CMAQ version 5.0 (February 2012 release) Technical Documentation

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Summary of Features and Enhancements in CMAQv5.0

The release version of CMAQ 5.0 builds upon the beta-version made available to the modeling community in May 2011 by the U.S. EPA's Atmospheric Modeling and Analysis Division. Feedback from the beta-testers is greatfully acknowledged, as these contributions have led to the development and release of a more robust model. Summarized below are the main enhancements to the modeling system.

Gas-phase Chemistry

CMAQv5.0 includes a new version of the SAPRC gas-phase chemical mechanism, namely SAPRC07TB (Carter, Development of the SAPRC-07 chemical mechanism, Atmos. Environ., 44, 5324–5335, 2010a; Carter, Development of a condensed SAPRC-07 chemical mechanism, Atmos. Environ., 44, 5336–5345, 2010b; Hutzell et al., Interpreting predictions from the SAPRC07 mechanism based on regional and continental simulations, Atmos. Environ., 46, 417–429, 2012). This mechanism includes fully updated representation of organic and inorganic reactions between various gas-phase species in the atmosphere, and is consistent with the current consensus knowledge on atmospheric kinetics (Carter, 2010a,b). The mechanism also explicitly represents organic species with either high emissions, high toxicity, or high secondary organic aerosol formation potential (e.g., xylene, α-pinene, benzene, 1,3-butadiene, etc.) (Hutzell et al., 2012; see also SAPRC-07 Chemical Mechanism and Emissions Assignment Files). Additionally, the CB05 mechanism has been updated to include the updated toluene chemistry recommended by Whitten et al. (A new condensed toluene mechanism for Carbon Bond: CB05-TU, Atmos. Environ., 44, 5346–5355, 2010). This update improves the simulation of O3 in urban plumes, though its impact on total fine particle mass predictions is small (Sarwar et al., Impact of a new condensed toluene mechanism on air quality model predictions in the US, Geosci. Model Dev., 4, 183–193, 2011).

Photolysis Rates

Previous versions of CMAQ relied on look-up tables for estimation of photolysis rates. The on-line photolysis rate module, which incorporates the radiative impacts of aerosol loading simulated by the model, has been further enhanced in CMAQv5.0. This treatment allows for inclusion of the effects of scattering and absorbing aerosols in modulating photolysis rates and atmospheric photochemistry regulating the formation of secondary air pollutants. Temperature and pressure corrections to the quantum yield and cross-sections used in the estimation of the photolysis rates were included to better represent these rates at higher altitudes. Additionally, the surface albedo is now estimated as a function of land-use, season, time of day and wavelength; this enhancement enables the model to more accurately represent the increase in photolysis due to reflection from snow surfaces, and consequently improves the applicability of the model for winter-time conditions and in addressing issues related to winter-time O3 in the Western States.

Aqueous and Heterogeneous Chemistry

The rate constants for the S(IV) to S(VI) conversion through in-cloud oxidation pathways were updated to be consistent with the current scientific consensus. Additionally, model simulated levels of Fe and Mn are used in the catalysis reactions instead of the previous background values, which would help in improved representation of spatial and seasonal variability in the relative importance of this reaction pathway.

Aerosol Chemistry and Speciation

Enhancements to the aerosol module in CMAQv5.0 were directed both at improving the aerosol chemistry as well as speciation. Recent evaluation studies have revealed that the largest biases in CMAQ PM2.5 results are driven by over predictions of the unspeciated PM2.5, referred to hereafter as PMother; this component constitutes over half of the National Emission Inventory (NEI) for PM2.5. Detailed speciation profiles derived from the work of Reff et al. (2009) were used to further subdivide emissions of PMother into primary ammonium (NH4+), sodium (Na+), chloride (Cl-), selected trace elements (Mg, Al, Si, K, Ca, Ti, Mn, and Fe), and non-carbon organic mass (NCOM). The CMAQ transport and chemistry operators were further modified to explicitly represent these 9 additional PM constituents. This additional speciation now allows for detailed characterization of the species, processes, and emission sector contributions to the model bias in primary and consequently total PM. The explicit treatment of Fe and Mn also allows for explicit representation of their catalysis effects on S(IV) to S(VI) conversion through aqueous chemistry, and consequently more consistent treatment of sulfate production pathways in the model. The representation of gas/particle partitioning of inorganic species was also improved through the incorporation of ISORROPIA version 2.0. Many of the numerical instabilities associated with the previous version of ISORROPIA have been eliminated/moderated in this new version. An additional advancement in ISORROPIAv2.0 is the treatment of Ca2+, K+, and Mg2+, species abundant in sea-salt and soil dust. In previous versions of CMAQ, contributions of natural windblown dust on airborne PM mass were not explicitly represented. CMAQv5.0 includes a module that dynamically estimates natural emissions of fine and coarse dust particles due to wind action over arid and agricultural land. The expanded speciation and incorporation of ISORROPIAv2.0 further facilitates the explicit representation of dust emission and PM composition simulated by CMAQv5.0. Finally, a scheme to represent the oxidation of primary organic aerosol has been included. The oxidation of organic carbon increases the non-carbon organic matter, thereby increasing PM2.5 mass concentrations. Comparison of modeled OM/OC ratios with those inferred from the IMPROVE measurements, show improved representation of both spatial and seasonal variability in the predicted OM/OC ratio.

