Aerosol-only simulation: Difference between revisions

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__FORCETOC__
'''''[[Simulations using KPP-built mechanisms|Previous]] | [[CH4 simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''
#[[Simulations using KPP-built mechanisms|Simulations using KPP-built mechanisms (carbon, fullchem, Hg)]]
#<span style="color:blue">'''Aerosol-only simulation'''</span>
#[[CH4 simulation]]
#[[CO2 simulation]]
#[[Metals simulation]]
#[[POPs simulation]]
#[[Tagged CO simulation]]
#[[Tagged O3 simulation]]
#[[TransportTracers simulation]]
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.


Line 4: Line 17:
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.


== Assumptions ==
NOTES:
# 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.
# The aerosol-only simuation is currently functional in GEOS-Chem Classic.
# 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.
# 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.
# 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.


== Practicalities ==
== Practicalities ==


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.
As with all other specialty 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.
 
=== Tracer list ===
 
==== GEOS-Chem v9-01-03 and earlier versions ====
 
In [[GEOS-Chem v9-01-03]] and earlier versions, there are 31 tracers in a complete aerosol-only simulation (see input.geos below). 
 
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:
 
Type of simulation      : 10
Number of Tracers      : 31
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    MSA    96.00
Tracer #5              : 5    NH3    17.00
Tracer #6              : 6    NH4    18.00
Tracer #7              : 7    NIT    62.00
Tracer #8              : 8    H2O2  34.00
Tracer #9              : 9    BCPI  12.00
Tracer #10              : 10  OCPI  12.00
Tracer #11              : 11  BCPO  12.00
Tracer #12              : 12  OCPO  12.00
Tracer #13              : 13  ALPH  136.23
Tracer #14              : 14  LIMO  136.23
Tracer #15              : 15  ALCO  142.00
Tracer #16              : 16  SOG1  150.00
Tracer #17              : 17  SOG2  160.00
Tracer #18              : 18  SOG3  220.00
Tracer #19              : 19  SOG4  130.00
Tracer #20              : 20  SOG5  150.00
Tracer #21              : 21  SOA1  150.00
Tracer #22              : 22  SOA2  160.00
Tracer #23              : 23  SOA3  220.00
Tracer #24              : 24  SOA4  130.00
Tracer #25              : 25  SOA5  150.00
Tracer #26              : 26  DST1  29.00
Tracer #27              : 27  DST2  29.00
Tracer #28              : 28  DST3  29.00
Tracer #29              : 29  DST4  29.00
Tracer #30              : 30  SALA  36.00
Tracer #31              : 31  SALC  36.00
 
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 (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).
 
==== GEOS-Chem v9-02 and later versions ====


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].
The 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].


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:
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:
Line 116: Line 84:
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).
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).


--[[User:Melissa Payer|Melissa Sulprizio]] 12:51, 5 November 2013 (EST)
----
 
'''''[[Simulations using KPP-built mechanisms|Previous]] | [[CH4 simulation|Next]] | [[Guide to GEOS-Chem simulations]]'''''
=== Run directories ===
 
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. 
 
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]]. 
 
Next, edit the TRACER MENU section of the <tt>input.geos</tt> file so that only the [[#Tracer list|aerosol tracers are listed]].
 
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:
 
  gamap, file=’restart.4x5.geos5.2004010100', 'IJ-AVG-$'
 
Then pick the tracers you want to save, and type
 
  S25-56    # this is DMS .. SALC in the 59-tracer SOA fullchem file
 
and when prompted for an output file name, type
 
  restart.4x5.geos5.2004010100.aer_only
 
and press "OK".  Make sure to add this restart file name to the SIMULATION MENU section of your input.geos file.
 
If you are using [[GEOS-Chem v9-01-03]] or earlier versions, 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. The SOA restart file is no longer needed in [[GEOS-Chem v9-02]], as part of the [[Secondary_organic_aerosols#SOA_simulation_with_semi-volatile_POA|SOA simulation updates]] by Havala Pye.
 
Please also see the following references:
 
# GEOS-Chem User's Guide: [http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html Chapter 5: GEOS-Chem run directories]
# 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]
 
--[[User:Bmy|Bob Y.]] 17:12, 3 March 2011 (EST)
 
== More Information ==
For more information, see the GEOS-Chem manual pages about offline aerosols:
[http://acmg.seas.harvard.edu/geos/doc/man/chapter_6.html#Aerosols http://acmg.seas.harvard.edu/geos/doc/man/chapter_6.html#6.1.6]
[http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html#Aerosols http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html#A1.2]
 
== Previous issues that have now been resolved ==
 
=== Error in ISOROPIAII when sulfate aerosols are turned off ===
 
<span style="color:green">'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem v9-02 benchmark history#1-month benchmark with GEOS-5 meteorology|v9-02r]] and approved on 14 Nov 2013.'''''</span>
 
'''''[mailto:cbuten@pdx.edu Chris Butenhoff] wrote:'''''
 
:I set ONLINE SULFATE AEROSOLS = F and removed the sulfate aerosols from the tracer list. However I now get the error "IDTSO4 is undefined" from  <tt>isoropia11_mod.F</tt> (line 207).
 
