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== Description ==
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__FORCETOC__
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'''''[[POPs simulation|Previous]] | [[Tagged O3 simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''
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#[[GEOS-Chem chemistry mechanisms|Simulations using KPP-built mechanisms]]
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#[[Aerosol-only simulation]]
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#[[CH4 simulation]]
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#[[CO2 simulation]]
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#[[Mercury|Hg simulation]]
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#[[POPs simulation]]
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#<span style="color:blue">'''Tagged CO simulation'''</span>
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#[[Tagged O3 simulation]]
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#[[TransportTracers simulation]]
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On this page, we describe the GEOS-Chem tagged CO simulation.
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== Overview ==
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=== Description ===
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The tagged CO simulation is an offline simulation that calculates CO concentrations only. It uses monthly mean OH concentrations archived from a previous full-chemistry simulation (more on that below). Because the simulation is linear, CO can be “tagged” by its source region/type. The regions and types used can be adapted to address different problems with a few simple code modifications.
 
The tagged CO simulation is an offline simulation that calculates CO concentrations only. It uses monthly mean OH concentrations archived from a previous full-chemistry simulation (more on that below). Because the simulation is linear, CO can be “tagged” by its source region/type. The regions and types used can be adapted to address different problems with a few simple code modifications.
  
== Assumptions ==
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=== Assumptions ===
1. The tagged CO simulation doesn’t include direct emissions of volatile organic compounds (VOCs), so CO sources are scaled to account for co-emitted VOCs. Fossil fuel and biofuel emissions are scaled by 19% and biomass burning emissions are scaled by 11%. More information is given in Duncan et al. (2007).<br><br>
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#The tagged CO simulation doesn’t include direct emissions of volatile organic compounds (VOCs), so CO sources are scaled to account for co-emitted VOCs. Fossil fuel and biofuel emissions are scaled by 19% and biomass burning emissions are scaled by 11%. More information is given in Duncan et al. (2007). See note below!<br><br>
2. Biogenic VOCs:<br>
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#Biogenic VOCs:<br>
  a. Isoprene: Yield of CO from isoprene is assumed to be 30% based on Miyoshi et al. (1994). Isoprene yield can also be computed as a<br>    function of NOx concentration by setting ALPHA_ISOP_FROM_NOX = .TRUE. in CHEM_TAGGED_CO, but this is not the default behavior.
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## Isoprene: Yield of CO from isoprene is assumed to be 30% based on Miyoshi et al. (1994). Isoprene yield can also be computed as a function of NOx concentration by setting <tt>ALPHA_ISOP_FROM_NOX = .TRUE.</tt> in CHEM_TAGGED_CO, but this is not the default behavior.
  b. Methanol: The CO flux from methanol is scaled to the isoprene flux
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##Methanol: The CO flux from methanol is scaled to the isoprene flux
  c. Monoterpene: Yield of CO from monoterpenes is assumed to be 20% based on Hatakeyama et al. (1991) and Vinckier et al. (1998).
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##Monoterpene: Yield of CO from monoterpenes is assumed to be 20% based on Hatakeyama et al. (1991) and Vinckier et al. (1998).
  d. Acetone: Yield of CO from acetone is assumed to be 2/3 and accounts for acetone loss from reaction with OH and photolysis.
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##Acetone: Yield of CO from acetone is assumed to be 2/3 and accounts for acetone loss from reaction with OH and photolysis.<br><br>
3. OH concentrations are taken from a previously run full chemistry simulation. The default is from a much earlier version of the model, when OH was thought to be more realistic. The standard code uses OH from version 5-07-08, with GEOS3 meteorology.<br><br>
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#OH concentrations are taken from a previously run full chemistry simulation. The default is from a much earlier version of the model, when OH was thought to be more realistic. The standard code uses OH from version 5-07-08, with GEOS3 meteorology.<br><br>
4. Methane concentrations are calculated based on measurements from the NOAA Global Monitoring Division network and are assumed constant over four latitudinal bands (30-90S, 0-30S, 0-30N, 30-90N). Yield is assumed to be one molecule CO per molecule CH4.<br><br>
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#Methane concentrations are calculated based on measurements from the NOAA Global Monitoring Division network and are assumed constant over four latitudinal bands (30-90S, 0-30S, 0-30N, 30-90N). Yield is assumed to be one molecule CO per molecule CH4.
  
