CMAQv5.0 Mechanism and Species

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Bill Hutzell

Version 5.0 of the CMAQ provides an updated version of a model that can simulate the atmospheric fate of mercury compounds and other Hazardous Air Pollutants (HAPs). Roselle et al. 2007 presented a prototype of this model and called its mechanism CB05TXHG_AE4_AQ. The mechanism included the same mercury compounds and HAPs in the CB05 based mechanisms for mercury compounds and HAPs in CMAQ version 4.7.1. Version 5.0 upgrades this version 4.7.1 based on the new science and algorithms for the photochemical mechanism, aerosol physics, and cloud chemistry. The result is a mechanism called CB05TUMP_AE6_AQ and specific build options need to use the new machanism.

In the Multi-Pollutant model, phase, i.e., gas or aerosol, determines the chemical and physical processes that they undergo. Each HAPs is transported and deposited. Wet deposition is determined by precipitation rate and the Henry's Law Constant or scavenging rate of the aerosol mode. Aerosol mode also determines dry deposition velocity for aerosol phase pollutants. For the gas phase HAPS, dry deposition has a nonzero velocity if the EPI Suite program (USEPA, 2011) and the SPECTRUM Laboratory database ( indicate dry deposition as a fate determining process. Check the NR and GC namelist files for which gas phase HAPs undergo dry deposition. In version 5.0 (as in 4.7.1), five HAPs in the NR species have explicitly calculated velocities.

The following paragraphs describe the Multiple Pollutant model, updates incorporated in version 5.0, and how to build the Multiple Pollutant model.


The CB05TUMP_AE6_AQ mechanism adapts the CB05TUCL_AE6_AQ mechanism (Whitten et al., 2010 and Sarwar et al., 2008) by adding the reactions for mercury compounds, acrolein, 1,3-butadiene and reactive tracers (Table 1) in CMAQ version 4.7.1. Check the mech_cb05tump_ae6_aq.def file for the reaction added. The adaption can affect predictions from the CB05TUCL mechanism because added reactions involving elemental mercury destory gas phase concentrations of O3, OH, CL and CL2. Acrolein and 1,3-butadiene reactions added are based on Yarwood et al. (2005). However, acrolein yields from 1,3-butadiene have been decreased based on the Master Chemical Mechanism (; Saunders et al., 2003). The reactive tracers track emissions such as formaldehyde, acetaldehyde, and acrolein emissions and allow determining photochemical production of the given pollutant. They also track emissions of toluene, alpha-pinene, beta-pinene and three xylene isomers (Table 2).  They do not alter ozone and radical concentrations. Check the mech_cb05tump_ae6_aq.def file for more information these modifications.   The GC namelist does define most of the gaseous HAPs (Table 1). The NR namelist defines them. These species do undergo chemical decay and Luecken et al. (2006) describes the method.


Adapting the new aerosol module added from adding aerosol species representing mercury, diesel emissions and other toxic metals (Table 3). Their concentrations are not used to determine the rates of aerosol microphysics and deposition but they do coagulate, mode merge and deposit from wet and dry processes. Species representing particulate mercury differ from these aerosols species because photochemistry produces mass for particulate mercury. The gas species, HGIIAER, represents the produced mass. HGIIAER goes directly into the accumulation mode and does not get divided between the fine modes. Species representing pariculate matter from diesel emissions have changed from CMAQ version 4.7.1 because the fine modes species have been divided into sulfate, nitrate, unspecified, elemental and organic carbon components.


Adapting the cloud module added in-cloud scavenging for metallic aerosol species and the cloud chemistry for mercury compounds. For the metallic species, the method follows the same approach as elemental carbon in the fine modes and unidentified material in the coarse mode. For mercury, in-cloud chemistry follows the method outlined in the Multipollutant release for CMAQ version 4.6 and 4.7.1. Although the reactions involving mercury do not directly change other aqueous species, mercury chemistry can alter particulate sulfate predictions because the mercury chemistry requires gas phase concentrations of HO2, HOCl and Cl2. These gas species affect pH and ion balance in cloud droplets based on Lin et al. (1998). Side effects increase wet deposition of each compound and possibly produce gaseous HOCL from clouds with low or no participation. The current GC namelist does not give the G2AQ_SUR for HO2 so the cloud chemistry does not use gas phase concentrations of HO2. The namelist does give the G2AQ_SUR for CL2 and HOCL so their gas concentration are used in cloud chemistry. If the user wants to change whether cloud chemistry uses these species concentrations, they should change their G2AQ values to their species name or a blank value, i.e., " ".


As mentioned above, building CMAQ with the Multi-Pollutant mechanism requires different build settings than the standard version of CMAQ. Table 4 shows the build settings needed to construct CCTM using this mechanism with its EBI solver. Settings not specified in Table 4 remain the same as the standard version. NOTE that the smvgear and ros3 options for the chem module also work for this mechanism.