Lightning NOx emissions

The application of the modeling system on annual time-scales as well as its use in applications examining more stringent NAAQS, necessitates that the model possess fidelity in simulating the entire range of atmospheric pollutant concentrations, from background levels to extreme values. Lightning can be a significant source of NOx in the mid-upper troposphere and can impact the distribution of reactive nitrogen as well as O3. A parameterization to estimate the vertical distribution of NOx emissions generated due to lightning is included in CMAQv5.0. For applications over the Continental U.S., the algorithm uses lightning flash totals from the National Lightning Detection Network (NLDN). For cases, where such data is not available, an alternate algorithm which estimates the number of lightning flashes based on the modeled convective precipitation can be invoked. Besides impacting ambient concentrations of reactive nitrogen species and O3 in the troposphere, initial simulations also show large improvements in nitrogen wet deposition simulations as a result of including lightning NOx emissions in the model.

Transport Processes

Physical process changes to CMAQv5.0 include updates to the representation of turbulent mixing during stable conditions and updates to the vertical advection scheme to reduce numerical diffusion in the upper model layers. Additionally, to facilitate the use of the model to simulate deposition fluxes for ecological assessment studies, an option to output the dry deposition flux for the different land-use categories within a grid cell has been included – this is referred to as the “Mosaic approach”.

Structural Updates

CMAQv5.0 also reflects the start of a concerted effort to review and update the model systems code structure and architectural design. As the complexity of the model system has increased since its initial release in 1998, some of the process level modularity has eroded and in some cases redundant calculations have been introduced. Two major structural enhancements have been introduced in CMAQv5.0. First, a complete redesign of the aerosol module was implemented which eliminated numerous dependencies and duplication across modules; the improved modularity has and will continue to further enhance the aerosol module and reduce the effort to ensure its correct linkage with other process modules. Second, a new approach to manage the model species via a namelist option has been introduced. This approach centralizes the specification of various attributes of the modeled chemical species and enables users to more easily modify and customize the modeled species set for specific applications.

Mercury and Air Toxics

Consistent with previous versions, CMAQv5.0 also contains the option to simulate the atmospheric fate of mercury compounds and 40 other Hazardous Air Pollutants (HAPs). The selection of HAPs was based on consultation with OAQPS and includes the 33 HAPs identified under the Integrated Urban Air Toxics Strategy as posing the greatest potential public health concern in the largest number of urban areas, as well as several additional HAPs which are significant contributors to ozone and secondary particulate matter formation. This extended capability allows model-based air quality assessment studies to transition from the traditional pollutant-by-pollutant approach to an integrated multi-pollutant air quality management approach, wherein benefits/dis-benefits of various control strategies can be more robustly examined.