== Standard Tracers ==
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<blockquote>NOTE: As described in bullet point 1 above, make sure that your <tt>HEMCO_Config.rc</tt> file contains these scale factors: </blockquote>
In a standard run, there are 17 tracers (see input.geos below).
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Tracer 1 (CO) is total CO; this is the sum of CO from all sources.
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      52 COPROD_FOSSIL  1.19 - - - xy 1 1
  Tracers 2-5 are CO from fossil fuel emissions in:
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      53 COPROD_BIOFUEL  1.189 - - - xy 1 1
  -COus: North America (172.5-17.5W, 24-88N)
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      54 COPROD_BIOMASS  1.11 - - - xy 1 1
  -COeur: Europe (17.5W-72.5E, 36-45N and 17.5W-172.5E, 45-88N)
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  -COasia: Asia (70-152.5E, 8-45N)
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  -COoth: everywhere else.
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  Tracers 6-11 are CO from biomass burning emissions in:
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  -CObbam: South America (112.5-32.5W, 56S-24N)
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  -CObbaf: Africa (17.5W-70E, 48S-36N)
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  -CObbas: Southeast Asia (70-152.5E, 8-45N)
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  -CObboc: Oceania (70-170E, 90S-8N)
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  -CObbeu: Europe (17.5W-72.5E, 36-45N and 17.5W-172.5E, 45-88N)
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  -CObbna: Everywhere else (basically North America)
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Tracer 12 (COch4) is CO produced from methane.
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Tracer 13 (CObiof) is CO from biofuel emissions (except if you are using the Streets inventory over Asia, where biofuel and fossil <br> fuel emissions are combined).
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Tracers 14-17 are CO produced from the following volatile organic compounds (in order): isoprene (COisop), monoterpenes (COmono), methanol <br>(COmeoh), and acetone (COacet).
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The regional definitions used for the fossil fuel and biomass burning tracers can be changed in DEFINE_FF_REGIONS and DEFINE_BB_REGIONS, respectively. The biofuel tracer can be removed by commenting lines in EMISS_TAGGED_CO (look for LSPLIT and tracer #13). The methane and VOC tracers can be removed by commenting lines in CHEM_TAGGED_CO (look for LSPLIT). Note that if you change the tracers you will also need to make the appropriate changes in your input.geos and restart files.<br>
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<blockquote>(i.e. fossil fuel/biofuel increased by ~19% and biomass by 11%). The <tt>HEMCO_Config.rc</tt> file that shipped with GEOS-Chem v11-01 contain incorrect values for these scale factors. This will be fixed for v11-02.</blockquote>
  
== Practicalities ==
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=== Standard Tracers ===
Tagged CO is simulation type 7. For tagged CO run with standard tracers, the input.geos should look like this:
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In a standard run, there are 17 tracers.
%%% TRACER MENU %%%    :
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Type of simulation      : 7
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Number of Tracers      : 17
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Tracer Entries -------> : TR#  Name    g/mole Tracer Members; () = emitted 
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Tracer #1              : 1    CO      28.0  (CO)
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Tracer #2              : 2    COus    28.0 
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Tracer #3              : 3    COeur  28.0 
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Tracer #4              : 4    COasia  28.0 
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Tracer #5              : 5    COoth  28.0 
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Tracer #6              : 6    CObbam  28.0 
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Tracer #7              : 7    CObbaf  28.0 
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Tracer #8              : 8    CObbas  28.0 
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Tracer #9              : 9    CObboc  28.0 
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Tracer #10              : 10    CObbeu  28.0 
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Tracer #11              : 11    CObbna  28.0 
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Tracer #12              : 12    COch4  28.0 
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Tracer #13              : 13    CObiof  28.0 
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Tracer #14              : 14    COisop  28.0 
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Tracer #15              : 15    COmono  28.0 
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Tracer #16              : 16    COmeoh  28.0 
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Tracer #17              : 17    COacet  28.0
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== Recent tagged CO updates ==
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{| border=1 cellspacing=0 cellpadding=5
1. Updated CO+OH rate constant to JPL2006 (Jenny Fisher): standard in v8-02-03<br>
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|-bgcolor="#CCCCCC"
2. Optional use of MEGAN biogenic emissions added (Prasad Kasibhatla and Jenny Fisher): standard in v8-02-03
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!width="30px"|#
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!width="75px"|Tracer
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!width="400px"|Description
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!width="300px"|Region
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|-valign="top
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|1  || CO      || Total CO from all sources                          || global
  
== Tagged CO development projects ==
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|-valign="top"
1. Flexible region masks (Dylan Jones and Prasad Kasibhatla)
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|2  || COus    || Anthropogenic + Biofuel CO emitted over the USA    || 172.5&deg;W - 17.0&deg;W; 24.0&deg;N - 88.0&deg;N
  
