Tagged CO simulation

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  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.



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.


  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.

--Bob Yantosca (talk) 14:44, 26 October 2017 (UTC)

Standard Tracers

In a standard run, there are 17 tracers (see input.geos below).

# 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:


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.

--Bob Yantosca (talk) 20:17, 23 March 2016 (UTC)

The input.geos file

Tagged CO is simulation type 7. For tagged CO run with standard tracers, the relevant settings in the input.geos (assuming GEOS-Chem v11-01) are:

Type of simulation      : 7
Number of Advected Spec.: 17
Species Entries ------->: Name
Species #1              : CO
Species #2              : COus
Species #3              : COeur
Species #4              : COasia
Species #5              : COoth
Species #6              : CObbam
Species #7              : CObbaf
Species #8              : CObbas
Species #9              : CObboc
Species #10             : CObbeu
Species #11             : CObboth
Species #12             : COch4
Species #13             : CObiof
Species #14             : COisop
Species #15             : COmono
Species #16             : COmeoh
Species #17             : COacet
Turn on Transport       : T
 => Fill Negative Values: T 
 => IORD, JORD, KORD    : 3  3  7
Transport Timestep [min]: 10   
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : T
Convect Timestep [min]  : 10
Turn on emissions?      : T
Emiss Timestep [min]    : 20
HEMCO Input file        : HEMCO_Config.rc

... set everything else to F ...
Turn on Dry Deposition? : T
Turn on Wet Deposition? : F
%%% CHEMISTRY MENU %%%  : 
Turn on Chemistry?      : T
Use linear. strat. chem?: F
 => Use Linoz for O3?   : F
Use UCX strat. chem?    : F
Online CH4 chemistry?   : F
Active strat. H2O?      : F
Chemistry Timestep [min]: 20
Use spec_rst (bpch only): F
 => CSPEC rst filename? : none
USE solver coded by KPP : F
Online O3 for FAST-JX?  : F
Gamma HO2               : 0.2

... etc ...
Binary punch file name  : trac_avg.geosfp_4x5_tagCO.YYYYMMDDhhmm
Diagnostic Entries ---> :  L   Tracers to print out for each diagnostic
... etc ...     
ND29: CO sources        : 47   all

... etc ...
ND45: Tracer Conc's     : 47   all 
 ==> ND45 Time range   :       0 24

--Bob Yantosca (talk) 15:18, 26 October 2017 (UTC)

The HEMCO_Config.rc file

In GEOS-Chem v11-01 and higher versions, the tagged CO emissions are now handled by the HEMCO emissions component. In the HEMCO_Config.rc file, you can add emissions from each data file to the regional CO tracers by adding a few extra lines below each data file.

For example, the following text will add emissions from one of the EDGAR inventory files into the relevant regional tracers:

0 EDGAR_CO_1A1a_6      $ROOT/EDGARv42/v2015-02/CO/EDGAR_v42_CO_IPCC_1A1a_6.generic.01x01.nc  emi_co  1970-2008/1/1/0 C xy kg/m2/s CO       6/41/26/52       1 2
0 EDGAR_CO_1A1a_6_us   -                                                                     -       -               - -  -       COus     6/41/26/52/1100  1 2
0 EDGAR_CO_1A1a_6_eur  -                                                                     -       -               - -  -       COeur    6/41/26/52/1101  1 2
0 EDGAR_CO_1A1a_6_asia -                                                                     -       -               - -  -       COasia   6/41/26/52/1102  1 2
0 EDGAR_CO_1A1a_6_oth         -                                                              -       -               - -  -       COoth    6/41/26/52/1103  1 2

Note that we simply add a mask number to the ScalId section (highlighted in RED) corresponding to each of the regional tracers. We repeat this process for all other anthropogenic data files that are read from disk.

The same methodology applies for splitting up biomass emissions into the CO regional tagged tracers. For example, this section of the HEMCO_Config.rc will put CO from the QFED biomass inventory into the biomass tagged CO tracers:

# --- QFED2 biomass burning ---
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# %%%   Set QFED2 to category 5 to match CATEGORY_BIOMASS in the  %%%
# %%%   include file GeosCore/hcoi_gc_diagn_include.H.            %%%
# %%%     -- Bob Yantosca (17 Mar 2016)                           %%%
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0 QFED_CO      $ROOT/QFED/v2014-09/$YYYY/$MM/qfed2.emis_co.005.$YYYY$MM$DD.nc4 biomass 2000-2013/1-12/1-31/0 C xy kg/m2/s CO      54/75       5 2 
0 QFED_CObbAm  -                                                               -       -                     - -  -       CObbam  54/75/1104  5 2 
0 QFED_CObbAf  -                                                               -       -                     - -  -       CObbaf  54/75/1105  5 2 
0 QFED_CObbAs  -                                                               -       -                     - -  -       CObbas  54/75/1106  5 2 
0 QFED_CObbOc  -                                                               -       -                     - -  -       CObboc  54/75/1107  5 2 
0 QFED_CObbEu  -                                                               -       -                     - -  -       CObbeu  54/75/1108  5 2 
0 QFED_CObbOth -                                                               -       -                     - -  -       CObboth 54/75/1109  5 2 

As for the anthropogenic emissions, we add the ID number of the appropriate mask (highlighted in PURPLE) corresponding to each biomass CO tagged tracer.

