Secondary organic aerosols

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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.

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]:

  1. Modifications to SOA formation (sincev8-03-01)
  2. SOA formation from aromatics (since v8-03-01)
  3. Speciated biogenic emissions from MEGAN v2.1 (since v8-03-01)
  4. Semi-volatile POA option (added to GEOS-Chem v9-02, public release 03 Mar 2014)

--Bob Y. (talk) 16:23, 26 October 2015 (UTC)

SOA schemes in v11-02 and later

These updates will be included in v11-02c.

The Aerosols Working Group decided on the following options for SOA in GEOS-Chem v11-02 and later.

Please refer to this user document for more details about the SOA options in GEOS-Chem v11-02.

Option 1: Simple SOA scheme

Option 2: Complex SOA scheme

  • Optional GEOS-Chem full-chemistry option
  • Built on the Havala Pye VBS scheme
  • May be used with or without semi-volatile POA (SVPOA is off by default)
  • IMPORTANT: When using the complex SOA scheme, the Aerosols WG warns that the PM2.5 and AOD calculations in GEOS-Chem currently includes all the SOA formed in both the Pye et al. (2010) and Marais et al. (2016) schemes and may include some double-counting of isoprene SOA.

Option 3

  • Used in the benchmark simulations as of v11-02c
  • Combines options 1 and 2 above
  • This option is used in the GEOS-Chem benchmarks so that the community can validate both SOA mechanisms on a regular basis
  • Users may choose to use options 1+2, but are should be aware of the implications listed below
    • This simulation will include *both* simple SOA (SOAP, SOAS) and complex SOA species (TSOA*, ISOA*, ASOA*)
    • Expert users need to think about how/if to combine the complex and simple SOA species
    • Beginner users should not use this option to avoid confusion
    • Colette Heald wrote, "I'm also not clear on what this implies for the gas-phase species as we go towards integrating the aerosol and gas phase chemistry (i.e. if we have simple monoterpene SOA as well as VBS monoterpene SOA produced (i.e. double counting), that messes up mass conservation)."

--Melissa Sulprizio (talk) 21:34, 31 August 2017 (UTC)

Simple SOA scheme

This update was included in v11-02c and approved on 21 Sep 2017.

The following sections describe the proposed SOA simulation updates for GEOS-Chem v11-02.

Starting in GEOS-Chem v11-02, we will have an option for "simple" SOA that forms irreversibly. This option will allow GEOS-Chem users to get approximate the "correct" amount of global SOA without detailed chemistry. This scheme introduces two SOA-related tracers: SOAP (SOA precursor) and SOAS ("simple" SOA in the particle phase). The emission of SOAP is tied directly to emissions of monoterpenes, isoprene, biomass burning CO, biofuel CO, and fossil fuel CO in HEMCO, and SOAP forms SOAS on a fixed timescale of 1 day. 50% of monoterpene and isoprene SOA is emitted directly as SOAS to reduce the average formation time for this SOA.

The default yields specified in the HEMCO configuration file are:

Each of the above yields may be adjusted in the HEMCO configuration file as follows (only the relevant lines are included):

Monoterpenes: 

 109     MEGAN_Mono        : on    CO/MONX/SOAP/SOAS
     --> Monoterp to SOAP  :       0.050
     --> Monoterp to SOAS  :       0.050

Isoprene: 

 108     MEGAN             : on    ISOP/ACET/PRPE/C2H4/ALD2/SOAP/SOAS
     --> Isoprene to SOAP  :       0.015
     --> Isoprene to SOAS  :       0.015

Fossil Fuel Combustion: 

 280      COtoSOAP_anth 0.069      -          -            -   xy    unitless 1

Biomass Burning: 

 111     GFED              : on    NO/CO/ALK4/ACET/MEK/ALD2/PRPE/C3H8/CH2O/C2H6/SO2/NH3/BCPO/BCPI/OCPO/OCPI/POG1/POG2/NAP/SOAP
     --> CO to SOAP        :       0.013
 #OR
 114     FINN              : on    NO/CO/ALK4/ACET/MEK/ALD2/PRPE/C3H8/CH2O/C2H6/SO2/NH3/BCPI/BCPO/OCPI/OCPO/GLYC/HAC/SOAP
     --> Scaling_SOAP      :       0.013
 #AND
 281      COtoSOAP_burn 0.013      -          -            -   xy    unitless 1


This simple SOA scheme works in both the tropchem and TOMAS-microphysics simulations. In TOMAS simulations the SOAS is added to the OCIL species in each size section (following kinetically limited irreversible condensation).

