GEOS-Chem chemistry mechanisms

On this page, we provide an overview of the chemistry mechanisms used in GEOS-Chem.

Overview

The following table provides links to information about the available chemistry mechanisms in GEOS-Chem. Please contact the relevant GEOS-Chem Working Group for more information.

Category	Simulation(s)	Mechanism file	Contact
Full-chemistry (troposphere + stratosphere)	Standard, Benchmark1	KPP/Standard/Standard.eqn	Chemistry Working Group
Full-chemistry (troposphere only)	Tropchem SOA complexSOA TOMAS APM RRTMG	KPP/Tropchem/Tropchem.eqn	Chemistry Working Group
SOA+semivoatile POA	complexSOA_SVPOA	KPP/SOA_SVPOA/SOA_SVPOA.eqn	Aerosols Working Group
Carbon Gases	CH4 tagCH4	GeosCore/global_ch4_mod.F	Carbon Cycle Working Group
Carbon Gases	tagCO	GeosCore/tagged_co_mod.F	Carbon Cycle Working Group
Carbon Gases	CO2	GeosCore/co2_mod.F	Carbon Cycle Working Group
Mercury	Hg tagHg Hg+GTMM	GeosCore/mercury_mod.F	Hg and POPs Working Group
Persistent Organic Pollutants	POPs	GeosCore/pops_mod.F	Hg and POPs Working Group
Ozone	tagO3	GeosCore/tagged_o3_mod.F	Chemistry Working Group
Radionuclides	Rn-Pb-Be TransportTracers	GeosCore/RnPbBe_mod.F	Transport Working Group
The following mechanisms are obsolete and have been removed:
Carbon Gases	C2H6	GeosCore/c2h6_mod.F	Carbon Cycle Working Group
Carbon Gases	CH3I	GeosCore/ch3i_mod.F in GEOS-Chem v9-02 and earlier	Carbon Cycle Working Group
Radionuclides	H2-HD	GeosCore/h2_h2_mod.F in GEOS-Chem v9-02 and earlier	Transport Working Group

¹The benchmark simulation is used for 1-month and 1-year benchmarks. It uses the Standard chemistry mechanism, but includes both the simple SOA and complex SOA species.

--Melissa Sulprizio (talk) 17:02, 22 February 2019 (UTC)

Chemistry updates

Updated isoprene and monoterpene chemistry

This update was included in v11-02c and approved on 21 Sep 2017.

Developers:

• Katie Travis (MIT, formerly Harvard)
• Jenny Fisher (U. Wollongong)
• Christopher Chan Miller (Smithsonian Astrophysical Observatory, formerly Harvard)
• Eloise Marais (U. Birminghan, formerly Harvard)

This document compiled by Katie Travis and Josh Cox describes the updated isoprene and monoterpene chemistry to be included in GEOS-Chem v11-02c (also see the list of modifications below). These updates include the monoterpene nitrate scheme and aqueous isoprene uptake and were originally implemented for simulation of the SEAC4RS data.

