Difference between revisions of "Aerosol-only simulation"

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__FORCETOC__
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'''''[[GEOS-Chem chemistry mechanisms|Previous]] | [[CH4 simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''
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#[[GEOS-Chem chemistry mechanisms|Simulations using KPP-built mechanisms]]
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#<span style="color:blue">'''Aerosol-only simulation'''</span>
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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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#[[Tagged CO simulation]]
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#[[Tagged O3 simulation]]
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#[[TransportTracers simulation]]
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On this page we describe the aerosol-only (a.k.a. offline aerosol) simulation.
 
On this page we describe the aerosol-only (a.k.a. offline aerosol) simulation.
  
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The aerosol simulation is an offline simulation for aerosol tracers only.  It uses archived monthly mean OH, NO3, O3 and total nitrate concentrations archived from a previous full-chemistry simulation (more on that below), as well as production and loss rates for H2O2. This simulation does not provide "tagged" capabilities, but reduces the suite of tracers from full chemistry.
 
The aerosol simulation is an offline simulation for aerosol tracers only.  It uses archived monthly mean OH, NO3, O3 and total nitrate concentrations archived from a previous full-chemistry simulation (more on that below), as well as production and loss rates for H2O2. This simulation does not provide "tagged" capabilities, but reduces the suite of tracers from full chemistry.
  
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== Assumptions ==
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NOTES:
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# OH concentrations are taken from a previously run full chemistry simulation. The default is from a much earlier version of the model, when OH thought to be more realistic. The standard code uses OH from version 5-07-08, with GEOS3 meteorology.
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# The aerosol-only simuation is currently functional in GEOS-Chem Classic.
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# O3, NO3 and total nitrate (HNO3+NIT) concentrations, as well as production rates and photolysis rates for H2O2 are taken from a previously run full chemistry simulation. The current default fields were produced from a GEOS-4, v7-02-03 simulation.  These files are generally located in the sulfate_sim_200508/offline/ directory in your GEOS-Chem data directories.
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# There is currently no aerosol-only run directory for GCHP. Interested users are encouraged to make this modification on their own.
 +
# OH concentrations are archived from the most recent 10-year benchmark simulation.
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# O3, NO3 and total nitrate (HNO3+NIT) concentrations, as well as production rates and photolysis rates for H2O2 are archived from the most recent 10-year benchmark simulation.
 +
 
 +
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 16:06, 25 August 2022 (UTC)
  
 
== Practicalities ==
 
== Practicalities ==
  
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As with all other [[Offline chemistry simulations]], the [http://acmg.seas.harvard.edu/geos/geos_people.html GEOS-Chem user community] shall be responsible for the scientific content and validation of the aerosol-only simulation.
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As with all other [[Offline chemistry simulations]], the [https://geoschem.github.io/geos-chem-people-projects-map/ GEOS-Chem user community] shall be responsible for the scientific content and validation of the aerosol-only simulation.
  
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=== Tracer list ===
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The [[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|SOA simulation]] was updated in [[GEOS-Chem_v9-02_benchmark_history#v9-02o|GEOS-Chem v9-02o]] to include a better tracer lumping scheme, as shown in Figure 1 of [http://www.atmos-chem-phys.net/10/11261/2010/acp-10-11261-2010.pdf Pye et al. 2010].
  
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In a complete aerosol-only simulation there are 31 tracers (see input.geos below). 
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The offline aerosol is simulation type 10. For a full set of aerosol tracers (based on the 100-tracer full-chemistry SOA simulation), the input.geos should look like this:
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The offline aerosol is simulation type 10. For a full set of aerosol tracers (based on the 59-tracer full-chemistry SOA simulation), the input.geos should look like this:  
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  Type of simulation      : 10
 