--Jeffrey Pierce (talk) 19:32, 11 May 2017 (UTC)
--Sal Farina (talk) 21:13, 13 May 2017 (UTC)

Complex SOA scheme

SOA simulation with semi-volatile POA

The following sections describe the current SOA simulation as of GEOS-Chem v9-02 and higher versions.

This update was tested in the 1-month benchmark simulation v9-02o and approved on 03 Sep 2013.

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)

Correction in v9-02

Parameters for the updated simulation follow values (alphas and C*) in Table 1 of Pye et al. 2010 with two exceptions. The low-NOx toluene and xylene SOA yields were updated to follow the data in Table 3 of Ng et al. 2007 ACP. Previous values were swapped. The correct values (corrected after v9-02o benchmark) are:

Species Oxidant alpha (yield) for nonvolatile
XYLE OH,HO2 0.36
TOLU OH,HO2 0.30

--havala 13:17, 5 September 2013 (EDT)

New data files

The following new data files are required for the SOA simulation with semi-volatile POA option:

  1. MEGAN_PFT_BT.geos.1x1
  2. MEGAN_PFT_CR.geos.1x1
  3. MEGAN_PFT_GR.geos.1x1
  4. MEGAN_PFT_NT.geos.1x1
  5. 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)

SOA formation from aqueous isoprene uptake

This update was included in v11-02c and approved on 21 Sep 2017.

Please refer to this user document for more details about the SOA options in GEOS-Chem v11-02.

Eloise Marais updated the online chemistry mechanism to account for SOA formation from aqueous isoprene uptake. The original code modifications were made in GEOS-Chem v9-02 and will be brought into the standard code in GEOS-Chem v11-02.

Reference:

Marais, E. A., D. J. Jacob, J. L. Jimenez, P. Campuzano-Jost, D. A. Day, W. Hu, J. Krechmer, L. Zhu, P. S. Kim, C. C. Miller, J. A. Fisher, K. Travis, K. Yu, T. F. Hanisco, G. M. Wolfe, H. L. Arkinson, H. O. T. Pye, K. D. Froyd, J. Liao, V. F. McNeill, Aqueous-phase mechanism for secondary organic aerosol formation from isoprene: application to the southeast United States and co-benefit of SO2 emission controls, Atmos. Chem. Phys., 16, 1603-1618, doi:10.5194/acp-16-1603-2016, 2016. PDF

The updates to the chemical mechanism are listed below:

