Difference between revisions of "FAST-JX v7.0 photolysis mechanism"

Revision as of 21:18, 30 May 2014

Sebastian Eastham (MIT) has introduced FAST-JX v7.0 into GEOS-Chem v10-01 concurrently with the UCX chemistry mechanism. FAST=JX v7.0 replaces the older FAST-J photolysis mechanism.

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:

--Bob Y. 13:42, 21 May 2014 (EDT)

Input files for FAST-JX v7.0

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

 GEOS_NATIVE/FastJ_201204/fastj.jv_atms_dat.nc

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

VOC photolysis in FAST-JX v7.0

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.

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

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

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

User:Sebastian Eastham replied:'

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

Daniel Jacob replied:

Thanks Jingqiu! If the 1-year benchmark run has already started just let it run - these changes will have very little effect except for HAC and we can just make a note of it. I'm glad that we resolved these J(VOC) issues thanks to Seb, Chris and Jingqiu. At this point we need to move on.

--Bob Y. 17:18, 30 May 2014 (EDT)

Use online ozone in FAST-JX v7.0 instead of scaling ozone climatology to archived TO3 values

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 copy the "online" O3 tracer concentration—contained in the State_Chm%TRACERS derived type object—directly into the FAST-JX module. O3 concentrations will be copied for all grid boxes starting at the surface and ending at the top of the chemistry grid, which is either the stratopause (for simulations using the UCX combined stratospheric-tropospheric chemistry mechanism) or the tropopause (for simulations not using UCX).

Using the online O3 option for FAST-JX v7.0 in conjunction with the UCX 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—that is, not using the UCX mechanism—you should still use the online O3 option for FAST-JX v7.0. GEOS-Chem simulations using the FAST-JX online O3 option do not differ significantly from simulations where the internal FAST-JX ozone profiles are scaled to monthly-mean TO3 from either the TOMS/SBUV archive or the GMAO met fields. Sebastian Eastham writes:

[The online O3 option in FAST-JX v7.0] 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 this option off (WHICH IS NOT RECOMMENDED):

Online O3 for FAST-JX?  : F

then FAST-JX will scale its internal ozone profiles to TO3 data as described in this section of our FAST-J photolysis mechanism wiki page.

--Bob Y. 14:24, 21 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. 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. 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)

Unresolved issues

The following are active areas of research in GEOS-Chem.

Carbonyl nitrate photolysis

Jingqiu Mao wrote:

We know that carbonyl nitrate should be photolyzed much faster than the current rates in FAST-JX, according to this paper. But updates in this rate should also be combined with updates in the OH rate in order to better reproduce the experimental results from chamber studies. This seems more like a research question, so we decided to leave this to the SEAC4RS team.

--Bob Y. 15:40, 27 May 2014 (EDT)

Acetaldehyde photolysis

Jingqiu Mao wrote:

We saw large discrepancies between observed(black) and modeled(red) J(ALD2), as shown in this plot by Chris Chan Miller:

This discrepancy is very likely due to the lack of pressure dependence on the quantum yield. But Michael Prather didn’t include this pressure dependence in any of the FAST-JX versions. So this remains as a problem in all GEOS-Chem versions, including GEOS-Chem v10-01c.

--Bob Y. 15:41, 27 May 2014 (EDT)

EP photolysis for dicarbonyls simulation

The code for EP photolysis found in calcrate.F needs to be updated for compatibility with FAST-JX v7.0. The EP photolysis code was left unchanged for now (as of GEOS-Chem v10-01c), but it is now executed only when LDICARB is true. This issue affects the dicarbonyls simulation.

        !==============================================================
        ! HARDWIRE the effect of branching ratio of HOC2H4O in EP photolysis
        !   HOC2H4O ------> HO2 + 2CH2O    : marked as I in P column of 
        !                                    'globchem.dat'
        !   HOC2H4O --O2--> HO2 + GLYC     : marked as J in P column of 
        !                                    'globchem.dat'
        !
        ! Add NCS index to NKHOROI and HKHOROJ for SMVGEARII (tmf, 12/16/06)
        !==============================================================

        ! Not yet modified this for compatibility with Fast-JX v7.0.
        ! (SDE 04/01/13)

        ! Now only do the following if using the dicarbonyls mechanism
        ! (sde, mps, 5/28/14)
        IF ( LDICARB ) THEN
           IF ( NKHOROI(NCS) > 0 ) THEN

              ! Put J(EP) in correct spot for SMVGEAR II
              PHOTVAL = NKHOROI(NCS) - NRATES(NCS)
              NKN     = NKNPHOTRT(PHOTVAL,NCS)

              DO KLOOP=1,KTLOOP
                 RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) *
    +               ( 1.D0-FYHORO(DENAIR(KLOOP), T3K(KLOOP)) )
              ENDDO
           ENDIF

           IF ( NKHOROJ(NCS) > 0 ) THEN

              ! Put J(EP) in correct spot for SMVGEAR II
              PHOTVAL = NKHOROJ(NCS) - NRATES(NCS)
              NKN     = NKNPHOTRT(PHOTVAL,NCS)

              DO KLOOP=1,KTLOOP
                 RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) *
    +               FYHORO(DENAIR(KLOOP), T3K(KLOOP)) 
              ENDDO
           ENDIF
        ENDIF

--Melissa Sulprizio 13:35, 28 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. 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)