Tagged CO simulation

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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).

  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.

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:

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.

--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 are:

------------------------+------------------------------------------------------
%%% TRACER MENU %%%     : 
Type of simulation      : 7 
Number of Tracers       : 17  
Tracer Entries -------> : TR#   Name     g/mole Tracer Members; () = emitted  
Tracer #1               : 1     CO       28.0   (CO) 
Tracer #2               : 2     COus     28.0  
Tracer #3               : 3     COeur    28.0  
Tracer #4               : 4     COasia   28.0  
Tracer #5               : 5     COoth    28.0  
Tracer #6               : 6     CObbam   28.0  
Tracer #7               : 7     CObbaf   28.0  
Tracer #8               : 8     CObbas   28.0  
Tracer #9               : 9     CObboc   28.0  
Tracer #10              : 10    CObbeu   28.0  
Tracer #11              : 11    CObboth  28.0  
Tracer #12              : 12    COch4    28.0  
Tracer #13              : 13    CObiof   28.0  
Tracer #14              : 14    COisop   28.0  
Tracer #15              : 15    COmono   28.0  
Tracer #16              : 16    COmeoh   28.0  
Tracer #17              : 17    COacet   28.0
------------------------+------------------------------------------------------
%%% TRANSPORT MENU %%%  :
Turn on Transport       : T
 => Fill Negative Values: T 
 => IORD, JORD, KORD    : 3  3  7
Transport Timestep [min]: 10   
------------------------+------------------------------------------------------
%%% CONVECTION MENU %%% :
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : T
Convect Timestep [min]  : 10
 ------------------------+------------------------------------------------------
%%% EMISSIONS MENU %%%  :
Turn on emissions?      : T
Emiss Timestep [min]    : 20
HEMCO Input file        : HEMCO_Config.rc

... etc ...
------------------------+------------------------------------------------------ 
%%% DEPOSITION MENU %%% :
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 ...
------------------------+------------------------------------------------------
%%% DIAGNOSTIC MENU %%% : 
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) 21:23, 23 March 2016 (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 lines below each data file that is read from disk.

For example, the following text will add emissions from an 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.

The same methodology applies for splitting up biomass emissions into the 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)                           %%%
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#==============================================================================
(((QFED2
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 
)))QFED2

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<tt>. But the tagged CO always reads the <tt>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)

Tagged CO science updates

The table below lists some important recent science updates to the tagged CO simulation.

Version Date Description Author
v8-02-03 Oct 2009 Updated CO+OH rate constant to JPL2006 Jenny Fisher (U. Wollongong)
v8-02-03 Oct 2009 Optional use of MEGAN biogenic emissions added Prasad Kasibhatla (Duke)
Jenny Fisher (U. Wollongong)
v9-01-02 Nov 2011 Bug fixes in biomass_mod.f, emep_mod.f, and nei2005_anthro_mod.f GCST
v9-02 Nov 2011 Addition of aircraft emissions of CO from the FAA/AEDT aircraft emissions inventory Steven Barrett (MIT)
GCST

--Bob Yantosca (talk) 21:15, 23 March 2016 (UTC)

Code updates made in GEOS-Chem v11-01

Code updates made in GEOS-Chem v10-01

These code updates were added to GEOS-Chem v10-01:

Now call INIT_TAGGED_CO from input_mod.F

This update was validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.

Prior to GEOS-Chem v10-01, routine INIT_TAGGED_CO (in module GeosCore/tagged_co_mod.F) was called from routine EMISS_TAGGED_CO on the first chemistry timestep.

In order to make the code more compatible with our Grid-Independent GEOS-Chem development, we now call INIT_TAGGED_CO from routine GIGC_INIT_EXTRA (in module GeosCore/input_mod.F). This is now called during the "Initialization" phase of GEOS-Chem rather than during the "Run" phase.

--Bob Y. 17:01, 30 May 2014 (EDT)

Reduce memory footprint of arrays

This update was validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.

In module GeosCore/tagged_co_mod.F, the following arrays:

     REAL*8,  ALLOCATABLE :: CO_PRODS  (:,:,:)   ! Strat P(CO) from CH4
     REAL*8,  ALLOCATABLE :: CO_LOSSS  (:,:,:)   ! Strat L(CO) from CO + OH

can be changed from REAL*8 to REAL*4:

     REAL*4,  ALLOCATABLE :: CO_PRODS  (:,:,:)   ! Strat P(CO) from CH4
     REAL*4,  ALLOCATABLE :: CO_LOSSS  (:,:,:)   ! Strat L(CO) from CO + OH

These arrays are meant to hold REAL*4 data that is read in from a netCDF file, so there is no need to keep them at REAL*8. This will half the amount of memory required to store this data.

