GEOS-Chem chemistry mechanisms: Difference between revisions

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On this page, we provide an overview of the chemistry mechanisms used in GEOS-Chem.
#REDIRECT [[Simulations using KPP-built mechanisms]]
 
== Overview ==
 
GEOS-Chem can perform many different types of chemical simulations, including:
 
*Several detailed ozone chemistry mechanisms
*Specialty simulations for tracers with simpler chemistry, including
**Radon-Lead-Beryllium
**Carbon gases (CO, CO2)
**Mercury
**Methane
**etc.
 
You may find more information about each of these mechanisms in the subsections below.
 
--[[User:Bmy|Bob Y.]] 10:08, 1 October 2013 (EDT)
 
== 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 v9-01-03 and prior versions ===
 
In [[GEOS-Chem v9-01-03]], users could select from one of four pre-defined tropospheric chemistry mechanisms:
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="100px"|Mechanism
!width="500x"|Description
!width="175px"|Nickname
!width="150px"|Solvers
 
|-valign="top"
|[[NOx-Ox-HC-aerosol|standard]]
|
*NOx-Ox-hydrocarbon-aerosol species
*PLUS [[Bromine chemistry mechanism|bromine species]]
|Full-chemistry,<br>fullchem
|
*SMVGEAR
*[[KPP solvers FAQ|KPP]]
 
|-valign="top"
|[[Secondary organic aerosols|SOA]]
|
*NOx-Ox-hydrocarbon-aerosol species
*PLUS secondary organic aerosol species
|SOA
|
*SMVGEAR
*[[KPP solvers FAQ|KPP]]
 
|-valign="top"
|[[Dicarbonyls simulation|Dicarbonyls]]
|
*NOx-Ox-hydrocarbon-aerosol species
*PLUS dicarbonyl species
|Dicarbonyls
|
*SMVGEAR only
 
|-valign="top"
|[[New isoprene scheme|isoprene]]
|
*NOx-Ox-hydrocarbon-aerosol species
*PLUS isoprene oxidation products
|Caltech isoprene scheme,<br>Paulot isoprene scheme
|
*SMVGEAR
*[[KPP solvers FAQ|KPP]]
|}
 
The [[Bromine chemistry mechanism|bromine tracers and species]] were added to the standard mechanism just prior to the release of [[GEOS-Chem v9-01-03]].
 
-[[User:Bmy|Bob Y.]] 17:00, 30 September 2013 (EDT)
 
=== Mechanisms in GEOS-Chem v9-02 and later versions ===
 
Several modifications were made to the [[#Mechanisms in GEOS-Chem v9-01-03 and prior versions|above-mentioned tropospheric chemistry mechanisms]] in [[GEOS-Chem v9-02]], as listed below:
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="100px"|Mechanism
!width="500px"|Description
!width="175px"|Nickname
!width="150px"|Solvers
 
|-valign="top"
|[[NOx-Ox-HC-aerosol|standard]]
|
*[[NOx-Ox-HC-aerosol|NOx-Ox-hydrocarbon-aerosol]] species
*PLUS [[Bromine chemistry mechanism|bromine species]]
*PLUS [[Updating_standard_chemistry_with_JPL_10-6|Updates to inorganic chemistry reactions (cf. JPL 10-6)]]
*PLUS [[Methyl peroxy nitrate chemistry]]
*PLUS [[New isoprene scheme|Isoprene oxidation species chemistry (aka "Caltech isoprene scheme")]]
*PLUS [[New_isoprene_scheme#Update_One_-_RO2.2BHO2_Reaction_Rate|Fix RO2+HO2 rate constant]]
*PLUS [[New_isoprene_scheme#NO3_aerosol_reactive_uptake_coefficient|Increase of NO3 uptake by aerosol]]
*PLUS [[NOx-Ox-HC-aerosol#Removal_of_NOx_and_Ox_partitioning|Removal of NOx and Ox partitioning]]
*PLUS [[ChemTelecon20111202|Inhibition of N2O5 uptake by nitrate aerosol]]
*PLUS [[NOx-Ox-HC-aerosol#Improved_HO2_uptake|Improved HO2 uptake by aerosol]]
|Full-chemistry,<br>fullchem
|
*SMVGEAR
*[[KPP solvers FAQ|KPP]]
 
|-valign="top"
|[[Secondary organic aerosols|SOA]]
|
*Everything in the "standard" simulation listed above
*PLUS Updated SOA species
*PLUS [[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|Semi-volatile primary organic aerosol (OPTIONAL)]]
|SOA
|
*SMVGEAR
*[[KPP solvers FAQ|KPP]]
 
|-valign="top"
|[[Dicarbonyls simulation|Dicarbonyls]]
|
*NOx-Ox-hydrocarbon-aerosol species
*PLUS dicarbonyl species
|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.
 