References

• Chan Miller, C., D.J.Jacob, E.A. Marais, K. Yu, K.R. Travis, P.S. Kim, J.A. Fisher, L. Zhu, G.M. Wolfe, F.N. Keutsch, J. Kaiser, K.-E. Min, S.S. Brown, R.A. Washenfelder, G. Gonzalez Abad, and K. Chance, Glyoxal yield from isoprene oxidation and relation to formaldehyde: chemical mechanism, constraints from SENEX aircraft observations, and interpretation of OMI satellite data, Atmos. Chem. Phys., 17, 8725-8738, https://doi.org/10.5194/acp-17-8725-2017, 2017. PDF
• Fisher, J.A., D.J. Jacob, K.R. Travis, P.S. Kim, E.A. Marais, C. Chan Miller, K. Yu, L. Zhu, R.M. Yantosca, M.P. Sulprizio, J. Mao, P.O. Wennberg, J.D. Crounse, A.P. Teng, T.B. Nguyen, J.M. St. Clair, R.C. Cohen, P. Romer, B.A. Nault, P.J. Wooldridge, J.L. Jimenez, P. Campuzano-Jost, D.A. Day, P.B. Shepson, F. Xiong, D.R. Blake, A.H. Goldstein, P.K. Misztal, T.F. Hanisco, G.M. Wolfe, T.B. Ryerson, A. Wisthaler, and T. Mikoviny. Organic nitrate chemistry and its implications for nitrogen budgets in an isoprene- and monoterpene-rich atmosphere: constraints from aircraft (SEAC4RS) and ground-based (SOAS) observations in the Southeast US. Atmos. Chem. Phys., 16, 2961-2990, 2016. PDF
• Marais, E. A., D. J. Jacob, J. L. Jimenez, P. Campuzano-Jost, D. A. Day, W. Hu, J. Krechmer, L. Zhu, P. S. Kim, C. C. Miller, J. A. Fisher, K. Travis, K. Yu, T. F. Hanisco, G. M. Wolfe, H. L. Arkinson, H. O. T. Pye, K. D. Froyd, J. Liao, V. F. McNeill, Aqueous-phase mechanism for secondary organic aerosol formation from isoprene: application to the southeast United States and co-benefit of SO2 emission controls, Atmos. Chem. Phys., 16, 1603-1618, 2016. PDF
• Travis, K. R., D. J. Jacob, J. A. Fisher, P. S. Kim, E. A. Marais, L. Zhu, K. Yu, C. C. Miller, R. M. Yantosca, M. P. Sulprizio, A. M. Thompson, P. O. Wennberg, J. D. Crounse, J. M. St. Clair, R. C. Cohen, J. L. Laughner, J. E. Dibb, S. R. Hall, K. Ullmann, G. M. Wolfe, J. A. Neuman, and X. Zhou, Why do models overestimate surface ozone in the Southeast United States, Atmos. Chem. Phys., 16, 13561-13577, doi:10.5194/acp-16-13561-2016, 2016. PDF, Supplement

--Melissa Sulprizio (talk) 18:06, 12 July 2017 (UTC)

Modifications to the original updates

The following modifications were made to the original updates listed in the above document following conversations with the developers. These modifications were included in v11-02c.

(1) Restore H2O2 Henry's law constant for wet deposition. Daniel Jacob wrote:

For wetdep of H2O2 we should restore the old Henry’s law constant of 8.3E4exp[7400(1/T – 1/298)] because as Dylan points out that’s the physical value. For drydep of H2O2 we can keep the value of 5E7 as parameterized by Nguyen to fit his drydep data.

(2) HC187 is advected

(3) The following species have different names from the original document:

• API is now MTPA (for consistency with existing SOA scheme)
• APIO2 is now PIO2 (for consistency with PAN updates added in v11-02a)
• LIM is now LIMO (for consistency with existing SOA scheme)
• PMN is now NPMN and IPMN (PMN from non-isoprene and isoprene sources; from aqueous isoprene uptake updates)
• ONITAam is now IONITA (Jenny Fisher recommended we change the names - they were originally daytime/nighttime species, but changed to isop/monot)
• ONITApm is now MONITA (Jenny Fisher recommended we change the names - they were originally daytime/nighttime species, but changed to isop/monot)

(4) Fix typos in the original document

   Orig:    ISNOHOO + MO2 = 0.660PROPNN + 0.700GLYX + 1.200HO2 + 0.750CH2O + 0.040ISN1OG
            Rate = 2.00e-13
   v11-02c: ISNOHOO + MO2 = 0.660PROPNN + 0.700GLYX + 1.200HO2 + 0.750CH2O + 0.250MOH + 0.040ISN1OG
            Rate = 2.06e-13

   Orig:    ISOPNB + OH = ISOPNBO2 + 0.100IEPOX + 0.100NO2 
   v11-02c: ISOPNB + OH = 0.900ISOPNBO2 + 0.100IEPOX + 0.100NO2

   Orig:    HONIT + OH = NO3 + HKET
   v11-02c: HONIT + OH = NO3 + HAC

   Orig:    HONIT + hv = HKET + NO2
   v11-02c: HONIT + hv = HAC + NO2

(5) Completely replace RIP with RIPA, RIPB, RIPD and IEPOX with IEPOXA, IEPOXB, IEPOXD

