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:
 
*[[#NOx-Ox-hydrocarbon-aerosol chemistry and variants|Several detailed NO, O3, hydrocarbon, and aerosol chemistry mechanisms (aka "full-chemistry")]]
*[[#Mechanisms for aerosol microphysics|"Full-chemistry" plus aerosol microphysics (i.e. accounting for aerosol number and size)]]
*[[#Specialty simulations|"Specialty simulations" for species with simpler chemistry]]
 
You may find more information about each of these mechanisms in the subsections below.
 
--[[User:Bmy|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 [[#Mechanisms in GEOS-Chem v9-02 and prior versions|above-mentioned tropospheric chemistry mechanisms]] in [[GEOS-Chem v10-01]], as listed below:
 
{| border=1 cellspacing=0 cellpadding=5
|-bgcolor="#CCCCCC"
!width="100px"|Mechanism
!width="450px"|Description
!width="150px"|Vertical grid
!width="150px"|Solvers
!width="225px"|Notes
 
|-valign="top"
|[[NOx-Ox-HC-aerosol|'''tropchem''']]
|From the surface to the tropopause:
*[[NOx-Ox-HC-Aer-Br_chemistry_mechanism|NOx-Ox-hydrocarbon-aerosol]] species
*PLUS [[Bromine chemistry mechanism|bromine species]]
*PLUS [[Methyl peroxy nitrate chemistry]]
 
From the tropopause to the top of the atmosphere:
*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
 
|
*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_reduced 47 levels]
*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 levels]
|
*SMVGEAR
*[[KPP solvers FAQ|KPP]]
|
*aka "[[NOx-Ox-HC-Aer-Br_chemistry_mechanism|NOx-Ox-HC-Aer-Br]]"
*aka "Full-chemistry"
*aka "Fullchem"
*aka "Trop-only"
 
|-valign="top"
|[[UCX chemistry mechanism|'''UCX''']]
|From the surface to the stratopause:
*[[NOx-Ox-HC-Aer-Br_chemistry_mechanism|All of the species in the '''tropchem''' mechanism]]
*PLUS [[UCX chemistry mechanism|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|'''LINOZ''' stratospheric ozone chemistry]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
 
|
*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 levels] only
|
*[[KPP solvers FAQ|KPP]]
*SMVGEAR is not recommended
|
 
|-valign="top"
|[[Secondary organic aerosols|'''SOA''']]
|From the surface to the tropopause:
*[[NOx-Ox-HC-Aer-Br_chemistry_mechanism|All of the species in the '''tropchem''' mechanism]]
*PLUS [[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|SOA species]]
*PLUS [[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|Semi-volatile primary organic aerosol (OPTIONAL)]]
 
From the tropopause to the top of the atmosphere:
*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
|
*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_reduced 47 levels]
*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 levels]
|
*SMVGEAR
*[[KPP solvers FAQ|KPP]]
|
 
|-valign="top" bgcolor="#CCFFFF"
|'''benchmark'''
|From the surface to the stratopause:
*[[NOx-Ox-HC-Aer-Br_chemistry_mechanism|All of the species in the '''tropchem''' mechanism]]
*PLUS [[UCX chemistry mechanism|all of the species in the '''UCX''' mechanism]]
*PLUS [[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|all of the species in the '''SOA''' mechanism]]
 
From the stratopause to the top of the atmosphere:
*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*All other species: [[Stratospheric_chemistry|GMI stratopsheric chemistry (archived P/L rates)]]
|
*[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 levels] only
|
*[[KPP solvers FAQ|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"
|}
 
For a list of tracers corresponding to each of these chemistry mecahnisms, please see [http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html#FullChem Appendix 1.1 of the GEOS-Chem Online User's Guide].
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:14, 26 May 2015 (UTC)<br>--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 14:21, 16 June 2015 (UTC)
 
=== Mechanisms in GEOS-Chem v9-02 ===
 
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''']]
|From the surface to the tropopause:
*[[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]]
 
From the tropopause to the top of the atmosphere:
*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
 
|Full-chemistry,<br>Fullchem
|
*SMVGEAR
*[[KPP solvers FAQ|KPP]]
 
|-valign="top"
|[[Secondary organic aerosols|'''SOA''']]
|From the surface to the tropopause:
*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)]]
 
From the tropopause to the top of the atmosphere:
*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
 
|SOA
|
*SMVGEAR
*[[KPP solvers FAQ|KPP]]
 
|-valign="top"
|[[Dicarbonyls simulation|'''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:
*Ozone: [[Linoz stratospheric ozone chemistry|'''LINOZ''' stratospheric ozone chemistry]]
*All other species: [[Stratospheric_chemistry|'''GMI''' stratopsheric chemistry (archived P/L rates)]]
|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.]] ([[User talk:Bmy|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:
 
{| 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)
 
=== Stratospheric chemistry ===
 
GEOS-Chem was historically developed as a model of tropospheric chemistry and composition.  The above-mentioned [[#Mechanisms in GEOS-Chem v9-01-03 and prior versions|chemistry mechamisms in GEOS-Chem v9-01-03]] and [[#Mechanisms in GEOS-Chem v9-02 and later versions|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:
 
# [[Linoz stratospheric ozone chemistry]]
# [[Stratospheric chemistry|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 [[UCX_chemistry_mechanism|'''Unified tropospheric-stratospheric Chemistry eXtension''' (UCX) mechanism]] into GEOS-Chem. UCX was developed by Seb Eastham and Steven Barrett at the [http://lae.mit.edu MIT Laboratory for Aviation and the Environment]. This mechanism combines the existing GEOS-Chem [[NOx-Ox-HC-aerosol|"NOx-Ox-HC-aerosol" mechanism]] with several new stratospheric species and reactions.
 
--[[User:Bmy|Bob Y.]] 12:11, 1 October 2013 (EDT)<br>--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:18, 26 May 2015 (UTC)
 
== Planned updates ==
 
The following chemistry updates are slated for inclusion to GEOS-Chem following the [[GEOS-Chem v10-01|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. <tt>globchem.dat</tt>, <tt>mglob.dat</tt>, etc.)
 
As of this writing (Oct 2015), Flexchem is still under development. It is scheduled for inclusion in [[GEOS-Chem v11-01 benchmark history|v11-01 history]].
 
--[[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 ===
 
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 [[NOx-Ox-HC-aerosol|standard GEOS-Chem "full-chemistry" simulation]].  For complete information about the TOMAS simulation, please see our [[TOMAS aerosol microphysics]] wiki page.
 
--[[User:Bmy|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#SOA_simulation_with_semi-volatile_POA|secondary organic aerosols with semi-volatile primary organic aerosols]].  The work is ongoing as of October 2013.
 
--[[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) 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 [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 O3 simulation]]
|Up-to-date
|[[Chemistry Issues|Oxidants and 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)
 
== Analytical tools ==
 
 
 
=== Process analysis diagnostics ===
 
[mailto:barronh@ufl.edu Barron Henderson] (U. Florida) has created a [[Process Analysis Diagnostics|software package for process analysis diagnostics]].  He writes:
 
<blockquote>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.</blockquote>
 
To obtain this software, [[Process_Analysis_Diagnostics#Installation_and_Application_-_How_can_I_use_it.3F|please contact Barron Henderson directly]].
 
--[[User:Bmy|Bob Y.]] 12:26, 1 October 2013 (EDT)

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