== Adjoint capabilities ==
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|-valign="top"
Tagged CO is one of the simulations supported in the adjoint code. See adjoint wiki page for more details.
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|3  || COeur  || Anthropogenic + Biofuel CO emitted over Europe      || 17.5&deg;W - 72.5&deg;E; 36.0&deg;N - 45.0&deg;N and<br>17.5&deg;W - 172.5&deg;E; 45.0&deg;N - 88.0&deg;N
http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_Adjoint
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== More Information ==
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|-valign="top"
For more information, see the GEOS-Chem manual pages about tagged CO:
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|4  || COasia  || Anthropogenic + Biofuel CO emitted over the SE Asia || 70.0&deg;E - 152.0&deg;E; 8.0&deg;N - 45.0&deg;N
  http://acmg.seas.harvard.edu/geos/doc/man/chapter_6.html#6.1.4
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  http://acmg.seas.harvard.edu/geos/doc/man/files/input.geos.tagco
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|-valign="top"
  http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html#A1.7
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|5  || COoth  || Anthropogenic + Biofuel CO emitted everywhere else  || rest of world
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|-valign="top"
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|6  || CObbam  || Biomass burning CO emitted over South America      || 112.5&deg;W - 32.5&deg;W; 56&deg;S - 24&deg;N
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|-valign="top"
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|7  || CObbaf  || Biomass burning CO emitted over Africa              || 17.5&deg;W -70.0&deg;E; 48.0&deg;S - 36.0&deg;N
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|-valign="top"
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|8  || CObbas  || Biomass burning CO emitted over SE Asia            || 70.0&deg;E - 152.5&deg;E; 8.0&deg;N - 45.0&deg;N
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|-valign="top"
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|9  || CObboc  || Biomass burning CO emitted over Oceania            || 70.0&deg;E - 170.0&deg;E;  90.0&deg;S - 8.0&deg;N
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|-valign="top"
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|10 || CObbeu  || Biomass burning CO emitted over SE Asia            || 17.5&deg;W - 72.5&deg;E; 36.0&deg;N - 45.0&deg;N and<br>17.5&deg;W - 172.5&deg;E; 45.0&deg;N - 88.0&deg;N
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|-valign="top"
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|11 || CObboth || Biomass burning CO emitted everywhere else          || rest of world
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|-valign="top"
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|12 || COch4  || CO chemically produced from methane                || global
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|-valign="top"
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|13 || CObbiof || CO produced from biofuel emissions                  || global<br>NOTE: This tracer is now obsolete, since via HEMCO we now lump anthropogenic and biofuel emissions together.  Some inventories cannot easily separate out biofuels from anthropogenic emissions, so the best thing to do is to lump biofuels in with anthropogenic emissions.
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|-valign="top"
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|14 || COisop || CO chemically produced from isoprene                || global
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|-valign="top"
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|15 || COmono || CO chemically produced CO from monoterpenes          || global
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|-valign="top"
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|16 || COmeoh || CO chemically produced from methanol                || global
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|-valign="top"
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|17 || COacet || CO chemically produced from acetone                  || global
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|}
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The regional definitions used for the fossil fuel and biomass burning tracers can be changed by modifying the HEMCO mask file:
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ExtData/HEMCO/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc
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The methane and VOC tracers can be removed by commenting lines in CHEM_TAGGED_CO (look for LSPLIT). Note that if you change the tracers you will also need to make the appropriate changes in your <tt>input.geos</tt> and restart files.
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=== Notes about using HEMCO with the tagged CO simulation ===
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In [[GEOS-Chem v11-01]] and higher versions, the HEMCO handles all emissions for the tagged CO simulation.  You should be aware of the following:
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#<p>HEMCO by default uses a binary masking (either 0 or 1).  If a grid box straddles the mask boundary, then HEMCO will count the entire box as part of the masked region. You can disable this behavior by setting <tt>Mask fractions: true</tt> in the SETTINGS section of the <tt>HEMCO_Config.rc</tt> file. But this may lead to some further discrepancies. It may be best to use the binary masking but use as fine resolution mask files e.g. 0.5 x 0.5) as possible.</p>
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#<p>For each file that is read from disk, we add underneath that file listing an entry to apply a regional mask to the total emissions, [[#The HEMCO_Config.rc file|as shown in the previous section]].</p>
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#<p>The Yevich & Logan biofuel emissions are added into the same CATEGORY & HIERARCHY as the EDGAR anthropogenic emissions. Because other inventories often do not separate biofuels from anthropogenic emisisons, it makes sense to lump them together.  This will make it easier for the tagged tracers to sum together.</p>
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#<p>At present, there is no way to apply regional masks to emissions that are computed from the GFED or FINN biomass burning emissions (which are implemented as HEMCO extensions). For this reason, we the default biomass burning emissions is the QFED inventory (which is simply read from disk, and thus can be separated into tagged tracers with regional masks, [[#The HEMCO_Config.rc file|as shown in the previous section]])Perhaps in a future HEMCO version we will be able to apply regional masks to extension-computed emissions.</p>
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#*<p>If you would like to use either GFED or FINN biomass emissions with the tagged CO simulation, then we recommend that you use the HEMCO standalone code to archive the total CO emissions for a given set of met fields (e.g. GEOS-FP, MERRA) and years. Then you can following the example of QFED ([[#The HEMCO_Config.rc file|shown above]]) to apply the regional masks to the total CO biomass emissions.</p>
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#<p>We have removed the <tt>+LinStratChem+</tt> block around the <tt>GMI_PROD_CO</tt> and <tt>GMI_LOSS_CO</tt>.  For full-chemistry simulations, <tt>+LinStratChem+</tt> is automatically toggled when stratospheric chemistry is turned on in <tt>input.geos</tt>But the tagged CO always reads the <tt>GMI_PROD_CO</tt> and <tt>GMI_LOSS_CO</tt> fields directly from HEMCO and applies them without using the normal stratospheric chemistry module. ithout having to invoke the strat chem module.<p>
  
