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"|Category
!width="175px"|Simulation(s)
!wigth="350px"|Mechanism file
!width="225px"|Contact
 
|-valign="top"
|Full-chemistry<br>([[Tropospheric_chemistry_mechanism#Recent_chemistry_updates|troposphere]] + [[UCX_chemistry_mechanism|stratosphere]])
|
*Standard
*Benchmark<sup>1</sup>
|[https://github.com/geoschem/geos-chem/blob/master/KPP/Standard/Standard.eqn <tt>KPP/Standard/Standard.eqn</tt>]
|[[Chemistry Working Group]]
 
|-valign="top"
|Full-chemistry<br>([[Tropospheric_chemistry_mechanism#Recent_chemistry_updates|troposphere]] only)
|
*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]]
|[https://github.com/geoschem/geos-chem/blob/master/KPP/Tropchem/Tropchem.eqn <tt>KPP/Tropchem/Tropchem.eqn</tt>]
|[[Chemistry Working Group]]
 
|-valign="top"
|Full-chemistry<br>([[Tropospheric_chemistry_mechanism#Recent_chemistry_updates|troposphere]] only + [[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|semivolatile POA]])
|
*[[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|complexSOA_SVPOA]]
|[https://github.com/geoschem/geos-chem/blob/master/KPP/SOA_SVPOA/SOA_SVPOA.eqn <tt>KPP/SOA_SVPOA/SOA_SVPOA.eqn</tt>]
|[[Aerosols Working Group]]
 
|-valign="top"
|Carbon Gases
|
*[[CH4 simulation|CH4]]
*[[CH4 simulation|tagCH4]]
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/global_ch4_mod.F <tt>GeosCore/global_ch4_mod.F</tt>]
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Carbon Gases
|
*[[Tagged CO simulation|tagCO]]
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/tagged_co_mod.F <tt>GeosCore/tagged_co_mod.F</tt>]
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Carbon Gases
|
*[[CO2 simulation|CO2]]
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/co2_mod.F <tt>GeosCore/co2_mod.F</tt>]
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Mercury
|
*[[Mercury|Hg]]
*[[Mercury|tagHg]]
*[[Mercury|Hg]]+[[Global Terrestrial Mercury Model|GTMM]]
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/mercury_mod.F <tt>GeosCore/mercury_mod.F</tt>]
|[[Hg and POPs Working Group]]
 
|-valign="top"
|Persistent Organic Pollutants
|
*[[POPs_simulation|POPs]]
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/pops_mod.F <tt>GeosCore/pops_mod.F</tt>]
|[[Hg and POPs Working Group]]
 
|-valign="top"
|Ozone
|
*[[Tagged O3 simulation|tagO3]]
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/tagged_o3_mod.F <tt>GeosCore/tagged_o3_mod.F</tt>]
|[[Chemistry Working Group]]
 
|-valign="top"
|Radionuclides
|
*[[Rn-Pb-Be simulation|Rn-Pb-Be]]<br>[[Transport_Working_Group#Transport_Tracers_simulation|TransportTracers]]
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/RnPbBe_mod.F <tt>GeosCore/RnPbBe_mod.F</tt>]
|[[Transport Working Group]]
 
|-
!colspan="5" bgcolor="#CCCCCC"|<span style="color:red">'''The following mechanisms are obsolete and have been removed:'''</span>
 
|-valign="top"
|Carbon Gases
|
*C2H6
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/c2h6_mod.F <tt>GeosCore/c2h6_mod.F</tt>]
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Carbon Gases
|
*CH3I
|<tt>GeosCore/ch3i_mod.F</tt><br>in [[GEOS-Chem v9-02]] and earlier
|[[Carbon Cycle Working Group]]
 
|-valign="top"
|Radionuclides
|
*H2-HD
|<tt>GeosCore/h2_h2_mod.F</tt><br>in [[GEOS-Chem v9-02]] and earlier
|[[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 ==
 
=== 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)
 
== Previous issues that have now been resolved ==
 
=== Centralizing chemistry time step===
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02q|v9-01-02q]] and approved on 18 Oct 2011.'''''</span>
 
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.
 
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)
 
=== Acetone photolysis ===
 
[[FAST-J_photolysis_mechanism#v9-02_post-release_patch_to_fix_bug_in_acetone_photolysis_pressure_dependency|This discussion has been moved to our ''FAST-J photolysis mechanism'' wiki page]].
 
