https://wiki.seas.harvard.edu/geos-chem/api.php?action=feedcontributions&user=Barronh&feedformat=atomGeos-chem - User contributions [en]2024-03-29T13:56:37ZUser contributionsMediaWiki 1.24.2https://wiki.seas.harvard.edu/geos-chem/index.php?title=Chemistry_Working_Group&diff=52664Chemistry Working Group2023-09-19T22:28:13Z<p>Barronh: /* Current GEOS-Chem Chemistry Projects (please add yours!) */</p>
<hr />
<div>All users interested in the GEOS-Chem chemistry scheme and associated processes (photolysis, heterogeneous, deposition) are encouraged to subscribe to the chemistry email list (click on the link in the [[#Contact information|contact information section]] below).<br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-valign="top"<br />
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs<br />
|width="600px"| <br />
*[http://www.barronh.com Barron Henderson] (GitHub: [https://github.com/barronh @barronh])<br />
*[http://hs.umt.edu/luhu/people.php Lu Hu] (GitHub: [https://github.com/luhu0 @luhu0])<br />
*[https://www.uaf.edu/chem/faculty/mao/ Jingqiu Mao] (Github: [https://github.com/jingqiumao @jingquimao])<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group email list<br />
|<tt>geos-chem-oxidants [at] g.harvard.edu</tt><br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To subscribe to email list<br />
|Either<br />
*Send an email to <tt>geos-chem-oxidants+subscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]<br />
*Click on '''Subscribe to this group'''<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To unsubscribe from email list<br />
|Either<br />
*Send an email to <tt>geos-chem-oxidants+unsubscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]<br />
*Click on the '''My Settings''' button<br />
*Click on '''Leave this group'''<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:29, 21 August 2015 (UTC)<br />
<br />
== Current GEOS-Chem Chemistry Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="200px"|User Group <br />
!width="600px"|Description <br />
!width="150px"|Contact Person<br />
!width="100px"|Date Added<br />
<br />
|-valign="top"<br />
|NASA LARC<br />
|Scheme for higher PN production from aromatics, MEK, monoterpenes, glycolaldehyde, and 1,3-butadiene <br />
|[mailto:katherine.travis@nasa.gov Katherine R. Travis]<br />
|19 Sep 2023<br />
<br />
<br />
|-valign="top"<br />
|Columbia University<br />
|Automated model reduction isoprene oxidation mechanism <br />
|[mailto:benjamin.yang@columbia.edu Benjamin Yang]<br><br />
[mailto:danielmw@ldeo.columbia.edu Dan Westervelt]<br />
|12 Sep 2023<br />
<br />
|-valign="top"<br />
|NOAA CSL<br />
|JPL Kinetic Review Update/C-N balance/stoichiometry update<br />
|[mailto:khbates@ucdavis.edu Kelvin Bates]<br />
|01 Jul 2023<br />
<br />
|-valign="top"<br />
|University of York<br />
|Nitrate Photolysis<br />
|[mailto:mat.evans@york.ac.ul Mat Evans]<br><br />
[mailto:matthew.rowlinson@york.ac.ul Matthew Rowlinson]<br />
|08 Jun 2022<br />
<br />
|-valign="top"<br />
|University of York<br />
|Halogen reverse reactions<br />
|[mailto:mat.evans@york.ac.ul Mat Evans]<br><br />
[mailto:hansen.cao@york.ac.ul Hansen Cao]<br />
|01 Jun 2022<br />
<br />
|-valign="top"<br />
|University of York<br />
|Chlorine chemistry<br />
|[mailto:mat.evans@york.ac.ul Mat Evans]<br><br />
[mailto:al1916@york.ac.uk Amy Lees]<br />
|01 Oct 2022<br />
<br />
|-valign="top"<br />
|Harvard University and<br>MPIC-Mainz<br />
|Further development of [https://kpp.readthedocs.io The Kinetic PreProcessor (KPP)]<br />
|[mailto:yantosca@seas.harvard.edu Bob Yantosca] (GCST)<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|Harvard University<br />
|Adding an adaptive solver capability into [https://kpp.readthedocs.io KPP]<br />
|[mailto:hplin@seas.harvard.edu Haipeng Lin]<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|GCST<br />
|Migrating the Hg chemistry mechanism to [https://kpp.readthedocs.io KPP]<br />
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|GCST<br />
|Adding a CO-CO2-CH4-OCS chemistry mechanism with [https://kpp.readthedocs.io KPP]<br />
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|U Montana<br />
|Formic acid and acetic acid formation in fire smoke<br />
|[mailto:wade.permar@umontana.edu Wade Permar]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]<br />
|21 May 2022<br />
<br />
|-valign="top"<br />
|U Montana<br />
|Furans chemistry in MCM and in GEOS-Chem<br />
|[mailto:lixu.jin@umontana.edu Lixu Jin]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]<br />
|21 May 2022<br />
<br />
|-valign="top"<br />
|U Wollongong<br />
|Evaluation of aromatic oxidation products using new observational constraints<br />
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]<br />
|9 June 2022<br />
<br />
|-valign="top"<br />
|UNSW, Sydney<br />
|Contribution of the unexplored photochemistry of aldehydes to the tropospheric levels of hydrogen<br />
|[mailto:m.perez_pena@unsw.edu.au Maria Paula Perez-Pena]<br />
|25 June 2021<br />
<br />
|-valign="top"<br />
|University of California, Riverside<br />
|Updates to DMS oxidation scheme<br />
|[mailto:wporter@ucr.edu William Porter]<br />
|26 August 2020<br />
<br />
|-valign="top"<br />
|Harvard University<br />
|Overhaul of cloud pH code including: use of Newton's method and addition of crustal cations and organic acids<br />
|[mailto:vshah@g.harvard.edu Viral Shah]<br>[mailto:jmoch@g.harvard.edu Jonathan Moch]<br />
|5 May 2019<br />
<br />
|-valign="top"<br />
|U Alaska Fairbanks<br />
|Monoterpene oxidation and its impact on SOA formation<br />
|[mailto:yzheng4@alaska.edu Yiqi Zheng]<br>[mailto:jmao2@alaska.edu Jingqiu Mao]<br />
|21 April 2019<br />
<br />
|-valign="top"<br />
|MIT<br />
|Simulating the global reactive carbon budget<br />
|[mailto:sarahsaf@mit.edu Sarah Safieddine]<br />
|12 April 2017<br />
<br />
|-valign="top"<br />
| FSU<br />
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry<br />
|[mailto:cdholmes@fsu.edu Chris Holmes]<br />
|May 2017<br />
<br />
|-valign="top"<br />
|FSU<br />
|Methane and methyl chloroform lifetimes<br />
|[mailto:cdholmes@fsu.edu Chris Holmes]<br />
|May 2017<br />
<br />
|-valign="top"<br />
|FSU<br />
|Arctic halogen & ozone chemistry<br />
|[mailto:cdholmes@fsu.edu Chris Holmes]<br />
|May 2017<br />
|}<br />
<br />
== Current GEOS-Chem Chemistry Issues (please add yours!) ==<br />
<br />
=== Working group telecom on the 13/3/2019 ===<br />
There was a telecon to discuss issues with the chemistry. The notes from the meeting are here [[Media:Chemistry_WG_March_2019..pdf ]] . '''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''<br />
<br />
=== Carbon balance ===<br />
<br />
==== Script for evaluating carbon balance ====<br />
<br />
'''''[http://www.barronh.com/ Barron Henderson] wrote:'''''<br />
<br />
<blockquote>[I created] an evaluation script to preserve balances going forward as the mechanism evolves (e.g., as isoprene gets updated). <br />
Currently, this done using an off-line script described in a [http://www.evernote.com/l/ATuCIZsKADFPPKnKQBlk07TFevitHHQ1Q_o/ linked note]. The approach is pretty straight-forward, but could be expanded to check conservation of functional groups as suggested by Mat.<br />
<br />
Longer term, the same technique would ideally be built-in to the standard KPP as an optional report. I discussed it with Michael Long and we both think that KPP has most of the capability for atom conservation (if not all). It may simply be a matter of defining the chemical formulas in the *.spc file.</blockquote><br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)<br />
<br />
==== Fixes for carbon creating reactions ====<br />
<br />
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span><br />
<br />
'''''Sarah Safieddine wrote:'''''<br />
<br />
<blockquote>Colette, Barron, Mat and myself modified 13 previous "carbon creating" reactions to preserve carbon. The [table below] lists all the corrections for the reactions in globchem.dat V902 that we corrected, with all the details.</blockquote><br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-bgcolor="#CCCCCC"<br />
!Reaction # in globchem.dat v9-02<br />
!Unbalanced Reaction<br />
!Rate constant<br />
!Issue<br>(R=Reactants, P=Products)<br />
!Fix and corrected reaction (in <span style="color:green">green</span>)<br />
<br />
|-valign="top<br />
|453 <br />
|R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2<br />
|K* (1-YN) where YN is returned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.5)<br />
|Creates carbon: R=4C P=4.26C<br />
|Replace 0.18B3O2 by 0.093B3O2 to achieve carbon closure (as suggested by Barron).<br><br />
<span style="color:green">R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + '''0.093B3O2''' + 0.32ETO2</span><br><br />
<span style="color:darkorange">'''Use Barron's [[Chemistry_Issues#Fixes_to_correct_ALK4_lumping_issue|fix to correct ALK4 lumping issue]] instead.'''</span><br />
<br />
|-valign="top<br />
|453<br />
|R4N1 + NO → 2NO2 + 0.39CH2O + 0.75ALD2 + 0.57RCHO + 0.3R4O2 <br />
|2.7E-12 exp(350/T)<br />
|Creates carbon: R=4C, P=4.8C<br />
|Fix, as suggested by Matt:<br><br />
<span style="color:green">R4N1 + NO → 2NO2 + 0.570RCHO + '''0.86ALD2''' + '''0.57CH2O'''</span><br />
<br />
|-valign="top<br />
|453<br />
|ATO2 + NO → 0.96NO2 + 0.96CH2O + 0.96MCO3 + 0.04R4N2 <br />
|2.8E-12 exp(300/T) <br />
|Creates carbon: R=3C, P=3.04 <br />
|Fix as suggested by Mat: ditch the R4N2 channel<br><br />
<span style="color:green">ATO2 + NO → NO2 + CH2O + MCO3<br />
<br />
|-valign="top<br />
|803<br />
|RIO2 → 2HO2 + CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.5HAC + OH <br />
|4.07E+08 exp(-7694/T)<br />
|Creates carbon: R=5C, P=7C<br>There was a [[Caltech_isoprene_scheme#Remove_duplicate_GLYX_product_from_RIO2_reaction|fix proposed on the isoprene scheme wiki page]] but still not enough<br />
|Fix as suggested by Sarah: remove CH2O<br><br />
<span style="color:green">RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''RIO2 → 0.5HPALD + 0.5DHPCARP''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|453<br />
|ISNOOB + NO3 → R4N2 + GLYX + 2NO2 <br />
|2.3E-12<br />
|Creates carbon: R=5C, P=6C<br />
|Fix as suggested by Barron: Replace R4N2 by PROPNN<br><br />
<span style="color:green">ISNOOB + NO3 → '''PROPNN''' + GLYX + 2NO2</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO3 → 0.94PROPNN + GLYX + 2NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|453<br />
|ISNOOB+NO → 0.94R4N2 +0.94GLYX +1.88NO2<br />
|2.6E-12 exp(380/T)<br />
|Creates carbon: R=5C, P=5.64C<br />
|Same as above<br><br />
<span style="color:green">ISNOOB + NO → '''0.06R4N2''' + ''''0.94PROPNN'''' + 0.94GLYX + 1.88NO2</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO → 0.9PROPNN + 0.94GLYX + 1.88NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|453<br />
|ISNOHOO + NO → 0.934R4N2 + 0.934HO2 + 0.919GLYX <br />
|2.6E-12 exp(380/T) <br />
|Creates carbon: R=5C, P=5.574C<br />
|Fix by Barron:<br><br />
<span style="color:green">ISNOHOO + NO → '''0.081R4N2''' + '''0.919PROPNN''' + 0.934HO2 + 0.919GLYX</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''ISNOHOO + NO3 → 0.894PROPNN + 0.934HO2 + 0.919GLYX + 0.4ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|472<br />
|MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85ISNP <br />
|2.91E-13*exp(1300/T)[1-exp(-0.245*n)],n=4<br />
|Creates carbon: R=4C, P=4.85C<br />
|Fix by both Mat and Barron: Replace ISNP with 0.85MAOP + 0.85NO2<br><br />
<span style="color:green">MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + '''0.85MAOP + 0.85NO2'''</span><br />
<br />
|-valign="top<br />
|719<br />
|ATO2 + MCO3 → MEK + ACTA <br />
|1.87E-13 exp(500/T)<br />
|Creates carbon: R=5C, P=6C<br />
|From the WIKI: replace MEK with MGLY<br><br />
<span style="color:green">ATO2 + MCO3 → '''MGLY''' + ACTA</span><br />
<br />
|-valign="top<br />
|817<br />
|Br + ALD2 → HBr + MCO3 + CO<br />
|1.3E-11 exp(-360/T)<br />
|Creates carbon: R=2C, P=3C<br />
|Remove CO Following Parrella et al., Table 2a, reactions R7 to R10 (also for the 3 reactions below)<br><br />
<span style="color:green">Br + ALD2 → HBr + MCO3</span><br />
<br />
|-valign="top<br />
|818<br />
|Br + ACET → HBr + ATO2 + CO<br />
|1.66E-10exp(-7000/T)<br />
|Creates carbon: R=3C, P=4C<br />
|Remove CO, same as above<br><br />
<span style="color:green">Br + ACET → HBr + ATO2</span><br />
<br />
|-valign="top<br />
|819<br />
|Br + C2H6 → HBr + ETO2 + CO<br />
|2.36E-10 exp(-6411/T)<br />
|Creates carbon: R=2C, P=3C<br />
|Remove CO, same as above<br><br />
<span style="color:green">Br + C2H6 → HBr + ETO2</span><br />
<br />
|-valign="top<br />
|820<br />
|Br + C3H8 → HBr + A3O2 + CO<br />
|8.77E-11 exp(-4330/T)<br />
|Creates carbon: R=3C, P=4C<br />
|Remove CO, same as above<br><br />
<span style="color:green">Br + C3H8 → HBr + A3O2</span><br />
<br />
|}<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:59, 27 July 2017 (UTC)<br />
<br />
==== Identification of carbon leaking reactions ====<br />
<br />
'''''Sarah Safieddine wrote:'''''<br />
<br />
<blockquote>76 other reactions leaked carbon, we enforced carbon conservation by tracking the lost carbon as CO2 (labeled as <tt>{CO2}</tt> in the document [http://onlinelibrary.wiley.com/store/10.1002/2017GL072602/asset/supinfo/grl55781-sup-0001-Supplementary.docx?v=1&s=21c96c26c411290d72b64fc4f9ecdc5e806af2c5 ROC_SI.docx], Table 2). This is the supplementary material for Safieddine, Heald and Henderson, 2017. It contains the corrections for both the carbon leaking and carbon creating reactions and all other information. The paper for reference can be found here: http://onlinelibrary.wiley.com/doi/10.1002/2017GL072602/abstract.</blockquote><br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)<br />
<br />
==== Fixes to correct ALK4 lumping issue ====<br />
<br />
<span style="color:green">'''''These fixes were included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span><br />
<br />
'''''[[User:Barronh|Barron Henderson]] wrote:'''''<br />
<br />
<blockquote>I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).<br />
<br />
Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy. When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.<br />
<br />
If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.<br />
<br />
I have [https://www.evernote.com/shard/s315/sh/f2ec9589-d827-4ee1-afcb-96ee5a2d2914/d84318450f729cd414e4a6653c03a296 extensive notes] on what I interpret as happening. To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.<br />
<br />
#Increase MO2 stoichiometry from 0.18 to 0.19<br />
#Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).<br />
#Modify the carbon count for ALK4 (i.e. the <tt>MolecRatio</tt> field in the [[GEOS-Chem species database]]) from 4 to 4.3.<br />
<br />
Fixes 1 and 2&mdash;which can be applied to the KPP <tt>globchem.eqn</tt> file&mdash;will make the carbon conservation consistent with Lurmann's. Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.</blockquote><br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:21, 31 January 2017 (UTC)<br />
<br />
=== JPL Released 18th Rate Coefficient Evaluation ===<br />
<br />
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span><br />
<br />
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page ([[Updates in JPL Publication 15-10]]) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10. <br />
<br />
:J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.<br />
<br />
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)<br />
<br />
=== Working Group Tele-con on the 2nd December 2011 ===<br />
[[ChemTelecon20111202]]<br />
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''<br />
<br />
=== Isoprene chemistry ===<br />
I've created a page with some of the recent literature on [[Isoprene|isoprene chemistry]]. Please add more papers as they come along! ([[User:mje| MJE Leeds]])<br />
<br />
=== HO2 + CH2O ===<br />
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)<br />
<br />
Hermans, I., et al. (2005), Kinetics of alpha-hydroxy-alkylperoxyl radicals in oxidation<br />
processes. HO2 center dot-initiated oxidation of ketones/aldehydes near the tropopause,<br />
Journal of Physical Chemistry A, 109(19), 4303-4311.<br />
<br />
According to this paper, this reaction is significant when Temperature is below 220K.<br />
<br />
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)<br />
<br />
== Previous issues that have now been resolved ==<br />
<br />
=== Centralizing chemistry time step===<br />
<br />
<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><br />
<br />
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)<br />
<br />
=== Acetone photolysis ===<br />
<br />
[[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]].<br />
<br />
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)<br />
<br />
== Documentation ==<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
*[http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf Updated chemical reactions] that will be used in [[GEOS-Chem v8-02-04]] and higher.<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v5.pdf Updated chemical reactions] now used in [[GEOS-Chem v8-02-01]] through [[GEOS-Chem v8-02-03]]. <br />
**All typos have now been corrected in the present file.<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jv_spec_format.pdf Format of FAST-J input file <tt>jv_spec.dat</tt>]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:41, 27 October 2009 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=Chemistry_Working_Group&diff=52600Chemistry Working Group2023-08-22T14:27:53Z<p>Barronh: /* Current GEOS-Chem Chemistry Projects (please add yours!) */</p>
<hr />
<div>All users interested in the GEOS-Chem chemistry scheme and associated processes (photolysis, heterogeneous, deposition) are encouraged to subscribe to the chemistry email list (click on the link in the [[#Contact information|contact information section]] below).<br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-valign="top"<br />
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs<br />
|width="600px"| <br />
*[http://www.barronh.com Barron Henderson] (GitHub: [https://github.com/barronh @barronh])<br />
*[http://hs.umt.edu/luhu/people.php Lu Hu] (GitHub: [https://github.com/luhu0 @luhu0])<br />
*[https://www.uaf.edu/chem/faculty/mao/ Jingqiu Mao] (Github: [https://github.com/jingqiumao @jingquimao])<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group email list<br />
|<tt>geos-chem-oxidants [at] g.harvard.edu</tt><br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To subscribe to email list<br />
|Either<br />
*Send an email to <tt>geos-chem-oxidants+subscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]<br />
*Click on '''Subscribe to this group'''<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To unsubscribe from email list<br />
|Either<br />
*Send an email to <tt>geos-chem-oxidants+unsubscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]<br />
*Click on the '''My Settings''' button<br />
*Click on '''Leave this group'''<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:29, 21 August 2015 (UTC)<br />
<br />
== Current GEOS-Chem Chemistry Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="200px"|User Group <br />
!width="600px"|Description <br />
!width="150px"|Contact Person<br />
!width="100px"|Date Added<br />
<br />
|-valign="top"<br />
|NOAA CSL<br />
|JPL Kinetic Review Update/C-N balance/stoichiometry update<br />
|[mailto:khbates@ucdavis.edu Kelvin Bates]<br />
|01 Jul 2023<br />
<br />
|-valign="top"<br />
|University of York<br />
|Nitrate Photolysis<br />
|[mailto:mat.evans@york.ac.ul Mat Evans]<br><br />
[mailto:matthew.rowlinson@york.ac.ul Matthew Rowlinson]<br />
|08 Jun 2022<br />
<br />
|-valign="top"<br />
|University of York<br />
|Halogen reverse reactions<br />
|[mailto:mat.evans@york.ac.ul Mat Evans]<br><br />
[mailto:hansen.cao@york.ac.ul Hansen Cao]<br />
|01 Jun 2022<br />
<br />
|-valign="top"<br />
|University of York<br />
|Chlorine chemistry<br />
|[mailto:mat.evans@york.ac.ul Mat Evans]<br><br />
[mailto:al1916@york.ac.uk Amy Lees]<br />
|01 Oct 2022<br />
<br />
|-valign="top"<br />
|Harvard University and<br>MPIC-Mainz<br />
|Further development of [https://kpp.readthedocs.io The Kinetic PreProcessor (KPP)]<br />
|[mailto:yantosca@seas.harvard.edu Bob Yantosca] (GCST)<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|Harvard University<br />
|Adding an adaptive solver capability into [https://kpp.readthedocs.io KPP]<br />
|[mailto:hplin@seas.harvard.edu Haipeng Lin]<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|GCST<br />
|Migrating the Hg chemistry mechanism to [https://kpp.readthedocs.io KPP]<br />
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|GCST<br />
|Adding a CO-CO2-CH4-OCS chemistry mechanism with [https://kpp.readthedocs.io KPP]<br />
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|U Montana<br />
|Formic acid and acetic acid formation in fire smoke<br />
|[mailto:wade.permar@umontana.edu Wade Permar]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]<br />
|21 May 2022<br />
<br />
|-valign="top"<br />
|U Montana<br />
|Furans chemistry in MCM and in GEOS-Chem<br />
|[mailto:lixu.jin@umontana.edu Lixu Jin]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]<br />
|21 May 2022<br />
<br />
|-valign="top"<br />
|U Wollongong<br />
|Evaluation of aromatic oxidation products using new observational constraints<br />
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]<br />
|9 June 2022<br />
<br />
|-valign="top"<br />
|UNSW, Sydney<br />
|Contribution of the unexplored photochemistry of aldehydes to the tropospheric levels of hydrogen<br />
|[mailto:m.perez_pena@unsw.edu.au Maria Paula Perez-Pena]<br />
|25 June 2021<br />
<br />
|-valign="top"<br />
|University of California, Riverside<br />
|Updates to DMS oxidation scheme<br />
|[mailto:wporter@ucr.edu William Porter]<br />
|26 August 2020<br />
<br />
|-valign="top"<br />
|Harvard University<br />
|Overhaul of cloud pH code including: use of Newton's method and addition of crustal cations and organic acids<br />
|[mailto:vshah@g.harvard.edu Viral Shah]<br>[mailto:jmoch@g.harvard.edu Jonathan Moch]<br />
|5 May 2019<br />
<br />
|-valign="top"<br />
|U Alaska Fairbanks<br />
|Monoterpene oxidation and its impact on SOA formation<br />
|[mailto:yzheng4@alaska.edu Yiqi Zheng]<br>[mailto:jmao2@alaska.edu Jingqiu Mao]<br />
|21 April 2019<br />
<br />
|-valign="top"<br />
|MIT<br />
|Simulating the global reactive carbon budget<br />
|[mailto:sarahsaf@mit.edu Sarah Safieddine]<br />
|12 April 2017<br />
<br />
|-valign="top"<br />
| FSU<br />
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry<br />
|[mailto:cdholmes@fsu.edu Chris Holmes]<br />
|May 2017<br />
<br />
|-valign="top"<br />
|FSU<br />
|Methane and methyl chloroform lifetimes<br />
|[mailto:cdholmes@fsu.edu Chris Holmes]<br />
|May 2017<br />
<br />
|-valign="top"<br />
|FSU<br />
|Arctic halogen & ozone chemistry<br />
|[mailto:cdholmes@fsu.edu Chris Holmes]<br />
|May 2017<br />
|}<br />
<br />
== Current GEOS-Chem Chemistry Issues (please add yours!) ==<br />
<br />
=== Working group telecom on the 13/3/2019 ===<br />
There was a telecon to discuss issues with the chemistry. The notes from the meeting are here [[Media:Chemistry_WG_March_2019..pdf ]] . '''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''<br />
<br />
=== Carbon balance ===<br />
<br />
==== Script for evaluating carbon balance ====<br />
<br />
'''''[http://www.barronh.com/ Barron Henderson] wrote:'''''<br />
<br />
<blockquote>[I created] an evaluation script to preserve balances going forward as the mechanism evolves (e.g., as isoprene gets updated). <br />
Currently, this done using an off-line script described in a [http://www.evernote.com/l/ATuCIZsKADFPPKnKQBlk07TFevitHHQ1Q_o/ linked note]. The approach is pretty straight-forward, but could be expanded to check conservation of functional groups as suggested by Mat.<br />
<br />
Longer term, the same technique would ideally be built-in to the standard KPP as an optional report. I discussed it with Michael Long and we both think that KPP has most of the capability for atom conservation (if not all). It may simply be a matter of defining the chemical formulas in the *.spc file.</blockquote><br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)<br />
<br />
==== Fixes for carbon creating reactions ====<br />
<br />
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span><br />
<br />
'''''Sarah Safieddine wrote:'''''<br />
<br />
<blockquote>Colette, Barron, Mat and myself modified 13 previous "carbon creating" reactions to preserve carbon. The [table below] lists all the corrections for the reactions in globchem.dat V902 that we corrected, with all the details.</blockquote><br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-bgcolor="#CCCCCC"<br />
!Reaction # in globchem.dat v9-02<br />
!Unbalanced Reaction<br />
!Rate constant<br />
!Issue<br>(R=Reactants, P=Products)<br />
!Fix and corrected reaction (in <span style="color:green">green</span>)<br />
<br />
|-valign="top<br />
|453 <br />
|R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2<br />
|K* (1-YN) where YN is returned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.5)<br />
|Creates carbon: R=4C P=4.26C<br />
|Replace 0.18B3O2 by 0.093B3O2 to achieve carbon closure (as suggested by Barron).<br><br />
<span style="color:green">R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + '''0.093B3O2''' + 0.32ETO2</span><br><br />
<span style="color:darkorange">'''Use Barron's [[Chemistry_Issues#Fixes_to_correct_ALK4_lumping_issue|fix to correct ALK4 lumping issue]] instead.'''</span><br />
<br />
|-valign="top<br />
|453<br />
|R4N1 + NO → 2NO2 + 0.39CH2O + 0.75ALD2 + 0.57RCHO + 0.3R4O2 <br />
|2.7E-12 exp(350/T)<br />
|Creates carbon: R=4C, P=4.8C<br />
|Fix, as suggested by Matt:<br><br />
<span style="color:green">R4N1 + NO → 2NO2 + 0.570RCHO + '''0.86ALD2''' + '''0.57CH2O'''</span><br />
<br />
|-valign="top<br />
|453<br />
|ATO2 + NO → 0.96NO2 + 0.96CH2O + 0.96MCO3 + 0.04R4N2 <br />
|2.8E-12 exp(300/T) <br />
|Creates carbon: R=3C, P=3.04 <br />
|Fix as suggested by Mat: ditch the R4N2 channel<br><br />
<span style="color:green">ATO2 + NO → NO2 + CH2O + MCO3<br />
<br />
|-valign="top<br />
|803<br />
|RIO2 → 2HO2 + CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.5HAC + OH <br />
|4.07E+08 exp(-7694/T)<br />
|Creates carbon: R=5C, P=7C<br>There was a [[Caltech_isoprene_scheme#Remove_duplicate_GLYX_product_from_RIO2_reaction|fix proposed on the isoprene scheme wiki page]] but still not enough<br />
|Fix as suggested by Sarah: remove CH2O<br><br />
<span style="color:green">RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''RIO2 → 0.5HPALD + 0.5DHPCARP''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|453<br />
|ISNOOB + NO3 → R4N2 + GLYX + 2NO2 <br />
|2.3E-12<br />
|Creates carbon: R=5C, P=6C<br />
|Fix as suggested by Barron: Replace R4N2 by PROPNN<br><br />
<span style="color:green">ISNOOB + NO3 → '''PROPNN''' + GLYX + 2NO2</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO3 → 0.94PROPNN + GLYX + 2NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|453<br />
|ISNOOB+NO → 0.94R4N2 +0.94GLYX +1.88NO2<br />
|2.6E-12 exp(380/T)<br />
|Creates carbon: R=5C, P=5.64C<br />
|Same as above<br><br />
<span style="color:green">ISNOOB + NO → '''0.06R4N2''' + ''''0.94PROPNN'''' + 0.94GLYX + 1.88NO2</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO → 0.9PROPNN + 0.94GLYX + 1.88NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|453<br />
|ISNOHOO + NO → 0.934R4N2 + 0.934HO2 + 0.919GLYX <br />
|2.6E-12 exp(380/T) <br />
|Creates carbon: R=5C, P=5.574C<br />
|Fix by Barron:<br><br />
<span style="color:green">ISNOHOO + NO → '''0.081R4N2''' + '''0.919PROPNN''' + 0.934HO2 + 0.919GLYX</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''ISNOHOO + NO3 → 0.894PROPNN + 0.934HO2 + 0.919GLYX + 0.4ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|472<br />
|MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85ISNP <br />
|2.91E-13*exp(1300/T)[1-exp(-0.245*n)],n=4<br />
|Creates carbon: R=4C, P=4.85C<br />
|Fix by both Mat and Barron: Replace ISNP with 0.85MAOP + 0.85NO2<br><br />
<span style="color:green">MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + '''0.85MAOP + 0.85NO2'''</span><br />
<br />
|-valign="top<br />
|719<br />
|ATO2 + MCO3 → MEK + ACTA <br />
|1.87E-13 exp(500/T)<br />
|Creates carbon: R=5C, P=6C<br />
|From the WIKI: replace MEK with MGLY<br><br />
<span style="color:green">ATO2 + MCO3 → '''MGLY''' + ACTA</span><br />
<br />
|-valign="top<br />
|817<br />
|Br + ALD2 → HBr + MCO3 + CO<br />
|1.3E-11 exp(-360/T)<br />
|Creates carbon: R=2C, P=3C<br />
|Remove CO Following Parrella et al., Table 2a, reactions R7 to R10 (also for the 3 reactions below)<br><br />
<span style="color:green">Br + ALD2 → HBr + MCO3</span><br />
<br />
|-valign="top<br />
|818<br />
|Br + ACET → HBr + ATO2 + CO<br />
|1.66E-10exp(-7000/T)<br />
|Creates carbon: R=3C, P=4C<br />
|Remove CO, same as above<br><br />
<span style="color:green">Br + ACET → HBr + ATO2</span><br />
<br />
|-valign="top<br />
|819<br />
|Br + C2H6 → HBr + ETO2 + CO<br />
|2.36E-10 exp(-6411/T)<br />
|Creates carbon: R=2C, P=3C<br />
|Remove CO, same as above<br><br />
<span style="color:green">Br + C2H6 → HBr + ETO2</span><br />
<br />
|-valign="top<br />
|820<br />
|Br + C3H8 → HBr + A3O2 + CO<br />
|8.77E-11 exp(-4330/T)<br />
|Creates carbon: R=3C, P=4C<br />
|Remove CO, same as above<br><br />
<span style="color:green">Br + C3H8 → HBr + A3O2</span><br />
<br />
|}<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:59, 27 July 2017 (UTC)<br />
<br />
==== Identification of carbon leaking reactions ====<br />
<br />
'''''Sarah Safieddine wrote:'''''<br />
<br />
<blockquote>76 other reactions leaked carbon, we enforced carbon conservation by tracking the lost carbon as CO2 (labeled as <tt>{CO2}</tt> in the document [http://onlinelibrary.wiley.com/store/10.1002/2017GL072602/asset/supinfo/grl55781-sup-0001-Supplementary.docx?v=1&s=21c96c26c411290d72b64fc4f9ecdc5e806af2c5 ROC_SI.docx], Table 2). This is the supplementary material for Safieddine, Heald and Henderson, 2017. It contains the corrections for both the carbon leaking and carbon creating reactions and all other information. The paper for reference can be found here: http://onlinelibrary.wiley.com/doi/10.1002/2017GL072602/abstract.</blockquote><br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)<br />
<br />
==== Fixes to correct ALK4 lumping issue ====<br />
<br />
<span style="color:green">'''''These fixes were included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span><br />
<br />
'''''[[User:Barronh|Barron Henderson]] wrote:'''''<br />
<br />
<blockquote>I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).<br />
<br />
Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy. When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.<br />
<br />
If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.<br />
<br />
I have [https://www.evernote.com/shard/s315/sh/f2ec9589-d827-4ee1-afcb-96ee5a2d2914/d84318450f729cd414e4a6653c03a296 extensive notes] on what I interpret as happening. To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.<br />
<br />
#Increase MO2 stoichiometry from 0.18 to 0.19<br />
#Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).<br />
#Modify the carbon count for ALK4 (i.e. the <tt>MolecRatio</tt> field in the [[GEOS-Chem species database]]) from 4 to 4.3.<br />
<br />
Fixes 1 and 2&mdash;which can be applied to the KPP <tt>globchem.eqn</tt> file&mdash;will make the carbon conservation consistent with Lurmann's. Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.</blockquote><br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:21, 31 January 2017 (UTC)<br />
<br />
=== JPL Released 18th Rate Coefficient Evaluation ===<br />
<br />
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span><br />
<br />
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page ([[Updates in JPL Publication 15-10]]) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10. <br />
<br />
:J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.<br />
<br />
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)<br />
<br />
=== Working Group Tele-con on the 2nd December 2011 ===<br />
[[ChemTelecon20111202]]<br />
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''<br />
<br />
=== Isoprene chemistry ===<br />
I've created a page with some of the recent literature on [[Isoprene|isoprene chemistry]]. Please add more papers as they come along! ([[User:mje| MJE Leeds]])<br />
<br />
=== HO2 + CH2O ===<br />
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)<br />
<br />
Hermans, I., et al. (2005), Kinetics of alpha-hydroxy-alkylperoxyl radicals in oxidation<br />
processes. HO2 center dot-initiated oxidation of ketones/aldehydes near the tropopause,<br />
Journal of Physical Chemistry A, 109(19), 4303-4311.<br />
<br />
According to this paper, this reaction is significant when Temperature is below 220K.<br />
<br />
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)<br />
<br />
== Previous issues that have now been resolved ==<br />
<br />
=== Centralizing chemistry time step===<br />
<br />
<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><br />
<br />
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)<br />
<br />
=== Acetone photolysis ===<br />
<br />
[[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]].<br />
<br />
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)<br />
<br />
== Documentation ==<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
*[http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf Updated chemical reactions] that will be used in [[GEOS-Chem v8-02-04]] and higher.<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v5.pdf Updated chemical reactions] now used in [[GEOS-Chem v8-02-01]] through [[GEOS-Chem v8-02-03]]. <br />
**All typos have now been corrected in the present file.<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jv_spec_format.pdf Format of FAST-J input file <tt>jv_spec.dat</tt>]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:41, 27 October 2009 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=Chemistry_Working_Group&diff=52570Chemistry Working Group2023-08-09T12:54:51Z<p>Barronh: /* Current GEOS-Chem Chemistry Projects (please add yours!) */</p>
<hr />
<div>All users interested in the GEOS-Chem chemistry scheme and associated processes (photolysis, heterogeneous, deposition) are encouraged to subscribe to the chemistry email list (click on the link in the [[#Contact information|contact information section]] below).<br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-valign="top"<br />
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs<br />
|width="600px"| <br />
*[http://www.barronh.com Barron Henderson] (GitHub: [https://github.com/barronh @barronh])<br />
*[http://hs.umt.edu/luhu/people.php Lu Hu] (GitHub: [https://github.com/luhu0 @luhu0])<br />
*[https://www.uaf.edu/chem/faculty/mao/ Jingqiu Mao] (Github: [https://github.com/jingqiumao @jingquimao])<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group email list<br />
|<tt>geos-chem-oxidants [at] g.harvard.edu</tt><br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To subscribe to email list<br />
|Either<br />
*Send an email to <tt>geos-chem-oxidants+subscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]<br />
*Click on '''Subscribe to this group'''<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To unsubscribe from email list<br />
|Either<br />
*Send an email to <tt>geos-chem-oxidants+unsubscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]<br />
*Click on the '''My Settings''' button<br />
*Click on '''Leave this group'''<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:29, 21 August 2015 (UTC)<br />
<br />
== Current GEOS-Chem Chemistry Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="200px"|User Group <br />
!width="600px"|Description <br />
!width="150px"|Contact Person<br />
!width="100px"|Date Added<br />
<br />
|-valign="top"<br />
|NOAA CSL<br />
|JPL Kinetic Review Update/C-N balance/stoichiometry update<br />
|[mailto:khbates@ucdavis.edu Kelvin Bates]<br />
|01 Jul 2023<br />
<br />
|-valign="top"<br />
|University of York<br />
|Nitrate Photolysis<br />
|[mailto:mat.evans@york.ac.ul Mat Evans]<br />
|08 Jun 2022<br />
<br />
|-valign="top"<br />
|Harvard University and<br>MPIC-Mainz<br />
|Further development of [https://kpp.readthedocs.io The Kinetic PreProcessor (KPP)]<br />
|[mailto:yantosca@seas.harvard.edu Bob Yantosca] (GCST)<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|Harvard University<br />
|Adding an adaptive solver capability into [https://kpp.readthedocs.io KPP]<br />
|[mailto:hplin@seas.harvard.edu Haipeng Lin]<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|GCST<br />
|Migrating the Hg chemistry mechanism to [https://kpp.readthedocs.io KPP]<br />
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|GCST<br />
|Adding a CO-CO2-CH4-OCS chemistry mechanism with [https://kpp.readthedocs.io KPP]<br />
|[mailto:yantosca@seas.harvard.eduard.edu Bob Yantosca] (GCST)<br />
|03 Jun 2022<br />
<br />
|-valign="top"<br />
|U Montana<br />
|Formic acid and acetic acid formation in fire smoke<br />
|[mailto:wade.permar@umontana.edu Wade Permar]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]<br />
|21 May 2022<br />
<br />
|-valign="top"<br />
|U Montana<br />
|Formic acid and acetic acid formation in fire smoke<br />
|[mailto:wade.permar@umontana.edu Wade Permar]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]<br />
|21 May 2022<br />
<br />
|-valign="top"<br />
|U Montana<br />
|Furans chemistry in MCM and in GEOS-Chem<br />
|[mailto:lixu.jin@umontana.edu Lixu Jin]<br>[mailto:lu.hu@mso.umt.edu Lu Hu]<br />
|21 May 2022<br />
<br />
|-valign="top"<br />
|U Wollongong<br />
|Evaluation of aromatic oxidation products using new observational constraints<br />
|[mailto:smm997@uowmail.edu.au Stephen MacFarlane]<br />
|9 June 2022<br />
<br />
|-valign="top"<br />
|UNSW, Sydney<br />
|Contribution of the unexplored photochemistry of aldehydes to the tropospheric levels of hydrogen<br />
|[mailto:m.perez_pena@unsw.edu.au Maria Paula Perez-Pena]<br />
|25 June 2021<br />
<br />
|-valign="top"<br />
|University of California, Riverside<br />
|Updates to DMS oxidation scheme<br />
|[mailto:wporter@ucr.edu William Porter]<br />
|26 August 2020<br />
<br />
|-valign="top"<br />
|Harvard University<br />
|Overhaul of cloud pH code including: use of Newton's method and addition of crustal cations and organic acids<br />
|[mailto:vshah@g.harvard.edu Viral Shah]<br>[mailto:jmoch@g.harvard.edu Jonathan Moch]<br />
|5 May 2019<br />
<br />
|-valign="top"<br />
|U Alaska Fairbanks<br />
|Monoterpene oxidation and its impact on SOA formation<br />
|[mailto:yzheng4@alaska.edu Yiqi Zheng]<br>[mailto:jmao2@alaska.edu Jingqiu Mao]<br />
|21 April 2019<br />
<br />
|-valign="top"<br />
|NIA / LaRC<br />
|Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis<br />
|[mailto:hyl@nianet.org Hongyu Liu]<br />
|5 May 2015<br />
<br />
|-valign="top"<br />
|MIT<br />
|Simulating the global reactive carbon budget<br />
|[mailto:sarahsaf@mit.edu Sarah Safieddine]<br />
|12 April 2017<br />
<br />
|-valign="top"<br />
|University of York <br />
|Halogen chemistry <br />
|[mailto:ts551@york.ac.uk Tomas Sherwen]<br />
|12 April 2017<br />
<br />
|-valign="top"<br />
|Harvard University<br />
|Halogen extension to include explicit phase partitioning and mass transfer<br />
|[mailto:seastham@fas.harvard.edu Sebastian D. Eastham]<br />
|12 April 2017<br />
<br />
<br />
|-valign="top"<br />
| FSU<br />
|Stratosphere-troposphere coupling, improvements to UCX & H2 chemistry<br />
|[mailto:cdholmes@fsu.edu Chris Holmes]<br />
|May 2017<br />
<br />
|-valign="top"<br />
|FSU<br />
|Methane and methyl chloroform lifetimes<br />
|[mailto:cdholmes@fsu.edu Chris Holmes]<br />
|May 2017<br />
<br />
|-valign="top"<br />
|FSU<br />
|Arctic halogen & ozone chemistry<br />
|[mailto:cdholmes@fsu.edu Chris Holmes]<br />
|May 2017<br />
|}<br />
<br />
== Current GEOS-Chem Chemistry Issues (please add yours!) ==<br />
<br />
=== Working group telecom on the 13/3/2019 ===<br />
There was a telecon to discuss issues with the chemistry. The notes from the meeting are here [[Media:Chemistry_WG_March_2019..pdf ]] . '''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''<br />
<br />
=== Carbon balance ===<br />
<br />
==== Script for evaluating carbon balance ====<br />
<br />
'''''[http://www.barronh.com/ Barron Henderson] wrote:'''''<br />
<br />
<blockquote>[I created] an evaluation script to preserve balances going forward as the mechanism evolves (e.g., as isoprene gets updated). <br />
Currently, this done using an off-line script described in a [http://www.evernote.com/l/ATuCIZsKADFPPKnKQBlk07TFevitHHQ1Q_o/ linked note]. The approach is pretty straight-forward, but could be expanded to check conservation of functional groups as suggested by Mat.<br />
<br />
Longer term, the same technique would ideally be built-in to the standard KPP as an optional report. I discussed it with Michael Long and we both think that KPP has most of the capability for atom conservation (if not all). It may simply be a matter of defining the chemical formulas in the *.spc file.</blockquote><br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)<br />
<br />
==== Fixes for carbon creating reactions ====<br />
<br />
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02c|v11-02c]] and approved on 21 Sep 2017.'''''</span><br />
<br />
'''''Sarah Safieddine wrote:'''''<br />
<br />
<blockquote>Colette, Barron, Mat and myself modified 13 previous "carbon creating" reactions to preserve carbon. The [table below] lists all the corrections for the reactions in globchem.dat V902 that we corrected, with all the details.</blockquote><br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-bgcolor="#CCCCCC"<br />
!Reaction # in globchem.dat v9-02<br />
!Unbalanced Reaction<br />
!Rate constant<br />
!Issue<br>(R=Reactants, P=Products)<br />
!Fix and corrected reaction (in <span style="color:green">green</span>)<br />
<br />
|-valign="top<br />
|453 <br />
|R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + 0.18B3O2 + 0.32ETO2<br />
|K* (1-YN) where YN is returned from fyrno3.f; K=2.7E-12 exp(350/T) (Xcarbn=4.5)<br />
|Creates carbon: R=4C P=4.26C<br />
|Replace 0.18B3O2 by 0.093B3O2 to achieve carbon closure (as suggested by Barron).<br><br />
<span style="color:green">R4O2 + NO → NO2 + 0.32ACET + 0.19MEK + 0.18MO2 + 0.27HO2 + 0.32ALD2 + 0.13RCHO + 0.05A3O2 + '''0.093B3O2''' + 0.32ETO2</span><br><br />
<span style="color:darkorange">'''Use Barron's [[Chemistry_Issues#Fixes_to_correct_ALK4_lumping_issue|fix to correct ALK4 lumping issue]] instead.'''</span><br />
<br />
|-valign="top<br />
|453<br />
|R4N1 + NO → 2NO2 + 0.39CH2O + 0.75ALD2 + 0.57RCHO + 0.3R4O2 <br />
|2.7E-12 exp(350/T)<br />
|Creates carbon: R=4C, P=4.8C<br />
|Fix, as suggested by Matt:<br><br />
<span style="color:green">R4N1 + NO → 2NO2 + 0.570RCHO + '''0.86ALD2''' + '''0.57CH2O'''</span><br />
<br />
|-valign="top<br />
|453<br />
|ATO2 + NO → 0.96NO2 + 0.96CH2O + 0.96MCO3 + 0.04R4N2 <br />
|2.8E-12 exp(300/T) <br />
|Creates carbon: R=3C, P=3.04 <br />
|Fix as suggested by Mat: ditch the R4N2 channel<br><br />
<span style="color:green">ATO2 + NO → NO2 + CH2O + MCO3<br />
<br />
|-valign="top<br />
|803<br />
|RIO2 → 2HO2 + CH2O + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5GLYX + 0.5HAC + OH <br />
