Aerosol-only 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.
Assumptions
- 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.
- 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:
- GEOS-Chem User's Guide: Chapter 5: GEOS-Chem run directories
- 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 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.
- Minor issue in emep_mod.f affecting the offline aerosol simulation
- 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.