  Type of simulation      : 10
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  Number of Tracers      : 31
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  Number of Tracers      : 47
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  Tracer Entries -------> : TR#  Name  g/mole Tracer Members; () = emitted  
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  Tracer Entries -------> : TR#  Name  g/mole   Tracer Members; () = emitted
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  Tracer #1              : 1   DMS   62.00
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  Tracer #1              : 1   DMS     62.00
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  Tracer #2              : 2   SO2   64.00
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  Tracer #2              : 2   SO2     64.00
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  Tracer #3              : 3   SO4   96.00
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  Tracer #3              : 3   SO4     96.00
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  Tracer #4              : 4   MSA   96.00
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  Tracer #4              : 4   SO4s   96.00
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  Tracer #5              : 5   NH3    17.00
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  Tracer #5              : 5   MSA    96.00
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  Tracer #6              : 6   NH4    18.00
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  Tracer #6              : 6   NH3    17.00
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  Tracer #7              : 7   NIT    62.00
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  Tracer #7              : 7   NH4    18.00
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  Tracer #8              : 8   H2O2   34.00
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  Tracer #8              : 8  NIT    62.00
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  Tracer #9              : 9   BCPI   12.00
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  Tracer #9              : 9  NITs    62.00
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  Tracer #10              : 10  OCPI  12.00
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  Tracer #10              : 10  H2O2    34.00
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  Tracer #11              : 11  BCPO  12.00
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  Tracer #11              : 11  BCPI    12.00
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  Tracer #12              : 12  OCPO  12.00
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  Tracer #12              : 12  OCPI    12.00
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  Tracer #13              : 13  ALPH  136.23
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  Tracer #13              : 13  BCPO    12.00
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  Tracer #14              : 14  LIMO  136.23
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  Tracer #14              : 14  OCPO    12.00
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  Tracer #15              : 15  ALCO  142.00
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  Tracer #15              : 15  DST1    29.00
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  Tracer #16              : 16  SOG1  150.00
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  Tracer #16              : 16  DST2    29.00
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  Tracer #17              : 17  SOG2  160.00
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  Tracer #17              : 17  DST3    29.00
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  Tracer #18              : 18  SOG3  220.00
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  Tracer #18              : 18  DST4    29.00
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  Tracer #19              : 19  SOG4  130.00
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  Tracer #19              : 19  SALA    36.00
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  Tracer #20              : 20  SOG5  150.00
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  Tracer #20              : 20  SALC    36.00
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  Tracer #21              : 21  SOA1   150.00
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  Tracer #21              : 21  MTPA   136.23
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  Tracer #22              : 22  SOA2   160.00
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  Tracer #22              : 22  LIMO   136.23
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  Tracer #23              : 23  SOA3   220.00
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  Tracer #23              : 23  MTPO   136.23
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  Tracer #24              : 24  SOA4  130.00
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  Tracer #24              : 24  TSOG1  150.00
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  Tracer #25              : 25  SOA5  150.00
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  Tracer #25              : 25  TSOG2  150.00
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  Tracer #26              : 26  DST1  29.00
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  Tracer #26              : 26  TSOG3  150.00
