CMAQ Chemical Mechanisms#

The CMAQ modeling system accounts for chemistry in three phases: gas, aerosol, and cloud droplets. Available mechanisms include variations of three photochemistry schemes such as different representations of secondary organic aerosols, additional model species representing Hazardous Air Pollutants, inclusion of dimethyl sulfide chemistry or detailed isoprene chemistry. Please consult the release notes for changes to mechanisms available in a specific version of CMAQ.

Fortran modules and namelists define a chemical mechanisms for the CMAQ model. Subdirectories of the $CMAQ_MODEL/CCTM/src/MECHS directory contain the files for available mechanisms. The species and emission control namelists enable setting runtime options for a mechanism. Species namelists define names, molecular weights and atmospheric processes (e.g., transport, cloud chemistry, and deposition). The files also determine whether the species concentrations and deposition results are written to output files. Emission control namelists define the emission inputs for model species. Two Fortran modules, RXNS_DATA_MODULE.F90 and RXNS_FUNC_MODULE.F90, define photochemistry for a mechanism. The data module specifies reactions and parameters. The functions module initializes photochemistry and calculates reaction rates constants. Because model source code define photochemistry for a mechanism, an executable version of the CMAQ model has a fixed photochemistry. To modify or change photochemistry, requires modifying or replacing the modules then recompiling. The approach may not work because data hardcoded within the photochemistry solver is not correct, if using an Euler Backward Interative (EBI) solver, or because data used to calculate photolysis rates is not complete.

Using predefined chemical mechanisms#

To select a predefined mechanism configuration in CMAQ, set the Mechanism variable in the build scripts to a one of the mechanism subdirectories located under $CMAQ_MODEL/CCTM/src/MECHS. The below table lists mechanisms available in this version of the CMAQ model.

Table 1. CMAQv5.4 Chemical Mechanisms

Mechanism Name	Photochemistry	Model Species^1,2	Cloud Chemistry Module³
cb6r3_ae7_aq	Carbon Bond 6 version r3 with aero7 treatment of SOA	species table	acm_ae7
cb6r5_ae7_aq	Carbon Bond 6 version r5 with aero7 treatment of SOA	species table	acm_ae7
cb6r5hap_ae7_aq	Carbon Bond 6 version r5 with air toxics and aero7 treatment of SOA	species table	acm_ae7
cb6r5_ae7_aqkmt2	Carbon Bond 6 version r5 with aero7 treatment of SOA	species table	acm_ae7_kmt2
cb6r5m_ae7_aq	Carbon Bond 6 version r5 with aero7 treatment of SOA and DMS and marine halogen chemistry	species table	acm_ae7_aq
racm2_ae6_aq	Regional Atmospheric Chemistry Mechanism version 2 with aero6 treatment of SOA	species table	acm_ae6
saprc07tic_ae7i_aq	State Air Pollution Research Center version 07tc with extended isoprene chemistry and aero7i treatment of SOA	species table	acm_ae7
saprc07tic_ae7i_aqkmt2	State Air Pollution Research Center version 07tc with extended isoprene chemistry and aero7i treatment of SOA	species table	acm_ae7_kmt2
saprc07tc_ae6_aq	State Air Pollution Research Center version 07tc with aero6 treatment of SOA	species table	acm_ae6
cracmm1_aq	Community Regional Atmospheric Chemistry Multiphase Mechanism version 1.0	species table	acm
cracmm1amore_aq	Community Regional Atmospheric Chemistry Multiphase Mechanism version 1.0 with AMORE isoprene condensation	species table	acm
cracmm2	Community Regional Atmospheric Chemistry Multiphase Mechanism version 2	species table	acm

mechanisms can share the same model species but differ cloud chemistry
species tables define model species in a mechanism’s GC, AE, and NR namelists.
kmt and acm refers to the kinetic mass transfer to cloud droplets and the convective cloud/transport representation, respectively

Creating or modifying a mechanism’s photochemistry#

Editing a mechanism’s Fortran modules is one way to make simple changes to thhe photochemistry scheme. More complex changes (adding reactions and model species) or creating a new scheme requires 1) creating new namelists with a text editor (if adding new model species) and 2) using the CMAQ chemical mechanism utility, CHEMMECH, to produce new Fortran modules. The CHEMMECH utility translates an ASCII file listing reactions for photochemistry into the Fortran modules used by CMAQ. For more information, consult the README file under $CMAQ_MODEL/UTIL/chemmech. Creating new mechanism modules may not be the last steps for the CMAQ model to use the photochemistry update. If changes add a new photolysis rate(s), the inline_phot_preproc or jproc utility has to create CMAQ input file(s) for the photolysis module used. If CMAQ is using an EBI solver to solve photochemistry, the create_ebi utility has to be used to create a new solver. These three utilities use the mechanism data module produced by the CHEMMECH utility.