   Orig:    RIP  + hv = 0.985OH + 0.985HO2 + 0.710CH2O + 0.425MVK + 0.285MACR + 0.275HC5 + 0.005LVOC
   v11-02c: RIPA + hv = 0.985OH + 0.985HO2 + 0.710CH2O + 0.425MVK + 0.285MACR + 0.275HC5 + 0.005LVOC
            RIPB + hv = 0.985OH + 0.985HO2 + 0.710CH2O + 0.425MVK + 0.285MACR + 0.275HC5 + 0.005LVOC
            RIPD + hv = 0.985OH + 0.985HO2 + 0.710CH2O + 0.425MVK + 0.285MACR + 0.275HC5 + 0.005LVOC

   Orig:    ISOPND + OH = 0.100IEPOX + 0.900ISOPNDO2 +0.100NO2
   v11-02c: ISOPND + OH = 0.100IEPOXD + 0.900ISOPNDO2 +0.100NO2

   Orig:    ISOPNB + OH = 0.900ISOPNBO2 + 0.100IEPOX + 0.100NO2
   v11-02c: ISOPNB + OH = 0.900ISOPNBO2 + 0.067IEPOXA + 0.033IEPOXB + 0.100NO2

   Orig:    IEPOX  = SOAIE : HET(ind_IEPOX,1);
   v11-02c: IEPOXA = SOAIE : HET(ind_IEPOXA,1);
            IEPOXB = SOAIE : HET(ind_IEPOXB,1);
            IEPOXD = SOAIE : HET(ind_IEPOXD,1);

(6) Add LVOC to RIP channels

   Orig:    RIPA + OH = 0.750 RIO2 + 0.250 HC5 + 0.125 (OH + H2O)
   v11-02c: RIPA + OH = 0.750 RIO2 + 0.245 HC5 + 0.125 (OH + H2O) + 0.005 LVOC
   
   Orig:    RIPA + OH = 0.850 OH + 0.578 IEPOXA + 0.272 IEPOXB + 0.150 HC5OO
   v11-02c: RIPA + OH = 0.850 OH + 0.578 IEPOXA + 0.272 IEPOXB + 0.145 HC5OO + 0.005 LVOC
   
   Orig:    RIPB + OH = 0.480 RIO2 + 0.520 HC5 + 0.26 (OH + H2O)
   v11-02c: RIPB + OH = 0.480 RIO2 + 0.515 HC5 + 0.26 (OH + H2O) + 0.005 LVOC
   
   Orig:    RIPD + OH = 0.250 RIO2 + 0.750 HC5 + 0.375 (OH + H2O)
   v11-02c: RIPD + OH = 0.250 RIO2 + 0.745 HC5 + 0.375 (OH + H2O) + 0.005 LVOC
   
   Orig:    RIPD + OH = 0.500 OH + 0.500 IEPOXD + 0.500 HC5OO
   v11-02c: RIPD + OH = 0.500 OH + 0.500 IEPOXD + 0.495 HC5OO + 0.005 LVOC
   
   The only reaction that wont have LVOC as a product is RIPB + OH = OH + IEPOXA + IEPOXB.

--Melissa Sulprizio (talk) 16:26, 7 September 2017 (UTC)

Stratospheric chemistry

GEOS-Chem was historically developed as a model of tropospheric chemistry and composition. The above-mentioned chemistry mechamisms in GEOS-Chem v9-01-03 and in GEOS-Chem v9-02 only solve the chemical reaction matrix within the troposphere. In order to prevent tropospheric species from accumulating in the stratosphere and being transported back into the troposphere, we have implemented the following simple stratospheric chemistry schemes:

1. Linoz stratospheric ozone chemistry
2. Application of monthly-mean prod/loss rates archived from the GMI model

Linoz only applied to ozone. The simple linearized stratospheric chemistry, which uses production and loss rates archived from the GMI model, is applied to all other species. (NOTE: The user has the option to disable Linoz and use the archived GMI prod/loss rates for ozone, but this is typically not done.)

In GEOS-Chem v10-01 we added the Unified tropospheric-stratospheric Chemistry eXtension (UCX) mechanism into GEOS-Chem. UCX was developed by Seb Eastham and Steven Barrett at the MIT Laboratory for Aviation and the Environment. This mechanism combines the existing GEOS-Chem "NOx-Ox-HC-aerosol" mechanism with several new stratospheric species and reactions.

--Bob Y. 12:11, 1 October 2013 (EDT)
--Melissa Sulprizio (talk) 17:18, 26 May 2015 (UTC)

Correcting ozone from the height of the lowest model level to 10m

This update is slated for inclusion in GEOS-Chem v11-02e.