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  Tracer #27              : 27  DST2  29.00
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  Tracer #27              : 27  TSOG0  150.00
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  Tracer #28              : 28  DST3  29.00
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  Tracer #28              : 28  TSOA1  150.00
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  Tracer #29              : 29  DST4  29.00
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  Tracer #29              : 29  TSOA2  150.00
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  Tracer #30              : 30  SALA  36.00
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  Tracer #30              : 30  TSOA3  150.00
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  Tracer #31              : 31  SALC  36.00
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  Tracer #31              : 31  TSOA0  150.00
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  Tracer #32              : 32  ISOG1  150.00
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This list can be reduced by turning off any aerosol species (eg. SOA, dust, SS, etc). You may also run without the secondary organic aerosols (ALPH, LIMO, ALCO, SOG{1,2,3,4,5}, SOA{1,2,3,4,5}) if you wish (but we recommend that you use them).
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  Tracer #33              : 33  ISOG2 150.00
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  Tracer #34              : 34  ISOG3 150.00
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=== Run directories ===
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  Tracer #34              : 35   ISOA1  150.00
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Tracer #36              : 36  ISOA2 150.00
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We recommend that you create the run directory for your aerosol-only (a.k.a offline aerosol simulation) from one of the GEOS-Chem full-chemistry run directories.  
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  Tracer #37              : 37  ISOA3  150.00
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Tracer #38              : 38  BENZ    12.00  (6C)
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First, use Git to download one of the [[Secondary organic aerosols#SOA run directories|full-chemistry run directories for the simulation with secondary organic aerosols]].  
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  Tracer #39              : 39  TOLU    12.00  (7C)
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  Tracer #40              : 40  XYLE    12.00  (8C)
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Next, edit the TRACER MENU section of the <tt>input.geos</tt> file so that only the [[#Tracer list|aerosol tracers are listed]].  
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Tracer #41             : 41  ASOG1  150.00
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  Tracer #42              : 42  ASOG2 150.00
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Next, create a new restart file that contains only the aerosol tracers. The easiest way to do this is with [http://acmg.seas.harvard.edu/gamap/ GAMAP]. Start GAMAP and Then all you’d have to do is change the number of tracers in “input.geos”.  You could also create a new restart file with GAMAP.  Start GAMAP with:
+
  Tracer #43              : 43  ASOG3 150.00
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Tracer #44              : 44  ASOAN  150.00
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   gamap, file=’restart.4x5.geos5.2004010100', 'IJ-AVG-$'
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Tracer #45              : 45  ASOA1  150.00
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Tracer #46              : 46  ASOA2  150.00
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Then pick the tracers you want to save, and type
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Tracer #47              : 47  ASOA3 150.00
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+
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  S25-56    # this is DMS .. SALC in the 59-tracer SOA fullchem file
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+
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and when prompted for an output file name, type
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+
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  restart.4x5.geos5.2004010100.aer_only
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+
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and press "OK". Make sure to add this restart file name to the SIMULATION MENU section of your input.geos file.
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You may also need to create an [[Secondary organic aerosols#The SOA restart file|SOA restart file]] which contains the concentrations of various short-lived secondary organic aerosol quantities.  
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Please also see the following references:
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+
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# GEOS-Chem User's Guide: [http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html Chapter 5: GEOS-Chem run directories]
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# GEOS-Chem User's Guide: [http://acmg.seas.harvard.edu/geos/doc/man/chapter_6.html#6.1.6 Chapter 6.1.6: Checklist for offline aerosol chemistry simulation]
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−
 