|4.07E+08 exp(-7694/T)<br />
|Creates carbon: R=5C, P=7C<br>There was a [[Caltech_isoprene_scheme#Remove_duplicate_GLYX_product_from_RIO2_reaction|fix proposed on the isoprene scheme wiki page]] but still not enough<br />
|Fix as suggested by Sarah: remove CH2O<br><br />
<span style="color:green">RIO2 → 2HO2 + 0.5MGLY + 0.5GLYC + 0.5GLYX + 0.5HAC + OH</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''RIO2 → 0.5HPALD + 0.5DHPCARP''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|453<br />
|ISNOOB + NO3 → R4N2 + GLYX + 2NO2 <br />
|2.3E-12<br />
|Creates carbon: R=5C, P=6C<br />
|Fix as suggested by Barron: Replace R4N2 by PROPNN<br><br />
<span style="color:green">ISNOOB + NO3 → '''PROPNN''' + GLYX + 2NO2</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO3 → 0.94PROPNN + GLYX + 2NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|453<br />
|ISNOOB+NO → 0.94R4N2 +0.94GLYX +1.88NO2<br />
|2.6E-12 exp(380/T)<br />
|Creates carbon: R=5C, P=5.64C<br />
|Same as above<br><br />
<span style="color:green">ISNOOB + NO → '''0.06R4N2''' + ''''0.94PROPNN'''' + 0.94GLYX + 1.88NO2</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''ISNOOB + NO → 0.9PROPNN + 0.94GLYX + 1.88NO2 + 0.04ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|453<br />
|ISNOHOO + NO → 0.934R4N2 + 0.934HO2 + 0.919GLYX <br />
|2.6E-12 exp(380/T) <br />
|Creates carbon: R=5C, P=5.574C<br />
|Fix by Barron:<br><br />
<span style="color:green">ISNOHOO + NO → '''0.081R4N2''' + '''0.919PROPNN''' + 0.934HO2 + 0.919GLYX</span><br><br />
<span style="color:darkorange">This reaction was replaced with '''ISNOHOO + NO3 → 0.894PROPNN + 0.934HO2 + 0.919GLYX + 0.4ISN1OG''' in the [[GEOS-Chem_chemistry_mechanisms#Updated_isoprene_and_monoterpene_chemistry|isoprene chemistry updates]] added in v11-02c</span><br />
<br />
|-valign="top<br />
|472<br />
|MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + 0.85ISNP <br />
|2.91E-13*exp(1300/T)[1-exp(-0.245*n)],n=4<br />
|Creates carbon: R=4C, P=4.85C<br />
|Fix by both Mat and Barron: Replace ISNP with 0.85MAOP + 0.85NO2<br><br />
<span style="color:green">MAN2 + HO2 → 0.075PROPNN + 0.075CO + 0.075HO2 + 0.075MGLY + 0.075CH2O + 0.075NO2 + 0.15OH + '''0.85MAOP + 0.85NO2'''</span><br />
<br />
|-valign="top<br />
|719<br />
|ATO2 + MCO3 → MEK + ACTA <br />
|1.87E-13 exp(500/T)<br />
|Creates carbon: R=5C, P=6C<br />
|From the WIKI: replace MEK with MGLY<br><br />
<span style="color:green">ATO2 + MCO3 → '''MGLY''' + ACTA</span><br />
<br />
|-valign="top<br />
|817<br />
|Br + ALD2 → HBr + MCO3 + CO<br />
|1.3E-11 exp(-360/T)<br />
|Creates carbon: R=2C, P=3C<br />
|Remove CO Following Parrella et al., Table 2a, reactions R7 to R10 (also for the 3 reactions below)<br><br />
<span style="color:green">Br + ALD2 → HBr + MCO3</span><br />
<br />
|-valign="top<br />
|818<br />
|Br + ACET → HBr + ATO2 + CO<br />
|1.66E-10exp(-7000/T)<br />
|Creates carbon: R=3C, P=4C<br />
|Remove CO, same as above<br><br />
<span style="color:green">Br + ACET → HBr + ATO2</span><br />
<br />
|-valign="top<br />
|819<br />
|Br + C2H6 → HBr + ETO2 + CO<br />
|2.36E-10 exp(-6411/T)<br />
|Creates carbon: R=2C, P=3C<br />
|Remove CO, same as above<br><br />
<span style="color:green">Br + C2H6 → HBr + ETO2</span><br />
<br />
|-valign="top<br />
|820<br />
|Br + C3H8 → HBr + A3O2 + CO<br />
|8.77E-11 exp(-4330/T)<br />
|Creates carbon: R=3C, P=4C<br />
|Remove CO, same as above<br><br />
<span style="color:green">Br + C3H8 → HBr + A3O2</span><br />
<br />
|}<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:59, 27 July 2017 (UTC)<br />
<br />
==== Identification of carbon leaking reactions ====<br />
<br />
'''''Sarah Safieddine wrote:'''''<br />
<br />
<blockquote>76 other reactions leaked carbon, we enforced carbon conservation by tracking the lost carbon as CO2 (labeled as <tt>{CO2}</tt> in the document [http://onlinelibrary.wiley.com/store/10.1002/2017GL072602/asset/supinfo/grl55781-sup-0001-Supplementary.docx?v=1&s=21c96c26c411290d72b64fc4f9ecdc5e806af2c5 ROC_SI.docx], Table 2). This is the supplementary material for Safieddine, Heald and Henderson, 2017. It contains the corrections for both the carbon leaking and carbon creating reactions and all other information. The paper for reference can be found here: http://onlinelibrary.wiley.com/doi/10.1002/2017GL072602/abstract.</blockquote><br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:06, 22 May 2017 (UTC)<br />
<br />
==== Fixes to correct ALK4 lumping issue ====<br />
<br />
<span style="color:green">'''''These fixes were included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span><br />
<br />
'''''[[User:Barronh|Barron Henderson]] wrote:'''''<br />
<br />
<blockquote>I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).<br />
<br />
Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy. When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.<br />
<br />
If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.<br />
<br />
I have [https://www.evernote.com/shard/s315/sh/f2ec9589-d827-4ee1-afcb-96ee5a2d2914/d84318450f729cd414e4a6653c03a296 extensive notes] on what I interpret as happening. To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.<br />
<br />
#Increase MO2 stoichiometry from 0.18 to 0.19<br />
#Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).<br />
#Modify the carbon count for ALK4 (i.e. the <tt>MolecRatio</tt> field in the [[GEOS-Chem species database]]) from 4 to 4.3.<br />
<br />
Fixes 1 and 2&mdash;which can be applied to the KPP <tt>globchem.eqn</tt> file&mdash;will make the carbon conservation consistent with Lurmann's. Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.</blockquote><br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:21, 31 January 2017 (UTC)<br />
<br />
=== JPL Released 18th Rate Coefficient Evaluation ===<br />
<br />
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02a|v11-02a]] and approved on 12 May 2017.'''''</span><br />
<br />
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page ([[Updates in JPL Publication 15-10]]) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10. <br />
<br />
:J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.<br />
<br />
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)<br />
<br />
=== Working Group Tele-con on the 2nd December 2011 ===<br />
[[ChemTelecon20111202]]<br />
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''<br />
<br />
=== Isoprene chemistry ===<br />
I've created a page with some of the recent literature on [[Isoprene|isoprene chemistry]]. Please add more papers as they come along! ([[User:mje| MJE Leeds]])<br />
<br />
=== HO2 + CH2O ===<br />
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)<br />
<br />
Hermans, I., et al. (2005), Kinetics of alpha-hydroxy-alkylperoxyl radicals in oxidation<br />
processes. HO2 center dot-initiated oxidation of ketones/aldehydes near the tropopause,<br />
Journal of Physical Chemistry A, 109(19), 4303-4311.<br />
<br />
According to this paper, this reaction is significant when Temperature is below 220K.<br />
<br />
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)<br />
<br />
== Previous issues that have now been resolved ==<br />
<br />
=== Centralizing chemistry time step===<br />
<br />
<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><br />
<br />
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)<br />
<br />
=== Acetone photolysis ===<br />
<br />
[[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]].<br />
<br />
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)<br />
<br />
== Documentation ==<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
*[http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf Updated chemical reactions] that will be used in [[GEOS-Chem v8-02-04]] and higher.<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v5.pdf Updated chemical reactions] now used in [[GEOS-Chem v8-02-01]] through [[GEOS-Chem v8-02-03]]. <br />
**All typos have now been corrected in the present file.<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jv_spec_format.pdf Format of FAST-J input file <tt>jv_spec.dat</tt>]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:41, 27 October 2009 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_vertical_grids&diff=39038GEOS-Chem vertical grids2018-10-01T13:57:58Z<p>Barronh: /* Hybrid grid definition */</p>
<hr />
<div>----<br />
----<br />
<big><strong>GEOS-Chem v11-02-final</strong> '''will also carry the designation''' <strong>GEOS-Chem 12.0.0</strong>'''.''' We are migrating to a purely numeric versioning system in order to adhere more closely to software development best practices. For a complete description of the new versioning system, please see [[GEOS-Chem version numbering system|our ''GEOS-Chem version numbering system'' wiki page]].</big><br />
----<br />
----<br />
<br />
<br />
On this page we provide information about the various vertical grids used in GEOS-Chem. We also invite you to visit our [[GEOS-Chem horizontal grids|''GEOS-Chem horizontal grids'' wiki page]].<br />
<br />
== Comparisons of vertical grids used by GEOS-Chem ==<br />
<br />
The table below compares the level structure of the various grids used by GEOS-Chem.<br />
<br />
<span style="color:red">'''''[[GEOS-Chem v11-02|GEOS-Chem v11-02 aka 12.0.0]] and later versions only support the [[GEOS-FP]] and [[MERRA-2]] met field products from NASA/GMAO. All other met field products mentioned below have been de-supported.'''''</span><br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top"<br />
!bgcolor="#CCCCCC" width="300px"|Description<br />
!bgcolor="#CCCCCC" width="700px"|Comparison<br />
<br />
|-valign="top"<br />
|Vertical grids up to 3 km:<br />
#[[#GCAP vertical grid|GCAP]]<br />
#[[#GEOS-3 vertical grid|GEOS-3]]<br />
#[[#Vertical grids for GEOS-4|GEOS-4]] and <br />
#[[#Vertical grids for GEOS-5, GEOS-FP, MERRA, and MERRA-2|GEOS-5 / GEOS-FP / MERRA / MERRA2]]<br />
|[[Image:Levels3km.png]]<br />
<br />
|-valign="top"<br />
|Vertical grids up to 10 km:<br />
#[[#GCAP vertical grid|GCAP]]<br />
#[[#GEOS-3 vertical grid|GEOS-3]]<br />
#[[#Vertical grids for GEOS-4|GEOS-4]] and <br />
#[[#Vertical grids for GEOS-5, GEOS-FP, MERRA, and MERRA-2|GEOS-5 / GEOS-FP / MERRA / MERRA2]]<br />
|[[Image:Levels10km.png]]<br />
<br />
|-valign="top"<br />
|Vertical grids up to 32 km:<br />
#[[#GCAP vertical grid|GCAP]]<br />
#[[#GEOS-3 vertical grid|GEOS-3]]<br />
#[[#Vertical grids for GEOS-4|GEOS-4]] and <br />
#[[#Vertical grids for GEOS-5, GEOS-FP, MERRA, and MERRA-2|GEOS-5 / GEOS-FP / MERRA / MERRA2]]<br />
|[[Image:Levels32km.png]]<br />
<br />
|-valign="top"<br />
|Vertical grids up to 80km:<br />
#[[#GCAP vertical grid|GCAP]]<br />
#[[#GEOS-3 vertical grid|GEOS-3]]<br />
#[[#Vertical grids for GEOS-4|GEOS-4]] and <br />
#[[#Vertical grids for GEOS-5, GEOS-FP, MERRA, and MERRA-2|GEOS-5 / GEOS-FP / MERRA / MERRA2]]<br />
|[[Image:Levels80km.png]]<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:47, 14 November 2016 (UTC)<br />
<br />
== Vertical grids for GEOS-FP and MERRA-2 ==<br />
<br />
The [[GEOS-FP]] and [[MERRA-2]] met field products from GMAO share the same vertical grid.<br />
<br />
<span style="color:red">'''''NOTE: The [[GEOS-5]] and [[MERRA]] met field products are placed on the same vertical grid as GEOS-FP and MERRA-2. But per request of NASA/GMAO, the GEOS-5 and MERRA met field products have been de-supported from [[GEOS-Chem v11-02]] and later versions.'''''</span><br />
<br />
=== 72-layer vertical grid ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
<br />
|-valign="top"<br />
!width="200px" bgcolor="#CCCCCC"|Used by <br />
|width="800px"|These met field products are currenlty used by GEOS-Chem:<br />
*[[GEOS-FP|GMAO GEOS-5 "forward processing" (aka GEOS-FP)]]<br />
*[[MERRA-2|GMAO MERRA-2 reanalysis product]]<br />
<br />
These met field products have been de-supported from [[GEOS-Chem v11-02]] and later versions:<br />
*[[GEOS-5|GMAO GEOS-5]]<br />
*[[MERRA|GMAO MERRA reanalysis product]]<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Number of layers<br />
|<br />
*72 centers<br />
*73 edges<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Indexing<br />
|<br />
*Surface upwards (in GEOS-Chem "Classic"); L=1 is the surface<br />
*Surface upwards (in met field files read in by GEOS-Chem); L=1 is the surface<br />
*Top down (in GMAO "raw" data files); L=1 is the atmosphere top<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Type of grid<br />
|<br />
*[[#Hybrid grid definition|Hybrid sigma-pressure]]<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Hybrid Ap parameter [hPa]<br />
|<br />
(surface)<br />
0.000000d+00, 4.804826d-02, 6.593752d+00, 1.313480d+01, 1.961311d+01, 2.609201d+01,<br />
3.257081d+01, 3.898201d+01, 4.533901d+01, 5.169611d+01, 5.805321d+01, 6.436264d+01,<br />
7.062198d+01, 7.883422d+01, 8.909992d+01, 9.936521d+01, 1.091817d+02, 1.189586d+02,<br />
1.286959d+02, 1.429100d+02, 1.562600d+02, 1.696090d+02, 1.816190d+02, 1.930970d+02,<br />
2.032590d+02, 2.121500d+02, 2.187760d+02, 2.238980d+02, 2.243630d+02, 2.168650d+02,<br />
2.011920d+02, 1.769300d+02, 1.503930d+02, 1.278370d+02, 1.086630d+02, 9.236572d+01,<br />
7.851231d+01, 6.660341d+01, 5.638791d+01, 4.764391d+01, 4.017541d+01, 3.381001d+01,<br />
2.836781d+01, 2.373041d+01, 1.979160d+01, 1.645710d+01, 1.364340d+01, 1.127690d+01,<br />
9.292942d+00, 7.619842d+00, 6.216801d+00, 5.046801d+00, 4.076571d+00, 3.276431d+00,<br />
2.620211d+00, 2.084970d+00, 1.650790d+00, 1.300510d+00, 1.019440d+00, 7.951341d-01,<br />
6.167791d-01, 4.758061d-01, 3.650411d-01, 2.785261d-01, 2.113490d-01, 1.594950d-01,<br />
1.197030d-01, 8.934502d-02, 6.600001d-02, 4.758501d-02, 3.270000d-02, 2.000000d-02,<br />
1.000000d-02<br />
(top of atmosphere)<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Hybrid Bp parameter [1]<br />
|<br />
(surface)<br />
1.000000d+00, 9.849520d-01, 9.634060d-01, 9.418650d-01, 9.203870d-01, 8.989080d-01,<br />
8.774290d-01, 8.560180d-01, 8.346609d-01, 8.133039d-01, 7.919469d-01, 7.706375d-01,<br />
7.493782d-01, 7.211660d-01, 6.858999d-01, 6.506349d-01, 6.158184d-01, 5.810415d-01,<br />
5.463042d-01, 4.945902d-01, 4.437402d-01, 3.928911d-01, 3.433811d-01, 2.944031d-01,<br />
2.467411d-01, 2.003501d-01, 1.562241d-01, 1.136021d-01, 6.372006d-02, 2.801004d-02,<br />
6.960025d-03, 8.175413d-09, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00,<br />
0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00,<br />
0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00,<br />
0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00,<br />
0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00,<br />
0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00,<br />
0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00,<br />
0.000000d+00<br />
(top of atmosphere)<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Pressures and altitudes for a column at atmospheric sea level, from surface upwards<br />
|<br />
<br />
L Eta Edge Eta Mid Altitude Pressure <br />
(unitless) (unitless) (km) (hPa) <br />
========================================================<br />
0.000000 80.581 0.010<br />
72 0.000005 78.146 0.015<br />
0.000010 76.357 0.020<br />
71 0.000016 74.594 0.026<br />
0.000022 73.180 0.033<br />
70 0.000030 71.812 0.040<br />
0.000037 70.657 0.048<br />
69 0.000046 69.440 0.057<br />
0.000055 68.392 0.066<br />
68 0.000067 67.243 0.078<br />
0.000078 66.245 0.089<br />
67 0.000093 65.115 0.105<br />
0.000108 64.130 0.120<br />
66 0.000128 63.004 0.140<br />
0.000148 62.021 0.159<br />
65 0.000173 60.902 0.185<br />
0.000199 59.924 0.211<br />
64 0.000232 58.816 0.245<br />
0.000265 57.846 0.279<br />
63 0.000308 56.752 0.322<br />
0.000350 55.794 0.365<br />
62 0.000405 54.717 0.420<br />
0.000460 53.773 0.476<br />
61 0.000529 52.716 0.546<br />
0.000599 51.788 0.617<br />
60 0.000687 50.754 0.706<br />
0.000775 49.844 0.795<br />
59 0.000886 48.835 0.907<br />
0.000996 47.946 1.019<br />
58 0.001135 46.962 1.160<br />
0.001274 46.092 1.301<br />
57 0.001446 45.134 1.476<br />
0.001619 44.286 1.651<br />
56 0.001834 43.355 1.868<br />
0.002048 42.529 2.085<br />
55 0.002312 41.627 2.353<br />
0.002576 40.825 2.620<br />
54 0.002900 39.951 2.948<br />
0.003224 39.173 3.276<br />
53 0.003619 38.328 3.677<br />
0.004013 37.574 4.077<br />
52 0.004492 36.759 4.562<br />
0.004971 36.030 5.047<br />
51 0.005548 35.244 5.632<br />
0.006126 34.539 6.217<br />
50 0.006818 33.782 6.918<br />
0.007510 33.101 7.620<br />
49 0.008336 32.372 8.456<br />
0.009162 31.716 9.293<br />
48 0.010141 31.015 10.285<br />
0.011120 30.382 11.277<br />
47 0.012287 29.701 12.460<br />
0.013455 29.085 13.643<br />
46 0.014844 28.423 15.050<br />
0.016232 27.824 16.457<br />
45 0.017878 27.180 18.124<br />
0.019523 26.596 19.792<br />
44 0.021467 25.971 21.761<br />
0.023410 25.402 23.730<br />
43 0.025699 24.794 26.049<br />
0.027987 24.240 28.368<br />
42 0.030673 23.648 31.089<br />
0.033358 23.108 33.810<br />
41 0.036499 22.531 36.993<br />
0.039641 22.004 40.175<br />
40 0.043326 21.438 43.910<br />
0.047011 20.920 47.644<br />
39 0.051326 20.364 52.016<br />
0.055641 19.855 56.388<br />
38 0.060682 19.309 61.496<br />
0.065723 18.807 66.603<br />
37 0.071600 18.269 72.558<br />
0.077477 17.773 78.512<br />
36 0.084313 17.243 85.439<br />
0.091149 16.753 92.366<br />
35 0.099191 16.222 100.514<br />
0.107233 15.731 108.663<br />
34 0.116695 15.198 118.250<br />
0.126157 14.706 127.837<br />
33 0.137287 14.170 139.115<br />
0.148418 13.674 150.393<br />
32 0.161513 13.134 163.661<br />
0.174608 12.633 176.930<br />
31 0.190061 12.086 192.587<br />
0.205513 11.578 208.244<br />
30 0.223772 11.021 226.745<br />
0.242032 10.504 245.246<br />
29 0.263587 9.936 267.087<br />
0.285142 9.409 288.927<br />
28 0.309854 8.846 313.966<br />
0.334566 8.320 339.005<br />
27 0.353349 7.943 358.038<br />
0.372133 7.582 377.070<br />
26 0.390927 7.237 396.112<br />
0.409720 6.905 415.155<br />
25 0.428528 6.585 434.212<br />
0.447337 6.277 453.269<br />
24 0.466153 5.980 472.335<br />
0.484970 5.692 491.401<br />
23 0.503795 5.413 510.475<br />
0.522620 5.142 529.550<br />
22 0.541449 4.879 548.628<br />
0.560278 4.623 567.706<br />
21 0.579115 4.375 586.793<br />
0.597953 4.132 605.880<br />
20 0.616790 3.896 624.967<br />
0.635628 3.665 644.054<br />
19 0.654471 3.439 663.146<br />
0.673314 3.219 682.239<br />
18 0.685878 3.074 694.969<br />
0.698442 2.932 707.699<br />
17 0.711006 2.792 720.429<br />
0.723570 2.654 733.160<br />
16 0.736134 2.517 745.890<br />
0.748698 2.382 758.621<br />
15 0.761265 2.249 771.354<br />
0.773832 2.118 784.088<br />
14 0.786400 1.988 796.822<br />
0.798967 1.860 809.556<br />
13 0.809021 1.759 819.743<br />
0.819075 1.659 829.929<br />
12 0.826616 1.584 837.570<br />
0.834157 1.510 845.211<br />
11 0.841698 1.436 852.852<br />
0.849239 1.363 860.493<br />
10 0.856781 1.290 868.135<br />
0.864323 1.218 875.776<br />
9 0.871864 1.146 883.418<br />
0.879406 1.075 891.059<br />
8 0.886948 1.004 898.701<br />
0.894489 0.934 906.342<br />
7 0.902031 0.864 913.984<br />
0.909573 0.795 921.626<br />
6 0.917116 0.726 929.268<br />
0.924658 0.657 936.911<br />
5 0.932200 0.589 944.553<br />
0.939743 0.521 952.195<br />
4 0.947285 0.454 959.837<br />
0.954828 0.387 967.480<br />
3 0.962370 0.320 975.122<br />
0.969913 0.254 982.765<br />
2 0.977456 0.189 990.408<br />
0.984999 0.123 998.051<br />
1 0.992500 0.058 1005.650<br />
1.000000 -0.006 1013.250<br />
|}<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:51, 14 November 2016 (UTC)<br />
<br />
=== 47-layer reduced vertical grid ===<br />
<br />
In order to save computational resources, GEOS-Chem "Classic" can collapse the 72 layer grid down to a 47-layer grid "on-the-fly". Groups of 2 and 4 layers are lumped together starting at ~70 hPa. See the table below for more information.<br />
<br />
<span style="color:red">'''''NOTE: The [[GEOS-5]] and [[MERRA]] met field products are placed on the same vertical grid as GEOS-FP and MERRA-2. But per request of NASA/GMAO, the GEOS-5 and MERRA met field products have been de-supported from [[GEOS-Chem v11-02]] and later versions.'''''</span><br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
<br />
|-valign="top"<br />
!width="200px" bgcolor="#CCCCCC"|Used by <br />
|width="800px"|These met field products are currently used by GEOS-Chem:<br />
*[[GEOS-FP|GMAO GEOS-5 "forward processing" (aka GEOS-FP)]]<br />
*[[MERRA-2|GMAO MERRA-2 reanalysis product]]<br />
<br />
These met field products have been de-supported from [[GEOS-Chem v11-02]] and later versions:<br />
*[[GEOS-5|GMAO GEOS-5]]<br />
*[[MERRA|GMAO MERRA reanalysis product]]<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Number of layers<br />
|<br />
*47 centers<br />
*48 edges<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Indexing<br />
|<br />
*Surface upwards (in GEOS-Chem "Classic"); L=1 is the surface<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Type of grid<br />
|<br />
*[[#Hybrid grid definition|Hybrid sigma-pressure]]<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Lumping of vertical levels<br />
|<br />
47-level reduced vertical grid<br />
<br />
Bottom Bottom # levels<br />
edge of edge prs lumped <br />
level (hPa) together<br />
<br />
PTOP 0.010 <br />
47 0.066 4<br />
46 0.211 4<br />
45 0.617 4<br />
44 1.651 4<br />
43 4.077 4<br />
42 9.293 4<br />
41 19.792 4<br />
40 28.368 2<br />
39 40.175 2<br />
38 56.388 2<br />
37 78.512 2<br />
%%%% START LUMPING LEVELS ABOVE HERE %%%%%<br />
36 92.366 <br />
35 108.663<br />
34 127.837<br />
33 150.393<br />
32 176.930<br />
%%%% FIXED-PRESSURE LEVELS BEGIN HERE %%%%<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Hybrid Ap parameter [hPa]<br />
|<br />
(surface)<br />
0.000000d+00, 4.804826d-02, 6.593752d+00, 1.313480d+01, 1.961311d+01, 2.609201d+01,<br />
3.257081d+01, 3.898201d+01, 4.533901d+01, 5.169611d+01, 5.805321d+01, 6.436264d+01,<br />
7.062198d+01, 7.883422d+01, 8.909992d+01, 9.936521d+01, 1.091817d+02, 1.189586d+02,<br />
1.286959d+02, 1.429100d+02, 1.562600d+02, 1.696090d+02, 1.816190d+02, 1.930970d+02,<br />
2.032590d+02, 2.121500d+02, 2.187760d+02, 2.238980d+02, 2.243630d+02, 2.168650d+02,<br />
2.011920d+02, 1.769300d+02, 1.503930d+02, 1.278370d+02, 1.086630d+02, 9.236572d+01,<br />
7.851231d+01, 5.638791d+01, 4.017541d+01, 2.836781d+01, 1.979160d+01, 9.292942d+00,<br />
4.076571d+00, 1.650790d+00, 6.167791d-01, 2.113490d-01, 6.600001d-02, 1.000000d-02<br />
(top of atmosphere)<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Hybrid Bp parameter [1]<br />
|<br />
(surface)<br />
1.000000d+00, 9.849520d-01, 9.634060d-01, 9.418650d-01, 9.203870d-01, 8.989080d-01,<br />
8.774290d-01, 8.560180d-01, 8.346609d-01, 8.133039d-01, 7.919469d-01, 7.706375d-01,<br />
7.493782d-01, 7.211660d-01, 6.858999d-01, 6.506349d-01, 6.158184d-01, 5.810415d-01,<br />
5.463042d-01, 4.945902d-01, 4.437402d-01, 3.928911d-01, 3.433811d-01, 2.944031d-01,<br />
2.467411d-01, 2.003501d-01, 1.562241d-01, 1.136021d-01, 6.372006d-02, 2.801004d-02,<br />
6.960025d-03, 8.175413d-09, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00,<br />
0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00,<br />
0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00, 0.000000d+00<br />
(top of atmosphere)<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Pressures and altitudes for a column at atmospheric sea level, from surface upwards<br />
|<br />
L Eta Edge Eta Mid Altitude Pressure<br />
(unitless) (unitless) (km) (hPa)<br />
========================================================<br />
0.000000 80.581 0.010<br />
47 0.000028 72.180 0.038<br />
0.000055 68.392 0.066<br />
46 0.000127 63.053 0.139<br />
0.000199 59.924 0.211<br />
45 0.000399 54.834 0.414<br />
0.000599 51.788 0.617<br />
44 0.001109 47.135 1.134<br />
0.001619 44.286 1.651<br />
43 0.002816 40.166 2.864<br />
0.004013 37.574 4.077<br />
42 0.006588 34.024 6.685<br />
0.009162 31.716 9.293<br />
41 0.014342 28.654 14.542<br />
0.019523 26.596 19.792<br />
40 0.023755 25.307 24.080<br />
0.027987 24.240 28.368<br />
39 0.033814 23.020 34.272<br />
0.039641 22.004 40.175<br />
38 0.047641 20.836 48.282<br />
0.055641 19.855 56.388<br />
37 0.066559 18.727 67.450<br />
0.077477 17.773 78.512<br />
36 0.084313 17.243 85.439<br />
0.091149 16.753 92.366<br />
35 0.099191 16.222 100.514<br />
0.107233 15.731 108.663<br />
34 0.116695 15.198 118.250<br />
0.126157 14.706 127.837<br />
33 0.137287 14.170 139.115<br />
0.148418 13.674 150.393<br />
32 0.161513 13.134 163.661<br />
0.174608 12.633 176.930<br />
31 0.190061 12.086 192.587<br />
0.205513 11.578 208.244<br />
30 0.223772 11.021 226.745<br />
0.242032 10.504 245.246<br />
29 0.263587 9.936 267.087<br />
0.285142 9.409 288.927<br />
28 0.309854 8.846 313.966<br />
0.334566 8.320 339.005<br />
27 0.353349 7.943 358.038<br />
0.372133 7.582 377.070<br />
26 0.390927 7.237 396.112<br />
0.409720 6.905 415.155<br />
25 0.428528 6.585 434.212<br />
0.447337 6.277 453.269<br />
24 0.466153 5.980 472.335<br />
0.484970 5.692 491.401<br />
23 0.503795 5.413 510.475<br />
0.522620 5.142 529.550<br />
22 0.541449 4.879 548.628<br />
0.560278 4.623 567.706<br />
21 0.579115 4.375 586.793<br />
0.597953 4.132 605.880<br />
20 0.616790 3.896 624.967<br />
0.635628 3.665 644.054<br />
19 0.654471 3.439 663.146<br />
0.673314 3.219 682.239<br />
18 0.685878 3.074 694.969<br />
0.698442 2.932 707.699<br />
17 0.711006 2.792 720.429<br />
0.723570 2.654 733.160<br />
16 0.736134 2.517 745.890<br />
0.748698 2.382 758.621<br />
15 0.761265 2.249 771.354<br />
0.773832 2.118 784.088<br />
14 0.786400 1.988 796.822<br />
0.798967 1.860 809.556<br />
13 0.809021 1.759 819.743<br />
0.819075 1.659 829.929<br />
12 0.826616 1.584 837.570<br />
0.834157 1.510 845.211<br />
11 0.841698 1.436 852.852<br />
0.849239 1.363 860.493<br />
10 0.856781 1.290 868.135<br />
0.864323 1.218 875.776<br />
9 0.871864 1.146 883.418<br />
0.879406 1.075 891.059<br />
8 0.886948 1.004 898.701<br />
0.894489 0.934 906.342<br />
7 0.902031 0.864 913.984<br />
0.909573 0.795 921.626<br />
6 0.917116 0.726 929.268<br />
0.924658 0.657 936.911<br />
5 0.932200 0.589 944.553<br />
0.939743 0.521 952.195<br />
4 0.947285 0.454 959.837<br />
0.954828 0.387 967.480<br />
3 0.962370 0.320 975.122<br />
0.969913 0.254 982.765<br />
2 0.977456 0.189 990.408<br />
0.984999 0.123 998.051<br />
1 0.992500 0.058 1005.650<br />
1.000000 -0.006 1013.250<br />
|}<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:33, 14 November 2016 (UTC)<br />
<br />
== Reference section for vertical grids ==<br />
<br />
In this section we provide more general information about the vertical grids used by GEOS-Chem.<br />
<br />
=== Sigma grid definition ===<br />
<br />
The sigma grid is a purely terrain-following coordinate. The following met data products are defined on the sigma grid:<br />
<br />
# [[Overview of GMAO met data products#GEOS-3|GMAO GEOS-3]] '''(NOTE: Now obsolete)'''''<br />
# [[GCAP|GCAP/GISS meteroloogy]]<br />
#*NOTE: GCAP met is really a hybrid grid, but it is defined as if it were a pure sigma grid (i.e. P<sub>TOP</sub>=150 hPa, and negative sigma edges at higher levels. <br />
<br />
The sigma grid is defined as follows:<br />
<br />
P(I,J,L) - P<sub>TOP</sub><br />
&sigma;(L)= ------------------------<br />
P<sub>surface</sub>(I,J) - P<sub>TOP</sub><br />
<br />
where:<br />
<br />
I,J,L are the longitude, latitude, level indices of the grid box<br />
P(I,J,L) is the pressure at a level edge or level center at grid box (I,J,L)<br />
P<sub>surface</sub>(I,J) is the surface pressure at grid box (I,J)<br />
P<sub>TOP</sub> is the pressure at the top of the atmosphere<br />
<br />
<tt>&sigma;(L)</tt> always varies between 0 and 1, with 1 being the surface and 0 being the atmosphere top. Therefore you can think of <tt>&sigma;(L)</tt> as the "fraction" of the atmosphere (measured from the top down) at which you are located.<br />
<br />
The <tt>&sigma;(L)</tt> therefore are independent of <tt>(I,J)</tt>. The sigma values are typically fixed for a given met field type. Knowing the sigma value allows you to compute the center or edge pressures as follows:<br />
<br />
P<sub>edge</sub>(I,J,L) = &sigma;<sub>edge</sub>(L) * [ P<sub>surface</sub>(I,J) - P<sub>TOP</sub> ] + P<sub>TOP</sub><br />
<br />
P<sub>center</sub>(I,J,L) = &sigma;<sub>center</sub>(L) * [ P<sub>surface</sub>(I,J) - P<sub>TOP</sub> ] + P<sub>TOP</sub><br />
<br />
Any sigma grid can also be computed with the [[#Hybrid grid|hybrid grid]] equation:<br />
<br />
P<sub>edge</sub>(I,J,L) = A<sub>p</sub>(L) + [ B<sub>p</sub>(L) * ( P<sub>surface</sub>(I,J) - P<sub>TOP</sub> ) ]<br />
<br />
P<sub>center</sub>(I,J,L) = [ P<sub>edge</sub>(I,J,L) + P<sub>edge</sub>(I,J,L+1) ] / 2 <br />
<br />
where<br />
<br />
P<sub>surface</sub>(I,J) = the "true" surface pressure at lon,lat (I,J)<br />
A<sub>p</sub>(L) = P<sub>TOP</sub> = model top pressure<br />
B<sub>p</sub>(L) = &sigma;<sub>edge</sub>(L) = bottom sigma edge of level L<br />
<br />
=== Hybrid grid definition ===<br />
<br />
Earlier versions of the GMAO met data products used a pure-sigma grid definition. The problem with a sigma-grid is that you still see the signature of the mountains at the very top of the atmosphere. This was the case in GEOS-3 and this caused a lot of noise in the stratospheric winds, which led to poor STE.<br />
<br />
The improvement on the sigma grid is the hybrid (or &eta;) grid. This grid is defined with A and B coefficients, which are specified by the makers of the met data products (e.g. GMAO).<br />
<br />
The following met data products use the hybrid grid formulation:<br />
<br />
#[[GEOS-FP|GMAO GEOS-FP]] (currently used in GEOS-Chem)<br />
#[[MERRA-2|GMAO MERRA-2]] (currently used in GEOS-Chem) <br />
#[[GMAO GEOS-4]] (de-supported in GEOS-Chem v11-02)<br />
#[[GEOS-5|GMAO GEOS-5]] (de-supported in GEOS-Chem v11-02)<br />
#[[MERRA|GMAO MERRA]] (de-supported in GEOS-Chem v11-02)<br />
<br />
The pressure at the bottom edge of grid box <tt>(I,J,L)</tt> is defined as follows:<br />
<br />
P<sub>edge</sub>(I,J,L) = A<sub>p</sub>(L) + [ B<sub>p</sub>(L) * P<sub>surface</sub>(I,J) ]<br />
<br />
P<sub>center</sub>(I,J,L) = [ P<sub>edge</sub>(I,J,L) + P<sub>edge</sub>(I,J,L+1) ] / 2<br />
where<br />
<br />
I,J,L are the lon, lat, level indices of the grid box<br />
P<sub>surface</sub>(I,J) is the "true" surface pressure at lon,lat (I,J)<br />
A<sub>p</sub>(L) has the same units as surface pressure [hPa]<br />
B<sub>p</sub>(L) is a unitless constant given at level edges<br />
<br />
The <tt>A<sub>p</sub>(L)</tt> and <tt>B<sub>p</sub>(L)</tt> for each met field type are listed in the GEOS-Chem source code file <tt>pressure_mod.f</tt>.<br />
<br />
=== The hybrid grid formula in more depth ===<br />
<br />
'''''[mailto:rb864@uowmail.edu.au Rebecca Buchholz] wrote:'''''<br />
<br />
:I'm having trouble conceptualising exactly how GEOS-Chem deals with the vertical grid. I'm using the [[GEOS-5]] reduced vertical resolution of 47 eta levels. I've seen the [http://amsglossary.allenpress.com/glossary/search?id=eta-vertical-coordinate1 AMS definition of eta].<br />
<br />
:I can see the first fraction is the sigma definition (which follows terrain). Is the second fraction essentially a scaling by the pressure at altitude relative to pressure at sea surface? I'm not sure how it fits in with the GEOS-Chem definition, i.e. when rearranging the equation, what becomes A_p and B_p.<br />
<br />
:The manual and wiki pages indicate GEOS-5 is a hybrid pressure-sigma grid. Are the first 31 levels pure sigma levels in both the reduced vertical 47 and native 72 level GEOS-5 fields? Does this mean GEOS-5 doesn't use the above eta definition of the levels - only sigma definition? Does GEOS-Chem then change the sigma levels to eta levels?<br />
<br />
'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] replied:'''''<br />
<br />
:Maybe we have used “eta” as a synonym for “hybrid” grid. Basically it refers to a grid that transitions smoothly from a sigma terrain-following coordinate near the surface to fixed pressure levels in the upper atmosphere. <br />
<br />
:Older met fields (e.g. GEOS-3) came on pure-sigma grids. However, the problem is that with a pure-sigma grid, you still see some signal of the mountains even at the top of the atmosphere. This makes the upper-atmosphere winds very noisy and it messes up the strat-trop exchange. (Or so GMAO tells us.)<br />
<br />
:The way I like to think of it is we specify the pressure at the bottom edge of grid box <tt>(I,J,L)</tt> with this formula:<br />
<br />
Pedge(I,J,L) = Ap(L) + [ Bp(L) * Psurface(I,J) ]<br />
<br />
:where <tt>Ap(L)</tt> and <tt>Bp(L)</tt> are specified by GMAO. Then you specify the pressures at the center of grid box <tt>(I,J,L)</tt> with this formula:<br />
<br />
Pcenter(I,J,L) = [ Pedge(I,J,L) + Pedge(I,J,L+1) ] / 2<br />
<br />
:i.e. it’s an average of the pressure at both edges. <br />
<br />
:Note that the <tt>Pedge(I,J,L)</tt> and <tt>Pcenter(I,J,L)</tt> vary w/ the topography up until about 170 hPa. That is where the first fixed-pressure levels occur. Skyward of that, then <tt>Pedge(I,J,L)</tt> and <tt>Pcenter(I,J,L)</tt> will be constant for all longitudes and latitudes <tt>(I,J)</tt>.<br />
<br />
:Once you have computed <tt>Pedge(I,J,L)</tt> and <tt>Pcenter(I,J,L)</tt>, you can construct an ETA coordinate such as:<br />
<br />
ETAedge(I,J,L) = [ Pedge(I,J,L) – Ptop ] / [ Psurface – Ptop ]<br />
<br />
ETAcenter(I,J,L) = [ Pcenter(I,J,L) – Ptop ] / [ Psurface – Ptop ]<br />
<br />
:but for the purposes of GEOS-Chem, we don’t really use the ETA values. We use the pressures computed from the <tt>Ap(L)</tt> and <tt>Bp(L)</tt> values. <br />
<br />
:The most important thing to note is that the thicknesses of the grid boxes near the surface vary with the surface pressure. When you come to a mountain, the levels all kind of bunch together and get small. When you are over flat land or ocean, the levels widen out.<br />
<br />
:Also note that a pure-sigma grid (like GEOS-3) can also be expressed using the same type of hybrid formulation:<br />
<br />
Pedge(I,J,L) = Ap(L) + [ Bp(L) * ( Psurface(I,J) – PTOP ) ]<br />
<br />
where <br />
<br />
Ap(L) = PTOP (for all L)<br />
Bp(L) = Sigma_Edge(L) = the bottom sigma edge for level L<br />
<br />
:In <tt>GeosUtil/pressure_mod.f</tt> we use the same hybrid formula but we use the <tt>Ap(L)</tt> and <tt>Bp(L)</tt> that pertain to each grid (GEOS-3, GEOS-4, GEOS-5, GCAP, etc). That simplifies the coding.<br />
<br />
--[[User:Bmy|Bob Y.]] 15:58, 6 April 2011 (EDT)<br />
<br />
=== Ordering of the vertical levels ===<br />
<br />
==== In the GMAO met field files ====<br />
<br />
The "raw" GMAO met data files&mdash;which we cut and/or regrid for input into GEOS-Chem&mdash;store data from the top of the atmopshere downward.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="120px"|GMAO data<br>product<br />
!width="120px"|Grid<br>type<br />
!width="100px"|Surface<br> level<br />
!width="100px"|Top-of-<br>atmosphere level<br />
!width="100px"| <br />
!width="100px"|Top-of-<br>atmosphere pressure<br />
<br />
|-valign="top" align="center"<br />
|[[Overview of GMAO met data products#GEOS-3|GEOS-3]]<br />
|Pure sigma<br />
|Level 48<br />
|Level 1<br />
| <br />
|0.01 hPa<br />
<br />
|-valign="top" align="center"<br />
|[[GMAO GEOS-4|GEOS-4]]<br />
|Hybrid<br />
|Level 55<br />
|Level 1<br />
| <br />
|0.01 hPa<br />
<br />
|-valign="top" align="center"<br />
|[[GEOS-5|GEOS-5.2.0]]<br>[[GEOS-FP]]<br>[[MERRA]]<br>[[MERRA-2]]<br />
|Hybrid<br />
|Level 72<br />
|Level 1<br />
| <br />
|0.01 hPa<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:51, 14 November 2016 (UTC)<br />
<br />
==== GEOS-Chem ====<br />
<br />
GEOS-Chem labels vertical levels starting from the surface and then moving upward&mdash;exactly in the opposite way as in the GMAO met field files.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="120px"|GMAO data<br>product<br />
!width="120px"|Grid<br>type<br />
!width="100px"|Surface<br> level<br />
!width="100px"|Top-of-<br>atmosphere level:<br>Full grid<br />
!width="100px"|Top-of-<br>atmosphere level:<br>[[#Collapsing of the vertical levels in GEOS-Chem|Reduced grid]]<br />
!width="100px"|Top-of<br>atmosphere pressure<br />
<br />
|-valign="top" align="center"<br />
|[[Overview of GMAO met data products#GEOS-3|GEOS-3]]<br />
|Pure sigma<br />
|Level 1 <br />
|Level 48<br />
|Level 30<br />
|0.01 hPa<br />
<br />
|-valign="top" align="center"<br />
|[[GMAO GEOS-4|GEOS-4]]<br />
|Hybrid<br />
|Level 1<br />
|Level 55<br />
|Level 30<br />
|0.01 hPa<br />
<br />
|-valign="top" align="center"<br />
|[[GEOS-5|GEOS-5.2.0]]<br>[[GEOS-FP]]<br>[[MERRA]]<br>[[MERRA-2]]<br />
|Hybrid<br />
|Level 1<br />
|Level 72<br />
|Level 47<br />
|0.01 hPa<br />
<br />
|}<br />
<br />
GEOS-Chem denotes the surface by L=1 because there are special processes (i.e. emissions, deposition, etc) that always happen at the surface level. The coding would be much more difficult if we kept L=1 for the atmosphere top and let the index of the surface vary. Also, in many instances it is more natural to think of processes as extending upward from the surface rather than as downward from the atmosphere top.<br />
<br />
The GEOS-Chem routines (in <tt>GeosUtil/pressure_mod.f</tt>):<br />
<br />
* <code>GET_PEDGE( I, J, L )</code><br />
* <code>GET_PCENTER( I, J, L )</code><br />
<br />
return the pressures in hPa at the edge and center, respectively, of grid box <tt>(I,J,L)</tt>.<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:18, 14 November 2016 (UTC)<br />
<br />
=== Vertical grids and GAMAP ===<br />
<br />
'''''[mailto:Ray.Nassar@ec.gc.ca Ray Nassar] wrote:'''''<br />
<br />
:[http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html Appendix 3 of the GEOS-Chem online manual] describes the different GEOS vertical grids.<br />
<br />
:These are based on a sigma/eta co-ordinate system, therefore equivalent altitudes can only be approximately defined by specifying a surface pressure. For example, altitudes for the GEOS-4 vertical grid and the reduced vertical grid are both shown in the online manual using a surface pressure of 1000 hPa (although the page incorrectly states that 1010 hPa was used).<br />
<br />
:Please note: Using the [http://acmg.seas.harvard.edu/gamap/ GAMAP software package], the altitudes provided in plot titles for the first 12 GEOS-4 levels differ from those specified in the GEOS-Chem online manual due to the specification of a different surface pressure. [[GAMAP_bugs_and_fixes#GAMAP_plot_titles_showing_.22incorrect.22_altitudes_for_plots|A correction for this apparent error]] can be found in the GAMAP bugs and fixes section of this wiki.<br />
<br />
'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] wrote:'''''<br />
<br />
:[http://acmg.seas.harvard.edu/gamap/ GAMAP v2-15] fixes many of the inconsistencies in the computation of the pressure and ETA coordinates for hybrid grids that were noted in previous GAMAP versions. If you are using an older version of GAMAP, then you should update.<br />
<br />
:For example:<br />
<br />
IDL> a = ctm_grid( ctm_type( 'gcap', res=4 ) )<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:14, 14 November 2016 (UTC)<br />
<br />
=== For more information ===<br />
<br />
Please see the following resources for more information about vertical grids:<br />
<br />
# [http://acmg.seas.harvard.edu/geos/wiki_docs/geos5/vertical_grids.pdf ''Overview of vertical grids'' by Bob Yantosca] (PDF)<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:16, 14 November 2016 (UTC)<br />
<br />
== Obsolete information ==<br />
<br />
The following sections correspond to vertical grids that have been de-supported in the most recent versions of GEOS-Chem. We shall keep this information here for reference.<br />
<br />
=== GCAP vertical grid ===<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<span style="color:red">'''''The original GCAP functionality in GEOS-Chem "Classic" is more or less obsolete. Most people use the ICECAP version of GEOS-Chem for climate-chemistry applications. We shall leave this information here for reference.'''''</span><br />
<br />
GCAP Native Vertical Grid (23 layers)<br />
<br />
L Sig Edge Sig Mid Altitude Pressure<br />
(unitless) (unitless) (km) (hPa)<br />
=======================================================<br />
0.000000 89.247 0.002<br />
23 0.000000 77.507 0.017<br />
0.000000 73.489 0.031<br />
22 0.000000 66.346 0.088<br />
0.000000 62.725 0.145<br />
21 0.000000 57.209 0.303<br />
0.000000 54.014 0.461<br />
20 0.000000 48.400 0.960<br />
0.000000 45.215 1.460<br />
19 0.000000 39.712 3.045<br />
0.000000 36.651 4.630<br />
18 0.000000 33.388 7.315<br />
0.000000 31.209 10.000<br />
17 0.000000 28.959 13.900<br />
0.000000 27.300 17.800<br />
16 0.000000 25.141 24.700<br />
0.000000 23.543 31.600<br />
15 0.000000 21.439 43.900<br />
0.000000 19.876 56.200<br />
14 0.000000 18.387 71.200<br />
0.000000 17.187 86.200<br />
13 0.000000 16.154 101.600<br />
0.000000 15.265 117.000<br />
12 0.000000 14.431 133.500<br />
0.000000 13.690 150.000<br />
11 0.000000 12.825 171.737<br />
0.000000 12.056 193.473<br />
10 0.000000 11.192 220.903<br />
0.000000 10.421 248.332<br />
9 0.000000 9.524 284.042<br />
0.000000 8.721 319.752<br />
8 0.000000 7.580 377.198<br />
0.000000 6.578 434.645<br />
7 0.000000 5.424 509.687<br />
0.000000 4.401 584.730<br />
6 0.000000 3.509 657.185<br />
0.000000 2.692 729.641<br />
5 0.000000 2.098 786.052<br />
0.000000 1.536 842.463<br />
4 0.000000 1.215 876.103<br />
0.000000 0.903 909.743<br />
3 0.000000 0.692 933.032<br />
0.000000 0.485 956.321<br />
2 0.000000 0.344 972.365<br />
0.000000 0.206 988.408<br />
1 0.000000 0.099 1000.829<br />
0.000000 -0.006 1013.250<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:12, 14 November 2016 (UTC)<br />
<br />
=== GEOS-3 vertical grid ===<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<span style="color:red">'''''GEOS-Chem no longer supports GEOS-3 meteorology. We shall keep this information here for future reference.'''''</span><br />
<br />
GEOS-3 is a [[#Sigma grid definition|pure-sigma grid]], unlike the [[#Hybrid grid definition|hybrid grids]] used in later met field products such as GEOS-4, GEOS-5, etc.) The vertical levels are lumped together in sigma-space as follows:<br />
<br />
Original Sigma Lumped <br />
levels edges, levels<br />
on the original on the<br />
48-L grid 48-L grid 30-L grid<br />
<br />
============== 0.000000 ==============<br />
48 <br />
0.000018 <br />
47 <br />
0.000048 30 <br />
46 <br />
0.000092 <br />
45 <br />
============== 0.000155 ==============<br />
44 <br />
0.000245 <br />
43 <br />
0.000370 29 <br />
42 <br />
0.000540 <br />
41 <br />
============== 0.000765 ==============<br />
40 <br />
0.001060 <br />
39 <br />
0.001440 28 <br />
38 <br />
0.001900 <br />
37 <br />
============== 0.002530 ==============<br />
36 <br />
0.003300 <br />
35 <br />
0.004280 27 <br />
34 <br />
0.005500 <br />
33 <br />
============== 0.007040 ============== <br />
32 <br />
0.008975 <br />
31 <br />
0.011405 26 <br />
30 <br />
0.014480 <br />
29 <br />
============== 0.018380 ==============<br />
28 <br />
0.023330 25 <br />
27 <br />
============== 0.029600 ============== <br />
26 <br />
0.037540 24 <br />
25 <br />
============== 0.047610 ==============<br />
24 <br />
0.060350 23 <br />
23 <br />
============== 0.076480 ==============<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:04, 14 November 2016 (UTC)<br />
<br />