Katie Travis created a diagnostic to correct daytime ozone values from the lowest model layer, ~60m, to 10m.

C(zC) = (1-Ra(z1,zC)vd(z1))C(z1)	            Eq. 1

where R_a(z₁,z_C) is the aerodynamic resistance between z₁ and z_C, and v_d(z₁) is the ozone deposition velocity at z₁, and C(z₁) is the ozone concentration at z₁.

R_a(z₁,z_C) is calculated to the lowest model level in drydep_mod.F. We recalculate R_a using z₁ = 10 m, which is the height of the CASTNET measurement for ozone. The new R_a is added to the diagnostic array AD_RA and passed to diag49.F for use in Equation 1.

This new diagnostic is called O3@10m-$, and can be called with tracer 539 in ND49 in input.geos.

References

• Travis, K.R., D.J. Jacob, C.A. Keller, S. Kuang, J. Lin, M.J. Newchurch, A.M. Thompson, Resolving ozone vertical gradients in air quality models, Atmos. Chem. Phys. Disc.,2017.
• Zhang, L., D.J. Jacob, E.M. Knipping, N. Kumar, J.W. Munger, C.C. Carouge, A. van Donkelaar, Y. Wang, and D. Chen, Nitrogen deposition to the United States: distribution, sources, and processes, Atmos. Chem. Phys., 12, 4,539-4,4554, 2012.

--Melissa Sulprizio (talk) 22:26, 17 November 2017 (UTC)

Analytical tools

Process analysis diagnostics

Barron Henderson (U. Florida) has created a software package for process analysis diagnostics. He writes:

Process-based Analysis examines the change in each species due to each process and reaction. Models predict atmospheric state, which in a time-series can be used to create net-change of each species. What this cannot tell us, is which processes led to that change. To supplement state (or concentration), GEOS-Chem has long archived emissions and employed advanced diagnostics to predict gross chemical production or loss. Process Analysis goes a step further archiving grid-cell budgets for each species, and decomposing gross production/loss into individual reaction contributions. Process Analysis extensions are currently available in CAMx, WRF-Chem, CMAQ, and now GEOS-Chem. This allows for direct comparisons of models at a fundamental, process level.

To obtain this software, please contact Barron Henderson directly.

--Bob Y. 12:26, 1 October 2013 (EDT)

Linking GEOS-Chem to CMAQ

Barron Henderson has created Python software that will let you translate GEOS-Chem output to the proper speciation for input to CMAQ. Please see our Linking GEOS-Chem to CMAQ wiki page for more information.

--Bob Y. (talk) 16:46, 26 October 2015 (UTC)

Previous issues that have now been resolved

Fixes for carbon creating reactions

This update was included in v11-02c and approved on 21 Sep 2017.

Sarah Safieddine wrote:

Colette, Barron, Mat and myself modified 13 previous "carbon creating" reactions to preserve carbon. The [table below] lists all the corrections for the reactions in globchem.dat V902 that we corrected, with all the details.