+
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--[[User:Bmy|Bob Y.]] 17:12, 3 March 2011 (EST)
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== More Information ==
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For more information, see the GEOS-Chem manual pages about offline aerosols:
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  http://acmg.seas.harvard.edu/geos/doc/man/chapter_6.html#6.1.6
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http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html#A1.8
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== Known issues ==
+
−
 
+
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=== Emissions not included when using non-local PBL mixing scheme ===
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−
 
+
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'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02l|v9-02l]] and approved on 26 Jun 2013.'''''
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−
 
+
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It was discovered in [[GEOS-Chem v9-01-03]] that the emissions were not being added into tracer concentration when the non-local PBL scheme was turned on in input.geos. To solve this problem, the following code needs to be added to routine VDIFFDR (vdiff_mod.F90) in the same loop where emissions are added for the full-chemistry simulation:
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−
 
+
−
      !----------------------------------------------------------------
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      ! Add emissions for offline aerosol simulation
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      !----------------------------------------------------------------
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      IF ( IS_AEROSOL ) THEN
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          ! add surface emis of aerosols
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          ! (after converting kg/box/timestep to kg/m2/s)
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          ! Should NOT use ID_EMITTED here, since it is only for gases
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          ! for SMVGEAR. (Lin, 06/10/08)
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          do N = 1, N_TRACERS
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             eflx(I,J,N) = eflx(I,J,N) + emis_save(I,J,N)      &
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                                      / GET_AREA_M2( I, J, 1 ) &
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                                      / GET_TS_EMIS() / 60.d0
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          enddo
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      ENDIF
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At the top of the same routine, <tt>IS_AEROSOL</tt> needs to be defined as:
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    LOGICAL :: IS_AEROSOL
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    IS_AEROSOL = ITS_AN_AEROSOL_SIM()
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--[[User:Melissa Payer|Melissa Payer]] 12:01, 19 June 2013 (EDT)
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=== Bugs in reading EMEP and EPA-NEI data from disk ===
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The following issues exist in [[GEOS-Chem v9-01-01]] and higher versions. These have not yet been resolved.
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# [[GEOS-Chem v9-01-02#Fixes in emep_mod.f|Minor issue in <tt>emep_mod.f</tt> affecting the offline aerosol simulation]]
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# [[GEOS-Chem v9-01-02#Fix for offline simulations in nei2005_anthro_mod.f|Minor issue in <tt>nei2005_anthro_mod.f</tt> affecting the offline aerosol simulation]]
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−
 
+
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--[[User:Bmy|Bob Y.]] 11:48, 8 August 2011 (EDT)
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=== ND05 diagnostic quantities zeroed unexpectedly ===
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'''''Helen McIntyre wrote:'''''
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:I'm running the new and old versions of GEOS-Chem, and both seem to not output all the ND05 diagnostics correctly. There are 10 prod/loss diagnostics in this category, but only the 5th, 6th and 7th work. All the rest come out as zero.
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:I've had a brief look though the code, and it seems that the ones that work are calculated in one part of the routine (<tt>sulfate_mod.f</tt>), and the zero ones in another (I don't know if this has anything to do with it).
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:I've just done a 1 day run, with [[GEOS-Chem v8-01-01]] at 4x5 resolution using GEOS-5 met fields. The old version I'm using is v7-02-04 and I get the same result.
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:The 'ctm.bpch', 'geos.log' and 'input.geos' files from the v8-01-01 run can be found here: http://homepages.see.leeds.ac.uk/~lechlm/files/
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'''''Claire Carouge replied:'''''
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:There are some problems in the calculations. For the 5th element of AD05 (in Fortran notations and not IDL), the diagnostic come from the value of L1 which is calculated line 1529 (v8-01-04):
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+
−
    L1    = ( SO20 - SO2_cd + PSO2_DMS(I,J,L) ) * RK1/RK
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+
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:But on line 1508, we have:
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+
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    RK1 = 0.d0
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:with the previous comment:
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  ! For online runs, SMVGEAR deals w/ this computation,
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  ! so we can simply set RK1 = 0 (rjp, bmy, 3/23/03)
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:So L1 is always 0. I have no idea what RK1 is for, you may have to go into the physics/chemistry behind the code and we are not qualified to help you with it.
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:The other values for AD05 are calculated in the routine CHEM_DMS and this routine is only called in an offline aerosol simulation (l. 545 in <tt>sulfate_mod.f</tt>).
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This list can be reduced by turning off any aerosol species (eg. SOA, dust, SS, etc). You may also run without the secondary organic aerosols (MTPA, LIMO, MTPO, TSOG0–3, TSOA0–3, ISOG1–3, ISOA1–3, ASOG1–3, ASOA1–3, ASOAN) if you wish (but we recommend that you use them).
  
−
:So my guess is that the ND05 diagnostic was designed for offline simulations and if you want it for online chemistry, you need to implement it.
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--[[User:Melissa Payer|Melissa Sulprizio]] 12:51, 5 November 2013 (EST)

Latest revision as of 21:01, 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 aerosol-only (a.k.a. offline aerosol) simulation.

Description

The aerosol simulation is an offline simulation for aerosol tracers only. It uses archived monthly mean OH, NO3, O3 and total nitrate concentrations archived from a previous full-chemistry simulation (more on that below), as well as production and loss rates for H2O2. This simulation does not provide "tagged" capabilities, but reduces the suite of tracers from full chemistry.

