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.

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)
  • Eloise Marais's isoprene aqueous uptake mechanism is added as an option to this scheme (it is on by default). This mechanism provides additional source of aq isoprene SOA, with new tracers identifying it as such, keeping existing SV isoprene SOA as well.
  • 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) scheme 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 is slated for inclusion into v11-02c.

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 will be added to v11-02c.

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. This option can be turned on/off via a switch in the Aerosol Menu of input.geos.

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)).

--Melissa Sulprizio (talk) 17:52, 15 June 2017 (UTC)

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)

References

  1. 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.
  2. Henze, D. K., and J. H. Seinfeld, Global secondary organic aerosol from isoprene oxidation,Geophys. Res. Lett., 33, L09812, 2006.
  3. 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.
  4. Liao, H., et al., Biogenic Secondary Organic Aerosol over the United States: Comparison of Climatological Simulations with Observations, J. Geophys. Res., 112, 2007. PDF
  5. 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
  6. 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

Fix diagnostics bugs in the SOA-SVPOA simulation

These fixes will be included in v11-02c.

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)