Reaction # in globchem.dat v9-02	Unbalanced Reaction	Rate constant	Issue (R=Reactants, P=Products)	Fix and corrected reaction (in green)
453	R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2	K* (1-YN) where YN is returned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.5)	Creates carbon: R=4C P=4.26C	Replace 0.18B3O2 by 0.093B3O2 to achieve carbon closure (as suggested by Barron). R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.093B3O2 + 0.32ETO2 Use Barron's fix to correct ALK4 lumping issue instead.
453	R4N1 + NO → 2NO2 + 0.39CH2O + 0.75ALD2 + 0.57RCHO + 0.3R4O2	2.7E-12 exp(350/T)	Creates carbon: R=4C, P=4.8C	Fix, as suggested by Matt: R4N1 + NO → 2NO2 + 0.570RCHO + 0.86ALD2 + 0.57CH2O
453	ATO2 + NO → 0.96NO2 + 0.96CH2O + 0.96MCO3 + 0.04R4N2	2.8E-12 exp(300/T)	Creates carbon: R=3C, P=3.04	Fix as suggested by Mat: ditch the R4N2 channel ATO2 + NO → NO2 + CH2O + MCO3
803	RIO2 → 2HO2 + CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.5HAC + OH	4.07E+08 exp(-7694/T)	Creates carbon: R=5C, P=7C There was a fix proposed on the isoprene scheme wiki page but still not enough	Fix as suggested by Sarah: remove CH2O RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH This reaction was replaced with RIO2 → 0.5HPALD + 0.5DHPCARP in the isoprene chemistry updates added in v11-02c
453	ISNOOB + NO3 → R4N2 + GLYX + 2NO2	2.3E-12	Creates carbon: R=5C, P=6C	Fix as suggested by Barron: Replace R4N2 by PROPNN ISNOOB + NO3 → PROPNN + GLYX + 2NO2 This reaction was replaced with ISNOOB + NO3 → 0.94PROPNN + GLYX + 2NO2 + 0.04ISN1OG in the isoprene chemistry updates added in v11-02c
453	ISNOOB+NO → 0.94R4N2 +0.94GLYX +1.88NO2	2.6E-12 exp(380/T)	Creates carbon: R=5C, P=5.64C	Same as above ISNOOB + NO → 0.06R4N2 + '0.94PROPNN' + 0.94GLYX + 1.88NO2 This reaction was replaced with ISNOOB + NO → 0.9PROPNN + 0.94GLYX + 1.88NO2 + 0.04ISN1OG in the isoprene chemistry updates added in v11-02c
453	ISNOHOO + NO → 0.934R4N2 + 0.934HO2 + 0.919GLYX	2.6E-12 exp(380/T)	Creates carbon: R=5C, P=5.574C	Fix by Barron: ISNOHOO + NO → 0.081R4N2 + 0.919PROPNN + 0.934HO2 + 0.919GLYX This reaction was replaced with ISNOHOO + NO3 → 0.894PROPNN + 0.934HO2 + 0.919GLYX + 0.4ISN1OG in the isoprene chemistry updates added in v11-02c
472	MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85ISNP	2.91E-13*exp(1300/T)[1-exp(-0.245*n)],n=4	Creates carbon: R=4C, P=4.85C	Fix by both Mat and Barron: Replace ISNP with 0.85MAOP + 0.85NO2 MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85MAOP + 0.85NO2
719	ATO2 + MCO3 → MEK + ACTA	1.87E-13 exp(500/T)	Creates carbon: R=5C, P=6C	From the WIKI: replace MEK with MGLY ATO2 + MCO3 → MGLY + ACTA
817	Br + ALD2 → HBr + MCO3 + CO	1.3E-11 exp(-360/T)	Creates carbon: R=2C, P=3C	Remove CO Following Parrella et al., Table 2a, reactions R7 to R10 (also for the 3 reactions below) Br + ALD2 → HBr + MCO3
818	Br + ACET → HBr + ATO2 + CO	1.66E-10exp(-7000/T)	Creates carbon: R=3C, P=4C	Remove CO, same as above Br + ACET → HBr + ATO2
819	Br + C2H6 → HBr + ETO2 + CO	2.36E-10 exp(-6411/T)	Creates carbon: R=2C, P=3C	Remove CO, same as above Br + C2H6 → HBr + ETO2
820	Br + C3H8 → HBr + A3O2 + CO	8.77E-11 exp(-4330/T)	Creates carbon: R=3C, P=4C	Remove CO, same as above Br + C3H8 → HBr + A3O2

--Melissa Sulprizio (talk) 19:59, 27 July 2017 (UTC)

Identification of carbon leaking reactions

Sarah Safieddine wrote:

76 other reactions leaked carbon, we enforced carbon conservation by tracking the lost carbon as CO2 (labeled as {CO2} in the document ROC_SI.docx, Table 2). This is the supplementary material for Safieddine, Heald and Henderson, 2017. It contains the corrections for both the carbon leaking and carbon creating reactions and all other information. The paper for reference can be found here: http://onlinelibrary.wiley.com/doi/10.1002/2017GL072602/abstract.

--Melissa Sulprizio (talk) 21:06, 22 May 2017 (UTC)

Fixes to correct ALK4 lumping issue

These fixes were included in v11-02a and approved on 12 May 2017.

Barron Henderson wrote:

I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).

Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy. When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.

If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.

I have extensive notes on what I interpret as happening. To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.