=== GEOS-4 55-layer vertical grid ===<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<span style="color:red">'''''NOTE: Per request of NASA/GMAO, the GEOS-4 met fields have been de-supported in [[GEOS-Chem v11-02]] and later versions.'''''</span><br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
<br />
|-valign="top"<br />
!width="200px" bgcolor="#CCCCCC"|Used by <br />
|width="800px"|<br />
*[[GMAO GEOS-4]]<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Number of layers<br />
|<br />
*55 centers<br />
*56 edges<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Indexing<br />
|<br />
*Surface upwards (in GEOS-Chem "Classic"); L=1 is the surface<br />
*Surface upwards (in met field files read in by GEOS-Chem); L=1 is the surface<br />
*Top down (in GMAO "raw" data files); L=1 is the atmosphere top<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Type of grid<br />
|<br />
*[[#Hybrid grid definition|Hybrid sigma-pressure]]<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Hybrid A parameter [hPa]<br />
|<br />
(surface)<br />
0.00000, 0.000000, 12.704939, 35.465965, 66.098427, 101.671654, <br />
138.744400, 173.403183, 198.737839, 215.417526, 223.884689, 224.362869,<br />
216.864929, 201.192093, 176.929993, 150.393005, 127.837006, 108.663429,<br />
92.365662, 78.512299, 66.603378, 56.387939, 47.643932, 40.175419, <br />
33.809956, 28.367815, 23.730362, 19.791553, 16.457071, 13.643393,<br />
11.276889, 9.292943, 7.619839, 6.216800, 5.046805, 4.076567, <br />
3.276433, 2.620212, 2.084972, 1.650792, 1.300508, 1.019442,<br />
0.795134, 0.616779, 0.475806, 0.365041, 0.278526, 0.211349, <br />
0.159495, 0.119703, 0.089345, 0.066000, 0.047585, 0.032700,<br />
0.020000, 0.010000<br />
(top of atmosphere)<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Hybrid B parameter [1]<br />
|<br />
(surface)<br />
1.000000, 0.985110, 0.943290, 0.867830, 0.764920, 0.642710,<br />
0.510460, 0.378440, 0.270330, 0.183300, 0.115030, 0.063720,<br />
0.028010, 0.006960, 0.000000, 0.000000, 0.000000, 0.000000,<br />
0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000,<br />
0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000,<br />
0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000,<br />
0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000,<br />
0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000,<br />
0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000,<br />
0.000000, 0.000000<br />
(top of atmosphere)<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Pressures and altitudes for a column at atmospheric sea level, from surface upwards<br />
|<br />
L Eta Edge Eta Mid Altitude Pressure<br />
(unitless) (unitless) (km) (hPa)<br />
<br />
========================================================<br />
0.000000 80.581 0.010<br />
55 0.000005 78.146 0.015<br />
0.000010 76.357 0.020<br />
54 0.000016 74.594 0.026<br />
0.000022 73.180 0.033<br />
53 0.000030 71.812 0.040<br />
0.000037 70.657 0.048<br />
52 0.000046 69.440 0.057<br />
0.000055 68.392 0.066<br />
51 0.000067 67.243 0.078<br />
0.000078 66.245 0.089<br />
50 0.000093 65.115 0.105<br />
0.000108 64.130 0.120<br />
49 0.000128 63.004 0.140<br />
0.000148 62.021 0.159<br />
48 0.000173 60.902 0.185<br />
0.000199 59.924 0.211<br />
47 0.000232 58.816 0.245<br />
0.000265 57.846 0.279<br />
46 0.000308 56.752 0.322<br />
0.000350 55.794 0.365<br />
45 0.000405 54.717 0.420<br />
0.000460 53.773 0.476<br />
44 0.000529 52.716 0.546<br />
0.000599 51.788 0.617<br />
43 0.000687 50.754 0.706<br />
0.000775 49.844 0.795<br />
42 0.000886 48.835 0.907<br />
0.000996 47.946 1.019<br />
41 0.001135 46.962 1.160<br />
0.001274 46.092 1.301<br />
40 0.001446 45.134 1.476<br />
0.001619 44.286 1.651<br />
39 0.001834 43.355 1.868<br />
0.002048 42.529 2.085<br />
38 0.002312 41.627 2.353<br />
0.002576 40.825 2.620<br />
37 0.002900 39.951 2.948<br />
0.003224 39.173 3.276<br />
36 0.003619 38.328 3.677<br />
0.004013 37.574 4.077<br />
35 0.004492 36.759 4.562<br />
0.004971 36.030 5.047<br />
34 0.005548 35.244 5.632<br />
0.006126 34.539 6.217<br />
33 0.006818 33.782 6.918<br />
0.007510 33.101 7.620<br />
32 0.008336 32.372 8.456<br />
0.009162 31.716 9.293<br />
31 0.010141 31.015 10.285<br />
0.011120 30.383 11.277<br />
30 0.012287 29.701 12.460<br />
0.013455 29.085 13.643<br />
29 0.014844 28.423 15.050<br />
0.016232 27.824 16.457<br />
28 0.017878 27.180 18.124<br />
0.019523 26.596 19.792<br />
27 0.021467 25.971 21.761<br />
0.023410 25.402 23.730<br />
26 0.025699 24.794 26.049<br />
0.027987 24.240 28.368<br />
25 0.030673 23.648 31.089<br />
0.033358 23.108 33.810<br />
24 0.036499 22.531 36.993<br />
0.039641 22.004 40.175<br />
23 0.043326 21.438 43.910<br />
0.047012 20.920 47.644<br />
22 0.051326 20.364 52.016<br />
0.055641 19.855 56.388<br />
21 0.060682 19.309 61.496<br />
0.065723 18.807 66.603<br />
20 0.071600 18.269 72.558<br />
0.077477 17.773 78.512<br />
19 0.084313 17.243 85.439<br />
0.091149 16.753 92.366<br />
18 0.099191 16.222 100.515<br />
0.107234 15.731 108.663<br />
17 0.116695 15.198 118.250<br />
0.126157 14.706 127.837<br />
16 0.137287 14.170 139.115<br />
0.148418 13.674 150.393<br />
15 0.161513 13.134 163.661<br />
0.174608 12.633 176.930<br />
14 0.190061 12.086 192.587<br />
0.205513 11.578 208.244<br />
13 0.223772 11.021 226.745<br />
0.242032 10.504 245.246<br />
12 0.263587 9.936 267.087<br />
0.285142 9.409 288.927<br />
11 0.310561 8.830 314.683<br />
0.335980 8.291 340.439<br />
10 0.365938 7.700 370.793<br />
0.395895 7.148 401.146<br />
9 0.431179 6.541 436.898<br />
0.466464 5.975 472.650<br />
8 0.508017 5.351 514.754<br />
0.549571 4.768 556.857<br />
7 0.598479 4.125 606.413<br />
0.647387 3.523 655.968<br />
6 0.695218 2.969 704.433<br />
0.743050 2.443 752.898<br />
5 0.786601 1.986 797.026<br />
0.830152 1.549 841.154<br />
4 0.866492 1.197 877.974<br />
0.902831 0.857 914.795<br />
3 0.929330 0.615 941.644<br />
0.955828 0.378 968.494<br />
2 0.970469 0.249 983.328<br />
0.985110 0.122 998.163<br />
1 0.992555 0.058 1005.706<br />
1.000000 -0.006 1013.250<br />
|}<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:50, 14 November 2016 (UTC)<br />
<br />
=== GEOS-4 30-level reduced vertical grid ===<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<span style="color:red">'''''NOTE: Per request of NASA/GMAO, the GEOS-4 met fields have been de-supported in [[GEOS-Chem v11-02]] and later versions.'''''</span><br />
<br />
In order to save computational resources, GEOS-Chem "Classic" can collapse the [[GMAO GEOS-4|GEOS-4]] 55 layer grid down to a 30-layer grid "on-the-fly". Groups of 2 and 4 layers are lumped together starting at ~70 hPa. See the table below for more information.<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
<br />
|-valign="top"<br />
!width="200px" bgcolor="#CCCCCC"|Used by <br />
|width="800px"|<br />
*[[GMAO GEOS-4]]<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Number of layers<br />
|<br />
*30 centers<br />
*31 edges<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Indexing<br />
|<br />
*Surface upwards (in GEOS-Chem "Classic"); L=1 is the surface<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Type of grid<br />
|<br />
*[[#Hybrid grid definition|Hybrid sigma-pressure]]<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Lumping of vertical levels<br />
|<br />
GEOS-4 30-level reduced vertical grid<br />
<br />
Bottom Bottom # levels<br />
edge of edge prs lumped <br />
level (hPa) together<br />
<br />
PTOP 0.010 <br />
30 0.066 4<br />
29 0.211 4<br />
28 0.617 4<br />
27 1.651 4<br />
26 4.077 4<br />
25 9.293 4<br />
24 19.792 4<br />
23 28.368 2<br />
22 40.175 2<br />
21 56.388 2<br />
20 78.512 2<br />
%%%% START LUMPING LEVELS ABOVE HERE %%%%%<br />
19 92.366 <br />
18 108.663<br />
17 127.837<br />
16 150.393<br />
15 176.930<br />
%%%% FIXED-PRESSURE LEVELS BEGIN HERE %%%%<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Hybrid Ap parameter [hPa]<br />
|<br />
(surface)<br />
0.000000, 0.000000, 12.704939, 35.465965, 66.098427, 101.671654,<br />
138.744400, 173.403183, 198.737839, 215.417526, 223.884689, 224.362869, <br />
216.864929, 201.192093, 176.929993, 150.393005, 127.837006, 108.663429,<br />
92.365662, 78.512299, 56.387939, 40.175419, 28.367815, 19.791553, <br />
9.292943, 4.076567, 1.650792, 0.616779, 0.211349, 0.066000,<br />
0.010000<br />
(top of atmosphere)<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Hybrid Bp parameter [1]<br />
|<br />
(surface)<br />
1.000000, 0.985110, 0.943290, 0.867830, 0.764920, 0.642710,<br />
0.510460, 0.378440, 0.270330, 0.183300, 0.115030, 0.063720, <br />
0.028010, 0.006960, 0.000000, 0.000000, 0.000000, 0.000000,<br />
0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, <br />
0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000,<br />
0.000000<br />
(top of atmosphere)<br />
<br />
|-valign="top"<br />
! bgcolor="#CCCCCC"|Pressures and altitudes for a column at atmospheric sea level, from surface upwards<br />
|<br />
L Eta Edge Eta Mid Altitude Pressure<br />
(unitless) (unitless) (km) (hPa)<br />
=======================================================<br />
0.000000 80.581 0.010<br />
30 0.000028 72.180 0.038<br />
0.000055 68.392 0.066<br />
29 0.000127 63.053 0.139<br />
0.000199 59.924 0.211<br />
28 0.000399 54.834 0.414<br />
0.000599 51.788 0.617<br />
27 0.001109 47.135 1.134<br />
0.001619 44.286 1.651<br />
26 0.002816 40.166 2.864<br />
0.004013 37.574 4.077<br />
25 0.006588 34.024 6.685<br />
0.009162 31.716 9.293<br />
24 0.014342 28.654 14.542<br />
0.019523 26.596 19.792<br />
23 0.023755 25.307 24.080<br />
0.027987 24.240 28.368<br />
22 0.033814 23.020 34.272<br />
0.039641 22.004 40.175<br />
21 0.047641 20.836 48.282<br />
0.055641 19.855 56.388<br />
20 0.066559 18.727 67.450<br />
0.077477 17.773 78.512<br />
19 0.084313 17.243 85.439<br />
0.091149 16.753 92.366<br />
18 0.099191 16.222 100.515<br />
0.107234 15.731 108.663<br />
17 0.116695 15.198 118.250<br />
0.126157 14.706 127.837<br />
16 0.137287 14.170 139.115<br />
0.148418 13.674 150.393<br />
15 0.161513 13.134 163.661<br />
0.174608 12.633 176.930<br />
14 0.190061 12.086 192.587<br />
0.205513 11.578 208.244<br />
13 0.223772 11.021 226.745<br />
0.242032 10.504 245.246<br />
12 0.263587 9.936 267.087<br />
0.285142 9.409 288.927<br />
11 0.310561 8.830 314.683<br />
0.335980 8.291 340.439<br />
10 0.365938 7.700 370.793<br />
0.395895 7.148 401.146<br />
9 0.431179 6.541 436.898<br />
0.466464 5.975 472.650<br />
8 0.508017 5.351 514.754<br />
0.549571 4.768 556.857<br />
7 0.598479 4.125 606.413<br />
0.647387 3.523 655.968<br />
6 0.695218 2.969 704.433<br />
0.743050 2.443 752.898<br />
5 0.786601 1.986 797.026<br />
0.830152 1.549 841.154<br />
4 0.866492 1.197 877.974<br />
0.902831 0.857 914.795<br />
3 0.929330 0.615 941.644<br />
0.955828 0.378 968.494<br />
2 0.970469 0.249 983.328<br />
0.985110 0.122 998.163<br />
1 0.992555 0.058 1005.706<br />
1.000000 -0.006 1013.250<br />
|}<br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:02, 14 November 2016 (UTC)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-Chem_Nested_Model&diff=32501GEOS-Chem Nested Model2017-05-04T15:07:53Z<p>Barronh: /* Current Regional Working Group Projects (Please add yours!) */</p>
<hr />
<div>All users interested in the GEOS-Chem regional air quality simulations (e.g. nested-grid, GEOS-Chem/CMAQ linkages, etc.) are encouraged to subscribe to the regional air quality email list (click on the link in the [[#Contact information|contact information section]] below).<br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-valign="top"<br />
!width="300px" bgcolor="#CCCCCC"|Nested Model Working Group Co-Chairs<br />
|width="600px"|<br />
*[http://www.uh.edu/nsm/earth-atmospheric/people/faculty/yuxuan-wang/ Yuxuan Wang]<br />
*[https://www.engineering.uiowa.edu/faculty-staff/jun-wang Jun Wang] and <br />
*[http://www.atmos.pku.edu.cn/lzhang/ Lin Zhang]<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Nested Model Working Group email list<br />
|<tt>geos-chem-regional [at] g.harvard.edu</tt><br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To subscribe to email list<br />
|Either<br />
*Send an email to <tt>geos-chem-regional+subscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-regional GEOS-Chem Nested Model Google Group]<br />
*Click on '''Subscribe to this group'''<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To unsubscribe from email list<br />
|Either<br />
*Send an email to <tt>geos-chem-regional+unsubscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-regional GEOS-Chem Nested Model Google Group]<br />
*Click on the '''My Settings''' button<br />
*Click on '''Leave this group'''<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:32, 21 August 2015 (UTC)<br />
<br />
== Current Regional Working Group Projects (Please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!User Group <br />
!Description <br />
!Funding<br />
!Contact Person<br />
|-<br />
|Tsinghua<br />
|Nested-grid GEOS-Chem model development; Regional air quality over East Asia and interactions with the globe<br />
|N/A<br />
|[mailto:yxw@mail.tsinghua.edu.cn Yuxuan Wang]<br />
|-<br />
|SNU<br />
|Regional PM simulations over East Asia<br />
|Ministry of Environment in Korea<br />
|[mailto:rjpark@snu.ac.kr Rokjin Park]<br />
|-<br />
|US EPA<br />
|<br />
|N/A<br />
|[mailto:Pinder.Rob@epamail.epa.gov Rob Pinder]<br />
|-<br />
|U. Tennessee<br />
|<br />
|N/A<br />
|[mailto:jsfu@utk.edu Joshua Fu]<br />
|-<br />
|Nat'l Obs. Athens <br />
|<br />
|N/A<br />
|[mailto:aprot@phys.uoa.gr Anna Protonotariou]<br />
|-<br />
|U. L'Aquila<br />
|Buondary conditions to CHIMERE model over Europe, focus on Saharan dust transport.<br />
|ASI (Italian Space Agency)<br />
|[mailto:gabriele.curci@aquila.infn.it Gabriele Curci]<br />
|-<br />
|Georgia Tech. <br />
|<br />
|N/A<br />
|[mailto:Tao.Zeng@dnr.state.ga.us Tao Zeng ]<br />
|-<br />
|U. Toronto<br />
|<br />
|N/A<br />
|[mailto:jliu@atmosp.physics.utoronto.ca Jane Liu]<br />
|-<br />
|Peking University<br />
|Regional air quality in East Asia, Inversion of trace gas emissions using satellite products<br />
|N/A<br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|-<br />
|Dalhousie U.<br />
|Surface PM2.5 retrieval using satellite products<br />
|N/A<br />
|[mailto:Aaron.van.Donkelaar@dal.ca Aaron van Donkelaar]<br />
|-<br />
|Dalhousie U.<br />
|Nested aerosol microphysics (TOMAS). NOx/ultrafine aerosol concentration relationships. Topographic influence on microphysics<br />
|N/A<br />
|[mailto:jeffrey.pierce@dal.ca Jeffrey Pierce]<br />
|-<br />
|SUNY-Albany<br />
|Regional particle formation, evolution, and properties: Nested-grid GEOS-Chem (with APM) simulations and comparisons with measurements<br />
|<br />
|[mailto:yfq@asrc.cestm.albany.edu Fangqun Yu]<br />
|-<br />
|U. Edinburgh<br />
|Quantify the impact of boreal biomass burning outflow on tropospheric chemistry over the North Atlantic: Nested grid simulations and evaluation with ground-based, aircraft, and satellite observations<br />
|<br />
|[mailto:mark.parrington@ed.ac.uk Mark Parrington]<br />
|-<br />
|Emory University<br />
|Improving MISR Aerosol retrieval with GEOS-Chem simulated aerosol composition<br />
|NASA<br />
|[mailto:yang.liu@emory.edu Yang Liu]<br />
|-<br />
|Peking University<br />
|Carbonaceous aerosols in China<br />
|<br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|-<br />
|Peking University<br />
|Two-way nesting model for GESO-Chem and impacts on regional air quality and long-range transport<br />
|<br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|-<br />
|CSU<br />
|Investigation of inorganic aerosol and role of NH3 during CalNex<br />
|<br />
|[mailto:lschifer@atmos.colostate.edu Luke Schiferl]<br />
|-<br />
|University of Wollongong<br />
|Nested grid for Australia<br />
|L'Oréal-UNESCO<br />
|[mailto:jennyf@uow.edu.au Jenny Fisher]<br />
|-<br />
|Harvard<br />
|Variability of HCHO Over the Southeastern United States Observed from Space<br />
| NASA AQAST<br />
|[mailto:leizhu@fas.harvard.edu Lei Zhu]<br />
|-<br />
|UNL<br />
|GEOS-Chem Satellite Simulator for future sensors<br />
|NASA<br />
|[mailto:jwang7@unl.edu Jun Wang]<br />
|-<br />
|Harvard, York, CSU<br />
|Develop 0.5&deg; x 0.67&deg; grid for continental Africa (Eloise) and 0.25&deg; x 0.3125&deg; grid for West Africa (Mat, Eleanor, Daven)<br />
|<br />
|[mailto:emarais@seas.harvard.edu Eloise Marais], [mailto:mat.evans@york.ac.uk Mat Evans], [mailto:erm552@york.ac.uk Eleanor Morris] [mailto:daven.henze@colorado.edu Daven Henze]<br />
|-<br />
|Purdue<br />
|Develop 0.5&deg; x 0.67&deg; grid for the Arctic<br />
|<br />
|[mailto:tan80@purdue.edu Zeli Tan]<br />
|-<br />
|Peking University<br />
|Regional ozone and PM pollution over Asia; Develop 0.25 x 0.3125 degree simulation in the adjoint model<br />
| <br />
|[mailto:zhanglg@pku.edu.cn Lin Zhang]<br />
|-<br />
|University of York<br />
|Evaluation of the GC European grid for AQ applications<br />
| <br />
|[mailto:mat.evans@york.ac.uk Mat Evans] [mailto:tg706@york.ac.uk Tim Garstin]<br />
|-<br />
|US EPA<br />
|Develop Boundary Conditions for USA Regional Chemical Transport Models for 2015 and 2016<br />
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]<br />
|}<br />
<br />
== Recent updates to nested GEOS-Chem ==<br />
<br />
=== Fixes to Streets emissions for model years 2005 and earlier ===<br />
<br />
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03f|v9-01-03f]] and approved on 17 Feb 2012.'''''<br />
<br />
We discovered two bugs in the implementation of Streets emissions for the nested model. These will affect all nested simulations at least through v9-01-02 for model years 2005 and earlier.<br />
<br />
1. The nested model was using Streets 2000 emissions for years 2001-2005 instead of Streets 2006 emissions, which the global model has been using since v8-03-01. This will be updated in [[GEOS-Chem v9-01-03]].<br />
<br />
2. Streets 2000 anthropogenic emissions include NOx, CO, and SO2 from ships, which leads to double-counting of ship emissions as well as improper treatment of NOx emissions. This problem is described in more detail on the [[Ship_emissions#Duplicate_ship_emissions_in_Asia_in_Streets_2000_inventory | ship emissions page]]. This will be updated in [[GEOS-Chem v9-01-03]].<br />
<br />
--Jenny Fisher, 1 February 2012<br />
<br />
=== Nested-grid capability for offline simulations ===<br />
<br />
The following offline simulations have been updated for the nested grid:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!Simulation <br />
!Author <br />
!Status<br />
|-<br />
|[[CO2 simulation#Nested-grid CO2 simulation|Nested-grid CO2 simulation]]<br />
|Yuxuan Wang (Tsinghua U.)<br />
|Added to [[GEOS-Chem v9-01-03]]; released 14 Sep 2012<br />
|-<br />
|[[CH4 simulation#Update methane emissions and add capability for North America nested grid|CH4 simulation]] (North America)<br />
|Kevin Wecht (Harvard)<br />
|Added to [[GEOS-Chem v9-01-03]]; released 14 Sep 2012<br />
|-<br />
|[[Mercury#Nested-grid Hg simulation over North_America|Hg simulation]] (North America)<br />
|Yanxu Zhang (U. Washington)<br />
|Slated for inclusion into [[GEOS-Chem v9-02]]<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 16:42, 14 September 2012 (EDT)<br />
<br />
===Nested grid model at 0.25&deg; x 0.3125&deg; resolution using GEOS-FP===<br />
<br />
====North America region====<br />
<br />
=====Developers=====<br />
*Patrick Kim (Harvard)<br />
*Lei Zhu (Harvard)<br />
*Karen Yu (Harvard)<br />
*Katie Travis (Harvard)<br />
*Jenny Fisher (U. Wollongong)<br />
<br />
=====Overview=====<br />
<br />
The 0.25&deg; x 0.3125&deg; nested-grid simulation over North America was implemented in [[GEOS-Chem v9-02]]. Data for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_NA GEOS-FP 0.25&deg; x 0.3125&deg; North America nested grid] can be downloaded from the Harvard or Dalhousie data archives via FTP. Please see our [[Available_met_data_for_nested_grid_simulations#GEOS-FP_2|''Available met data for nested grid simulations'' wiki page]] for more information.<br />
<br />
====China region====<br />
<br />
=====Developers=====<br />
*Patrick Kim (Harvard)<br />
*Libao Chai (Tsinghua)<br />
*Yu Yao (Tsinghua)<br />
*Yuxuan Wang ((Tsinghua and Texas A&M Galveston)<br />
*Lin Zhang (Peking University)<br />
<br />
=====Overview=====<br />
<br />
Data for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_CH GEOS-FP 0.25&deg; x 0.3125&deg; China nested grid] can be downloaded from the Dalhousie data archives via FTP. Please see our [[Available_met_data_for_nested_grid_simulations#GEOS-FP|''Available met data for nested grid simulations'' wiki page]] for more information.<br />
<br />
=====Bug fixes for the 0.25 x 0.3125 nested CH simulation=====<br />
<br />
'''''These updates were validated with the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01f|v10-01f]] and approved on Approved 13 Jan 2015.'''''<br />
<br />
'''''Yuxuan Wang wrote:'''''<br />
<br />
:I’m happy to report that we’ve finally implemented all the bug fixes and necessary input files to successfully run the 0.25 nested_CH full chemistry simulation on the Tsinghua platform. We’ve done a 10-day test run and the simulation results look reasonable, so I thought it’s a good time to submit our code updates to the GC Support Team so that they can be incorporated in the next code release. <br />
<br />
:[http://wiki.seas.harvard.edu/geos-chem/images/Bug_fix_NEST_CH_025.txt Attached] please find a summary list of the code fixes we’ve implemented on the basis of v9-02 public release. The codes and input data are located at ftp://166.111.42.70/share/v9-02_CH025/. <br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:07, 18 November 2014 (EST)<br />
<br />
====Europe region====<br />
<br />
=====Developers=====<br />
*Junwei Xu (Dalhhousie)<br />
*Anna Protonatariou (Athens)<br />
<br />
=====Overview=====<br />
<br />
Data for the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_EU GEOS-FP 0.25&deg; x 0.3125&deg; Europe nested grid] can be downloaded from the Dalhousie data archives via FTP. Please see our [[Available_met_data_for_nested_grid_simulations#GEOS-FP_3|''Available met data for nested grid simulations'' wiki page]] for more information.<br />
<br />
=====Bug fixes for the 0.25 x 0.3125 nested EU simulation=====<br />
<br />
<span style="color:green">'''''These fixes were included in the [[GEOS-Chem v10-01#Fixes and updates added during the public comment period|GEOS-Chem v10-01 public release]].'''''</span><br />
<br />
'''''Anna Protonatariou wrote:'''''<br />
<br />
:1. I updated the Headers/CMN_SIZE_mod.F to define IGLOB, JGLOB for the European region at 0.25x0.3125 resolution by adding similar code as for CH and NA. The correct numbers are:<br />
<br />
INTEGER :: IGLOB = 177<br />
INTEGER :: JGLOB = 115<br />
<br />
:2. Then I got another compilation error in strat_chem_mod.F90<br />
<br />
:A. I found that the problem was in line 1613, which was only for CH and NA:<br />
<br />
#if defined( NESTED_CH ) || defined( NESTED_NA )<br />
<br />
:So I added the European part and now it is:<br />
<br />
#if defined( NESTED_CH ) || defined( NESTED_NA )|| defined(NESTED_EU)<br />
<br />
:B. Lines 1603-1609 were:<br />
<br />
#elif defined( GRID025x03125 )<br />
#if defined( NESTED_CH )<br />
INTEGER, PARAMETER :: J30S = 1, J30N = 161<br />
#elif defined( NESTED_NA )<br />
INTEGER, PARAMETER :: J30S = 1, J30N = 161<br />
#endif<br />
<br />
:I added the European part and now it is :<br />
<br />
#elif defined( GRID025x03125 )<br />
#if defined( NESTED_CH )<br />
INTEGER, PARAMETER :: J30S = 1, J30N = 161<br />
#elif defined( NESTED_NA )<br />
INTEGER, PARAMETER :: J30S = 1, J30N = 161<br />
#elif defined( NESTED_EU )<br />
INTEGER, PARAMETER :: J30S = 1, J30N = 115<br />
#endif<br />
<br />
:However, I think NA should be 202 and not 161 (which is the grid number for CH)!<br />
<br />
:Compilation is now successfully ended!! So happy with that:) I send you attached the routines. Unfortunately I get errors when I tried to run the model.<br />
<br />
Anna is following up with the Nested Model Working Group to resolve issues encountered while trying to run the 0.25&deg; x 0.3125&deg; European nested grid simulation. Development is ongoing.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 21:45, 20 May 2015 (UTC)<br />
<br />
== Recent linking tool updates for GEOS-Chem and CMAQ ==<br />
<br />
<br />
== On-going Developments ==<br />
<br />
'''[[##lists|1. Modified for Code.v8-02-01]]'''<br />
<br />
1). main.f, add following lines after DO_CHEMISTRY in line 941:<br />
<pre><br />
! check STT (yxw) <br />
#if defined( GEOS_5 ) && defined( GRID05x0666 )<br />
! Loop over grid boxes<br />
!$OMP PARALLEL DO <br />
!$OMP+DEFAULT( SHARED )<br />
!$OMP+PRIVATE( I, J, L, N )<br />
DO N = 1, N_TRACERS<br />
DO L = 1, LLPAR<br />
DO J = 1, JJPAR<br />
DO I = 1, IIPAR<br />
!---------------------------<br />
! Check for Negatives<br />
!---------------------------<br />
IF ( STT(I,J,L,N) < 0d0 ) THEN <br />
!$OMP CRITICAL<br />
WRITE( 6, 100 ) I, J, L, N, STT(I,J,L,N)<br />
PRINT*, 'Neg STT after chemistry ' // <br />
& 'SET STT TO BE ZERO'<br />
STT(I,J,L,N) = 0d0<br />
!$OMP END CRITICAL<br />
!---------------------------<br />
! Check for NaN's<br />
!---------------------------<br />
ELSE IF ( IT_IS_NAN( STT(I,J,L,N) ) ) THEN <br />
!$OMP CRITICAL<br />
WRITE( 6, 100 ) I, J, L, N, STT(I,J,L,N)<br />
PRINT*, 'NaN STT after chemistry ' //<br />
& 'SET STT TO BE LOWER LEVEL'<br />
STT(I,J,L,N) = STT(I,J,L-1,N)<br />
!$OMP END CRITICAL<br />
!----------------------------<br />
! Check STT's for Infinities<br />
!----------------------------<br />
ELSE IF ( .not. IT_IS_FINITE( STT(I,J,L,N) ) ) THEN<br />
!$OMP CRITICAL<br />
WRITE( 6, 100 ) I, J, L, N, STT(I,J,L,N)<br />
PRINT*, 'Inf STT after chemistry ' //<br />
& 'SET STT TO BE LOWER LEVEL'<br />
STT(I,J,L,N) = STT(I,J,L-1,N)<br />
!$OMP END CRITICAL <br />
<br />
ENDIF<br />
ENDDO<br />
ENDDO<br />
ENDDO<br />
ENDDO<br />
!$OMP END PARALLEL DO<br />
#endif<br />
</pre><br />
<br />
2). main.f, add following lines after ITS_TIME_FOR_DIAG in line 1021:<br />
<pre><br />
! Sometimes STT in the stratosphere can be negative at <br />
! the nested-grid domain edges. Force them to be zero before<br />
! CHECK_STT (yxw)<br />
#if defined( GEOS_5 ) && defined( GRID05x0666 )<br />
! Loop over grid boxes<br />
!$OMP PARALLEL DO <br />
!$OMP+DEFAULT( SHARED )<br />
!$OMP+PRIVATE( I, J, L, N )<br />
DO N = 1, N_TRACERS<br />
DO L = 1, LLPAR<br />
DO J = 1, JJPAR<br />
DO I = 1, IIPAR<br />
<br />
!---------------------------<br />
! Check for Negatives<br />
!---------------------------<br />
IF ( STT(I,J,L,N) < 0d0 ) THEN<br />
!$OMP CRITICAL<br />
WRITE( 6, 100 ) I, J, L, N, STT(I,J,L,N)<br />
PRINT*, 'Neg STT after dynamics step ' //<br />
& 'SET STT TO BE ZERO'<br />
STT(I,J,L,N) = 0d0<br />
!$OMP END CRITICAL<br />
ENDIF<br />
ENDDO<br />
ENDDO<br />
ENDDO<br />
ENDDO<br />
!$OMP END PARALLEL DO<br />
100 FORMAT( ' STT(',i3,',',i3,',',i3,',',i3,') = ', f13.6 )<br />
<br />
#endif<br />
<br />
</pre><br />
<br />
--[[User:Yuxuan|Wang]],[[User:Dan|Chen]], 05:13, 25 June 2009 (EDT)<br />
--[[User:Aaron van Donkelaar], March 4, 2010<br />
<br />
== How to run the 0.5x0.667 nested-grid for GEOS-5 ==<br />
<br />
We have moved this discussion to the following wiki pages:<br />
<br />
#[[GEOS-Chem nested grid simulations]] <br />
#[[Setting up GEOS-Chem nested grid simulations]]<br />
<br />
--[[User:Bmy|Bob Y.]] 14:07, 15 November 2010 (EST)<br />
<br />
== About linking tools ==<br />
<br />
TBD</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=Chemistry_Working_Group&diff=32500Chemistry Working Group2017-05-04T15:05:54Z<p>Barronh: /* Current GEOS-Chem Chemistry Projects (please add yours!) */</p>
<hr />
<div><big><big><strong>Oxidants and Chemistry Working Group</strong></big></big><br />
<br />
All users interested in the GEOS-Chem chemistry scheme and associated processes (photolysis, heterogeneous, deposition) are encouraged to subscribe to the chemistry email list (click on the link in the [[#Contact information|contact information section]] below).<br />
<br />
== Contact information ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-valign="top"<br />
!width="300px" bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group Co-Chairs<br />
|width="600px"|<br />
*[http://www.york.ac.uk/chemistry/staff/academic/d-g/evansm/ Mat Evans] and <br />
*[http://www.barronh.com Barron Henderson]<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Oxidants and Chemistry Working Group email list<br />
|<tt>geos-chem-oxidants [at] g.harvard.edu</tt><br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To subscribe to email list<br />
|Either<br />
*Send an email to <tt>geos-chem-oxidants+subscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]<br />
*Click on '''Subscribe to this group'''<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To unsubscribe from email list<br />
|Either<br />
*Send an email to <tt>geos-chem-oxidants+unsubscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-oxidants GEOS-Chem Oxidants and Chemistry]<br />
*Click on the '''My Settings''' button<br />
*Click on '''Leave this group'''<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:29, 21 August 2015 (UTC)<br />
<br />
== Current GEOS-Chem Chemistry Projects (please add yours!) ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="200px"|User Group <br />
!width="600px"|Description <br />
!width="150px"|Contact Person<br />
!width="100px"|Date Added<br />
|-<br />
|NIA / LaRC<br />
|Tropospheric ozone over East Asia: Ozonesonde observations and modeling analysis<br />
|[mailto:hyl@nianet.org Hongyu Liu]<br />
|5 May 2015<br />
|-<br />
|MIT<br />
|Exploring the impact of monoterpene and aromatic chemistry on ozone and OH reactivity<br />
|[mailto:wporter@mit.edu Will Porter]<br />
|12 April 2017<br />
|-<br />
|MIT<br />
|Simulating the global reactive carbon budget<br />
|[mailto:sarahsaf@mit.edu Sarah Safieddine]<br />
|12 April 2017<br />
|-<br />
|University of York <br />
|Halogen chemistry <br />
|[mailto:ts551@york.ac.uk Tomas Sherwen]<br />
|12 April 2017<br />
|-<br />
|University of York <br />
|Isoprene over Borneo<br />
|[mailto:sag527@york.ac.uk Shani Garraway]<br />
|12 April 2017<br />
|-<br />
|University of York <br />
|Impacts of uncertainty in chemical kinetics <br />
|[mailto:bn506@york.ac.uk Ben Newsome]<br />
|12 April 2017<br />
|-<br />
|University of York <br />
|Impacts of resolution in GEOS-Chem <br />
|[mailto:bn506@york.ac.uk Ben Newsome]<br />
|12 April 2017<br />
|-<br />
|University of York <br />
|Updates to the kinetics of Criegee chemistry based on new chamber experiments<br />
|[mailto:mat.evans@york.ac.uk Mat Evans]<br />
|12 April 2017<br />
|-<br />
|University of Wollongong <br />
|Simulation of small (methyl, ethyl, propyl) alkyl nitrates in GEOS-Chem<br />
|[mailto:jennyf@uow.edu.au Jenny Fisher]<br />
|12 April 2017<br />
|-<br />
|Harvard University<br />
|Halogen extension to include explicit phase partitioning and mass transfer<br />
|[mailto:seastham@fas.harvard.edu Sebastian D. Eastham]<br />
|12 April 2017<br />
|-<br />
| US EPA<br />
|Alkane chemistry and product yields as a function of temperature/pressure.<br />
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]<br />
|4 May 2017<br />
|-<br />
| US EPA<br />
|Carbon and Nitrogen Balance and checking software.<br />
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]<br />
|4 May 2017<br />
|-<br />
| US EPA<br />
|Update DSMACC for v11 GEOS-Chem Chemistry and Emissions to facilitate chemical experiments<br />
|[mailto:Henderson.Barron@epa.gov Barron H. Henderson]<br />
|4 May 2017<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 15:08, 25 April 2014 (EDT)<br />
<br />
== Current GEOS-Chem Chemistry Issues (please add yours!) ==<br />
<br />
=== Fixes to correct ALK4 lumping issue ===<br />
<br />
<span style="color:darkorange">'''''NOTE: This update is currently slated for [[GEOS-Chem v11-02#v11-02a|v11-02a]].'''''</span><br />
<br />
'''''[[User:Barronh|Barron Henderson]] wrote:'''''<br />
<br />
<blockquote>I have a lumping-related issue that I know some of you are already aware of. There is a chemical carbon source (and secondary ETO2 source).<br />
<br />
Right now, ALK4 (via R4O2) produces 4.26 moles carbon products per reaction. The ALK4 representation can be traced back to a paper by Frederick Lurmann. That paper refers to a report that I have been unable to obtain. In fact, Frederick Lurmann no longer has a copy. When we spoke, however, he confirmed my suspicion that ALK4 is based on a 70% butane and 30% pentane mixture. Our 4.26 carbon product appears to be based on two differences (typos?) from the paper that alter the yields.<br />
<br />
If ALK4 emissions are introduced using a 4C assumption, then ALK4 chemistry is acting as a 7% carbon source. From a ozone reactivity standpoint, this is not a major issue. First, the speciation of VOC is highly uncertain and most of the atmosphere is NOx-limited. Even so, it represents another reason to revisit our lumped species.<br />
<br />
I have [https://www.evernote.com/shard/s315/sh/f2ec9589-d827-4ee1-afcb-96ee5a2d2914/d84318450f729cd414e4a6653c03a296 extensive notes] on what I interpret as happening. To the best of my knowledge, we need to make three modifications to R4O2 + NO. The first two are to make R4O2 correctly linked to Lurmann and the third is to correctly connect the mass emissions with the molar conservation.<br />
<br />
#Increase MO2 stoichiometry from 0.18 to 0.19<br />
#Increase RCHO stoichiometry from 0.13 to 0.14 (or A3O2 from 0.05 to 0.06 -- it is not clear to me when this was introduced).<br />
#Modify the carbon count for ALK4 (i.e. the <tt>MolecRatio</tt> field in the [[GEOS-Chem species database]]) from 4 to 4.3.<br />
<br />
Fixes 1 and 2&mdash;which can be applied to the KPP <tt>globchem.eqn</tt> file&mdash;will make the carbon conservation consistent with Lurmann's. Right now, it looks like there were a couple changes that could have been inadvertent (i.e., 0.18 instead of 0.19). If there was a reason for these changes, I have been unable to find it.</blockquote><br />
<br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:21, 31 January 2017 (UTC)<br />
<br />
=== JPL Released 18th Rate Coefficient Evaluation ===<br />
<br />
<span style="color:darkorange">'''''NOTE: This update is currently slated for [[GEOS-Chem v11-02|v11-02a]].'''''</span><br />
<br />
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page ([[Updates in JPL Publication 15-10]]) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10. <br />
<br />
:J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.<br />
<br />
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)<br />
<br />
=== Working Group Tele-con on the 2nd December 2011 ===<br />
[[ChemTelecon20111202]]<br />
'''''[mailto:mat.evans@york.ac.uk Mat Evans]'''''<br />
<br />
=== Isoprene chemistry ===<br />
I've created a page with some of the recent literature on [[Isoprene|isoprene chemistry]]. Please add more papers as they come along! ([[User:mje| MJE Leeds]])<br />
<br />
=== HO2 + CH2O ===<br />
Scheme does not contain the HO2 + CH2O --> Adduct reaction (MJE Leeds)<br />
<br />
Hermans, I., et al. (2005), Kinetics of alpha-hydroxy-alkylperoxyl radicals in oxidation<br />
processes. HO2 center dot-initiated oxidation of ketones/aldehydes near the tropopause,<br />
Journal of Physical Chemistry A, 109(19), 4303-4311.<br />
<br />
According to this paper, this reaction is significant when Temperature is below 220K.<br />
<br />
--[[User:Jmao|J Mao.]] 15:00, 10 Aug 2009 (EDT)<br />
<br />
== Previous issues that have now been resolved ==<br />
<br />
=== Centralizing chemistry time step===<br />
<br />
<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><br />
<br />
Please see the full discussion on the [[Centralized chemistry time step]] wiki page.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:01, 4 November 2011 (EDT)<br />
<br />
=== Acetone photolysis ===<br />
<br />
[[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]].<br />
<br />
--[[User:Bmy|Bob Y.]] 15:20, 20 May 2014 (EDT)<br />
<br />
== Issues that have been since rendered obsolete by newer code updates ==<br />
<br />
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]]).<br />
<br />
=== NIT should be converted to molec/cm3 in calcrate.F ===<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<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><br />
<br />
In <tt>calcrate.F</tt>, we have:<br />
<br />
! Nitrate effect; reduce the gamma on nitrate by a<br />
! factor of 10 (lzh, 10/25/2011)<br />
IF ( N == 8 ) THEN<br />
TMP1 = State_Chm%Tracers(IX,IY,IZ,IDTSO4) +<br />
& State_Chm%Tracers(IX,IY,IZ,IDTNIT)<br />
TMP2 = State_Chm%tracers(IX,IY,IZ,IDTNIT)<br />
IF ( TMP1 .GT. 0.0 ) THEN<br />
XSTKCF = XSTKCF * ( 1.0e+0_fp - 0.9e+0_fp<br />
& *TMP2/TMP1 )<br />
ENDIF<br />
ENDIF<br />
<br />
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>.<br />
<br />
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>).<br />
<br />
--[[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)<br />
<br />
=== rate of HNO4 ===<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<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><br />
<br />
[mailto:ecbrow@berkeley.edu Ellie Browne] found a typo in the globchem.dat ([[GEOS-Chem v8-02-01]] and beyond)<br />
<pre><br />
A 73 9.52E-05 3.2E+00 -10900 1 P 0.60 0. 0. <br />
1.38E+15 1.4E+00 -10900 0 0.00 0. 0. <br />
HNO4 + M <br />
=1.000HO2 +1.000NO2 + +<br />
</pre><br />
This should be corrected as:<br />
<pre><br />
A 73 9.52E-05 3.4E+00 -10900 1 P 0.60 0. 0. <br />
1.38E+15 1.1E+00 -10900 0 0.00 0. 0. <br />
HNO4 + M <br />
=1.000HO2 +1.000NO2 + + <br />
</pre><br />
The difference is within 2%.<br />
<br />
--[[User:Jmao|J Mao.]] 19:04, 30 Aug 2010 (EDT)<br><br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:29, 31 January 2017 (UTC)<br />
<br />
=== near-IR photolysis of HNO4 ===<br />
<br />
<span style="color:green">'''''This update was added to [[GEOS-Chem v8-02-04]].'''''</span><br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<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><br />
<br />
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:<br />
<br />
!---------------------------------------------------------------------<br />
! Prior to 10/27/09:<br />
! FastJX has taken near-IR photolysis into account with<br />
! cross section at 574nm, so we don't need to add 1e-5 anymore.<br />
! According to Jimenez et al., "Quantum yields of OH, HO2 and<br />
! NO3 in the UV photolysis of HO2NO2", PCCP, 2005, we also<br />
! changed the branch ratio from 0.67(HO2)/0.33(OH) to 0.95/0.05<br />
! This will put most weight of near-IR photolysis on HO2 channel.<br />
! (jmao, bmy, 10/27/09)<br />
!<br />
!!==============================================================<br />
!! HARDWIRE addition of 1e-5 s-1 photolysis rate to <br />
!! HNO4 -> HO2+NO2 to account for HNO4 photolysis in near-IR -- <br />
!! see Roehl et al. 'Photodissociation of peroxynitric acid in <br />
!! the near-IR', 2002. (amf, bmy, 1/7/02)<br />
!!<br />
!! Add NCS index to NKHNO4 for SMVGEAR II (gcc, bmy, 4/1/03)<br />
!!==============================================================<br />
!IF ( NKHNO4(NCS) > 0 ) THEN<br />
!<br />
! ! Put J(HNO4) in correct spot for SMVGEAR II<br />
! PHOTVAL = NKHNO4(NCS) - NRATES(NCS)<br />
! NKN = NKNPHOTRT(PHOTVAL,NCS)<br />
!<br />
! DO KLOOP=1,KTLOOP<br />
! RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) + 1d-5<br />
! ENDDO<br />
!ENDIF<br />
!---------------------------------------------------------------------<br />
<br />
<br />
2. We need to change the branch ratio of HNO4 photolysis in <tt>ratj.d</tt>. Change these lines from:<br />
<br />
13 HNO4 PHOTON OH NO3 0.00E+00 0.00 33.3 HO2NO2 <br />
14 HNO4 PHOTON HO2 NO2 0.00E+00 0.00 66.7 HO2NO2 <br />
<br />
to:<br />
<br />
13 HNO4 PHOTON OH NO3 0.00E+00 0.00 5.0 HO2NO2 <br />
14 HNO4 PHOTON HO2 NO2 0.00E+00 0.00 95.0 HO2NO2<br />
<br />
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.<br />
<br />
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).<br />
<br />
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].<br />
<br />
--[[User:Jmao|J Mao.]] 11:00, 26 Oct 2009 (EDT)<br><br />
--[[User:Bmy|Bob Y.]] 16:08, 4 November 2011 (EDT)<br />
<br />
=== yield of isoprene nitrates ===<br />
<br />
<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><br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<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><br />
<br />
[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%. <br />
<br />
A 453 2.70E-12 0.0E+00 350 1 B 0.00 0. 0. <br />
5.00E+00 0.0E+00 0 0 0.00 0. 0. <br />
RIO2 + NO <br />
=0.900NO2 +0.900HO2 +0.340IALD +0.340MVK <br />
+0.220MACR +0.560CH2O + + <br />
<br />
A 453 2.70E-12 0.0E+00 350 1 A 0.00 0. 0. <br />
5.00E+00 0.0E+00 0 0 0.00 0. 0. <br />
RIO2 + NO <br />
=1.000HNO3 + + + <br />
<br />
So it should be corrected as (no channel A):<br />
<br />
A 453 2.70E-12 0.0E+00 350 0 0 0.00 0. 0. <br />
RIO2 + NO <br />
=0.900NO2 +0.900HO2 +0.340IALD +0.340MVK <br />
+0.220MACR +0.560CH2O + + <br />
<br />
D 453 2.70E-12 0.0E+00 350 1 A 0.00 0. 0. <br />
5.00E+00 0.0E+00 0 0 0.00 0. 0. <br />
RIO2 + NO <br />
=1.000HNO3 + + + <br />
<br />
--[[User:Jmao|J Mao.]] 18:04, 30 Aug 2010 (EDT)<br><br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:31, 31 January 2017 (UTC)<br />
<br />
=== Potential issue with reading restart.cspec file ===<br />
<br />
<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><br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<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><br />
<br />
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.<br />
<br />
--[[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)<br />
<br />
=== GLCO3, GLPAN bug in standard mechanism ===<br />
<br />
<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><br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<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><br />
<br />
'''''[mailto:fabienpaulot@gmail.com Fabien Paulot] wrote:'''''<br />
<br />
: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.<br />
<br />
: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.<br />
<br />
:To fix the error, I made the following modifications in <tt>globchem.dat</tt>:<br />
<br />
:#I set GLPAN and GLCO3 rxns from active to dead. These rxns were causing an artificial loss of NOx.<br />
:#I have physically removed GLCO3, GLP, GLPAN, GPAN, ISNO3, MNO3, O2CH2OH, MVN2 and their associated reactions. <br />
:#I have made GLYX active. I'm not sure why it's not active by default.<br />
<br />
:and to <tt>ratj.d</tt>:<br />
<br />
:# I deleted photolysis reactions for MNO3 and GLP, since these species have also now been deleted in <tt>globchem.dat</tt><br />
<br />
--[[User:Bmy|Bob Y.]] 14:51, 10 November 2011 (EST)<br><br />
--[[User:Melissa Payer|Melissa Payer]] 10:49, 15 December 2011 (EST)<br><br />
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:35, 31 January 2017 (UTC)<br />
<br />
=== Bug in routine ARSL1K ===<br />
<br />
<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><br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
<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><br />
<br />
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.<br />
<br />
'''''[mailto:mat.evans@york.ac.uk Mat Evans] wrote:'''''<br />
<br />
: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. <br />
<br />
:The simulations show virtually no difference between the two simulations.<br />
