Difference between revisions of "GEOS-Chem chemistry mechanisms"

From Geos-chem
Jump to: navigation, search
(Overview)
(Overview)
(47 intermediate revisions by 4 users not shown)
Line 1: Line 1:
On this page, we provide an overview of the chemistry mechanisms used in GEOS-Chem.
+
__FORCETOC__
 +
'''''[[Guide to GEOS-Chem simulations|Previous]] | [[Aerosol-only simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''
 +
#<span style="color:blue">'''Simulations using KPP-built mechanisms'''</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 information about GEOS-Chem simulations that use chemistry mechanism solver code built by the [https://kpp.readthedocs.io Kinetic PreProcessor (KPP)].
  
 
== Overview ==
 
== 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.
+
The following table provides links to information about the available full-chemistry mechanisms in GEOS-Chem.  
 
+
 
{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="250x"|Category
+
!width="100px"|Mechanism
!width="175px"|Simulation(s)
+
!width="300px"|Description
!wigth="350px"|Mechanism file
+
!width="250px"|Mechanism file
!width="225px"|Contact
+
!width="175px"|Extra options
  
 
|-valign="top"
 
|-valign="top"
|Full-chemistry<br>([[Tropospheric_chemistry_mechanisms|troposphere]] + [[UCX_chemistry_mechanism|stratosphere]])
+
|fullchem
 +
|NOx + Ox + Br + Cl + I + aerosols chemistry in the [[Tropospheric_chemistry_mechanism|troposphere]] and [[UCX_chemistry_mechanism|stratosphere]]
 +
|[https://github.com/geoschem/geos-chem/blob/main/KPP/fullchem/fullchem.eqn <tt>KPP/fullchem/fullchem.eqn</tt>]
 
|
 
|
*Standard
+
*[[GEOS-Chem_benchmarking|benchmark]]
*Benchmark<sup>1</sup>
+
*[[Secondary_organic_aerosols#Simple_SOA_scheme|simple SOA]]
|[https://github.com/geoschem/geos-chem/blob/master/KPP/Standard/Standard.eqn <tt>KPP/Standard/Standard.eqn</tt>]
+
*[[Secondary_organic_aerosols#Complex_SOA_scheme|complex SOA]]
|[[Chemistry Working Group]]
+
*[[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|complex SOA + SVPOA]]
 
+
|-valign="top"
+
|Full-chemistry<br>([[Tropospheric_chemistry_mechanism|troposphere]] only)
+
|
+
*Tropchem
+
*[[Secondary_organic_aerosols#Simple_SOA_scheme|SOA]]
+
*[[Secondary_organic_aerosols#Complex_SOA_scheme|complexSOA]]
+
 
*[[#TOMAS|TOMAS]]
 
*[[#TOMAS|TOMAS]]
 
*[[#APM|APM]]
 
*[[#APM|APM]]
 
*[[Coupling_GEOS-Chem_with_RRTMG|RRTMG]]
 
*[[Coupling_GEOS-Chem_with_RRTMG|RRTMG]]
|[https://github.com/geoschem/geos-chem/blob/master/KPP/Tropchem/Tropchem.eqn <tt>KPP/Tropchem/Tropchem.eqn</tt>]
+
*Aciduptake
|[[Chemistry Working Group]]
+
*Marine POA
  
 
|-valign="top"
 
|-valign="top"
|Full-chemistry<br>([[Tropospheric_chemistry_mechanism|troposphere]] only + [[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|semivolatile POA]])
+
|Hg
 +
|[[Mercury|Mercury chemistry]]
 +
*Introduced in [[GEOS-Chem 13.4.0|13.4.0]] as a KPP mechanism
 +
|[https://github.com/geoschem/geos-chem/blob/main/KPP/fullchem/fullchem.eqn <tt>KPP/Hg/Hg.eqn</tt>]
 
|
 
|
*[[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"
 
|-valign="top"
|Carbon Gases
+
|carboncycle
 +
|[https://github.com/geoschem/geos-chem/blob/main/KPP/carboncycle/carboncycle.eqn <tt>KPP/carboncycle/carboncycle.eqn</tt>]
 +
*Will debut in [[GEOS-Chem 14.1.0|14.1.0]] as a KPP mechanism
 
|
 
|
*[[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"
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:22, 20 September 2022 (UTC)
|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"
+
== Updates to the fullchem mechanism ==
|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"
+
=== Updates to heterogeneous and cloud chemistry ===
|Ozone
+
|
+
<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>
*[[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"
+
This combines model updates described by Holmes et al. (2019) and McDuffie et al (2018a, b).
|Radionuclides
+
|
+
==== Cloud heterogeneous chemistry ====
*[[Rn-Pb-Be simulation|Rn-Pb-Be]]<br>[[Transport_Working_Group#Transport_Tracers_simulation|TransportTracers]]
+
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.
|[https://github.com/geoschem/geos-chem/blob/master/GeosCore/RnPbBe_mod.F <tt>GeosCore/RnPbBe_mod.F</tt>]
+
|[[Transport Working Group]]
+
==== 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 ===
!colspan="5" bgcolor="#CCCCCC"|<span style="color:red">'''The following mechanisms are obsolete and have been removed:'''</span>
+
  
|-valign="top"
+
<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>
|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"
+
'''''Tomas Sherwen wrote:'''''
|Carbon Gases
+
|
+
*CH3I
+
|<tt>GeosCore/ch3i_mod.F</tt><br>in [[GEOS-Chem v9-02]] and earlier
+
|[[Carbon Cycle Working Group]]
+
  
|-valign="top"
+
: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:
|Radionuclides
+
   
|
+
    Photolyse nitrate aer.? : F
*H2-HD
+
    => NIT Jscale (JHNO3)  : 0.0
|<tt>GeosCore/h2_h2_mod.F</tt><br>in [[GEOS-Chem v9-02]] and earlier
+
    => NITs Jscale (JHNO3) : 0.0
|[[Transport Working Group]]
+
    => % 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.
<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]]) 16:52, 27 June 2019 (UTC)
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 17:02, 22 February 2019 (UTC)
+
 