Bi-directional Exchange of Ammonia and Mercury

Unlike most gas phase pollutants, which are consistently deposited, species such as NH3 and Hg could be both emitted from and deposited to land and water surfaces. Measurement data suggest that depending on whether the difference between NH3 concentrations in the air and those in the depositing surface is positive or negative, either dry deposition or emission from the surface could occur. The Hg bidirectional exchange model estimates fluxes as a function of the mercury content in environmental media and redox reactions between elemental and oxidized Hg in soil and surface waters based on published field scale experiments (Bash, Description and initial simulation of a dynamic bidirectional air-surface exchange model for mercury in Community Multiscale Air Quality (CMAQ model), J. Geophys. Res. 115, D06305, 2010). The NH3 bidirectional exchange model parameterizations were developed based on published field scale models and an intensive measurement campaign in which AMAD collaborated with measurement scientists to measure the parameters necessary for a regional scale model parameterization (Bash et al. Estimation of in-canopy ammonia sources and sinks in a fertilized Zea mays field, Environ. Sci. Technol. 44, 1683-1689, 2010). This bidirectional exchange model was linked to agricultural management practices and fertilization rates through a collaboration in which a USDA agro-ecosystem model was evaluated against field observations (Cooter et al. Estimation of NH3 bi-directional flux from managed agricultural soils, Atmos. Environ. 44, 2107-2115, 2010) and coupled to CMAQ linking agricultural management practices to regional transportation and deposition of gaseous NH3 and ammonium aerosols. This parameterization was applied on a regional scale by representing bi-directional exchange of NH3 and Hg based on varying land-use, soil, and plant compensation points and is included in CMAQv5.0. The inclusion of NH3 bidirectional exchange in CMAQ significantly reduces the models annual bias in NHx wet deposition (Appel et al., A multi-resolution assessment of the Community Multiscale Air Quality (CMAQ) model v4.7 wet deposition estimates for 2002-2006, Geosci. Model. Dev, 4, 357-371, 2011 ). This parameterization is based on field intensive data and has also been rigorously evaluated against NH3 flux measurements as well as thoroughly assessed as to its impact on model performance of ambient nitrogen levels and wet deposition amounts.

Two-way Coupled WRF-CMAQ

Previous versions of CMAQ were run in a sequential off-line manner, wherein, archived output on the dynamical state of the atmosphere simulated using the meteorology model was used to drive CMAQ’s chemistry-transport-transformation-deposition calculations. A modeling system that facilitates coupled air quality and meteorology execution is desirable because it (1) provides consistent treatment of the dynamical processes occurring in the real-world while reducing many redundant calculations, (2) provides ability to couple dynamical and chemical calculations at finer time-steps that are needed for the application of CMAQ at smaller horizontal grid cells, (3) reduces the disk-storage requirements typically associated with uncoupled sequential operation, and (4) provides opportunities to represent and assess potentially important radiative effects of pollutant loading on simulated dynamical features. CMAQv5.0 includes the option to run the model in the traditional off-line mode or in a 2-way coupled (i.e., on-line) mode with the Weather Research and Forecast (WRF) model. In the on-line mode, the WRF and CMAQ modeling systems are coupled through the use of memory-resident buffer data files, which provide flexibility both in the frequency of data communication between the two models as well as for accommodating both coupled and uncoupled modeling paradigms with minimal changes in the basic code and structure of the two modeling systems. This approach also mitigates the need to maintain separate versions of the models for on-line and off-line modeling. Thus, both WRF and CMAQ can evolve independently benefitting from their individual user and development communities; updated versions of the individual models can be easily incorporated in the evolving coupled WRF-CMAQ modeling system.

Coupling the modeling systems provides a natural means for finer scale applications, wherein higher frequency of data exchange between the meteorological and chemistry-transport calculations is desirable. Additionally, it provides opportunities to model common physical processes in a consistent manner, thereby better simulating the atmospheric processes.

In the 2-way coupled WRF-CMAQ system, simulated aerosol composition and size distribution are used to estimate the optical properties of aerosols which are then used in the radiation calculations in WRF. Thus, direct radiative effects of absorbing and scattering aerosols in the troposphere estimated from the spatially and temporally varying simulated aerosol distributions, can be fed-back to the WRF radiation calculations, resulting in a “2-way” coupling between the meteorology and atmospheric chemisty modeling components. This extended capability enables more realistic representation of the impacts of atmospheric loading of radiatively important trace species on the simulated dynamics as well as the earth’s radiation budget. Consequently, besides supporting traditional air quality applications, this evolving modeling system is also expected to play a critical role in the Agency’s future research and regulatory applications exploring air quality-climate interactions.