<br />
:mean and stddev ratio of all grid boxes with and without the fix are shown below<br />
NOx 0.999996 0.000409291<br />
Ox 1.00000 1.27233e-05<br />
O3 1.00000 1.52284e-05<br />
PAN 0.997849 0.0111997<br />
CO 1.00000 4.21768e-06<br />
ALK4 0.990514 0.0351941<br />
ISOP 0.999979 0.0108033<br />
H2O2 0.992067 0.0264659<br />
DST1 1.00000 0.00000<br />
HO2 0.999996 0.00309464<br />
OH 1.00003 0.00767954<br />
<br />
: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.<br />
<br />
--[[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)<br />
<br />
== Documentation ==<br />
<br />
[[Image:Obsolete.jpg]]<br />
<br />
*[http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v6.pdf Updated chemical reactions] that will be used in [[GEOS-Chem v8-02-04]] and higher.<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/chemistry_updates_v5.pdf Updated chemical reactions] now used in [[GEOS-Chem v8-02-01]] through [[GEOS-Chem v8-02-03]]. <br />
**All typos have now been corrected in the present file.<br />
* [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jv_spec_format.pdf Format of FAST-J input file <tt>jv_spec.dat</tt>]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:41, 27 October 2009 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:JPL201510andGCv10_OHplOClO_eq_HOClplO2.png&diff=30802File:JPL201510andGCv10 OHplOClO eq HOClplO2.png2017-02-16T19:54:32Z<p>Barronh: Barronh uploaded a new version of File:JPL201510andGCv10 OHplOClO eq HOClplO2.png</p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:JPL201510andGCv10_OHplOClO_eq_HOClplO2.png&diff=30801File:JPL201510andGCv10 OHplOClO eq HOClplO2.png2017-02-16T19:53:33Z<p>Barronh: Barronh uploaded a new version of File:JPL201510andGCv10 OHplOClO eq HOClplO2.png</p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:JPL201510andGCv10_OHplOClO_eq_HOClplO2.png&diff=30800File:JPL201510andGCv10 OHplOClO eq HOClplO2.png2017-02-16T19:51:57Z<p>Barronh: Barronh uploaded a new version of File:JPL201510andGCv10 OHplOClO eq HOClplO2.png</p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:JPL201510andGCv10_OHplOClO_eq_HOClplO2.png&diff=30799File:JPL201510andGCv10 OHplOClO eq HOClplO2.png2017-02-16T19:51:02Z<p>Barronh: Barronh uploaded a new version of File:JPL201510andGCv10 OHplOClO eq HOClplO2.png</p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:JPL201510andGCv10_OHplOClO_eq_HOClplO2.png&diff=30798File:JPL201510andGCv10 OHplOClO eq HOClplO2.png2017-02-16T19:50:30Z<p>Barronh: Barronh uploaded a new version of File:JPL201510andGCv10 OHplOClO eq HOClplO2.png</p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:JPL201510andGCv10_OHplOClO_eq_HOClplO2.png&diff=30797File:JPL201510andGCv10 OHplOClO eq HOClplO2.png2017-02-16T19:49:39Z<p>Barronh: Barronh uploaded a new version of File:JPL201510andGCv10 OHplOClO eq HOClplO2.png</p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=Updates_in_JPL_Publication_15-10&diff=30796Updates in JPL Publication 15-102017-02-16T19:36:45Z<p>Barronh: /* Table 1F - Bimolecular ClOx */</p>
<hr />
<div>= Summary = <br />
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page ([[Updates in JPL Publication 15-10]]) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10. A similar comparison was done for JPL Publication 10-6 ([[Updating standard chemistry with JPL 10-6]]). For each reaction coefficient that was updated, we will note the rate expression currently used in v10, the updated expression in JPL 15-10, and provide a plot of the two rate coefficients. For expressions that are only temperature dependent, rates will be plotted as a function of temperature between 220 K and 320 K. For termolecular reactions, expressions will be plotted as a function of altitude with temperature and pressure following the 1976 US Standard Atmosphere.<br />
<br />
J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.<br />
<br />
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)<br />
<br />
= JPL Updated Rates Compared to GC v10 =<br />
<br />
NOTE: These tables are a work in progress.<br />
<br />
=== Table 1A - Bimolecular Ox ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|No quantitative updates || || ||<br />
<br />
|}<br />
<br />
=== Table 1A - Bimolecular O1D ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|CH3Cl + O1D || not active || || <br />
<br />
|-valign="top"<br />
|CH3CCl3 + O1D || not active || || <br />
<br />
|-valign="top"<br />
|O1D + HCFC22 = O + HCFC22 + ClO + Cl<br />
|1e-10<br />
|1.02e-10<br />
|[[File:JPL201510andGCv10_O1DplHCFC22_eq_OplHCFC22plClOplCl.png|200px|thumb|left|JPL201510andGCv10_O1DplHCFC22_eq_OplHCFC22plClOplCl.png]]<br />
<br />
|-valign="top"<br />
|O1D + HCFC142b<br />
|2.20E-10<br />
|2.00E-10<br />
|[[File:JPL201510andGCv10_O1DplHCFC142b.png|200px|thumb|left|JPL201510andGCv10_O1DplHCFC142b.png]]<br />
<br />
|-valign="top"<br />
|O1D + CFC113<br />
|2.00E-10<br />
|2.32E-10<br />
|[[File:JPL201510andGCv10_O1DplCFC113.png|200px|thumb|left|JPL201510andGCv10_O1DplCFC113.png]]<br />
<br />
|-valign="top"<br />
|O1D + CFC114<br />
|1.30E-10<br />
|1.3E-10*exp(-25/T)<br />
|[[File:JPL201510andGCv10_O1DplCFC114.png|200px|thumb|left|JPL201510andGCv10_O1DplCFC114.png]]<br />
<br />
|-valign="top"<br />
|O1D + CFC115<br />
|5.0E-11<br />
|5.4E-11*exp(-30/T)<br />
|[[File:JPL201510andGCv10_O1DplCFC115.png|200px|thumb|left|JPL201510andGCv10_O1DplCFC115.png]]<br />
<br />
|}<br />
<br />
=== Table 1A - Bimolecular Singlet O2 ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|No quantitative updates || || ||<br />
<br />
|}<br />
<br />
=== Table 1B - Bimolecular HOx ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|No quantitative updates || || ||<br />
<br />
|}<br />
<br />
=== Table 1C - Bimolecular NOx ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|No quantitative updates || || ||<br />
<br />
|}<br />
<br />
=== Table 1D - Bimolecular Organic ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|MACR + O3 = OH + HO2 + HCOOH + CO + MGLY + CH2O<br />
|1.40E-15*exp(-2100/T)<br />
|1.5e-15*exp(-2110/T)<br />
|[[File:JPL201510andGCv10_MACRplO3_eq_OHplHO2plHCOOHplCOplMGLYplCH2O.png|200px|thumb|left|JPL201510andGCv10_MACRplO3_eq_OHplHO2plHCOOHplCOplMGLYplCH2O.png]]<br />
<br />
|-valign="top"<br />
|MVK + O3 = OH + HO2 + HCOOH + CO + ALD2 + MGLY + CH2O<br />
|8.50E-16*exp(-1520/T)<br />
|8.5e-16*exp(-1520/T)<br />
|[[File:JPL201510andGCv10_MVKplO3_eq_OHplHO2plHCOOHplCOplALD2plMGLYplCH2O.png|200px|thumb|left|JPL201510andGCv10_MVKplO3_eq_OHplHO2plHCOOHplCOplALD2plMGLYplCH2O.png]]<br />
<br />
|-valign="top"<br />
|MACR + OH = MAO3 + MRO2\<br />
|8.0E-12*exp(380/T)<br />
|9.6e-12*exp(360./T)<br />
|[[File:JPL201510andGCv10_MACRplOH_eq_MAO3plMRO2.png|200px|thumb|left|JPL201510andGCv10_MACRplOH_eq_MAO3plMRO2.png]]<br />
<br />
|-valign="top"<br />
|MVK + OH = VRO2\<br />
|2.6e-12*exp(610/T)<br />
|2.7e-12*exp(580./T)<br />
|[[File:JPL201510andGCv10_MVKplOH_eq_VRO2.png|200px|thumb|left|JPL201510andGCv10_MVKplOH_eq_VRO2.png]]<br />
<br />
|-valign="top"<br />
|ISOP + OH = RIO2<br />
|3.1e-11*exp(350/T)<br />
|3.0e-11*exp(360./T)<br />
|[[File:JPL201510andGCv10_ISOPplOH_eq_RIO2.png|200px|thumb|left|JPL201510andGCv10_ISOPplOH_eq_RIO2.png]]<br />
<br />
|-valign="top"<br />
|MACR + NO3 = MAN2<br />
|2.30e-15<br />
|3.4e-15<br />
|[[File:JPL201510andGCv10_MACRplNO3_eq_MAN2.png|200px|thumb|left|JPL201510andGCv10_MACRplNO3_eq_MAN2.png]]<br />
<br />
|-valign="top"<br />
|ISOP + NO3 = INO2<br />
|3.3E-12*exp(-450/T)<br />
|3.5e-12*exp(-450/T)<br />
|[[File:JPL201510andGCv10_ISOPplNO3_eq_INO2.png|200px|thumb|left|JPL201510andGCv10_ISOPplNO3_eq_INO2.png]]<br />
<br />
|}<br />
<br />
=== Table 1F - Bimolecular ClOx ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|OH + HCFC22 = Cl + H2O<br />
|1.05E-12*exp(-1600./T)<br />
|9.2e-13*exp(-1560./T)<br />
|[[File:JPL201510andGCv10_OHplHCFC22_eq_ClplH2O.png|200px|thumb|left|JPL201510andGCv10_OHplHCFC22_eq_ClplH2O.png]]<br />
<br />
|-valign="top"<br />
|OH + HCFC123 = Cl + H2O<br />
|6.30E-13*exp(-850./T)<br />
|7.4e-13*exp(-900./T)<br />
|[[File:JPL201510andGCv10_OHplHCFC123_eq_ClplH2O.png|200px|thumb|left|JPL201510andGCv10_OHplHCFC123_eq_ClplH2O.png]]<br />
<br />
|-valign="top"<br />
|MO2 + ClO = ClOO + HO2 + CH2O<br />
|3.3E-12*exp(-115./T)<br />
|1.8e-12*exp(-600./T)<br />
|[[File:JPL201510andGCv10_MO2plClO_eq_ClOOplHO2plCH2O.png|200px|thumb|left|JPL201510andGCv10_MO2plClO_eq_ClOOplHO2plCH2O.png]]<br />
<br />
|-valign="top"<br />
|OH + CH3Cl = Cl + HO2 + H2O<br />
|2.4E-12*exp(-1250./T)<br />
|1.96e-12*exp(-1200./T)<br />
|[[File:JPL201510andGCv10_OHplCH3Cl_eq_ClplHO2plH2O.png|200px|thumb|left|JPL201510andGCv10_OHplCH3Cl_eq_ClplHO2plH2O.png]]<br />
<br />
|-valign="top"<br />
|OH + OClO = HOCl + O2<br />
|1.5E-12*exp(600./T)<br />
|1.4e-12*exp(600./T)<br />
|needs updating[[File:JPL201510andGCv10_OHplOClO_eq_HOClplO2.png|200px|thumb|left|JPL201510andGCv10_OHplOClO_eq_HOClplO2.png]]<br />
<br />
|-valign="top"<br />
|Cl + C3H8 = HCl + A3O2<br />
|7.85E-11*exp(-80./T)<br />
|8.12e-11*exp(-90./T)<br />
|[[File:JPL201510andGCv10_ClplC3H8_eq_HClplA3O2.png|200px|thumb|left|JPL201510andGCv10_ClplC3H8_eq_HClplA3O2.png]]<br />
<br />
|-valign="top"<br />
|Cl + C3H8 = HCl + B3O2<br />
|6.54E-11<br />
|6.54e-11*exp(-60./T)<br />
|[[File:JPL201510andGCv10_ClplC3H8_eq_HClplB3O2.png|200px|thumb|left|JPL201510andGCv10_ClplC3H8_eq_HClplB3O2.png]]<br />
<br />
|-valign="top"<br />
|Cl + ACET = HCl + ATO2<br />
|7.7E-11*exp(-1000./T)<br />
|1.63e-11*exp(-610./T)<br />
|[[File:JPL201510andGCv10_ClplACET_eq_HClplATO2.png|200px|thumb|left|JPL201510andGCv10_ClplACET_eq_HClplATO2.png]]<br />
<br />
|-valign="top"<br />
|Cl + ISOP = HCl + RIO2<br />
|7.7E-11*exp(-500./T)<br />
|7.6E-11*exp(-500./T)<br />
|[[File:JPL201510andGCv10_ClplISOP_eq_HClplRIO2.png|200px|thumb|left|JPL201510andGCv10_ClplISOP_eq_HClplRIO2.png]]<br />
<br />
|-valign="top"<br />
|Cl + CH4 = products <br />
|7.3E-12*exp(-1280./T)<br />
|7.1E-11*exp(-1270./T)<br />
|[[File:JPL201510andGCv10_ClplCH4_eq_products.png|200px|thumb|left|JPL201510andGCv10_ClplCH4_eq_products.png]]<br />
<br />
|}<br />
<br />
=== Table 1G - Bimolecular BrOx ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|OH + CH3Br = 3Br + products<br />
|1.35E-12*exp(-600./T)<br />
|9.0e-13*exp(-360./T)<br />
|[[File:JPL201510andGCv10_OHplCH3Br_eq_3Brplproducts.png|200px|thumb|left|JPL201510andGCv10_OHplCH3Br_eq_3Brplproducts.png]]<br />
<br />
|-valign="top"<br />
|Br + ALD2 = HBr + MCO3 + CO<br />
|1.3e-11*exp(-360./T)<br />
|1.8e-11*exp(-460./T)<br />
|[[File:JPL201510andGCv10_BrplALD2_eq_HBrplMCO3plCO.png|200px|thumb|left|JPL201510andGCv10_BrplALD2_eq_HBrplMCO3plCO.png]]<br />
<br />
|}<br />
<br />
=== Table 1H - Bimolecular IOx ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|IO + HO2 = HOI + O2<br />
|8.4E-11<br />
|1.3e-11*exp(-570./T)<br />
|[[File:JPL201510andGCv10_IOplHO2_eq_HOIplO2.png|200px|thumb|left|JPL201510andGCv10_IOplHO2_eq_HOIplO2.png]]<br />
<br />
|-valign="top"<br />
|IO + NO = I + NO2<br />
|9.1e-12*exp(-249./T)<br />
|9.12e-11*exp(-240./T)<br />
|[[File:JPL201510andGCv10_IOplNO_eq_IplNO2.png|200px|thumb|left|JPL201510andGCv10_IOplNO_eq_IplNO2.png]]<br />
<br />
|}<br />
<br />
=== Table 1I - Bimolecular SOx ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|colspan="4"|Needs review. (volunteer by putting your name here)<br />
<br />
<br />
|}<br />
<br />
=== Table 2-1 - Termolecular ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|HO2 + NO2 + M = HNO4<br />
|GP(A0 = 2.e-31, B0 = 3.4, A1 = 2.9e-12, B1 = 1.1)<br />
|GP(A0 = 1.9e-31, B0 = 3.4, A1 = 4e-12, B1 = 0.3)<br />
|[[File:JPL201510andGCv10_HO2plNO2plM_eq_HNO4.png|200px|thumb|left|JPL201510andGCv10_HO2plNO2plM_eq_HNO4.png]]<br />
<br />
|-valign="top"<br />
|NO2 + NO3 + M = N2O5<br />
|GP(A0 = 2.00E-30, B0 = 4.4E+00, A1 = 1.40E-12, B1 = 7.0E-01)<br />
|GP(A0 = 2.4e-30, B0 = 3., A1 = 1.6e-12, B1 = -0.1)<br />
|[[File:JPL201510andGCv10_NO2plNO3plM_eq_N2O5.png|200px|thumb|left|JPL201510andGCv10_NO2plNO3plM_eq_N2O5.png]]<br />
<br />
|-valign="top"<br />
|OH + CO + M = H + CO2<br />
|GY(A0 = 5.9e-33, B0 = 1.4e0, A1 = 1.1e-12, B1 = -1.3e0, A2 = 1.5e-13, B2 = -0.6e0, A3 = 2.1e09, B3 = -6.1e0)<br />
|GY(A0 = 5.9e-33, B0 = 1., A1 = 1.1e-12, B1 = -1.3e0, A2 = 1.5e-13, B2 = 0., A3 = 2.1e09, B3 = -6.1e0)<br />
|[[File:JPL201510andGCv10_OHplCOplM_eq_HplCO2.png|200px|thumb|left|JPL201510andGCv10_OHplCOplM_eq_HplCO2.png]]<br />
<br />
|-valign="top"<br />
|OH + PRPE + M = PO2<br />
|GP(A0 = 8.00E-27, B0 = 3.5E+00, A1 = 3.00E-11, B1 = 1.0E+00)<br />
|GP(A0 = 4.6e-27, B0 = 4., A1 = 2.6e-11, B1 = 1.3)<br />
|[[File:JPL201510andGCv10_OHplPRPEplM_eq_PO2.png|200px|thumb|left|JPL201510andGCv10_OHplPRPEplM_eq_PO2.png]]<br />
<br />
|-valign="top"<br />
|ClO + ClO + M = Cl2O2<br />
|GP(1.60E-32, 4.5E+00 , 3.00E-12, 2.0E+00)<br />
|GP(A0 = 1.9e-32, B0 = 3.6, A1 = 3.7e-12, B1 = 1.6)<br />
|[[File:JPL201510andGCv10_ClOplClOplM_eq_Cl2O2.png|200px|thumb|left|JPL201510andGCv10_ClOplClOplM_eq_Cl2O2.png]]<br />
<br />
|-valign="top"<br />
|BrO + NO2 + M = BrNO3<br />
|GP(5.20E-31, 3.2E+00 , 6.90E-12, 2.9E+00)<br />
|GP(A0 = 5.4e-31, B0 = 3.1, A1 = 6.5e-12, B1 = 2.9)<br />
|[[File:JPL201510andGCv10_BrOplNO2plM_eq_BrNO3.png|200px|thumb|left|JPL201510andGCv10_BrOplNO2plM_eq_BrNO3.png]]<br />
<br />
<br />
<br />
|-valign="top"<br />
|colspan="4"|<br />
#Termolecular rates coefficients are evaluated from -0.5km to 11km in the 1976 US Std Atmosphere temperature and pressures<br />
#GP is short hand for the GEOS-Chem rate form denoted by P in globchem.dat and corresponding to the JPL termolecular rate defined as k_f([M],T) in Section 2.1<br />
#GY is short hand for the GEOS-Chem rate form denoted by Y in globchem.dat and corresponding to the JPL termolecular rate defined as k^{ca}_f([M],T) in Section 2.1<br />
<br />
|}<br />
<br />
=== Table 3-1 ===<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-valign="top" bgcolor="#CCCCCC"<br />
!width="275px"|GEOS-Chem Reaction<br />
!width="275px"|v10 (JPL 10-6)<br />
!width="275px"|JPL 15-10<br />
!width="275px"|Comparison<br />
<br />
|-valign="top"<br />
|N2O5 = NO2 + NO3<br />
|GP(A0 = 7.40E-04, B0 = 4.4E+00, C0 = -11000., A1 = 5.18E+14, B1 = 7.0E-01, C1 = -11000.)<br />
|GP(A0 = 2.4e-30/5.8e-27, B0 = 3., C0 = -10840, A1 = 1.6e-12/5.8e-27, B1 = -0.1, C1 = -10840)<br />
|[[File:JPL201510andGCv10_N2O5_eq_NO2plNO3.png|200px|thumb|left|JPL201510andGCv10_N2O5_eq_NO2plNO3.png]]<br />
<br />
|-valign="top"<br />
|HNO4 = HO2 + NO2<br />
|GP(A0 = 2.e-31 / 2.1e-27, B0 = 3.4, C0 = -10900., A1 = 2.9e-12 / 2.1e-27, B1 = 1.1, C1 = -10900.)<br />
|GP(A0 = 1.9e-31 / 2.1e-27, B0 = 3.4, C0 = -10900., A1 = 4e-12 / 2.1e-27, B1 = 0.3, C1 = -10900.)<br />
|[[File:JPL201510andGCv10_HNO4_eq_HO2plNO2.png|200px|thumb|left|JPL201510andGCv10_HNO4_eq_HO2plNO2.png]]<br />
<br />
|-valign="top"<br />
|colspan="4"|<br />
#GP is short hand for the GEOS-Chem rate form denoted by P in globchem.dat and corresponding to the JPL termolecular rate defined as k_f([M],T) in Section 2.1<br />
#GY is short hand for the GEOS-Chem rate form denoted by Y in globchem.dat and corresponding to the JPL termolecular rate defined as k^{ca}_f([M],T) in Section 2.1<br />
<br />
|}<br />
<br />
=== Notes ===<br />
<br />
* Skipping CH2OO + ... on 1-93<br />
* Skipping syn-CH3CHOO and anti-CH3CHOO on 1-94<br />
* Skipping FOx reactions<br />
* Skipped ClOx reactions, needs review<br />
* Skipped BrOx reactions, needs review<br />
* SOx reactions need further consideration perhaps with overlap of Iodine IO and DMS? IO + CH3SCH3 -> products</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28196MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T20:19:04Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I explored both the MODIS product using very basic processing and the product described by Yuan et al. 2011. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I processed LAI for 2008-2010 and simulated isoprene emissions for 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing LAI from 2008, we can understand the difference between LAI products. Looking at isoprene emissions from 2010 estimates the difference due to LAI product and the effect of interannual variability.<br />
<br />
:The differences between products (the product we currently use, basic processing of MODIS, and Yuan) is larger than the differences between years. The Yuan product having been used in Sindelarova (2014) with Guenther as a co-author and explicit discussion of better gap filling leads me to select the Yuan product.<br />
<br />
:Using the Yuan product reduces isoprene emissions by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different, gap filling, and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The largest differences occur in areas with the lowest emissions. <br />
<br />
{|<br />
|- style="text-align:center;"<br />
|[[File:STD_LAI_2010.png|250px|Standard]] <br />
|[[File:BNU_LAI_2010.png|250px|Yuan]] <br />
|[[File:MFB_LAI_2010.png|250px|2*(Yuan - STD)/(Yuan+STD)Mean fractional bias]] <br />
|- style="text-align:center;"<br />
|Standard <br />
|From Yuan<br />
|2*(Yuan - STD)/(Yuan+STD)<br />
|}<br />
<br />
:For 2010, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28195MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T20:10:11Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The largest differences occur in areas with the lowest emissions. The differences between products is larger than the differences between years.<br />
<br />
<br />
{|<br />
|- style="text-align:center;"<br />
|[[File:STD_LAI_2010.png|250px|Standard]] <br />
|[[File:BNU_LAI_2010.png|250px|BNU]] <br />
|[[File:MFB_LAI_2010.png|250px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
|- style="text-align:center;"<br />
|Standard <br />
|From Yuan (BNU) <br />
|2*(BNU - STD)/(BNU+STD)<br />
|}<br />
<br />
:For 2010, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28192MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T20:09:49Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The largest differences occur in areas with the lowest emissions. The differences between products is larger than the differences between years.<br />
<br />
<br />
{|<br />
|- style="text-align:center;"<br />
|[[File:STD_LAI_2010.png|250px|Standard]] <br />
|[[File:BNU_LAI_2010.png|250px|BNU]] <br />
|[[File:MFB_LAI_2010.png|250px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
|- style="text-align:center;"<br />
|From Yuan (BNU) <br />
|Standard <br />
|2*(BNU - STD)/(BNU+STD)<br />
|}<br />
<br />
:For 2010, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28188MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T20:05:01Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The largest differences occur in areas with the lowest emissions. The differences between products is larger than the differences between years.<br />
<br />
{|<br />
|-[[File:BNU_LAI_2010.png|250px|BNU]] <br />
| [[File:STD_LAI_2010.png|250px|Standard]] <br />
| [[File:MFB_LAI_2010.png|250px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
|- From Yuan (BNU) | Standard | 2*(BNU - STD)/(BNU+STD)<br />
|}<br />
<br />
:For 2010, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28187MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T20:02:42Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The largest differences occur in areas with the lowest emissions. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2010.png|250px|BNU]] <br />
[[File:STD_LAI_2010.png|250px|Standard]] <br />
[[File:MFB_LAI_2010.png|250px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
<br />
:For 2010, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28174MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T19:11:05Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2010.png|250px|BNU]] <br />
[[File:STD_LAI_2010.png|250px|Standard]] <br />
[[File:MFB_LAI_2010.png|250px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
<br />
:For 2010, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28173MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T19:10:45Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2010.png|30%|BNU]] <br />
[[File:STD_LAI_2010.png|250px|Standard]] <br />
[[File:MFB_LAI_2010.png|250px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
<br />
:For 2010, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28170MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T18:59:45Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2010.png|250px|BNU]] <br />
[[File:STD_LAI_2010.png|250px|Standard]] <br />
[[File:MFB_LAI_2010.png|250px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
<br />
:For 2010, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28169MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T18:59:17Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2010.png|250px|BNU]] <br />
[[File:STD_LAI_2010.png|250px|Standard]] <br />
[[File:MFB_LAI_2010.png|250px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
<br />
:For 2008, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:MFB_LAI_2010.png&diff=28168File:MFB LAI 2010.png2016-11-04T18:58:53Z<p>Barronh: Mean fractional bias between standard GEOS-Chem ISOP emissions and new Yuan product.</p>
<hr />
<div>Mean fractional bias between standard GEOS-Chem ISOP emissions and new Yuan product.</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28167MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T18:58:15Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2010.png|100px|BNU]] <br />
[[File:STD_LAI_2010.png|100px|Standard]] <br />
[[File:MFB_LAI_2010.png|100px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
<br />
:For 2008, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:STD_LAI_2010.png&diff=28165File:STD LAI 2010.png2016-11-04T18:58:00Z<p>Barronh: </p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28164MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T18:57:37Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2010.png|100px|BNU]] <br />
[[File:BU_LAI_2010.png|100px|Standard]] <br />
[[File:MFB_LAI_2010.png|100px|2*(BNU - STD)/(BNU+STD)Mean fractional bias]] <br />
<br />
:For 2008, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:BNU_LAI_2010.png&diff=28163File:BNU LAI 2010.png2016-11-04T18:56:28Z<p>Barronh: </p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28162MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T18:55:58Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated isoprene emissions for 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2010.png|100px|Standard]] <br />
[[File:BU_LAI_2010.png|100px|BNU]] <br />
[[File:MFB_LAI_2010.png|100px|Mean fractional bias]] <br />
<br />
:For 2008, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28161MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T18:49:52Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2008.png|100px|]] <br />
[[File:BU_LAI_2008.png|100px|]] <br />
[[File:MFB_LAI_2008.png|100px|]] <br />
<br />
:For 2008, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28157MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T18:10:50Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences. The differences between products is larger than the differences between years.<br />
<br />
[[File:BNU_LAI_2008.png]] <br />
[[File:BU_LAI_2008.png]] <br />
<br />
:For 2008, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28156MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T18:10:09Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated 2008 and 2010 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences.<br />
<br />
[[File:BNU_LAI_2008.png]] <br />
[[File:BU_LAI_2008.png]] <br />
<br />
:For 2008, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28155MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T18:09:02Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources, some of which are more recent than the ones in GEOS-Chem at this time. I propose updating LAI to the product described by Yuan et al. 2011. This product is available from 2000 through 2015 and was previously applied with MEGAN by Sindelarova et al. (2014). I performed tests with GEOS-Chem v9-02 and saw generally consistent results.<br />
<br />
:I simulated 2008 and 2015 using both the product already in GEOS-Chem and the Yuan et al. (2011) product. LAI varies both intra and inter-annually. GEOS-Chem currently applies year-specific LAI for 2005-2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. By comparing both a year-specific run and an extrapolated run, I can estimate both the difference due to LAI product differences and the effect of interannual variability.<br />
<br />
:The year-specific comparison shows patch differences that are large and smaller differences overall. The global total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU.txt]]). In specific locations, the differences can be quite high. These may be a combination of edge effects where spatial processing was different and a difference in the LAI maximum. Sindelarova et al (2014) applied the Yuan dataset with a 7 m2/m2 maximum, which was not applied in my tests and may account for some large differences.<br />
<br />
[[File:BNU_LAI_2008.png]] <br />
[[File:BU_LAI_2008.png]] <br />
<br />
:For 2008, there is not a huge difference that motivates a high priority implementation. However, upon further reflection, this update seems easy and practical. It also has the added benefit of providing a consistent product for a 15-year period.<br />
<br />
#Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001, <br />
#Sindelarova, K., Granier, C., Bouarar, I., Guenther, A., Tilmes, S., Stavrakou, T., Müller, J.-F., Kuhn, U., Stefani, P., and Knorr, W.: Global data set of biogenic VOC emissions calculated by the MEGAN model over the last 30 years, Atmos. Chem. Phys., 14, 9317-9341, doi:10.5194/acp-14-9317-2014, 2014.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT) edited drastically at 2:08pm.<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:README_LAI_BNU.txt&diff=28146File:README LAI BNU.txt2016-11-04T16:00:42Z<p>Barronh: Description of simulations with BNU LAI and the results.</p>
<hr />
<div>Description of simulations with BNU LAI and the results.</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28144MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T15:47:06Z<p>Barronh: /* Discussion of LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources. I originally proposed updating to newer LAI for current years. It is no longer clear to me that this is an imperative, but I wanted to document my exploration into the issue and get feedback from the community.<br />
<br />
:LAI varies both intra and inter-annually and GEOS-Chem currently has LAI for years 2005 and 2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. There are many source of LAI for past and future years. I've explored a few options including the direct MODIS product and the Yuan et al., 2011 product.<br />
<br />
:I simulated 2008 and 2015 using both the product already in GEOS-Chem and the BNU product. Using the Yuan product, I found that the LAI can be quite different in specific locations, but the total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU]]). The spatial variability of change is patchy likely due to edge effects in the processing methodology<br />
<br />
[[File:BNU_LAI_2008.png]] <br />
[[File:BU_LAI_2008.png]] <br />
<br />
<br />
:While I was doing tests, I spoke with Alex Guenther who suggested that gap filling may be more important than interannual variability. Gap filling is done on the satellite product specifically for urban environments where the LAI product might be biased. The gap filling on the BNU product is described in their publication, but is less specific to the needs of MEGAN.<br />
<br />
:In summary, it is not an obvious improvement to use a more current LAI product with a different gap filling technique. For near-term (2019-2015ish), I do not find an immediate need to update LAI. If GEOS-Chem is used for future-scenarios, then using consistent LAI would provide meaningful changes.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT)<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28143MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T15:44:41Z<p>Barronh: /* LAI Data Sources */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
:LAI products from MODIS come from many sources. I originally proposed updating to newer LAI for current years. It is no longer clear to me that this is an imperative, but I wanted to document my exploration into the issue and get feedback from the community.<br />
<br />
:LAI varies both intra and inter-annually and GEOS-Chem currently has LAI for years 2005 and 2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. There are many source of LAI for past and future years. I've explored a few options including the direct MODIS product and the Yuan et al., 2011 product.<br />
<br />
:I simulated 2008 and 2015 using both the product already in GEOS-Chem and the BNU product. Using the Yuan product, I found that the LAI can be quite different in specific locations, but the total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU]]). The spatial variability of change is patchy likely due to edge effects in the processing methodology<br />
<br />
[[File:BNU_LAI_2008.png]] <br />
[[File:BNU_LAI_2008.png]] <br />
<br />
<br />
:While I was doing tests, I spoke with Alex Guenther who suggested that gap filling may be more important than interannual variability. Gap filling is done on the satellite product specifically for urban environments where the LAI product might be biased. The gap filling on the BNU product is described in their publication, but is less specific to the needs of MEGAN.<br />
<br />
:In summary, it is not an obvious improvement to use a more current LAI product with a different gap filling technique. For near-term (2019-2015ish), I do not find an immediate need to update LAI. If GEOS-Chem is used for future-scenarios, then using consistent LAI would provide meaningful changes.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT)<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions&diff=28142MEGAN v2.1 plus Guenther 2012 biogenic emissions2016-11-04T15:42:12Z<p>Barronh: /* Discussion following 1-month benchmark v10-01h */</p>
<hr />
<div>On this page we describe the MEGAN v2.1 plus Guenther et al 2012 biogenic emissions, which are used in [[GEOS-Chem v10-01]] and newer versions. The MEGAN emissions are fed into GEOS-Chem via the [[HEMCO|HEMCO emissions component]].<br />
<br />
== Overview ==<br />
<br />
=== Description ===<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
<blockquote>GEOS-Chem emission routines for biogenic VOCs have been updated to MEGAN2.1 as described in Guenther et al., <u>Geosci. Model Dev.</u>, '''5''', 1471–1492, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html (Article)] The net result is a 11-12% decrease in the global flux for isoprene, and a 30% increase in the global flux for total monoterpenes. Biogenic alkene emissions are now computed using MEGAN instead of by scaling to isoprene, as was done previously. Biogenic emissions of acetaldehyde are now included. Annual emission totals at 2x2.5 resolution for the different compounds are within ~20% of the values in Table 6 of Guenther et al., within the expected uncertainty associated with differing meteorology, years, etc. Note that global emissions can also change by 10% or more when running at 2x2.5 versus 4x5 degree horizontal resolution (for both the updated and the standard emission routines).</blockquote><br />
<br />
<blockquote>One of the ‘under-the-hood’ changes is that there is now a single driver routine for calculating MEGAN emissions across all compounds (GET_MEGAN_EMISSIONS). Previously we had separate driver routines for each individual compound. GET_MEGAN_EMISSIONS is passed the compound name, looks up or computes the appropriate parameters, and returns the corresponding emissions. This should hopefully make it much easier to add new compounds in the future, since one just has to add the appropriate parameter values for that compound. There are parameters included for a number of compounds not presently in the standard chemistry scheme - for use in specialized simulations and/or future inclusion in standard fullchem. Another under-the-hood change is that the PCEEA/PECCA flag is no longer needed since we use this scheme exclusively now.</blockquote><br />
<br />
<blockquote>The new MEGAN implementation computes emissions for certain compounds based on pre-defined emission factor maps provided with the MEGAN source code. For other compounds emissions are computed in GEOS-Chem based on CLM4 plant functional type distributions combined with PFT-specific emission factors. This PFT approach can be used for all MEGAN compounds if desired (by adding in the corresponding emission factors for each PFT), which may be useful for applications using different vegetation maps or dynamically shifting vegetation.</blockquote><br />
<br />
<blockquote>The updated emissions lead to lower CO concentrations in the Northern Hemisphere during summer. A [[GEOS-Chem v9-01-03]] 4x5 run for 2006 gave CO mixing ratios averaged for P>800 hPa) that were lower by a few ppb over much of the Northern Hemisphere during ummer months. Maximum decreases of about 10ppb occur over certain source regions. Ox changes are small (< 2ppb for P > 800hPa) using the standard v9-1-3 (non-Caltech) chemistry scheme.</blockquote><br />
<br />
Please contact [mailto:dbm@umn.edu Dylan Millet] with any further questions about these emissions.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:05, 25 February 2015 (EST)<br />
<br />
=== Documentation ===<br />
<br />
*[http://wiki.seas.harvard.edu/geos-chem/images/Readme_megan21.pdf Readme]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (year-2006):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_2x25.pdf 2x2.5]<br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2006_4x5.pdf 4x5]<br />
<br />
*<u>Comparison between previous and updated BVOC emissions for standard tracers (nested NA, year-2011):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissComp_2011_05x067_NA.pdf 0.5x0.67]<br />
<br />
*<u>Updated emissions for all BVOCs, including non-standard tracers:</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/EmissAll_2x25.pdf 2x25]<br />
<br />
*<u>Monthly CO comparison for previous and updated MEGAN implementation (year-2006; 4x5 resolution):</u><br />
**[http://wiki.seas.harvard.edu/geos-chem/images/COComp_2006_4x5.pdf 4x5]<br />
<br />
--[[User:Dbm|Dbm]] 14:18, 22 January 2013 (EST)<br />
<br />
=== Data files ===<br />
<br />
In [[GEOS-Chem v10-01]] and newer versions, the MEGAN v2.1 plus Guenther (2012) biogenic emissions are read with the [[HEMCO|HEMCO emissions component]]. We have created [http://ftp.as.harvard.edu/gcgrid/data/ExtData/HEMCO/MEGAN/v2015-02/README new MEGAN data files] (in [[Preparing data files for use with HEMCO|COARDS-compliant netCDF format]]) for use with HEMCO. These new data files are contained in the [[HEMCO data directories|HEMCO data directory tree]]. For detailed instructions on how to download these data files to your disk server, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''Downloading the HEMCO data directories'' wiki post]].<br />
<br />
--[[User:Bmy|Bob Y.]] 13:19, 3 March 2015 (EST)<br />
<br />
=== Discussion following 1-month benchmark v10-01h ===<br />
<br />
This emission scheme was validated in [[GEOS-Chem_v10-01_benchmark_history#v10-01h|GEOS-Chem v10-01h]]. The following discussion ensued.<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:A few comments and questions below.<br />
<br />
:1. Acetone<br />
:Based on the benchmarking I did earlier biogenic acetone emissions should increase 6-7% globally & annually with the MEGAN update. But the emission ratio plot for ACET in the new benchmark shows a >2x increase everywhere. On the emission summary page, the "biogenic and natural' acetone sources look to have increased from 1.6 to 5.2. But if we look on the same page at the "acetone sources" the two simulations are very similar and the sum is consistent with a ~7% increase. In other words the large discrepancy in the emission ratio plot and in the "biogenic and natural sources" table for acetone just looks to be a correction to the way the diagnostics are being done. Is that right? Consistent with that, the concentration ratios are not very different.<br />
<br />
:2. Isoprene<br />
:I'd expect about a 10-12% isoprene decrease globally & annually for isoprene emissions. The new benchmark has a ~30% decrease. I'm not sure why that would be. It could just be the difference between a 1-month run and a full year, or interannual variability, I suppose, though the discrepancy seems large for that. Does the 10-01f benchmark we're comparing to use the (old) standard canopy treatment, or does it use the PCEEA parameterization? That was an option before, but we got rid of it with the MEGAN update (which only uses PCEEA). If we're switching canopy schemes that might explain the difference. <br />
<br />
:3. For propene I expect about a 50% increase globally. The change we see in the benchmark is larger (67%) but not dramatically.<br />
<br />
:4. Since we now have biogenic emissions of ALD2 we should add the appropriate biogenic benchmark diagnostics.<br />
<br />
'''''[[User:Melissa Payer|Melissa Sulprizio]] wrote:'''''<br />
<br />
:1. Acetone<br />
:That is correct. Prior to this version, there was a bug in diag3.F in the conversion to atomsC/cm2/s that affected the biogenic acetone diagnostic (ND46). The error appears to have come in with the implementation of HEMCO. We corrected the unit conversion in this version and the biogenic acetone emissions are now more consistent with pre-HEMCO values.<br />
<br />
:2. Isoprene<br />
:The PECCA/PCEEA model was turned off in the old benchmarks, so that may explain the difference. From the <tt>HEMCO.log</tt> file for the previous benchmark ([[GEOS-Chem_v10-01_benchmark_history#v10-01h|v10-01f_UCX]]), we have:<br />
<br />
Use MEGAN biogenic emissions (extension module)<br />
'''- Use PECCA model: F'''<br />
- Use the following species:<br />
Isoprene = ISOP 1<br />
Acetone = ACET 26<br />
C3 Alkenes = PRPE 23<br />
Ethene = C2H4 -1<br />
--> Isoprene scale factor is 1.00000000000000<br />
- MEGAN monoterpene option enabled:<br />
CO = CO 31<br />
OC aorosol = OCPI 16<br />
Monoterp. = MONX -1<br />
<br />
:3. Propene<br />
:Could it be that the difference in meteorology fields is causing this difference? It looks like your benchmarks used GEOS-5 met fields for 2006. In v10-01h, we are using GEOS-FP met fields for July 2013.<br />
<br />
:4. Diagnostics<br />
:I have added ALD2 to the benchmark plotting routines. We were unable to make difference plots for this version since v10-01f_UCX didn’t include biogenic emissions of ALD2 so I have that update commented out for now, but we will include differences of ALD2 biogenic emissions in future benchmarks. For your reference, I have included a map of the ALD2 biogenic emissions from v10-01h below:<br />
<br />
:[[Image:V10-01h_ALD2_biogenic_emissions.gif]]<br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
:Ok, that all seems reasonable. The only question left in my mind is the 30% isoprene decrease compared to 10% that I saw earlier. I've started a run testing the impact of switching canopy schemes to see if that accounts for it.<br />
<br />
:Based on my original implementation of the MEGAN update, changing the MEGAN algorithms and EFs gives a 10-11% reduction in global emissions. Changing the canopy scheme gives another 7-8% decrease. So the total expected decrease (18%) is still less than we see with the new benchmark (30%), but close enough that it could be due to 1 month versus 1 year, different met fields, interannual variability, etc. I vote for moving ahead and having a look at the 1-y benchmark.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:12, 27 March 2015 (EDT)<br />
<br />
=== Discussion of LAI Data Sources ===<br />
<br />
== LAI Data Sources ==<br />
<br />
'''''[[User:barronh|Barron Henderson]] wrote:'''''<br />
<br />
LAI products from MODIS come from many sources. I originally proposed updating to newer LAI for current years. It is no longer clear to me that this is an imperative, but I wanted to document my exploration into the issue and get feedback from the community.<br />
<br />
LAI varies both intra and inter-annually and GEOS-Chem currently has LAI for years 2005 and 2009. Beyond 2009, GEOS-Chem currently uses LAI from 2008. Before 2005, GEOS-Chem currently uses LAI from 2005. There are many source of LAI for past and future years. I've explored a few options including the direct MODIS product and the Yuan et al., 2011 product.<br />
<br />
I simulated 2008 and 2015 using both the product already in GEOS-Chem and the BNU product. Using the Yuan product, I found that the LAI can be quite different in specific locations, but the total ISOP emissions are reduced by 4-7% per month (see [[File:README_LAI_BNU]]). The spatial variability of change is patchy likely due to edge effects in the processing methodology<br />
<br />
[[File:BNU_LAI_2008.png]] <br />
[[File:BNU_LAI_2008.png]] <br />
<br />
<br />
While I was doing tests, I spoke with Alex Guenther who suggested that gap filling may be more important than interannual variability. Gap filling is done on the satellite product specifically for urban environments where the LAI product might be biased. The gap filling on the BNU product is described in their publication, but is less specific to the needs of MEGAN.<br />
<br />
In summary, it is not an obvious improvement to use a more current LAI product with a different gap filling technique.<br />
to be more current ithis update would provide a significant improvement for near-present day modeling. If there was a long-term future projection, then it would provide meaningful changes and the application should ingest forcast LAI and PFT from CLM.<br />
<br />
--[[User:barronh|barronh]] 11:30, 4 Nov 2016 (EDT)<br />
<br />
== CO2 direct effect on isoprene emissions ==<br />
<br />
<span style="color:green">'''''This update was validated with [[GEOS-Chem_v11-01_benchmark_history#v11-01d|1-month benchmark simulation v11-01d]] and [[GEOS-Chem_v11-01_benchmark_history#v11-01d-Run1|1-year benchmark simulation v11-01d-Run1]]. This version was approved on 12 Dec 2015.'''''</span><br />
<br />
Amos Tai developed code updates to include CO2 inhibition of isoprene emissions in MEGAN. <br />
<br />
The reference for this work is:<br />
<br />
:Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:45, 23 January 2014 (EST)<br />
<br />
== References ==<br />
<br />
#Barkley, M., ''Description of MEGAN biogenic VOC emissions in GEOS-Chem'', 2010. [http://acmg.seas.harvard.edu/geos/wiki_docs/emissions/megan.pdf PDF]<br />
#Buermann, W., Wang, Y.J., Dong, J.R., Zhou, L.M., Zeng, X.B., Dickinson, R.E., Potter, C.S., and Myneni, R.B.: ''Analysis of a multiyear global vegetation leaf area index data set'', <u>J. Geophys. Res.</u>, 107, 4646, doi:10.1029/2001JD000975, 2002.<br />
#Guenther, A., Baugh, B., Brasseur, G., Greenberg, J., Harley, P., Klinger, L., Serca, D., and Vierling, L.: ''Isoprene emission estimates and uncertainties for the Central African EXPRESSO study domain'', <u>J. Geophys. Res.</u>, 104, 30625-30639, 1999.<br />
#Guenther, A., Karl, T., Harley, P., Wiedinmyer, C., Palmer, P.I., and Geron, C.: ''Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature)'', <u>Atmos. Chem. Phys.</u>, '''6''', 3181-3210, 2006.<br />
#Guenther, A., and C. Wiedinmyer, ''User's guide to the Model of Emissions of Gases and Aerosols from Nature (MEGAN), Version 2.01'', 2007.<br />
#Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: ''The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions'', <u>Geosci. Model Dev.</u>, '''5''', 1471-1492, doi:10.5194/gmd-5-1471-2012, 2012. [http://www.geosci-model-dev.net/5/1471/2012/gmd-5-1471-2012.html Article]<br />
#Millet, D.B., Jacob, D.J., Boersma, K.F., Fu, T.M., Kurosu, T.P., Chance, K., Heald, C.L., and Guenther, A.: ''Spatial distribution of isoprene emissions from North America derived from formaldehyde column measurements by the OMI satellite sensor'', <u>J. Geophys. Res.</u>, 113, D02307, doi:10.1029/2007JD008950, 2008. [http://acmg.seas.harvard.edu/publications/millet_2008.pdf PDF]<br />
#Mueller, J.-F., et al. ''Global isoprene emissions estimated using MEGAN, ECMWF analyses and a detailed canopy environment model'', <u>Atmos. Chem. Phys.</u>, '''8''', 1329-1341, 2008.<br />
#Myneni, R. B., et al., ''Large seasonal swings in leaf area of Amazon rainforests'', <u>Proceedings of the National Academy of Sciences</u>, '''104'''(12), 4820{4823, doi:10.1073/pnas.0611338104, 2007.<br />
#Palmer, P.I., Abbot, D.S., Fu, T.M., Jacob, D.J., Chance, K., Kurosu, T.P., Guenther, A., Wiedinmyer, C., Stanton, J.C., Pilling, M.J., Pressley, S.N., Lamb, B., and Sumner, A.L.: ''Quantifying the seasonal and interannual variability of North American isoprene emissions using satellite observations of the formaldehyde column'', <u>J. Geophys. Res.</u>, 111, D12315, doi:10.1029/2005JD006689, 2006. [http://acmg.seas.harvard.edu/publications/palmer2006_gome.pdf PDF]<br />
#Sakulyanontvittaya, T., T. Duhl, C. Wiedinmyer, D. Helmig, S. Matsunaga, M. Potosnak, J. Milford, and A. Guenther, ''Monoterpene and Sesquiterpene Emission Estimates for the United States'', <u>Environ. Sci. Technol.</u>, '''42'''(5), 1623{1629, doi:10.1021/es702274e, 2008.<br />
#Tai, A.P.K., L.J. Mickley, C.L. Heald, S. Wu, ''Effect of CO2 inhibition on biogenic isoprene emission: Implications for air quality under 2000-to-2050 changes in climate, vegetation, and land use'', <u>Geophys. Res. Let.</u>, '''40''', 3479-3483, 2013. [[http://acmg.seas.harvard.edu/publications/2013/Tai_grl_2013.pdf pdf]]<br />
<br />
--[[User:Bmy|Bob Y.]] 15:49, 25 February 2015 (EST)<br />
<br />
== Previous issues that are now resolved == <br />
<br />
=== Bug fix for monoterpenes in ND46 diagnostic ===<br />
<br />
<span style="color:green">'''''This fix was validated with the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01c|v11-01c]] and approved on 14 Sept 2015.'''''</span><br />
<br />
'''''Jared Brewer wrote:'''''<br />
<br />
:I'm now working with the public release of [[GEOS-Chem v10-01]], and I'm reaching out to you regarding a possible bug that I've identified in the monoterpene outputs in the <tt>BIOGSRCE</tt> diagnostic in <tt>diag3.F</tt> - specifically the <tt>FACTOR</tt> code in line 4028. At this line, the program claims it is converting from KgC/m2/s to AtomsC/cm2/s, but includes the factor of 10 for conversion from Kg monoterpene to atoms C (IE, 10 carbons/monoterpene). This bug would appear to be common in all the different monoterpene emissions as well (A-Pinene, Ocimene, etc.).<br />
<br />
To resolve this issue, we have removed the number of carbons per molecume (10 for monoterpenes, 15 for sesquiterpenes, etc.( from the conversion factors in <tt>diag3.F</tt>.<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 18:36, 9 September 2015 (UTC)<br />
<br />
=== Minor bug fix in MEGAN_Mono extension ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Christoph Keller|Christoph Keller]] wrote:'''''<br />
<br />
:I came across a small bug in MEGAN: I tried to run the "standard" MEGAN only, i.e. without the monoterpenes, but this would give me zeros for all emissions except isoprene because the <tt>CLM4</tt> arrays were only being read if MEGAN extension 109 (<tt>MEGAN_mono</tt>) was enabled. So in the configuration file, we need to link the <tt>CLM4</tt> arrays to extension 108, not 109:<br />
<br />
108 CLM4_PFT_BARE $ROOT/MEGAN/v2015-02/CLM4_PFT.geos.1x1.nc PFT_BARE 2000/1/1/0 C xy 1 * - 1 1<br />
<br />
:etc. Furthermore, I made two small updates in <tt>HEMCO/Extensions/hcox_megan_mod.F</tt> for better error trapping and to avoid out-of-bounds errors:<br />
<br />
:1. In the run driver (<tt>HCOX_Megan_Run</tt>), evaluate the error return code of <tt>CALC_AEF</tt> and <tt>CALC_NORM_FAC</tt>:<br />
<br />
IF ( FIRST ) THEN<br />
! Generate annual emission factors for MEGAN inventory<br />
CALL CALC_AEF( am_I_Root, HcoState, ExtState, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
<br />
! Calculate normalization factor (dbm, 11/2012)<br />
CALL CALC_NORM_FAC( am_I_Root, RC )<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
ENDIF<br />
<br />
:2. In routine <tt>CALC_AEF</tt>, check if arrays are really used:<br />
<br />
! Convert AEF arrays to [kgC/m2/s]<br />
! Multiply arrays by FACTOR and ratio [g C/g compound]<br />
! NOTE: AEFs for ISOP, MBOX, BPIN, CARE, LIMO, OCIM, SABI <br />
! are read from file in [kgC/m2/s], so no need to convert here<br />
IF ( ExtNrMono > 0 ) THEN<br />
AEF_APIN(I,J) = AEF_APIN(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_MYRC(I,J) = AEF_MYRC(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
AEF_OMON(I,J) = AEF_OMON(I,J)<br />
& * FACTOR * 120.0_hp / 136.234_hp<br />
ENDIF<br />
<br />
:Note that these fixes do not affect the benchmarks since the benchmarks run with MEGAN_Mono turned on.<br />
<br />
--[[User:Bmy|Bob Y.]] 16:54, 28 April 2015 (EDT)<br />
<br />
=== Restore missing BIOGENIC_CO diagnostics ===<br />
<br />
<span style="color:green">'''''This update was added as a last-minute fix to [[GEOS-Chem v10-01]]. It was included in the GEOS-Chem v10-01 public release (17 Jun 2015).'''''</span><br />
<br />
'''''[[User:Dbm|Dylan Millet]] wrote:'''''<br />
<br />
CO SOURCES<br />
Tracer v10-01e-geosfp-Run1 v10-01h-geosfp-Run0 v10-01i-geosfp-Run0<br />
============================================================================<br />
COan+bf 527.122265 598.575584 608.052597 Tg<br />
CObb 283.579062 296.993630 293.039311 Tg<br />
'''COmono 34.826250 41.440323 0.000000 Tg'''<br />
<br />
:Why did the CO source from terpenes change [in GEOS-Chem v10-01]? It looks like it went to zero? Is that just a change in the diagnostic?<br />
<br />
'''''[[User:Bmy|Bob Yantosca]] replied:'''''<br />
<br />
:The zero CO from monoterpenes is a diagnostic issue. I looked through the logs from a recent simulation and I saw:<br />
<br />
HEMCO WARNING: Diagnostics counter is zero - return empty array: BIOGENIC_CO<br />
--> LOCATION: DiagnCont_PrepareOutput (hco_diagn_mod.F90)<br />
<br />
:Melissa and I just traced this to an omission in the HEMCO MEGAN extension (module <tt>HEMCO/Extensions/hcox_megan_mod.F</tt>). HEMCO was computing the CO emissions from monoterpenes properly. But these emissions were not being added to the proper diagnostic container (called <tt>BIOGENIC_CO</tt>) in HEMCO’s data structure. Therefore, when we went to print out these emissions, they showed up as all zeroes.<br />
<br />
:It appears that the subroutine call to add the CO emissions from monoterpenes to the diagnostics had been somehow removed from the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i]] code. We think that this may have been “clobbered” by a recent Git merge. In any case, adding the lines in <span style="color:green">GREEN</span> correct this issue:<br />
<br />
! ----------------------------------------------------------------<br />
! CO<br />
IF ( ( ExtNrMono > 0 ) .AND. ( IDTCO > 0 ) ) THEN<br />
<br />
! Add flux to emission array<br />
CALL HCO_EmisAdd( am_I_Root, HcoState, FLUXCO, IDTCO, <br />
& RC, ExtNr=ExtNr )<br />
IF ( RC /= HCO_SUCCESS ) THEN<br />
CALL HCO_ERROR( 'HCO_EmisAdd error: FLUXCO', RC )<br />
RETURN <br />
ENDIF<br />
<br />
<span style="color:green">! Also archive the BIOGENIC_CO diagnostic (bmy, 4/29/15)<br />
Arr2D => FLUXCO<br />
DiagnName = 'BIOGENIC_CO'<br />
CALL Diagn_Update( am_I_Root, ExtNr=ExtNrMono,<br />
& cName=TRIM(DiagnName), Array2D=Arr2D, RC=RC)<br />
IF ( RC /= HCO_SUCCESS ) RETURN<br />
Arr2D => NULL()</span><br />
ENDIF<br />
<br />
:With the fix installed, HEMCO now successfully adds the CO emitted from monoterpenes to the <tt>BIOGENIC_CO</tt> diagnostic instead of printing out all zeroes. <br />
<br />
--[[User:Bmy|Bob Y.]] 12:01, 29 April 2015 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=Emissions_Working_Group&diff=28134Emissions Working Group2016-11-04T14:51:44Z<p>Barronh: /* Discussions Related to Sources and Sinks (please add!) */</p>
<hr />
<div><u>The purpose of this Working Group</u> is to provide a forum to discuss current and new developments in GEOS-Chem associated with land-atmosphere and ocean-atmosphere sources, sinks, and fluxes of trace gases and aerosols.<br />
<br />
All users interested in adding/updating the GEOS-Chem emissions inventories are encouraged to subscribe to the emissions email list (click on the link in the [[#Contact information|contact information section]] below).<br />
<br />
== Primary Working Group Contacts ==<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|-valign="top"<br />
!width="300px" bgcolor="#CCCCCC"|Sources and Surface Uptake<br>Working Group Co-Chairs<br />
|width="600px"|<br />
*[http://www.atmos.pku.edu.cn/acm/contact.html Jintai Lin] and<br />
* [http://www.tsinghua.edu.cn/publish/cessen/5346/2010/20101226113024726624747/20101226113024726624747_.html Qiang Zhang]<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|Sources and Surface Uptake<br>Working Group email list<br />
|<tt>geos-chem-emissions [at] g.harvard.edu</tt><br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To subscribe to email list<br />
|Either<br />
*Send an email to <tt>geos-chem-emissions+subscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-emissions GEOS-Chem Sources and Surface Uptake Google Group]<br />
*Click on '''Subscribe to this group'''<br />
<br />
|-valign="top"<br />
!bgcolor="#CCCCCC"|To unsubscribe from email list<br />
|Either<br />
*Send an email to <tt>geos-chem-emissions+unsubscribe [at] g.harvard.edu</tt><br />
Or<br />
*Go to the [https://groups.google.com/a/g.harvard.edu/forum/#!forum/geos-chem-emissions GEOS-Chem Sources and Surface Uptake Google Group]<br />
*Click on the '''My Settings''' button<br />
*Click on '''Leave this group'''<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 18:35, 21 August 2015 (UTC)<br />
<br />
== Who's doing what and where? [Current GEOS-Chem Research Projects on Sources and Sinks] ==<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="150px"|User Group <br />
!width="600px"|Description <br />
!width="150px"|Contact Person<br />
!width="100px"|Date Added<br />
|-<br />
|Dalhousie<br />
|Top-down constraints on surface NOx emissions<br />
|[mailto:mcooper@dal.ca Matthew Cooper]<br />
|27 April 2011<br />
|-<br />
|Harvard<br />
|Methane sources in the Arctic<br />
|[mailto:cpickett@as.harvard.edu Christopher Pickett-Heaps]<br />
|<br />
|-<br />
|Harvard<br />
|Mechanistic Lightning Parameterization <br />
|[mailto:ltmurray@fas.harvard.edu Lee Murray]<br />
|<br />
|-<br />
|JPL<br />
|Comparison of adjoint and mass balance for NOx emissions <br />
|[mailto:changsub.shim@jpl.nasa.gov Changsub Shim]<br />
|<br />
|-<br />
|U. East Anglia<br />
|COS Emissions<br />
|[mailto:P.Suntharalingam@uea.ac.uk Parvadha Suntharalingam]<br />
|<br />
|-<br />
|U. Edinburgh<br />
|Biogenic VOC emissions from tropical ecosystems<br />
|[mailto:michael.barkley@ed.ac.uk Michael Barkley]<br />
|<br />
|-<br />
|U. Edinburgh<br />
|Regional methane sources using surface in situ and GOSAT and IASI satellite observations and an ensemble Kalman filter<br />
|[mailto:ac.fraser@ed.ac.uk Annemarie Fraser]<br />
|<br />
|-<br />
|U. Edinburgh<br />
|Quantifying the impact of boreal biomass burning emissions on tropospheric oxidant chemistry <br />
|[mailto:mark.parrington@ed.ac.uk Mark Parrington]<br />
|<br />
|-<br />
|U. Eindhoven<br />
|Constraining ship emissions using OMI NO2 observations / Soil NOx emissions <br />
|[mailto:g.c.m.vinken@tue.nl Geert Vinken]<br />
|21 June 2012<br />
|-<br />
|U. Toronto / Env Canada<br />
|CO2 sources and sinks (fossil fuels including shipping/aviation, biosphere, ocean, etc.)<br />
|[mailto:ray.nassar@ec.gc.ca Ray Nassar]<br />
|<br />
|-<br />
|U. Toronto<br />
|Adjoint analysis of CO sources from MOPITT<br />
|[mailto:zjiang@atmosp.physics.utoronto.ca Zhe Jiang]<br />
|<br />
|-<br />
|Peking University<br />
|Top-down constraints on Asia VOCs<br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|<br />
|-<br />
|Peking University<br />
|Air-sea exchange and top-down constraints on global acetone<br />
|[mailto:tmfu@pku.edu.cn May Fu]<br />
|29 April 2011<br />
|-<br />
|CSU<br />
|IASI constraints on NHx<br />
|[mailto:heald@atmos.colostate.edu Colette Heald]<br />
|<br />
|-<br />
|Tsinghua University<br />
|Bottom-up/top-down anthropogenic inventory over East Asia <br />
|[mailto:qiangzhang@tsinghua.edu.cn Qiang Zhang]<br />
|<br />
|-<br />
|CU Boulder<br />
|Top-down constraints on NH3<br />
|[mailto:julietboulder@gmail.com Juliet Zhu]<br />
|<br />
|-<br />
|US EPA<br />
|Top-down constraints on NO2<br />
|[mailto:Pye.Havala@epamail.epa.gov Havala Pye]<br />
|<br />
|-<br />
|U. Nebraska Lincoln<br />
|Top-down constraints on aerosols over Asia using MODIS<br />
|[mailto:xxu@huskers.unl.edu Richard Zu]<br />
|<br />
|-<br />
|Peking University<br />
|Natural sources (soil, lightning, bb) of NOx over China: top-down vs bottom-up<br />
|[mailto:linjt@pku.edu.cn Jintai Lin]<br />
|01 Nov 2010<br />
|-<br />
|UW<br />
|Snow NOx source in Greenland and Antarctica<br />
|[mailto:beckya@uw.edu Becky Alexander]<br />
|07 May 2015<br />
|}<br />
<br />
== Ongoing GEOS-Chem Developments Related to Sources and Sinks (please add yours!) ==<br />
<br />
Here is the list of updates that are slated to be added to GEOS-Chem in the next few releases:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5<br />
|- bgcolor="#cccccc"<br />
!width="400"|Update<br />
!width="200"|Authors<br />
!width="400"|Planned release<br />
<br />
|-valign="top"<br />
|[[HEMCO|HEMCO emissions component]]<br />
|Christoph Keller (Harvard)<br />
|<br />
*Implemented into [[GEOS-Chem v10-01]], updated as needed<br />
<br />
|-valign="top"<br />
|[[MEGAN biogenic emissions]]<br />
|Michael Barkley (Leicester)<br />
|<br />
*Updates ongoing<br />
<br />
|-valign="top"<br />
|Updated Southeast Asian emissions for SEAC4RS<br />
|Jenny Fisher (Wollongong)<br>Patrick Kim (Harvard)<br />
|<br />
*Updates ongoing<br />
<br />
|-valign="top"<br />
|Australian anthropogenic emissions<br />
|Jenny Fisher (Wollongong)<br />
|<br />
*Updates ongoing<br />
<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 18:55, 14 January 2015 (EST)<br />
<br />
== Recent GEOS-Chem Updates Related to Sources and Sinks ==<br />
<br />
We have added the following updates pertaining to sources and sinks to recent GEOS-Chem versions:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|-bgcolor="#CCCCCC" valign="top"<br />
!width="75px"|Version<br />
!width="75px"|Released<br />
!width="550px"|Description<br />
!width="250px"|Contact<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v10-01|v10-01]]<br />
|Jun 2015<br />
|The [[HEMCO|HEMCO emissions component]] now handles all GEOS-Chem emissions.<br />
|Christoph Keller (Harvard)<br>[[GCST]]<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v10-01|v10-01]]<br />
|Jun 2015<br />
|Daily anthropogenic emissions broken down by sector from the EPA NEI2008 inventory (via [[HEMCO]])<br />
|Katie Travis (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v10-01|v10-01]]<br />
|Jun 2015<br />
|[[Biomass_burning_emissions#FINNv1|FINNv1 biomass burning emissions]] (via [[HEMCO]])<br />
|Jenny Fisher (Wollongong)<br>Min Huang (JPL)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v10-01|v10-01]]<br />
|Jun 2015<br />
|[[MEGAN_v2.1_plus_Guenther_2012_biogenic_emissions|MEGAN v2.1 plus Guenther 2012 biogenic emissions]] (via [[HEMCO]])<br />
|Dylan Millet (Minnesota)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Soil NOx emissions#Updated soil NOx emissions algorithm|New soil NOx emission module]]<br />
|Rynda Hudman Kay (EPA)<br>Neil Moore (formerly of Dalhousie)<br>Bram Maasakkers (Harvard) <br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Mercury#Nested-grid Hg simulation over North America|EPA/NEI05 North American Hg emissions]]<br />
|Yanxu Zhang (U. Washington)<br>Lyatt Jaegl&eacute; (U. Washington) <br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Mercury#Streets future Hg emissions|Hg anthropogenic emissions options for the year 2006 or 2050 following SRES scenarios A1B, A2, B1, and B2 from Streets et al. 2009.]]<br />
|Bess Corbitt (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[EPA/NEI05 North American emissions#Updated NH3 seasonal scaling factors in_v9-02|Updated NH3 seasonal scaling factors over the US]]<br />
|Lin Zhang (PKU)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Anthropogenic emissions#CAC|Updated Canadian NH3 inventory]]<br />
|Wai-Ho Lo (Dalhousie)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Wet_deposition#Bug_in_Henry.27s_constant|Bug in wet deposition Henry's constant]]<br />
|Fabien Paulot (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[GEOS-Chem_v9-02#Bug fixes in_biofuel_mod.F and emfossil.F|Fix diurnal NOx scale factors and fix double counting of biofuels over Mexico, Canada, and Europe]]<br />
|Christoph Keller (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Ship emissions#Bugs in ship emissions and non-local PBL mixing|Correct bugs in ship emissions w/ non-local PBL mixing]]<br />
|Chris Holmes (UC Irvine)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[GEOS-Chem v9-02#Bug fixes in day-of-week computation|Bug fixes in day-of-week computation]]<br />
|[[GEOS-Chem Support Team]]<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Historical and Future Emissions#RCP future emission scenarios|RCP future emission scenarios]]<br />
|Chris Holmes (UC Irvine)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[CH4 simulation#Update CH4 emissions to EDGAR v4.2|EDGAR v4.2 emissions for CH4 simulation]]<br />
|Kevin Wecht (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Scale factors for anthropogenic emissions|Update anthropogenic scale factors through 2010]]<br />
|Aaron van Donkelaar (Dalhoisie)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Biomass burning emissions#Update GFED3 emissions to 2011|Update GFED3 emissions to 2011]]<br />
|Prasad Kasibhatla (Duke)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Aircraft emissions#MIT aviation emissions inventory|AEIC aircraft emissions inventory]]<br />
|Sebastian Eastham (MIT)<br>Steven Barrett (MIT) <br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[Dry deposition#Error in definition of RIP and IEPOX drydep species|Fix molecular weights of RIP and IEPOX used in drydep_mod.F]]<br />
|[[GEOS-Chem Support Team]]<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-02|v9-02]]<br />
|Mar 2014<br />
|[[EPA/NEI05 North American emissions#Bug fix for NEI2005 SO4 emissions in sulfate_mod.F|Bug fix for NEI2005 SO4 emissions in sulfate_mod.F]]<br />
|Jenny Fisher (U. Wollongong)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|[[Acetone|Improved acetone simulation]]<br />
|Emily Fischer (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|[[Biogenic emissions#Retirement of obsolete GEIA biogenic emissions|Complete shift of biogenic VOC emissions from GEIA to MEGAN; retire GEIA]]<br />
|Dylan Millet<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|[[Dry deposition#OVOCs dry deposition|OVOC's dry deposition]]<br />
|Jingqiu Mao (NOAA/GFDL) <br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|[[#Available Historical and Future Emissions|Historical emission inventories of SO2, NOx, BC, and POA]]<br />
|Eric Leibensperger (MIT)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|[[Ship emissions#PARANOX_ship_plume_model|PARANOX model for evolution of ship exhaust plumes]]<br />
|Geert Vinken (Eindhoven)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|Improved [[Wet deposition#Add scavenging by snow|snow scavenging]] and [[Wet deposition#Updates for aerosol scavenging efficiency|washout parameterization]]<br />
|Qiaoqiao Wang (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|[[Lightning NOx emissions|Constraining the lightning NOx source with satellite data]]<br />
|Lee Murray (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|[[Regridding in GEOS-Chem#Modification of MAP_A2A for use within GEOS-Chem|MAP_A2A algorithm to regrid emissions on the fly]]<br />
|Prasad Kasibhatla (Duke)<br>Matt Cooper (Dalhousie)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|Sep 2012<br />
|[[Scale factors for anthropogenic emissions#Anthropogenic NOx scaling factors from OMI|Anthropogenic NOx scaling factors from OMI]]<br />
|Lok Lamsal (NASA)<br>Matt Cooper (Dalhousie)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-02|v9-01-02]]<br />
|Nov 2011<br />
|[[Mercury#Anthropogenic Emissions|GEIA 2005 Hg emissions]]<br />
|Bess Corbitt (Harvard)<br>Noelle Selin (MIT)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-02|v9-01-02]]<br />
|Nov 2011<br />
|[[EPA/NEI05_North_American_emissions#Biofuel_emissions|Bug fix for biofuel emissions when using EPA/NEI05]]<br />
|[[GEOS-Chem Support Team]]<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-02|v9-01-02]]<br />
|Nov 2011<br />
|[[Biomass burning emissions#GFED3|Update to GFED3 biomass burning]]<br />
|[mailto:psk9@duke.edu Prasad Kasibhatla] (Duke)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-02|v9-01-02]]<br />
|Nov 2011<br />
|[[Implementation of RETRO Anthropogenic Emissions|Anthropogenic VOCs]]<br />
|[mailto:dbm@umn.edu Dylan Millet] (UMN)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-02|v9-01-02]]<br />
|Nov 2011<br />
|[[Anthropogenic_emissions#Streets_2000|Added seasonality to Streets NH3 emissions over Asia]]<br />
|[mailto:jafisher@fas.harvard.edu Jenny Fisher] (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-01|v9-01-01]]<br />
|May 2011<br />
|Updated Hg simulation <br />
||Bess Corbitt (Harvard)<br>Jenny Fisher (Harvard)<br>Helen Amos (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-01|v9-01-01]]<br />
|May 2011<br />
|[[EPA/NEI05_North_American_emissions#Biofuel_emissions|Bug fix for biofuel emissions when using EPA/NEI05]]<br />
|[[GEOS-Chem Support Team]]<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-01|v9-01-01]]<br />
|May 2011<br />
|Bug fixes for [[Ship emissions#Bug for ship emissions in emfossil.f|ship emissions]] and [[Ship emissions#Inconsistent mask file for EMEP ship emissions|EMEP ship emissions mask file]]<br />
|[[GEOS-Chem Support Team]]<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-01|v9-01-01]]<br />
|May 2011<br />
|[http://seas.harvard.edu/~ltmurray/LNOx.v9-01-01.Release.Notes.pdf Updated lightning parameterization and fix for cloud-top-height algorithm]<br />
|L. Murray, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-01|v9-01-01]]<br />
|May 2011<br />
|[[Volcanic SO2 emissions from Aerocom#Data for v9-01-01 and newer versions|Updated volcanic SO2 emissions from Aerocom]]<br />
| J. Fisher (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v9-01-01|v9-01-01]]<br />
|May 2011<br />
|[http://acmg.seas.harvard.edu/geos/wiki_docs/deposition/v9-01-01_wetdep.pdf Updated wet scavenging and convective updraft scavenging algorithms] and<br>[[Wet deposition#Allow both washout and rainout when precipitation forms|Allow both washout and rainout when precipitation forms]]<br />
|H. Amos (Harvard)<br>Bess Corbitt (Harvard)<br>Q. Wang (Harvard)<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-02|v8-03-02]]<br />
|Sep 2010<br />
|[[CO2_simulation| Updated CO2 Emissions]]<br />
|R. Nassar, Environment Canada<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|[[Scale factors for anthropogenic emissions| Extension of annual anthropogenic scale factors to 2006]]<br />
|A. van Donkelaar, Dalhousie<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|EMEP emissions extended to 2007 and seasonality extended to SOx, CO, and NH3<br />
|A. van Donkelaar, Dalhousie<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|Emissions for Nested NA/EU Simulations [[GEOS-Chem nested grid simulations|Nested Grid]]<br />
|A. van Donkelaar, Dalhousie<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|Emissions for Global 1 x 1.25 simulation capability<br />
|L. Lamsal, Dalhousie<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-03-01|v8-03-01]]<br />
|May 2010<br />
|[[Secondary organic aerosols#Speciated biogenic emissions from MEGAN|Speciated biogenic emissions from MEGAN v2.1 now used in SOA code]]<br />
|H. Pye, Caltech<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-02-04|v8-02-04]]<br />
|Feb 2010<br />
|[[EPA/NEI05 North American emissions|EPA/NEI2005 regional emissions inventory for North America]]<br />
|P. Le Sager (formerly Harvard),<br>A. van Donkelaar (Dalhousie)<br />
<br />
|-valign="top"align="center"<br />
|[[GEOS-Chem v8-02-04|v8-02-04]]<br />
|Feb 2010<br />
|[[MEGAN biogenic emissions#MEGAN in GEOS-Chem v8-02-04 and later versions|MEGAN v2.1 biogenic emissions]]<br />
|Mike Barkley, Edinburgh<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-02-04|v8-02-04]]<br />
|Feb 2010<br />
|[[Volcanic SO2 emissions from Aerocom|Updated inventory of volcanic SO2 emissions from AeroCom]]<br />
|Jenny Fisher, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-02-03|v8-02-03]]<br />
|Oct 2009<br />
|[[Ship emissions#ICOADS|ICOADS ship emissions]]<br />
|Chulkyu Lee, Dalhousie<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-02-03|v8-02-03]]<br />
|Oct 2009<br />
|[[Lightning NOx emissions#Updated OTD.2FLIS local redistribution for GEOS-5|Updated OTD/LIS redistribution factors for GEOS-5]]<br />
|Lee Murray, Harvard<br />
<br />
|-valign="top"<br />
|[[GEOS-Chem v8-02-02|v8-02-02]]<br />
|Jun 2009 <br />
|[[#Error in the Bond BC/OC emissons|BOND inventory for BC and OC with monthly variations]]<br />
|Eric Leibensperger, Harvard<br />
<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 10:43, 17 January 2014 (EST)<br />
<br />
== Discussions Related to Sources and Sinks (please add!) ==<br />
<br />
#[[Scale factors for anthropogenic emissions]]<br />
#[[Carbon_Gases_and_Organics_Working_Group#GEIA_anthropogenic_scaling_factors | GEIA Anthropogenic Scaling Factors]]<br />
#[[Biogenic Parameter Input Sources]]<br />
<br />
== Isoprene Emission Estimates in the Literature ==<br />
'''<br />
'''Recent Papers'''<br />
<br />
'''Evaluation of the global oceanic isoprene source and its impacts on marine organic carbon aerosol'''. Arnold SR, Spracklen DV, Williams J, Yassaa N, Sciare J, Bonsang B, Gros V, Peeken I, Lewis AC, Alvain S, Moulin C. ATMOSPHERIC CHEMISTRY AND PHYSICS, Volume: 9, Issue: 4, Pages: 1253-1262, Published: 2009. We have combined the first satellite maps of the global distribution of phytoplankton functional type and new measurements of phytoplankton-specific isoprene productivities, with available remote marine isoprene observations and a global model, to evaluate our understanding of the marine isoprene source and its impacts on organic aerosol abundances. Using satellite products to scale up data on phytoplankton-specific isoprene productivity to the global oceans, we infer a mean "bottom-up" oceanic isoprene emission of 0.31 +/- 0.08 (1 sigma) Tg/yr. By minimising the mean bias between the model and isoprene observations in the marine atmosphere remote from the continents, we produce a "top-down" oceanic isoprene source estimate of 1.9 Tg/yr. We suggest our reliance on limited atmospheric isoprene data, difficulties in simulating in-situ isoprene production rates in laboratory phytoplankton cultures, and limited knowledge of isoprene production mechanisms across the broad range of phytoplankton communities in the oceans under different environmental conditions as contributors to this difference between the two estimates. Inclusion of secondary organic aerosol (SOA) production from oceanic isoprene in the model with a 2% yield produces small contributions (0.01-1.4%) to observed organic carbon (OC) aerosol mass at three remote marine sites in the Northern and Southern Hemispheres. Based on these findings we suggest an insignificant role for isoprene in modulating remote marine aerosol abundances, giving further support to a recently postulated primary OC source in the remote marine atmosphere.<br />
<br />
For current discussions of isoprene oxidation in the literature, please see our [[Isoprene|Isoprene: Recent Papers]] page.<br />
<br />
== Available Historical and Future Emissions ==<br />
<br />
Please visit our [[Historical and Future Emissions|Historical and Future Emissions wiki page]] for the latest information about the historical and future emissions, including any bug fixes or updates.<br />
<br />
--[[User:Melissa Payer|Melissa Payer]] 15:53, 9 January 2013 (EST)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=FAST-JX_v7.0_photolysis_mechanism&diff=27104FAST-JX v7.0 photolysis mechanism2016-07-23T11:59:04Z<p>Barronh: /* Fix for TOMS to address strange cycle in OH output */</p>
<hr />
<div>Sebastian Eastham (MIT) has introduced FAST-JX v7.0 into [[GEOS-Chem v10-01]] concurrently with the [[UCX chemistry mechanism]]. FAST-JX v7.0 replaces the older [[FAST-J photolysis mechanism]].<br />
<br />
== Overview ==<br />
<br />
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
Sebastian Eastham incorporated Fast-JX v7.0a into the [[UCX chemistry mechanism|GEOS-Chem UCX mechanism]]. From [http://www.sciencedirect.com/science/article/pii/S1352231014000971 Eastham et al. (2014)]:<br />
<br />
:GEOS-Chem uses a customized version of the [[FAST-JX v6.2 photolysis mechanism]] (Wild et al., 2000), which efficiently estimates tropospheric photolysis. The customized version uses the wavelength bands from the older Fast-J tropospheric photolysis scheme and does not consider wavelengths shorter than 289 nm, assuming they are attenuated above the tropopause. However, these high-energy photons are responsible for the release of ozone-depleting agents in the stratosphere. The standard Fast-JX model (Prather, 2012) addresses this limitation by expanding the spectrum analyzed to 18 wavelength bins covering 177–850 nm, extending the upper altitude limit to approximately 60 km. We therefore incorporate Fast-JX v7.0a into [[UCX chemistry mechanism|GEOS-Chem UCX]]. Fast-JX includes cross-section data for many species relevant to the troposphere and stratosphere. However, accurately representing sulfur requires calculation of gaseous H2SO4 photolysis, a reaction which is not present in Fast-JX but which acts as a source of sulfur dioxide in the upper stratosphere. Based on a study by Mills (2005), the mean cross-section between 412.5 and 850 nm is estimated at 2.542 × 10−25 cm2. We also add photolysis of ClOO and ClNO2, given their importance in catalytic ozone destruction, using data from JPL 10-06 (Sander et al., 2011). Fast-JX v7.0a includes a correction to calculated acetone cross sections. Accordingly, where hydroxyacetone cross-sections were previously estimated based on one branch of the acetone decomposition, a distinct set of cross sections from JPL 10-06 are used.<br />
<br />
:The base version of GEOS-Chem uses satellite observations of total ozone columns when determining ozone-related scattering and extinction. The UCX allows either this approach, as was used for the production of the results shown, or can employ calculated ozone mixing ratios instead, allowing photolysis rates to respond to changes in the stratospheric ozone layer.<br />
<br />
=== Timeline ===<br />
<br />
The following table displays a timeline of important milestones in FAST-JX v7.0 development:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|- bgcolor="#CCCCCC"<br />
!width="150px"|Version<br />
!width="100px"|Date<br />
!width="800px"|Features / Improvements<br />
|-valign="top"<br />
|[[GEOS-Chem v10-01]]<br />
|Jun 2015<br />
|<br />
*Retired the [[FAST-J photolysis mechanism]] in v10-01c ''(GEOS-Chem Support Team)''<br />
*Implemented FAST-JX v7.0 into GEOS-Chem, concurrent with [[UCX chemistry mechanism]] in v10-01c ''(S. Eastham + GEOS-Chem Support Team)''<br />
*Corrected the following errors in the original FAST-JX v7.0 implementation:<br />
**[[FAST-JX_v7.0_photolysis_mechanism#Reactivation_of_bromine_species_photolysis_for_tropospheric_simulation|Reactivation of Br species for tropospheric simulation]]<br />
**[[FAST-JX_v7.0_photolysis_mechanism#Error_in_reducing_wavelength_bins_for_tropospheric_simulation|Bug fix for reducing wavelength bins for tropospheric simulation]]<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 13:42, 21 May 2014 (EDT)<br />
<br />
== Input files for FAST-JX v7.0 ==<br />
<br />
The following input files are required for the FAST-JX v7.0 photolysis mechanism:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|- bgcolor="#CCCCCC"<br />
!width="180px"|File<br />
!width="75px"|Introduced<br />
!width="75px"|Retired<br />
!width="700px"|Description<br />
<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#JvAtms <tt>fastj.jv_atms.dat.nc</tt>]<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|still used<br />
|<br />
*This netCDF file (originally created for the [[FAST-J photolysis mechanism]]) specifies the reference O3 and T climatologies for FAST-J.<br />
*This file is located in data directory:<br />
GEOS_NATIVE/FastJ_201204/fastj.jv_atms_dat.nc<br />
*NOTE: Where such data exists, GEOS-Chem will overwrite the reference O3 climatology as follows:<br />
*#The online O3 tracer (carried in (<tt>State_Chm%TRACERS(:,:,1:LLCHEM,IDTO3</tt>) '''(RECOMMENDED)''', or<br />
*#Archived O3 profiles sclaed to TOMS/SBUV monthly-mean total ozone column (TO3) data, or<br />
*#Archived TO3 data from the [[GEOS-5]] or [[GEOS-FP]] met field archives.<br />
<br />
|-valign="top"<br />
|<tt>FJX_j2j.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01c|v10-01c]]<br />
|still used<br />
|<br />
*Links GEOS-Chem chemical species to Fast-JX species. Replaces the following file:<br />
**<tt>ratj.d</tt> from the [[FAST-J photolysis mechanism]], used in versions prior to [[GEOS-Chem v10-01]]<br />
<br />
|-valign="top"<br />
|<tt>FJX_spec.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01c|v10-01c]]<br />
|still used<br />
|<br />
*Fast-JX cross-sections, which replaces the following files:<br />
**<tt>jv_spec.dat</tt> from the [[FAST-J photolysis mechanism]], used in versions prior to [[GEOS-Chem v10-01]]<br />
**<tt>spec2008.dat</tt> from the [[FAST-JX v6.4 photolysis mechanism|FAST-JX v6.x photolysis mechanism]], used in several research implementations of GEOS-Chem<br />
<br />
|-valign="top"<br />
|<tt>jv_spec.mie.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01c|v10-01c]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties at 5 wavelengths<br />
<br />
|-valign="top"<br />
|<tt>jv_spec_aod.dat</tt><br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|<br />
*The <tt>jv_spec_aod.dat</tt> file contains the optical properties for aerosols at a single wavelength to be used in the online calculation of the aerosol optical depth diagnostics. The default properties are provided at 550 nm. These properties have been calculated using the same size and optical properties as the <tt>jv_spec.dat</tt> file used for the FAST–J photolysis calculations.<br />
*[[#Scaling_of_AOD_diagnostic_output_to_other_wavelengths|The user can exchange this set of properties with those at another wavelength]]. We recommend that the wavelength used be included in the first line of the header for traceability (this line is output to the GEOS–Chem log file during run time). <br />
<br />
|-valign="top"<br />
|<tt>dust.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for dust at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>org.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for organic carbon at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>so4.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for sulfate at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>soot.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for black carbon at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>ssa.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for accumulation mode sea salt aerosol at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>ssc.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for coarse mode sea salt aerosol at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>h2so4.dat</tt><br />
|[[GEOS-Chem_v10-01#Fixes_and_updates_added_during_the_public_comment_period|v10-01 public comment period]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for sulfuric acid at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
*This file is only needed if the [[UCX chemistry mechanism]] is enabled.<br />
<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:07, 1 June 2015 (UTC)<br />
<br />
== VOC photolysis in FAST-JX v7.0 ==<br />
<br />
<span style="color:green">'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
In the table below, we summarize VOC photolysis in Fast-JX v7.0. We also invite you to view our [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jrates.pdf ''Comparison of GEOS-Chem Photolysis Rates'' document] prepared by Chris Chan Miller.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5"<br />
|-bgcolor="#cccccc"<br />
! width="300px" |Old reaction<br />
! width="300px" |New reaction<br />
! width="200px" |New rate<br />
! width="300px" |Note<br />
|-valign="top"<br />
| CH2O = HO2 + HO2 + CO (channel a) ||same ||New cross sections leads to an increase by 10% to 20% || This increase is consistent with JPL 2010.<br />
|-<br />
| CH2O = H2 + CO (channel b) ||same ||increase by 6% to 15% || This increase is consistent with JPL 2010.<br />
|-<br />
| PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2 + 0.4NO3 ||PAN = 0.7MCO3 + 0.7NO2 + 0.3MO2 + 0.3NO3 ||same || JPL2010 suggests two channels(only one channel in FastJX-v7.0), branching ratio follows JPL2010<br />
|-<br />
| ALD2 = MO2 + HO2 + CO||ALD2 = 0.88MO2 + HO2 + 0.88CO + 0.12MCO3 || || large discrepancy is found between obs and model (see [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jrates.pdf Chris's slides]), pressure dependence is probably needed. The cross section is now updated by Michael Prather.<br />
|-<br />
| ALD2 = CH4 + CO || this channel is turned off || || this channel is not included in FastJX-v7.0<br />
|-<br />
| RCHO = ETO2 + HO2 + CO ||same || || No pressure dependence is observed, according to JPL2010.<br />
|-<br />
| MP = CH2O + HO2 + OH||same || || change is small.<br />
|-<br />
| GLYX = 0.5H2 + CO + 0.5CH2O + 0.5CO ||GLYX = H2 + 2CO <br> GLYX = CH2O + CO || Pressure dependence is now included, rate is higher ||now 3 channels, Stern-Volmer expression: Qtotal = 1/[6.80 + 251.8e-4 P(Torr)], Increases quantum yields at low P, but ONLY specified for 390-470 nm. Assume that 220K has P = 0.18 atm and higher q.(From FJX v7.0 notes)<br />
|-<br />
| GLYX = 2.0CO + 2.0HO2 ||same ||Pressure dependence is now included, rate is higher || <br />
|-<br />
| MACR = CO + HO2 + CH2O + MCO3 <br> branching ratio = 0.5 ||same ||rate is significantly reduced, as Qy is reduced from 0.008 to 0.003 ||this channel is dominant,the third channel (C3H6 + CO), is ignored, to be consistent with Fast-JX v7.0<br />
|-<br />
| MACR = MAO3 + HO2 <br> branching ratio = 0.5 ||remove this channel || ||suggested by IUPAC, also consistent with Fast-JX v7.0<br />
|-<br />
| MVK = PRPE + CO <br> branching ratio = 0.6 || ||pressure dependence is now included ||<br />
|-<br />
| MVK = MCO3 + CH2O + CO + HO2 <br> branching ratio = 0.2|| ||pressure dependence is now included ||<br />
|-<br />
| MVK = MO2 + MAO3<br> branching ratio = 0.2 ||MVK = MO2 + RCO3 || ||this channel was removed in FJX v7.0, but it shouldn't according to IUPAC. MAO3 is changed to RCO3 for carbon balance.<br />
|- <br />
| GLYC = CH2O + 2.0HO2 + CO ||GLYC = 0.9CH2O + 1.73HO2 + 0.07OH + 1.0CO + 0.1MOH ||Significant increase in X sections || merge from three channels GLYC =CH2O + 2.0HO2 + CO(QY = 0.83), GLYC =CH3OH + CO (QY=0.10), GLYC =OH + CH2O + HO2 + CO (QY =0.07) JPL 2010<br />
|-<br />
| MEK = 0.85MCO3 + 0.85ETO2 + 0.15MO2 + 0.15RCO3 ||same || ||two channels are merged into one reaction<br />
|-<br />
| HAC = MCO3 + CH2O + HO2 || ||rate is lower ||the old rate was using Acetone X sections.This species is not in FastJX v7.0. Seb added X sections based on JPL2010. Need to multiply 0.6 for quantum yield.The bins above 335nm must be zeroed out, otherwise J(HAC) would be too high. The major removal process is its reaction with OH, photolysis is of minor importance (see Orlando et al., 1999). <br />
|}<br />
<br />
--[[User:Jmao|Jmao]] 15:54, 20 May 2014 (EDT)<br />
<br />
=== Final recommendation for J(HAC) and J(PAN) ===<br />
<br />
<span style="color:green">'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01d|v10-01d]] and approved on 03 Jun 2014.'''''</span><br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:I have two more suggestions to the code and I think we then can finalize v10-01c. We can deal with unresolved J(VOC) later. Seb, please let me know if you think otherwise.<br />
<br />
:#For HAC, keep the QY as 0.6, but zero out the bins >335 nm. <br />
:#For PAN, change the reaction from <br />
<br />
PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2 + 0.4NO3 <br />
<br />
:to <br />
<br />
PAN = 0.7MCO3 + 0.7NO2 + 0.3MO2 + 0.3NO3<br />
<br />
'''''[[User:Sebastian D. Eastham|Sebastian Eastham]] replied:'''''<br />
<br />
:These sound good to me, and I’m not aware of any other pressing issues regarding J-values.<br />
<br />
'''''Daniel Jacob replied:<br />
<br />
:Thanks Jingqiu! If the 1-year benchmark run has already started just let it run - these changes will have very little effect except for HAC and we can just make a note of it. I'm glad that we resolved these J(VOC) issues thanks to Seb, Chris and Jingqiu. At this point we need to move on. <br />
<br />
--[[User:Bmy|Bob Y.]] 17:18, 30 May 2014 (EDT)<br />
<br />
== Overhead ozone columns for use with FAST-JX ==<br />
<br />
=== Use online ozone in FAST-JX v7.0 instead of scaling ozone climatology to archived TO3 values ===<br />
<br />
When using FAST-JX v7.0 with met data other than GEOS-5, we recommend that you select the following option in the CHEMISTRY MENU section of <tt>input.geos</tt>:<br />
<br />
Online O3 for FAST-JX? : T <br />
<br />
Selecting this option will cause FAST-JX v7.0 to copy the "online" O3 tracer concentration&mdash;contained in the <tt>State_Chm%TRACERS</tt> derived type object&mdash;directly into the FAST-JX module. O3 concentrations will be copied for all grid boxes starting at the surface and ending at the top of the chemistry grid, which is either the stratopause (for simulations using the [[UCX chemistry mechanism|UCX combined stratospheric-tropospheric chemistry mechanism]]) or the tropopause (for simulations not using UCX).<br />
<br />
Using the online O3 option for FAST-JX v7.0 in conjunction with the UCX chemistry mechanism will allow photolysis rates to respond to the changes in the dynamically-evolving stratospheric ozone layer. This will result in a more accurate simulation.<br />
<br />