 
== Studies that used Tagged CO simulation ==
 
== Studies that used Tagged CO simulation ==
1. Palmer, P. I., D. J. Jacob, D. B. A. Jones, C. L. Heald, R. M. Yantosca, J. A. Logan, G. W. Sachse, and D. G. Streets (2003), Inverting for emissions of carbon monoxide from Asia using aircraft observations over the western Pacific, Journal of Geophysical Research, 108(D21), 4180, doi: 10.1029/2003JD003397.<br>
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#Palmer, P. I., D. J. Jacob, D. B. A. Jones, C. L. Heald, R. M. Yantosca, J. A. Logan, G. W. Sachse, and D. G. Streets (2003), Inverting for emissions of carbon monoxide from Asia using aircraft observations over the western Pacific, Journal of Geophysical Research, 108(D21), 4180, doi: 10.1029/2003JD003397.
2. Heald, C. L., D. J. Jacob, D. B. A. Jones, P. I. Palmer, J. A. Logan, D. G. Streets, G. W. Sachse, J. C. Gille, R. N. Hoffman, and T. Nehrkorn (2004), Comparative inverse analysis of satellite (MOPITT) and aircraft (TRACE-P) observations to estimate Asian sources of carbon monoxide, Journal of Geophysical Research, 109(D15S04), doi: 10.1029/2004JD005185.<br>
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#Heald, C. L., D. J. Jacob, D. B. A. Jones, P. I. Palmer, J. A. Logan, D. G. Streets, G. W. Sachse, J. C. Gille, R. N. Hoffman, and T. Nehrkorn (2004), Comparative inverse analysis of satellite (MOPITT) and aircraft (TRACE-P) observations to estimate Asian sources of carbon monoxide, Journal of Geophysical Research, 109(D15S04), doi: 10.1029/2004JD005185.
3. Arellano, A. F., P. S. Kasibhatla, L. Giglio, G. R. van der Werf, and J. T. Randerson (2004), Top-down estimates of global CO sources using MOPITT measurements, Geophysical Research Letters, 31(L01104), doi: 10.1029/2003GL018609.<br>
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#Arellano, A. F., P. S. Kasibhatla, L. Giglio, G. R. van der Werf, and J. T. Randerson (2004), ''Top-down estimates of global CO sources using MOPITT measurements'', <u>Geophysical Research Letters</u>, '''31'''(L01104), doi: 10.1029/2003GL018609.
4. Arellano, A. F., P. S. Kasibhatla, L. Giglio, G. R. van der Werf, J. T. Randerson, and G. J. Collatz (2006), Time-dependent inversion estimates of global biomass-burning CO emissions using Measurement of Pollution in the Troposphere (MOPITT) measurements, Journal of Geophysical Research, 111(D09303), doi: 10.1029/2005JD006613.<br>
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#Arellano, A. F., P. S. Kasibhatla, L. Giglio, G. R. van der Werf, J. T. Randerson, and G. J. Collatz (2006), ''Time-dependent inversion estimates of global biomass-burning CO emissions using Measurement of Pollution in the Troposphere (MOPITT) measurements'', <u>J. Geophys. Res.</u>, '''111'''(D09303), doi: 10.1029/2005JD006613.
5. Duncan, B. N., Logan, J. A., Bey, I., Megretskaia, I. A., Yantosca, R. M., Novelli, P. C., Jones, N. B., and Rinsland, C. P.: Global budget of CO, 1988–1997: Source estimates and validation with a global model, J. Geophys. Res., 112, D22301, doi:10.1029/2007JD008459, 2007.<br>
+
#Duncan, B. N., Logan, J. A., Bey, I., Megretskaia, I. A., Yantosca, R. M., Novelli, P. C., Jones, N. B., and Rinsland, C. P., ''Global budget of CO, 1988–1997: Source estimates and validation with a global model'', <u>J. Geophys. Res.</u>, '''112''', D22301, doi:10.1029/2007JD008459, 2007.
