GEOS-Chem chemistry mechanisms

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

Overview

GEOS-Chem can perform many different types of chemical simulations, including:

• Several detailed NO, O3, hydrocarbon, and aerosol chemistry mechanisms (aka "full-chemistry")
• "Full-chemistry" plus aerosol microphysics (i.e. accounting for aerosol number and size)
• "Specialty simulations" for species with simpler chemistry

You may find more information about each of these mechanisms in the subsections below.

--Bob Y. 11:56, 24 February 2014 (EST)

NOx-Ox-hydrocarbon-aerosol chemistry and variants

The NOx-Ox-hydrocarbon-aerosol (aka "full-chemistry") simulations have undergone several updates in recent GEOS-Chem versions. We provide a summary of these updates in this section.

Mechanisms in GEOS-Chem v10-01 and later versions

Several modifications were made to the above-mentioned tropospheric chemistry mechanisms in GEOS-Chem v10-01, as listed below:

Mechanism	Description	Vertical grid	Solvers	Notes
tropchem	From the surface to the tropopause: NOx-Ox-hydrocarbon-aerosol species PLUS bromine species PLUS Methyl peroxy nitrate chemistry From the tropopause to the top of the atmosphere: Ozone: Linoz stratospheric ozone chemistry All other species: GMI stratopsheric chemistry (archived P/L rates)	47 levels 72 levels	SMVGEAR KPP	aka "NOx-Ox-HC-Aer-Br" aka "Full-chemistry" aka "Fullchem" aka "Trop-only"
UCX	From the surface to the stratopause: All of the species in tropchem mechanism PLUS online stratospheric chemistry PLUS long-lived species such as N2O, CH4, OCS, CFCs, HCFCs, and halons From the stratopause to the top of the atmosphere: Ozone: Linoz stratospheric ozone chemistry All other species: GMI stratopsheric chemistry (archived P/L rates)	72 levels only	KPP SMVGEAR is not recommended
SOA	From the surface to the tropopause: All of the species in tropchem mechanism PLUS SOA species PLUS Semi-volatile primary organic aerosol (OPTIONAL) From the tropopause to the top of the atmosphere: Ozone: Linoz stratospheric ozone chemistry All other species: GMI stratopsheric chemistry (archived P/L rates)	47 levels 72 levels	SMVGEAR KPP
benchmark	From the surface to the stratopause: All of the species in the tropchem mechanism PLUS all of the species in the UCX mechanism PLUS all of the species in the SOA mechanism From the stratopause to the top of the atmosphere: Ozone: Linoz stratospheric ozone chemistry All other species: GMI stratopsheric chemistry (archived P/L rates)	72 levels only	KPP SMVGEAR is not recommended	This is now the chemistry mechanism that will be used when you run GEOS-Chem "out-of-the-box" This is now the chemistry mechanism that will be used for benchmark simulations aka "standard"

--Melissa Sulprizio (talk) 17:14, 26 May 2015 (UTC)
--Bob Y. (talk) 14:52, 28 May 2015 (UTC)

Mechanisms in GEOS-Chem v9-02

Several modifications were made to the above-mentioned tropospheric chemistry mechanisms in GEOS-Chem v9-02, as listed below:

Mechanism	Description	Nickname	Solvers
standard	NOx-Ox-hydrocarbon-aerosol species PLUS bromine species PLUS Updates to inorganic chemistry reactions (cf. JPL 10-6) PLUS Methyl peroxy nitrate chemistry PLUS Isoprene oxidation species chemistry (aka "Caltech isoprene scheme") PLUS Fix RO2+HO2 rate constant PLUS Increase of NO3 uptake by aerosol PLUS Removal of NOx and Ox partitioning PLUS Inhibition of N2O5 uptake by nitrate aerosol PLUS Improved HO2 uptake by aerosol	Full-chemistry, Fullchem	SMVGEAR KPP
SOA	Everything in the "standard" simulation listed above PLUS Updated SOA species PLUS Semi-volatile primary organic aerosol (OPTIONAL)	SOA	SMVGEAR KPP
Dicarbonyls	NOx-Ox-hydrocarbon-aerosol species PLUS dicarbonyl species This chemical mechanism is in need of updating	Dicarbonyls	SMVGEAR only

Starting with v9-02, family tracers (NOx, Ox) have now been removed from all GEOS-Chem mechanisms. The individual family members (NO, NO2, O3, etc.) are now carried as individual advected tracers and chemical species. Also, the isoprene mechanism from v9-01-03 now has been folded into the standard mechanism.

