FAST-JX v7.0 photolysis mechanism

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Overview

This update was validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.

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 Jun 2015

Input files for FAST-JX v7.0

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

File Description
fastj.jv_atms.dat.nc Purpose:

Location:

  • CHEM_INPUTS/FastJ_201204/

NOTE: Where such data exists, GEOS-Chem will overwrite the reference O3 climatology as follows:

  1. The online O3 tracer (carried in State_Chm%Species (RECOMMENDED), or
  2. Archived O3 profiles sclaed to TOMS/SBUV monthly-mean total ozone column (TO3) data, or
  3. Archived TO3 data from the GEOS-5 or GEOS-FP met field archives.
FJX_j2j.dat Purpose:
  • Links GEOS-Chem chemical species to Fast-JX species. See below for more information.

Location:

FJX_spec.dat Purpose
  • Fast-JX cross-sections

Location:

jv_spec.mie.dat Purpose:
  • Contains aerosol optical properties at 5 wavelengths

Location:

Notes:

  • In this file the column labeled "Q" contains the extinction efficiencies
brc.dat Purpose:
  • Contains aerosol optical properties for brown carbon at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of input.geos.
  • These properties are also used for in the RRTMG radiative transfer model (if enabled).

Location:

dust.dat Purpose:
  • Contains aerosol optical properties for dust at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of input.geos.
  • These properties are also used for in the RRTMG radiative transfer model (if enabled).

Location:

org.dat Purpose:
  • Contains aerosol optical properties for organic carbon at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of input.geos.
  • These properties are also used for in the RRTMG radiative transfer model (if enabled).

Location:

so4.dat Purpose:
  • Contains aerosol optical properties for sulfate at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelengths can be selected in the Radiation Menu of input.geos.
  • These properties are also used for in the RRTMG radiative transfer model (if enabled).

Location:

soot.dat Purpose:
  • Contains aerosol optical properties for black carbon at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of input.geos.
  • These properties are also used for in the RRTMG radiative transfer model (if enabled).

Location:

ssa.dat Purpose:
  • Contains aerosol optical properties for accumulation mode sea salt aerosol at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of input.geos.
  • These properties are also used for in the RRTMG radiative transfer model (if enabled).

Location:

ssc.dat Purpose:
  • Contains aerosol optical properties for coarse mode sea salt aerosol at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of input.geos.
  • These properties are also used for in the RRTMG radiative transfer model (if enabled).

Location:

h2so4.dat Purpose:
  • Contains aerosol optical properties for sulfuric acid at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of input.geos.
  • These properties are also used for in the RRTMG radiative transfer model (if enabled).
  • This file is only needed if the UCX chemistry mechanism is enabled.

Location:


FJX_j2j.dat

Seb Eastham wrote:

Each row in FJX_j2j.dat can be broken down as follows. Taking the ETP photolysis reaction as an example:

     80 ETP       PHOTON    OH        HO2       ALD2          0.500 /CH3OOH/

The elements mean the following in terms of how the code parses them:

  • 80: This is the internal index used by Fast-JX. When setting up the reaction in globchem.eqn, this is the number you need when indexing PHOTOL.
  • ETP: This is the GEOS-Chem species that will undergo photolysis.
  • PHOTON: This just makes clear that the reaction is photolysis.
  • 0.500: This is the quantum yield of the reaction. Specifically, it is a flat multiplier applied to the first-order rate returned by Fast-JX for this reaction specifically.
  • CH3OOH: This is the cross-section (from FJX_spec.dat) which will be used to calculate the first-order reaction rate.

As you can see, the product list is not used – in theory you could put anything here! However, it is very helpful for other users if the product list is correctly specified, so that they can cross check between FJX_j2j.dat and globchem.eqn (where the product list must be correct). The actual calculation order would go as follows:

  1. Fast-JX calculates the cross section data for CH3OOH, then applies the local actinic flux in the grid box to derive a first-order reaction rate. Let’s call this rate "R".
  2. Every reaction listed in FJX_j2j.dat which uses the "CH3OOH" cross section in the final column would take the rate "R" as its rate of reaction, and then multiply it by the quantum yield. In the case of ETP, we end up with an overall photolysis rate of 0.500*R.
  3. The rate is stored in PHOTOL based on the first column of the FJX_j2j.dat entry, specifically PHOTOL(80) = 0.500*R
  4. When performing chemistry, KPP will retrieve the reaction rate from PHOTOL(80) (see reaction 544 in the standard globchem.eqn file). It ignores the "hv" reactant, yielding a final loss rate for ETP + hv of: d[ETP]/dt = -0.500 * R * [ETP].

The short version of all this is:

  1. The stoichiometric coefficients do not need to be included in FJX_j2j.dat, but it helps for clarity
  2. Only the globchem.eqn products are important in terms of the calculation, but again having the products right in FJX_j2j.dat does help in terms of clarity

VOC photolysis in FAST-JX v7.0

These updates were validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.

In the table below, we summarize VOC photolysis in Fast-JX v7.0. We also invite you to view our Comparison of GEOS-Chem Photolysis Rates document prepared by Chris Chan Miller.