6. Duncan, B. N., J. A. Logan, I. Bey, I. A. Megretskaia, R. M. Yantosca, P. C. Novelli, N. B. Jones, and C. P. Rinsland (2008), Model analysis of the factors regulating the trends and variability of carbon monoxide between 1988 and 1997, Atmos. Chem. Phys, 8, 7389-3403.<br>
+
#Duncan, B. N., J. A. Logan, I. Bey, I. A. Megretskaia, R. M. Yantosca, P. C. Novelli, N. B. Jones, and C. P. Rinsland (2008), ''Model analysis of the factors regulating the trends and variability of carbon monoxide between 1988 and 1997'', <u>Atmos. Chem. Phys</u>, '''8''', 7389-3403.
7. Kopacz, M., D. J. Jacob, D. K. Henze, C. L. Heald, D. G. Streets, and Q. Zhang (2009), Comparison of adjoint and analytical Bayesian inversion methods for constraining Asian sources of carbon monoxide using satellite (MOPITT) measurements of CO columns, Journal Of Geophysical Research, 114(D04305), doi: 10.1029/2007JD009264. <br>
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#Kopacz, M., D. J. Jacob, D. K. Henze, C. L. Heald, D. G. Streets, and Q. Zhang (2009), ''Comparison of adjoint and analytical Bayesian inversion methods for constraining Asian sources of carbon monoxide using satellite (MOPITT) measurements of CO columns'', <u>J. Geophys. Res.</u>, '''114'''(D04305), doi: 10.1029/2007JD009264.  
8. Fisher, J.A., D.J. Jacob, M.T. Purdy, M. Kopacz, P. Le Sager, C. Carouge, C.D. Holmes, R.M. Yantosca, R.L. Batchelor, K. Strong, G.S. Diskin, H.E. Fuelberg, J.S. Holloway, E.J. Hyer, W.W. McMillan, J. Warner, D.G. Streets, Q. Zhang, Y. Wang, S. Wu, Source attribution and interannual variability of Arctic pollution in spring constrained by aircraft (ARCTAS, ARCPAC) and satellite (AIRS) observations of carbon monoxide, Atmospheric Chememistry and Physics Discussions, (9) 19035-19080, 2009 <br> 
+
#Fisher, J.A., D.J. Jacob, M.T. Purdy, M. Kopacz, P. Le Sager, C. Carouge, C.D. Holmes, R.M. Yantosca, R.L. Batchelor, K. Strong, G.S. Diskin, H.E. Fuelberg, J.S. Holloway, E.J. Hyer, W.W. McMillan, J. Warner, D.G. Streets, Q. Zhang, Y. Wang, S. Wu, ''Source attribution and interannual variability of Arctic pollution in spring constrained by aircraft (ARCTAS, ARCPAC) and satellite (AIRS) observations of carbon monoxide'', <u>Atm. Chem. Phys. Discuss.</u>, '''9''', 19035-19080, 2009.
9. Kopacz, M., D.J. Jacob, J.A. Fisher, J.A. Logan, L. Zhang, I.A. Megretskaia, R.M. Yantosca, K. Singh, D.K. Henze, J.P. Burrows, M. Buchwitz, I. Khlystova, W.W. McMillan, J.C. Gille, D.P. Edwards, A. Eldering, V. Thouret, P. Nedelec, Global estimates of CO sources with high resolution by adjoint inversion of multiple satellite datasets (MOPITT, AIRS, SCIAMACHY and TES), Atmospheric Chemistry and Physics Discussions, (9) 19967-20018, 2009 <br>
+
#Kopacz, M., D.J. Jacob, J.A. Fisher, J.A. Logan, L. Zhang, I.A. Megretskaia, R.M. Yantosca, K. Singh, D.K. Henze, J.P. Burrows, M. Buchwitz, I. Khlystova, W.W. McMillan, J.C. Gille, D.P. Edwards, A. Eldering, V. Thouret, P. Nedelec, ''Global estimates of CO sources with high resolution by adjoint inversion of multiple satellite datasets (MOPITT, AIRS, SCIAMACHY and TES)'', <u>Atm. Chem. Phys. Discuss.</u>, '''9''', 19967-20018, 2009.
  