  • Modifications for updated irreversible SOA uptake and better treatment of gas-phase expoxide oxidation:
  • Add species IMAE and update PMN reaction rates with Lin et al., PNAS, 2013.
  • Update products of the RIO2+HO2, RIO2+NO reaction rates using laboratory data from Liu et al., ACP, 2013.
  • Update products of the IEPOXOO+HO2 and IEPOXOO+NO reactions using lab data from Bates et al., JPC, 2014.
  • Update isoprene nitrate chemistry with mechanism provided in Lee et al., JPC-A (2014). New species is DHDN - a potential SOA precursor.
  • Update to Bates mechanism to replace non-reactive carbon (CO2) with reactive carbon (i.e. the m/z 187 and 189 compounds identified by Bates et al. (2014)). The new species is HC187 and it replaces MOBA as a tracer in GEOS-Chem. Its rate of reaction with OH and products and yields of products are a somewhat informed guess at this stage and will require updating in the future.
  • Update RIO2 self-reaction with new reaction rate (faster than previous) and new product yields from Xie et al., ACP, 2013.
  • Update photolysis reactions and OH-oxidation reactions of carbonyl nitrates based on findings of Muller et al., ACP, 2014.
  • Update isoprene nitrate chemistry to include the formation of IEPOX from ISOPNBO2 and ISOPNDO2 reactions with NO from Jacobs et al., ACP, 2014.
  • Update RIO2 isomerization to be consistent with Stavrakou et al. (2010).
  • Added GLYX, MGLY, and GLYC heterogeneous reactions.
  • Update alkyl nitrates. Assume they form a diol (INDIOL) and HNO3 (based on lab findings by Jacobs et al., 2014). Molecular weight of INDIOL is the molecular weight of the diol formed from ISOPN.
  • Update IEPOX uptake with Joel Thornton's work (Gaston et al., 2014). Added IEPOX het reaction. NOTE the stoichiometric values are arbitary and change depending on H+, SO4, and NITR concentrations.
  • Add low-volatility SOA precursor formed from oxidation of ISOPOOH (RIP). This requires adjusting the yield IEPOX and OH from ISOPOOH+OH and HC5 and OH from the other ISOPOOH+OH pathway and ISOPOOH photolysis. The change is small, but important for SOA yields (Krechmer et al., 2015).
  • Add other loss pathways for ISOPOOH-SOA precursor, LVOC. These should be very small in comparison with aerosol uptake.
  • Include the formation of organic nitrate aerosol from oxidation of isoprene by NO3. The mass yield from nocturnal isoprene should be ~14%. Data for including this in GEOS-Chem is from Ng et al. (2008) and Rollins et al. (2009).
  • Use faster reaction kinetics of IEPOX+OH (Jacobs et al., 2013) (scale IEPOX+OH Arrhenius factor up for a factor of 2.85 relative to the Bates value previously used).
  • Reduced IEPOX yield from ISOPOOH+OH to 75% (low end of Paulot et al. (2009)).

This update was included in v11-02e (Approved 24 Mar 2018).

Colette Heald wrote:

We recommended a switch to turn on/off Eloise's mechanism, but it appears that this chemistry is always on (I don't think we thought through at the time that such a switch would require a whole new set of chemical mechanism files, etc.) and the only difference is whether it is included in the AOD and PM2.5 calculations. We think that this might cause some confusion in the community (and the expert user can always go into the code and make these adjustments themselves). So we'd like to recommend removing this switch prior to the release of v11.02 (and have all the SOA species included in the PM2.5 and AOD calculations in the complex scheme). Obviously this is a somewhat superficial functional change, so it is less urgent.

--Melissa Sulprizio (talk) 22:32, 5 January 2018 (UTC)

Calculation of PM2.5, AOD, and aerosol mass

This update was included in v11-02e (approved 24 Mar 2018).

Daniel Jacob wrote:

The UCX benchmark includes both simple and complex SOA so that we can monitor changes in both, but we decided when finalizing v11-02c that simple SOA should be the GEOS-Chem default. But it turns out that the UCX benchmark currently uses the complex SOA for heterogeneous chemistry, PM2.5, and AOD. That seems to be a mistake – it should be using simple SOA for these calculations. We will make that change unless you object.

--Melissa Sulprizio (talk) 18:57, 12 December 2017 (UTC)

References

  1. Chung, S. H., and J. H. Seinfeld, Global distribution and climate forcing of carbonaceous aerosols, J. Geophys. Res., 107(D19), 4407, DOI, 2002.
  2. Henze, D. K., and J. H. Seinfeld, Global secondary organic aerosol from isoprene oxidation,Geophys. Res. Lett., 33, L09812, 2006. DOI,
  1. 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. DOI,
  2. Liao, H., et al., Biogenic Secondary Organic Aerosol over the United States: Comparison of Climatological Simulations with Observations, J. Geophys. Res., 112, 2007. PDF
  3. 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
  4. 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)

Previous issues that are now resolved

Only add ISOAAQ species to PM2.5 diagnostics for simulations using the complex SOA option

This update will be included during the GEOS-Chem v11-02 provisional release period.

Jenny Fisher wrote:

I am (still) trying to understand the treatment of SOA options in v11-02. Eloise & I thought we had worked it all out when we put together that document a month ago, but looking through the bleeding edge code, there seem to be some inconsistencies between our understanding and the actual implementation.