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)
 
== Issues that have been since rendered obsolete by newer code updates ==
 
Most of the issues described below pertained to the SMVGEAR chemical solver (which was replaced by FlexChem in [[GEOS-Chem v11-01|v11-01]]) and/or the FAST-J photolysis mechanism (which was replaced by FAST-JX in [[GEOS-Chem v10-01|v10-01]]).
 
=== NIT should be converted to molec/cm3 in calcrate.F ===
 
[[Image:Obsolete.jpg]]
 
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The code in <tt>calcrate.F</tt> will be replaced by the KPP master equation file.'''''</span>
 
In <tt>calcrate.F</tt>, we have:
 
                    ! Nitrate effect; reduce the gamma on nitrate by a
                    ! factor of 10 (lzh, 10/25/2011)
                    IF ( N == 8 ) THEN
                        TMP1 = State_Chm%Tracers(IX,IY,IZ,IDTSO4) +
    &                        State_Chm%Tracers(IX,IY,IZ,IDTNIT)
                        TMP2 = State_Chm%tracers(IX,IY,IZ,IDTNIT)
                        IF ( TMP1 .GT. 0.0 ) THEN
                          XSTKCF = XSTKCF * ( 1.0e+0_fp - 0.9e+0_fp
    &                            *TMP2/TMP1 )
                        ENDIF
                    ENDIF
 
Here NIT is added to SO4 but NIT is in different units than SO4. This unit difference can be traced to the definition of IDTRMB, which is only nonzero for species that are in the SMVGEAR mechanism. Since NIT is not a SMVGEAR species, IDTRMB = 0 for NIT and it is therefore skipped in the unit conversion from kg --> molec/cm3 in <tt>partition.F</tt>.
 
This issue was discovered during the implementation of [[FlexChem]]. In [[GEOS-Chem v11-01#v11-01g|GEOS-Chem v11-01g]] and later versions, units of NIT are properly accounted for in routine <tt>HETN2O5</tt> (found in <tt>gckpp_HetRates.F90</tt>).
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 20:25, 12 September 2016 (UTC)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:27, 31 January 2017 (UTC)
 
=== rate of HNO4 ===
 
[[Image:Obsolete.jpg]]
 
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The <tt>globchem.dat</tt> file is now replaced by the KPP master equation file.'''''</span>
 
[mailto:ecbrow@berkeley.edu Ellie Browne] found a typo in the globchem.dat ([[GEOS-Chem v8-02-01]] and beyond)
<pre>
A  73 9.52E-05  3.2E+00 -10900 1 P  0.60    0.    0.       
      1.38E+15  1.4E+00 -10900 0    0.00    0.    0.       
      HNO4          +                        M                               
=1.000HO2          +1.000NO2          +                  +
</pre>
This should be corrected as:
<pre>
A  73 9.52E-05  3.4E+00 -10900 1 P  0.60    0.    0.       
      1.38E+15  1.1E+00 -10900 0    0.00    0.    0.       
      HNO4          +                        M                               
=1.000HO2          +1.000NO2          +                  +
</pre>
The difference is within 2%.
 
--[[User:Jmao|J Mao.]] 19:04, 30 Aug 2010 (EDT)<br>
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:29, 31 January 2017 (UTC)
 
=== near-IR photolysis of HNO4 ===
 
<span style="color:green">'''''This update was added to [[GEOS-Chem v8-02-04]].'''''</span>
 
[[Image:Obsolete.jpg]]
 
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The <tt>globchem.dat</tt> file is now replaced by the KPP master equation file.  Also, FAST-JX has now replaced FAST-J photolysis.'''''</span>
 
1. Since FastJX already takes this into account with cross section data at 574nm, we do not need to redo this in <tt>calcrate.f</tt>.  We can therefore comment out this entire IF block:
        !---------------------------------------------------------------------
        ! Prior to 10/27/09:
        ! FastJX has taken near-IR photolysis into account with
        ! cross section at 574nm, so we don't need to add 1e-5 anymore.
        ! According to Jimenez et al., "Quantum yields of OH, HO2 and
        ! NO3 in the UV photolysis of HO2NO2", PCCP, 2005, we also
        ! changed the branch ratio from 0.67(HO2)/0.33(OH) to 0.95/0.05
        ! This will put most weight of near-IR photolysis on HO2 channel.
        ! (jmao, bmy, 10/27/09)
        !
        !!==============================================================
        !! HARDWIRE addition of 1e-5 s-1 photolysis rate to
        !! HNO4 -> HO2+NO2 to account for HNO4 photolysis in near-IR --
        !! see Roehl et al. 'Photodissociation of peroxynitric acid in
        !! the near-IR', 2002. (amf, bmy, 1/7/02)
        !!
        !! Add NCS index to NKHNO4 for SMVGEAR II (gcc, bmy, 4/1/03)
        !!==============================================================
        !IF ( NKHNO4(NCS) > 0 ) THEN
        !
        !  ! Put J(HNO4) in correct spot for SMVGEAR II
        !  PHOTVAL = NKHNO4(NCS) - NRATES(NCS)
        !  NKN    = NKNPHOTRT(PHOTVAL,NCS)
        !
        !  DO KLOOP=1,KTLOOP
        !      RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) + 1d-5
        !  ENDDO
        !ENDIF
        !---------------------------------------------------------------------
 
