View source for GEOS-Chem chemistry mechanisms

__FORCETOC__
'''''[[Simulations overview|Previous]] | [[Aerosol-only simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''
#[[Simulations overview]]
#<span style="color:blue">'''Mechanisms for full-chemistry simulations (e.g. Standard, Tropchem, etc.)'''</span>
#[[Aerosol-only simulation]]
#[[CH4 simulation]]
#[[CO2 simulation]]
#[[Mercury|Hg simulation]]
#[[POPs simulation]]
#[[Tagged CO simulation]]
#[[Tagged O3 simulation]]
#[[TransportTracers simulation]]

On this page, we provide an overview of the chemistry mechanisms used in GEOS-Chem.

== Overview ==

The following table provides links to information about the available full-chemistry mechanisms in GEOS-Chem. 
{| 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
*[[GEOS-Chem_benchmarking|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]]

|}

For more information about GEOS-Chem "specialty simulations", please see our ''[[Simulations overview]]'' wiki page.

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:36, 13 August 2019 (UTC)

== Chemistry updates ==

=== Updates to heterogeneous and cloud chemistry ===
 
<span style="color:green">'''''This update was included in [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]], which was released on 18 Oct 2019.'''''</span>

This combines model updates described by Holmes et al. (2019) and McDuffie et al (2018a, b).
 
==== Cloud heterogeneous chemistry ====
These changes are described by Holmes et al. (2019). The effective radius and surface area of ice cloud particles have been updated based on aircraft observations (Heymsfield et al., 2014). Entrainment-limited uptake in clouds, as defined by Holmes et al. (2019), is implemented. This method accounts for cloud fraction and entrainment within the chemical loss rates. Losses of NO3 and N2O5 in clouds are currently included and the method and code can also be applied to other species that react in clouds. The changes in the cloud and ice surface areas had significant impact on the cycling of HCl to ClOx species increasing them in the UT. 
 
==== N2O5 uptake on aerosol ====
N2O5 uptake on sulfate-nitrate-ammonium-organic aerosol is calculated with gamma for combined SNA+ORG aerosol in in which a SNA core is coated with an organic shell (McDuffie et al. 2018b). Parameters in the gamma expression are fitted to aircraft observations. This parameterization generally follows the Bertram and Thornton ACP (2009) functional form for SNA aerosol (excluding chloride enhancement) and treats aerosol organics as a resistive coating. The gamma values of SNA and ORG components are calculated separately and combined  using a resistor model framework: 1/gamma_total = 1/gamma_SNA + 1/gamma_ORG. The ClNO2 yield is currently treated as 1 on sea salt aerosol and 0 on SNA+ORG aerosol. Planned updates to chlorine chemistry will modify the ClNO2 yields in a future model version.
 
The gamma for N2O5 uptake on other aerosols is updated according to IUPAC and JPL recommendations, as documented by Holmes et al. (2019).
 
==== NO2 and NO3 uptake on aerosol ====
Gamma parameters are updated according to IUPAC and JPL recommendations, as documented by Holmes et al. (2019). Notable changes compared to prior model versions include reduction of NO2 and NO3 gammas on all aerosol types,
 
==== Aerosol water content ====
Within the heterogeneous chemistry, we now use the aerosol water content of sulfate-nitrate-ammonium aerosol from the ISORROPIA II aerosol thermodynamics. This water content is then used to infer the volume and surface area of sulfate-nitrate-ammonium for heterogeneous chemistry. The aerosol optics used for FastJ and RRTMG continue to use lookup tables for hygroscopic growth so that the optical properties (phase function, index of refraction) are consistent with the assumptions about aerosol composition and size.
 
==== Heterogeneous chemistry diagnostics ====
Aerosol water content and N2O5 gamma coefficients are now saved as StateChem variables for diagnostic output through HISTORY.rc
 