Old reaction New reaction New rate Note
CH2O = HO2 + HO2 + CO (channel a) same New cross sections leads to an increase by 10% to 20% This increase is consistent with JPL 2010.
CH2O = H2 + CO (channel b) same increase by 6% to 15% This increase is consistent with JPL 2010.
PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2 + 0.4NO3 PAN = 0.7MCO3 + 0.7NO2 + 0.3MO2 + 0.3NO3 same JPL2010 suggests two channels(only one channel in FastJX-v7.0), branching ratio follows JPL2010
ALD2 = MO2 + HO2 + CO ALD2 = 0.88MO2 + HO2 + 0.88CO + 0.12MCO3 large discrepancy is found between obs and model (see Chris's slides), pressure dependence is probably needed. The cross section is now updated by Michael Prather.
ALD2 = CH4 + CO this channel is turned off this channel is not included in FastJX-v7.0
RCHO = ETO2 + HO2 + CO same No pressure dependence is observed, according to JPL2010.
MP = CH2O + HO2 + OH same change is small.
GLYX = 0.5H2 + CO + 0.5CH2O + 0.5CO GLYX = H2 + 2CO
GLYX = CH2O + CO		 Pressure dependence is now included, rate is higher now 3 channels, Stern-Volmer expression: Qtotal = 1/[6.80 + 251.8e-4 P(Torr)], Increases quantum yields at low P, but ONLY specified for 390-470 nm. Assume that 220K has P = 0.18 atm and higher q.(From FJX v7.0 notes)
GLYX = 2.0CO + 2.0HO2 same Pressure dependence is now included, rate is higher
MACR = CO + HO2 + CH2O + MCO3
branching ratio = 0.5		 same rate is significantly reduced, as Qy is reduced from 0.008 to 0.003 this channel is dominant,the third channel (C3H6 + CO), is ignored, to be consistent with Fast-JX v7.0
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		 pressure dependence is now included
MVK = MCO3 + CH2O + CO + HO2
branching ratio = 0.2		 pressure dependence is now included
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 GLYC = 0.9CH2O + 1.73HO2 + 0.07OH + 1.0CO + 0.1MOH Significant increase in X sections merge from three channels GLYC =CH2O + 2.0HO2 + CO(QY = 0.83), GLYC =CH3OH + CO (QY=0.10), GLYC =OH + CH2O + HO2 + CO (QY =0.07) JPL 2010
MEK = 0.85MCO3 + 0.85ETO2 + 0.15MO2 + 0.15RCO3 same two channels are merged into one reaction
HAC = MCO3 + CH2O + HO2 rate is lower the old rate was using Acetone X sections.This species is not in FastJX v7.0. Seb added X sections based on JPL2010. Need to multiply 0.6 for quantum yield.The bins above 335nm must be zeroed out, otherwise J(HAC) would be too high. The major removal process is its reaction with OH, photolysis is of minor importance (see Orlando et al., 1999).

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

Final recommendation for J(HAC) and J(PAN)

These updates were validated in the 1-month benchmark simulation v10-01d and approved on 03 Jun 2014.

Jingqiu Mao wrote:

I have two more suggestions to the code and I think we then can finalize v10-01c. We can deal with unresolved J(VOC) later. Seb, please let me know if you think otherwise.
  1. For HAC, keep the QY as 0.6, but zero out the bins >335 nm.
  2. For PAN, change the reaction from
       PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2 + 0.4NO3
to
       PAN = 0.7MCO3 + 0.7NO2 + 0.3MO2 + 0.3NO3

Sebastian Eastham replied:

These sound good to me, and I’m not aware of any other pressing issues regarding J-values.

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. Because this option is computationally intensive, it remains a research option rather than a standard supported feature.

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

Discussion

We invite you 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. They are defined in the .dat files previously stored in the GEOS-Chem run directories, and now stored in ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/. Please see the Input files for FAST-JX v7.0 section above for details on the contents of the .dat files for each aerosol species.

--Melissa Sulprizio (talk) 18:29, 27 June 2019 (UTC)

Updated aerosol hygroscopicity and optics

This update was included in GEOS-Chem 12.6.0, which was released on 18 Oct 2019.

The aerosol hygroscopicity and optics tables have been updated following work by Latimer and Martin (2019). The FAST_JX/v2019-06/ directory contains the updated aerosol optical property tables for secondary inorganic aerosol (so4.dat) and organic aerosol (org.dat).

The one-month (July 2016) comparison of AOD between default (v12.3.2) and revised as follows:

AOD compare July revised default.png

--Melissa Sulprizio (talk) 18:29, 27 June 2019 (UTC)

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. Magneron, I., A. Mellouki, G. Le Bras, G. K. Moortgat, A. Horowitz, and K. Wirtz , Photolysis and OH-Initiated Oxidation of Glycolaldehyde under Atmospheric Conditions, The Journal of Physical Chemistry A, 109(20), 4552-4561, doi:10.1021/jp044346y, 2005.
  7. Müller, J.-F., Peeters, J., and Stavrakou, T., Fast photolysis of carbonyl nitrates from isoprene, Atmos. Chem. Phys., 14, 2497-2508, doi:10.5194/acp-14-2497-2014, 2014.
  8. Orlando, J. J., G. S. Tyndall, J.-M. Fracheboud, E. G. Estupiñan, S. Haberkorn, and A. Zimmer, The rate and mechanism of the gas-phase oxidation of hydroxyacetone, Atmos. Environ., 33(10), 1621-1629, doi:10.1016/S1352-2310(98)00386-0,1999.
  9. 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.
  10. 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.
  11. 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. 15:01, 27 May 2014 (EDT)

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