Even if you are performing a tropospheric-only chemistry simulation&mdash;that is, not using the UCX mechanism&mdash;you should still use the online O3 option for FAST-JX v7.0. GEOS-Chem simulations using the FAST-JX online O3 option do not differ significantly from simulations where the internal FAST-JX ozone profiles are scaled to monthly-mean TO3 from either the TOMS/SBUV archive or the GMAO met fields. Sebastian Eastham writes:<br />
<br />
:[The online O3 option in FAST-JX v7.0] should only affect the impact of tropospheric ozone when comparing between [1-month benchmarks] v10-01b and v10-01c_trop, right? The stratospheric ozone estimate from the point of view of Fast-JX should be identical between v10-01b and v10-01c_trop regardless of the online ozone option. My personal thoughts are that leaving the option on should be fine as long as we trust the tropospheric ozone estimates, although it shouldn’t make much of a difference (and if it does that is probably something I should look into). <br />
<br />
Of course, if you turn this option off (WHICH IS NOT RECOMMENDED):<br />
<br />
Online O3 for FAST-JX? : F<br />
<br />
then FAST-JX will scale its internal ozone profiles to TO3 data [[FAST-J_photolysis_mechanism#Overhead_ozone_columns_for_use_with_FAST-J| as described in this section of our ''FAST-J photolysis mechanism'' wiki page]].<br />
<br />
=== Use TOMS ozone for all years when running simulations with GEOS-5 ===<br />
<br />
<span style="color:darkorange">'''''NOTE: This update will be added to [[GEOS-Chem v11-01]].'''''</span><br />
<br />
'''''[[User:Jaf|Jenny Fisher]] wrote:'''''<br />
<br />
:I have been doing some test runs of the tropchem simulation using v11-01f (I know this isn’t recommended, but it was what I had easy access to and I figured I might as well trial it since the 1-year benchmarks have already been done). I was running 2010-2011 — which requires GEOS-5 — and noticed a weird behaviour in the log files: global mean OH jumps up by nearly 50% between December 2010 and Jan 2011 (see output from log files at the end of this email). I haven’t looked super carefully, but I have a hunch that this is because TOMS O3 availability ends after 2010, and starting in 2011 the code therefore uses the O3 column from the met files instead (and I see this switch in the log files).<br />
<br />
:I know it makes sense to use the met field O3 in GEOS-FP, but has anyone looked carefully at the O3 columns in GEOS-5? Given GEOS-5 only goes through the end of 2012 (and GEOS-FP doesn’t start until partway through 2012), I think it would be safer to treat all GEOS-5 runs the same with respect to O3 columns. Even if this isn’t responsible for the OH jump, it would ensure continuity for people running multi-year GEOS-5 simulations, which is still pretty common, especially for interpreting existing observational records. This shouldn’t be hard to do — looks like the TOMS O3 data files have been updated through 2015: http://acdb-ext.gsfc.nasa.gov/Data_services/merged/<br />
<br />
--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 15:30, 5 May 2016 (UTC)<br />
<br />
=== Fix for TOMS to address strange cycle in OH output ===<br />
<br />
<span style="color:darkorange">'''''NOTE: This update will be added to [[GEOS-Chem v11-01]].'''''</span><br />
<br />
'''''Ben Brown-Steiner wrote:'''''<br />
<br />
:I've been running [[GEOS-Chem v10-01|GEOS-Chem v10]] "out of the box" (geos5_2x25_tropchem) and started to look at the daily output via the ND50 diagnostic (although this also happens with daily output to the main file). More that one person here at MIT has found the same behavior within their own simulations, so I'm pretty sure it's not just me.<br />
<br />
:Monthly averages look fine, and daily averages follow the long-term monthly behavior, but with a very weird cycle. At the 15th of each month, something just...stops. Certain species start to decay (e.g. OH) while others spike (e.g. O3).<br />
<br />
:I've attached a few files demonstrating the strange behavior. <br />
<br />
:First is [http://wiki.seas.harvard.edu/geos-chem/images/c/c0/Surface.O3.globalave.1year.png global surface O3] (this is every day for a year, January - December, the plotted dates are wonky, please ignore).<br />
<br />
:Next is [http://wiki.seas.harvard.edu/geos-chem/images/d/dc/Surface.OH.globalave.1year.png surface OH], with a similar strange behavior.<br />
<br />
:I've also plotted POX at the [http://wiki.seas.harvard.edu/geos-chem/images/4/4a/Surface.POX.globalave.1year.png surface] and in the [http://wiki.seas.harvard.edu/geos-chem/images/4/46/Upperatm.POX.globalave.1year.png upper atmosphere].<br />
<br />
:It seems that this happens most prominently over the oceans that over the land, and influences almost every tracer (NO, CO, PRPE, ISOP).<br />
<br />
:We don't know what's going on, but we suspect that it's not an emissions problem (as a similar pattern exists in the upper atmosphere). Perhaps something with radiation?<br />
<br />
:Do you know what's going on? Or point me to someone who does?<br />
<br />
'''''[[User:Barronh|Barron Henderson]] responded:'''''<br />
<br />
:Got it and I think there is an easy fix. (@Ben: see test below)<br />
<br />
:After reviewing HEMCO/Core/hco_calc_mod.F90, I agree that this is almost certainly a HEMCO/TOMS compatibility issue. HEMCO identifies missing values based on the HCO_MISSVAL (hco_calc_mod.F90:849-856). All masked values are returned as 0 (hco_calc_mod.F90:1534-1536). However, I think that the TOMS NetCDF files are not masked appropriately.<br />
<br />
:The TOMS netcdf files use -999 as the "missing_value" and "_FillValue" parameter, but... the actual missing values are set to -999.99. As a result, these values are not getting masked. <br />
<br />
:Since the -999.99 values are not masked, they are used in the aggregation to a new resolution. The result is a value slightly higher than -999 and therefore not caught in toms_mod (toms_mod.F:418-426)<br />
<br />
:The solution is quite simple. We just update the "missing_value" and "_FillValue" in the netcdf file. This will change the way the NetCDF library passes data to HEMCO.<br />
<br />
:Updating the properties can be done with ncatted from nco with the command below.<br />
<br />
ncatted -a _FillValue,DTOMS2,o,f,-999.99 -a missing_value,DTOMS2,o,f,-999.99 -a _FillValue,DTOMS1,o,f,-999.99 -a missing_value,DTOMS1,o,f,-999.99 -a _FillValue,TOMS,o,f,-999.99 -a missing_value,TOMS,o,f,-999.99 /path/to/yourfiles/ExtData/HEMCO/TOMS_SBUV/v2015-03/TOMS_O3col_2004.geos.1x1.nc<br />
<br />
:I have tested that ncdump correctly identifies the values as masked after the update, but I have not seen if HEMCO does. <br />
<br />
:@Ben - Can you try this simple fix? Just update the path and run the command above for 2003-2006 (if you don't have NCO, I can make the edits and post a file for you). Then, re-run 2004.<br />
<br />
'''''[[User:Jaf|Jenny Fisher]] wrote:'''''<br />
<br />
:Thanks for the solution!! Looking at this, I wonder if there is also going to be a problem associated with these lines:<br />
<br />
IF ( TOMS(I,J) > -999e+0_f4 .AND.<br />
& DTOMS2(I,J) > -999e+0_f4 ) THEN<br />
<br />
:I took a quick look back at the code, it looks as though by default we set the ozone column to 0 then overwrite if there is data. I assume having zero overhead ozone column could be a problem…<br />
<br />
:Should we set to a more sensible default value?<br />
<br />
:I had this issue with the Hg simulation and created the files with long-term mean and present day mean values. But they still have missing values at the poles in winter, so a default value might be a better option…<br />
<br />
'''''Ben Brown-Steiner wrote:'''''<br />
<br />
:I've changed the "_FillValue" and "missing_value" for all the TOMS datasets, but am still getting the identical cycles.<br />
<br />
:I copied over the TOMS_O3col* files and made the changes, and redirected the HEMCO config file to use the altered files. Should I have done something else?<br />
<br />
'''''[[User:Barronh|Barron Henderson]] responded:'''''<br />
<br />
:I am proposing a fix for the TOMS/HEMCO issue that tries to address the immediate issue and the unobserved problem. Karl Seltzer tested the fix. I also want to note that the same problem may be in other parts of the system as well.<br />
<br />
:The attached figures show J(O3) for the US ([http://wiki.seas.harvard.edu/geos-chem/images/d/dc/Old_new_us.png old_new_us.png], 20-60N and 110W-60W) and the world ([http://wiki.seas.harvard.edu/geos-chem/images/c/c1/Old_new_global.png old_new_global.png]) as a function of time. Note the drastically improved pattern and higher average for the world. The higher average for the world is due to using a fill value for the unobserved poles.<br />
<br />
:This is a three step fix: (1) process TOMS files; (2) prepare HEMCO rc for new TOMS; (3) update toms module. The steps are described below and supplemented by the attachments. I welcome input on the proposed fix, particularly with respect to the "fill value" approach.<br />
<br />
:'''STEP 1 - Reprocess TOMS'''<br />
<br />
::(processing: [http://wiki.seas.harvard.edu/geos-chem/images/0/0e/Toms2edges.txt toms2edges.txt]; result figure: [http://wiki.seas.harvard.edu/geos-chem/images/a/a2/TOMS_O3col_2004.a.geos.1x1.TOMS1.png TOMS_O3col_2004.a.geos.1x1.TOMS1.png])<br />
::1) Fixes missing flag.<br />
::2) Switches from monthly mean (center) and two delta's to two edges. <br />
::3) Fills data forward in time assuming missing data is best represented by the last value available.<br />
::4) Any cells with no preceding valid value (e.g., January) with the annual mean.<br />
::5) Filling missing latitude to address missing data. (See below)<br />
::: a) I am making a bad assumption as a quick fix/proof of concept. I am using the South pole values as a surrogate for missing north pole values -- matching season with a simple 6 month offset. If both the north and south are missing (e.g., 2003), fill the data poleward.<br />
::: b) This can be replaced with a better fill value later. <br />
<br />
:'''STEP 2 - Edit 1 line and add 2 to HEMCO rc'''<br />
<br />
::Edit the TOMS input line to add ".a" after the year<br />
::Was:<br />
* TOMS_O3_COL $ROOT/TOMS_SBUV/v2015-03/TOMS_O3col_$YYYY.geos.1x1.nc TOMS 1971-2010/1-12/1/0 C xy dobsons * - 1 1<br />
::Would be<br />
* TOMS_O3_COL $ROOT/TOMS_SBUV/v2015-03/TOMS_O3col_$YYYY.a.geos.1x1.nc TOMS 1971-2010/1-12/1/0 C xy dobsons * - 1 1<br />
<br />
::Additions:<br />
* TOMS1_O3_COL - TOMS1 - - - dobsons/day * - 1 1<br />
* TOMS2_O3_COL - TOMS2 - - - dobsons/day * - 1 1<br />
<br />
:'''STEP 3 - Replace [http://wiki.seas.harvard.edu/geos-chem/index.php/File:Toms_mod.F.txt toms_mod.F] with the attached version. Recompile and run.'''<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 13:51, 21 July 2016 (UTC)<br />
<br />
== Cloud overlap options in FAST-JX v7.0 ==<br />
<br />
You may use the following cloud overlap options with the FAST-JX v7.0 photolysis mechanism:<br />
<br />
=== Approximate random overlap assumption === <br />
<br />
The approximate random overlap option (which is the default setting) is:<br />
<br />
Grid Box Optical Depth = In-Cloud Optical Depth * ( Cloud Fraction )^1.5 <br />
<br />
To select this option, make sure the following lines at the top of <tt>GeosCore/fast_jx_mod.F</tt> are uncommented:<br />
<br />
! Approximate random overlap (balance between accuracy & speed)<br />
#define USE_APPROX_RANDOM_OVERLAP 1<br />
<br />
As this is the default option, these lines should already be uncommented for you when you download the GEOS-Chem source code.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:49, 20 May 2014 (EDT)<br />
<br />
=== Linear cloud overlap assumption === <br />
<br />
The linear cloud overlap option is:<br />
<br />
Grid Box Optical depth = In-cloud optical depth * Cloud fraction. <br />
<br />
To select this option you must uncomment these lines at the top of <tt>GeosCore/fast_jx_mod.F</tt>:<br />
<br />
!! Linear overlap<br />
!#define USE_LINEAR_OVERLAP 1 <br />
<br />
and then recompile GEOS-Chem.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:49, 20 May 2014 (EDT)<br />
<br />
=== Maximum random overlap assumption === <br />
<br />
At present, the maximum random overlap assumption has not been implemented into FAST-JX v7.0. Because this option is computationally intensive, it remains a research option rather than a standard supported feature.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:49, 20 May 2014 (EDT)<br />
<br />
=== Discussion ===<br />
<br />
We invite you to read [[FAST-J photolysis mechanism#Discussion|this discussion about cloud overlap options on our ''FAST-J photolysis mechanism wiki page'']].<br />
<br />
--[[User:Bmy|Bob Y.]] 16:13, 20 May 2014 (EDT)<br />
<br />
== Aerosol optical properties in FAST-JX v7.0 ==<br />
<br />
The aerosol optical properties have been updated from the older [[FAST-J photolysis mechanism]]. '''TEXT NEEDED'''<br />
<br />
The ability to scale aerosol optical depth diagnostic output from 550 nm to other wavelengths (originally implemented for the older FAST-J mechanism in [[GEOS-Chem v8-03-01]]) is still compatible for FAST-JX v7.0. Please see [[FAST-J_photolysis_mechanism#Scaling_of_AOD_diagnostic_output_to_other_wavelengths|this section on our ''FAST-J photolysis mechanism'' wiki page]] for more information.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:12, 20 May 2014 (EDT)<br />
<br />
== Previous issues that have now been resolved ==<br />
<br />
In this section we discuss issues that have been recently fixed in the implementation of FAST-JX v7.0:<br />
<br />
=== Reactivation of bromine species photolysis for tropospheric simulation ===<br />
<br />
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
'''''[mailto:seastham@mit.edu Sebastian Eastham] wrote:'''''<br />
<br />
:Bromine species photolysis should probably be reactivated in the tropospheric version – given that it was online in the pre-UCX version, we may as well keep it online. Doing so is just a question of removing the 'x' in the <tt>FJX_spec.dat</tt> file for the relevant species.<br />
<br />
In <tt>FJX_spec.dat</tt> change the following lines from:<br />
<br />
BrO x300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 0.000E+00 5.620E-19 1.202E-18 2.008E-18<br />
3.239E-18 4.520E-18 5.064E-18 5.809E-18 7.350E-19 0.000E+00<br />
BrNO3 x200 0.000E+00 0.000E+00 5.484E-19 7.245E-19 3.702E-18 3.475E-18 J10<br />
3.182E-18 2.978E-18 5.304E-19 6.086E-19 4.489E-19 1.963E-19<br />
1.584E-19 1.307E-19 1.110E-19 8.033E-20 3.377E-20 1.270E-21<br />
BrNO3 x300 0.000E+00 0.000E+00 8.026E-19 1.071E-18 5.166E-18 4.190E-18 J10<br />
3.467E-18 3.039E-18 5.567E-19 5.989E-19 4.528E-19 2.098E-19<br />
1.705E-19 1.425E-19 1.207E-19 8.648E-20 3.716E-20 1.445E-21<br />
HOBr x300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 1.324E-19 2.011E-19 2.202E-19 2.196E-19<br />
1.726E-19 1.367E-19 1.157E-19 1.125E-19 6.197E-20 2.755E-21<br />
<br />
to:<br />
<br />
BrO 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 0.000E+00 5.620E-19 1.202E-18 2.008E-18<br />
3.239E-18 4.520E-18 5.064E-18 5.809E-18 7.350E-19 0.000E+00<br />
BrNO3 200 0.000E+00 0.000E+00 5.484E-19 7.245E-19 3.702E-18 3.475E-18 J10<br />
3.182E-18 2.978E-18 5.304E-19 6.086E-19 4.489E-19 1.963E-19<br />
1.584E-19 1.307E-19 1.110E-19 8.033E-20 3.377E-20 1.270E-21<br />
BrNO3 300 0.000E+00 0.000E+00 8.026E-19 1.071E-18 5.166E-18 4.190E-18 J10<br />
3.467E-18 3.039E-18 5.567E-19 5.989E-19 4.528E-19 2.098E-19<br />
1.705E-19 1.425E-19 1.207E-19 8.648E-20 3.716E-20 1.445E-21<br />
HOBr 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 1.324E-19 2.011E-19 2.202E-19 2.196E-19<br />
1.726E-19 1.367E-19 1.157E-19 1.125E-19 6.197E-20 2.755E-21<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:33, 14 May 2014 (EDT)<br />
<br />
=== Error in reducing wavelength bins for tropospheric simulation === <br />
<br />
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
'''''[mailto:seastham@mit.edu Sebastian Eastham] wrote:'''''<br />
<br />
:In <tt>fast_jx_mod</tt>, specifically <tt>RD_XXX</tt>, there is a transformation to reduce 18 cross sections to 12. Since bin 18 now corresponds to bin 12 and so on, the wavelengths are moved within the cross section array QQQ. However, the 12-bin capability is rarely used (if ever), so when Fast-JX was extended to allow cross sections with 1 or 3 sets of data, the 12 and 8 bin codes were not updated accordingly. This results in very large cross sections for acetone at long wavelengths, because the shorter wavelength data is being used instead.<br />
<br />
:I've notified Michael Prather - he did not know about this bug and is putting together a fix ASAP. I've written my own fix in the meantime, which results in the acetone cross sections matching much more closely, at least between the two [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c versions]].<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 10:39, 12 May 2014 (EDT)<br />
<br />
=== Use proper org.dat file with updates for OC growth ===<br />
<br />
<span style="color:green">'''''This update was added to the official release of [[GEOS-Chem v10-01]] (approved 15 Jun 2015).'''''</span><br />
<br />
After the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i benchmarks]] were submitted, we learned that we were using a version of the FAST-JX input file <tt>org.dat</tt> that did not have [[Aerosol optical properties#Better representation of OC growth with RH and correction to sulfate optics|Randall Martin's updates for better representation of OC growth with RH]].<br />
<br />
'''''[[User:David_Ridley|David Ridley]] wrote:'''''<br />
<br />
<blockquote>So it looks like I’d assumed you didn’t have the organics updates yet, so the <tt>org.dat</tt> I sent you doesn’t include Randall’s updates in there, sorry! I do have the multi-wavelength version that does include those. The change in the org optics seems to tie in with the reduction in the organic AOD we’re seeing, so that makes sense.</blockquote><br />
<blockquote>The BC optics are the same, so the differences seen there shouldn’t be coming from the optics. There may have been a change in the density because of a lot of BC tweaks around the same time. I’ll double check that.</blockquote><br />
<br />
We will make sure that the updated <tt>org.dat</tt> file ships with the publicly-released version of [[GEOS-Chem v10-01]]. <br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:53, 11 May 2015 (EDT)<br />
<br />
== Unresolved issues ==<br />
<br />
The following are active areas of research in GEOS-Chem.<br />
<br />
=== Carbonyl nitrate photolysis ===<br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:We know that carbonyl nitrate should be photolyzed much faster than the current rates in FAST-JX, [http://www.atmos-chem-phys.net/14/2497/2014/acp-14-2497-2014.html according to this paper]. But updates in this rate should also be combined with updates in the OH rate in order to better reproduce the experimental results from chamber studies. This seems more like a research question, so we decided to leave this to the SEAC4RS team.<br />
--[[User:Bmy|Bob Y.]] 15:40, 27 May 2014 (EDT)<br />
<br />
=== Acetaldehyde photolysis ===<br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:We saw large discrepancies between observed(black) and modeled(red) J(ALD2), as shown in this plot by Chris Chan Miller: <br />
<br />
:[[Image:ALD2_photolysis.png]]<br />
<br />
:This discrepancy is very likely due to the lack of pressure dependence on the quantum yield. But Michael Prather didn’t include this pressure dependence in any of the FAST-JX versions. So this remains as a problem in all GEOS-Chem versions, including [[GEOS-Chem v10-01 benchmark history#v10-01c|GEOS-Chem v10-01c]]. <br />
<br />
==== Solution ====<br />
<br />
<span style="color:green">'''''These updates were validated with the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01f|v10-01f]] and approved on Approved 13 Jan 2015.'''''</span><br />
<br />
The solution is to update the entries for acetaldehyde in the FAST-JX input file <tt>FJX_spec_dat</tt>, as follows:<br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:Michael Prather just provided a new set of cross section with pressure dependence for acetaldehyde:<br />
<br />
ActAldp177 0.000E+00 0.000E+00 1.989E-23 0.000E+00 3.699E-22 4.938E-22 CH3CO IUPAC 2014<br />
4.737E-22 4.659E-22 2.450E-20 3.409E-20 3.820E-20 3.732E-20 sheet P2 298K<br />
2.707E-20 1.579E-20 6.566E-21 3.883E-22 5.683E-26 0.000E+00 q2=0.88 (CH3+HCO)<br />
ActAldp566 0.000E+00 0.000E+00 1.903E-23 0.000E+00 3.539E-22 4.725E-22 q3=0.12 (H+CH3CO)<br />
4.533E-22 4.458E-22 2.270E-20 2.985E-20 3.199E-20 2.987E-20 q1=0.00 (CH4+CO)<br />
1.923E-20 9.497E-21 3.450E-21 1.914E-22 3.762E-26 0.000E+00 q's based on 1 bar<br />
ActAldp999 0.000E+00 0.000E+00 1.822E-23 0.000E+00 3.389E-22 4.525E-22 wave > 300 nm<br />
4.340E-22 4.269E-22 2.112E-20 2.647E-20 2.740E-20 2.479E-20<br />
1.485E-20 6.739E-21 2.319E-21 1.258E-22 2.790E-26 0.000E+00 <br />
<br />
:We should use this instead. The reaction is also updated from <br />
<br />
ALD2 = MO2 + HO2 + CO<br />
<br />
:to <br />
<br />
ALD2 = 0.88MO2 + HO2 + 0.88CO + 0.12MCO3 <br />
<br />
--[[User:Bmy|Bob Y.]] 15:19, 6 June 2014 (EDT)<br />
<br />
==== Validation ====<br />
<br />
'''''[[User:Emarais|Eloise Marais]] wrote:'''''<br />
<br />
:I have implemented Michael Prather's pressure-dependent cross-sections for acetaldehyde (ALD2) in GEOS-Chem. The photolysis of ALD2 to form CH4 + CO is turned off. The product yields of the other ALD2 photolysis channel are also updated (see above). Pressure-dependent ALD2 photolysis leads to a decrease in J(ALD2) at the surface and an increase at 500 hPa. The effect on PAN is small (1-5 pptv increase at the surface and <2 pptv at 500 hPa in July 2005).<br />
<br />
:The comparison for SEAC4RS (from a simulation by Katie Travis) is shown below:<br />
:[[Image:Seac4rs_jval_PratherXSect.png]]<br />
<br />
=== EP photolysis for dicarbonyls simulation ===<br />
<br />
<span style="color:red">'''''The SMVGEAR solver will be removed from [[GEOS-Chem v11-01]], when the FlexChem solver package is implemented. At that time, routine <tt>calcrate.F</tt> will be removed from GEOS_Chem.'''''</span><br />
<br />
The code for EP photolysis found in <tt>calcrate.F</tt> needs to be updated for compatibility with FAST-JX v7.0. The EP photolysis code was left unchanged for now (as of [[GEOS-Chem_v10-01_benchmark_history#v10-01c|GEOS-Chem v10-01c]]), but it is now executed only when <tt>LDICARB</tt> is true. This issue affects the [[Dicarbonyls_simulation|dicarbonyls simulation]].<br />
<br />
!==============================================================<br />
! HARDWIRE the effect of branching ratio of HOC2H4O in EP photolysis<br />
! HOC2H4O ------> HO2 + 2CH2O : marked as I in P column of <br />
! 'globchem.dat'<br />
! HOC2H4O --O2--> HO2 + GLYC : marked as J in P column of <br />
! 'globchem.dat'<br />
!<br />
! Add NCS index to NKHOROI and HKHOROJ for SMVGEARII (tmf, 12/16/06)<br />
!==============================================================<br />
<br />
! Not yet modified this for compatibility with Fast-JX v7.0.<br />
! (SDE 04/01/13)<br />
<br />
! Now only do the following if using the dicarbonyls mechanism<br />
! (sde, mps, 5/28/14)<br />
IF ( LDICARB ) THEN<br />
IF ( NKHOROI(NCS) > 0 ) THEN<br />
<br />
! Put J(EP) in correct spot for SMVGEAR II<br />
PHOTVAL = NKHOROI(NCS) - NRATES(NCS)<br />
NKN = NKNPHOTRT(PHOTVAL,NCS)<br />
<br />
DO KLOOP=1,KTLOOP<br />
RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) *<br />
+ ( 1.D0-FYHORO(DENAIR(KLOOP), T3K(KLOOP)) )<br />
ENDDO<br />
ENDIF<br />
<br />
IF ( NKHOROJ(NCS) > 0 ) THEN<br />
<br />
! Put J(EP) in correct spot for SMVGEAR II<br />
PHOTVAL = NKHOROJ(NCS) - NRATES(NCS)<br />
NKN = NKNPHOTRT(PHOTVAL,NCS)<br />
<br />
DO KLOOP=1,KTLOOP<br />
RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) *<br />
+ FYHORO(DENAIR(KLOOP), T3K(KLOOP)) <br />
ENDDO<br />
ENDIF<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:35, 28 May 2014 (EDT)<br />
<br />
== References ==<br />
<br />
#Blitz, M. A., D. E. Heard, M. J. Pilling, S. R. Arnold, M. P. Chipperfield, ''Pressure and temperature-dependent quantum yields for the photodissociation of acetone between 279 and 327.5 nm'', <u>Geophys. Res. Lett.</u>, '''31''', 9, L09104, 2004.<br />
#Eastham, S. D., D. K. Weisenstein, S. R. H. Barrett, ''Development and evaluation of the unified tropospheric–stratospheric chemistry extension (UCX) for the global chemistry-transport model GEOS-Chem'', <u>Atmos. Environ</u>, '''89''', 52-63, doi:10.1016/j.atmosenv.2014.02.001, 2014.<br />
#Feng, Y., et al., ''Effects of cloud overlap in photochemical models'', <u>J. Geophys. Res.</u>, '''109''', D04310, doi:10.1029/2003JD004040, 2004.<br />
#Liang, X.-Z., and W.-C. Wang, ''Cloud overlap effects on general circulation model climate simulations'', <u>J. Geophys. Res.</u>, '''102''' (D10), 11,039–11,047, 1997.<br />
#Liu, H., et al., ''Radiative effect of clouds on tropospheric chemistry in a global three-dimensional chemical transport model'', <u>J. Geophys. Res.</u>, '''111''', D20303, doi:10.1029/2005JD006403, 2006.<br />
#Magneron, I., A. Mellouki, G. Le Bras, G. K. Moortgat, A. Horowitz, and K. Wirtz , ''Photolysis and OH-Initiated Oxidation of Glycolaldehyde under Atmospheric Conditions'', <u>The Journal of Physical Chemistry A</u>, '''109'''(20), 4552-4561, doi:10.1021/jp044346y, 2005.<br />
#Müller, J.-F., Peeters, J., and Stavrakou, T., ''Fast photolysis of carbonyl nitrates from isoprene'', <u>Atmos. Chem. Phys.</u>, '''14''', 2497-2508, doi:10.5194/acp-14-2497-2014, 2014.<br />
#Orlando, J. J., G. S. Tyndall, J.-M. Fracheboud, E. G. Estupiñan, S. Haberkorn, and A. Zimmer, ''The rate and mechanism of the gas-phase oxidation of hydroxyacetone'', <u>Atmos. Environ.</u>, '''33'''(10), 1621-1629, doi:10.1016/S1352-2310(98)00386-0,1999.<br />
#Tie, X., et al., ''Effect of clouds on photolysis and oxidants in the troposphere'', <u>J. Geophys. Res.</u>, '''108'''(D20), 4642, doi:10.1029/2003JD003659, 2003.<br />
#Stubenrauch, C.J., et al., ''Implementation of subgrid cloud vertical structure inside a GCM and its effect on the radiation budget'', <u>J. Clim.</u>, '''10''', 273-287, 1997.<br />
#Wild, O., X. Zhu, and M. J. Prather, ''Fast-J: Accurate simulation of in- and below-cloud photolysis in tropospheric chemical models'', <u>J. Atmos. Chem.</u>, '''37''', 245–282, 2000.<br />
<br />
--[[User:Bmy|Bob Y.]] 15:01, 27 May 2014 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:Toms_mod.F.txt&diff=27103File:Toms mod.F.txt2016-07-23T11:58:32Z<p>Barronh: This file contains updates to toms_mod.F. It is stored as a .txt file to allow upload. The file should be saved as GeosCore/toms_mod.F in the v10-01 code. This issue is ongoing at present so, it may apply to later versions as well.</p>
<hr />
<div>This file contains updates to toms_mod.F. It is stored as a .txt file to allow upload. The file should be saved as GeosCore/toms_mod.F in the v10-01 code. This issue is ongoing at present so, it may apply to later versions as well.</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:Toms_mod_patch.txt&diff=27102File:Toms mod patch.txt2016-07-23T11:55:51Z<p>Barronh: Barronh uploaded a new version of File:Toms mod patch.txt</p>
<hr />
<div>This patch contains fixes for v10-01 GeosCore/toms_mod.F that address an inconsistency between TOMS column ozone interpolation and HEMCO processing of input files.</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:Toms_mod_patch.txt&diff=27101File:Toms mod patch.txt2016-07-23T11:50:56Z<p>Barronh: This patch contains fixes for v10-01 GeosCore/toms_mod.F that address an inconsistency between TOMS column ozone interpolation and HEMCO processing of input files.</p>
<hr />
<div>This patch contains fixes for v10-01 GeosCore/toms_mod.F that address an inconsistency between TOMS column ozone interpolation and HEMCO processing of input files.</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=FAST-JX_v7.0_photolysis_mechanism&diff=27100FAST-JX v7.0 photolysis mechanism2016-07-23T11:43:01Z<p>Barronh: /* Fix for TOMS to address strange cycle in OH output */</p>
<hr />
<div>Sebastian Eastham (MIT) has introduced FAST-JX v7.0 into [[GEOS-Chem v10-01]] concurrently with the [[UCX chemistry mechanism]]. FAST-JX v7.0 replaces the older [[FAST-J photolysis mechanism]].<br />
<br />
== Overview ==<br />
<br />
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
Sebastian Eastham incorporated Fast-JX v7.0a into the [[UCX chemistry mechanism|GEOS-Chem UCX mechanism]]. From [http://www.sciencedirect.com/science/article/pii/S1352231014000971 Eastham et al. (2014)]:<br />
<br />
:GEOS-Chem uses a customized version of the [[FAST-JX v6.2 photolysis mechanism]] (Wild et al., 2000), which efficiently estimates tropospheric photolysis. The customized version uses the wavelength bands from the older Fast-J tropospheric photolysis scheme and does not consider wavelengths shorter than 289 nm, assuming they are attenuated above the tropopause. However, these high-energy photons are responsible for the release of ozone-depleting agents in the stratosphere. The standard Fast-JX model (Prather, 2012) addresses this limitation by expanding the spectrum analyzed to 18 wavelength bins covering 177–850 nm, extending the upper altitude limit to approximately 60 km. We therefore incorporate Fast-JX v7.0a into [[UCX chemistry mechanism|GEOS-Chem UCX]]. Fast-JX includes cross-section data for many species relevant to the troposphere and stratosphere. However, accurately representing sulfur requires calculation of gaseous H2SO4 photolysis, a reaction which is not present in Fast-JX but which acts as a source of sulfur dioxide in the upper stratosphere. Based on a study by Mills (2005), the mean cross-section between 412.5 and 850 nm is estimated at 2.542 × 10−25 cm2. We also add photolysis of ClOO and ClNO2, given their importance in catalytic ozone destruction, using data from JPL 10-06 (Sander et al., 2011). Fast-JX v7.0a includes a correction to calculated acetone cross sections. Accordingly, where hydroxyacetone cross-sections were previously estimated based on one branch of the acetone decomposition, a distinct set of cross sections from JPL 10-06 are used.<br />
<br />
:The base version of GEOS-Chem uses satellite observations of total ozone columns when determining ozone-related scattering and extinction. The UCX allows either this approach, as was used for the production of the results shown, or can employ calculated ozone mixing ratios instead, allowing photolysis rates to respond to changes in the stratospheric ozone layer.<br />
<br />
=== Timeline ===<br />
<br />
The following table displays a timeline of important milestones in FAST-JX v7.0 development:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|- bgcolor="#CCCCCC"<br />
!width="150px"|Version<br />
!width="100px"|Date<br />
!width="800px"|Features / Improvements<br />
|-valign="top"<br />
|[[GEOS-Chem v10-01]]<br />
|Jun 2015<br />
|<br />
*Retired the [[FAST-J photolysis mechanism]] in v10-01c ''(GEOS-Chem Support Team)''<br />
*Implemented FAST-JX v7.0 into GEOS-Chem, concurrent with [[UCX chemistry mechanism]] in v10-01c ''(S. Eastham + GEOS-Chem Support Team)''<br />
*Corrected the following errors in the original FAST-JX v7.0 implementation:<br />
**[[FAST-JX_v7.0_photolysis_mechanism#Reactivation_of_bromine_species_photolysis_for_tropospheric_simulation|Reactivation of Br species for tropospheric simulation]]<br />
**[[FAST-JX_v7.0_photolysis_mechanism#Error_in_reducing_wavelength_bins_for_tropospheric_simulation|Bug fix for reducing wavelength bins for tropospheric simulation]]<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 13:42, 21 May 2014 (EDT)<br />
<br />
== Input files for FAST-JX v7.0 ==<br />
<br />
The following input files are required for the FAST-JX v7.0 photolysis mechanism:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|- bgcolor="#CCCCCC"<br />
!width="180px"|File<br />
!width="75px"|Introduced<br />
!width="75px"|Retired<br />
!width="700px"|Description<br />
<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#JvAtms <tt>fastj.jv_atms.dat.nc</tt>]<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|still used<br />
|<br />
*This netCDF file (originally created for the [[FAST-J photolysis mechanism]]) specifies the reference O3 and T climatologies for FAST-J.<br />
*This file is located in data directory:<br />
GEOS_NATIVE/FastJ_201204/fastj.jv_atms_dat.nc<br />
*NOTE: Where such data exists, GEOS-Chem will overwrite the reference O3 climatology as follows:<br />
*#The online O3 tracer (carried in (<tt>State_Chm%TRACERS(:,:,1:LLCHEM,IDTO3</tt>) '''(RECOMMENDED)''', or<br />
*#Archived O3 profiles sclaed to TOMS/SBUV monthly-mean total ozone column (TO3) data, or<br />
*#Archived TO3 data from the [[GEOS-5]] or [[GEOS-FP]] met field archives.<br />
<br />
|-valign="top"<br />
|<tt>FJX_j2j.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01c|v10-01c]]<br />
|still used<br />
|<br />
*Links GEOS-Chem chemical species to Fast-JX species. Replaces the following file:<br />
**<tt>ratj.d</tt> from the [[FAST-J photolysis mechanism]], used in versions prior to [[GEOS-Chem v10-01]]<br />
<br />
|-valign="top"<br />
|<tt>FJX_spec.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01c|v10-01c]]<br />
|still used<br />
|<br />
*Fast-JX cross-sections, which replaces the following files:<br />
**<tt>jv_spec.dat</tt> from the [[FAST-J photolysis mechanism]], used in versions prior to [[GEOS-Chem v10-01]]<br />
**<tt>spec2008.dat</tt> from the [[FAST-JX v6.4 photolysis mechanism|FAST-JX v6.x photolysis mechanism]], used in several research implementations of GEOS-Chem<br />
<br />
|-valign="top"<br />
|<tt>jv_spec.mie.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01c|v10-01c]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties at 5 wavelengths<br />
<br />
|-valign="top"<br />
|<tt>jv_spec_aod.dat</tt><br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|<br />
*The <tt>jv_spec_aod.dat</tt> file contains the optical properties for aerosols at a single wavelength to be used in the online calculation of the aerosol optical depth diagnostics. The default properties are provided at 550 nm. These properties have been calculated using the same size and optical properties as the <tt>jv_spec.dat</tt> file used for the FAST–J photolysis calculations.<br />
*[[#Scaling_of_AOD_diagnostic_output_to_other_wavelengths|The user can exchange this set of properties with those at another wavelength]]. We recommend that the wavelength used be included in the first line of the header for traceability (this line is output to the GEOS–Chem log file during run time). <br />
<br />
|-valign="top"<br />
|<tt>dust.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for dust at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>org.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for organic carbon at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>so4.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for sulfate at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>soot.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for black carbon at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>ssa.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for accumulation mode sea salt aerosol at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>ssc.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for coarse mode sea salt aerosol at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>h2so4.dat</tt><br />
|[[GEOS-Chem_v10-01#Fixes_and_updates_added_during_the_public_comment_period|v10-01 public comment period]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for sulfuric acid at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
*This file is only needed if the [[UCX chemistry mechanism]] is enabled.<br />
<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:07, 1 June 2015 (UTC)<br />
<br />
== VOC photolysis in FAST-JX v7.0 ==<br />
<br />
<span style="color:green">'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
In the table below, we summarize VOC photolysis in Fast-JX v7.0. We also invite you to view our [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jrates.pdf ''Comparison of GEOS-Chem Photolysis Rates'' document] prepared by Chris Chan Miller.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5"<br />
|-bgcolor="#cccccc"<br />
! width="300px" |Old reaction<br />
! width="300px" |New reaction<br />
! width="200px" |New rate<br />
! width="300px" |Note<br />
|-valign="top"<br />
| CH2O = HO2 + HO2 + CO (channel a) ||same ||New cross sections leads to an increase by 10% to 20% || This increase is consistent with JPL 2010.<br />
|-<br />
| CH2O = H2 + CO (channel b) ||same ||increase by 6% to 15% || This increase is consistent with JPL 2010.<br />
|-<br />
| PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2 + 0.4NO3 ||PAN = 0.7MCO3 + 0.7NO2 + 0.3MO2 + 0.3NO3 ||same || JPL2010 suggests two channels(only one channel in FastJX-v7.0), branching ratio follows JPL2010<br />
|-<br />
| ALD2 = MO2 + HO2 + CO||ALD2 = 0.88MO2 + HO2 + 0.88CO + 0.12MCO3 || || large discrepancy is found between obs and model (see [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jrates.pdf Chris's slides]), pressure dependence is probably needed. The cross section is now updated by Michael Prather.<br />
|-<br />
| ALD2 = CH4 + CO || this channel is turned off || || this channel is not included in FastJX-v7.0<br />
|-<br />
| RCHO = ETO2 + HO2 + CO ||same || || No pressure dependence is observed, according to JPL2010.<br />
|-<br />
| MP = CH2O + HO2 + OH||same || || change is small.<br />
|-<br />
| GLYX = 0.5H2 + CO + 0.5CH2O + 0.5CO ||GLYX = H2 + 2CO <br> GLYX = CH2O + CO || Pressure dependence is now included, rate is higher ||now 3 channels, Stern-Volmer expression: Qtotal = 1/[6.80 + 251.8e-4 P(Torr)], Increases quantum yields at low P, but ONLY specified for 390-470 nm. Assume that 220K has P = 0.18 atm and higher q.(From FJX v7.0 notes)<br />
|-<br />
| GLYX = 2.0CO + 2.0HO2 ||same ||Pressure dependence is now included, rate is higher || <br />
|-<br />
| MACR = CO + HO2 + CH2O + MCO3 <br> branching ratio = 0.5 ||same ||rate is significantly reduced, as Qy is reduced from 0.008 to 0.003 ||this channel is dominant,the third channel (C3H6 + CO), is ignored, to be consistent with Fast-JX v7.0<br />
|-<br />
| MACR = MAO3 + HO2 <br> branching ratio = 0.5 ||remove this channel || ||suggested by IUPAC, also consistent with Fast-JX v7.0<br />
|-<br />
| MVK = PRPE + CO <br> branching ratio = 0.6 || ||pressure dependence is now included ||<br />
|-<br />
| MVK = MCO3 + CH2O + CO + HO2 <br> branching ratio = 0.2|| ||pressure dependence is now included ||<br />
|-<br />
| MVK = MO2 + MAO3<br> branching ratio = 0.2 ||MVK = MO2 + RCO3 || ||this channel was removed in FJX v7.0, but it shouldn't according to IUPAC. MAO3 is changed to RCO3 for carbon balance.<br />
|- <br />
| GLYC = CH2O + 2.0HO2 + CO ||GLYC = 0.9CH2O + 1.73HO2 + 0.07OH + 1.0CO + 0.1MOH ||Significant increase in X sections || merge from three channels GLYC =CH2O + 2.0HO2 + CO(QY = 0.83), GLYC =CH3OH + CO (QY=0.10), GLYC =OH + CH2O + HO2 + CO (QY =0.07) JPL 2010<br />
|-<br />
| MEK = 0.85MCO3 + 0.85ETO2 + 0.15MO2 + 0.15RCO3 ||same || ||two channels are merged into one reaction<br />
|-<br />
| HAC = MCO3 + CH2O + HO2 || ||rate is lower ||the old rate was using Acetone X sections.This species is not in FastJX v7.0. Seb added X sections based on JPL2010. Need to multiply 0.6 for quantum yield.The bins above 335nm must be zeroed out, otherwise J(HAC) would be too high. The major removal process is its reaction with OH, photolysis is of minor importance (see Orlando et al., 1999). <br />
|}<br />
<br />
--[[User:Jmao|Jmao]] 15:54, 20 May 2014 (EDT)<br />
<br />
=== Final recommendation for J(HAC) and J(PAN) ===<br />
<br />
<span style="color:green">'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01d|v10-01d]] and approved on 03 Jun 2014.'''''</span><br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:I have two more suggestions to the code and I think we then can finalize v10-01c. We can deal with unresolved J(VOC) later. Seb, please let me know if you think otherwise.<br />
<br />
:#For HAC, keep the QY as 0.6, but zero out the bins >335 nm. <br />
:#For PAN, change the reaction from <br />
<br />
PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2 + 0.4NO3 <br />
<br />
:to <br />
<br />
PAN = 0.7MCO3 + 0.7NO2 + 0.3MO2 + 0.3NO3<br />
<br />
'''''[[User:Sebastian D. Eastham|Sebastian Eastham]] replied:'''''<br />
<br />
:These sound good to me, and I’m not aware of any other pressing issues regarding J-values.<br />
<br />
'''''Daniel Jacob replied:<br />
<br />
:Thanks Jingqiu! If the 1-year benchmark run has already started just let it run - these changes will have very little effect except for HAC and we can just make a note of it. I'm glad that we resolved these J(VOC) issues thanks to Seb, Chris and Jingqiu. At this point we need to move on. <br />
<br />
--[[User:Bmy|Bob Y.]] 17:18, 30 May 2014 (EDT)<br />
<br />
== Overhead ozone columns for use with FAST-JX ==<br />
<br />
=== Use online ozone in FAST-JX v7.0 instead of scaling ozone climatology to archived TO3 values ===<br />
<br />
When using FAST-JX v7.0 with met data other than GEOS-5, we recommend that you select the following option in the CHEMISTRY MENU section of <tt>input.geos</tt>:<br />
<br />
Online O3 for FAST-JX? : T <br />
<br />
Selecting this option will cause FAST-JX v7.0 to copy the "online" O3 tracer concentration&mdash;contained in the <tt>State_Chm%TRACERS</tt> derived type object&mdash;directly into the FAST-JX module. O3 concentrations will be copied for all grid boxes starting at the surface and ending at the top of the chemistry grid, which is either the stratopause (for simulations using the [[UCX chemistry mechanism|UCX combined stratospheric-tropospheric chemistry mechanism]]) or the tropopause (for simulations not using UCX).<br />
<br />
Using the online O3 option for FAST-JX v7.0 in conjunction with the UCX chemistry mechanism will allow photolysis rates to respond to the changes in the dynamically-evolving stratospheric ozone layer. This will result in a more accurate simulation.<br />
<br />
Even if you are performing a tropospheric-only chemistry simulation&mdash;that is, not using the UCX mechanism&mdash;you should still use the online O3 option for FAST-JX v7.0. GEOS-Chem simulations using the FAST-JX online O3 option do not differ significantly from simulations where the internal FAST-JX ozone profiles are scaled to monthly-mean TO3 from either the TOMS/SBUV archive or the GMAO met fields. Sebastian Eastham writes:<br />
<br />
:[The online O3 option in FAST-JX v7.0] should only affect the impact of tropospheric ozone when comparing between [1-month benchmarks] v10-01b and v10-01c_trop, right? The stratospheric ozone estimate from the point of view of Fast-JX should be identical between v10-01b and v10-01c_trop regardless of the online ozone option. My personal thoughts are that leaving the option on should be fine as long as we trust the tropospheric ozone estimates, although it shouldn’t make much of a difference (and if it does that is probably something I should look into). <br />
<br />
Of course, if you turn this option off (WHICH IS NOT RECOMMENDED):<br />
<br />
Online O3 for FAST-JX? : F<br />
<br />
then FAST-JX will scale its internal ozone profiles to TO3 data [[FAST-J_photolysis_mechanism#Overhead_ozone_columns_for_use_with_FAST-J| as described in this section of our ''FAST-J photolysis mechanism'' wiki page]].<br />
<br />
=== Use TOMS ozone for all years when running simulations with GEOS-5 ===<br />
