FAST-JX v7.0 photolysis mechanism

FAST-JX v7.0 has been introduced into the GEOS-Chem v10-01, along with the UCX chemistry mechanism, by Sebastian Eastham (MIT).

Overview

This update is being tested in the 1-month benchmark simulation v10-01c.

Sebastian Eastham incorporated Fast-JX v7.0a into the GEOS-Chem UCX mechanism. From Eastham et al. (2014):

GEOS-Chem uses a customized version of the Fast-JX v6.2 photolysis rate solver (Wild et al., 2000), which efficiently estimates tropospheric photolysis. The customized version uses the wavelength bands from the older Fast-J tropospheric photolysis scheme and does not consider wavelengths shorter than 289 nm, assuming they are attenuated above the tropopause. However, these high-energy photons are responsible for the release of ozone-depleting agents in the stratosphere. The standard Fast-JX model (Prather, 2012) addresses this limitation by expanding the spectrum analyzed to 18 wavelength bins covering 177–850 nm, extending the upper altitude limit to approximately 60 km. We therefore incorporate Fast-JX v7.0a into GEOS-Chem UCX. Fast-JX includes cross-section data for many species relevant to the troposphere and stratosphere. However, accurately representing sulfur requires calculation of gaseous H2SO4 photolysis, a reaction which is not present in Fast-JX but which acts as a source of sulfur dioxide in the upper stratosphere. Based on a study by Mills (2005), the mean cross-section between 412.5 and 850 nm is estimated at 2.542 × 10−25 cm2. We also add photolysis of ClOO and ClNO2, given their importance in catalytic ozone destruction, using data from JPL 10-06 (Sander et al., 2011). Fast-JX v7.0a includes a correction to calculated acetone cross sections. Accordingly, where hydroxyacetone cross-sections were previously estimated based on one branch of the acetone decomposition, a distinct set of cross sections from JPL 10-06 are used.

The base version of GEOS-Chem uses satellite observations of total ozone columns when determining ozone-related scattering and extinction. The UCX allows either this approach, as was used for the production of the results shown, or can employ calculated ozone mixing ratios instead, allowing photolysis rates to respond to changes in the stratospheric ozone layer.

Timeline

The following table displays a timeline of important milestones in FAST-JX v7.0 development:

Version	Date	Features / Improvements
GEOS-Chem v10-01	TBD 2014	Retirement of FAST-J photolysis mechanism (in v10-01c) Implementation of FAST-JX v7.0 into GEOS-Chem, concurrent with UCX chemistry mechanism (in v10-01c) Fixed the following errors in the original FAST-JX v7.0 implementation: Reactivation of Br species for tropospheric simulation Bug fix for reducing wavelength bins for tropospheric simulation

--Bob Y. 11:01, 20 May 2014 (EDT)

Input files for FAST-JX v7.0

The following input files are required for the FAST-JX v7.0 photolysis mechanism:

File	Introduced	Retired	Description
fastj.jv_atms.dat.nc	v9-01-03	still used	This netCDF file (originally created for the FAST-J photolysis mechanism) specifies the reference O3 and T climatologies for FAST-J. This file is located in data directory: GEOS_NATIVE/FastJ_201204/fastj.jv_atms_dat.nc NOTE: Where such data exists, GEOS-Chem will overwrite the reference O3 climatology with either: TOMS/SBUV total ozone column (TO3) data, or TO3 data from the GEOS-5 or GEOS-FP met field archives.
FJX_j2j.dat	v10-01	still used	Links GEOS-Chem chemical species to Fast-JX species. Replaces the following file: ratj.d from the FAST-J photolysis mechanism, used in versions prior to GEOS-Chem v10-01
FJX_spec.dat	v10-01	still used	Fast-JX cross-sections, which replaces the following files: jv_spec.dat from the FAST-J photolysis mechanism, used in versions prior to GEOS-Chem v10-01 spec2008.dat from the FAST-JX v6.x photolysis mechanism, used in several research implementations of GEOS-Chem
jv_spec_aod.dat	v9-01-03	still used	The jv_spec_aod.dat file contains the optical properties for aerosols at a single wavelength to be used in the online calculation of the aerosol optical depth diagnostics. The default properties are provided at 550 nm. These properties have been calculated using the same size and optical properties as the jv_spec.dat file used for the FAST–J photolysis calculations. The user can exchange this set of properties with those at another wavelength. We recommend that the wavelength used be included in the first line of the header for traceability (this line is output to the GEOS–Chem log file during run time).
jv_spec.mie.dat	v10=01	still used	Contains aerosol optical properties at 5 wavelengths

--Bob Y. 10:35, 20 May 2014 (EDT)

Overhead ozone columns for use with FAST-JX v7.0

The treatment of overhead ozone columns for FAST-JX v7.0 is identical to that of the older FAST-J mechanism. Please see this section on our FAST-J photolysis mechanism wiki page for more information.