The question is around the treatment in tropchem & standard simulations of Eloise’s aqueous isoprene SOA species (abbreviated in the code to ISOAAQ = SOAGX + SOAMG + SOAIE + SOAME + LVOCOA + ISN1OA).

Our previous impression was that these SOA species were only being included in the Complex SOA simulations (but that the associated gas-phase chemistry would be included in all simulations).

However, I’ve pulled v11-02e from the bleeding edge code & run directories and have noticed the following in Tropchem (same in Standard):

  1. All ISOAAQ species listed above are included in the species list in input.geos (presumably meaning they are defined with id_ > 0)
  2. There are no differences between Tropchem.eqn and SOA_SVPOA.eqn in the KPP subdirectories that involve any of these species
  3. In aerosol_mod.F:
    • All ISOAAQ species listed above are added to the ISOAAQ array as long as the species ID is > 0, whether or not Complex SOA or Simple SOA is being used.
    • ISOAAQ is then added to the OCPISOA array, again irrespective of whether or not Complex SOA or Simple SOA is being used.
    • ISOAAQ is also added to the PM25 array, again irrespective of whether or not Complex SOA or Simple SOA is being used.

So – my questions are:

  1. Have I misunderstood the behaviour anywhere here?
  2. Is the code actually doing what is intended (i.e. is the intention to include the ISOAAQ in ALL simulations)?
  3. Does this mean there is now double-counting of isoprene SOA between SOAS and the ISOAAQ species?

Colette Heald replied:

Per Jenny's initial email, my understanding is that the simple scheme includes SOA aerosol tracers it should not, and that these are included in the PM2.5 (and possibly AOD?) diagnostics. This is an error. In the meantime, it seems like the simplest thing to do would be to remove those extra SOA species from the PM2.5 (and AOD?) diagnostics for the simple SOA version of v11-02. The tracers will still be there (when they shouldn't be) but we could put a warning on the wiki to tell folks not to double-count these.

Following Colette's recommendation above, to avoid double-counting of SOA, we now add 

 ISOAAQ = SOAGX + SOAMG + SOAIE + SOAME + LVOCOA + ISN10A

to the AOD diagnostics only when the complex SOA option is turned on.

Furthermore, for the PM2.5 diagnostic, we do the following:

  1. For simulations using Simple SOA only (Standard, Tropchem), then SOAS (but not ISOAAQ) will be added to the PM2.5 diagnostic;

  2. For simulations using Complex SOA only (complexSOA and complexSOA_SVPOA), then ISOAAQ (but not SOAS) will be added to the PM2.5 diagnostic;

  3. For the Benchmark simulation (which turns on both simple and complex SOA simultaneously) SOAS but not ISOAAQ will be added to the PM2.5 diagnostic. (This is to avoid double-counting.)

This update will cause the Standard, Tropchem, and Benchmark simulations to have differences in the PM2.5 diagnostic w/r/t the prior commit (because SOAS and ISOAAQ together were added to the PM2.5 diagnostic).

The complexSOA and complexSOA_SVPOA simulations will have identical PM2.5 diagnostics w/r/t the prior commit (because ISOAAQ was already being added to the PM2.5 diagnostic).

--Bob Yantosca (talk) 20:31, 14 May 2018 (UTC)

Only add ISOAAQ species to OCPISOA when using the complex SOA option

This update will be included during the GEOS-Chem v11-02 provisional release period.

Jenny Fisher wrote:

The only thing I am wondering about is the continued use of ISOAAQ in the following line 982 for ALL simulations:
        ! Add mechanistic isoprene OA (eam, 08/2015)
        OCPISOA(I,J,L) = OCPISOA(I,J,L) + ISOAAQ(I,J,L)
I don’t know enough about the SOA simulation to know how OCIPSOA is used, and whether this a problem. Can someone more familiar weigh in?

Colette Heald wrote:

I think Jenny is correct that as far as simple SOA is concerned ISOAAQ shouldn't exist, so it would be smart to put an if statement here too.