To run the CMAQ with the Multi-Pollutant mechanism, the user needs emissions files containing rates listed in the GC, NR and AE namelists files. The files contain emissions that are not identical to the original CB05TUCL_AE6_AQ mechanisms. A user must complete SMOKE processing with correct ancillary files such as GSREF and GSPRO and the merged NEI/Toxics database. To obtain these items contact the CMAS Help desk at

The Multi-Pollutant mechanism allows simulating a bi-directional fluxes for atmospheric mercury in addition to ammonia. The environment variable, CTM_HGBIDI, determines whether a model execution  uses this capacity. To use the bi-directional fluxes for atmospheric mercury, add the below line to the runscript.


The default value is F. Consult the bidirectional notes for more information about using this option.

The MP model can subset or eliminate Hazardous Air Pollutants (HAPs) that are simulated. Users can then tailor their applications based on the HAPs of interest. Guidelines follow. For the NR namelist, any or all HAPs can be eliminated by deleting the rows that define them. Users can have to be more careful when removing HAPs from the AE namelist. They have to delete the group of rows that define all the aerosol modes for the HAP (Table 3). For example, the user wants to only simulate toxics metals and not the diesel species in particulate matter. To accomplish this objective, the AE namelist will not contain the rows that define the model species representing to the modes of DE_SO4, DE_NO3, DE_EC, DE_OC, DE_OTHR, and DE. The namelist retains the rows defining modes of the toxic metals. Note that NR namelist remains the same. The test case supplied with the CMAQ release is an application of this example. An alternative example edits both namelists to simulate the fate and transport of atmospheric mercury. For the NR namelist, the user deletes rows that defined all of its HAPs (see Table 1 and its footnote) and the result is equivalent to NR namelist for the CB05TUCL mechanism. For the AE namelist, the user deletes the rows that represent the HAPs in Table 3, EXCEPT FOR ROWS FOR PHG.


Lin, C.-J. and Pehkonen, S.O., 1998. Oxidation of elemental mercury by aqueous chlorine: implications for tropospheric mercury chemistry. Journal of Geophysical Research, 103 (D21), 28,093-28,102.

Luecken, D. J., W. T. Hutzell and G. L. Gipson 2006. Development and analysis of air quality modeling simulations for hazardous air pollutants. Atmospheric Environment, 40, 5087-5096.

Roselle, S.J., D.J. Luecken, W.T. Hutzell, O.R. Bullock, G. Sarwar, and K.L. Schere, 2007.  Development of a multipollutant version of the community multiscale air quality (CMAQ) modeling system. Extended Absract for the 5th Annual CMAS Conference, Chapel Hill, NC.

Sarwar, G., D. Luecken, G. Yarwood, G. Whitten, B. Carter, 2008. Impact of an updated Carbon Bond mechanism on air quality using the Community Multiscale Air Quality modeling system: preliminary assessment. Journal of Applied Meteorology and Climatology, 47, 3-14.

Saunders, S. M., Jenkin, M. E., Derwent, R. G., Pilling, M. J., 2003. Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): tropospheric degradation of non-aromatic volatile organic compounds, Atmospheric Chemistry and Physics, 3, 161-180, doi:10.5194/acp-3-161-2003.

US Environmental Protection Agency, cited 2011. Estimations Programs Interface for Windows (EIPWIN), version 4.10. Available online at

Yarwood, G., S. Rao, M. Yocke, and G.Z. Whitten, 2005. Updates to the Carbon Bond Mechanism: CB05. Report to the U.S. Environmental Protection Agency, RT-04- 00675. Available online at

Whitten, G.Z., Heo, G., Kimura, Y., McDonald-Buller, E., Allen, D.T., Carter, W.P.L, Yarwood, G, 2010. A new condensed toluene mechanism for Carbon Bond: CB05-TU. Atmospheric Environment, 44, 5346-5355.

