GEOS-Chem chemistry mechanisms: Difference between revisions

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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 16:26, 7 September 2017 (UTC)
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 16:26, 7 September 2017 (UTC)


== Planned updates ==
=== 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)


== Mechanisms for aerosol microphysics ==
== Mechanisms for aerosol microphysics ==

Revision as of 18:32, 21 March 2018

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 v11-02 and later versions

Several modifications were made to the chemistry mechanisms in v11-02, as listed below:

Mechanism Description Vertical grid Solvers Notes
standard From the surface to the stratopause:

From the stratopause to the top of the atmosphere:

benchmark Same as Standard, but turns includes both the simple SOA and complex SOA species.
tropchem From the surface to the tropopause:

From the tropopause to the top of the atmosphere:

Complex SOA From the surface to the tropopause:

From the tropopause to the top of the atmosphere:

Updated isoprene and monoterpene chemistry

This update was included in v11-02c and approved on 21 Sep 2017.

Developers:

  • Katie Travis (MIT, formerly Harvard)
  • Jenny Fisher (U. Wollongong)
  • Christopher Chan Miller (Smithsonian Astrophysical Observatory, formerly Harvard)
  • Eloise Marais (U. Birminghan, formerly Harvard)

This document compiled by Katie Travis and Josh Cox describes the updated isoprene and monoterpene chemistry to be included in GEOS-Chem v11-02c (also see the list of modifications below). These updates include the monoterpene nitrate scheme and aqueous isoprene uptake and were originally implemented for simulation of the 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. 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. 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. 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. PDF, Supplement

--Melissa Sulprizio (talk) 18:06, 12 July 2017 (UTC)

Modifications to the original updates

The following modifications were made to the original updates listed in the above document following conversations with the developers. These modifications were included in 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 existing SOA scheme)
  • APIO2 is now PIO2 (for consistency with PAN updates added in v11-02a)
  • LIM is now LIMO (for consistency with existing SOA scheme)
  • PMN is now NPMN and IPMN (PMN from non-isoprene and isoprene sources; from 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
            Rate = 2.00e-13
   v11-02c: ISNOHOO + MO2 = 0.660PROPNN + 0.700GLYX + 1.200HO2 + 0.750CH2O + 0.250MOH + 0.040ISN1OG
            Rate = 2.06e-13

   Orig:    ISOPNB + OH = ISOPNBO2 + 0.100IEPOX + 0.100NO2 
   v11-02c: ISOPNB + OH = 0.900ISOPNBO2 + 0.100IEPOX + 0.100NO2

   Orig:    HONIT + OH = NO3 + HKET
   v11-02c: HONIT + OH = NO3 + HAC

   Orig:    HONIT + hv = HKET + NO2
   v11-02c: HONIT + hv = HAC + NO2

(5) Completely replace RIP with RIPA, RIPB, RIPD and IEPOX with IEPOXA, IEPOXB, IEPOXD 

   Orig:    RIP  + hv = 0.985OH + 0.985HO2 + 0.710CH2O + 0.425MVK + 0.285MACR + 0.275HC5 + 0.005LVOC
   v11-02c: 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

   Orig:    ISOPND + OH = 0.100IEPOX + 0.900ISOPNDO2 +0.100NO2
   v11-02c: ISOPND + OH = 0.100IEPOXD + 0.900ISOPNDO2 +0.100NO2

   Orig:    ISOPNB + OH = 0.900ISOPNBO2 + 0.100IEPOX + 0.100NO2
   v11-02c: ISOPNB + OH = 0.900ISOPNBO2 + 0.067IEPOXA + 0.033IEPOXB + 0.100NO2

   Orig:    IEPOX  = SOAIE : HET(ind_IEPOX,1);
   v11-02c: IEPOXA = SOAIE : HET(ind_IEPOXA,1);
            IEPOXB = SOAIE : HET(ind_IEPOXB,1);
            IEPOXD = SOAIE : HET(ind_IEPOXD,1);

(6) Add LVOC to RIP channels 

   Orig:    RIPA + OH = 0.750 RIO2 + 0.250 HC5 + 0.125 (OH + H2O)
   v11-02c: RIPA + OH = 0.750 RIO2 + 0.245 HC5 + 0.125 (OH + H2O) + 0.005 LVOC
   
   Orig:    RIPA + OH = 0.850 OH + 0.578 IEPOXA + 0.272 IEPOXB + 0.150 HC5OO
   v11-02c: RIPA + OH = 0.850 OH + 0.578 IEPOXA + 0.272 IEPOXB + 0.145 HC5OO + 0.005 LVOC
   
   Orig:    RIPB + OH = 0.480 RIO2 + 0.520 HC5 + 0.26 (OH + H2O)
   v11-02c: RIPB + OH = 0.480 RIO2 + 0.515 HC5 + 0.26 (OH + H2O) + 0.005 LVOC
   
   Orig:    RIPD + OH = 0.250 RIO2 + 0.750 HC5 + 0.375 (OH + H2O)
   v11-02c: RIPD + OH = 0.250 RIO2 + 0.745 HC5 + 0.375 (OH + H2O) + 0.005 LVOC
   
   Orig:    RIPD + OH = 0.500 OH + 0.500 IEPOXD + 0.500 HC5OO
   v11-02c: RIPD + OH = 0.500 OH + 0.500 IEPOXD + 0.495 HC5OO + 0.005 LVOC
   
   The only reaction that wont have LVOC as a product is RIPB + OH = OH + IEPOXA + IEPOXB.

--Melissa Sulprizio (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 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)

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)

Obsolete mechanisms

Obsolete.jpg


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 and is obsolete in v11-01 and later
tropchem From the surface to the tropopause:

From the tropopause to the top of the atmosphere:

  • KPP
  • SMVGEAR (obsolete in v11-01 and later)
UCX From the surface to the stratopause:

From the stratopause to the top of the atmosphere:

  • KPP
  • SMVGEAR is not recommended and is obsolete in v11-01 and later
SOA From the surface to the tropopause:

From the tropopause to the top of the atmosphere:

  • 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 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)

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