Difference between revisions of "Tagged CO simulation"

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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.
 +
 
 +
== 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.
 
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 ==
+
=== Assumptions ===
#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>
+
#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>
 
#Biogenic VOCs:<br>
 
#Biogenic VOCs:<br>
 
## 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.
 
## 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.
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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.
 
#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 ==
+
<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).
+
  
Tracer 1 (CO) is total CO; this is the sum of CO from all sources.
+
      52 COPROD_FOSSIL  1.19 - - - xy 1 1
  Tracers 2-5 are CO from fossil fuel emissions in:
+
      53 COPROD_BIOFUEL  1.189 - - - xy 1 1
  -COus: North America (172.5-17.5W, 24-88N)
+
      54 COPROD_BIOMASS  1.11 - - - xy 1 1
  -COeur: Europe (17.5W-72.5E, 36-45N and 17.5W-172.5E, 45-88N)
+
  -COasia: Asia (70-152.5E, 8-45N)
+
  -COoth: everywhere else.
+
  Tracers 6-11 are CO from biomass burning emissions in:
+
  -CObbam: South America (112.5-32.5W, 56S-24N)
+
  -CObbaf: Africa (17.5W-70E, 48S-36N)
+
  -CObbas: Southeast Asia (70-152.5E, 8-45N)
+
  -CObboc: Oceania (70-170E, 90S-8N)
+
  -CObbeu: Europe (17.5W-72.5E, 36-45N and 17.5W-172.5E, 45-88N)
+
  -CObbna: Everywhere else (basically North America)
+
Tracer 12 (COch4) is CO produced from methane.
+
Tracer 13 (CObiof) is CO from biofuel emissions (except if you are using the Streets inventory over Asia, where biofuel and fossil fuel emissions are combined).
+
Tracers 14-17 are CO produced from the following volatile organic compounds (in order): isoprene (COisop), monoterpenes (COmono), methanol (COmeoh), and acetone (COacet).
+
  
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.
+
<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 ==
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 14:44, 26 October 2017 (UTC)
Tagged CO is simulation type 7. For tagged CO run with standard tracers, the input.geos should look like this:
+
%%% 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    CObbna  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
+
  
== Recent tagged CO updates ==
+
=== Standard Tracers ===
 +
In a standard run, there are 17 tracers (see input.geos below).
  
The following updates were recently added to the GEOS-Chem tagged CO simulation:
+
{| border=1 cellspacing=0 cellpadding=5
 +
|-bgcolor="#CCCCCC"
 +
!width="30px"|#
 +
!width="75px"|Tracer
 +
!width="400px"|Description
 +
!width="300px"|Region
 +
|-valign="top
 +
|1  || CO      || Total CO from all sources                          || global
  
=== Science updates ===
+
|-valign="top"
 +
|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
  
These scientific updates were added to the tagged CO simulation:
+
|-valign="top"
 +
|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
  
# Updated CO+OH rate constant to JPL2006 (Jenny Fisher): standard in [[GEOS-Chem v8-02-03]]<br>
+
|-valign="top"
# Optional use of [[MEGAN biogenic emissions]] added (Prasad Kasibhatla and Jenny Fisher): standard in [[GEOS-Chem v8-02-03]]
+
|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
# [[GEOS-Chem v9-01-02#Bug fixes for offline simulations|Bug fixes in biomass_mod.f, emep_mod.f, and nei2005_anthro_mod.f]]: standard in [[GEOS-Chem v9-01-02]]
+
# Addition of aircraft emissions of CO from the [[Aircraft_emissions#FAA_aircraft_emissions_inventory|FAA/AEDT aircraft emissions inventory]] (in [[GEOS-Chem v9-02]] and higher)
+
  
--[[User:Bmy|Bob Y.]] 15:00, 11 April 2014 (EDT)
+
|-valign="top"
 +
|5  || COoth  || Anthropogenic + Biofuel CO emitted everywhere else  || rest of world
  
=== Code Updates ===
+
|-valign="top"
 +
|6  || CObbam  || Biomass burning CO emitted over South America      || 112.5&deg;W - 32.5&deg;W; 56&deg;S - 24&deg;N
  
These code updates were added to [[GEOS-Chem v10-01]]:
+
|-valign="top"
 +
|7  || CObbaf  || Biomass burning CO emitted over Africa              || 17.5&deg;W -70.0&deg;E; 48.0&deg;S - 36.0&deg;N
  
==== Now call INIT_TAGGED_CO from input_mod.F ====
+
|-valign="top"
 +
|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
  
'''''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.'''''
+
|-valign="top"
 +
|9  || CObboc  || Biomass burning CO emitted over Oceania            || 70.0&deg;E - 170.0&deg;E;  90.0&deg;S - 8.0&deg;N
  