<br />
<span style="color:darkorange">'''''NOTE: This update will be added to [[GEOS-Chem v11-01]].'''''</span><br />
<br />
'''''[[User:Jaf|Jenny Fisher]] wrote:'''''<br />
<br />
:I have been doing some test runs of the tropchem simulation using v11-01f (I know this isn’t recommended, but it was what I had easy access to and I figured I might as well trial it since the 1-year benchmarks have already been done). I was running 2010-2011 — which requires GEOS-5 — and noticed a weird behaviour in the log files: global mean OH jumps up by nearly 50% between December 2010 and Jan 2011 (see output from log files at the end of this email). I haven’t looked super carefully, but I have a hunch that this is because TOMS O3 availability ends after 2010, and starting in 2011 the code therefore uses the O3 column from the met files instead (and I see this switch in the log files).<br />
<br />
:I know it makes sense to use the met field O3 in GEOS-FP, but has anyone looked carefully at the O3 columns in GEOS-5? Given GEOS-5 only goes through the end of 2012 (and GEOS-FP doesn’t start until partway through 2012), I think it would be safer to treat all GEOS-5 runs the same with respect to O3 columns. Even if this isn’t responsible for the OH jump, it would ensure continuity for people running multi-year GEOS-5 simulations, which is still pretty common, especially for interpreting existing observational records. This shouldn’t be hard to do — looks like the TOMS O3 data files have been updated through 2015: http://acdb-ext.gsfc.nasa.gov/Data_services/merged/<br />
<br />
--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 15:30, 5 May 2016 (UTC)<br />
<br />
=== Fix for TOMS to address strange cycle in OH output ===<br />
<br />
<span style="color:darkorange">'''''NOTE: This update will be added to [[GEOS-Chem v11-01]].'''''</span><br />
<br />
'''''Ben Brown-Steiner wrote:'''''<br />
<br />
:I've been running [[GEOS-Chem v10-01|GEOS-Chem v10]] "out of the box" (geos5_2x25_tropchem) and started to look at the daily output via the ND50 diagnostic (although this also happens with daily output to the main file). More that one person here at MIT has found the same behavior within their own simulations, so I'm pretty sure it's not just me.<br />
<br />
:Monthly averages look fine, and daily averages follow the long-term monthly behavior, but with a very weird cycle. At the 15th of each month, something just...stops. Certain species start to decay (e.g. OH) while others spike (e.g. O3).<br />
<br />
:I've attached a few files demonstrating the strange behavior. <br />
<br />
:First is [http://wiki.seas.harvard.edu/geos-chem/images/c/c0/Surface.O3.globalave.1year.png global surface O3] (this is every day for a year, January - December, the plotted dates are wonky, please ignore).<br />
<br />
:Next is [http://wiki.seas.harvard.edu/geos-chem/images/d/dc/Surface.OH.globalave.1year.png surface OH], with a similar strange behavior.<br />
<br />
:I've also plotted POX at the [http://wiki.seas.harvard.edu/geos-chem/images/4/4a/Surface.POX.globalave.1year.png surface] and in the [http://wiki.seas.harvard.edu/geos-chem/images/4/46/Upperatm.POX.globalave.1year.png upper atmosphere].<br />
<br />
:It seems that this happens most prominently over the oceans that over the land, and influences almost every tracer (NO, CO, PRPE, ISOP).<br />
<br />
:We don't know what's going on, but we suspect that it's not an emissions problem (as a similar pattern exists in the upper atmosphere). Perhaps something with radiation?<br />
<br />
:Do you know what's going on? Or point me to someone who does?<br />
<br />
'''''[[User:Barronh|Barron Henderson]] responded:'''''<br />
<br />
:Got it and I think there is an easy fix. (@Ben: see test below)<br />
<br />
:After reviewing HEMCO/Core/hco_calc_mod.F90, I agree that this is almost certainly a HEMCO/TOMS compatibility issue. HEMCO identifies missing values based on the HCO_MISSVAL (hco_calc_mod.F90:849-856). All masked values are returned as 0 (hco_calc_mod.F90:1534-1536). However, I think that the TOMS NetCDF files are not masked appropriately.<br />
<br />
:The TOMS netcdf files use -999 as the "missing_value" and "_FillValue" parameter, but... the actual missing values are set to -999.99. As a result, these values are not getting masked. <br />
<br />
:Since the -999.99 values are not masked, they are used in the aggregation to a new resolution. The result is a value slightly higher than -999 and therefore not caught in toms_mod (toms_mod.F:418-426)<br />
<br />
:The solution is quite simple. We just update the "missing_value" and "_FillValue" in the netcdf file. This will change the way the NetCDF library passes data to HEMCO.<br />
<br />
:Updating the properties can be done with ncatted from nco with the command below.<br />
<br />
ncatted -a _FillValue,DTOMS2,o,f,-999.99 -a missing_value,DTOMS2,o,f,-999.99 -a _FillValue,DTOMS1,o,f,-999.99 -a missing_value,DTOMS1,o,f,-999.99 -a _FillValue,TOMS,o,f,-999.99 -a missing_value,TOMS,o,f,-999.99 /path/to/yourfiles/ExtData/HEMCO/TOMS_SBUV/v2015-03/TOMS_O3col_2004.geos.1x1.nc<br />
<br />
:I have tested that ncdump correctly identifies the values as masked after the update, but I have not seen if HEMCO does. <br />
<br />
:@Ben - Can you try this simple fix? Just update the path and run the command above for 2003-2006 (if you don't have NCO, I can make the edits and post a file for you). Then, re-run 2004.<br />
<br />
'''''[[User:Jaf|Jenny Fisher]] wrote:'''''<br />
<br />
:Thanks for the solution!! Looking at this, I wonder if there is also going to be a problem associated with these lines:<br />
<br />
IF ( TOMS(I,J) > -999e+0_f4 .AND.<br />
& DTOMS2(I,J) > -999e+0_f4 ) THEN<br />
<br />
:I took a quick look back at the code, it looks as though by default we set the ozone column to 0 then overwrite if there is data. I assume having zero overhead ozone column could be a problem…<br />
<br />
:Should we set to a more sensible default value?<br />
<br />
:I had this issue with the Hg simulation and created the files with long-term mean and present day mean values. But they still have missing values at the poles in winter, so a default value might be a better option…<br />
<br />
'''''Ben Brown-Steiner wrote:'''''<br />
<br />
:I've changed the "_FillValue" and "missing_value" for all the TOMS datasets, but am still getting the identical cycles.<br />
<br />
:I copied over the TOMS_O3col* files and made the changes, and redirected the HEMCO config file to use the altered files. Should I have done something else?<br />
<br />
'''''[[User:Barronh|Barron Henderson]] responded:'''''<br />
<br />
:I am proposing a fix for the TOMS/HEMCO issue that tries to address the immediate issue and the unobserved problem. Karl Seltzer tested the fix. I also want to note that the same problem may be in other parts of the system as well.<br />
<br />
:The attached figures show J(O3) for the US ([http://wiki.seas.harvard.edu/geos-chem/images/d/dc/Old_new_us.png old_new_us.png], 20-60N and 110W-60W) and the world ([http://wiki.seas.harvard.edu/geos-chem/images/c/c1/Old_new_global.png old_new_global.png]) as a function of time. Note the drastically improved pattern and higher average for the world. The higher average for the world is due to using a fill value for the unobserved poles.<br />
<br />
:This is a three step fix: (1) process TOMS files; (2) prepare HEMCO rc for new TOMS; (3) update toms module. The steps are described below and supplemented by the attachments. I welcome input on the proposed fix, particularly with respect to the "fill value" approach.<br />
<br />
:'''STEP 1 - Reprocess TOMS'''<br />
<br />
::(processing: [http://wiki.seas.harvard.edu/geos-chem/images/0/0e/Toms2edges.txt toms2edges.txt]; result figure: [http://wiki.seas.harvard.edu/geos-chem/images/a/a2/TOMS_O3col_2004.a.geos.1x1.TOMS1.png TOMS_O3col_2004.a.geos.1x1.TOMS1.png])<br />
::1) Fixes missing flag.<br />
::2) Switches from monthly mean (center) and two delta's to two edges. <br />
::3) Fills data forward in time assuming missing data is best represented by the last value available.<br />
::4) Any cells with no preceding valid value (e.g., January) with the annual mean.<br />
::5) Filling missing latitude to address missing data. (See below)<br />
::: a) I am making a bad assumption as a quick fix/proof of concept. I am using the South pole values as a surrogate for missing north pole values -- matching season with a simple 6 month offset. If both the north and south are missing (e.g., 2003), fill the data poleward.<br />
::: b) This can be replaced with a better fill value later. <br />
<br />
:'''STEP 2 - Edit 1 line and add 2 to HEMCO rc'''<br />
<br />
::Edit the TOMS input line to add ".a" after the year<br />
::Was:<br />
* TOMS_O3_COL $ROOT/TOMS_SBUV/v2015-03/TOMS_O3col_$YYYY.geos.1x1.nc TOMS 1971-2010/1-12/1/0 C xy dobsons * - 1 1<br />
::Would be<br />
* TOMS_O3_COL $ROOT/TOMS_SBUV/v2015-03/TOMS_O3col_$YYYY.a.geos.1x1.nc TOMS 1971-2010/1-12/1/0 C xy dobsons * - 1 1<br />
<br />
::Additions:<br />
* TOMS1_O3_COL - TOMS1 - - - dobsons/day * - 1 1<br />
* TOMS2_O3_COL - TOMS2 - - - dobsons/day * - 1 1<br />
<br />
:'''STEP 3 - Replace [toms_mod.F] with the attached version. Recompile and run.'''<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 13:51, 21 July 2016 (UTC)<br />
<br />
== Cloud overlap options in FAST-JX v7.0 ==<br />
<br />
You may use the following cloud overlap options with the FAST-JX v7.0 photolysis mechanism:<br />
<br />
=== Approximate random overlap assumption === <br />
<br />
The approximate random overlap option (which is the default setting) is:<br />
<br />
Grid Box Optical Depth = In-Cloud Optical Depth * ( Cloud Fraction )^1.5 <br />
<br />
To select this option, make sure the following lines at the top of <tt>GeosCore/fast_jx_mod.F</tt> are uncommented:<br />
<br />
! Approximate random overlap (balance between accuracy & speed)<br />
#define USE_APPROX_RANDOM_OVERLAP 1<br />
<br />
As this is the default option, these lines should already be uncommented for you when you download the GEOS-Chem source code.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:49, 20 May 2014 (EDT)<br />
<br />
=== Linear cloud overlap assumption === <br />
<br />
The linear cloud overlap option is:<br />
<br />
Grid Box Optical depth = In-cloud optical depth * Cloud fraction. <br />
<br />
To select this option you must uncomment these lines at the top of <tt>GeosCore/fast_jx_mod.F</tt>:<br />
<br />
!! Linear overlap<br />
!#define USE_LINEAR_OVERLAP 1 <br />
<br />
and then recompile GEOS-Chem.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:49, 20 May 2014 (EDT)<br />
<br />
=== Maximum random overlap assumption === <br />
<br />
At present, the maximum random overlap assumption has not been implemented into FAST-JX v7.0. Because this option is computationally intensive, it remains a research option rather than a standard supported feature.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:49, 20 May 2014 (EDT)<br />
<br />
=== Discussion ===<br />
<br />
We invite you to read [[FAST-J photolysis mechanism#Discussion|this discussion about cloud overlap options on our ''FAST-J photolysis mechanism wiki page'']].<br />
<br />
--[[User:Bmy|Bob Y.]] 16:13, 20 May 2014 (EDT)<br />
<br />
== Aerosol optical properties in FAST-JX v7.0 ==<br />
<br />
The aerosol optical properties have been updated from the older [[FAST-J photolysis mechanism]]. '''TEXT NEEDED'''<br />
<br />
The ability to scale aerosol optical depth diagnostic output from 550 nm to other wavelengths (originally implemented for the older FAST-J mechanism in [[GEOS-Chem v8-03-01]]) is still compatible for FAST-JX v7.0. Please see [[FAST-J_photolysis_mechanism#Scaling_of_AOD_diagnostic_output_to_other_wavelengths|this section on our ''FAST-J photolysis mechanism'' wiki page]] for more information.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:12, 20 May 2014 (EDT)<br />
<br />
== Previous issues that have now been resolved ==<br />
<br />
In this section we discuss issues that have been recently fixed in the implementation of FAST-JX v7.0:<br />
<br />
=== Reactivation of bromine species photolysis for tropospheric simulation ===<br />
<br />
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
'''''[mailto:seastham@mit.edu Sebastian Eastham] wrote:'''''<br />
<br />
:Bromine species photolysis should probably be reactivated in the tropospheric version – given that it was online in the pre-UCX version, we may as well keep it online. Doing so is just a question of removing the 'x' in the <tt>FJX_spec.dat</tt> file for the relevant species.<br />
<br />
In <tt>FJX_spec.dat</tt> change the following lines from:<br />
<br />
BrO x300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 0.000E+00 5.620E-19 1.202E-18 2.008E-18<br />
3.239E-18 4.520E-18 5.064E-18 5.809E-18 7.350E-19 0.000E+00<br />
BrNO3 x200 0.000E+00 0.000E+00 5.484E-19 7.245E-19 3.702E-18 3.475E-18 J10<br />
3.182E-18 2.978E-18 5.304E-19 6.086E-19 4.489E-19 1.963E-19<br />
1.584E-19 1.307E-19 1.110E-19 8.033E-20 3.377E-20 1.270E-21<br />
BrNO3 x300 0.000E+00 0.000E+00 8.026E-19 1.071E-18 5.166E-18 4.190E-18 J10<br />
3.467E-18 3.039E-18 5.567E-19 5.989E-19 4.528E-19 2.098E-19<br />
1.705E-19 1.425E-19 1.207E-19 8.648E-20 3.716E-20 1.445E-21<br />
HOBr x300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 1.324E-19 2.011E-19 2.202E-19 2.196E-19<br />
1.726E-19 1.367E-19 1.157E-19 1.125E-19 6.197E-20 2.755E-21<br />
<br />
to:<br />
<br />
BrO 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 0.000E+00 5.620E-19 1.202E-18 2.008E-18<br />
3.239E-18 4.520E-18 5.064E-18 5.809E-18 7.350E-19 0.000E+00<br />
BrNO3 200 0.000E+00 0.000E+00 5.484E-19 7.245E-19 3.702E-18 3.475E-18 J10<br />
3.182E-18 2.978E-18 5.304E-19 6.086E-19 4.489E-19 1.963E-19<br />
1.584E-19 1.307E-19 1.110E-19 8.033E-20 3.377E-20 1.270E-21<br />
BrNO3 300 0.000E+00 0.000E+00 8.026E-19 1.071E-18 5.166E-18 4.190E-18 J10<br />
3.467E-18 3.039E-18 5.567E-19 5.989E-19 4.528E-19 2.098E-19<br />
1.705E-19 1.425E-19 1.207E-19 8.648E-20 3.716E-20 1.445E-21<br />
HOBr 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 1.324E-19 2.011E-19 2.202E-19 2.196E-19<br />
1.726E-19 1.367E-19 1.157E-19 1.125E-19 6.197E-20 2.755E-21<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:33, 14 May 2014 (EDT)<br />
<br />
=== Error in reducing wavelength bins for tropospheric simulation === <br />
<br />
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
'''''[mailto:seastham@mit.edu Sebastian Eastham] wrote:'''''<br />
<br />
:In <tt>fast_jx_mod</tt>, specifically <tt>RD_XXX</tt>, there is a transformation to reduce 18 cross sections to 12. Since bin 18 now corresponds to bin 12 and so on, the wavelengths are moved within the cross section array QQQ. However, the 12-bin capability is rarely used (if ever), so when Fast-JX was extended to allow cross sections with 1 or 3 sets of data, the 12 and 8 bin codes were not updated accordingly. This results in very large cross sections for acetone at long wavelengths, because the shorter wavelength data is being used instead.<br />
<br />
:I've notified Michael Prather - he did not know about this bug and is putting together a fix ASAP. I've written my own fix in the meantime, which results in the acetone cross sections matching much more closely, at least between the two [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c versions]].<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 10:39, 12 May 2014 (EDT)<br />
<br />
=== Use proper org.dat file with updates for OC growth ===<br />
<br />
<span style="color:green">'''''This update was added to the official release of [[GEOS-Chem v10-01]] (approved 15 Jun 2015).'''''</span><br />
<br />
After the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i benchmarks]] were submitted, we learned that we were using a version of the FAST-JX input file <tt>org.dat</tt> that did not have [[Aerosol optical properties#Better representation of OC growth with RH and correction to sulfate optics|Randall Martin's updates for better representation of OC growth with RH]].<br />
<br />
'''''[[User:David_Ridley|David Ridley]] wrote:'''''<br />
<br />
<blockquote>So it looks like I’d assumed you didn’t have the organics updates yet, so the <tt>org.dat</tt> I sent you doesn’t include Randall’s updates in there, sorry! I do have the multi-wavelength version that does include those. The change in the org optics seems to tie in with the reduction in the organic AOD we’re seeing, so that makes sense.</blockquote><br />
<blockquote>The BC optics are the same, so the differences seen there shouldn’t be coming from the optics. There may have been a change in the density because of a lot of BC tweaks around the same time. I’ll double check that.</blockquote><br />
<br />
We will make sure that the updated <tt>org.dat</tt> file ships with the publicly-released version of [[GEOS-Chem v10-01]]. <br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:53, 11 May 2015 (EDT)<br />
<br />
== Unresolved issues ==<br />
<br />
The following are active areas of research in GEOS-Chem.<br />
<br />
=== Carbonyl nitrate photolysis ===<br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:We know that carbonyl nitrate should be photolyzed much faster than the current rates in FAST-JX, [http://www.atmos-chem-phys.net/14/2497/2014/acp-14-2497-2014.html according to this paper]. But updates in this rate should also be combined with updates in the OH rate in order to better reproduce the experimental results from chamber studies. This seems more like a research question, so we decided to leave this to the SEAC4RS team.<br />
--[[User:Bmy|Bob Y.]] 15:40, 27 May 2014 (EDT)<br />
<br />
=== Acetaldehyde photolysis ===<br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:We saw large discrepancies between observed(black) and modeled(red) J(ALD2), as shown in this plot by Chris Chan Miller: <br />
<br />
:[[Image:ALD2_photolysis.png]]<br />
<br />
:This discrepancy is very likely due to the lack of pressure dependence on the quantum yield. But Michael Prather didn’t include this pressure dependence in any of the FAST-JX versions. So this remains as a problem in all GEOS-Chem versions, including [[GEOS-Chem v10-01 benchmark history#v10-01c|GEOS-Chem v10-01c]]. <br />
<br />
==== Solution ====<br />
<br />
<span style="color:green">'''''These updates were validated with the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01f|v10-01f]] and approved on Approved 13 Jan 2015.'''''</span><br />
<br />
The solution is to update the entries for acetaldehyde in the FAST-JX input file <tt>FJX_spec_dat</tt>, as follows:<br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:Michael Prather just provided a new set of cross section with pressure dependence for acetaldehyde:<br />
<br />
ActAldp177 0.000E+00 0.000E+00 1.989E-23 0.000E+00 3.699E-22 4.938E-22 CH3CO IUPAC 2014<br />
4.737E-22 4.659E-22 2.450E-20 3.409E-20 3.820E-20 3.732E-20 sheet P2 298K<br />
2.707E-20 1.579E-20 6.566E-21 3.883E-22 5.683E-26 0.000E+00 q2=0.88 (CH3+HCO)<br />
ActAldp566 0.000E+00 0.000E+00 1.903E-23 0.000E+00 3.539E-22 4.725E-22 q3=0.12 (H+CH3CO)<br />
4.533E-22 4.458E-22 2.270E-20 2.985E-20 3.199E-20 2.987E-20 q1=0.00 (CH4+CO)<br />
1.923E-20 9.497E-21 3.450E-21 1.914E-22 3.762E-26 0.000E+00 q's based on 1 bar<br />
ActAldp999 0.000E+00 0.000E+00 1.822E-23 0.000E+00 3.389E-22 4.525E-22 wave > 300 nm<br />
4.340E-22 4.269E-22 2.112E-20 2.647E-20 2.740E-20 2.479E-20<br />
1.485E-20 6.739E-21 2.319E-21 1.258E-22 2.790E-26 0.000E+00 <br />
<br />
:We should use this instead. The reaction is also updated from <br />
<br />
ALD2 = MO2 + HO2 + CO<br />
<br />
:to <br />
<br />
ALD2 = 0.88MO2 + HO2 + 0.88CO + 0.12MCO3 <br />
<br />
--[[User:Bmy|Bob Y.]] 15:19, 6 June 2014 (EDT)<br />
<br />
==== Validation ====<br />
<br />
'''''[[User:Emarais|Eloise Marais]] wrote:'''''<br />
<br />
:I have implemented Michael Prather's pressure-dependent cross-sections for acetaldehyde (ALD2) in GEOS-Chem. The photolysis of ALD2 to form CH4 + CO is turned off. The product yields of the other ALD2 photolysis channel are also updated (see above). Pressure-dependent ALD2 photolysis leads to a decrease in J(ALD2) at the surface and an increase at 500 hPa. The effect on PAN is small (1-5 pptv increase at the surface and <2 pptv at 500 hPa in July 2005).<br />
<br />
:The comparison for SEAC4RS (from a simulation by Katie Travis) is shown below:<br />
:[[Image:Seac4rs_jval_PratherXSect.png]]<br />
<br />
=== EP photolysis for dicarbonyls simulation ===<br />
<br />
<span style="color:red">'''''The SMVGEAR solver will be removed from [[GEOS-Chem v11-01]], when the FlexChem solver package is implemented. At that time, routine <tt>calcrate.F</tt> will be removed from GEOS_Chem.'''''</span><br />
<br />
The code for EP photolysis found in <tt>calcrate.F</tt> needs to be updated for compatibility with FAST-JX v7.0. The EP photolysis code was left unchanged for now (as of [[GEOS-Chem_v10-01_benchmark_history#v10-01c|GEOS-Chem v10-01c]]), but it is now executed only when <tt>LDICARB</tt> is true. This issue affects the [[Dicarbonyls_simulation|dicarbonyls simulation]].<br />
<br />
!==============================================================<br />
! HARDWIRE the effect of branching ratio of HOC2H4O in EP photolysis<br />
! HOC2H4O ------> HO2 + 2CH2O : marked as I in P column of <br />
! 'globchem.dat'<br />
! HOC2H4O --O2--> HO2 + GLYC : marked as J in P column of <br />
! 'globchem.dat'<br />
!<br />
! Add NCS index to NKHOROI and HKHOROJ for SMVGEARII (tmf, 12/16/06)<br />
!==============================================================<br />
<br />
! Not yet modified this for compatibility with Fast-JX v7.0.<br />
! (SDE 04/01/13)<br />
<br />
! Now only do the following if using the dicarbonyls mechanism<br />
! (sde, mps, 5/28/14)<br />
IF ( LDICARB ) THEN<br />
IF ( NKHOROI(NCS) > 0 ) THEN<br />
<br />
! Put J(EP) in correct spot for SMVGEAR II<br />
PHOTVAL = NKHOROI(NCS) - NRATES(NCS)<br />
NKN = NKNPHOTRT(PHOTVAL,NCS)<br />
<br />
DO KLOOP=1,KTLOOP<br />
RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) *<br />
+ ( 1.D0-FYHORO(DENAIR(KLOOP), T3K(KLOOP)) )<br />
ENDDO<br />
ENDIF<br />
<br />
IF ( NKHOROJ(NCS) > 0 ) THEN<br />
<br />
! Put J(EP) in correct spot for SMVGEAR II<br />
PHOTVAL = NKHOROJ(NCS) - NRATES(NCS)<br />
NKN = NKNPHOTRT(PHOTVAL,NCS)<br />
<br />
DO KLOOP=1,KTLOOP<br />
RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) *<br />
+ FYHORO(DENAIR(KLOOP), T3K(KLOOP)) <br />
ENDDO<br />
ENDIF<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:35, 28 May 2014 (EDT)<br />
<br />
== References ==<br />
<br />
#Blitz, M. A., D. E. Heard, M. J. Pilling, S. R. Arnold, M. P. Chipperfield, ''Pressure and temperature-dependent quantum yields for the photodissociation of acetone between 279 and 327.5 nm'', <u>Geophys. Res. Lett.</u>, '''31''', 9, L09104, 2004.<br />
#Eastham, S. D., D. K. Weisenstein, S. R. H. Barrett, ''Development and evaluation of the unified tropospheric–stratospheric chemistry extension (UCX) for the global chemistry-transport model GEOS-Chem'', <u>Atmos. Environ</u>, '''89''', 52-63, doi:10.1016/j.atmosenv.2014.02.001, 2014.<br />
#Feng, Y., et al., ''Effects of cloud overlap in photochemical models'', <u>J. Geophys. Res.</u>, '''109''', D04310, doi:10.1029/2003JD004040, 2004.<br />
#Liang, X.-Z., and W.-C. Wang, ''Cloud overlap effects on general circulation model climate simulations'', <u>J. Geophys. Res.</u>, '''102''' (D10), 11,039–11,047, 1997.<br />
#Liu, H., et al., ''Radiative effect of clouds on tropospheric chemistry in a global three-dimensional chemical transport model'', <u>J. Geophys. Res.</u>, '''111''', D20303, doi:10.1029/2005JD006403, 2006.<br />
#Magneron, I., A. Mellouki, G. Le Bras, G. K. Moortgat, A. Horowitz, and K. Wirtz , ''Photolysis and OH-Initiated Oxidation of Glycolaldehyde under Atmospheric Conditions'', <u>The Journal of Physical Chemistry A</u>, '''109'''(20), 4552-4561, doi:10.1021/jp044346y, 2005.<br />
#Müller, J.-F., Peeters, J., and Stavrakou, T., ''Fast photolysis of carbonyl nitrates from isoprene'', <u>Atmos. Chem. Phys.</u>, '''14''', 2497-2508, doi:10.5194/acp-14-2497-2014, 2014.<br />
#Orlando, J. J., G. S. Tyndall, J.-M. Fracheboud, E. G. Estupiñan, S. Haberkorn, and A. Zimmer, ''The rate and mechanism of the gas-phase oxidation of hydroxyacetone'', <u>Atmos. Environ.</u>, '''33'''(10), 1621-1629, doi:10.1016/S1352-2310(98)00386-0,1999.<br />
#Tie, X., et al., ''Effect of clouds on photolysis and oxidants in the troposphere'', <u>J. Geophys. Res.</u>, '''108'''(D20), 4642, doi:10.1029/2003JD003659, 2003.<br />
#Stubenrauch, C.J., et al., ''Implementation of subgrid cloud vertical structure inside a GCM and its effect on the radiation budget'', <u>J. Clim.</u>, '''10''', 273-287, 1997.<br />
#Wild, O., X. Zhu, and M. J. Prather, ''Fast-J: Accurate simulation of in- and below-cloud photolysis in tropospheric chemical models'', <u>J. Atmos. Chem.</u>, '''37''', 245–282, 2000.<br />
<br />
--[[User:Bmy|Bob Y.]] 15:01, 27 May 2014 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=FAST-JX_v7.0_photolysis_mechanism&diff=27099FAST-JX v7.0 photolysis mechanism2016-07-23T11:40:03Z<p>Barronh: /* Fix for TOMS to address strange cycle in OH output */</p>
<hr />
<div>Sebastian Eastham (MIT) has introduced FAST-JX v7.0 into [[GEOS-Chem v10-01]] concurrently with the [[UCX chemistry mechanism]]. FAST-JX v7.0 replaces the older [[FAST-J photolysis mechanism]].<br />
<br />
== Overview ==<br />
<br />
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
Sebastian Eastham incorporated Fast-JX v7.0a into the [[UCX chemistry mechanism|GEOS-Chem UCX mechanism]]. From [http://www.sciencedirect.com/science/article/pii/S1352231014000971 Eastham et al. (2014)]:<br />
<br />
:GEOS-Chem uses a customized version of the [[FAST-JX v6.2 photolysis mechanism]] (Wild et al., 2000), which efficiently estimates tropospheric photolysis. The customized version uses the wavelength bands from the older Fast-J tropospheric photolysis scheme and does not consider wavelengths shorter than 289 nm, assuming they are attenuated above the tropopause. However, these high-energy photons are responsible for the release of ozone-depleting agents in the stratosphere. The standard Fast-JX model (Prather, 2012) addresses this limitation by expanding the spectrum analyzed to 18 wavelength bins covering 177–850 nm, extending the upper altitude limit to approximately 60 km. We therefore incorporate Fast-JX v7.0a into [[UCX chemistry mechanism|GEOS-Chem UCX]]. Fast-JX includes cross-section data for many species relevant to the troposphere and stratosphere. However, accurately representing sulfur requires calculation of gaseous H2SO4 photolysis, a reaction which is not present in Fast-JX but which acts as a source of sulfur dioxide in the upper stratosphere. Based on a study by Mills (2005), the mean cross-section between 412.5 and 850 nm is estimated at 2.542 × 10−25 cm2. We also add photolysis of ClOO and ClNO2, given their importance in catalytic ozone destruction, using data from JPL 10-06 (Sander et al., 2011). Fast-JX v7.0a includes a correction to calculated acetone cross sections. Accordingly, where hydroxyacetone cross-sections were previously estimated based on one branch of the acetone decomposition, a distinct set of cross sections from JPL 10-06 are used.<br />
<br />
:The base version of GEOS-Chem uses satellite observations of total ozone columns when determining ozone-related scattering and extinction. The UCX allows either this approach, as was used for the production of the results shown, or can employ calculated ozone mixing ratios instead, allowing photolysis rates to respond to changes in the stratospheric ozone layer.<br />
<br />
=== Timeline ===<br />
<br />
The following table displays a timeline of important milestones in FAST-JX v7.0 development:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|- bgcolor="#CCCCCC"<br />
!width="150px"|Version<br />
!width="100px"|Date<br />
!width="800px"|Features / Improvements<br />
|-valign="top"<br />
|[[GEOS-Chem v10-01]]<br />
|Jun 2015<br />
|<br />
*Retired the [[FAST-J photolysis mechanism]] in v10-01c ''(GEOS-Chem Support Team)''<br />
*Implemented FAST-JX v7.0 into GEOS-Chem, concurrent with [[UCX chemistry mechanism]] in v10-01c ''(S. Eastham + GEOS-Chem Support Team)''<br />
*Corrected the following errors in the original FAST-JX v7.0 implementation:<br />
**[[FAST-JX_v7.0_photolysis_mechanism#Reactivation_of_bromine_species_photolysis_for_tropospheric_simulation|Reactivation of Br species for tropospheric simulation]]<br />
**[[FAST-JX_v7.0_photolysis_mechanism#Error_in_reducing_wavelength_bins_for_tropospheric_simulation|Bug fix for reducing wavelength bins for tropospheric simulation]]<br />
|}<br />
<br />
--[[User:Bmy|Bob Y.]] 13:42, 21 May 2014 (EDT)<br />
<br />
== Input files for FAST-JX v7.0 ==<br />
<br />
The following input files are required for the FAST-JX v7.0 photolysis mechanism:<br />
<br />
{| border=1 cellspacing=0 cellpadding=5 <br />
|- bgcolor="#CCCCCC"<br />
!width="180px"|File<br />
!width="75px"|Introduced<br />
!width="75px"|Retired<br />
!width="700px"|Description<br />
<br />
|-valign="top"<br />
|[http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#JvAtms <tt>fastj.jv_atms.dat.nc</tt>]<br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|still used<br />
|<br />
*This netCDF file (originally created for the [[FAST-J photolysis mechanism]]) specifies the reference O3 and T climatologies for FAST-J.<br />
*This file is located in data directory:<br />
GEOS_NATIVE/FastJ_201204/fastj.jv_atms_dat.nc<br />
*NOTE: Where such data exists, GEOS-Chem will overwrite the reference O3 climatology as follows:<br />
*#The online O3 tracer (carried in (<tt>State_Chm%TRACERS(:,:,1:LLCHEM,IDTO3</tt>) '''(RECOMMENDED)''', or<br />
*#Archived O3 profiles sclaed to TOMS/SBUV monthly-mean total ozone column (TO3) data, or<br />
*#Archived TO3 data from the [[GEOS-5]] or [[GEOS-FP]] met field archives.<br />
<br />
|-valign="top"<br />
|<tt>FJX_j2j.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01c|v10-01c]]<br />
|still used<br />
|<br />
*Links GEOS-Chem chemical species to Fast-JX species. Replaces the following file:<br />
**<tt>ratj.d</tt> from the [[FAST-J photolysis mechanism]], used in versions prior to [[GEOS-Chem v10-01]]<br />
<br />
|-valign="top"<br />
|<tt>FJX_spec.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01c|v10-01c]]<br />
|still used<br />
|<br />
*Fast-JX cross-sections, which replaces the following files:<br />
**<tt>jv_spec.dat</tt> from the [[FAST-J photolysis mechanism]], used in versions prior to [[GEOS-Chem v10-01]]<br />
**<tt>spec2008.dat</tt> from the [[FAST-JX v6.4 photolysis mechanism|FAST-JX v6.x photolysis mechanism]], used in several research implementations of GEOS-Chem<br />
<br />
|-valign="top"<br />
|<tt>jv_spec.mie.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01c|v10-01c]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties at 5 wavelengths<br />
<br />
|-valign="top"<br />
|<tt>jv_spec_aod.dat</tt><br />
|[[GEOS-Chem v9-01-03|v9-01-03]]<br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|<br />
*The <tt>jv_spec_aod.dat</tt> file contains the optical properties for aerosols at a single wavelength to be used in the online calculation of the aerosol optical depth diagnostics. The default properties are provided at 550 nm. These properties have been calculated using the same size and optical properties as the <tt>jv_spec.dat</tt> file used for the FAST–J photolysis calculations.<br />
*[[#Scaling_of_AOD_diagnostic_output_to_other_wavelengths|The user can exchange this set of properties with those at another wavelength]]. We recommend that the wavelength used be included in the first line of the header for traceability (this line is output to the GEOS–Chem log file during run time). <br />
<br />
|-valign="top"<br />
|<tt>dust.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for dust at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>org.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for organic carbon at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>so4.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for sulfate at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>soot.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for black carbon at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>ssa.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for accumulation mode sea salt aerosol at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>ssc.dat</tt><br />
|[[GEOS-Chem v10-01#v10-01i|v10-01i]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for coarse mode sea salt aerosol at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
<br />
|-valign="top"<br />
|<tt>h2so4.dat</tt><br />
|[[GEOS-Chem_v10-01#Fixes_and_updates_added_during_the_public_comment_period|v10-01 public comment period]]<br />
|still used<br />
|<br />
*Contains aerosol optical properties for sulfuric acid at multiple wavelengths to be used in the online calculation of the aerosol optical depth diagnostics. Up to three wavelentghs can be selected in the Radiation Menu of <tt>input.geos</tt>.<br />
*These properties are also used for in the [[Coupling GEOS-Chem with RRTMG|RRTMG radiative transfer model]] (if enabled).<br />
*This file is only needed if the [[UCX chemistry mechanism]] is enabled.<br />
<br />
|}<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 19:07, 1 June 2015 (UTC)<br />
<br />
== VOC photolysis in FAST-JX v7.0 ==<br />
<br />
<span style="color:green">'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
In the table below, we summarize VOC photolysis in Fast-JX v7.0. We also invite you to view our [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jrates.pdf ''Comparison of GEOS-Chem Photolysis Rates'' document] prepared by Chris Chan Miller.<br />
<br />
{| border="1" cellspacing="0" cellpadding="5"<br />
|-bgcolor="#cccccc"<br />
! width="300px" |Old reaction<br />
! width="300px" |New reaction<br />
! width="200px" |New rate<br />
! width="300px" |Note<br />
|-valign="top"<br />
| CH2O = HO2 + HO2 + CO (channel a) ||same ||New cross sections leads to an increase by 10% to 20% || This increase is consistent with JPL 2010.<br />
|-<br />
| CH2O = H2 + CO (channel b) ||same ||increase by 6% to 15% || This increase is consistent with JPL 2010.<br />
|-<br />
| PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2 + 0.4NO3 ||PAN = 0.7MCO3 + 0.7NO2 + 0.3MO2 + 0.3NO3 ||same || JPL2010 suggests two channels(only one channel in FastJX-v7.0), branching ratio follows JPL2010<br />
|-<br />
| ALD2 = MO2 + HO2 + CO||ALD2 = 0.88MO2 + HO2 + 0.88CO + 0.12MCO3 || || large discrepancy is found between obs and model (see [http://acmg.seas.harvard.edu/geos/wiki_docs/chemistry/jrates.pdf Chris's slides]), pressure dependence is probably needed. The cross section is now updated by Michael Prather.<br />
|-<br />
| ALD2 = CH4 + CO || this channel is turned off || || this channel is not included in FastJX-v7.0<br />
|-<br />
| RCHO = ETO2 + HO2 + CO ||same || || No pressure dependence is observed, according to JPL2010.<br />
|-<br />
| MP = CH2O + HO2 + OH||same || || change is small.<br />
|-<br />
| GLYX = 0.5H2 + CO + 0.5CH2O + 0.5CO ||GLYX = H2 + 2CO <br> GLYX = CH2O + CO || Pressure dependence is now included, rate is higher ||now 3 channels, Stern-Volmer expression: Qtotal = 1/[6.80 + 251.8e-4 P(Torr)], Increases quantum yields at low P, but ONLY specified for 390-470 nm. Assume that 220K has P = 0.18 atm and higher q.(From FJX v7.0 notes)<br />
|-<br />
| GLYX = 2.0CO + 2.0HO2 ||same ||Pressure dependence is now included, rate is higher || <br />
|-<br />
| MACR = CO + HO2 + CH2O + MCO3 <br> branching ratio = 0.5 ||same ||rate is significantly reduced, as Qy is reduced from 0.008 to 0.003 ||this channel is dominant,the third channel (C3H6 + CO), is ignored, to be consistent with Fast-JX v7.0<br />
|-<br />
| MACR = MAO3 + HO2 <br> branching ratio = 0.5 ||remove this channel || ||suggested by IUPAC, also consistent with Fast-JX v7.0<br />
|-<br />
| MVK = PRPE + CO <br> branching ratio = 0.6 || ||pressure dependence is now included ||<br />
|-<br />
| MVK = MCO3 + CH2O + CO + HO2 <br> branching ratio = 0.2|| ||pressure dependence is now included ||<br />
|-<br />
| MVK = MO2 + MAO3<br> branching ratio = 0.2 ||MVK = MO2 + RCO3 || ||this channel was removed in FJX v7.0, but it shouldn't according to IUPAC. MAO3 is changed to RCO3 for carbon balance.<br />
|- <br />
| GLYC = CH2O + 2.0HO2 + CO ||GLYC = 0.9CH2O + 1.73HO2 + 0.07OH + 1.0CO + 0.1MOH ||Significant increase in X sections || merge from three channels GLYC =CH2O + 2.0HO2 + CO(QY = 0.83), GLYC =CH3OH + CO (QY=0.10), GLYC =OH + CH2O + HO2 + CO (QY =0.07) JPL 2010<br />
|-<br />
| MEK = 0.85MCO3 + 0.85ETO2 + 0.15MO2 + 0.15RCO3 ||same || ||two channels are merged into one reaction<br />
|-<br />
| HAC = MCO3 + CH2O + HO2 || ||rate is lower ||the old rate was using Acetone X sections.This species is not in FastJX v7.0. Seb added X sections based on JPL2010. Need to multiply 0.6 for quantum yield.The bins above 335nm must be zeroed out, otherwise J(HAC) would be too high. The major removal process is its reaction with OH, photolysis is of minor importance (see Orlando et al., 1999). <br />
|}<br />
<br />
--[[User:Jmao|Jmao]] 15:54, 20 May 2014 (EDT)<br />
<br />
=== Final recommendation for J(HAC) and J(PAN) ===<br />
<br />
<span style="color:green">'''''These updates were validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01d|v10-01d]] and approved on 03 Jun 2014.'''''</span><br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:I have two more suggestions to the code and I think we then can finalize v10-01c. We can deal with unresolved J(VOC) later. Seb, please let me know if you think otherwise.<br />
<br />
:#For HAC, keep the QY as 0.6, but zero out the bins >335 nm. <br />
:#For PAN, change the reaction from <br />
<br />
PAN = 0.6MCO3 + 0.6NO2 + 0.4MO2 + 0.4NO3 <br />
<br />
:to <br />
<br />
PAN = 0.7MCO3 + 0.7NO2 + 0.3MO2 + 0.3NO3<br />
<br />
'''''[[User:Sebastian D. Eastham|Sebastian Eastham]] replied:'''''<br />
<br />
:These sound good to me, and I’m not aware of any other pressing issues regarding J-values.<br />
<br />
'''''Daniel Jacob replied:<br />
<br />
:Thanks Jingqiu! If the 1-year benchmark run has already started just let it run - these changes will have very little effect except for HAC and we can just make a note of it. I'm glad that we resolved these J(VOC) issues thanks to Seb, Chris and Jingqiu. At this point we need to move on. <br />
<br />
--[[User:Bmy|Bob Y.]] 17:18, 30 May 2014 (EDT)<br />
<br />
== Overhead ozone columns for use with FAST-JX ==<br />
<br />
=== Use online ozone in FAST-JX v7.0 instead of scaling ozone climatology to archived TO3 values ===<br />
<br />
When using FAST-JX v7.0 with met data other than GEOS-5, we recommend that you select the following option in the CHEMISTRY MENU section of <tt>input.geos</tt>:<br />
<br />
Online O3 for FAST-JX? : T <br />
<br />
Selecting this option will cause FAST-JX v7.0 to copy the "online" O3 tracer concentration&mdash;contained in the <tt>State_Chm%TRACERS</tt> derived type object&mdash;directly into the FAST-JX module. O3 concentrations will be copied for all grid boxes starting at the surface and ending at the top of the chemistry grid, which is either the stratopause (for simulations using the [[UCX chemistry mechanism|UCX combined stratospheric-tropospheric chemistry mechanism]]) or the tropopause (for simulations not using UCX).<br />
<br />
Using the online O3 option for FAST-JX v7.0 in conjunction with the UCX chemistry mechanism will allow photolysis rates to respond to the changes in the dynamically-evolving stratospheric ozone layer. This will result in a more accurate simulation.<br />
<br />
Even if you are performing a tropospheric-only chemistry simulation&mdash;that is, not using the UCX mechanism&mdash;you should still use the online O3 option for FAST-JX v7.0. GEOS-Chem simulations using the FAST-JX online O3 option do not differ significantly from simulations where the internal FAST-JX ozone profiles are scaled to monthly-mean TO3 from either the TOMS/SBUV archive or the GMAO met fields. Sebastian Eastham writes:<br />
<br />
:[The online O3 option in FAST-JX v7.0] should only affect the impact of tropospheric ozone when comparing between [1-month benchmarks] v10-01b and v10-01c_trop, right? The stratospheric ozone estimate from the point of view of Fast-JX should be identical between v10-01b and v10-01c_trop regardless of the online ozone option. My personal thoughts are that leaving the option on should be fine as long as we trust the tropospheric ozone estimates, although it shouldn’t make much of a difference (and if it does that is probably something I should look into). <br />
<br />
Of course, if you turn this option off (WHICH IS NOT RECOMMENDED):<br />
<br />
Online O3 for FAST-JX? : F<br />
<br />
then FAST-JX will scale its internal ozone profiles to TO3 data [[FAST-J_photolysis_mechanism#Overhead_ozone_columns_for_use_with_FAST-J| as described in this section of our ''FAST-J photolysis mechanism'' wiki page]].<br />
<br />
=== Use TOMS ozone for all years when running simulations with GEOS-5 ===<br />
<br />
<span style="color:darkorange">'''''NOTE: This update will be added to [[GEOS-Chem v11-01]].'''''</span><br />
<br />
'''''[[User:Jaf|Jenny Fisher]] wrote:'''''<br />
<br />
:I have been doing some test runs of the tropchem simulation using v11-01f (I know this isn’t recommended, but it was what I had easy access to and I figured I might as well trial it since the 1-year benchmarks have already been done). I was running 2010-2011 — which requires GEOS-5 — and noticed a weird behaviour in the log files: global mean OH jumps up by nearly 50% between December 2010 and Jan 2011 (see output from log files at the end of this email). I haven’t looked super carefully, but I have a hunch that this is because TOMS O3 availability ends after 2010, and starting in 2011 the code therefore uses the O3 column from the met files instead (and I see this switch in the log files).<br />
<br />
:I know it makes sense to use the met field O3 in GEOS-FP, but has anyone looked carefully at the O3 columns in GEOS-5? Given GEOS-5 only goes through the end of 2012 (and GEOS-FP doesn’t start until partway through 2012), I think it would be safer to treat all GEOS-5 runs the same with respect to O3 columns. Even if this isn’t responsible for the OH jump, it would ensure continuity for people running multi-year GEOS-5 simulations, which is still pretty common, especially for interpreting existing observational records. This shouldn’t be hard to do — looks like the TOMS O3 data files have been updated through 2015: http://acdb-ext.gsfc.nasa.gov/Data_services/merged/<br />
<br />
--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 15:30, 5 May 2016 (UTC)<br />
<br />
=== Fix for TOMS to address strange cycle in OH output ===<br />
<br />
<span style="color:darkorange">'''''NOTE: This update will be added to [[GEOS-Chem v11-01]].'''''</span><br />
<br />
'''''Ben Brown-Steiner wrote:'''''<br />
<br />
:I've been running [[GEOS-Chem v10-01|GEOS-Chem v10]] "out of the box" (geos5_2x25_tropchem) and started to look at the daily output via the ND50 diagnostic (although this also happens with daily output to the main file). More that one person here at MIT has found the same behavior within their own simulations, so I'm pretty sure it's not just me.<br />
<br />