Therefore we have added the code in GREEN to GeosCore/aerosol_mod.F at approx. line 982: 

        ! Add mechanistic isoprene OA (eam, 08/2015)
        IF ( Is_ComplexSOA ) THEN
           OCPISOA(I,J,L) = OCPISOA(I,J,L) + ISOAAQ(I,J,L)
        ENDIF

This bug fix does not affect the benchmark simulation, which uses the Complex SOA option. Here is the log file from a difference test using the benchmark simulation w/r/t the prior commit: 

###############################################################################
### VALIDATION OF GEOS-CHEM OUTPUT FILES
### Run ID: geosfp_4x5_benchmark
##@
### IDENTICAL : GEOSChem_restart.201307010200.nc.{Ref,Dev}
### IDENTICAL : HEMCO_diagnostics.201307010000.nc.{Ref,Dev}
### IDENTICAL : HEMCO_restart.201307010200.nc.{Ref,Dev}
### IDENTICAL : trac_avg.geosfp_4x5_benchmark.201307010000.{Ref,Dev}
##%
###############################################################################

--Bob Yantosca (talk) 15:45, 17 May 2018 (UTC)

Fixes for isoprene SOA for consistency with Marais et al. (2016)

This update was included in v11-02e (approved 24 Mar 2018).

Eloise Marais wrote:

The bug fixes that Seb found in the KPP implementation of the heterogeneous chemistry mean that the isoprene SOA is now no longer consistent with the version that I used to implement this chemistry. This is concerning, as I will no doubt receive emails asking why isoprene SOA in the public release isn’t consistent with what’s reported in my paper. This now requires that I provide updated effective Henry’s Law constants and possibly also yields of SOA precursors.
Here are the scaling factors for the isoprene SOA compounds:
(1) LVOCOA:
LVOC is a factor of 1.4 lower in v11-02d simulation. This can be addressed by updating the gas-phase chemistry reactions leading to LVOC formation. I’ve indicated the changes below [that need to be made to Standard.eqn, Tropchem.eqn, and SOA_SVPOA.eqn]:
 Current (v11-02d): RIPA + OH -> 0.750 RIO2 + 0.245 HC5 + 0.125 (OH + H2O) + 0.005 LVOC
 Update  (v11-02e): RIPA + OH -> 0.750 RIO2 + 0.243 HC5 + 0.125 (OH + H2O) + 0.007 LVOC

 Current (v11-02d): RIPA + OH -> 0.850 OH + 0.578 IEPOXA + 0.272 IEPOXB + 0.145 HC5OO + 0.005 LVOC
 Update  (v11-02e): RIPA + OH -> 0.850 OH + 0.578 IEPOXA + 0.272 IEPOXB + 0.143 HC5OO + 0.007 LVOC

 Current (v11-02d): RIPB + OH -> 0.480 RIO2 + 0.515 HC5 + 0.26 (OH + H2O) + 0.005 LVOC
 Update  (v11-02e): RIPB + OH -> 0.480 RIO2 + 0.513 HC5 + 0.26 (OH + H2O) + 0.007 LVOC

 Current (v11-02d): RIPD + OH -> 0.250 RIO2 + 0.745 HC5 + 0.375 (OH + H2O) + 0.005 LVOC
 Update  (v11-02e): RIPD + OH -> 0.250 RIO2 + 0.743 HC5 + 0.375 (OH + H2O) + 0.007 LVOC

 Current (v11-02d): RIPD + OH -> 0.500 OH + 0.500 IEPOXD + 0.495 HC5OO + 0.005 LVOC
 Update  (v11-02e): RIPD + OH -> 0.500 OH + 0.500 IEPOXD + 0.493 HC5OO + 0.007 LVOC
(2) SOAGX:
SOAGX is a factor of 1.5 lower in v11-02d and can be addressed by updating the uptake coefficients [in function HETGLYX found in gckpp_HetRates.F90] as follows:
Day-time gamma: change to 4.4d-3
Night-time gamma: change to 8d-6.
(3) SOAIE:
SOAIE is a factor of 2 too low and can be addressed by changing the Henry’s law constant [HSTAR_EPOX in gckpp_HetRates.F90] from 5d6 to 1.7d7.
(4) INDIOL:
I find really large mass concentrations of INDIOL in the Southeast US boundary layer during SEAC4RS (2.9 ug/m3) compared to the value I obtained in my v9-02 simulation (0.1 ug/m3). I looked back at the benchmark output and this also shows very high INDIOL concentrations compared to SOAIE (IEPOX SOA) and SOAGX (glyoxal SOA).
Jenny, do these high INDIOL mass concentrations seem reasonable? Perhaps in your mechanism you account for additional sources that would lead to these high concentrations?