Prior to [[GEOS-Chem v10-01]], routine <tt>INIT_TAGGED_CO</tt> (in module <tt>GeosCore/tagged_co_mod.F</tt>) was called from routine <tt>EMISS_TAGGED_CO</tt> on the first chemistry timestep.  
+
|-valign="top"
 +
|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
  
In order to make the code more compatible with our [[Grid-Independent GEOS-Chem]] development, we now call <tt>INIT_TAGGED_CO</tt> from routine <tt>GIGC_INIT_EXTRA</tt> (in module <tt>GeosCore/input_mod.F</tt>).  This is now called during the "Initialization" phase of GEOS-Chem rather than during the "Run" phase.
+
|-valign="top"
 +
|11 || CObboth || Biomass burning CO emitted everywhere else          || rest of world
  
--[[User:Bmy|Bob Y.]] 17:01, 30 May 2014 (EDT)
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|-valign="top"
 +
|12 || COch4  || CO chemically produced from methane                || global
  
==== Reduce memory footprint of arrays ====
+
|-valign="top"
 +
|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.
  
'''''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.'''''
+
|-valign="top"
 +
|14 || COisop || CO chemically produced from isoprene                || global
  
In module <tt>GeosCore/tagged_co_mod.F</tt>, the following arrays:
+
|-valign="top"
 +
|15 || COmono || CO chemically produced CO from monoterpenes          || global
  
      REAL*8,  ALLOCATABLE :: CO_PRODS  (:,:,:)  ! Strat P(CO) from CH4
+
|-valign="top"
      REAL*8,  ALLOCATABLE :: CO_LOSSS  (:,:,:)  ! Strat L(CO) from CO + OH
+
|16 || COmeoh || CO chemically produced from methanol                || global
  
can be changed from <tt>REAL*8</tt> to <tt>REAL*4</tt>:
+
|-valign="top"
 +
|17 || COacet || CO chemically produced from acetone                  || global
  
      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 <tt>REAL*4</tt> data that is read in from a netCDF file, so there is no need to keep them at <tt>REAL*8</tt>.  This will half the amount of memory required to store this data.
+
The regional definitions used for the fossil fuel and biomass burning tracers can be changed by modifying the HEMCO mask file:
  
--[[User:Bmy|Bob Y.]] 17:01, 30 May 2014 (EDT)
+
ExtData/HEMCO/MASKS/v2014-07/tagged_CO_masks.generic.0.5x0.5.nc
  
==== Bug fix: Make sure to define the DTCHEM variable ====
+
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.
  
'''''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.'''''
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 20:17, 23 March 2016 (UTC)
  
In routine <tt>CHEM_TAGGED_CO</tt> (in module file <tt>GeosCore/tagged_co_mod.F</tt>, variable <tt>DTCHEM</tt> was never assigned any value.  This caused the tagged CO to halt with an error when running in the [[GEOS-Chem Unit Tester]].
+
=== The input.geos file ===
  
The solution was to change this line:
+
Tagged CO is simulation type 7. For tagged CO run with standard tracers, the relevant settings in the <tt>input.geos</tt> (assuming [[GEOS-Chem v11-01]]) are:
  
      ! DTCHEM is the number of seconds per chemistry timestep
+
------------------------+------------------------------------------------------
       DTSRCE   = GET_TS_EMIS() * 60d0
+
%%% ADVECTED SPECIES MENU %%%:
 +
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
 +
------------------------+------------------------------------------------------
 +
%%% 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
 +
 +
... set everything else to F ...
 +
------------------------+------------------------------------------------------
 +
%%% 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
 +
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:18, 26 October 2017 (UTC)
  
to this:
+
=== The HEMCO_Config.rc file ===
  
      ! DTCHEM is the number of seconds per chemistry timestep
+
In [[GEOS-Chem v11-01]] and higher versions, the tagged CO emissions are now handled by the [[HEMCO|HEMCO emissions component]].  In the <tt>HEMCO_Config.rc</tt> file, you can add emissions from each data file to the regional CO tracers by adding a few extra lines below each data file.
      DTCHEM    = GET_TS_CHEM() * 60d0
+
  
--[[User:Bmy|Bob Y.]] 17:01, 30 May 2014 (EDT)
+
For example, the following text will add emissions from one of the EDGAR inventory files into the relevant regional tracers:
  
