View source for Secondary organic aerosols

== Overview ==

=== Original formulation ===

From [http://acmg.seas.harvard.edu/publications/liao2006/Liao2007.pdf ''Liao et al'' <nowiki>[2007]</nowiki>]:

<blockquote>Formation of SOA in the GEOS-Chem model is predicted based upon rate constants and aerosol yield parameters determined from laboratory chamber studies [''Seinfeld and Pankow'', 2003]. SOA formation from isoprene photooxidation follows the work of ''Henze and Seinfeld'' [2006], which is based on chamber experiments of reaction of isoprene with OH at low NOx condition [Kroll et al., 2006]. Simulation of SOA from monoterpenes and other reactive VOCs (ORVOCs) is described by ''Chung and Seinfeld [2002]''; for computational efficiency we have reduced the number of tracers from 33 in that work to 9 by lumping oxidation products together. As in the work by ''Chung and Seinfeld'' [2002], monoterpenes and ORVOCs are
divided into five hydrocarbon classes according to the values of their experimentally measured aerosol yield parameters [''Griffin et al.'', 1999a].  In this study, each of the hydrocarbon classes I, II and IV is treated as a tracer, while classes III and V are diagnosed at each time step based on emissions. Hydrocarbon classes III and V are not transported in the model because of their high reactivity. For each of the first four primary reactive hydrocarbon classes, there are three oxidation products, two for combined O3 and OH oxidation and one for NO3 oxidation. In the case of hydrocarbon class V (sesquiterpenes), only two products are required (one for combined O3 and OH oxidation and one for NO3 oxidation). All products are semivolatile and partition between the gas and aerosol phases, leading to a total of 28 oxidation products. During chemistry simulation, the chemical reactions and the number of SOA-related species in the GEOS-Chem are exactly
the same as those of ''Chung and Seinfeld'' [2002]. When the chemistry calculation is finished, the gas phase products
from the oxidation of hydrocarbon classes I, II, and III are lumped into one tracer, because they will have the same behavior during transport since they are assumed to have the same molecular weight and Henry's law constant. The mass
ratios of the individual oxidation products to the total mass of lumped products in each grid cell are then used to
partition the tracer back into individual products before the chemistry simulation of the next time step. Similarly,
we aggregate all the aerosol phase products from the oxidation of hydrocarbon classes I, II, and III into one tracer, and treat the gas phase and aerosol phase oxidation products from each of hydrocarbon group IV, hydrocarbon group V, and isoprene as one tracer.</blockquote>

=== Updates ===

Additions since [http://acmg.seas.harvard.edu/publications/liao2006/Liao2007.pdf ''Liao et al'' <nowiki>[2007]</nowiki>]:

# [[#Modification to SOA formation|Modifications to SOA formation]] (in [[GEOS-Chem v8-03-01|v8-03-01]])
# [[#SOA formation from aromatics|SOA formation from aromatics]] (in [[GEOS-Chem v8-03-01|v8-03-01]])

--[[User:Bmy|Bob Y.]] 12:46, 17 March 2010 (EDT)

==Current Parent Hydrocarbons Treated==
The following parent hydrocarbons form SOA according to absorptive paritioning following the framework by Chung and Seinfeld 2002:
{| border=1 cellspacing=0 cellpadding=5
|- bgcolor="#cccccc"
!Parent HC Class	
!Parent Hydrocarbons	
!Oxidants
!NOx Levels Considered
!Tracers
!Reference
!GEOS-Chem version 
|-
|1
|pinene, sabinene, carene, terpenoid ketones
|OH, O3, NO3
|1
|SOA/G1
|Chung and Seinfeld 2002
| 
|-
|2
|limonene
|OH, O3, NO3
|1
|SOA/G1
|Chung and Seinfeld 2002
| 
|-
|3
|terpinene, terpinolene
|OH, O3, NO3
|1
|SOA/G1
|Chung and Seinfeld 2002
| 
|-
|4
|myrcene, terpenoid alcohols, ocimene
|OH, O3, NO3
|1
|SOA/G2
|Chung and Seinfeld 2002
|
|-
|5
|sesquiterpenes
|OH, O3, NO3
|1
|SOA/G3
|Chung and Seinfeld 2002
| 
|-
|6
|isoprene
|OH
|1 (low NOx)
|SOA/G4
|Henze and Seinfeld 2006
| 
|-
|7
|benzene
|OH followed by HO2 or NO
|2 (high and low NOx)
|SOA/G5
|Henze et al. 2008
|planned [[GEOS-Chem v8-03-01|v8-03-01]]
|-
|8
|toluene
|OH followed by HO2 or NO
|2 (high and low NOx)
|SOA/G5
|Henze et al. 2008
|planned v8-03-01
|-
|9
|xylene
|OH followed by HO2 or NO
|2 (high and low NOx)
|SOA/G5
|Henze et al. 2008
|planned v8-03-01
|-
|}

Additional Important Parameters (based on Chung and Seinfeld):
:Henry's Law Coefficient for SOG species: 10^5 M/atm
:Enthalpy of Vaporization for equilibrium partitioning coefficient adjustment: 42 kJ/mol

--[[User:Havala|havala]] 13:11, 24 February 2010 (EST)

== The SOA restart file ==
The SOA restart files have been introduced in v7-04-11. They are required for GEOS-Chem [http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html#A1.3 full-chemistry] and/or [http://acmg.seas.harvard.edu/geos/doc/man/appendix_1.html#A1.8 offline aerosol simulations] that use the secondary organic aerosol tracers.

