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 v11-02 and later versions ===
 
 
Several modifications were made to the [[#Mechanisms in GEOS-Chem v9-02 and prior versions|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" bgcolor="#CCFFFF"
|'''standard''' (v11-01)<br>'''benchmark''' (v10-01)
|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)]]
|
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]] only
|
*[[KPP solvers FAQ|KPP]]
*SMVGEAR is not recommended and is obsolete in v11-01 and later
|
*Used when you run GEOS-Chem "out-of-the-box"
*Used for [http://acmg.seas.harvard.edu/geos/geos_benchmark.html GC benchmark simulations]
 
|-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)]]
|
*[[GEOS-Chem_vertical_grids#47-layer_reduced_vertical_grid|47 levels]]
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]]
|
*[[KPP solvers FAQ|KPP]]
*SMVGEAR (obsolete in v11-01 and later)
|
*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)]]
|
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]] only
|
*[[KPP solvers FAQ|KPP]]
*SMVGEAR is not recommended and is obsolete in v11-01 and later
|
 
|-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)]]
|
*[[GEOS-Chem_vertical_grids#47-layer_reduced_vertical_grid|47 levels]]
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]]
|
*[[KPP solvers FAQ|KPP]]
*SMVGEAR (obsolete in v11-01 and later)
|
 
|}
 
 
=== Mechanisms in GEOS-Chem v10-01 and later versions ===
 
Several modifications were made to the [[#Mechanisms in GEOS-Chem v9-02 and prior versions|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" bgcolor="#CCFFFF"
|'''standard''' (v11-01)<br>'''benchmark''' (v10-01)
|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)]]
|
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]] only
|
*[[KPP solvers FAQ|KPP]]
*SMVGEAR is not recommended and is obsolete in v11-01 and later
|
*Used when you run GEOS-Chem "out-of-the-box"
*Used for [http://acmg.seas.harvard.edu/geos/geos_benchmark.html GC benchmark simulations]
 
|-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)]]
|
*[[GEOS-Chem_vertical_grids#47-layer_reduced_vertical_grid|47 levels]]
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]]
|
*[[KPP solvers FAQ|KPP]]
*SMVGEAR (obsolete in v11-01 and later)
|
*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)]]
|
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]] only
|
*[[KPP solvers FAQ|KPP]]
*SMVGEAR is not recommended and is obsolete in v11-01 and later
|
 
|-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)]]
|
*[[GEOS-Chem_vertical_grids#47-layer_reduced_vertical_grid|47 levels]]
*[[GEOS-Chem_vertical_grids#72-layer_vertical_grid|72 levels]]
|
*[[KPP solvers FAQ|KPP]]
*SMVGEAR (obsolete in v11-01 and later)
|
 
|}
 
For a list of tracers corresponding to each of these chemistry mecahnisms, please see [[Species_in_GEOS-Chem#Full-chemistry|Species in GEOS-Chem: Full-chemistry mechanisms]].
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:14, 26 May 2015 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|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 v11-01#v11-01g|GEOS-Chem v11-01g]].  We expect that [[GEOS-Chem v11-01]] will be officially released in January 2017.
 
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:45, 5 December 2016 (UTC)
 
=== Mechanisms in GEOS-Chem v9-02 ===
 
Several modifications were made to the [[#Mechanisms in GEOS-Chem v9-01-03 and prior versions|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 ==
 
=== Updated isoprene and monoterpene chemistry ===
 
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span>
 
'''Developers:'''
* Katie Travis (MIT, formerly Harvard)
* Jenny Fisher (U. Wollongong)
* Christopher Chan Miller (Smithsonian Astrophysical Observatory, formerly Harvard)
* Eloise Marais (U. Birminghan, formerly Harvard)
 
[[Media:NewChemistry 030917.pdf|'''This document''']] compiled by Katie Travis and Josh Cox describes the updated isoprene and monoterpene chemistry to be included in [[GEOS-Chem v11-02#v11-02c|GEOS-Chem v11-02c]] (also see the [[#Modifications to the original updates|list of modifications below]]). These updates include the [[monoterpene nitrate scheme]] and [[Secondary_organic_aerosols#SOA_formation_from_aqueous_isoprene_uptake|aqueous isoprene uptake]] and were originally implemented for simulation of the [https://www.nasa.gov/seac4rs/ 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. [http://acmg.seas.harvard.edu/publications/2016/miller2016_seac4rs.pdf 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. [http://acmg.seas.harvard.edu/publications/2016/fisher2016.pdf 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. [http://acmg.seas.harvard.edu/publications/2016/Marais_SEUS_isopSOA_ACP_2016.pdf 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. [http://acmg.seas.harvard.edu/publications/2016/Travis_ACPD_2016.pdf PDF], [http://acmg.seas.harvard.edu/publications/2016/Travis_ACPD_2016_sup.pdf Supplement]
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:06, 12 July 2017 (UTC)
 