--[[User:Bmy|Bob Y.]] 09:56, 1 October 2013 (EDT)
 
=== Mechanisms in GEOS-Chem v10 ===
 
We propose adding the [[UCX chemistry mechanism|'''Unified tropospheric-stratospheric Chemistry eXtension''' (UCX) mechanism]] into the release following [[GEOS-Chem v9-02]].  UCX, which was developed by Steven Barrett's group (the [http://lae.mit.edu MIT Laboratory for Aviation and the Environment]), combines the existing GEOS-Chem [[NOx-Ox-HC-aerosol|"standard" mechanism]] (based on [[GEOS-Chem v9-01-03|v9-01-03]]) with several new stratospheric species and reactions.
 
Because UCX will be a major update to GEOS-Chem, we propose naming the version in which it ships to GEOS-Chem v10-01.  This will make it easier to denote versions that contain UCX from versions that do not.
 
--[[User:Bmy|Bob Y.]] 10:04, 1 October 2013 (EDT)
 
=== 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. <tt>globchem.dat</tt>, <tt>mglob.dat</tt>, 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.
 
--[[User:Bmy|Bob Y.]] 10:17, 1 October 2013 (EDT)
 
== Mechanisms for aerosol microphysics ==
 
GEOS-Chem contains two different aerosol microphysics packages: [[TOMAS aerosol microphysics|TOMAS]] and [[APM aerosol microphysics|APM]].
 
=== TOMAS ===
 
As of this writing (Oct 2012), the [[TOMAS aerosol microphysics]] scheme has been more tightly integrated into [[GEOS-Chem v9-02]].  It adds several size-resolved aerosols (you may select from 12, 15, 30, or 40 size bins) to the [[NOx-Ox-HC-aerosol|standard GEOS-Chem "full-chemistry" simulation]].
 
--[[User:Bmy|Bob Y.]] 11:34, 1 October 2013 (EDT)
 
=== 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#SOA_simulation_with_semi-volatile_POA|secondary organic aerosols with semi-volatile primary organic aerosols]].  The work is ongoing as of October 2012.
 
--[[User:Bmy|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) saved out 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 [http://acmg.seas.harvard.edu/geos/geos_working_groups.html GEOS-Chem Working Group] for more information.
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="125px"|Category
!width="400px"|Simulation
!width="125px"|Status
!width="250px"|Contact
 
|-valign="top"
|Aerosols
|[[Aerosol-only simulation]]<br>(can be customized to include only the aerosol species you want)
|Up-to-date
|[[Aerosols Working Group]]
 
|-valign="top"
|Carbon Gases
|C2H6 simulation
|Needs attention
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Carbon Gases
|CH3I simulation
|Needs attention
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Carbon Gases
|[[CH4 simulation]]
|Up-to-date
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Carbon Gases
|[[Tagged CO simulation]]
|Up-to-date
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Carbon Gases
|[[CO2 simulation]]
|Up-to-date
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Carbon Gases
|OCS simulation
|Under development
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Hg and POPs
|[[Mercury|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]]
 
|-valign="top"
|Hg and POPs
|[[POPs_simulation|Persistent Organic Pollutants (POPs) simulation]]
|Up-to-date
|[[Hg and POPs Working Group]]
 
|-valign="top"
|Ozone
|[[Tagged Ox simulation]]
|Needs attention
|[[Chemistry Issues|Chemistry Working Group]]
 
|-valign="top"
|Radionuclides
|[[Rn-Pb-Be simulation]]
|Up-to-date
|[[Transport Working Group]]
 
|-valign="top"
|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 [http://acmg.seas.harvard.edu/geos/geos_people.html GEOS-Chem user community] to be responsible for the scientific content and validation of offline simulations, and shall:
 
# Provide the appropriate code, data, and documentation for offline simulations to the GEOS-Chem Support Team
# Benchmark and evaluate GEOS-Chem offline simulations
# Notify the GEOS-Chem support team of any bugs or technical issues.
 
--[[User:Bmy|Bob Y.]] 10:59, 1 October 2013 (EDT)

Latest revision as of 15:32, 21 May 2024

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