 
== References ==
 
== References ==
1. Duncan, B. N., Logan, J. A., Bey, I., Megretskaia, I. A., Yantosca, R. M., Novelli, P. C., Jones, N. B., and Rinsland, C. P.: Global budget of CO, 1988–1997: Source estimates and validation with a global model, J. Geophys. Res., 112, D22301, doi:10.1029/2007JD008459, 2007.<br>
+
#Duncan, B. N., Logan, J. A., Bey, I., Megretskaia, I. A., Yantosca, R. M., Novelli, P. C., Jones, N. B., and Rinsland, C. P., ''Global budget of CO, 1988–1997: Source estimates and validation with a global model'', <u>J. Geophys. Res.</u>, '''112''', D22301, doi:10.1029/2007JD008459, 2007.
2. Hatakeyama, S., Izumi, K., Fukuyama, T., Akimoto, H. Washida, N.: Reactions of OH with alpha-pinene and beta-pinene in air: Estimate of global CO production from the atmospheric oxidation of terpenes, J. Geophys. Res., 96(D1), 947-958, 1991.<br>
+
#Hatakeyama, S., Izumi, K., Fukuyama, T., Akimoto, H. Washida, N., ''Reactions of OH with alpha-pinene and beta-pinene in air: Estimate of global CO production from the atmospheric oxidation of terpenes'', <u>J. Geophys. Res.</u>, '''96'''(D1), 947-958, 1991.
3. Miyoshi, A., Hatakeyama, S., Washida, N.: OH radical-initiated photooxidation of isoprene: An estimate of global CO production, J. Geophs. Res., 99(D9), 18779-18787, 1994.<br>
+
#Miyoshi, A., Hatakeyama, S., Washida, N., ''OH radical-initiated photooxidation of isoprene: An estimate of global CO production'', <u>J. Geophs. Res.</u>, '''99'''(D9), 18779-18787, 1994.
4. Vinckier, C., Compernolle, F., Saleh, A. M., Van Hoof, N., Van Hees, I.: Product yields of the alpha -pinene reaction with hydroxyl radicals and the implication on the global emission of trace compounds in the atmosphere, Fresenius Env. Bull., 7(5-6), 361-368, 1998.<br>
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#Vinckier, C., Compernolle, F., Saleh, A. M., Van Hoof, N., Van Hees, I., ''Product yields of the alpha -pinene reaction with hydroxyl radicals and the implication on the global emission of trace compounds in the atmosphere'', <u>Fresenius Env. Bull.</u>, '''7'''(5-6), 361-368, 1998.
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'''''[[POPs simulation|Previous]] | [[Tagged O3 simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''

Latest revision as of 17:33, 24 October 2023

Previous | Next | Guide to GEOS-Chem simulations

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


On this page, we describe the GEOS-Chem tagged CO simulation.

Overview

Description

The tagged CO simulation is an offline simulation that calculates CO concentrations only. It uses monthly mean OH concentrations archived from a previous full-chemistry simulation (more on that below). Because the simulation is linear, CO can be “tagged” by its source region/type. The regions and types used can be adapted to address different problems with a few simple code modifications.

Assumptions

  1. The tagged CO simulation doesn’t include direct emissions of volatile organic compounds (VOCs), so CO sources are scaled to account for co-emitted VOCs. Fossil fuel and biofuel emissions are scaled by 19% and biomass burning emissions are scaled by 11%. More information is given in Duncan et al. (2007). See note below!

  2. Biogenic VOCs:
    1. Isoprene: Yield of CO from isoprene is assumed to be 30% based on Miyoshi et al. (1994). Isoprene yield can also be computed as a function of NOx concentration by setting ALPHA_ISOP_FROM_NOX = .TRUE. in CHEM_TAGGED_CO, but this is not the default behavior.
    2. Methanol: The CO flux from methanol is scaled to the isoprene flux
    3. Monoterpene: Yield of CO from monoterpenes is assumed to be 20% based on Hatakeyama et al. (1991) and Vinckier et al. (1998).
    4. Acetone: Yield of CO from acetone is assumed to be 2/3 and accounts for acetone loss from reaction with OH and photolysis.

  3. OH concentrations are taken from a previously run full chemistry simulation. The default is from a much earlier version of the model, when OH was thought to be more realistic. The standard code uses OH from version 5-07-08, with GEOS3 meteorology.

  4. Methane concentrations are calculated based on measurements from the NOAA Global Monitoring Division network and are assumed constant over four latitudinal bands (30-90S, 0-30S, 0-30N, 30-90N). Yield is assumed to be one molecule CO per molecule CH4.
NOTE: As described in bullet point 1 above, make sure that your HEMCO_Config.rc file contains these scale factors:
     52 COPROD_FOSSIL   1.19  - - - xy 1 1
     53 COPROD_BIOFUEL  1.189 - - - xy 1 1
     54 COPROD_BIOMASS  1.11  - - - xy 1 1
(i.e. fossil fuel/biofuel increased by ~19% and biomass by 11%). The HEMCO_Config.rc file that shipped with GEOS-Chem v11-01 contain incorrect values for these scale factors. This will be fixed for v11-02.

Standard Tracers

In a standard run, there are 17 tracers.

