Secondary organic aerosols
From Geos-chem
This page describes the GEOS-Chem "full-chemistry" simulation with secondary organic aerosols. You may also run a "lighter" aerosol-only simulation with prescribed oxidant fields with secondary organic aerosols.
Contents |
Overview
Original formulation
From Liao et al [2007]:
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.
Updates
Additions since Liao et al [2007]:
- Modifications to SOA formation (in v8-03-01)
- SOA formation from aromatics (in v8-03-01)
- Speciated biogenic emissions from MEGAN v2.1 (in v8-03-01)
- Semi-volatile POA option (slated for v9-01-03)
--Bob Y. 13:54, 2 August 2011 (EDT)
The current SOA simulation
The following sections describe the current SOA simulation as of GEOS-Chem v8-03-01 and higher versions.
Current Parent Hydrocarbons Treated
The following parent hydrocarbons form SOA according to absorptive paritioning following the framework by Chung and Seinfeld 2002 and Henze et al 2008:
| Parent HC Class | Parent Hydrocarbons | Oxidants | NOx Levels Considered | Tracers | Reference | GEOS-Chem version |
|---|---|---|---|---|---|---|
| 1 | pinene, sabinene, carene, terpenoid ketones | OH, O3, NO3 | 1 | SOA1 SOG1 | Chung and Seinfeld 2002 | Prior to v7-04-04 |
| 2 | limonene | OH, O3, NO3 | 1 | SOA1 SOG1 | Chung and Seinfeld 2002 | " " |
| 3 | terpinene, terpinolene | OH, O3, NO3 | 1 | SOA1 SOG1 | Chung and Seinfeld 2002 | " " |
| 4 | myrcene, terpenoid alcohols, ocimene | OH, O3, NO3 | 1 | SOA2 SOG2 | Chung and Seinfeld 2002 | " " |
| 5 | sesquiterpenes | OH, O3, NO3 | 1 | SOA3 SOG3 | Chung and Seinfeld 2002 | " " |
| 6 | isoprene | OH | 1 (low NOx) | SOA4 SOG4 | Henze and Seinfeld 2006 | Introduced in v7-04-04 |
| 7 | benzene | OH followed by HO2 or NO | 2 (high and low NOx) | SOA5 SOG5 | Henze et al. 2008 | Introduced in v8-03-01 |
| 8 | toluene | OH followed by HO2 or NO | 2 (high and low NOx) | SOA5 SOG5 | Henze et al. 2008 | " " |
| 9 | xylene | OH followed by HO2 or NO | 2 (high and low NOx) | SOA5 SOG5 | Henze et al. 2008 | " " |
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
--havala 13:15, 24 February 2010 (EST)
--Bob Y. 11:43, 8 March 2011 (EST)
Modification to SOA formulation
This modification is included in GEOS-Chem v8-03-01 and higher versions:
Colette Heald wrote:
- SOA formation should not depend on the mass on inorganics. Specifically, in carbon_mod.f, 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 v8-02-04) did include absorption into inorganics. (Colette Heald, 12/3/09)
--Bob Y. 11:43, 8 March 2011 (EST)
SOA formation from aromatics
This modification is included in GEOS-Chem v8-03-01 and higher versions:
... Text needs to be added here ...
--Bob Y. 11:43, 8 March 2011 (EST)
Speciated biogenic emissions from MEGAN
This modification is included in GEOS-Chem v8-03-01 and higher versions:
The MEGAN v2.1 biogenic emissions inventory now contains speciated emissions for secondary organic aerosols. Havala Pye has modified carbon_mod.f to use these speciated emissions.
The table reflects emission totals generated from a GEOS-Chem run with GCAP meteorology for the year 2000:
| HC Class | MEGAN v2.1 (Tg/yr) | MEGAN v2.0 (Tg/yr) |
|---|---|---|
| ALPH | 84 | 92 |
| LIMO | 10 | 27 |
| TERP | 3.2 | 3.5 |
| ALCO | 47 | 38 |
| SESQ | 15 | 15 |
| Total | 159 | 176 |
--Bob Y. 11:43, 8 March 2011 (EST)
SOA simulation with semi-volatile POA
NOTE: This simulation was developed by Havala Pye. This is currently slated for inclusion into GEOS-Chem v9-01-03, along with several other chemistry updates.
Description
Havala Pye wrote:
This simulation updates the traditional SOA simulation to include SOA from isoprene+NO3, NOx dependent monoterpene and sesquiterpene yields, and a better tracer lumping scheme so that different volatility species are not lumped together for transport (old code probably had errors ~30% on a global basis in terms of global aerosol production). The code also allows for the option to replace OCPI and OCPO with a semivolatile aerosol that can age in the gas-phase to form lower volatility products. The semivolatile POA simulation also includes aerosol from intermediate volatility organic compounds (IVOCs) that behave like naphthalene in terms of their aerosol yields and are spatially distributed like naphthalene. Emissions of the POA and naphthalene-like IVOC can be scaled up/down in input.geos relative to the default inventory (default inventories would be indicated with a 1.0). More information can be found in Pye and Seinfeld 2010 and Pye et al. 2010 (both ACP).
In particular, figure 1 of Pye et al. 2010 shows the tracer lumping scheme. The same executable can be used for traditional (OCPO/OCPI) and semivolatile POA simulations; the treatment is determined by which tracers are in input.geos. Emissions of sesquiterpenes are updated to follow MEGAN 2.0.