Using species namelist files#

Species namelists define the four groups of model species: gas (GC), aerosol (AE), non-reactive (NR), and tracer (TR) species simulated by the CMAQ model. It reads namelists to define processes determining concentrations. For example, species namelists can be used to apply uniform scaling factors to several physical processes. Dry deposition of NO can be reduced by 50% by applying a factor of 0.5 to the dry deposition velocity for NO. Similarly, the boundary conditions of O₃ can be increased by 50% by applying a factor of 1.5. The gas, aerosol, and non-reactive namelists define a specific mechanism. The tracer namelist is generally interchangable between mechanisms. It can be employed for transport and deposition studies. Example tracer namelists are under $CMAQ_MODEL/CCTM/src/MECHS/trac0 (the version most often used) and $CMAQ_MODEL/CCTM/src/MECHS/trac1.

Points to emphasize on chemical mechanisms#

The Euler Backward Iterative (EBI) solver for photochemistry is hardcoded to the Fortran data module representing photochemistry and specific names in the species namelists. If either change, a new or different EBI solver source code is needed.
The Rosenbrock and SMVGEAR photochemistry solvers are not hardcoded the above files so they are more easily allow changing these files.

Sulfur Tracking Method (STM) option#

This release of CMAQ includes a runtime option that provides detailed information on the modeled sulfur budget. This option, referred to as the “Sulfur Tracking Method (STM)”, tracks sulfate production from gas- and aqueous-phase chemical reactions, as well as contributions from emissions and initial and boundary conditions. The STM option is activated by setting an environment variable in the CTM runscript:

setenv STM_SO4TRACK Y

Sulfur tracking species are added to the AE and NR groups at runtime if you enable this option. Table 2 provides a list of inorganic sulfur tracking species. Table 3 lists additional tracking species for the loss of inorganic sulfate to organosulfate for chemical mechanisms that include this loss pathway (SAPRC07TIC_AE6I, SAPRC07TIC_AE7I, CB6R3_AE7, or CB6R5M_AE7 mechanisms).

Table 2. Sulfur Tracking Species

Species Group	Species Name	MW	Description
AE	ASO4AQH2O2J	96.0	Accumulation mode sulfate (ASO4J) produced by aqueous-phase hydrogen peroxide oxidation reaction: H₂O₂ + S(IV) -> S(VI) + H₂O
AE	ASO4AQO3J	96.0	ASO4J produced by aqueous-phase ozone oxidation reaction: O₃ + S(IV) -> S(VI) + O₂
AE	ASO4AQFEMNJ	96.0	ASO4J produced by aqueous-phase oxygen catalyzed by Fe³⁺ and Mn²⁺ oxidation reaction: O₂ + S(IV) -> S(VI)
AE	ASO4AQMHPJ	96.0	ASO4J produced by aqueous-phase methyl hydrogen peroxide oxidation reaction: MHP + S(IV) -> S(VI)
AE	ASO4AQPAAJ	96.0	ASO4J produced by aqueous-phase peroxyacetic acid oxidation reaction: PAA + S(IV) -> S(VI)
AE	ASO4GASJ	96.0	ASO4J condensation following gas-phase reaction: OH + SO₂ -> SULF + HO₂
AE	ASO4EMISJ	96.0	ASO4J from source emissions
AE	ASO4ICBCJ	96.0	ASO4J from boundary and initial conditions
AE	ASO4GASI	96.0	Aitken mode sulfate (ASO4I) nucleation and/or condensation following gas-phase reaction: OH + SO₂ -> SULF + HO₂
AE	ASO4EMISI	96.0	ASO4I from source emissions
AE	ASO4ICBCI	96.0	ASO4I from boundary and initial conditions
AE	ASO4GASK	96.0	Coarse mode sulfate (ASO4K) condensation following gas-phase reaction: OH + SO₂ -> SULF + HO₂
AE	ASO4EMISK	96.0	ASO4K from source emissions
AE	ASO4ICBCK	96.0	ASO4K from boundary and initial conditions
NR	SULF_ICBC	98.0	Sulfuric acid vapor (SULF) from boundary and initial conditions

Table 3. Additional Tracking Species Representing Loss of Inorganic Sulfate to Organosulfate (only included if using SAPRC07TIC_AE6I, SAPRC07TIC_AE7I, CB6R3_AE7, or CB6R5M_AE7 mechanisms).

Species Group	Species Name	MW	Description
AE	OSO4J	96.0	Loss of ASO4J to organosulfate
AE	OSO4AQH2O2J	96.0	Loss of ASO4AQH2O2J to organosulfate
AE	OSO4AQO3J	96.0	Loss of ASO4AQO3J to organosulfate
AE	OSO4AQFEMNJ	96.0	Loss of ASO4AQFEMNJ to organosulfate
AE	OSO4AQMHPJ	96.0	Loss of ASO4AQMHPJ to organosulfate
AE	OSO4AQPAAJ	96.0	Loss of ASO4AQPAAJ to organosulfate
AE	OSO4GASJ	96.0	Loss of ASO4GASJ to organosulfate
AE	OSO4EMISJ	96.0	Loss of ASO4EMISJ to organosulfate
AE	OSO4ICBCJ	96.0	Loss of ASO4ICBCJ to organosulfate