1. Increase MO2 stoichiometry from 0.18 to 0.19
2. Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).
3. Modify the carbon count for ALK4 (i.e. the MolecRatio field in the GEOS-Chem species database) from 4 to 4.3.

Fixes 1 and 2—which can be applied to the KPP globchem.eqn file—will make the carbon conservation consistent with Lurmann's. Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.

--Bob Yantosca (talk) 20:21, 31 January 2017 (UTC)

JPL Released 18th Rate Coefficient Evaluation

This update was included in v11-02a and approved on 12 May 2017.

JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page (Updates in JPL Publication 15-10) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10.

J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.

---B. Henderson 2016-05-03 15:25 (EDT)

Centralizing chemistry time step

This update was tested in the 1-month benchmark simulation v9-01-02q and approved on 18 Oct 2011.

Please see the full discussion on the Centralized chemistry time step wiki page.

--Bob Y. 16:01, 4 November 2011 (EDT)

Acetone photolysis

This discussion has been moved to our FAST-J photolysis mechanism wiki page.

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

Issues that have been since rendered obsolete by newer code updates

Most of the issues described below pertained to the SMVGEAR chemical solver (which was replaced by FlexChem in v11-01) and/or the FAST-J photolysis mechanism (which was replaced by FAST-JX in v10-01).

NIT should be converted to molec/cm3 in calcrate.F

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The code in calcrate.F will be replaced by the KPP master equation file.

In calcrate.F, we have:

                    ! Nitrate effect; reduce the gamma on nitrate by a
                    ! factor of 10 (lzh, 10/25/2011)
                    IF ( N == 8 ) THEN
                       TMP1 = State_Chm%Tracers(IX,IY,IZ,IDTSO4) +
    &                         State_Chm%Tracers(IX,IY,IZ,IDTNIT)
                       TMP2 = State_Chm%tracers(IX,IY,IZ,IDTNIT)
                       IF ( TMP1 .GT. 0.0 ) THEN
                          XSTKCF = XSTKCF * ( 1.0e+0_fp - 0.9e+0_fp
    &                            *TMP2/TMP1 )
                       ENDIF
                    ENDIF

Here NIT is added to SO4 but NIT is in different units than SO4. This unit difference can be traced to the definition of IDTRMB, which is only nonzero for species that are in the SMVGEAR mechanism. Since NIT is not a SMVGEAR species, IDTRMB = 0 for NIT and it is therefore skipped in the unit conversion from kg --> molec/cm3 in partition.F.

This issue was discovered during the implementation of FlexChem. In GEOS-Chem v11-01g and later versions, units of NIT are properly accounted for in routine HETN2O5 (found in gckpp_HetRates.F90).

--Melissa Sulprizio (talk) 20:25, 12 September 2016 (UTC)
--Bob Yantosca (talk) 20:27, 31 January 2017 (UTC)

rate of HNO4

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The globchem.dat file is now replaced by the KPP master equation file.

Ellie Browne found a typo in the globchem.dat (GEOS-Chem v8-02-01 and beyond)

A   73 9.52E-05  3.2E+00 -10900 1 P   0.60     0.     0.         
       1.38E+15  1.4E+00 -10900 0     0.00     0.     0.         
      HNO4          +                         M                                
=1.000HO2           +1.000NO2           +                   +

This should be corrected as:

A   73 9.52E-05  3.4E+00 -10900 1 P   0.60     0.     0.         
       1.38E+15  1.1E+00 -10900 0     0.00     0.     0.         
      HNO4          +                         M                                
=1.000HO2           +1.000NO2           +                   + 

The difference is within 2%.

--J Mao. 19:04, 30 Aug 2010 (EDT)
--Bob Yantosca (talk) 20:29, 31 January 2017 (UTC)

near-IR photolysis of HNO4

This update was added to GEOS-Chem v8-02-04.

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The globchem.dat file is now replaced by the KPP master equation file. Also, FAST-JX has now replaced FAST-J photolysis.

