.8
r_eff (um)	10.1	1.7
Qext (at 300nm)	2.07	2.22
Qext (at 600nm)	2.11	2.43

Issues

It is likely that organic aerosol at ultraviolet wavelengths is more absorbing than included here as based on GADS [Koepke et al., 1997].

Aerosols are often internally mixed, in contast with their implementation as an external mixture in jv_spec.dat.

References

1. Drury, E., D.J. Jacob, R.J.D. Spurr, J. Wang, Y. Shinozuka, B.E. Anderson, A.D. Clarke, J. Dibb, C. McNaughton, and R. Weber, Synthesis of satellite (MODIS), aircraft (ICARTT), and surface (IMPROVE, EPA-AQS, AERONET) aerosol observations over North America to improve MODIS aerosol retrievals and constrain surface aerosol concentrations and sources , J. Geophys. Res., submitted.
2. Koepke, P., M. Hess, I. Schult, and E. P. Shettle, (1997). Global Aerosol Data Set, Report No. 243, Max-Planck-Institut fur Meteorologie, Hamburg, ISSN 0937-1060.
3. Martin, R.V., D.J. Jacob, R.M. Yantosca, M. Chin, and P. Ginoux, Global and regional decreases in tropospheric oxidants from photochemical effects of aerosols, J. Geophys. Res., 108, 4097, doi:10.1029/2002JD002622, 2003.
4. Mishchenko, M.I., J.M. Dlugach, E.G. Yanovitskij, and N.T. Zakharova, Bidirectional reflectance of flat optically thick particulate layers: an efficient radiative transfer solution and applications to snow and soil surfaces, J. Quant. Spectrosc. Radiat. Transfer, 63, 409-432, 1999.
5. Wang, J., S.A. Christopher, F. Brechtel, J. Kim, B. Schmid, J. Redemann, P.B. Russell, P. Quinn, and B.N. Holben, Geostationary satellite rtrievals of aerosol optical thickness during ACE-Asia, J. Geophys. Res., 108, 8657, doi:10.1029/2003JD003580, 2003.
6. Wang, J., S.A. Christopher, J.S. Reid, H. Maring, D. Savoie, B.H. Holben, J.M. Livingston, P.B. Russell, and S.K. Yang, GOES-8 retrieval of dust aerosol optical thickness over the Atlantic Ocean during PRIDE, J. Geophys. Res., 108, 8595, doi:10.1029/2002JD002494, 2003.

--Bob Y. 16:46, 14 January 2010 (EST)

Too many levels in photolysis code

The scattering module (OPMIE.f) for Fast-J requires many additional vertical levels. It happens that the limit (NL set in jv_mie.h) can be reached in some situations, causing the program to stop with a "Too many levels in photolysis code.." error message. Sometimes you can increase NL to solve the problem. Now a new version of OPMIE.f is available, which still warns you if NL is reached, but works with that limit.

Before being released into the standard model, you can find the new OPMIE.f at: ftp://ftp.as.harvard.edu/pub/geos-chem/patches/v8-01-01/OPMIE.f

--phs 11:29, 17 June 2008 (EDT)

This can also be an indication that there may be a problem in your visual optical depths, dust emissions, or aerosol emissions. Dust and aerosol optical depths are computed from the concentration array STT. If for some reason you end up emitting too much aerosol or dust (i.e. a unit conversion error), then this will result in an abnormally high dust or aerosol optical depth. A very high optical depth will cause FAST-J to want to keep adding points to the Gaussian quadrature in OPMIE.f. You can get into a situation where the number of points that FAST-J wants to add is greater than the array parameter NL (it may want to add thousands of points!).

Therefore, if you encounter this type of error, it is a good idea to doublecheck your aerosol & dust emissions to make sure that the monthly and annual totals are reasonable.

--Bob Y. 11:03, 26 June 2008 (EDT)