For full-chemistry simulations, we only call routine <tt>DO_ISOROPIAII</tt> if sulfate aerosols are used (i.e. LSULF = T). However, no such check exists when running the offline aerosol simulation. This was probably an oversight and we should add the following fix to routine <tt>DO_CHEMISTRY</tt> (in <tt>GeosCore/chemistry_mod.F</tt>):
 
            !*** AEROSOL THERMODYNAMIC EQUILIBRIUM ***
            '''IF ( LSULF ) THEN'''
              IF ( LSSALT ) THEN
#if  !defined( NO_ISORROPIA )
                  ! ISOROPIA takes Na+, Cl- into account
                  CALL DO_ISOROPIAII
    &              ( am_I_Root, Input_Opt, State_Met, State_Chm, RC )
#endif
              ELSE
                  ! RPMARES does not take Na+, Cl- into account
                  ! (skip for crystalline & aqueous offline run)
                  IF ( .not. LCRYST ) THEN
                    CALL DO_RPMARES( am_I_Root, Input_Opt,
    &                                State_Met, State_Chm, RC )
                  ENDIF
              ENDIF
            '''ENDIF'''
 
--[[User:Bmy|Bob Y.]] 15:29, 14 November 2013 (EST)
 
=== Bug in routine GET_WETDEP_NMAX when using SOA ===
 
The following issue exists in [[GEOS-Chem v9-01-03]] and earlier versions. This issue was resolved in [[GEOS-Chem v9-02]].
 
'''''[mailto:cbuten@pdx.edu Chris Butenhoff] wrote:'''''
 
:There appears to be a bug in <tt>wetscav_mod.F</tt>. In line 6978 the number of carbon + SOA aerosols in the tracer list should be 17 not 15. This is set correctly for the fullchem simulation but not offline simulations.
 
The corrected code is shown below:
 
      ELSE IF ( ITS_AN_AEROSOL_SIM() ) THEN
        !-----------------------
        ! Offline simulation
        !-----------------------
        NMAX = 0
        IF ( LSULF  )  NMAX = NMAX + 9        ! add 9 sulfur species
        IF ( LCRYST )  NMAX = NMAX + 5        ! add 5 cryst & aq species
        IF ( LDUST  )  NMAX = NMAX + NDSTBIN  ! Add number of dust bins
        IF ( LSSALT )  NMAX = NMAX + 2        ! plus 2 seasalts
        IF ( LSOA ) THEN
            IF ( LCARB ) NMAX = NMAX + '''17'''      ! carbon + SOA aerosols
        ELSE
            IF ( LCARB ) NMAX = NMAX + 4        ! just carbon aerosols
        ENDIF
 
--[[User:Melissa Payer|Melissa Sulprizio]] 11:17, 5 November 2013 (EST)
 
=== Emissions not included when using non-local PBL mixing scheme ===
 
<span style="color:green">'''''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.'''''</span>
 
<span style="color:red">'''''This code was removed from [[GEOS-Chem v10-01]] and newer versions.  All emissions are now implemented via the [[HEMCO|HEMCO emissions component]].'''''</span>
 
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:
 
      !----------------------------------------------------------------
      ! Add emissions for offline aerosol simulation
      !----------------------------------------------------------------
      IF ( IS_AEROSOL ) THEN
          ! add surface emis of aerosols
          ! (after converting kg/box/timestep to kg/m2/s)
          ! Should NOT use ID_EMITTED here, since it is only for gases
          ! for SMVGEAR. (Lin, 06/10/08)
          do N = 1, N_TRACERS
            eflx(I,J,N) = eflx(I,J,N) + emis_save(I,J,N)      &
                                      / GET_AREA_M2( I, J, 1 ) &
                                      / GET_TS_EMIS() / 60.d0
          enddo
      ENDIF
 
At the top of the same routine, <tt>IS_AEROSOL</tt> needs to be defined as:
 
    LOGICAL :: IS_AEROSOL
    IS_AEROSOL  = ITS_AN_AEROSOL_SIM()
 
--[[User:Melissa Payer|Melissa Payer]] 12:01, 19 June 2013 (EDT)
 
=== Bugs in reading EMEP and EPA-NEI data from disk ===
 
<span style="color:red">'''''In [[GEOS-Chem v10-01]] and higher versions, EMEP and EPA/NEI emissions are handled by the [[HEMCO|HEMCO emissions component]].'''''</span>
 
The following issues exist in [[GEOS-Chem v9-01-01]] and higher versions. These issues were resolved in [[GEOS-Chem v9-01-03]].
 
# [[GEOS-Chem v9-01-02#Fixes in emep_mod.f|Minor issue in <tt>emep_mod.f</tt> affecting the offline aerosol simulation]]
# [[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]]
 
--[[User:Bmy|Bob Y.]] 11:48, 8 August 2011 (EDT)
 
== Known issues ==
 
=== ND05 diagnostic quantities zeroed unexpectedly ===
 
<span style="color:red">'''''In [[GEOS-Chem v11-01]], we shall be implementing netCDF-based diagnostics.  These will render the "binary punch" format diagnostics obsolete.'''''</span>
 
'''''Helen McIntyre wrote:'''''
: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.
 
: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).
 
: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.
 
: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/
 
'''''Claire Carouge replied:'''''
 
: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):
 
    L1    = ( SO20 - SO2_cd + PSO2_DMS(I,J,L) ) * RK1/RK
 
:But on line 1508, we have:
 
    RK1 = 0.d0
 
:with the previous comment:
 
  ! For online runs, SMVGEAR deals w/ this computation,
  ! so we can simply set RK1 = 0 (rjp, bmy, 3/23/03)
 
: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.
 
: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>).
 
: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.

Latest revision as of 15:43, 21 May 2024

Previous | Next | Guide to GEOS-Chem simulations

  1. Simulations using KPP-built mechanisms (carbon, fullchem, Hg)
  2. Aerosol-only simulation
  3. CH4 simulation
  4. CO2 simulation
  5. Metals 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.

Practicalities

As with all other specialty 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).

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