==== References ====
#Heymsfield, A., Winker, D., Avery, M., Vaughan, M., Diskin, G., Deng, M., et al., ''Relationships between ice water content and volume extinction coefficient from in situ observations for temperatures from 0° to –86 °C: Implications for spaceborne lidar retrievals'', <u>Journal of Applied Meteorology and Climatology</u>, 53(2), 479–505. https://doi.org/10.1175/JAMC‐D‐13‐087.1, 2014.
#Holmes, C. D., Bertram, T. H., Confer, K. L., Graham, K. A., Ronan, A. C., Wirks, C. K., & Shah, V., ''The role of clouds in the tropospheric NOx cycle: A new modeling approach for cloud chemistry and its global implications'', <u>Geophysical Research Letters</u>, 46(9), 4980–4990. https://doi.org/10.1029/2019GL081990, 2019.
#McDuffie, E. E., Fibiger, D. L., Dubé, W. P., Lopez-Hilfiker, F., Lee, B. H., Jaeglé, L., et al., ''ClNO2 yields from aircraft measurements during the 2015 WINTER campaign and critical evaluation of the current parameterization'', <u>Journal of Geophysical Research</u>, 123(22), 12,994–13,015. https://doi.org/10.1029/2018JD029358, 2018a.
#McDuffie, E. E., Fibiger, D. L., Dubé, W. P., Lopez-Hilfiker, F., Lee, B. H., Thornton, J. A., et al., ''Heterogeneous N2O5 Uptake During Winter: Aircraft Measurements During the 2015 WINTER Campaign and Critical Evaluation of Current Parameterizations'', <u>Journal of Geophysical Research</u>, 123(8), 4345–4372. https://doi.org/10.1002/2018JD028336, 2018b.

=== Aerosol nitrate photolysis option ===

<span style="color:darkorange">'''''This update (Git ID: [https://github.com/geoschem/geos-chem/commit/407dcd6d550f1540856b3876ab0d48af6f2dcbb8 407dcd6d]) will be included in [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]].'''''</span>

'''''Tomas Sherwen wrote:'''''

:This update allows for optional photolysis of aerosol nitrate (NIT(s)) yielding HNO2+NO2. '''This set to off as default.''' The photolysis rate is scaled the photolysis rates of HNO3 (JHNO3) as described by Kasibhatla et al (2018). The photolysis rate and product split is set in the input.geos file with the lines as below:
    
    Photolyse nitrate aer.? : F
     => NIT Jscale (JHNO3)  : 0.0
     => NITs Jscale (JHNO3) : 0.0
     => % channel A (HONO)  : 66.667
     => % channel B (NO2)   : 33.333
    
:As the code is off by default no notable changes are expected in the model's output. To reproduce the results of Kasibhatla et al 2018, updates to nitrate partitioning (e.g. from Xuan Wang's chlorine updates) and updates to the heterogeneous uptake and hydrolysis of NO2 need to be included as well. 

'''Reference:'''
*Kasibhatla, P., Sherwen, T., Evans, M. J., Carpenter, L. J., Alexander, B., Chen, Q., Sulprizio, M. P., Lee, J. D., Read, K. A., Bloss, W., Crilley, L. R., Keene, W. C., Pszenny, A. A. P., and Hodzic, A.: ''Global impact of nitrate photolysis in sea-salt aerosol on NOx, OH, and O4 in the marine boundary layer'', <u>Atmos. Chem. Phys.</u>, '''18''', 11185-11203, https://doi.org/10.5194/acp-18-11185-2018, 2018.
    
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 16:52, 27 June 2019 (UTC)

=== 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 (Git ID: [https://github.com/geoschem/geos-chem/commit/7891271b5047f3a4fc4735926ee0815201884045 7891271b]) is slated for inclusion in [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]].'''''</span>

Katie Travis created a diagnostic to correct daytime ozone and HNO3 values from the lowest model layer, ~60m, to a user-defined altitude such as 10m (which corresponds to the height of certain observational instruments at surface stations).  This altitude can be selected in the [[GEOS-Chem input files#Deposition Menu|DEPOSITION MENU of the <tt>input.geos</tt> file]].

 ''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 <tt>GeosCore/drydep_mod.F</tt>. We recalculate <tt>''R<sub>a</sub>''</tt> using <tt>''z<sub>1</sub>''</tt> = user defined height (such as 10m) 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 has been implemented in as [[History_collections_for_dry_deposition#The_ConcAboveSfc_collection|the ConcAboveSfc collection]] of the [[Guide to GEOS-Chem History diagnostics|GEOS-Chem History diagnostics]].

Here is a sample plot of O3 at the midpoint of the 1st model level (~60m) and O3 at 10m at Centerville, AL (32.94N, 87.18W), as generated with this diagnostic:

[[Image:O3_10m.png]]

'''References'''
#Travis, K.R., and D.J. Jacob,Systematic bias in evaluating chemical transport models with maximum daily 8-hour average (MDA8) surface ozone for air quality applications, Geophys. Model Dev. Discuss., https://doi.org/10.5194/gmd-2019-78, in review, 2019.
#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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