Aerosol-only simulation

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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.

Assumptions

  1. 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.
  2. 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.

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.

Tracer list

In a complete aerosol-only simulation there are 31 tracers (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).

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 full-chemistry run directories for the simulation with secondary organic aerosols.

Next, edit the TRACER MENU section of the input.geos file so that only the aerosol tracers are listed.

Next, create a new restart file that contains only the aerosol tracers. The easiest way to do this is with 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.

You may also need to create an SOA restart file which contains the concentrations of various short-lived secondary organic aerosol quantities.

Please also see the following references:

  1. GEOS-Chem User's Guide: Chapter 5: GEOS-Chem run directories
  2. GEOS-Chem User's Guide: Chapter 6.1.6: Checklist for offline aerosol chemistry simulation

--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#6.1.6
http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html#A1.8

Known issues

Emissions are not included when using non-local PBL mixing scheme

NOTE: This bug fix is slated for inclusion in GEOS-Chem v9-02.

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, IS_AEROSOL needs to be defined as:

   LOGICAL :: IS_AEROSOL
   IS_AEROSOL  = ITS_AN_AEROSOL_SIM()

--Melissa Payer 12:01, 19 June 2013 (EDT)

Bugs in reading EMEP and EPA-NEI data from disk

The following issues exist in GEOS-Chem v9-01-01 and higher versions. These have not yet been resolved.

  1. Minor issue in emep_mod.f affecting the offline aerosol simulation
  2. Minor issue in nei2005_anthro_mod.f affecting the offline aerosol simulation

--Bob Y. 11:48, 8 August 2011 (EDT)

ND05 diagnostic quantities zeroed unexpectedly

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 (sulfate_mod.f), 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 sulfate_mod.f).
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.