For versions '''v7-04-11 to v8-02-04''', this restart file is named restart_gprod_aprod.YYYYMMDDhh.

For versions '''v8-03-01 and after''', this restart file is named soaprod.YYYYMMDDhh

restart_gprod_aprod.YYYYMMDDhh files only have data about the SOA/G1 to SOA/G4 species. In soaprod.YYYYMMDDhh files there is additional data for SOA/G5. 


The following explanation is valid for the SOA restart files of any version.

'''''[mailto:havala@caltech.edu Havala Olson Taylor Pye] wrote:'''''

:Before [the restart_gprod_aprod.YYYYMMDDhh files were introduced in v7-04-11], if you started a run from a restart file (even one from a run that was well initialized), the global SOA burden would drop dramatically in the first time step to about half of what the restart file said it should be. The GPROD/APROD values were not being stored.  These values relate to how much gas or aerosol phase product belongs to each hydrocarbon/oxidant combination.

:SOA is somewhat unique in that in the model, it can evaporate and exist in the same chemical form (SOG). I didn't notice a dip in the burden for SO4, NIT (gas phase form would be HNO3), or NH4 (gas phase form would be NH3).

Note that the restart_gprod_aprod.YYYYMMDDhh are strict in their usage.  They cannot change name, and the dates in the filename, of the simulation, and in the data block headers inside the file, must all be the same. 

See the following note about [[File_I/O_with_GAMAP#Renaming_and_Regridding_APROD.2FGPROD_restart_files|renaming and regridding restart_gprod_aprod.YYYYMMDDhh files.]]

Also see the following note about a [[Common_GEOS-Chem_error_messages#Error_when_reading_the_.22restart_gprod_aprod.22_file|common error message that can occur]] with the restart_gprod_aprod.YYYYMMDDhh files.

--[[User:Bmy|Bob Y.]] 16:07, 19 February 2010 (EST)

Note that the restart file is require because species of different volatilities are lumped together into the same tracer. Unless you know how much of each volatility species is in the tracer, the partitioning will be incorrect upon restart. restart_gprod_aprod keeps track of how much of each individual species is in the lumped SOA and SOG tracers.
--[[User:Havala|havala]] 13:39, 24 February 2010 (EST)

The restart file name was changed from v8-03-01 to soaprod.YYYYMMDDhh.

== Modification to SOA formulation ==

The following modification will be added to [[GEOS-Chem v8-03-01]].

'''''[mailto:heald@atmos.colostate.edu Colette Heald] wrote:'''''

:SOA formation should not depend on the mass on inorganics.  Specifically, in <tt>carbon_mod.f</tt>, MPOC in the code should only consist of organic aerosol.

:We carry carbon mass only in the STT array and multiply by 2.1 to account for non-carbon mass in the SOA.

:Partitioning theory (Pankow, 1994) describes organic phase partitioning assuming absorption into pre-existing organic mass.  There is currently no theoretical or laboratory support for absorption of organics into inorganics. 

:Note that previous versions of the standard code (v7-04-07 through [[GEOS-Chem v8-02-04|v8-02-04]]) did include absorption into inorganics. (Colette Heald, 12/3/09)

--[[User:Bmy|Bob Y.]] 12:29, 17 March 2010 (EDT)

== SOA formation from aromatics ==

The following modification will be added to [[GEOS-Chem v8-03-01]]:

... Text needs to be added here ...

== References ==

#Chung, S. H., and J. H. Seinfeld, ''Global distribution and climate forcing of carbonaceous aerosols'', <u>J. Geophys. Res.</u>, '''107'''(D19), 4407, doi:10.1029/2001JD001397, 2002.
#Liao, H., et al., ''Biogenic Secondary Organic Aerosol over the United States: Comparison of Climatological Simulations with Observations'', <u>J. Geophys. Res.</u>, '''112''', 2007. [http://acmg.seas.harvard.edu/publications/liao2006/Liao2007.pdf PDF]
#Henze, D. K., and J. H. Seinfeld, ''Global secondary organic aerosol from isoprene oxidation'',<u>Geophys. Res. Lett.</u>, '''33''', L09812, 2006.
#Seinfeld, J. H., and J. F. Pankow, ''Organic atmospheric particulate material'', <u>Ann. Rev. Phys. Chem.</u>, 54, 121–140, 2003.
#Henze, D. K., et al., ''Global modeling of secondary organic aerosol formation from aromatic hydrocarbons: High- vs. low-yield pathways'', <u>Atmos. Chem. Phys.</u>, '''8''', 2405-2420, 2008.

--[[User:Bmy|Bob Y.]] 16:07, 19 February 2010 (EST)

--[[User:Havala|havala]] 13:15, 24 February 2010 (EST)