--Bob Y. 10:44, 20 May 2014 (EDT)

Cloud overlap options in FAST-JX v7.0

The treatment of cloud overlap in FAST-JX v7.0 is identical to that of the older FAST-J mechanism, with the exception that the maximum cloud overlap option has not yet been implemented. For more information, please see this section on our FAST-J photolysis mechanism wiki page.

--Bob Y. 10:54, 20 May 2014 (EDT)

Previous issues that have now been resolved

In this section we discuss issues that have been recently fixed in the implementation of FAST-JX v7.0:

Reactivation of bromine species photolysis for tropospheric simulation

This update will be tested in the 1-month benchmark simulation v10-01c.

Sebastian Eastham wrote:

Bromine species photolysis should probably be reactivated in the tropospheric version – given that it was online in the pre-UCX version, we may as well keep it online. Doing so is just a question of removing the 'x' in the FJX_spec.dat file for the relevant species.

In FJX_spec.dat change the following lines from:

BrO   x300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00  J10
           0.000E+00 0.000E+00 0.000E+00 5.620E-19 1.202E-18 2.008E-18
           3.239E-18 4.520E-18 5.064E-18 5.809E-18 7.350E-19 0.000E+00
BrNO3 x200 0.000E+00 0.000E+00 5.484E-19 7.245E-19 3.702E-18 3.475E-18  J10
           3.182E-18 2.978E-18 5.304E-19 6.086E-19 4.489E-19 1.963E-19
           1.584E-19 1.307E-19 1.110E-19 8.033E-20 3.377E-20 1.270E-21
BrNO3 x300 0.000E+00 0.000E+00 8.026E-19 1.071E-18 5.166E-18 4.190E-18  J10
           3.467E-18 3.039E-18 5.567E-19 5.989E-19 4.528E-19 2.098E-19
           1.705E-19 1.425E-19 1.207E-19 8.648E-20 3.716E-20 1.445E-21
HOBr  x300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00  J10
           0.000E+00 0.000E+00 1.324E-19 2.011E-19 2.202E-19 2.196E-19
           1.726E-19 1.367E-19 1.157E-19 1.125E-19 6.197E-20 2.755E-21

to:

BrO    300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00  J10
           0.000E+00 0.000E+00 0.000E+00 5.620E-19 1.202E-18 2.008E-18
           3.239E-18 4.520E-18 5.064E-18 5.809E-18 7.350E-19 0.000E+00
BrNO3  200 0.000E+00 0.000E+00 5.484E-19 7.245E-19 3.702E-18 3.475E-18  J10
           3.182E-18 2.978E-18 5.304E-19 6.086E-19 4.489E-19 1.963E-19
           1.584E-19 1.307E-19 1.110E-19 8.033E-20 3.377E-20 1.270E-21
BrNO3  300 0.000E+00 0.000E+00 8.026E-19 1.071E-18 5.166E-18 4.190E-18  J10
           3.467E-18 3.039E-18 5.567E-19 5.989E-19 4.528E-19 2.098E-19
           1.705E-19 1.425E-19 1.207E-19 8.648E-20 3.716E-20 1.445E-21
HOBr   300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00  J10
           0.000E+00 0.000E+00 1.324E-19 2.011E-19 2.202E-19 2.196E-19
           1.726E-19 1.367E-19 1.157E-19 1.125E-19 6.197E-20 2.755E-21

--Melissa Sulprizio 13:33, 14 May 2014 (EDT)

Error in reducing wavelength bins for tropospheric simulation

This update will be tested in the 1-month benchmark simulation v10-01c.

Sebastian Eastham wrote:

In fast_jx_mod, specifically RD_XXX, there is a transformation to reduce 18 cross sections to 12. Since bin 18 now corresponds to bin 12 and so on, the wavelengths are moved within the cross section array QQQ. However, the 12-bin capability is rarely used (if ever), so when Fast-JX was extended to allow cross sections with 1 or 3 sets of data, the 12 and 8 bin codes were not updated accordingly. This results in very large cross sections for acetone at long wavelengths, because the shorter wavelength data is being used instead.

I've notified Michael Prather - he did not know about this bug and is putting together a fix ASAP. I've written my own fix in the meantime, which results in the acetone cross sections matching much more closely, at least between the two v10-01c versions.

--Melissa Sulprizio 10:39, 12 May 2014 (EDT)