RELEASE_NOTES for CMAQv5.0 - February 2012

Changes and new features

  1. Aerosol Module
    • Redesign
      • Eliminated dependencies and duplication across modules
    • AERO6
      • PMother speciation
        • Addition of 9 new PM2.5 species: APNCOMI/J, AFEJ, AALJ, ASIJ, ATIJ, ACAJ, AMGJ, AKJ, AMNJ
        • Anthropogenic emissions of 4 existing PM2.5 species: ANAJ, ACLJ, AH2OJ, ANH4J
        • Changed names of 2 species: AORGPAI/J --> APOCI/J and A25I/J --> AOTHRI/J
        • Note: When preparing emissions for AERO6, emissions must be specified for 13 new species. CMAQ will crash if any emitted PM species is not included in the emissions input files. See PM emitted species list for details on naming species in the emissions file. Emission Changes for this release of CMAQ including changes needed for AERO6 are summarized in Emission Changes for CMAQv5.0
      • POA aging
        • Oxidative aging of POC leads to increases in APNCOMI/J.
        • Aging is modeled as a second order reaction between OH and POCR (reduced primary organic carbon: calculated as moles of POC minus moles of primary organic oxygen).
      • ISORROPIA2
      • Sulfur Chemistry
      • Windblown dust
    • Updates to SOA yield parametrization (AERO5 and AERO6)
  2. Chemistry
    • CB05
      • Replaced existing toluene chemistry in CB05 with updated toluene chemistry (CB05-TU, Whitten et al., 2010)
      • Revised rate constants for N2O5 hydrolysis in CB05 based on the latest recommendation of IUPAC
      • Added reactions of toluene and xylene with chlorine radical (CL)
    • SAPRC07(TB & TC)
      • Fully updated organic and inorganic reactions
      • Updated photolysis rates
      • Use operator species to better represent chemical reactions in low-NOx conditions
      • Additional species with high emission, high toxicity, or high SOA formation are treated explicitly
    • In-line Option for Photolysis Rates
      • Moved opacity and photolysis data (absorption cross sections and quantum yield data) to an ASCII input file, that is created by a pre-processor and depends only on the mechanism for gas chemistry (not time).
        • Allows more flexibility to change/introduce data for photolysis rates or create/modify a chemical mechanism.
        • The ASCII file also defines the number of wavelength and temperature interpolation points, allowing for adjustments to improve the accuracy of the radiative transfer calculation.
        • The CCTM runscript specifies the new input file by using the environment variable called CSQY_DATA.
      • Introduced an algorithm that calculates the surface albedo based on land use categories, zenith angle, seasonal vegetation, snow and sea ice coverage.
  3. Vertical Diffusion (ACM2)
    • Default read of C-staggered wind components from MET_DOT_3D
    • Corrected component-wise shear to properly use B-staggered winds; removed map-scale factor from wind shear calculation
    • Modified eddy diffusivity for stable conditions. Same modifications will be included in ACM2 in the next release of WRF (v3.4?)
    • Also reduced minimum eddy diffusivity from 0.5 m2s-1 to 0.01 m2s-1 and from 2.0 m2s-1 to 1.0 m2s-1 for urban areas. Minimum eddy diffusivity in WRF/ACM2 is 0.01 m2s-1 everywhere.
  4. Vertical Advection
    • A new method for computing the vertical velocity has been implemented which follows the omega calculation in WRF but using CMAQ's advection schemes (ppm) to compute horizontal mass divergence. It's a 2 step process where first we integrate the continuity equation through the column to get the change in column mass and then solve for omega layer-by-layer using the horizontal mass divergence. See equation 2.27 in the WRF Tech Doc: The new scheme is much less diffusive in the upper layers because it is constrained to have zero flux at the model top. However, mass conservation is not guaranteed. Testing has shown very small mass errors.
  5. Production of nitrogen oxide (NO) from lightning
    • Four settings are supported: off, read a 4-D file, inline informed by lightning detection network data, and fully inline
    • Has a substantial impact on summer nitrogen deposition, minor impact on surface concentrations
  6. Dry Deposition
  7. Structural Updates
  8. Multi-Pollutant Modeling
  9. Clouds
    • In coordination with MCIPv4.0, the CMAQ cloud module was updated to only simulate subgrid clouds when the meteorological driver used a convective cloud parameterization. (The minimum horizontal grid resolution restriction that had existed in previous versions of CMAQ was removed).

Two-way Coupled WRF 3.3 and CMAQ 5.0

  1. WRF 3.3 + CMAQ 5.0 Two-way Model Release Notes

Known Issues

  1. When using the inline option for biogenic emissions, only one hour output timesteps are supported for the diagnostic file.
  2. The inline lightning NO emissions algorithm assumes a 1-hr timestep for the meteorology data provided in the MCIP files.

Other Documentation

  1. README File
  2. Parallel Information
  3. SMOKE