--Bob Y. 13:55, 2 August 2011 (EDT)
New data files
The following new data files are required for the SOA simulation with semi-volatile POA option:
- MEGAN_PFT_BT.geos.1x1
- MEGAN_PFT_CR.geos.1x1
- MEGAN_PFT_GR.geos.1x1
- MEGAN_PFT_NT.geos.1x1
- MEGAN_PFT_SH.geos.1x1
These contain the coverage of plant functional types based on MEGAN v2.0 on GEOS 1x1 grid for broadleaf trees (BT), crops (CR), grasslands (GR), needleleaf trees (NT), and shrubs (SH). These are needed as input for MEGAN emission calculations.
--Bob Y. 11:54, 8 March 2011 (EST)
The SOA restart file
This section describes the initial conditions files that are required for the SOA simulation.
NOTE: The semi-volatile POA option does not use the SOA restart file and APROD/GPROD arrays because in this simulation, different volatility species are not lumped together.
Overview
The SOA restart files have been introduced in v7-04-11. They are required for GEOS-Chem full-chemistry and/or 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.
The restart_gprod_aprod.YYYYMMDDhh files only have data about the SOA1..SOA4 and SOG1..SOG4 species. In soaprod.YYYYMMDDhh files there is additional data for SOA5 and SOG5.
The following explanation is valid for the SOA restart files of any version.
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 creating, renaming and regridding restart_gprod_aprod.YYYYMMDDhh files.
Also see the following note about a common error message that can occur with the restart_gprod_aprod.YYYYMMDDhh files.
--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.
--havala 13:39, 24 February 2010 (EST)
The restart file name was changed from v8-03-01 to soaprod.YYYYMMDDhh.
Creating a SOA restart file from scratch
Colette Heald wrote:
- I am doing a 2001 GEOS-4 run with SOA using v8-03-01. I downloaded the run directory for this from Harvard using GIT and then used rewrite_agprod to re-date the soaprod file from 20040101 to 20010101 to start my spin-up. However when I start the run it crashes with the "BAD GPROD" messages in the log file. I did download the file a second time to ensure it wasn't due to corruption during the git transfer. Have you guys seen this before? A search on the wiki didn't turn anything up... Do you have any other soa_agprod files for GEOS-4 and v8-03-01 or beyond that I could try out? Other suggestions?
Claire Carouge replied:
- With the new SOA simulation, someone (Havala maybe) added a possibility to create the first SOA restart file from scratch using GEOS-Chem. See this wiki post for more information.
--Bob Y. 15:07, 14 December 2010 (EST)
SOA run directories
As described in Chapter 2.3: Downloading the GEOS-Chem Run Directories in the GEOS-Chem Online User's Guide, you can use a Git Clone command to download run directories for the SOA simulation. Each run directory contains a SOA restart file soaprod.YYYYMMDDhh, a tracer restart file restart.YYYYMMDDhh, and the various input files used to customize the chemical mechanism and simulation options.
We no longer distribute the run directories via TARBALL (*.tar.gz) files. You must use the Git version control software to download the run directories. The download command takes the form:
git clone git://git.as.harvard.edu/bmy/GEOS-Chem-rundirs/DIR-OPTION LOCAL-DIR-NAME
Where:
LOCAL-DIR-NAME is the name under which the run directory will be stored in your disk space.
DIR-OPTION may be one of the following:
Run directories for current SOA simulation
| DIR-OPTION | Description |
|---|---|
| 2x2.5/geos4/SOA | 2 x 2.5 GEOS-4 fullchem w/ secondary organic aerosols option |
| 2x2.5/geos5/SOA | 2 x 2.5 GEOS-5 fullchem w/ secondary organic aerosols option |
| 4x5/geos4/SOA | 4 x 5 GEOS-4 fullchem w/ secondary organic aerosols option |
| 4x5/geos5/SOA | 4 x 5 GEOS-5 fullchem w/ secondary organic aerosols option |
| 4x5/merra/SOA | 4 x 5 MERRA fullchem w/ secondary organic aerosols option |
Run directories for SOA w/ semi-volatile POA
Text to be added
--Bob Y. 11:58, 8 March 2011 (EST)
References
- Chung, S. H., and J. H. Seinfeld, Global distribution and climate forcing of carbonaceous aerosols, J. Geophys. Res., 107(D19), 4407, doi:10.1029/2001JD001397, 2002.
- Henze, D. K., and J. H. Seinfeld, Global secondary organic aerosol from isoprene oxidation,Geophys. Res. Lett., 33, L09812, 2006.
- Henze, D. K., et al., Global modeling of secondary organic aerosol formation from aromatic hydrocarbons: High- vs. low-yield pathways, Atmos. Chem. Phys., 8, 2405-2420, 2008.
- Liao, H., et al., Biogenic Secondary Organic Aerosol over the United States: Comparison of Climatological Simulations with Observations, J. Geophys. Res., 112, 2007. PDF
- Pye, H. O. T., Chan, A. W. H., Barkley, M. P., and Seinfeld, J. H., Global modeling of organic aerosol: the importance of reactive nitrogen (NOx and NO3), Atmos. Chem. Phys., 10, 11261-11276, doi:10.5194/acp-10-11261-2010, 2010. PDF
- Seinfeld, J. H., and J. F. Pankow, Organic atmospheric particulate material, Ann. Rev. Phys. Chem., 54, 121–140, 2003.
--havala 13:15, 24 February 2010 (EST)
--Bob Y. 11:43, 8 March 2011 (EST)