 
2. We need to change the branch ratio of HNO4 photolysis in <tt>ratj.d</tt>.  Change these lines from:
 
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00    33.3  HO2NO2
14 HNO4      PHOTON    HO2        NO2                  0.00E+00  0.00    66.7  HO2NO2
 
to:
 
13 HNO4      PHOTON    OH        NO3                  0.00E+00  0.00      5.0  HO2NO2
14 HNO4      PHOTON    HO2        NO2                  0.00E+00  0.00    95.0  HO2NO2
 
This is based on Jimenez et al. (Quantum yields of OH, HO2 and NO3 in the UV photolysis of HO2NO2, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2005) shows that HO2 yield should be 0.95 and OH yield should be 0.05 for wavelength above 290nm.
 
This way all the near-IR photolysis will have most weight on HO2 channel(Stark et al., Overtone dissociation of peroxynitric acid (HO2NO2): Absorption cross sections and photolysis products, JOURNAL OF PHYSICAL CHEMISTRY A, 2008).
 
This update has now been added to the [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf chemistry mechanism documentation file].
 
--[[User:Jmao|J Mao.]] 11:00, 26 Oct 2009 (EDT)<br>
--[[User:Bmy|Bob Y.]] 16:08, 4 November 2011 (EDT)
 
=== yield of isoprene nitrates ===
 
<span style="color:green">'''''This update was added to [[GEOS-Chem v8-03-02]] as a post-release patch, and standardized in [[GEOS-Chem v9-01-01]].'''''</span>
 
[[Image:Obsolete.jpg]]
 
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The <tt>globchem.dat</tt> file is now replaced by the KPP master equation file.'''''</span>
 
[mailto:paulot@caltech.edu Fabien Paulot] found a problem in current chemistry scheme.  In [[GEOS-Chem v8-02-01]] and beyond, isoprene nitrates are produced twice: one through channel A and one through 10% loss in channel B. This makes the loss of NOx larger than it should be (18.7% vs. 10%) and also reduces the yield of MVK/MACR/CH2O by about 13%.
 
A  453 2.70E-12  0.0E+00    350 1 B  0.00    0.    0.       
        5.00E+00  0.0E+00      0 0    0.00    0.    0.       
      RIO2          +    NO                                             
=0.900NO2          +0.900HO2          +0.340IALD          +0.340MVK   
+0.220MACR          +0.560CH2O          +                  + 
         
A  453 2.70E-12  0.0E+00    350 1 A  0.00    0.    0.       
        5.00E+00  0.0E+00      0 0    0.00    0.    0.       
      RIO2          +    NO                                             
=1.000HNO3          +                  +                  +           
 
So it should be corrected as (no channel A):
 
A  453 2.70E-12  0.0E+00    350 0 0  0.00    0.    0.       
      RIO2          +    NO                                             
=0.900NO2          +0.900HO2          +0.340IALD          +0.340MVK   
+0.220MACR          +0.560CH2O          +                  +     
D  453 2.70E-12  0.0E+00    350 1 A  0.00    0.    0.       
        5.00E+00  0.0E+00      0 0    0.00    0.    0.       
      RIO2          +    NO                                             
=1.000HNO3          +                  +                  + 
 
--[[User:Jmao|J Mao.]] 18:04, 30 Aug 2010 (EDT)<br>
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:31, 31 January 2017 (UTC)
 
=== Potential issue with reading restart.cspec file ===
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-02_benchmark_history#v9-01-02c|v9-01-02c]] and approved on 21 Jul 2011.'''''</span>
 
[[Image:Obsolete.jpg]]
 
<span style="color:red">'''''The binary-punch format <tt>restart.cspec.YYYYMMDDhh</tt> file is slated to be replaced by a netCDF-format restart file, starting in [[GEOS-Chem v11-01]] and higher versions.  But during a transition period, you can still request binary-punch format output.'''''</span>
 
Jingqiu Mao discovered a mis-indexing problem when using the <tt>restart.cspec.YYYYMMDDhh</tt> file.  Please see [[Restart files#Potential issue with reading restart.cspec_file|this wiki post]] for more information.
 