                                                            Table 1.
                                Gas Phase HAP Species in CB05TUMP_AE6_AQ
 Species Name                               Compound                                 CAS#        In mech.def1
 FORM                                   total FORMALDEHYDE                     50-00-0           Yes
 ALD2                                    total ACETALDEHYDE                       75-07-0           Yes
 BENZENE                             BENZENE                                         71-43-2           Yes
 ACROLEIN                            total ACROLEIN                               107-02-8           Yes
 BUTADIENE13                      1,3-BUTADIENE                               106-99-0           Yes
 HG                                       Elemental Mercury                                 NA              Yes
 HGIIGAS                               Reactive Gaseous Mercury                     NA              Yes
 HGIIAER                               Particulate Mercury Precursor                 NA              Yes
 FORM_PRIMARY                  FORMALDEHYDE emissions              50-00-0           Yes
 ALD2_PRIMARY                   ACETALDEHYDE emissions               75-07-0            Yes
 ACROLEIN_PRIMARY           ACROLEIN emissions                       107-02-8            Yes
 ACRYLONITRILE                   ACRYLONITRILE                              107-13-1            No
 CARBONTET                        CARBON TETRACHLORIDE                56-23-5            No
 PROPDICHLORIDE               PROPYLENE DICHLORIDE                 78-87-5            No
 DICHLOROPROPENE           1,3-DICHLOROPROPENE                  542-75-6           No
 CL4_ETHANE1122                1,1,2,2-TETRACHLOROETHANE          79-34-5           No
 CHCL3                                  CHLOROFORM                                  67-66-3           No
 BR2_C2_12                           1,2-DIBROMOETHANE                      106-93-4           No
 CL2_C2_12                           1,2-DICHLOROETHANE                     107-06-2           No
 ETOX                                    ETHYLENE OXIDE                              75-21-8           No
 CL2_ME                                METHYLENE CHLORIDE                    75-09-2           No
 CL4_ETHE                             PERCHLOROETHYLENE                  127-18-4           No
 CL3_ETHE                             TRICHLOROETHYLENE                      79-01-6           No
 CL_ETHE                               VINYL CHLORIDE                               75-01-4           No
 NAPHTHALENE                      NAPHTHALENE                                 91-20-3           No
 QUINOLINE                            QUINOLINE                                        91-22-5           No
 HYDRAZINE                           Hydrazine                                         302-01-2           No
 TOL_DIIS                               2,4-Toluene Diisocyanate                   584-84-9           No
 HEXAMETHY_DIIS                 Hexamethylene 1,6-Diisocyanate        822-06-0           No
 MAL_ANHYDRIDE                 Maleic Anhydride                               108-31-6           No
 TRIETHYLAMINE                   Triethylamine                                     121-44-8           No
 DICHLOROBENZENE             1,4-Dichlorobenzene                          106-46-7           No

1) The GC namelist defines the gas phase species in the mech.def file. Gas phase species not in

the mech.def file is defined in the NR namelist.

                                                          Table 2.
                            Additional Gas Phase Species in CB05TUMP_AE6_AQ
Species Name                             Compound                                CAS#           In mech.def
TOLU                                    Toluene Emissions                        108-88-3              YES
MXYL                                    M-Xylene Emissions                      108-38-3              YES
OXYL                                    O-Xylene Emissions                        95-47-6              YES
PXYL                                    P-Xylene Emissions                       106-42-3              YES
APIN                                    Alpha-Pinene Emissions                   80-56-8              YES
BPIN                                    Beta-Pinene Emissions                   127-91-3              YES

                                                             Table 3.
                               Aerosol Phase HAP species in CB05TUMP_AE6_AQ
String in Aerosol Species                         Modes1                  Represents
        PHG                                                 I,J,K              Mercury Compounds
        BE                                                   I,J,K              Beryllium Compounds
        NI                                                    I,J,K               Nickel Compounds
        CR_III                                               I,J,K              Chromium (III) Compounds
        CR_VI                                              I,J,K              Chromium (VI) Compounds
        PB                                                   I,J,K              Lead Compounds
        CD                                                   I,J,K              Cadmium Compounds
        MN_HAPS                                        I,J,K              Manganese Compounds via HAPS Inventory
        DE_SO4                                            J                  Diesel Fine Sulfate Emissions
        DE_NO3                                            J                  Diesel Fine Nitrate Emissions
        DE_EC                                            I,J                  Diesel Fine Elemental Carbon Emissions
        DE_OC                                            I,J                  Diesel Fine Organic Carbon Emissions
        DE_OTHR                                        I,J                  Remainder of Diesel Fine PM Emissions
        DE                                                    K                 Diesel Coarse Mode PM Emissions
1) I = Aitken mode, J = Accumulation mode and K = Coarse mode

                                                               Table 4.
                           Option setting needed in CCTM build scrip if using EBI solver.
                      NOTE that unspecific options remain same as CCTM with aerosols.

  1. Select a HAP mechanism
    set Mechanism = cb05tump_ae6_aq
  2. Select correct EBI solver
    # NOTE THAT ros3 and smvgear options also work
    set ModChem   = ( module ebi_cb05tump_ae6     $Revision; )
  3. AERO option required
    set ModAero   = ( module aero6_mp                    $Revision; )
  4. cloud processing and aqueous chemistry setting
    set ModCloud  = ( module cloud_acm_ae6_mp   $Revision; )
  5. vertical diffusion setting
     set ModVdiff  = ( module acm2_mp                     $Revision; )
  6. dry deposition setting
     set ModDepv   = ( module m3dry_mp                  $Revision; )
    #NOTE compiling and linking with the m3dry_mp option requires the
    #LAPACK and BLAS libraries. The user can download and compile these
    #libraries or may use already compiled versions for their FORTRAN
    #compiler if available. Check the compiler manual for the latter