1. Since FastJX already takes this into account with cross section data at 574nm, we do not need to redo this in calcrate.f. We can therefore comment out this entire IF block:

        !---------------------------------------------------------------------
        ! Prior to 10/27/09:
        ! FastJX has taken near-IR photolysis into account with
        ! cross section at 574nm, so we don't need to add 1e-5 anymore.
        ! According to Jimenez et al., "Quantum yields of OH, HO2 and
        ! NO3 in the UV photolysis of HO2NO2", PCCP, 2005, we also
        ! changed the branch ratio from 0.67(HO2)/0.33(OH) to 0.95/0.05
        ! This will put most weight of near-IR photolysis on HO2 channel.
        ! (jmao, bmy, 10/27/09)
        !
        !!==============================================================
        !! HARDWIRE addition of 1e-5 s-1 photolysis rate to 
        !! HNO4 -> HO2+NO2 to account for HNO4 photolysis in near-IR -- 
        !! see Roehl et al. 'Photodissociation of peroxynitric acid in 
        !! the near-IR', 2002. (amf, bmy, 1/7/02)
        !!
        !! Add NCS index to NKHNO4 for SMVGEAR II (gcc, bmy, 4/1/03)
        !!==============================================================
        !IF ( NKHNO4(NCS) > 0 ) THEN
        !
        !   ! Put J(HNO4) in correct spot for SMVGEAR II
        !   PHOTVAL = NKHNO4(NCS) - NRATES(NCS)
        !   NKN     = NKNPHOTRT(PHOTVAL,NCS)
        !
        !   DO KLOOP=1,KTLOOP
        !      RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) + 1d-5
        !   ENDDO
        !ENDIF
        !---------------------------------------------------------------------

2. We need to change the branch ratio of HNO4 photolysis in ratj.d. Change these lines from:

13 HNO4       PHOTON     OH         NO3                  0.00E+00  0.00     33.3  HO2NO2 
14 HNO4       PHOTON     HO2        NO2                  0.00E+00  0.00     66.7  HO2NO2 

to:

13 HNO4       PHOTON     OH         NO3                  0.00E+00  0.00      5.0  HO2NO2 
14 HNO4       PHOTON     HO2        NO2                  0.00E+00  0.00     95.0  HO2NO2

This is based on Jimenez et al. (Quantum yields of OH, HO2 and NO3 in the UV photolysis of HO2NO2, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2005) shows that HO2 yield should be 0.95 and OH yield should be 0.05 for wavelength above 290nm.

This way all the near-IR photolysis will have most weight on HO2 channel(Stark et al., Overtone dissociation of peroxynitric acid (HO2NO2): Absorption cross sections and photolysis products, JOURNAL OF PHYSICAL CHEMISTRY A, 2008).

This update has now been added to the chemistry mechanism documentation file.

--J Mao. 11:00, 26 Oct 2009 (EDT)
--Bob Y. 16:08, 4 November 2011 (EDT)

yield of isoprene nitrates

This update was added to GEOS-Chem v8-03-02 as a post-release patch, and standardized in GEOS-Chem v9-01-01.

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The globchem.dat file is now replaced by the KPP master equation file.

Fabien Paulot found a problem in current chemistry scheme. In GEOS-Chem v8-02-01 and beyond, isoprene nitrates are produced twice: one through channel A and one through 10% loss in channel B. This makes the loss of NOx larger than it should be (18.7% vs. 10%) and also reduces the yield of MVK/MACR/CH2O by about 13%.

A  453 2.70E-12  0.0E+00    350 1 B   0.00     0.     0.         
       5.00E+00  0.0E+00      0 0     0.00     0.     0.         
      RIO2          +     NO                                              
=0.900NO2           +0.900HO2           +0.340IALD          +0.340MVK     
+0.220MACR          +0.560CH2O          +                   +  
          
A  453 2.70E-12  0.0E+00    350 1 A   0.00     0.     0.         
       5.00E+00  0.0E+00      0 0     0.00     0.     0.         
      RIO2          +     NO                                              
=1.000HNO3          +                   +                   +             

So it should be corrected as (no channel A):

A  453 2.70E-12  0.0E+00    350 0 0   0.00     0.     0.         
      RIO2          +     NO                                              
=0.900NO2           +0.900HO2           +0.340IALD          +0.340MVK     
+0.220MACR          +0.560CH2O          +                   +       

D  453 2.70E-12  0.0E+00    350 1 A   0.00     0.     0.         
       5.00E+00  0.0E+00      0 0     0.00     0.     0.         
      RIO2          +     NO                                              
=1.000HNO3          +                   +                   +  

--J Mao. 18:04, 30 Aug 2010 (EDT)
--Bob Yantosca (talk) 20:31, 31 January 2017 (UTC)

Potential issue with reading restart.cspec file

This update was tested in the 1-month benchmark simulation v9-01-02c and approved on 21 Jul 2011.