--Bob Y. 17:01, 30 May 2014 (EDT)

Bug fix: Make sure to define the DTCHEM variable

This update was validated in the 1-month benchmark simulation v10-01c and approved on 29 May 2014.

In routine CHEM_TAGGED_CO (in module file GeosCore/tagged_co_mod.F, variable DTCHEM was never assigned any value. This caused the tagged CO to halt with an error when running in the GEOS-Chem Unit Tester.

The solution was to change this line:

      ! DTCHEM is the number of seconds per chemistry timestep
      DTSRCE    = GET_TS_EMIS() * 60d0			 

to this:

     ! DTCHEM is the number of seconds per chemistry timestep
     DTCHEM    = GET_TS_CHEM() * 60d0			 

--Bob Y. 17:01, 30 May 2014 (EDT)

Tagged CO development projects

  1. Flexible region masks (Dylan Jones and Prasad Kasibhatla)
  2. 3-D chemical production source (Jenny Fisher and Lee Murray)

Adjoint capabilities

Tagged CO is one of the simulations supported in the adjoint code. See the GEOS-Chem Adjoint wiki page for more details.

Setting up a tagged CO simulation on the GEOS-5 72-level grid

If you wish to run the tagged CO simulation on the GEOS-5 (or MERRA or GEOS-FP) 72-level vertical grid, then follow these steps:

  1. In file Headers/define.h
    • Turn off (e.g. comment out) the GRIDREDUCED switch
  2. In file Headers/CMN_SIZE
  3. Make sure that the various files are interpolated to 72 vertical levels, including
    • Mean OH file
    • P(CO) and L(CO) rates
    • NOx fields

More Information

For more information, see the GEOS-Chem manual pages about tagged CO:

  1. Checklist for Tagged CO simulation (Chapter 6.1.4 of the GEOS-Chem User's Guide)
  2. Sample input.geos file for Tagged CO simulation
  3. Tracers for Tagged CO simulation (Appendix 1.7 of the GEOS-Chem User's Guide)

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.

Previous issues that are now resolved

We have found and fixed the following issues with the Tagged CO simulation:

Bug fixes and updates for tagged CO in v9-02

These updates were validated with the 1-month benchmark simulation v10-01f and approved on Approved 13 Jan 2015.

Jenny Fisher wrote:

  1. Major bug fix
    • DTCHEM: At some point in v9-02 implementation, the call that assigned a number to DTCHEM was removed from subroutine CHEM_TAGGED_CO. DTCHEM is used all over that subroutine, so there were a lot of unexpected zeros and infinities. I've restored the call the assign DTCHEM and removed DTSRCE (which was I think the intention of the original change since DTSRCE isn't used in that subroutine).
    • Update: this bug was fixed in GEOS-Chem v10-01c.
  2. Minor bug fixes / inconsistencies
    • SUNCOS: Tagged CO uses the same calls to get MEGAN emissions as full chemistry. When the full chem code was updated to use SUNCOSmid rather than SUNCOS in these calls, the updates should have also been applied here but weren't.
    • Monoterpenes: Similarly, at some point full chem treatment of monoterpene emissions were updated but these weren't applied in tagged CO. The two are now consistent.
    • Non-local PBL mixing: This was never implemented in tagged CO, although there was no documentation anywhere of that fact (except in vdiff_mod.F90). I've now added it.
  3. Structural changes
    • Obsolete variables: I've removed some obsolete variables, cleaned up a few really old comments, and also moved a few things that were being defined (as constants) in loops into parameter declarations.
    • I've replaced FIRSTEMISS and FIRSTCHEM with a new logical called FIRSTTIME that is used for the initialisation routines so that tagged CO can still be initialised and run even if emissions are turned off.
      • Update: in GEOS-Chem v10-01c we now call INIT_TAGGED_CO during the initialization phase (i.e. before the model starts timestepping), rather than on the first emissions or chemistry call. This is also required for running GEOS-Chem in an ESMF environment (i.e. in the GEOS-5 DAS).
  4. Objective science changes
    • I've added a diurnal cycle for the offline OH used both for CO production from CH4 and CO loss. This is done in all the other offline simulations, but for some reason was never implemented in tagged CO. This is an objective improvement.

