GEOS-Chem chemistry mechanisms

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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.

Mechanism Mechanism file Simulation(s) Contact
Standard

(full-chemistry in troposphere + stratosphere)

KPP/Standard/Standard.eqn Chemistry Working Group
Tropchem

(full-chemistry in troposphere only)

KPP/Tropchem/Tropchem.eqn Chemistry Working Group
SOA_SVPOA

(full chemistry in troposphere only + semivolatile POA)

KPP/SOA_SVPOA/SOA_SVPOA.eqn Aerosols Working Group
Methane GeosCore/global_ch4_mod.F Carbon Cycle Working Group
CO GeosCore/tagged_co_mod.F Carbon Cycle Working Group
CO2 GeosCore/co2_mod.F Carbon Cycle Working Group
Mercury GeosCore/mercury_mod.F Hg and POPs Working Group
Persistent Organic Pollutants GeosCore/pops_mod.F Hg and POPs Working Group
Ozone GeosCore/tagged_o3_mod.F Chemistry Working Group
Radionuclides GeosCore/RnPbBe_mod.F Transport Working Group
The following mechanisms are obsolete and have been removed:
Ethane GeosCore/c2h6_mod.F
  • C2H6
Carbon Cycle Working Group
Methyl iodide GeosCore/ch3i_mod.F
in GEOS-Chem v9-02 and earlier
  • CH3I
Carbon Cycle Working Group
H2-HD isotopes GeosCore/h2_h2_mod.F
in GEOS-Chem v9-02 and earlier
  • H2-HD
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 Ra(z1,zC) is the aerodynamic resistance between z1 and zC, and vd(z1) is the ozone deposition velocity at z1, and C(z1) is the ozone concentration at z1.

Ra(z1,zC) is calculated to the lowest model level in drydep_mod.F. We recalculate Ra using z1 = 10 m, which is the height of the CASTNET measurement for ozone. The new Ra 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

Carbon balance

Barron Henderson has created a script for evaluating carbon balance. Please see this post on the Chemistry Working Group wiki page for more information.

--Melissa Sulprizio (talk) 17:31, 22 February 2019 (UTC)

Process analysis diagnostics

Barron Henderson 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)