FAST-JX v7.0 photolysis mechanism

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FAST-JX v7.0 has been introduced into 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 mechanism (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

--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
FJX_spec.dat v10-01 still used
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)

VOC photolysis in FAST-JX v7.0

Here I summarize VOC photolysis in Fast-JX v7.0:

Old reaction Old rate New reaction New rate Note
CH2O = HO2 + HO2 + CO same Significant increase by 10% to 20% channel a
CH2O = H2 + CO same increase by 6% to 15% channel b
PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2 + 0.4NO3 same JPL2010 suggests two channels, in contrast to FastJX-v7.0, branching ratio follows IUPAC
ALD2 = MO2 + HO2 + CO same
ALD2 = CH4 + CO same
GLYX = 0.5H2 + CO + 0.5CH2O + 0.5CO GLYX = H2 + 2CO
GLYX = CH2O + CO
Pressure dependence is now included now 3 channels
GLYX = 2.0CO + 2.0HO2 same Pressure dependence is now included
MACR = CO + HO2 + CH2O + MCO3
branching ratio = 0.5
same
MACR = MAO3 + HO2
branching ratio = 0.5
remove this channel suggested by IUPAC, also consistent with Fast-JX v7.0
MVK = PRPE + CO
branching ratio = 0.6
MVK = MCO3 + CH2O + CO + HO2
branching ratio = 0.2
MVK = MO2 + MAO3
branching ratio = 0.2
MVK = MO2 + RCO3 this channel was removed in FJX v7.0, but it shouldn't according to IUPAC. MAO3 is changed to RCO3 for carbon balance.
GLYC = CH2O + 2.0HO2 + CO same
GLYC = CH3OH + CO two more channels were added in FJX v7.0, but IUPAC only recommends this one
MEK = 0.85MCO3 + 0.85ETO2 + 0.15MO2 + 0.15RCO3 same two channels are merged into one reaction

--Jmao 15:54, 20 May 2014 (EDT)

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

When using FAST-JX v7.0, we recommend that you select the following option in the CHEMISTRY MENU section of input.geos:

Online O3 for FAST-JX?  : T  

Selecting this option will cause FAST-JX v7.0 to compute the total overhead ozone columns (aka TO3) from the "online" ozone tracer concentration contained in the State_Chm%TRACERS(:,:,:,IDTO3) derived type object. (In some older GEOS-Chem routines, this is referred to as STT(:,:,:,IDTO3).)

Using FAST-JX v7.0 in conjunction with the UCX combined stratospheric-tropospheric chemistry mechanism will allow photolysis rates to respond to the changes in the dynamically-evolving stratospheric ozone layer. This will result in a more accurate simulation.

Even if you are performing a tropospheric-only chemistry simulation (i.e. with the UCX chemistry mechanism turned off), you should still use the online O3 option for FAST-JX v7.0. Using the online O3 does not cause the results to significantly differ than than if you had obtained TO3 from the TOMS/SBUV or GMAO met data archives. Sebastian Eastham writes:

This should only affect the impact of tropospheric ozone when comparing between (1-month benchmarks) v10-01b and v10-01c_trop, right? The stratospheric ozone estimate from the point of view of Fast-JX should be identical between v10-01b and v10-01c_trop regardless of the online ozone option. My personal thoughts are that leaving the option on should be fine as long as we trust the tropospheric ozone estimates, although it shouldn’t make much of a difference (and if it does that is probably something I should look into).

Of course, if you turn off the online O3 for FAST-JX option (NOT RECOMMENDED):

Online O3 for FAST-JX?  : F

then FAST-JX will revert to computing TO3 in the same way as for the older FAST-J photolysis mechanism.

--Bob Y. 15:50, 20 May 2014 (EDT)

Cloud overlap options in FAST-JX v7.0

You may use the following cloud overlap options with the FAST-JX v7.0 photolysis mechanism:

Approximate random overlap assumption

The approximate random overlap option (which is the default setting) is:

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

To select this option, make sure the following lines at the top of GeosCore/fast_jx_mod.F are uncommented:

! Approximate random overlap (balance between accuracy & speed)
#define USE_APPROX_RANDOM_OVERLAP 1

As this is the default option, these lines should already be uncommented for you when you download the GEOS-Chem source code.

--Bob Y. 11:49, 20 May 2014 (EDT)

Linear cloud overlap assumption

The linear cloud overlap option is:

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

To select this option you must uncomment these lines at the top of GeosCore/fast_jx_mod.F:

!! Linear overlap
!#define USE_LINEAR_OVERLAP 1	

and then recompile GEOS-Chem.

--Bob Y. 11:49, 20 May 2014 (EDT)

Maximum random overlap assumption

At present, the maximum random overlap assumption has not been implemented into FAST-JX v7.0.

--Bob Y. 11:49, 20 May 2014 (EDT)

Discussion

We invite to read this discussion about cloud overlap options on our FAST-J photolysis mechanism wiki page.

--Bob Y. 16:13, 20 May 2014 (EDT)

Aerosol optical properties in FAST-JX v7.0

The aerosol optical properties have been updated from the older FAST-J photolysis mechanism. TEXT NEEDED

The ability to scale aerosol optical depth diagnostic output from 550 nm to other wavelengths (originally implemented for the older FAST-J mechanism in GEOS-Chem v8-03-01) is still compatible for FAST-JX v7.0. Please see this section on our FAST-J photolysis mechanism wiki page for more information.

--Bob Y. 11:12, 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)

References

  1. Blitz, M. A., D. E. Heard, M. J. Pilling, S. R. Arnold, M. P. Chipperfield, Pressure and temperature-dependent quantum yields for the photodissociation of acetone between 279 and 327.5 nm, Geophys. Res. Lett., 31, 9, L09104, 2004.
  2. Eastham, S. D., D. K. Weisenstein, S. R. H. Barrett, Development and evaluation of the unified tropospheric–stratospheric chemistry extension (UCX) for the global chemistry-transport model GEOS-Chem, Atmos. Environ, 89, 52-63, doi:10.1016/j.atmosenv.2014.02.001, 2014.
  3. Feng, Y., et al., Effects of cloud overlap in photochemical models, J. Geophys. Res., 109, D04310, doi:10.1029/2003JD004040, 2004.
  4. Liang, X.-Z., and W.-C. Wang, Cloud overlap effects on general circulation model climate simulations, J. Geophys. Res., 102 (D10), 11,039–11,047, 1997.
  5. 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.
  6. 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.
  7. 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.
  8. Wild, O., X. Zhu, and M. J. Prather, Fast-J: Accurate simulation of in- and below-cloud photolysis in tropospheric chemical models, J. Atmos. Chem., 37, 245–282, 2000.

--Bob Y. 11:06, 20 May 2014 (EDT)