Jenny Fisher wrote:

All the organic nitrate aerosols from our mechanism hydrolyse with a lifetime of 1 hr to form INDIOL + HNO3. We weren’t particularly concerned with the INDIOL that came out, basically just a place to dump the excess.
If INDIOL only comes from these alkyl nitrate reactions and we are only using my constant uptake, then perhaps we just leave as INDIOL but remove from the calculations of aerosol mass and AOD.

As a solution in v11-02e, INDIOL will be excluded from the aerosol mass and AOD calculations. It is important to note that this results in lost mass. As noted in Fisher et al. (2016, ACP), this is a source of uncertainty and would benefit from an update when more information about this process becomes available.

--Melissa Sulprizio (talk) 17:12, 5 January 2018 (UTC)

Add MTPO as an advected and chemical species to all full-chemistry simulations

This update was included in v11-02e (approved 24 Mar 2018).

Melissa Sulprizio wrote:

The monoterpene and limonene chemistry added in v11-02a and v11-02c introduced MTPA and LIMO as species that are both advected and included in the chemistry mechanism. However, MTPO is currently only an advected species in the complex SOA mechanism (we use simple SOA by default in the Standard simulation that will ship with v11-02). It would be very simple to add MTPO as an advected species to all full-chemistry simulations so that the monoterpene species are treated consistently.

Colette Heald responded:

It seems like for simplicity we should add MTPO as an advected species in all simulations. Maybe we should be incorporating MTPO into the simple SOA too.
MTPO is included in the Pye et al. scheme with the same yields as MTPA (from alpha-pinene, based off of the Shilling et al. data). Prior to that in the Chung and Seinfeld 2-product formulation, there were in fact different yield parameters for each of these categories. This was based on the original lab work by Griffin et al. - a quick look at those 1999 papers shows that the yields of these species were maybe just a bit higher than alpha and beta pinene (but the yields of terpinene and terpinolene were lower...). I don't think that there is any more recent lab work on these compounds. I can't find anything in Pye et al. about the oxidation rates used, so I'm not sure if she stuck to the rates from Chung and Seinfeld (which are from Atkinson), but if there is no update, presumably we can just stick with those to get the approximately right concentration of MTPO (and someone can build out the explicit chemistry in the future if there is more info).

Eloise Marais wrote:

MTPO lumps all other monoterpenes, so myrcene (MYRC), ocimene (OCIM), and other (OMON) (according to megan_mod). Ocimene and myrcene have 8-chain carbon backbones (no rings) that include 3 double bonds.
I did a quick search for chemistry in MCM. There’s nothing for myrcene and ocimene. I’d imagine with all those double bonds there would be a cascade of reactions to rival isoprene’s.

Mat Evans wrote:

So just to confirm the conversation:
The problem:
  • We currently have a species called MTPA which represents lumped chemistry of alpha-pinene, beta-pinene, sabine, carene
  • We currently have a species call LIMO which represents emissions of limonene
  • We currently also have a species called MONX which is meant to represent all of the monoterpenes and just generates CH2O.
There is an inconsistency here as we seem to not conserve carbon for an important carbon source.
The suggestion is:
  • We should retire the total monoterpene species MONX from the chemistry scheme.
  • We should include a new monoterpenes species called MPTO which represents all the monoterpenes not covered by alpha-pinene, beta-pinene, sabine, carene, and limonene.
  • The MPTO chemistry should follow that of MPTA until somebody wants to take on this problem. That would be. 
    MTPO + OH = PIO2 :                          GCARR(1.21E-11, 0.0E+00, 440.0);    {2017/03/23; IUPAC2010; EVF}
    MTPO + O3 = 0.850OH + 0.100HO2 +
     0.620KO2 + 0.140CO + 0.020H2O2 +
     0.650RCHO + 0.530MEK :                     GCARR(5.00E-16, 0.0E+00, -530.0);  {2017/07/14; Atkinson2003; KRT,JAF,CCM,EAM,KHB,RHS}
    MTPO + NO3 = 0.100OLNN + 0.900OLND :        GCARR(8.33E-13, 0.0E+00, 490.0);   {2017/07/14; Fisher2016; KRT,JAF,CCM,EAM,KHB,RHS}