The binary-punch format restart.cspec.YYYYMMDDhh file is slated to be replaced by a netCDF-format restart file, starting in GEOS-Chem v11-01 and higher versions. But during a transition period, you can still request binary-punch format output.

Jingqiu Mao discovered a mis-indexing problem when using the restart.cspec.YYYYMMDDhh file. Please see this wiki post for more information.

--Bob Y. 16:02, 4 November 2011 (EDT)
--Bob Yantosca (talk) 20:33, 31 January 2017 (UTC)

GLCO3, GLPAN bug in standard mechanism

This update was tested in the 1-month benchmark simulation v9-01-03a and approved on 08 Dec 2011.

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The globchem.dat file is now replaced by the KPP master equation file.

Fabien Paulot wrote:

I think there is a relatively serious bug in the standard chemistry. GLPAN and GLCO3 are set to inactive but their production and loss reactions are active. As a result they never reach equilibrium and this results in an artificial loss of NOx.

If this is the only cause of the imbalance between sources and sinks of NOx in my simulations, this would account for ~5% of NOy losses. I don't see that problem in a simulation with a different chemistry that among other changes does not feature those reactions. So hopefully that's it.

To fix the error, I made the following modifications in globchem.dat:

1. I set GLPAN and GLCO3 rxns from active to dead. These rxns were causing an artificial loss of NOx.
2. I have physically removed GLCO3, GLP, GLPAN, GPAN, ISNO3, MNO3, O2CH2OH, MVN2 and their associated reactions.
3. I have made GLYX active. I'm not sure why it's not active by default.

and to ratj.d:

1. I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in globchem.dat

--Bob Y. 14:51, 10 November 2011 (EST)
--Melissa Payer 10:49, 15 December 2011 (EST)
--Bob Yantosca (talk) 20:35, 31 January 2017 (UTC)

Bug in routine ARSL1K

This update was tested in the 1-month benchmark simulation v9-01-03m and approved on 06 Jun 2012.

SMVGEAR was removed from GEOS-Chem v11-01 and higher versions. The ARSL1K routine was replaced by an equivalent function in KPP's rate law library.

A bug in routine ARSL1K became problematic in the implementation of Justin Parrella's tropospheric bromine chemistry mechanism for GEOS-Chem v9-01-03. In the bromine chemistry mechanism, a sticking coefficient of 0.0 is passed to the routine ARSL1K for non-sulfate, non-sea salt aerosol. The IF statement modified in GEOS-Chem v8-02-04 resulted in the reaction rate being set to the default value of 1.0d-3. A 1-month benchmark for July 2005 indicated that the simulated BrO was a little more than twice the expected zonal mean. Modifying the default value from 1.0d-3 to 1.0d-30 resulted in reasonable simulated BrO values.

Mat Evans wrote:

I've re-run two 2 month simulation [using GEOS-Chem v9-01-02]. One with the error handling value of 1e-3 (standard) and one with it being 1e-30. There are 5127 time and space points where the model traps the problem and invokes the 1e-3 or 1e-30 value. There are 30*24*2*37*72*46 (roughly 200 million) time and space points when the error could have occurred so we are looking at a relatively infrequent event.

The simulations show virtually no difference between the two simulations.

mean and stddev ratio of all grid boxes with and without the fix are shown below

    NOx     0.999996  0.000409291
    Ox      1.00000   1.27233e-05
    O3      1.00000   1.52284e-05
    PAN     0.997849  0.0111997
    CO      1.00000   4.21768e-06
    ALK4    0.990514  0.0351941
    ISOP    0.999979  0.0108033
    H2O2    0.992067  0.0264659
    DST1    1.00000   0.00000
    HO2     0.999996  0.00309464
    OH      1.00003   0.00767954

So although there are some differences they are very minor. For completeness we should put this in as a bug fix (make the error value 1d-30 rather than 1d-3). But it is not a major problem.

--Melissa Payer 17:52, 14 May 2012 (EDT)
--Bob Yantosca (talk) 20:35, 31 January 2017 (UTC)