== Tagged CO development projects ==
+
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
#Flexible region masks (Dylan Jones and Prasad Kasibhatla)
+
0 EDGAR_CO_1A1a_6_us  -                                                                    -      -              - -  -      COus    6/41/26/52/<span style="color:red">1100</span>  1 2
 +
0 EDGAR_CO_1A1a_6_eur  -                                                                    -      -              - -  -      COeur    6/41/26/52/<span style="color:red">1101</span>  1 2
 +
0 EDGAR_CO_1A1a_6_asia -                                                                    -      -              - -  -      COasia  6/41/26/52/<span style="color:red">1102</span>  1 2
 +
0 EDGAR_CO_1A1a_6_oth        -                                                              -      -              - -  -      COoth    6/41/26/52/<span style="color:red">1103</span>  1 2
  
== Adjoint capabilities ==
+
Note that we simply add a mask number to the <tt>ScalId</tt> section (highlighted in <span style="color:red">RED</span>) corresponding to each of the regional tracers.  We repeat this process for all other anthropogenic data files that are read from disk.
  
Tagged CO is one of the simulations supported in the adjoint code. See the [[GEOS-Chem Adjoint]] wiki page for more details.
+
The same methodology applies for splitting up biomass emissions into the CO regional tagged tracers.  For example, this section of the <tt>HEMCO_Config.rc</tt> will put CO from the QFED biomass inventory into the biomass tagged CO tracers:
  
== Setting up a tagged CO simulation on the GEOS-5 72-level grid ==
+
#==============================================================================
 +
# --- 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/<span style="color:purple">1104</span>  5 2
 +
0 QFED_CObbAf  -                                                              -      -                    - -  -      CObbaf  54/75/<span style="color:purple">1105</span>  5 2
 +
0 QFED_CObbAs  -                                                              -      -                    - -  -      CObbas  54/75/<span style="color:purple">1106</span>  5 2
 +
0 QFED_CObbOc  -                                                              -      -                    - -  -      CObboc  54/75/<span style="color:purple">1107</span>  5 2
 +
0 QFED_CObbEu  -                                                              -      -                    - -  -      CObbeu  54/75/<span style="color:purple">1108</span>  5 2
 +
0 QFED_CObbOth -                                                              -      -                    - -  -      CObboth 54/75/<span style="color:purple">1109</span>  5 2
 +
)))QFED2
  
If you wish to run the tagged CO simulation on the [[GEOS-5]] (or [[MERRA]] or [[GEOS-FP]]) [http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#A3.5 72-level vertical grid], then follow these steps:
+
As for the anthropogenic emissions, we add the ID number of the appropriate mask (highlighted in <span style="color:purple">PURPLE</span>) corresponding to each biomass CO tagged tracer.
  
# In file <tt>Headers/define.h</tt>
+
Mask definitions corresponding to each regional tagged tracer are read from a netCDF file. These masks are listed in the MASKS section of the <tt>HEMCO_Config.rc</tt> file:
#* Turn off (e.g. comment out) the <tt>GRIDREDUCED</tt> switch
+
# In file <tt>Headers/CMN_SIZE</tt>
+
#* If you are using a version of GEOS-Chem prior to v9-01-01, increase the value of <tt>LLTROP</tt> from 38 to 40.  For complete instructions, please see [[Dynamic tropopause#Defining LLTROP for GEOS-5 72-layer grid|this wiki post on our Dynamic Tropopause page]].
+
# 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 ==
+
#==============================================================================
 +
# Tagged CO regions
 +
#==============================================================================
 +
<span style="color:red">1100 TAGCO_USA_MASK</span>  $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
 +
<span style="color:red">1101 TAGCO_EUR_MASK</span>  $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
 +
<span style="color:red">1102 TAGCO_ASIA_MASK</span>  $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
 +
<span style="color:red">1103 TAGCO_OTH_MASK</span>  $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
 +
<span style="color:purple">1104 TAGCO_BBAM_MASK</span>  $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
 +
<span style="color:purple">1105 TAGCO_BBAF_MASK</span>  $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
 +
<span style="color:purple">1106 TAGCO_BBAS_MASK</span>  $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
 +
<span style="color:purple">1107 TAGCO_BBOC_MASK</span>  $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
 +
<span style="color:purple">1108 TAGCO_BBEU_MASK</span>  $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
 +
<span style="color:purple">1109 TAGCO_BBOTH_MASK</span> $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
  
For more information, see the GEOS-Chem manual pages about tagged CO:
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:16, 23 March 2016 (UTC)
  
# [http://acmg.seas.harvard.edu/geos/doc/man/chapter_6.html#6.1.4 Checklist for Tagged CO simulation (Chapter 6.1.4 of the GEOS-Chem User's Guide) ]
+
=== Notes about using HEMCO with the tagged CO simulation ===
# [http://acmg.seas.harvard.edu/geos/doc/man/files/input.geos.tagco Sample <tt>input.geos</tt> file for Tagged CO simulation]
+
# [http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html#A1.7 Tracers for Tagged CO simulation (Appendix 1.7 of the GEOS-Chem User's Guide)]
+
  
