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.
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
- 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
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.
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.
- 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.
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 |