# Tracer Description Region
1 CO Total CO from all sources global
2 COus Anthropogenic + Biofuel CO emitted over the USA 172.5°W - 17.0°W; 24.0°N - 88.0°N
3 COeur Anthropogenic + Biofuel CO emitted over Europe 17.5°W - 72.5°E; 36.0°N - 45.0°N and
17.5°W - 172.5°E; 45.0°N - 88.0°N
4 COasia Anthropogenic + Biofuel CO emitted over the SE Asia 70.0°E - 152.0°E; 8.0°N - 45.0°N
5 COoth Anthropogenic + Biofuel CO emitted everywhere else rest of world
6 CObbam Biomass burning CO emitted over South America 112.5°W - 32.5°W; 56°S - 24°N
7 CObbaf Biomass burning CO emitted over Africa 17.5°W -70.0°E; 48.0°S - 36.0°N
8 CObbas Biomass burning CO emitted over SE Asia 70.0°E - 152.5°E; 8.0°N - 45.0°N
9 CObboc Biomass burning CO emitted over Oceania 70.0°E - 170.0°E; 90.0°S - 8.0°N
10 CObbeu Biomass burning CO emitted over SE Asia 17.5°W - 72.5°E; 36.0°N - 45.0°N and
17.5°W - 172.5°E; 45.0°N - 88.0°N
11 CObboth Biomass burning CO emitted everywhere else rest of world
12 COch4 CO chemically produced from methane global
13 CObbiof CO produced from biofuel emissions global
NOTE: This tracer is now obsolete, since via HEMCO we now lump anthropogenic and biofuel emissions together. Some inventories cannot easily separate out biofuels from anthropogenic emissions, so the best thing to do is to lump biofuels in with anthropogenic emissions.
14 COisop CO chemically produced from isoprene global
15 COmono CO chemically produced CO from monoterpenes global
16 COmeoh CO chemically produced from methanol global
17 COacet CO chemically produced from acetone global

The regional definitions used for the fossil fuel and biomass burning tracers can be changed by modifying the HEMCO mask file:

ExtData/HEMCO/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc

The methane and VOC tracers can be removed by commenting lines in CHEM_TAGGED_CO (look for LSPLIT). Note that if you change the tracers you will also need to make the appropriate changes in your input.geos and restart files.

Notes about using HEMCO with the tagged CO simulation

In GEOS-Chem v11-01 and higher versions, the HEMCO handles all emissions for the tagged CO simulation. You should be aware of the following:

  1. HEMCO by default uses a binary masking (either 0 or 1). If a grid box straddles the mask boundary, then HEMCO will count the entire box as part of the masked region. You can disable this behavior by setting Mask fractions: true in the SETTINGS section of the HEMCO_Config.rc file. But this may lead to some further discrepancies. It may be best to use the binary masking but use as fine resolution mask files e.g. 0.5 x 0.5) as possible.

  2. For each file that is read from disk, we add underneath that file listing an entry to apply a regional mask to the total emissions, as shown in the previous section.

  3. The Yevich & Logan biofuel emissions are added into the same CATEGORY & HIERARCHY as the EDGAR anthropogenic emissions. Because other inventories often do not separate biofuels from anthropogenic emisisons, it makes sense to lump them together. This will make it easier for the tagged tracers to sum together.

  4. At present, there is no way to apply regional masks to emissions that are computed from the GFED or FINN biomass burning emissions (which are implemented as HEMCO extensions). For this reason, we the default biomass burning emissions is the QFED inventory (which is simply read from disk, and thus can be separated into tagged tracers with regional masks, as shown in the previous section). Perhaps in a future HEMCO version we will be able to apply regional masks to extension-computed emissions.

    • If you would like to use either GFED or FINN biomass emissions with the tagged CO simulation, then we recommend that you use the HEMCO standalone code to archive the total CO emissions for a given set of met fields (e.g. GEOS-FP, MERRA) and years. Then you can following the example of QFED (shown above) to apply the regional masks to the total CO biomass emissions.

  5. We have removed the +LinStratChem+ block around the GMI_PROD_CO and GMI_LOSS_CO. For full-chemistry simulations, +LinStratChem+ is automatically toggled when stratospheric chemistry is turned on in input.geos. But the tagged CO always reads the GMI_PROD_CO and GMI_LOSS_CO fields directly from HEMCO and applies them without using the normal stratospheric chemistry module. ithout having to invoke the strat chem module.<p>