:Monthly averages look fine, and daily averages follow the long-term monthly behavior, but with a very weird cycle. At the 15th of each month, something just...stops. Certain species start to decay (e.g. OH) while others spike (e.g. O3).<br />
<br />
:I've attached a few files demonstrating the strange behavior. <br />
<br />
:First is [http://wiki.seas.harvard.edu/geos-chem/images/c/c0/Surface.O3.globalave.1year.png global surface O3] (this is every day for a year, January - December, the plotted dates are wonky, please ignore).<br />
<br />
:Next is [http://wiki.seas.harvard.edu/geos-chem/images/d/dc/Surface.OH.globalave.1year.png surface OH], with a similar strange behavior.<br />
<br />
:I've also plotted POX at the [http://wiki.seas.harvard.edu/geos-chem/images/4/4a/Surface.POX.globalave.1year.png surface] and in the [http://wiki.seas.harvard.edu/geos-chem/images/4/46/Upperatm.POX.globalave.1year.png upper atmosphere].<br />
<br />
:It seems that this happens most prominently over the oceans that over the land, and influences almost every tracer (NO, CO, PRPE, ISOP).<br />
<br />
:We don't know what's going on, but we suspect that it's not an emissions problem (as a similar pattern exists in the upper atmosphere). Perhaps something with radiation?<br />
<br />
:Do you know what's going on? Or point me to someone who does?<br />
<br />
'''''[[User:Barronh|Barron Henderson]] responded:'''''<br />
<br />
:Got it and I think there is an easy fix. (@Ben: see test below)<br />
<br />
:After reviewing HEMCO/Core/hco_calc_mod.F90, I agree that this is almost certainly a HEMCO/TOMS compatibility issue. HEMCO identifies missing values based on the HCO_MISSVAL (hco_calc_mod.F90:849-856). All masked values are returned as 0 (hco_calc_mod.F90:1534-1536). However, I think that the TOMS NetCDF files are not masked appropriately.<br />
<br />
:The TOMS netcdf files use -999 as the "missing_value" and "_FillValue" parameter, but... the actual missing values are set to -999.99. As a result, these values are not getting masked. <br />
<br />
:Since the -999.99 values are not masked, they are used in the aggregation to a new resolution. The result is a value slightly higher than -999 and therefore not caught in toms_mod (toms_mod.F:418-426)<br />
<br />
:The solution is quite simple. We just update the "missing_value" and "_FillValue" in the netcdf file. This will change the way the NetCDF library passes data to HEMCO.<br />
<br />
:Updating the properties can be done with ncatted from nco with the command below.<br />
<br />
ncatted -a _FillValue,DTOMS2,o,f,-999.99 -a missing_value,DTOMS2,o,f,-999.99 -a _FillValue,DTOMS1,o,f,-999.99 -a missing_value,DTOMS1,o,f,-999.99 -a _FillValue,TOMS,o,f,-999.99 -a missing_value,TOMS,o,f,-999.99 /path/to/yourfiles/ExtData/HEMCO/TOMS_SBUV/v2015-03/TOMS_O3col_2004.geos.1x1.nc<br />
<br />
:I have tested that ncdump correctly identifies the values as masked after the update, but I have not seen if HEMCO does. <br />
<br />
:@Ben - Can you try this simple fix? Just update the path and run the command above for 2003-2006 (if you don't have NCO, I can make the edits and post a file for you). Then, re-run 2004.<br />
<br />
'''''[[User:Jaf|Jenny Fisher]] wrote:'''''<br />
<br />
:Thanks for the solution!! Looking at this, I wonder if there is also going to be a problem associated with these lines:<br />
<br />
IF ( TOMS(I,J) > -999e+0_f4 .AND.<br />
& DTOMS2(I,J) > -999e+0_f4 ) THEN<br />
<br />
:I took a quick look back at the code, it looks as though by default we set the ozone column to 0 then overwrite if there is data. I assume having zero overhead ozone column could be a problem…<br />
<br />
:Should we set to a more sensible default value?<br />
<br />
:I had this issue with the Hg simulation and created the files with long-term mean and present day mean values. But they still have missing values at the poles in winter, so a default value might be a better option…<br />
<br />
'''''Ben Brown-Steiner wrote:'''''<br />
<br />
:I've changed the "_FillValue" and "missing_value" for all the TOMS datasets, but am still getting the identical cycles.<br />
<br />
:I copied over the TOMS_O3col* files and made the changes, and redirected the HEMCO config file to use the altered files. Should I have done something else?<br />
<br />
'''''[[User:Barronh|Barron Henderson]] responded:'''''<br />
<br />
:I am proposing a fix for the TOMS/HEMCO issue that tries to address the immediate issue and the unobserved problem. Karl Seltzer tested the fix. I also want to note that the same problem may be in other parts of the system as well.<br />
<br />
:The attached figures show J(O3) for the US ([http://wiki.seas.harvard.edu/geos-chem/images/d/dc/Old_new_us.png old_new_us.png], 20-60N and 110W-60W) and the world ([http://wiki.seas.harvard.edu/geos-chem/images/c/c1/Old_new_global.png old_new_global.png]) as a function of time. Note the drastically improved pattern and higher average for the world. The higher average for the world is due to using a fill value for the unobserved poles.<br />
<br />
:This is a three step fix: (1) process TOMS files; (2) prepare HEMCO rc for new TOMS; (3) update toms module. The steps are described below and supplemented by the attachments. I welcome input on the proposed fix, particularly with respect to the "fill value" approach.<br />
<br />
:'''STEP 1 - Reprocess TOMS'''<br />
<br />
::(processing: [http://wiki.seas.harvard.edu/geos-chem/images/0/0e/Toms2edges.txt toms2edges.txt]; result figure: [http://wiki.seas.harvard.edu/geos-chem/images/a/a2/TOMS_O3col_2004.a.geos.1x1.TOMS1.png TOMS_O3col_2004.a.geos.1x1.TOMS1.png])<br />
::1) Fixes missing flag.<br />
::2) Switches from monthly mean (center) and two delta's to two edges. <br />
::3) Fills data forward in time assuming missing data is best represented by the last value available.<br />
::4) Any cells with no preceding valid value (e.g., January) with the annual mean.<br />
::5) Filling missing latitude to address missing data. (See below)<br />
::: a) I am making a bad assumption as a quick fix/proof of concept. I am using the South pole values as a surrogate for missing north pole values -- matching season with a simple 6 month offset. If both the north and south are missing (e.g., 2003), fill the data poleward.<br />
::: b) This can be replaced with a better fill value later. <br />
<br />
:'''STEP 2 - Edit 1 line and add 2 to HEMCO rc'''<br />
<br />
::Edit the TOMS input line to add ".a" after the year<br />
::Was:<br />
* TOMS_O3_COL $ROOT/TOMS_SBUV/v2015-03/TOMS_O3col_$YYYY.geos.1x1.nc TOMS 1971-2010/1-12/1/0 C xy dobsons * - 1 1<br />
::Would be<br />
* TOMS_O3_COL $ROOT/TOMS_SBUV/v2015-03/TOMS_O3col_$YYYY.a.geos.1x1.nc TOMS 1971-2010/1-12/1/0 C xy dobsons * - 1 1<br />
<br />
::Additions:<br />
* TOMS1_O3_COL - TOMS1 - - - dobsons/day * - 1 1<br />
* TOMS2_O3_COL - TOMS2 - - - dobsons/day * - 1 1<br />
<br />
:'''STEP 3 - Replace toms_mod.F with the [[File:attached version]]. Recompile and run.'''<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 13:51, 21 July 2016 (UTC)<br />
<br />
== Cloud overlap options in FAST-JX v7.0 ==<br />
<br />
You may use the following cloud overlap options with the FAST-JX v7.0 photolysis mechanism:<br />
<br />
=== Approximate random overlap assumption === <br />
<br />
The approximate random overlap option (which is the default setting) is:<br />
<br />
Grid Box Optical Depth = In-Cloud Optical Depth * ( Cloud Fraction )^1.5 <br />
<br />
To select this option, make sure the following lines at the top of <tt>GeosCore/fast_jx_mod.F</tt> are uncommented:<br />
<br />
! Approximate random overlap (balance between accuracy & speed)<br />
#define USE_APPROX_RANDOM_OVERLAP 1<br />
<br />
As this is the default option, these lines should already be uncommented for you when you download the GEOS-Chem source code.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:49, 20 May 2014 (EDT)<br />
<br />
=== Linear cloud overlap assumption === <br />
<br />
The linear cloud overlap option is:<br />
<br />
Grid Box Optical depth = In-cloud optical depth * Cloud fraction. <br />
<br />
To select this option you must uncomment these lines at the top of <tt>GeosCore/fast_jx_mod.F</tt>:<br />
<br />
!! Linear overlap<br />
!#define USE_LINEAR_OVERLAP 1 <br />
<br />
and then recompile GEOS-Chem.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:49, 20 May 2014 (EDT)<br />
<br />
=== Maximum random overlap assumption === <br />
<br />
At present, the maximum random overlap assumption has not been implemented into FAST-JX v7.0. Because this option is computationally intensive, it remains a research option rather than a standard supported feature.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:49, 20 May 2014 (EDT)<br />
<br />
=== Discussion ===<br />
<br />
We invite you to read [[FAST-J photolysis mechanism#Discussion|this discussion about cloud overlap options on our ''FAST-J photolysis mechanism wiki page'']].<br />
<br />
--[[User:Bmy|Bob Y.]] 16:13, 20 May 2014 (EDT)<br />
<br />
== Aerosol optical properties in FAST-JX v7.0 ==<br />
<br />
The aerosol optical properties have been updated from the older [[FAST-J photolysis mechanism]]. '''TEXT NEEDED'''<br />
<br />
The ability to scale aerosol optical depth diagnostic output from 550 nm to other wavelengths (originally implemented for the older FAST-J mechanism in [[GEOS-Chem v8-03-01]]) is still compatible for FAST-JX v7.0. Please see [[FAST-J_photolysis_mechanism#Scaling_of_AOD_diagnostic_output_to_other_wavelengths|this section on our ''FAST-J photolysis mechanism'' wiki page]] for more information.<br />
<br />
--[[User:Bmy|Bob Y.]] 11:12, 20 May 2014 (EDT)<br />
<br />
== Previous issues that have now been resolved ==<br />
<br />
In this section we discuss issues that have been recently fixed in the implementation of FAST-JX v7.0:<br />
<br />
=== Reactivation of bromine species photolysis for tropospheric simulation ===<br />
<br />
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
'''''[mailto:seastham@mit.edu Sebastian Eastham] wrote:'''''<br />
<br />
:Bromine species photolysis should probably be reactivated in the tropospheric version – given that it was online in the pre-UCX version, we may as well keep it online. Doing so is just a question of removing the 'x' in the <tt>FJX_spec.dat</tt> file for the relevant species.<br />
<br />
In <tt>FJX_spec.dat</tt> change the following lines from:<br />
<br />
BrO x300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 0.000E+00 5.620E-19 1.202E-18 2.008E-18<br />
3.239E-18 4.520E-18 5.064E-18 5.809E-18 7.350E-19 0.000E+00<br />
BrNO3 x200 0.000E+00 0.000E+00 5.484E-19 7.245E-19 3.702E-18 3.475E-18 J10<br />
3.182E-18 2.978E-18 5.304E-19 6.086E-19 4.489E-19 1.963E-19<br />
1.584E-19 1.307E-19 1.110E-19 8.033E-20 3.377E-20 1.270E-21<br />
BrNO3 x300 0.000E+00 0.000E+00 8.026E-19 1.071E-18 5.166E-18 4.190E-18 J10<br />
3.467E-18 3.039E-18 5.567E-19 5.989E-19 4.528E-19 2.098E-19<br />
1.705E-19 1.425E-19 1.207E-19 8.648E-20 3.716E-20 1.445E-21<br />
HOBr x300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 1.324E-19 2.011E-19 2.202E-19 2.196E-19<br />
1.726E-19 1.367E-19 1.157E-19 1.125E-19 6.197E-20 2.755E-21<br />
<br />
to:<br />
<br />
BrO 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 0.000E+00 5.620E-19 1.202E-18 2.008E-18<br />
3.239E-18 4.520E-18 5.064E-18 5.809E-18 7.350E-19 0.000E+00<br />
BrNO3 200 0.000E+00 0.000E+00 5.484E-19 7.245E-19 3.702E-18 3.475E-18 J10<br />
3.182E-18 2.978E-18 5.304E-19 6.086E-19 4.489E-19 1.963E-19<br />
1.584E-19 1.307E-19 1.110E-19 8.033E-20 3.377E-20 1.270E-21<br />
BrNO3 300 0.000E+00 0.000E+00 8.026E-19 1.071E-18 5.166E-18 4.190E-18 J10<br />
3.467E-18 3.039E-18 5.567E-19 5.989E-19 4.528E-19 2.098E-19<br />
1.705E-19 1.425E-19 1.207E-19 8.648E-20 3.716E-20 1.445E-21<br />
HOBr 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10<br />
0.000E+00 0.000E+00 1.324E-19 2.011E-19 2.202E-19 2.196E-19<br />
1.726E-19 1.367E-19 1.157E-19 1.125E-19 6.197E-20 2.755E-21<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:33, 14 May 2014 (EDT)<br />
<br />
=== Error in reducing wavelength bins for tropospheric simulation === <br />
<br />
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c]] and approved on 29 May 2014.'''''</span><br />
<br />
'''''[mailto:seastham@mit.edu Sebastian Eastham] wrote:'''''<br />
<br />
:In <tt>fast_jx_mod</tt>, specifically <tt>RD_XXX</tt>, there is a transformation to reduce 18 cross sections to 12. Since bin 18 now corresponds to bin 12 and so on, the wavelengths are moved within the cross section array QQQ. However, the 12-bin capability is rarely used (if ever), so when Fast-JX was extended to allow cross sections with 1 or 3 sets of data, the 12 and 8 bin codes were not updated accordingly. This results in very large cross sections for acetone at long wavelengths, because the shorter wavelength data is being used instead.<br />
<br />
:I've notified Michael Prather - he did not know about this bug and is putting together a fix ASAP. I've written my own fix in the meantime, which results in the acetone cross sections matching much more closely, at least between the two [[GEOS-Chem v10-01 benchmark history#v10-01c|v10-01c versions]].<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 10:39, 12 May 2014 (EDT)<br />
<br />
=== Use proper org.dat file with updates for OC growth ===<br />
<br />
<span style="color:green">'''''This update was added to the official release of [[GEOS-Chem v10-01]] (approved 15 Jun 2015).'''''</span><br />
<br />
After the [[GEOS-Chem v10-01 benchmark history#v10-01i|GEOS-Chem v10-01i benchmarks]] were submitted, we learned that we were using a version of the FAST-JX input file <tt>org.dat</tt> that did not have [[Aerosol optical properties#Better representation of OC growth with RH and correction to sulfate optics|Randall Martin's updates for better representation of OC growth with RH]].<br />
<br />
'''''[[User:David_Ridley|David Ridley]] wrote:'''''<br />
<br />
<blockquote>So it looks like I’d assumed you didn’t have the organics updates yet, so the <tt>org.dat</tt> I sent you doesn’t include Randall’s updates in there, sorry! I do have the multi-wavelength version that does include those. The change in the org optics seems to tie in with the reduction in the organic AOD we’re seeing, so that makes sense.</blockquote><br />
<blockquote>The BC optics are the same, so the differences seen there shouldn’t be coming from the optics. There may have been a change in the density because of a lot of BC tweaks around the same time. I’ll double check that.</blockquote><br />
<br />
We will make sure that the updated <tt>org.dat</tt> file ships with the publicly-released version of [[GEOS-Chem v10-01]]. <br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 15:53, 11 May 2015 (EDT)<br />
<br />
== Unresolved issues ==<br />
<br />
The following are active areas of research in GEOS-Chem.<br />
<br />
=== Carbonyl nitrate photolysis ===<br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:We know that carbonyl nitrate should be photolyzed much faster than the current rates in FAST-JX, [http://www.atmos-chem-phys.net/14/2497/2014/acp-14-2497-2014.html according to this paper]. But updates in this rate should also be combined with updates in the OH rate in order to better reproduce the experimental results from chamber studies. This seems more like a research question, so we decided to leave this to the SEAC4RS team.<br />
--[[User:Bmy|Bob Y.]] 15:40, 27 May 2014 (EDT)<br />
<br />
=== Acetaldehyde photolysis ===<br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:We saw large discrepancies between observed(black) and modeled(red) J(ALD2), as shown in this plot by Chris Chan Miller: <br />
<br />
:[[Image:ALD2_photolysis.png]]<br />
<br />
:This discrepancy is very likely due to the lack of pressure dependence on the quantum yield. But Michael Prather didn’t include this pressure dependence in any of the FAST-JX versions. So this remains as a problem in all GEOS-Chem versions, including [[GEOS-Chem v10-01 benchmark history#v10-01c|GEOS-Chem v10-01c]]. <br />
<br />
==== Solution ====<br />
<br />
<span style="color:green">'''''These updates were validated with the 1-month benchmark simulation [[GEOS-Chem v10-01 benchmark history#v10-01f|v10-01f]] and approved on Approved 13 Jan 2015.'''''</span><br />
<br />
The solution is to update the entries for acetaldehyde in the FAST-JX input file <tt>FJX_spec_dat</tt>, as follows:<br />
<br />
'''''[[User:Jmao|Jingqiu Mao]] wrote:'''''<br />
<br />
:Michael Prather just provided a new set of cross section with pressure dependence for acetaldehyde:<br />
<br />
ActAldp177 0.000E+00 0.000E+00 1.989E-23 0.000E+00 3.699E-22 4.938E-22 CH3CO IUPAC 2014<br />
4.737E-22 4.659E-22 2.450E-20 3.409E-20 3.820E-20 3.732E-20 sheet P2 298K<br />
2.707E-20 1.579E-20 6.566E-21 3.883E-22 5.683E-26 0.000E+00 q2=0.88 (CH3+HCO)<br />
ActAldp566 0.000E+00 0.000E+00 1.903E-23 0.000E+00 3.539E-22 4.725E-22 q3=0.12 (H+CH3CO)<br />
4.533E-22 4.458E-22 2.270E-20 2.985E-20 3.199E-20 2.987E-20 q1=0.00 (CH4+CO)<br />
1.923E-20 9.497E-21 3.450E-21 1.914E-22 3.762E-26 0.000E+00 q's based on 1 bar<br />
ActAldp999 0.000E+00 0.000E+00 1.822E-23 0.000E+00 3.389E-22 4.525E-22 wave > 300 nm<br />
4.340E-22 4.269E-22 2.112E-20 2.647E-20 2.740E-20 2.479E-20<br />
1.485E-20 6.739E-21 2.319E-21 1.258E-22 2.790E-26 0.000E+00 <br />
<br />
:We should use this instead. The reaction is also updated from <br />
<br />
ALD2 = MO2 + HO2 + CO<br />
<br />
:to <br />
<br />
ALD2 = 0.88MO2 + HO2 + 0.88CO + 0.12MCO3 <br />
<br />
--[[User:Bmy|Bob Y.]] 15:19, 6 June 2014 (EDT)<br />
<br />
==== Validation ====<br />
<br />
'''''[[User:Emarais|Eloise Marais]] wrote:'''''<br />
<br />
:I have implemented Michael Prather's pressure-dependent cross-sections for acetaldehyde (ALD2) in GEOS-Chem. The photolysis of ALD2 to form CH4 + CO is turned off. The product yields of the other ALD2 photolysis channel are also updated (see above). Pressure-dependent ALD2 photolysis leads to a decrease in J(ALD2) at the surface and an increase at 500 hPa. The effect on PAN is small (1-5 pptv increase at the surface and <2 pptv at 500 hPa in July 2005).<br />
<br />
:The comparison for SEAC4RS (from a simulation by Katie Travis) is shown below:<br />
:[[Image:Seac4rs_jval_PratherXSect.png]]<br />
<br />
=== EP photolysis for dicarbonyls simulation ===<br />
<br />
<span style="color:red">'''''The SMVGEAR solver will be removed from [[GEOS-Chem v11-01]], when the FlexChem solver package is implemented. At that time, routine <tt>calcrate.F</tt> will be removed from GEOS_Chem.'''''</span><br />
<br />
The code for EP photolysis found in <tt>calcrate.F</tt> needs to be updated for compatibility with FAST-JX v7.0. The EP photolysis code was left unchanged for now (as of [[GEOS-Chem_v10-01_benchmark_history#v10-01c|GEOS-Chem v10-01c]]), but it is now executed only when <tt>LDICARB</tt> is true. This issue affects the [[Dicarbonyls_simulation|dicarbonyls simulation]].<br />
<br />
!==============================================================<br />
! HARDWIRE the effect of branching ratio of HOC2H4O in EP photolysis<br />
! HOC2H4O ------> HO2 + 2CH2O : marked as I in P column of <br />
! 'globchem.dat'<br />
! HOC2H4O --O2--> HO2 + GLYC : marked as J in P column of <br />
! 'globchem.dat'<br />
!<br />
! Add NCS index to NKHOROI and HKHOROJ for SMVGEARII (tmf, 12/16/06)<br />
!==============================================================<br />
<br />
! Not yet modified this for compatibility with Fast-JX v7.0.<br />
! (SDE 04/01/13)<br />
<br />
! Now only do the following if using the dicarbonyls mechanism<br />
! (sde, mps, 5/28/14)<br />
IF ( LDICARB ) THEN<br />
IF ( NKHOROI(NCS) > 0 ) THEN<br />
<br />
! Put J(EP) in correct spot for SMVGEAR II<br />
PHOTVAL = NKHOROI(NCS) - NRATES(NCS)<br />
NKN = NKNPHOTRT(PHOTVAL,NCS)<br />
<br />
DO KLOOP=1,KTLOOP<br />
RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) *<br />
+ ( 1.D0-FYHORO(DENAIR(KLOOP), T3K(KLOOP)) )<br />
ENDDO<br />
ENDIF<br />
<br />
IF ( NKHOROJ(NCS) > 0 ) THEN<br />
<br />
! Put J(EP) in correct spot for SMVGEAR II<br />
PHOTVAL = NKHOROJ(NCS) - NRATES(NCS)<br />
NKN = NKNPHOTRT(PHOTVAL,NCS)<br />
<br />
DO KLOOP=1,KTLOOP<br />
RRATE(KLOOP,NKN)=RRATE(KLOOP,NKN) *<br />
+ FYHORO(DENAIR(KLOOP), T3K(KLOOP)) <br />
ENDDO<br />
ENDIF<br />
ENDIF<br />
<br />
--[[User:Melissa Payer|Melissa Sulprizio]] 13:35, 28 May 2014 (EDT)<br />
<br />
== References ==<br />
<br />
#Blitz, M. A., D. E. Heard, M. J. Pilling, S. R. Arnold, M. P. Chipperfield, ''Pressure and temperature-dependent quantum yields for the photodissociation of acetone between 279 and 327.5 nm'', <u>Geophys. Res. Lett.</u>, '''31''', 9, L09104, 2004.<br />
#Eastham, S. D., D. K. Weisenstein, S. R. H. Barrett, ''Development and evaluation of the unified tropospheric–stratospheric chemistry extension (UCX) for the global chemistry-transport model GEOS-Chem'', <u>Atmos. Environ</u>, '''89''', 52-63, doi:10.1016/j.atmosenv.2014.02.001, 2014.<br />
#Feng, Y., et al., ''Effects of cloud overlap in photochemical models'', <u>J. Geophys. Res.</u>, '''109''', D04310, doi:10.1029/2003JD004040, 2004.<br />
#Liang, X.-Z., and W.-C. Wang, ''Cloud overlap effects on general circulation model climate simulations'', <u>J. Geophys. Res.</u>, '''102''' (D10), 11,039–11,047, 1997.<br />
#Liu, H., et al., ''Radiative effect of clouds on tropospheric chemistry in a global three-dimensional chemical transport model'', <u>J. Geophys. Res.</u>, '''111''', D20303, doi:10.1029/2005JD006403, 2006.<br />
#Magneron, I., A. Mellouki, G. Le Bras, G. K. Moortgat, A. Horowitz, and K. Wirtz , ''Photolysis and OH-Initiated Oxidation of Glycolaldehyde under Atmospheric Conditions'', <u>The Journal of Physical Chemistry A</u>, '''109'''(20), 4552-4561, doi:10.1021/jp044346y, 2005.<br />
#Müller, J.-F., Peeters, J., and Stavrakou, T., ''Fast photolysis of carbonyl nitrates from isoprene'', <u>Atmos. Chem. Phys.</u>, '''14''', 2497-2508, doi:10.5194/acp-14-2497-2014, 2014.<br />
#Orlando, J. J., G. S. Tyndall, J.-M. Fracheboud, E. G. Estupiñan, S. Haberkorn, and A. Zimmer, ''The rate and mechanism of the gas-phase oxidation of hydroxyacetone'', <u>Atmos. Environ.</u>, '''33'''(10), 1621-1629, doi:10.1016/S1352-2310(98)00386-0,1999.<br />
#Tie, X., et al., ''Effect of clouds on photolysis and oxidants in the troposphere'', <u>J. Geophys. Res.</u>, '''108'''(D20), 4642, doi:10.1029/2003JD003659, 2003.<br />
#Stubenrauch, C.J., et al., ''Implementation of subgrid cloud vertical structure inside a GCM and its effect on the radiation budget'', <u>J. Clim.</u>, '''10''', 273-287, 1997.<br />
#Wild, O., X. Zhu, and M. J. Prather, ''Fast-J: Accurate simulation of in- and below-cloud photolysis in tropospheric chemical models'', <u>J. Atmos. Chem.</u>, '''37''', 245–282, 2000.<br />
<br />
--[[User:Bmy|Bob Y.]] 15:01, 27 May 2014 (EDT)</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:Pnc_trac_avg.geosfp_4x5_benchmark.20130701000_pncprofile_IJ-AVG_O3.png&diff=26830File:Pnc trac avg.geosfp 4x5 benchmark.20130701000 pncprofile IJ-AVG O3.png2016-05-16T16:39:26Z<p>Barronh: Barronh uploaded a new version of File:Pnc trac avg.geosfp 4x5 benchmark.20130701000 pncprofile IJ-AVG O3.png</p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:Pnc_trac_avg.geosfp_4x5_benchmark.20130701000_pncprofile_IJ-AVG_O3.png&diff=26824File:Pnc trac avg.geosfp 4x5 benchmark.20130701000 pncprofile IJ-AVG O3.png2016-05-16T15:08:48Z<p>Barronh: </p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:Pnc_trac_avg.geosfp_4x5_benchmark.20130701000_IJ-AVG_O3.png&diff=26818File:Pnc trac avg.geosfp 4x5 benchmark.20130701000 IJ-AVG O3.png2016-05-16T14:37:23Z<p>Barronh: </p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=Updates_in_JPL_Publication_15-10&diff=26815Updates in JPL Publication 15-102016-05-16T14:26:24Z<p>Barronh: /* JPL Updated Rates Compared to GC v10 */</p>
<hr />
<div>= Summary = <br />
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page ([[Updates in JPL Publication 15-10]]) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10. A similar comparison was done for JPL Publication 10-6 ([[Updating standard chemistry with JPL 10-6]]). For each reaction coefficient that was updated, we will note the rate expression currently used in v10, the updated expression in JPL 15-10, and provide a plot of the two rate coefficients. For expressions that are only temperature dependent, rates will be plotted as a function of temperature between 220 K and 320 K. For termolecular reactions, expressions will be plotted as a function of altitude with temperature and pressure following the 1976 US Standard Atmosphere.<br />
<br />
J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.<br />
<br />
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)<br />
<br />
= JPL Updated Rates Compared to GC v10 =<br />
<br />
This table is a work in progress.<br />
<br />
<table border="1"><br />
<tr><th width="20%">GEOS-Chem Reaction</th><th>v10 (JPL 10-6)</th><th>JPL 15-10</th><th>Comparison</th></tr><br />
<tr><th colspan=4>Table 1A - Bimolecular Ox </th></tr><br />
<tr><td colspan=4>No quantitative updates.</td></tr><br />
<tr><th colspan=4>Table 1A - Bimolecular O1D</th></tr><br />
<tr><td>CH3Cl + O1D</td><td>not active </td><td></td><td></td></tr><br />
<tr><td>CH3CCl3 + O1D</td><td>not active </td><td></td><td></td></tr><br />
<tr><td>O1D + HCFC22 = O + HCFC22 + ClO + Cl</td><td>1e-10</td><td>1.02e-10</td><td width="30%">[[File:JPL201510andGCv10_O1DplHCFC22_eq_OplHCFC22plClOplCl.png|200px|thumb|left|JPL201510andGCv10_O1DplHCFC22_eq_OplHCFC22plClOplCl.png]]</td></tr><br />
<tr><td>O1D + HCFC142b</td><td>2.20E-10</td><td>2.00E-10</td><td width="30%">[[File:JPL201510andGCv10_O1DplHCFC142b.png|200px|thumb|left|JPL201510andGCv10_O1DplHCFC142b.png]]</td></tr><br />
<tr><td>O1D + CFC113</td><td>2.00E-10</td><td>2.32E-10</td><td width="30%">[[File:JPL201510andGCv10_O1DplCFC113.png|200px|thumb|left|JPL201510andGCv10_O1DplCFC113.png]]</td></tr><br />
<tr><td>O1D + CFC114</td><td>1.30E-10</td><td>1.3E-10*exp(-25/T)</td><td width="30%">[[File:JPL201510andGCv10_O1DplCFC114.png|200px|thumb|left|JPL201510andGCv10_O1DplCFC114.png]]</td></tr><br />
<tr><td>O1D + CFC115</td><td>5.0E-11</td><td>5.4E-11*exp(-30/T)</td><td width="30%">[[File:JPL201510andGCv10_O1DplCFC115.png|200px|thumb|left|JPL201510andGCv10_O1DplCFC115.png]]</td></tr><br />
<tr><th colspan=4>Table 1A - Bimolecular Singlet O2 </th></tr><br />
<tr><td colspan=4>No quantitative updates.</td></tr><br />
<tr><th colspan=4>Table 1B - Bimolecular HOx </th></tr><br />
<tr><td colspan=4>No quantitative updates.</td></tr><br />
<tr><th colspan=4>Table 1C - Bimolecular NOx </th></tr><br />
<tr><td colspan=4>No quantitative updates.</td></tr><br />
<tr><th colspan=4>Table 1D - Bimolecular Organic</th></tr><br />
<tr><th width="20%">GEOS-Chem Reaction</th><th>v10 (JPL 10-6)</th><th>JPL 15-10</th><th>Comparison</th></tr><br />
<tr><td>MACR + O3 = OH + HO2 + HCOOH + CO + MGLY + CH2O</td><td>1.40E-15*exp(-2100/T)</td><td>1.5e-15*exp(-2110/T)</td><td width="30%">[[File:JPL201510andGCv10_MACRplO3_eq_OHplHO2plHCOOHplCOplMGLYplCH2O.png|200px|thumb|left|JPL201510andGCv10_MACRplO3_eq_OHplHO2plHCOOHplCOplMGLYplCH2O.png]]</td></tr><br />
<tr><td>MVK + O3 = OH + HO2 + HCOOH + CO + ALD2 + MGLY + CH2O</td><td>8.50E-16*exp(-1520/T)</td><td>8.5e-16*exp(-1520/T)</td><td width="30%">[[File:JPL201510andGCv10_MVKplO3_eq_OHplHO2plHCOOHplCOplALD2plMGLYplCH2O.png|200px|thumb|left|JPL201510andGCv10_MVKplO3_eq_OHplHO2plHCOOHplCOplALD2plMGLYplCH2O.png]]</td></tr><br />
<tr><td>MACR + OH = MAO3 + MRO2</td><td>8.0E-12*exp(380/T)</td><td>9.6e-12*exp(360./T)</td><td width="30%">[[File:JPL201510andGCv10_MACRplOH_eq_MAO3plMRO2.png|200px|thumb|left|JPL201510andGCv10_MACRplOH_eq_MAO3plMRO2.png]]</td></tr><br />
<tr><td>MVK + OH = VRO2</td><td>2.6e-12*exp(610/T)</td><td>2.7e-12*exp(580./T)</td><td width="30%">[[File:JPL201510andGCv10_MVKplOH_eq_VRO2.png|200px|thumb|left|JPL201510andGCv10_MVKplOH_eq_VRO2.png]]</td></tr><br />
<tr><td>ISOP + OH = RIO2</td><td>3.1e-11*exp(350/T)</td><td>3.0e-11*exp(360./T)</td><td width="30%">[[File:JPL201510andGCv10_ISOPplOH_eq_RIO2.png|200px|thumb|left|JPL201510andGCv10_ISOPplOH_eq_RIO2.png]]</td></tr><br />
<tr><td>MACR + NO3 = MAN2</td><td>2.30e-15</td><td>3.4e-15</td><td width="30%">[[File:JPL201510andGCv10_MACRplNO3_eq_MAN2.png|200px|thumb|left|JPL201510andGCv10_MACRplNO3_eq_MAN2.png]]</td></tr><br />
<tr><td>ISOP + NO3 = INO2</td><td>3.3E-12*exp(-450/T)</td><td>3.5e-12*exp(-450/T)</td><td width="30%">[[File:JPL201510andGCv10_ISOPplNO3_eq_INO2.png|200px|thumb|left|JPL201510andGCv10_ISOPplNO3_eq_INO2.png]]</td></tr><br />
<tr><th colspan=4>Table 1F - Bimolecular ClOx </th></tr><br />
<tr><td colspan=4>Non CFC/HCFC ClOx needs review. (volunteer by putting your name here)</td></tr><br />
<tr><td>OH + HCFC22 = Cl + H2O</td><td>1.05E-12*exp(-1600./T)</td><td>9.2e-13*exp(-1560./T)</td><td width="30%">[[File:JPL201510andGCv10_OHplHCFC22_eq_ClplH2O.png|200px|thumb|left|JPL201510andGCv10_OHplHCFC22_eq_ClplH2O.png]]</td></tr><br />
<tr><td>OH + HCFC123 = Cl + H2O</td><td>6.30E-13*exp(-850./T)</td><td>7.4e-13*exp(-900./T)</td><td width="30%">[[File:JPL201510andGCv10_OHplHCFC123_eq_ClplH2O.png|200px|thumb|left|JPL201510andGCv10_OHplHCFC123_eq_ClplH2O.png]]</td></tr><br />
<tr><th colspan=4>Table 1G - Bimolecular BrOx </th></tr><br />
<tr><td colspan=4>Needs review. (volunteer by putting your name here)</td></tr><br />
<tr><th colspan=4>Table 1H - Bimolecular IOx </th></tr><br />
<tr><td colspan=4>Needs review. (volunteer by putting your name here)</td></tr><br />
<tr><th colspan=4>Table 1I - Bimolecular SOx </th></tr><br />
<tr><td colspan=4>Needs review. (volunteer by putting your name here)</td></tr><br />
<tr><th colspan=4>Table 2-1 - Termolecular</th></tr><br />
<tr><th width="20%">GEOS-Chem Reaction</th><th>v10 (JPL 10-6)</th><th>JPL 15-10</th><th>Comparison</th></tr><br />
<tr><td>HO2 + NO2 + M = HNO4</td><td>GP(A0 = 2.e-31, B0 = 3.4, A1 = 2.9e-12, B1 = 1.1)</td><td>GP(A0 = 1.9e-31, B0 = 3.4, A1 = 4e-12, B1 = 0.3)</td><td width="30%">[[File:JPL201510andGCv10_HO2plNO2plM_eq_HNO4.png|200px|thumb|left|JPL201510andGCv10_HO2plNO2plM_eq_HNO4.png]]</td></tr><br />
<tr><td>NO2 + NO3 + M = N2O5</td><td>GP(A0 = 2.00E-30, B0 = 4.4E+00, A1 = 1.40E-12, B1 = 7.0E-01)</td><td>GP(A0 = 2.4e-30, B0 = 3., A1 = 1.6e-12, B1 = -0.1)</td><td width="30%">[[File:JPL201510andGCv10_NO2plNO3plM_eq_N2O5.png|200px|thumb|left|JPL201510andGCv10_NO2plNO3plM_eq_N2O5.png]]</td></tr><br />
<tr><td>OH + CO + M = H + CO2</td><td>GY(A0 = 5.9e-33, B0 = 1.4e0, A1 = 1.1e-12, B1 = -1.3e0, A2 = 1.5e-13, B2 = -0.6e0, A3 = 2.1e09, B3 = -6.1e0)</td><td>GY(A0 = 5.9e-33, B0 = 1., A1 = 1.1e-12, B1 = -1.3e0, A2 = 1.5e-13, B2 = 0., A3 = 2.1e09, B3 = -6.1e0)</td><td width="30%">[[File:JPL201510andGCv10_OHplCOplM_eq_HplCO2.png|200px|thumb|left|JPL201510andGCv10_OHplCOplM_eq_HplCO2.png]]</td></tr><br />
<tr><td>OH + PRPE + M = PO2</td><td>GP(A0 = 8.00E-27, B0 = 3.5E+00, A1 = 3.00E-11, B1 = 1.0E+00)</td><td>GP(A0 = 4.6e-27, B0 = 4., A1 = 2.6e-11, B1 = 1.3)</td><td width="30%">[[File:JPL201510andGCv10_OHplPRPEplM_eq_PO2.png|200px|thumb|left|JPL201510andGCv10_OHplPRPEplM_eq_PO2.png]]</td></tr><br />
<tr><td>ClO + ClO + M = Cl2O2</td><td>GP(1.60E-32, 4.5E+00 , 3.00E-12, 2.0E+00)</td><td>GP(A0 = 1.9e-32, B0 = 3.6, A1 = 3.7e-12, B1 = 1.6)</td><td width="30%">[[File:JPL201510andGCv10_ClOplClOplM_eq_Cl2O2.png|200px|thumb|left|JPL201510andGCv10_ClOplClOplM_eq_Cl2O2.png]]</td></tr><br />
<tr><th colspan=4>Table 3-1</th></tr><br />
<tr><td>N2O5 = NO2 + NO3</td><td>GP(A0 = 7.40E-04, B0 = 4.4E+00, C0 = -11000., A1 = 5.18E+14, B1 = 7.0E-01, C1 = -11000.)</td><td>GP(A0 = 2.4e-30/5.8e-27, B0 = 3., C0 = -10840, A1 = 1.6e-12/5.8e-27, B1 = -0.1, C1 = -10840)</td><td width="30%">[[File:JPL201510andGCv10_N2O5_eq_NO2plNO3.png|200px|thumb|left|JPL201510andGCv10_N2O5_eq_NO2plNO3.png]]</td></tr><br />
<tr><td>HNO4 = HO2 + NO2</td><td>GP(A0 = 2.e-31 / 2.1e-27, B0 = 3.4, C0 = -10900., A1 = 2.9e-12 / 2.1e-27, B1 = 1.1, C1 = -10900.)</td><td>GP(A0 = 1.9e-31 / 2.1e-27, B0 = 3.4, C0 = -10900., A1 = 4e-12 / 2.1e-27, B1 = 0.3, C1 = -10900.)</td><td width="30%">[[File:JPL201510andGCv10_HNO4_eq_HO2plNO2.png|200px|thumb|left|JPL201510andGCv10_HNO4_eq_HO2plNO2.png]]</td></tr><br />
<tr><td colspan=4>1. Termolecular rates coefficients are evaluated from -0.5km to 11km in the 1976 US Std Atmosphere temperature and pressures</td></tr><br />
<tr><td colspan=4>2. GP is short hand for the GEOS-Chem rate form denoted by P in globchem.dat and corresponding to the JPL termolecular rate defined as k_f([M],T) in Section 2.1</td></tr><br />
<tr><td colspan=4>3. GY is short hand for the GEOS-Chem rate form denoted by Y in globchem.dat and corresponding to the JPL termolecular rate defined as k^{ca}_f([M],T) in Section 2.1</td></tr><br />
</table><br />
<br />
Notes:<br />
<br />
* Skipping CH2OO + ... on 1-93<br />
* Skipping syn-CH3CHOO and anti-CH3CHOO on 1-94<br />
* Skipping FOx reactions<br />
* Skipped ClOx reactions, needs review<br />
* Skipped BrOx reactions, needs review<br />
* Skipped IOx reactions, needs review<br />
* SOx reactions need further consideration perhaps with overlap of Iodine IO and DMS? IO + CH3SCH3 -> products</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=Updates_in_JPL_Publication_15-10&diff=26814Updates in JPL Publication 15-102016-05-13T21:06:01Z<p>Barronh: /* JPL Updated Rates Compared to GC v10 */</p>
<hr />
<div>= Summary = <br />
JPL has released its 18th evaluation of chemical rate coefficients for atmospheric studies (Burkholder et al., 2015)." A new page ([[Updates in JPL Publication 15-10]]) is being created to compare rates between GEOS-Chem v10 and JPL Publication 15-10. A similar comparison was done for JPL Publication 10-6 ([[Updating standard chemistry with JPL 10-6]]). For each reaction coefficient that was updated, we will note the rate expression currently used in v10, the updated expression in JPL 15-10, and provide a plot of the two rate coefficients. For expressions that are only temperature dependent, rates will be plotted as a function of temperature between 220 K and 320 K. For termolecular reactions, expressions will be plotted as a function of altitude with temperature and pressure following the 1976 US Standard Atmosphere.<br />
<br />
J. B. Burkholder, S. P. Sander, J. Abbatt, J. R. Barker, R. E. Huie, C. E. Kolb, M. J. Kurylo, V. L. Orkin, D. M. Wilmouth, and P. H. Wine "Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation No. 18," JPL Publication 15-10, Jet Propulsion Laboratory, Pasadena, 2015 http://jpldataeval.jpl.nasa.gov.<br />
<br />
---[[User:barronh|B. Henderson]] 2016-05-03 15:25 (EDT)<br />
<br />
= JPL Updated Rates Compared to GC v10 =<br />
<br />
This table is a work in progress.<br />
<br />
<table border="1"><br />
<tr><th width="20%">GEOS-Chem Reaction</th><th>v10 (JPL 10-6)</th><th>JPL 15-10</th><th>Comparison</th></tr><br />
<tr><th colspan=4>Table 1A - Bimolecular Ox </th></tr><br />
<tr><td colspan=4>No quantitative updates.</td></tr><br />
<tr><th colspan=4>Table 1A - Bimolecular O1D</th></tr><br />
<tr><td>CH3Cl + O1D</td><td>not active </td><td></td><td></td></tr><br />
<tr><td>CH3CCl3 + O1D</td><td>not active </td><td></td><td></td></tr><br />
<tr><td>O1D + HCFC22 = O + HCFC22 + ClO + Cl</td><td>1e-10</td><td>1.02e-10</td><td width="30%">[[File:JPL201510andGCv10_O1DplHCFC22_eq_OplHCFC22plClOplCl.png|200px|thumb|left|JPL201510andGCv10_O1DplHCFC22_eq_OplHCFC22plClOplCl.png]]</td></tr><br />
<tr><td>O1D + HCFC142b</td><td>2.20E-10</td><td>2.00E-10</td><td width="30%">[[File:JPL201510andGCv10_O1DplHCFC142b.png|200px|thumb|left|JPL201510andGCv10_O1DplHCFC142b.png]]</td></tr><br />
<tr><td>O1D + CFC113</td><td>2.00E-10</td><td>2.32E-10</td><td width="30%">[[File:JPL201510andGCv10_O1DplCFC113.png|200px|thumb|left|JPL201510andGCv10_O1DplCFC113.png]]</td></tr><br />
<tr><td>O1D + CFC114</td><td>1.30E-10</td><td>1.3E-10*exp(-25/T)</td><td width="30%">[[File:JPL201510andGCv10_O1DplCFC114.png|200px|thumb|left|JPL201510andGCv10_O1DplCFC114.png]]</td></tr><br />
<tr><td>O1D + CFC115</td><td>5.0E-11</td><td>5.4E-11*exp(-30/T)</td><td width="30%">[[File:JPL201510andGCv10_O1DplCFC115.png|200px|thumb|left|JPL201510andGCv10_O1DplCFC115.png]]</td></tr><br />
<tr><th colspan=4>Table 1A - Bimolecular Singlet O2 </th></tr><br />
<tr><td colspan=4>No quantitative updates.</td></tr><br />
<tr><th colspan=4>Table 1B - Bimolecular HOx </th></tr><br />
<tr><td colspan=4>No quantitative updates.</td></tr><br />
<tr><th colspan=4>Table 1C - Bimolecular NOx </th></tr><br />
<tr><td colspan=4>No quantitative updates.</td></tr><br />
<tr><th colspan=4>Table 1D - Bimolecular Organic</th></tr><br />
<tr><th width="20%">GEOS-Chem Reaction</th><th>v10 (JPL 10-6)</th><th>JPL 15-10</th><th>Comparison</th></tr><br />
<tr><td>MACR + O3 = OH + HO2 + HCOOH + CO + MGLY + CH2O</td><td>1.40E-15*exp(-2100/T)</td><td>1.5e-15*exp(-2110/T)</td><td width="30%">[[File:JPL201510andGCv10_MACRplO3_eq_OHplHO2plHCOOHplCOplMGLYplCH2O.png|200px|thumb|left|JPL201510andGCv10_MACRplO3_eq_OHplHO2plHCOOHplCOplMGLYplCH2O.png]]</td></tr><br />
<tr><td>MVK + O3 = OH + HO2 + HCOOH + CO + ALD2 + MGLY + CH2O</td><td>8.50E-16*exp(-1520/T)</td><td>8.5e-16*exp(-1520/T)</td><td width="30%">[[File:JPL201510andGCv10_MVKplO3_eq_OHplHO2plHCOOHplCOplALD2plMGLYplCH2O.png|200px|thumb|left|JPL201510andGCv10_MVKplO3_eq_OHplHO2plHCOOHplCOplALD2plMGLYplCH2O.png]]</td></tr><br />
<tr><td>MACR + OH = MAO3 + MRO2</td><td>8.0E-12*exp(380/T)</td><td>9.6e-12*exp(360./T)</td><td width="30%">[[File:JPL201510andGCv10_MACRplOH_eq_MAO3plMRO2.png|200px|thumb|left|JPL201510andGCv10_MACRplOH_eq_MAO3plMRO2.png]]</td></tr><br />
<tr><td>MVK + OH = VRO2</td><td>2.6e-12*exp(610/T)</td><td>2.7e-12*exp(580./T)</td><td width="30%">[[File:JPL201510andGCv10_MVKplOH_eq_VRO2.png|200px|thumb|left|JPL201510andGCv10_MVKplOH_eq_VRO2.png]]</td></tr><br />
<tr><td>ISOP + OH = RIO2</td><td>3.1e-11*exp(350/T)</td><td>3.0e-11*exp(360./T)</td><td width="30%">[[File:JPL201510andGCv10_ISOPplOH_eq_RIO2.png|200px|thumb|left|JPL201510andGCv10_ISOPplOH_eq_RIO2.png]]</td></tr><br />
<tr><td>MACR + NO3 = MAN2</td><td>2.30e-15</td><td>3.4e-15</td><td width="30%">[[File:JPL201510andGCv10_MACRplNO3_eq_MAN2.png|200px|thumb|left|JPL201510andGCv10_MACRplNO3_eq_MAN2.png]]</td></tr><br />
<tr><td>ISOP + NO3 = INO2</td><td>3.3E-12*exp(-450/T)</td><td>3.5e-12*exp(-450/T)</td><td width="30%">[[File:JPL201510andGCv10_ISOPplNO3_eq_INO2.png|200px|thumb|left|JPL201510andGCv10_ISOPplNO3_eq_INO2.png]]</td></tr><br />
<tr><th colspan=4>Table 1F - Bimolecular ClOx </th></tr><br />
<tr><td colspan=4>Non CFC/HCFC ClOx needs review. (volunteer by putting your name here)</td></tr><br />
<tr><td>OH + HCFC22 = Cl + H2O</td><td>1.05E-12*exp(-1600./T)</td><td>9.2e-13*exp(-1560./T)</td><td width="30%">[[File:JPL201510andGCv10_OHplHCFC22_eq_ClplH2O.png|200px|thumb|left|JPL201510andGCv10_OHplHCFC22_eq_ClplH2O.png]]</td></tr><br />
**PNC://anaconda/lib/python3.5/site-packages/matplotlib/pyplot.py:516:RuntimeWarning:<br />
More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).<br />
<tr><td>OH + HCFC123 = Cl + H2O</td><td>6.30E-13*exp(-850./T)</td><td>7.4e-13*exp(-900./T)</td><td width="30%">[[File:JPL201510andGCv10_OHplHCFC123_eq_ClplH2O.png|200px|thumb|left|JPL201510andGCv10_OHplHCFC123_eq_ClplH2O.png]]</td></tr><br />
<tr><th colspan=4>Table 1G - Bimolecular BrOx </th></tr><br />
<tr><td colspan=4>Needs review. (volunteer by putting your name here)</td></tr><br />
<tr><th colspan=4>Table 1H - Bimolecular IOx </th></tr><br />
<tr><td colspan=4>Needs review. (volunteer by putting your name here)</td></tr><br />
<tr><th colspan=4>Table 1I - Bimolecular SOx </th></tr><br />
<tr><td colspan=4>Needs review. (volunteer by putting your name here)</td></tr><br />
<tr><th colspan=4>Table 2-1 - Termolecular</th></tr><br />
<tr><th width="20%">GEOS-Chem Reaction</th><th>v10 (JPL 10-6)</th><th>JPL 15-10</th><th>Comparison</th></tr><br />
<tr><td>HO2 + NO2 + M = HNO4</td><td>GP(A0 = 2.e-31, B0 = 3.4, A1 = 2.9e-12, B1 = 1.1)</td><td>GP(A0 = 1.9e-31, B0 = 3.4, A1 = 4e-12, B1 = 0.3)</td><td width="30%">[[File:JPL201510andGCv10_HO2plNO2plM_eq_HNO4.png|200px|thumb|left|JPL201510andGCv10_HO2plNO2plM_eq_HNO4.png]]</td></tr><br />
<tr><td>NO2 + NO3 + M = N2O5</td><td>GP(A0 = 2.00E-30, B0 = 4.4E+00, A1 = 1.40E-12, B1 = 7.0E-01)</td><td>GP(A0 = 2.4e-30, B0 = 3., A1 = 1.6e-12, B1 = -0.1)</td><td width="30%">[[File:JPL201510andGCv10_NO2plNO3plM_eq_N2O5.png|200px|thumb|left|JPL201510andGCv10_NO2plNO3plM_eq_N2O5.png]]</td></tr><br />
<tr><td>OH + CO + M = H + CO2</td><td>GY(A0 = 5.9e-33, B0 = 1.4e0, A1 = 1.1e-12, B1 = -1.3e0, A2 = 1.5e-13, B2 = -0.6e0, A3 = 2.1e09, B3 = -6.1e0)</td><td>GY(A0 = 5.9e-33, B0 = 1., A1 = 1.1e-12, B1 = -1.3e0, A2 = 1.5e-13, B2 = 0., A3 = 2.1e09, B3 = -6.1e0)</td><td width="30%">[[File:JPL201510andGCv10_OHplCOplM_eq_HplCO2.png|200px|thumb|left|JPL201510andGCv10_OHplCOplM_eq_HplCO2.png]]</td></tr><br />
<tr><td>OH + PRPE + M = PO2</td><td>GP(A0 = 8.00E-27, B0 = 3.5E+00, A1 = 3.00E-11, B1 = 1.0E+00)</td><td>GP(A0 = 4.6e-27, B0 = 4., A1 = 2.6e-11, B1 = 1.3)</td><td width="30%">[[File:JPL201510andGCv10_OHplPRPEplM_eq_PO2.png|200px|thumb|left|JPL201510andGCv10_OHplPRPEplM_eq_PO2.png]]</td></tr><br />
<tr><td>ClO + ClO + M = Cl2O2</td><td>GP(1.60E-32, 4.5E+00 , 3.00E-12, 2.0E+00)</td><td>GP(A0 = 1.9e-32, B0 = 3.6, A1 = 3.7e-12, B1 = 1.6)</td><td width="30%">[[File:JPL201510andGCv10_ClOplClOplM_eq_Cl2O2.png|200px|thumb|left|JPL201510andGCv10_ClOplClOplM_eq_Cl2O2.png]]</td></tr><br />
<tr><th colspan=4>Table 3-1</th></tr><br />
<tr><td>N2O5 = NO2 + NO3</td><td>GP(A0 = 7.40E-04, B0 = 4.4E+00, C0 = -11000., A1 = 5.18E+14, B1 = 7.0E-01, C1 = -11000.)</td><td>GP(A0 = 2.4e-30/5.8e-27, B0 = 3., C0 = -10840, A1 = 1.6e-12/5.8e-27, B1 = -0.1, C1 = -10840)</td><td width="30%">[[File:JPL201510andGCv10_N2O5_eq_NO2plNO3.png|200px|thumb|left|JPL201510andGCv10_N2O5_eq_NO2plNO3.png]]</td></tr><br />
<tr><td>HNO4 = HO2 + NO2</td><td>GP(A0 = 2.e-31 / 2.1e-27, B0 = 3.4, C0 = -10900., A1 = 2.9e-12 / 2.1e-27, B1 = 1.1, C1 = -10900.)</td><td>GP(A0 = 1.9e-31 / 2.1e-27, B0 = 3.4, C0 = -10900., A1 = 4e-12 / 2.1e-27, B1 = 0.3, C1 = -10900.)</td><td width="30%">[[File:JPL201510andGCv10_HNO4_eq_HO2plNO2.png|200px|thumb|left|JPL201510andGCv10_HNO4_eq_HO2plNO2.png]]</td></tr><br />
<tr><td colspan=4>1. Termolecular rates coefficients are evaluated from -0.5km to 11km in the 1976 US Std Atmosphere temperature and pressures</td></tr><br />
<tr><td colspan=4>2. GP is short hand for the GEOS-Chem rate form denoted by P in globchem.dat and corresponding to the JPL termolecular rate defined as k_f([M],T) in Section 2.1</td></tr><br />
<tr><td colspan=4>3. GY is short hand for the GEOS-Chem rate form denoted by Y in globchem.dat and corresponding to the JPL termolecular rate defined as k^{ca}_f([M],T) in Section 2.1</td></tr><br />
</table><br />
<br />
Notes:<br />
<br />
* Skipping CH2OO + ... on 1-93<br />
* Skipping syn-CH3CHOO and anti-CH3CHOO on 1-94<br />
* Skipping FOx reactions<br />
* Skipped ClOx reactions, needs review<br />
* Skipped BrOx reactions, needs review<br />
* Skipped IOx reactions, needs review<br />
* SOx reactions need further consideration perhaps with overlap of Iodine IO and DMS? IO + CH3SCH3 -> products</div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:JPL201510andGCv10_OHplHCFC123_eq_ClplH2O.png&diff=26813File:JPL201510andGCv10 OHplHCFC123 eq ClplH2O.png2016-05-13T21:03:32Z<p>Barronh: </p>
<hr />
<div></div>Barronhhttps://wiki.seas.harvard.edu/geos-chem/index.php?title=File:JPL201510andGCv10_OHplHCFC22_eq_ClplH2O.png&diff=26812File:JPL201510andGCv10 OHplHCFC22 eq ClplH2O.png2016-05-13T21:02:47Z<p>Barronh: </p>
<hr />
<div></div>Barronh