==== Modifications to the original updates ====
 
The following modifications were made to the original updates listed in the [[Media:NewChemistry 030917.pdf|above document]] following conversations with the developers. These modifications were included in [[GEOS-Chem v11-02#v11-02c|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 [[Secondary_organic_aerosols#Complex_SOA_scheme|existing SOA scheme]])
:*APIO2 is now PIO2 (for consistency with [[PAN|PAN updates]] added in [[GEOS-Chem v11-02#v11-02a|v11-02a]])
:*LIM is now LIMO (for consistency with [[Secondary_organic_aerosols#Complex_SOA_scheme|existing SOA scheme]])
:*PMN is now NPMN and IPMN (PMN from non-isoprene and isoprene sources; from [[Secondary_organic_aerosols#SOA_formation_from_aqueous_isoprene_uptake|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
            <span style="color:red">Rate = 2.00e-13</span>
    v11-02c: ISNOHOO + MO2 = 0.660PROPNN + 0.700GLYX + 1.200HO2 + 0.750CH2O + <span style="color:green">0.250MOH</span> + 0.040ISN1OG
            <span style="color:green">Rate = 2.06e-13</span>
    Orig:    ISOPNB + OH = <span style="color:red">ISOPNBO2</span> + 0.100IEPOX + 0.100NO2
    v11-02c: ISOPNB + OH = <span style="color:green">0.900ISOPNBO2</span> + 0.100IEPOX + 0.100NO2
    Orig:    HONIT + OH = NO3 + <span style="color:red">HKET</span>
    v11-02c: HONIT + OH = NO3 + <span style="color:green">HAC</span>
    Orig:    HONIT + hv = <span style="color:red">HKET</span> + NO2
    v11-02c: HONIT + hv = <span style="color:green">HAC</span> + NO2
 
(5) Completely replace RIP with RIPA, RIPB, RIPD and IEPOX with IEPOXA, IEPOXB, IEPOXD
 
    Orig:    <span style="color:red">RIP  + hv = 0.985OH + 0.985HO2 + 0.710CH2O + 0.425MVK + 0.285MACR + 0.275HC5 + 0.005LVOC</span>
    v11-02c: <span style="color:green">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</span>
    Orig:    ISOPND + OH = <span style="color:red">0.100IEPOX</span> + 0.900ISOPNDO2 +0.100NO2
    v11-02c: ISOPND + OH = <span style="color:green">0.100IEPOXD</span> + 0.900ISOPNDO2 +0.100NO2
    Orig:    ISOPNB + OH = 0.900ISOPNBO2 + <span style="color:red">0.100IEPOX</span> + 0.100NO2
    v11-02c: ISOPNB + OH = 0.900ISOPNBO2 + <span style="color:green">0.067IEPOXA + 0.033IEPOXB</span> + 0.100NO2
    Orig:    <span style="color:red">IEPOX  = SOAIE : HET(ind_IEPOX,1);</span>
    v11-02c: <span style="color:green">IEPOXA = SOAIE : HET(ind_IEPOXA,1);
            IEPOXB = SOAIE : HET(ind_IEPOXB,1);
            IEPOXD = SOAIE : HET(ind_IEPOXD,1);</span>
 
(6) Add LVOC to RIP channels
 
    Orig:    RIPA + OH = 0.750 RIO2 + <span style="color:red">0.250 HC5</span> + 0.125 (OH + H2O)
    v11-02c: RIPA + OH = 0.750 RIO2 + <span style="color:green">0.245 HC5</span> + 0.125 (OH + H2O) + <span style="color:green">0.005 LVOC</span>
   
    Orig:    RIPA + OH = 0.850 OH + 0.578 IEPOXA + 0.272 IEPOXB + <span style="color:red">0.150 HC5OO</span>
    v11-02c: RIPA + OH = 0.850 OH + 0.578 IEPOXA + 0.272 IEPOXB + <span style="color:green">0.145 HC5OO + 0.005 LVOC</span>
   
    Orig:    RIPB + OH = 0.480 RIO2 + <span style="color:red">0.520 HC5</span> + 0.26 (OH + H2O)
    v11-02c: RIPB + OH = 0.480 RIO2 + <span style="color:green">0.515 HC5</span> + 0.26 (OH + H2O) + <span style="color:green">0.005 LVOC</span>
   
    Orig:    RIPD + OH = 0.250 RIO2 + <span style="color:red">0.750 HC5</span> + 0.375 (OH + H2O)
    v11-02c: RIPD + OH = 0.250 RIO2 + <span style="color:green">0.745 HC5</span> + 0.375 (OH + H2O) + <span style="color:green">0.005 LVOC</span>
   
    Orig:    RIPD + OH = 0.500 OH + 0.500 IEPOXD + <span style="color:red">0.500 HC5OO</span>
    v11-02c: RIPD + OH = 0.500 OH + 0.500 IEPOXD + <span style="color:green">0.495 HC5OO + 0.005 LVOC</span>
   
    The only reaction that wont have LVOC as a product is RIPB + OH = OH + IEPOXA + IEPOXB.
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 16:26, 7 September 2017 (UTC)
 
== 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]] (with optional passive tracer)
|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)
 
=== Linking GEOS-Chem to CMAQ ===
 
[mailto:barronh@ufl.edu Barron Henderson] has created Python software that will let you translate GEOS-Chem output to the proper speciation for input to CMAQ.  Please see [[Linking_GEOS-Chem_to_CMAQ|our ''Linking GEOS-Chem to CMAQ'' wiki page]] for more information.
 
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 16:46, 26 October 2015 (UTC)

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