GEOS-Chem chemistry mechanisms: Difference between revisions

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*All other species: [[Stratospheric_chemistry|GMI stratopsheric chemistry (archived P/L rates)]]
*All other species: [[Stratospheric_chemistry|GMI stratopsheric chemistry (archived P/L rates)]]
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*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 levels] only
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*[[KPP solvers FAQ|KPP]]  
*[[KPP solvers FAQ|KPP]]  
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*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
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*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_reduced 47 levels]
*[[GEOS-Chem_vertical_grids#47-layer_reduced_vertical_grid|47 levels]]
*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 levels]
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]]
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*SMVGEAR
*SMVGEAR
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*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
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*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 levels] only
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]] only
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*[[KPP solvers FAQ|KPP]]
*[[KPP solvers FAQ|KPP]]
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*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
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*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_reduced 47 levels]
*[[GEOS-Chem_vertical_grids#47-layer_reduced_vertical_grid|47 levels]]
*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 levels]
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]]
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*SMVGEAR
*SMVGEAR

Revision as of 22:49, 5 December 2016

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:

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 tropospheric chemistry mechanisms in GEOS-Chem v10-01, as listed below:

Mechanism Description Vertical grid Solvers Notes
standard (v11-01)
benchmark (v10-01)
From the surface to the stratopause:

From the stratopause to the top of the atmosphere:

  • KPP
  • SMVGEAR is not recommended
tropchem From the surface to the tropopause:

From the tropopause to the top of the atmosphere:

UCX From the surface to the stratopause:

From the stratopause to the top of the atmosphere:

  • KPP
  • SMVGEAR is not recommended
SOA From the surface to the tropopause:

From the tropopause to the top of the atmosphere:

For a list of tracers corresponding to each of these chemistry mecahnisms, please see Species in GEOS-Chem: Full-chemistry mechanisms.

--Melissa Sulprizio (talk) 17:14, 26 May 2015 (UTC)
--Bob Yantosca (talk) 22:42, 5 December 2016 (UTC)

FlexChem

In GEOS-Chem v11-01, the above mechanisms have been added to our FlexChem implementation of KPP. The legacy SMVGEAR solver has now been removed.

Flexchem was implemented into GEOS-Chem v11-01g. We expect that GEOS-Chem v11-01 will be officially released in January 2017.

--Bob Yantosca (talk) 22:45, 5 December 2016 (UTC)

Mechanisms in GEOS-Chem v9-02

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

Mechanism Description Nickname Solvers
standard From the surface to the tropopause:

From the tropopause to the top of the atmosphere:

Full-chemistry,
Fullchem
SOA From the surface to the tropopause:

From the tropopause to the top of the atmosphere:

SOA
Dicarbonyls From the surface to the tropopause:
  • NOx-Ox-hydrocarbon-aerosol species
  • PLUS dicarbonyl species
  • This chemical mechanism is in need of updating

From the tropopause to the top of the atmosphere:

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. (talk) 14:58, 28 May 2015 (UTC)

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 Full-chemistry,
Fullchem
SOA
  • NOx-Ox-hydrocarbon-aerosol species
  • PLUS secondary organic aerosol species
SOA
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

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.

Monoterpene Nitrate Chemistry

An experimental monoterpene nitrate chemistry scheme has been implemented for simulation of the SEAC4RS data. The paper describing the implementation (Fisher et al., 2016) has not yet been peer reviewed. If you are interested in using this scheme in advance of possible eventual inclusion in GEOS-Chem, you can see the detailed monoterpene nitrate scheme or contact Jenny Fisher (jennyf@uow.edu.au).

--Jenny Fisher, 15 January 2015

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
  1. Total Hg tracers: Hg0, Hg2, HgP
  2. Tagged Hg tracers
  3. 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 (with optional passive tracer) 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)

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)