--Melissa Sulprizio 09:22, 10 July 2014 (EDT)

Bug fixes for tagged CO simulation

This update was tested in the 1-month benchmark simulation v9-02b and approved on 29 Oct 2012.

We have corrected the following minor issues in the Tagged CO simulation. These bugs were present in GEOS-Chem v9-01-03. The full-chemistry simulation is not affected by these issues.

(1) In emissdr.F, bracket AD46 diagnostics with IF statements in order to avoid out-of-bounds errors caused by undefined bromine tracer flags:

               ! CHBr3 emissions [kg/m2/s] -- tracer #14
               IF ( IDECHBr3 > 0 ) THEN
                  AD46(I,J,14) = AD46(I,J,14) 
     &                         + ( EMISRR(I,J,IDECHBr3)  / AREA_M2 ) 
     &                         * ( MWT_CHBr3             / AVG     )
              ENDIF
 
               ! CH2Br2 emissions [kg/m2/s] -- tracer #15
               IF ( IDECH2Br2 > 0 ) THEN
                  AD46(I,J,15) = AD46(I,J,15) 
     &                         + ( EMISRR(I,J,IDECH2Br2) / AREA_M2 ) 
     &                         * ( MWT_CH2Br2            / AVG     )
               ENDIF


(2) We needed to pass the am_I_Root = .TRUE. value to routine GET_GLOBAL_CH4 from tagged_co_mod.F. We changed this line:

         CALL GET_GLOBAL_CH4( GET_YEAR(), .TRUE., 
     &                        A3090S, A0030S, A0030N, A3090N )

to:

         CALL GET_GLOBAL_CH4( GET_YEAR(), .TRUE.,             
     &                        A3090S, A0030S, A0030N, A3090N, .TRUE. )


(3) The CO_PRODS and CO_LOSSS arrays need to be made 3-dimensional for compatibility with the new GMI stratospheric chemistry data. Change these lines:

      REAL*8,  ALLOCATABLE :: CO_PRODS(:,:)
      REAL*8,  ALLOCATABLE :: CO_LOSSS(:,:)
      . . .
      ALLOCATE( CO_PRODS( JJPAR, LLPAR ), STAT=AS )
      . . .
      ALLOCATE( CO_LOSSS( JJPAR, LLPAR ), STAT=AS )
      . . .
      IF ( IS_PROD ) THEN
         RATE = CO_PRODS(J,L)   ! P(CO) from CH4 + OH in [v/v/s]
      ELSE
         RATE = CO_LOSSS(J,L)   ! L(CO) from CO + OH  in [s^-1]
      ENDIF

to:

      REAL*8,  ALLOCATABLE :: CO_PRODS(:,:,:)
      REAL*8,  ALLOCATABLE :: CO_LOSSS(:,:,:)
      . . .
      ALLOCATE( CO_PRODS( IIPAR, JJPAR, LLPAR ), STAT=AS )
      . . .
      ALLOCATE( CO_LOSSS( IIPAR, JJPAR, LLPAR ), STAT=AS )
      . . .
      IF ( IS_PROD ) THEN
         RATE = CO_PRODS(I,J,L)   ! P(CO) from CH4 + OH in [v/v/s]
      ELSE
         RATE = CO_LOSSS(I,J,L)   ! L(CO) from CO + OH  in [s^-1]
      ENDIF

Thanks to Jenny Fisher for her assistance in correcting these issues.

--Bob Y. 10:58, 20 December 2012 (EST)

Outstanding issues that are not yet resolved

  1. No diurnal variability in OH fields -- other offline simulations scale OH diurnally based on the cosine of the SZA. I have implemented this in a working version of GEOS-Chem and will submit to the standard code shortly.
  2. Centralized chemistry timestep not fully implemented -- Tagged CO has some lingering calls to SUNCOS instead of SUNCOS_MID. I've fixed these and will submit with #1.
  3. Non-local PBL mixing doesn't work -- Right now, selecting non-local PBL mixing has no effect on the tagged CO code as the model ignores this. I've fixed this as well and will submit with #1-3.
  4. 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