== Studies that used Tagged CO simulation ==
+
In [[GEOS-Chem v11-01]] and higher versions, the [[HEMCO|HEMCO emissions component]] now handles all emissions for the tagged CO simulation. You should be aware of the following:
#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.
+
#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.
+
#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.
+
#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.
+
#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.
+
#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.
+
#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.
+
#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.
+
#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 ==
+
#<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>
#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.
+
#<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>
#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.
+
#<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>
#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.
+
#<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>
#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.
+
#*<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>
 +
#<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>
  
== Previous issues that are now resolved ==
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:07, 23 March 2016 (UTC)
  
We have found and fixed the following issues with the Tagged CO simulation:
+
== New tagged CO simulation in v11-02 and later ==
  
=== Bug fixes for tagged CO simulation ===
+
<span style="color:green">'''''This update was included in [[GEOS-Chem v11-02#v11-02f|v11-02f]] (approved 17 May 2018).'''''</span>
  
'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02b|v9-02b]] and approved on 29 Oct 2012.'''''
+
'''''[[User:Jaf|Jenny Fisher]] wrote:'''''
  
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.
+
<blockquote>My paper describing the updated Tagged CO simulation is now published: https://www.geosci-model-dev.net/10/4129/2017/
  
(1) In <tt>emissdr.F</tt>, bracket AD46 diagnostics with IF statements in order to avoid out-of-bounds errors caused by undefined bromine tracer flags:
+
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.
  
                ! CHBr3 emissions [kg/m2/s] -- tracer #14
+
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.
                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
+
  
 +
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)
  
(2) We needed to pass the <tt>am_I_Root = .TRUE.</tt> value to routine <tt>GET_GLOBAL_CH4</tt> from <tt>tagged_co_mod.F</tt>.  We changed this line:
+
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.</blockquote>
  
          CALL GET_GLOBAL_CH4( GET_YEAR(), .TRUE.,
+
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:00, 17 May 2018 (UTC)
      &                        A3090S, A0030S, A0030N, A3090N )
+
  
to:
+
=== Process for creating tagged CO input files ===
          CALL GET_GLOBAL_CH4( GET_YEAR(), .TRUE.,           
+
      &                        A3090S, A0030S, A0030N, A3090N, .TRUE. )
+
  
 +
Jenny Fisher developed scripts for creating input files for the tagged CO simulation in [[GEOS-Chem v11-02]] and later versions.
  
(3) The <tt>CO_PRODS</tt> and <tt>CO_LOSSS</tt> arrays need to be made 3-dimensional for compatibility with the new GMI stratospheric chemistry data.  Change these lines:
+
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)
  
      REAL*8,  ALLOCATABLE :: CO_PRODS(:,:)
+
2. In IDL, run script <tt>prepare_tagCO_IDL.pro</tt>
      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:
+
:This will loop over 12 months to run
 +
:*<tt>merge_oh_3d_v11</tt>
 +
:*<tt>extract_pco_3d_v11</tt>
 +
:Defaults including directory for trac_avg files, model, resolution, year should be specified in that script.
  
      REAL*8,  ALLOCATABLE :: CO_PRODS(:,:,:)
+
: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.
      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.
+
3. Run the script <tt>nco_for_taggedCO</tt> to combined the monthly files and fix the netcdf files for HEMCO.
  
--[[User:Bmy|Bob Y.]] 10:58, 20 December 2012 (EST)
+
--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 14:53, 10 August 2018 (UTC)
 +
 
 +
== Studies that used Tagged CO simulation ==
 +
#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.
 +
#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.
 +
#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.
 +
#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.
 +
#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.
 +
#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.
 +
#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.
 +
#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.
 +
#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 ==
 +
#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.
 +
#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.
 +
#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.
 +
#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.
  
 
== Outstanding issues that are not yet resolved ==
 
== Outstanding issues that are not yet resolved ==
  
None at this time.
+
#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<br>--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:40, 23 March 2016 (UTC)
 +
 
  
--[[User:Bmy|Bob Y.]] 10:58, 20 December 2012 (EST)
+
----
 +
'''''[[POPs simulation|Previous]] | [[Tagged O3 simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''

Latest revision as of 14:20, 20 September 2022

Previous | Next | Guide to GEOS-Chem simulations

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


On this page, we 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.

--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:

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 (assuming GEOS-Chem v11-01) are:

------------------------+------------------------------------------------------
%%% ADVECTED SPECIES MENU %%%:
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
------------------------+------------------------------------------------------
%%% 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

... set everything else to F ...
------------------------+------------------------------------------------------ 
%%% 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) 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)                           %%%
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#==============================================================================
(((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. 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.

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.

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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