FAST-JX v7.0 photolysis mechanism: Difference between revisions
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'''''These updates are being validated with the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01f|v10-01f]].''''' | |||
'''''[[User:Jmao|Jingqiu Mao]] wrote:''''' | '''''[[User:Jmao|Jingqiu Mao]] wrote:''''' | ||
Revision as of 20:30, 19 December 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 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 | TBD 2014 |
|
--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:
| File | Introduced | Retired | Description |
|---|---|---|---|
| fastj.jv_atms.dat.nc | v9-01-03 | still used |
GEOS_NATIVE/FastJ_201204/fastj.jv_atms_dat.nc
|
| FJX_j2j.dat | v10-01 | still used |
|
| FJX_spec.dat | v10-01 | still used |
|
| jv_spec_aod.dat | v9-01-03 | still used |
|
| jv_spec.mie.dat | v10=01 | still used |
|
--Bob Y. 10:35, 20 May 2014 (EDT)
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.
- For HAC, keep the QY as 0.6, but zero out the bins >335 nm.
- 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.
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 was validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.
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 was validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.
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.
Solution
These updates are being validated with the 1-month benchmark simulation v10-01f.
Jingqiu Mao wrote:
- Michael Prather just provided a new set of cross section with pressure dependence for acetaldehyde:
ActAldp177 0.000E+00 0.000E+00 1.989E-23 0.000E+00 3.699E-22 4.938E-22 CH3CO IUPAC 2014
4.737E-22 4.659E-22 2.450E-20 3.409E-20 3.820E-20 3.732E-20 sheet P2 298K
2.707E-20 1.579E-20 6.566E-21 3.883E-22 5.683E-26 0.000E+00 q2=0.88 (CH3+HCO)
ActAldp566 0.000E+00 0.000E+00 1.903E-23 0.000E+00 3.539E-22 4.725E-22 q3=0.12 (H+CH3CO)
4.533E-22 4.458E-22 2.270E-20 2.985E-20 3.199E-20 2.987E-20 q1=0.00 (CH4+CO)
1.923E-20 9.497E-21 3.450E-21 1.914E-22 3.762E-26 0.000E+00 q's based on 1 bar
ActAldp999 0.000E+00 0.000E+00 1.822E-23 0.000E+00 3.389E-22 4.525E-22 wave > 300 nm
4.340E-22 4.269E-22 2.112E-20 2.647E-20 2.740E-20 2.479E-20
1.485E-20 6.739E-21 2.319E-21 1.258E-22 2.790E-26 0.000E+00
- We should use this instead. The reaction is also updated from
ALD2 = MO2 + HO2 + CO
- to
ALD2 = 0.88MO2 + HO2 + 0.88CO + 0.12MCO3
--Bob Y. 15:19, 6 June 2014 (EDT)
Validation
Eloise Marais wrote:
- I have implemented Michael Prather's pressure-dependent cross-sections for acetaldehyde (ALD2) in GEOS-Chem. The photolysis of ALD2 to form CH4 + CO is turned off. The product yields of the other ALD2 photolysis channel are also updated (see above). Pressure-dependent ALD2 photolysis leads to a decrease in J(ALD2) at the surface and an increase at 500 hPa. The effect on PAN is small (1-5 pptv increase at the surface and <2 pptv at 500 hPa in July 2005).
- The comparison for SEAC4RS (from a simulation by Katie Travis) is shown below:
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
- 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.
- 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.
- Feng, Y., et al., Effects of cloud overlap in photochemical models, J. Geophys. Res., 109, D04310, doi:10.1029/2003JD004040, 2004.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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)