--Melissa Sulprizio (talk) 15:39, 22 February 2018 (UTC)

Update simple SOA entries in HEMCO to follow MTPA+LIMO+MTPO

This update was included in v11-02e (approved 24 Mar 2018).

Following the bug fix to remove MONX from the chemical mechanisms and the update to add MTPO as an advected species to all full-chemistry simulations, Jeff Pierce indicated the simple SOA (SOAP and SOAS) entries in HEMCO should be updated to follow MTPA+LIMO+MTPO rather than MONX. The SOAP and SOAS entries from isoprene, biofuel and biomass burning will be left as is.

--Melissa Sulprizio (talk) 17:23, 1 December 2017 (UTC)

Fix diagnostics bugs in the SOA-SVPOA simulation

This update was included in v11-02c and approved on 21 Sep 2017.

Katie Travis wrote:

While running the SOA-SVPOA simulation, I found a few bugs in the diagnostics.
1. Diag3.F is missing a call for id_NAP under ND28. Add the following code:
       !%%%%% NAP %%%%%
        IF ( id_NAP > 0 ) THEN
           DiagnName = 'BIOMASS_NAP'
           UNIT      = 'molec/cm2/s'
           N         = id_NAP
           SpcInfo => State_Chm%SpcData(N)%Info
           FACTOR    = AVO / ( SpcInfo%emMW_g * 1.e-3_fp) / CM2PERM2
           CALL DIAG2BPCH( am_I_Root, HcoState, DiagnName, CATEGORY,
    &                      UNIT,      N, 1, -1, .TRUE.,    FACTOR, RC )
           IF ( RC /= HCO_SUCCESS ) CALL ERROR_STOP( DiagnName, LOC)
        ENDIF
This means hcoi_gc_diagn_mod.F also needs a call to NAP.
2. In the SOA-SVPOA simulation, emissions of POG1 and POG2 are also not in diag3.F, instead emissions of POA1 are called. But in HEMCO, emissions in the SOA simulation are of POG1 and POG2, not POA1 and POA2. I believe this is also a problem in gamap_mod.F and hcoi_gc_diagn_mod.F90.

--Melissa Sulprizio (talk) 20:43, 25 August 2017 (UTC)

Incorrect concentrations in SOA-SVPOA simulation

This update was included in v11-01f (approved 16 Apr 2016).

Prasad Kasibhatla wrote:

It looks like there are some problems in the implementation of the semi-volatile POA option in v10-01. I ran 2 one month simulations (2009 July) using GEOS-5 meteorology and out-of-the-box set up of v10-01 (using run directories created by gcCopyRunDirs) - one simulation used the traditional nonvolatile POA option and the other (with the same executable) used the semivolatile POA option.

Attached are plots from the restart file after 1 month of simulation. OCPI and OCPO are from the traditional nonvolatile POA run, and the remainder [are] from the semivolatile POA run. The OCPI and OCPO plots from the traditional nonvolatile POA run are as expected, but the plots from the semivolatile POA run are not.

Looking at the code (GeosCore/carbon_mod.F) it looks like one problem is that SVOC emissions are allocated to POG1 and POA1, instead of to POG1 and POG2 as they should be in the semivolatile POA simulation. But the patterns seen in the some of the plots from the semivolatile POA simulation suggest other problems as well.