Mask definitions corresponding to each regional tagged tracer are read from a netCDF file. These masks are listed in the MASKS section of the HEMCO_Config.rc file:

# Tagged CO regions
1100 TAGCO_USA_MASK   $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_USA_MASK   2000/1/1/0 C xy 1 1 -172/24/-18/88
1101 TAGCO_EUR_MASK   $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_EUR_MASK   2000/1/1/0 C xy 1 1 -17/36/172/88
1102 TAGCO_ASIA_MASK  $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_ASIA_MASK  2000/1/1/0 C xy 1 1  70/8/152/44
1103 TAGCO_OTH_MASK   $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_OTH_MASK   2000/1/1/0 C xy 1 1 -180/-90/180/90
1104 TAGCO_BBAM_MASK  $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_BBAM_MASK  2000/1/1/0 C xy 1 1 -112/-56/-33/24
1105 TAGCO_BBAF_MASK  $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_BBAF_MASK  2000/1/1/0 C xy 1 1 -17/-48/70/36
1106 TAGCO_BBAS_MASK  $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_BBAS_MASK  2000/1/1/0 C xy 1 1  70/8/153/45
1107 TAGCO_BBOC_MASK  $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_BBOC_MASK  2000/1/1/0 C xy 1 1  70/8/170/90
1108 TAGCO_BBEU_MASK  $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_BBEU_MASK  2000/1/1/0 C xy 1 1 -17/45/173/88 
1109 TAGCO_BBOTH_MASK $ROOT/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc TAGCO_BBOTH_MASK 2000/1/1/0 C xy 1 1 -180/-90/180/90

--Bob Yantosca (talk) 21:16, 23 March 2016 (UTC)

Notes about using HEMCO with the tagged CO simulation

In GEOS-Chem v11-01 and higher versions, the HEMCO emissions component now 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>

--Bob Yantosca (talk) 21:07, 23 March 2016 (UTC)

New tagged CO simulation in v11-02 and later

This update was included in v11-02f (approved 17 May 2018).

Jenny Fisher wrote:

My paper describing the updated Tagged CO simulation is now published: https://www.geosci-model-dev.net/10/4129/2017/

While the version described in the paper was based on v9, I have ported all the code into v11-01 and created a git patch along with relevant input files. Bea Bukosa has tested these out in v11-01 and all appears to be working as expected. FYI, this version maintains the possibility of using the “old” method for tagged CO with a switch in the input file.

There is one minor thing… The HEMCO files (OH and P(CO)) are for the year 2013 and v11-01. For a very interested user, these should in theory be re-created from full chem using the same year / met fields / emissions / etc. that they will run tagged CO with. However, we do show in the paper that for most applications, using a default file will be fine – and we suggest that these files can be created during the 1-year benchmarking process for the standard simulation.

I can bring this up with GCSC, but in principle could this be added to the benchmarking process? I think it would only require minor additions to what is already being saved as we need:

  • OH
  • Pressure edges
  • Box height
  • PCO chemical family
  • LCH4 chemical family (which I added in my KPP files in the patch)
There are then some IDL & NCO scripts to run to create the files, which I guess will need to be updated for netcdf diagnostics, but I imagine that won’t be hard. The scripts & associated readme are attached here.

--Bob Yantosca (talk) 16:00, 17 May 2018 (UTC)

Process for creating tagged CO input files

Jenny Fisher developed scripts for creating input files for the tagged CO simulation in GEOS-Chem v11-02 and later versions.

1. Run GEOS-Chem for 1-year (presumably benchmark simulation) saving:

  • OH (ND43, all levels, tracer 1)
  • PEDGE (ND31, all levels, tracer all)
  • BXHGHT (ND68, all levels, tracer 4)
  • PCO (ND65)
  • LCH4 (ND65)

2. In IDL, run script prepare_tagCO_IDL.pro

This will loop over 12 months to run
  • merge_oh_3d_v11
  • extract_pco_3d_v11
Defaults including directory for trac_avg files, model, resolution, year should be specified in that script.
You should check that PCO_CH4 is tracer 7 and PCO_NMVOC is tracer 8. If not, you can specify these in the script as well.

3. Run the script nco_for_taggedCO to combined the monthly files and fix the netcdf files for HEMCO.

--Melissa Sulprizio (talk) 14:53, 10 August 2018 (UTC)

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.


  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.

Outstanding issues that are not yet resolved

  1. No CO dry deposition -- this is actually true in both full chemistry and tagged CO, and Chris Holmes has pointed out it can be up to 10% of the CO sink. I have started looking into this but have made no serious progress yet.

--Jenny Fisher, 3 Jun 2014
--Bob Yantosca (talk) 21:40, 23 March 2016 (UTC)

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