+
== Chemistry updates ==
+
  
 
=== Updated isoprene and monoterpene chemistry ===
 
=== Updated isoprene and monoterpene chemistry ===
Line 230: Line 215:
 
=== Correcting ozone from the height of the lowest model level to 10m ===
 
=== 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>
+
<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>
  
Katie Travis created a diagnostic to correct daytime ozone values from the lowest model layer, ~60m, to 10m.
+
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
 
  ''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
Line 238: Line 223:
 
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>.
 
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.  
+
<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 is called <tt>O3@10m-$</tt>, and can be called with tracer 539 in ND49 in input.geos.
+
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'''
 
'''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.  
+
#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.
+
#Lapina, K., D. K. Henze, J. B. Milford and K. Travis (2016), Impacts of foreign, domestic and state-level emissions on ozone-induced vegetation loss in the U.S., Environ. Sci. Technol., 50 (2), 806-813, doi:10.1021/acs.est.5b04887.
 +
#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)
 
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 22:26, 17 November 2017 (UTC)
  
 
== Analytical tools ==
 
== 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 ===
 
=== 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:
+
[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>  
 
<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>  
Line 266: Line 262:
 
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 16:46, 26 October 2015 (UTC)
 
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 16:46, 26 October 2015 (UTC)
  
== Previous issues that have now been resolved ==
+
----
 
+
'''''[[Guide to GEOS-Chem simulations|Previous]] | [[Aerosol-only simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''
=== 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)
+

Revision as of 20:51, 20 September 2022

Previous | Next | Guide to GEOS-Chem simulations

  1. Simulations using KPP-built mechanisms
  2. Aerosol-only simulation
  3. CH4 simulation
  4. CO2 simulation
  5. Hg simulation
  6. POPs simulation
  7. Tagged CO simulation
  8. Tagged O3 simulation
  9. TransportTracers simulation

On this page, we provide information about GEOS-Chem simulations that use chemistry mechanism solver code built by the Kinetic PreProcessor (KPP).

Overview

The following table provides links to information about the available full-chemistry mechanisms in GEOS-Chem.

Mechanism Description Mechanism file Extra options
fullchem NOx + Ox + Br + Cl + I + aerosols chemistry in the troposphere and stratosphere KPP/fullchem/fullchem.eqn
Hg Mercury chemistry
  • Introduced in 13.4.0 as a KPP mechanism
KPP/Hg/Hg.eqn
carboncycle KPP/carboncycle/carboncycle.eqn
  • Will debut in 14.1.0 as a KPP mechanism

--Bob Yantosca (talk) 14:22, 20 September 2022 (UTC)

Updates to the fullchem mechanism

Updates to heterogeneous and cloud chemistry

This update was included in GEOS-Chem 12.6.0, which was released on 18 Oct 2019.

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

  1. 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, Journal of Applied Meteorology and Climatology, 53(2), 479–505. https://doi.org/10.1175/JAMC‐D‐13‐087.1, 2014.
  2. 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, Geophysical Research Letters, 46(9), 4980–4990. https://doi.org/10.1029/2019GL081990, 2019.
  3. 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, Journal of Geophysical Research, 123(22), 12,994–13,015. https://doi.org/10.1029/2018JD029358, 2018a.
  4. 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, Journal of Geophysical Research, 123(8), 4345–4372. https://doi.org/10.1002/2018JD028336, 2018b.

Aerosol nitrate photolysis option

This update was included in GEOS-Chem 12.6.0, which was released on 18 Oct 2019.

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, Atmos. Chem. Phys., 18, 11185-11203, https://doi.org/10.5194/acp-18-11185-2018, 2018.

--Melissa Sulprizio (talk) 16:52, 27 June 2019 (UTC)

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)

Correcting ozone from the height of the lowest model level to 10m

This update was included in GEOS-Chem 12.6.0, which was released on 18 Oct 2019.

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 DEPOSITION MENU of the input.geos file.

C(zC) = (1-Ra(z1,zC)vd(z1))C(z1)	            Eq. 1

where Ra(z1,zC) is the aerodynamic resistance between z1 and zC, and vd(z1) is the ozone deposition velocity at z1, and C(z1) is the ozone concentration at z1.

Ra(z1,zC) is calculated to the lowest model level in GeosCore/drydep_mod.F. We recalculate Ra using z1 = user defined height (such as 10m) for ozone. The new Ra 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 the ConcAboveSfc collection of the 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:

O3 10m.png

References

  1. 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.
  2. Lapina, K., D. K. Henze, J. B. Milford and K. Travis (2016), Impacts of foreign, domestic and state-level emissions on ozone-induced vegetation loss in the U.S., Environ. Sci. Technol., 50 (2), 806-813, doi:10.1021/acs.est.5b04887.
  3. 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, Atmos. Chem. Phys., 12, 4,539-4,4554, 2012.

--Melissa Sulprizio (talk) 22:26, 17 November 2017 (UTC)

Analytical tools

Carbon balance

Barron Henderson has created a script for evaluating carbon balance. Please see this post on the Chemistry Working Group wiki page for more information.

--Melissa Sulprizio (talk) 17:31, 22 February 2019 (UTC)

Process analysis diagnostics

Barron Henderson 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)


Previous | Next | Guide to GEOS-Chem simulations