--[[User:Bmy|Bob Y.]] 16:02, 4 November 2011 (EDT)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:33, 31 January 2017 (UTC)
 
=== GLCO3, GLPAN bug in standard mechanism ===
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03a|v9-01-03a]] and approved on 08 Dec 2011.'''''</span>
 
[[Image:Obsolete.jpg]]
 
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The <tt>globchem.dat</tt> file is now replaced by the KPP master equation file.'''''</span>
 
'''''[mailto:fabienpaulot@gmail.com Fabien Paulot] wrote:'''''
 
:I think there is a relatively serious bug in the standard chemistry.  GLPAN and GLCO3 are set to inactive but their production and loss reactions are active.  As a result they never reach equilibrium and this results in an artificial loss of NOx.
 
:If this is the only cause of the imbalance between sources and sinks of NOx in my simulations, this would account for ~5% of NOy losses.  I don't see that problem in a simulation with a different chemistry that among other changes does not feature those reactions. So hopefully that's it.
 
:To fix the error, I made the following modifications in <tt>globchem.dat</tt>:
 
:#I set GLPAN and GLCO3 rxns from active to dead.  These rxns were causing an artificial loss of NOx.
:#I have physically removed GLCO3, GLP, GLPAN, GPAN, ISNO3, MNO3, O2CH2OH, MVN2 and their associated reactions. 
:#I have made GLYX active.  I'm not sure why it's not active by default.
 
:and to <tt>ratj.d</tt>:
 
:# I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in <tt>globchem.dat</tt>
 
--[[User:Bmy|Bob Y.]] 14:51, 10 November 2011 (EST)<br>
--[[User:Melissa Payer|Melissa Payer]] 10:49, 15 December 2011 (EST)<br>
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:35, 31 January 2017 (UTC)
 
=== Bug in routine ARSL1K ===
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem v9-01-03 benchmark history#v9-01-03m|v9-01-03m]] and approved on 06 Jun 2012.'''''</span>
 
[[Image:Obsolete.jpg]]
 
<span style="color:red">'''''SMVGEAR was removed from [[GEOS-Chem v11-01]] and higher versions.  The <tt>ARSL1K</tt> routine was replaced by an equivalent function in KPP's rate law library.'''''</span>
 
A bug in routine ARSL1K became problematic in the implementation of Justin Parrella's [[Bromine_chemistry_mechanism|tropospheric bromine chemistry mechanism]] for [[GEOS-Chem v9-01-03]]. In the bromine chemistry mechanism, a sticking coefficient of 0.0 is passed to the routine ARSL1K for non-sulfate, non-sea salt aerosol. The IF statement modified in [[GEOS-Chem_v8-02-04#Div-by-zero_error_encountered_in_arsl1k.f|GEOS-Chem v8-02-04]] resulted in the reaction rate being set to the default value of 1.0d-3. A 1-month benchmark for July 2005 indicated that the simulated BrO was a little more than twice the expected zonal mean. Modifying the default value from 1.0d-3 to 1.0d-30 resulted in reasonable simulated BrO values.
 
'''''[mailto:mat.evans@york.ac.uk Mat Evans] wrote:'''''
 
:I've re-run two 2 month simulation [using [[GEOS-Chem v9-01-02]]]. One with the error handling value of 1e-3 (standard) and one with it being 1e-30. There are 5127 time and space points where the model traps the problem and invokes the 1e-3 or 1e-30 value. There are 30*24*2*37*72*46 (roughly 200 million) time and space points when the error could have occurred so we are looking at a relatively infrequent event. 
 
:The simulations show virtually no difference between the two simulations.
 
:mean and stddev ratio of all grid boxes with and without the fix are shown below
    NOx    0.999996  0.000409291
    Ox      1.00000  1.27233e-05
    O3      1.00000  1.52284e-05
    PAN    0.997849  0.0111997
    CO      1.00000  4.21768e-06
    ALK4    0.990514  0.0351941
    ISOP    0.999979  0.0108033
    H2O2    0.992067  0.0264659
    DST1    1.00000  0.00000
    HO2    0.999996  0.00309464
    OH      1.00003  0.00767954
 
:So although there are some differences they are very minor. For completeness we should put this in as a bug fix (make the error value 1d-30 rather than 1d-3). But it is not a major problem.
 
--[[User:Melissa Payer|Melissa Payer]] 17:52, 14 May 2012 (EDT)<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:35, 31 January 2017 (UTC)

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