Studies that used Tagged CO simulation

  1. Palmer, P. I., D. J. Jacob, D. B. A. Jones, C. L. Heald, R. M. Yantosca, J. A. Logan, G. W. Sachse, and D. G. Streets (2003), Inverting for emissions of carbon monoxide from Asia using aircraft observations over the western Pacific, Journal of Geophysical Research, 108(D21), 4180, doi: 10.1029/2003JD003397.
  2. Heald, C. L., D. J. Jacob, D. B. A. Jones, P. I. Palmer, J. A. Logan, D. G. Streets, G. W. Sachse, J. C. Gille, R. N. Hoffman, and T. Nehrkorn (2004), Comparative inverse analysis of satellite (MOPITT) and aircraft (TRACE-P) observations to estimate Asian sources of carbon monoxide, Journal of Geophysical Research, 109(D15S04), doi: 10.1029/2004JD005185.
  3. Arellano, A. F., P. S. Kasibhatla, L. Giglio, G. R. van der Werf, and J. T. Randerson (2004), Top-down estimates of global CO sources using MOPITT measurements, Geophysical Research Letters, 31(L01104), doi: 10.1029/2003GL018609.
  4. Arellano, A. F., P. S. Kasibhatla, L. Giglio, G. R. van der Werf, J. T. Randerson, and G. J. Collatz (2006), Time-dependent inversion estimates of global biomass-burning CO emissions using Measurement of Pollution in the Troposphere (MOPITT) measurements, J. Geophys. Res., 111(D09303), doi: 10.1029/2005JD006613.
  5. Duncan, B. N., Logan, J. A., Bey, I., Megretskaia, I. A., Yantosca, R. M., Novelli, P. C., Jones, N. B., and Rinsland, C. P., Global budget of CO, 1988–1997: Source estimates and validation with a global model, J. Geophys. Res., 112, D22301, doi:10.1029/2007JD008459, 2007.
  6. Duncan, B. N., J. A. Logan, I. Bey, I. A. Megretskaia, R. M. Yantosca, P. C. Novelli, N. B. Jones, and C. P. Rinsland (2008), Model analysis of the factors regulating the trends and variability of carbon monoxide between 1988 and 1997, Atmos. Chem. Phys, 8, 7389-3403.
  7. Kopacz, M., D. J. Jacob, D. K. Henze, C. L. Heald, D. G. Streets, and Q. Zhang (2009), Comparison of adjoint and analytical Bayesian inversion methods for constraining Asian sources of carbon monoxide using satellite (MOPITT) measurements of CO columns, J. Geophys. Res., 114(D04305), doi: 10.1029/2007JD009264.
  8. Fisher, J.A., D.J. Jacob, M.T. Purdy, M. Kopacz, P. Le Sager, C. Carouge, C.D. Holmes, R.M. Yantosca, R.L. Batchelor, K. Strong, G.S. Diskin, H.E. Fuelberg, J.S. Holloway, E.J. Hyer, W.W. McMillan, J. Warner, D.G. Streets, Q. Zhang, Y. Wang, S. Wu, Source attribution and interannual variability of Arctic pollution in spring constrained by aircraft (ARCTAS, ARCPAC) and satellite (AIRS) observations of carbon monoxide, Atm. Chem. Phys. Discuss., 9, 19035-19080, 2009.
  9. Kopacz, M., D.J. Jacob, J.A. Fisher, J.A. Logan, L. Zhang, I.A. Megretskaia, R.M. Yantosca, K. Singh, D.K. Henze, J.P. Burrows, M. Buchwitz, I. Khlystova, W.W. McMillan, J.C. Gille, D.P. Edwards, A. Eldering, V. Thouret, P. Nedelec, Global estimates of CO sources with high resolution by adjoint inversion of multiple satellite datasets (MOPITT, AIRS, SCIAMACHY and TES), Atm. Chem. Phys. Discuss., 9, 19967-20018, 2009.

References

  1. Duncan, B. N., Logan, J. A., Bey, I., Megretskaia, I. A., Yantosca, R. M., Novelli, P. C., Jones, N. B., and Rinsland, C. P., Global budget of CO, 1988–1997: Source estimates and validation with a global model, J. Geophys. Res., 112, D22301, doi:10.1029/2007JD008459, 2007.
  2. Hatakeyama, S., Izumi, K., Fukuyama, T., Akimoto, H. Washida, N., Reactions of OH with alpha-pinene and beta-pinene in air: Estimate of global CO production from the atmospheric oxidation of terpenes, J. Geophys. Res., 96(D1), 947-958, 1991.
  3. Miyoshi, A., Hatakeyama, S., Washida, N., OH radical-initiated photooxidation of isoprene: An estimate of global CO production, J. Geophs. Res., 99(D9), 18779-18787, 1994.
  4. Vinckier, C., Compernolle, F., Saleh, A. M., Van Hoof, N., Van Hees, I., Product yields of the alpha -pinene reaction with hydroxyl radicals and the implication on the global emission of trace compounds in the atmosphere, Fresenius Env. Bull., 7(5-6), 361-368, 1998.

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