NOTES:

  1. The aerosol-only simuation is currently functional in GEOS-Chem Classic.
  2. There is currently no aerosol-only run directory for GCHP. Interested users are encouraged to make this modification on their own.
  3. OH concentrations are archived from the most recent 10-year benchmark simulation.
  4. O3, NO3 and total nitrate (HNO3+NIT) concentrations, as well as production rates and photolysis rates for H2O2 are archived from the most recent 10-year benchmark simulation.

--Bob Yantosca (talk) 16:06, 25 August 2022 (UTC)

Practicalities

As with all other Offline chemistry simulations, the GEOS-Chem user community shall be responsible for the scientific content and validation of the aerosol-only simulation.

The SOA simulation was updated in GEOS-Chem v9-02o to include a better tracer lumping scheme, as shown in Figure 1 of Pye et al. 2010.

The offline aerosol is simulation type 10. For a full set of aerosol tracers (based on the 100-tracer full-chemistry SOA simulation), the input.geos should look like this: 

Type of simulation      : 10
Number of Tracers       : 47
Tracer Entries -------> : TR#  Name   g/mole   Tracer Members; () = emitted
Tracer #1               :  1   DMS     62.00
Tracer #2               :  2   SO2     64.00
Tracer #3               :  3   SO4     96.00
Tracer #4               :  4   SO4s    96.00
Tracer #5               :  5   MSA     96.00
Tracer #6               :  6   NH3     17.00
Tracer #7               :  7   NH4     18.00
Tracer #8               :  8   NIT     62.00
Tracer #9               :  9   NITs    62.00
Tracer #10              : 10   H2O2    34.00
Tracer #11              : 11   BCPI    12.00
Tracer #12              : 12   OCPI    12.00
Tracer #13              : 13   BCPO    12.00
Tracer #14              : 14   OCPO    12.00
Tracer #15              : 15   DST1    29.00
Tracer #16              : 16   DST2    29.00
Tracer #17              : 17   DST3    29.00
Tracer #18              : 18   DST4    29.00
Tracer #19              : 19   SALA    36.00
Tracer #20              : 20   SALC    36.00
Tracer #21              : 21   MTPA   136.23
Tracer #22              : 22   LIMO   136.23
Tracer #23              : 23   MTPO   136.23
Tracer #24              : 24   TSOG1  150.00
Tracer #25              : 25   TSOG2  150.00
Tracer #26              : 26   TSOG3  150.00
Tracer #27              : 27   TSOG0  150.00
Tracer #28              : 28   TSOA1  150.00
Tracer #29              : 29   TSOA2  150.00
Tracer #30              : 30   TSOA3  150.00
Tracer #31              : 31   TSOA0  150.00
Tracer #32              : 32   ISOG1  150.00
Tracer #33              : 33   ISOG2  150.00
Tracer #34              : 34   ISOG3  150.00
Tracer #34              : 35   ISOA1  150.00
Tracer #36              : 36   ISOA2  150.00
Tracer #37              : 37   ISOA3  150.00
Tracer #38              : 38   BENZ    12.00   (6C)
Tracer #39              : 39   TOLU    12.00   (7C)
Tracer #40              : 40   XYLE    12.00   (8C)
Tracer #41              : 41   ASOG1  150.00
Tracer #42              : 42   ASOG2  150.00
Tracer #43              : 43   ASOG3  150.00
Tracer #44              : 44   ASOAN  150.00
Tracer #45              : 45   ASOA1  150.00
Tracer #46              : 46   ASOA2  150.00
Tracer #47              : 47   ASOA3  150.00

This list can be reduced by turning off any aerosol species (eg. SOA, dust, SS, etc). You may also run without the secondary organic aerosols (MTPA, LIMO, MTPO, TSOG0–3, TSOA0–3, ISOG1–3, ISOA1–3, ASOG1–3, ASOA1–3, ASOAN) if you wish (but we recommend that you use them).

--Melissa Sulprizio 12:51, 5 November 2013 (EST)

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