The implementation of the HEMCO emissions component in GEOS-Chem v10-01 appears to have caused problems for the SOA-SVPOA simulation. The cause was traced to a missing unit conversion in routine EMISSCARBON (GeosCore/carbon_mod.F). Emissions are obtained from HEMCO in units kg/m2/s and need to be converted to kg for array POAEMISS. To resolve the issue in GEOS-Chem v10-01, you can add the following code in GREEN: 

        ! For POA, add emissions to POAEMISS array. Mix entire
        ! column emissions evenly in the PBL.
        IF ( HCOPOA1 > 0 ) THEN
           ! Units from HEMCO are kgC/m2/s. Convert to kgC/box here.
           TMPFLX = SUM(HcoState%Spc(HCOPOA1)%Emis%Val(I,J,:))
    &               * GET_TS_EMIS() * 60.0e+0_fp  * GET_AREA_M2(I,J,1)
           POAEMISS(I,J,L,1) = F_OF_PBL * TMPFLX
        ENDIF 
        IF ( HCOPOG1 > 0 ) THEN
           ! Units from HEMCO are kgC/m2/s. Convert to kgC/box here.
           TMPFLX = SUM(HcoState%Spc(HCOPOG1)%Emis%Val(I,J,:))
    &               * GET_TS_EMIS() * 60.0e+0_fp  * GET_AREA_M2(I,J,1)
           POAEMISS(I,J,L,2) = F_OF_PBL * TMPFLX
        ENDIF

Furthermore, in GEOS-Chem v10-01, biofuel and biomass burning SVOC emissions were added to species POA1 and anthropogenic SVOC emissions were added to species POG1. According to Pye et al. (2010), the SVOC emissions should be added to the two gas-phase species (POG1 and POG2). To avoid confusion, in v11-01f we updated HEMCO_Config.template and the code in carbon_mod.F and hcox_gfed_mod.F90 so that all SVOC emissions are now assigned to the POG1 and POG2 species in HEMCO using a ratio of 0.49:0.51 (ALPHA in carbon_mod.F). The total (anthropogenic + biofuel + biomass burning) emissions of POG1 and POG2 are added to array POAEMISS in EMISSCARBON and then added to the two gas-phase species concentrations in routine CHEM_NVOC.

--Melissa Sulprizio (talk) 15:51, 15 January 2016 (UTC)
--Bob Yantosca (talk) 15:32, 30 March 2016 (UTC)

SOA in older versions of GEOS-Chem

The following sections describe information about the SOA simulations in older (now obsolete) versions of GEOS-Chem. We shall preserve this information here for reference.

The SOA simulation prior to v9-02

Obsolete.jpg

This information is now obsolete. We shall leave this here for reference.

The following sections describe the current SOA simulation as of GEOS-Chem v8-03-01 and higher versions. We shall leave this section here for reference.

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):

  1. Henry's Law Coefficient for SOG species: 10^5 M/atm
  2. 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)

The SOA restart file

Obsolete.jpg

NOTE: In GEOS-Chem v9-02 and later versions, the soaprod restart file and APROD/GPROD arrays no longer exist since different volatility species are not lumped together in the updated SOA simulation. Therefore, the APROD/GPROD restart file is no longer needed for SOA simulations done with GEOS-Chem v9-02 and later versions.

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.

  1. For versions v7-04-11 to v8-02-04, this restart file is named restart_gprod_aprod.YYYYMMDDhh.
  1. 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

Obsolete.jpg

NOTE: In GEOS-Chem v10-01 and later versions, run directories can be generated from the GEOS-Chem Unit Tester. The information below is now obsolete.

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 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/geosfp/SOA 4 x 5 GEOS-FP 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

DIR-OPTION Description
4x5/geos5/SOA_SVPOA 4 x 5 GEOS-5 fullchem w/ secondary organic aerosols option and semivolatile POA
4x5/geosfp/SOA_SVPOA 4 x 5 GEOS-FP fullchem w/ secondary organic aerosols option and semivolatile POA
4x5/merra/SOA_SVPOA 4 x 5 MERRA fullchem w/ secondary organic aerosols option and semivolatile POA

--Melissa Sulprizio 16:38, 21 January 2014 (EST)

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