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 ==
 
The following table provides links to information about the available chemistry mechanisms in GEOS-Chem. Please 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="250x"|Mechanism
!wigth="350px"|Mechanism file
!width="175px"|Simulation(s)
!width="225px"|Contact
 
|-valign="top"
|Standard
(full-chemistry in [[Tropospheric_chemistry_mechanism|troposphere]] + [[UCX_chemistry_mechanism|stratosphere]])
|[https://github.com/geoschem/geos-chem/blob/master/KPP/Standard/Standard.eqn <tt>KPP/Standard/Standard.eqn</tt>]
|
*Standard
*Benchmark<sup>1</sup>
|[[Chemistry Working Group]]
 
|-valign="top"
|Tropchem
(full-chemistry in [[Tropospheric_chemistry_mechanism|troposphere]] only)
|[https://github.com/geoschem/geos-chem/blob/master/KPP/Tropchem/Tropchem.eqn <tt>KPP/Tropchem/Tropchem.eqn</tt>]
|
*Tropchem
*[[Secondary_organic_aerosols#Simple_SOA_scheme|SOA]]
*[[Secondary_organic_aerosols#Complex_SOA_scheme|complexSOA]]
*[[#TOMAS|TOMAS]]
*[[#APM|APM]]
*[[Coupling_GEOS-Chem_with_RRTMG|RRTMG]]
|[[Chemistry Working Group]]
 
|-valign="top"
|SOA_SVPOA
(full chemistry in [[Tropospheric_chemistry_mechanism|troposphere]] only + [[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|semivolatile POA]])
|[https://github.com/geoschem/geos-chem/blob/master/KPP/SOA_SVPOA/SOA_SVPOA.eqn <tt>KPP/SOA_SVPOA/SOA_SVPOA.eqn</tt>]
|
*[[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|complexSOA_SVPOA]]
|[[Aerosols Working Group]]
 
|-valign="top"
|Methane
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/global_ch4_mod.F <tt>GeosCore/global_ch4_mod.F</tt>]
|
*[[CH4 simulation|CH4]]
*[[CH4 simulation|tagCH4]]
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|CO
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/tagged_co_mod.F <tt>GeosCore/tagged_co_mod.F</tt>]
|
*[[Tagged CO simulation|tagCO]]
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|CO2
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/co2_mod.F <tt>GeosCore/co2_mod.F</tt>]
|
*[[CO2 simulation|CO2]]
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Mercury
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/mercury_mod.F <tt>GeosCore/mercury_mod.F</tt>]
|
*[[Mercury|Hg]]
*[[Mercury|tagHg]]
*[[Mercury|Hg]]+[[Global Terrestrial Mercury Model|GTMM]]
|[[Hg and POPs Working Group]]
 
|-valign="top"
|Persistent Organic Pollutants
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/pops_mod.F <tt>GeosCore/pops_mod.F</tt>]
|
*[[POPs_simulation|POPs]]
|[[Hg and POPs Working Group]]
 
|-valign="top"
|Ozone
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/tagged_o3_mod.F <tt>GeosCore/tagged_o3_mod.F</tt>]|
*[[Tagged O3 simulation|tagO3]]
|[[Chemistry Working Group]]
 
|-valign="top"
|Radionuclides
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/RnPbBe_mod.F <tt>GeosCore/RnPbBe_mod.F</tt>]
|
*[[Rn-Pb-Be simulation|Rn-Pb-Be]]<br>[[Transport_Working_Group#Transport_Tracers_simulation|TransportTracers]]
|[[Transport Working Group]]
 
|-
!colspan="5" bgcolor="#CCCCCC"|<span style="color:red">'''The following mechanisms are obsolete and have been removed:'''</span>
 
|-valign="top"
|Ethane
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/c2h6_mod.F <tt>GeosCore/c2h6_mod.F</tt>]
|
*C2H6
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Methyl iodide
|<tt>GeosCore/ch3i_mod.F</tt><br>in [[GEOS-Chem v9-02]] and earlier
|
*CH3I
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|H2-HD isotopes
|<tt>GeosCore/h2_h2_mod.F</tt><br>in [[GEOS-Chem v9-02]] and earlier
|
*H2-HD
|[[Transport Working Group]]
 
|}
 
<sup>1</sup>The benchmark simulation is used for [[GEOS-Chem_benchmarking|1-month and 1-year benchmarks]]. It uses the Standard chemistry mechanism, but includes both the [[Secondary_organic_aerosols#Simple_SOA_scheme|simple SOA]] and [[Secondary_organic_aerosols#Complex_SOA_scheme|complex SOA]] species.
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:02, 22 February 2019 (UTC)
 
== Chemistry 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)
 
=== 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)
 
=== Correcting ozone from the height of the lowest model level to 10m ===
 
<span style="color:darkorange">'''''This update is slated for inclusion in [[GEOS-Chem v11-02#v11-02e|GEOS-Chem v11-02e]].'''''</span>
 
Katie Travis created a diagnostic to correct daytime ozone values from the lowest model layer, ~60m, to 10m.
 
''C''(''z<sub>C</sub>'') = (1-''R<sub>a</sub>''(''z<sub>1</sub>'',''z<sub>C</sub>'')''v<sub>d</sub>(''z<sub>1</sub>))''C''(''z<sub>1</sub>'')             Eq. 1
 
where <tt>''R<sub>a</sub>''(''z<sub>1</sub>'',''z<sub>C</sub>'')</tt> is the aerodynamic resistance between <tt>''z<sub>1</sub>''</tt> and <tt>''z<sub>C</sub>''</tt>, and <tt>''v<sub>d</sub>''(''z<sub>1</sub>'')</tt> is the ozone deposition velocity at <tt>''z<sub>1</sub>''</tt>, and <tt>''C''(''z<sub>1</sub>'')</tt> is the ozone concentration at <tt>''z<sub>1</sub>''</tt>.
 
<tt>''R<sub>a</sub>''(''z<sub>1</sub>'',''z<sub>C</sub>'')</tt> is calculated to the lowest model level in drydep_mod.F. We recalculate <tt>''R<sub>a</sub>''</tt> using <tt>''z<sub>1</sub>''</tt> = 10 m, which is the height of the CASTNET measurement for ozone.  The new <tt>''R<sub>a</sub>''</tt> is added to the diagnostic array AD_RA and passed to diag49.F for use in Equation 1.
 
This new diagnostic is called <tt>O3@10m-$</tt>, and can be called with tracer 539 in ND49 in input.geos.
 
'''References'''
*Travis, K.R., D.J. Jacob, C.A. Keller, S. Kuang, J. Lin, M.J. Newchurch, A.M. Thompson, ''Resolving ozone vertical gradients in air quality models'', <u>Atmos. Chem. Phys. Disc.</u>,2017.
*Zhang, L., D.J. Jacob, E.M. Knipping, N. Kumar, J.W. Munger, C.C. Carouge, A. van Donkelaar, Y. Wang, and D. Chen, ''Nitrogen deposition to the United States: distribution, sources, and processes'', <u>Atmos. Chem. Phys.</u>, '''12''', 4,539-4,4554, 2012.
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 22:26, 17 November 2017 (UTC)
 
== Analytical tools ==
 
=== Carbon balance ===
 
[http://www.barronh.com/ Barron Henderson] has created a script for evaluating carbon balance. Please see [[Chemistry_Working_Group#Script_for_evaluating_carbon_balance|this post on the ''Chemistry Working Group'' wiki page]] for more information.
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:31, 22 February 2019 (UTC)
 
=== Process analysis diagnostics ===
 
[http://www.barronh.com/ Barron Henderson] 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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