--Bob Y. 09:56, 1 October 2013 (EDT)

Mechanisms in GEOS-Chem v9-01-03 and prior versions

In GEOS-Chem v9-01-03, users could select from one of four pre-defined tropospheric chemistry mechanisms:

Mechanism	Description	Nickname	Solvers
standard	NOx-Ox-hydrocarbon-aerosol species PLUS bromine species	Full-chemistry, Fullchem	SMVGEAR KPP
SOA	NOx-Ox-hydrocarbon-aerosol species PLUS secondary organic aerosol species	SOA	SMVGEAR KPP
Dicarbonyls	NOx-Ox-hydrocarbon-aerosol species PLUS dicarbonyl species	Dicarbonyls	SMVGEAR only
isoprene	NOx-Ox-hydrocarbon-aerosol species PLUS isoprene oxidation products	Caltech isoprene scheme, Paulot isoprene scheme	SMVGEAR KPP

The bromine tracers and species were added to the standard mechanism just prior to the release of GEOS-Chem v9-01-03.

-Bob Y. 17:00, 30 September 2013 (EDT)

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)

Planned updates

The following chemistry updates are slated for inclusion to GEOS-Chem following the v10-01 release.

Flexchem

We also propose to add a cleaner implementation of KPP into GEOS-Chem. This implementation, which we have named Flexchem, will allow users to customize the chemical mechanism according to their research interests. Flexchem will remove the existing SMVGEAR and KPP infrastructure, and all related input files (i.e. globchem.dat, mglob.dat, etc.)

As of this writing (Oct 2013), Flexchem is still under development. We hope to have it installed in a version of GEOS-Chem sometime in 2014.

--Bob Y. 10:17, 1 October 2013 (EDT)

Mechanisms for aerosol microphysics

GEOS-Chem contains two different aerosol microphysics packages: TOMAS and APM.

TOMAS

The TOMAS aerosol microphysics scheme has been fully integrated with GEOS-Chem v9-02. It adds several size-resolved aerosols (you may select from 12, 15, 30, or 40 size bins) to the standard GEOS-Chem "full-chemistry" simulation. For complete information about the TOMAS simulation, please see our TOMAS aerosol microphysics wiki page.

--Bob Y. 11:57, 24 February 2014 (EST)

APM

The APM aerosol microphysics is currently being re-integrated into GEOS-Chem. APM needs to be brought up to date with the recent update for secondary organic aerosols with semi-volatile primary organic aerosols. The work is ongoing as of October 2013.

--Bob Y. 11:32, 1 October 2013 (EDT)

Specialty simulations

GEOS-Chem can also perform "specialty simulations" (aka "offline simulations"). These are simulations for species having simpler chemistry mechanisms that do not require the use of a full chemical solver such as SMVGEAR or KPP. Many of these simulations rely on oxidant fields (O3, OH) archived from a previous "full-chemistry" simulation.

List of specialty simulations

The following table provides links to information about the available specialty simulations in GEOS-Chem. Please note that some of these simulations are out of date and will require some work in order to be brought back to the state-of-the-science. Contact the relevant GEOS-Chem Working Group for more information.

Category	Simulation	Status	Contact
Aerosols	Aerosol-only simulation (can be customized to include only the aerosol species you want)	Up-to-date	Aerosols Working Group
Carbon Gases	C2H6 simulation	Needs attention	Carbon Cycle Working Group
Carbon Gases	CH3I simulation	Needs attention	Carbon Cycle Working Group
Carbon Gases	CH4 simulation	Up-to-date	Carbon Cycle Working Group
Carbon Gases	Tagged CO simulation	Up-to-date	Carbon Cycle Working Group
Carbon Gases	CO2 simulation	Up-to-date	Carbon Cycle Working Group
Carbon Gases	OCS simulation	Under development	Carbon Cycle Working Group
Hg and POPs	Hg simulations Total Hg tracers: Hg0, Hg2, HgP Tagged Hg tracers Hg simulation + Global Terrestrial Mercury Model	Up-to-date	Hg and POPs Working Group
Hg and POPs	Persistent Organic Pollutants (POPs) simulation	Up-to-date	Hg and POPs Working Group
Ozone	Tagged O3 simulation	Up-to-date	Oxidants and Chemistry Working Group
Radionuclides	Rn-Pb-Be simulation	Up-to-date	Transport Working Group
Radionuclides	H2-HD isotope simulation	Needs attention	Transport Working Group

Note to developers

The GEOS-Chem Support Team will be happy to assist you with technical issues (i.e. debugging, or answering questions about coding) pertaining to specialty simulations. However, we expect the GEOS-Chem user community to be responsible for the scientific content and validation of offline simulations, and shall:

1. Provide the appropriate code, data, and documentation for offline simulations to the GEOS-Chem Support Team
2. Benchmark and evaluate GEOS-Chem offline simulations
3. Notify the GEOS-Chem support team of any bugs or technical issues.

--Bob Y. 10:59, 1 October 2013 (EDT)

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)