CMAQ version 5.0 (February 2012 release) Technical Documentation- cmaqwiki 

CMAQ version 5.0 (February 2012 release) 

Technical Documentation 

From cmaqwiki 

Contents 

• 1 Summary of Features and Enhancements in CMAQv5.0 

• 1.1 Gas-phase Chemistry: 

• 1.2 Photolysis Rates: 

• 1.3 Aqueous and Heterogeneous Chemistry: 

• 1.4 Aerosol Chemistry and Speciation: 

• 1.5 Lightning NOx emissions: 

• 1.6 Transport Processes: 

• 1. 7 Structural Updates: 

• 1.8 Mercury and Air Toxics: 

• 1.9 Bi-directional Exchange of Ammonia and Mercury: I 

• 1.10 Two-way Coupled WRF-CMAQ 

• 2 RELEASE_NOTES for CMAQv5.0- February 2012 

• 2.1 Changes and new features 

• 2.2 Two-way Coupled WRF 3.3 and CMAQ 5.0 

• 2.3 Known Issues 

• 2.4 Other Documentation 

Summary of Features and Enhancements in CMAQvS.O 

Page 1 of8 

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, Atrnos. Environ., 44, 5324 

- 5335, 201 Oa; Carter, Development of a condensed SAPRC-07 chemical mechanism, Atmos. Environ., 

44, 5336-5345, 201 Ob; Hutzell et al., Interpreting predictions from the SAPRC07 mechanism based on 

regional and continental simulations, Atmos. Environ., 46, 417-429, 20 12). 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, 

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201 Oa,b ). The mechanism also explicitly represents organic species with either high emissions, high 

toxicity, or high secondary organic aerosol formation potential (e.g., xylene, a-pinene, benzene, 

lj3-butadiene, etc.) (Hutzell et al.~ 2012; see also SAPRC-07 Chemical Mechanism and Emissions 

Assignment Files (http://www.cert.ucr.edu/~carter/SAPRC/fi es.htm) ). 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, 

201 0). This update improves the simulation of 03 in urban plumes, though its impact on total fme 

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 03 

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 ofF e 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 i~proving the aerosol 

chemistry as well as speciation. Recent evaluation studies have revealed that the largest biases in CMAQ 

PM2.s results are driven by over predictions of the unspeciated PM2.s, referred to hereafter as PMother; 

this component constitutes over half of the National Emission Inventory (NEI) for PM2.S· Detailed 

speciation profiles derived from the work of Reff et al. (2009) were used to further subdivide emissions 

ofPMother into primary ammonium (NH/), sodium (Na+), chloride (Cr), selected trace elements (Mg, 

AI, 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 oftheir catalysis effects on S(IV) to S(VI) 

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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 ofiSORROPIA version 2.0. Many of the numerical 

instabilities associated with the previous version ofiSORROPIA have been eliminated/moderated in this · 

new version. An additional advancement in ISORROPIAv2.0 is the treatment ofCa2

+, K+, and Mg2+, 

. species abundant in sea-sC).lt 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 ofiSORROPIA v2.0 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 ofNOx in the mid-upper troposphere and can impact the distribution of reactive 

nitrogen as well as 03. A parameterization to estimate the vertical distribution ofNOx 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 0 3 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 

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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 managem~nt 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 ofthe 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 si~ulation 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. Techno I. 44, 1683-1689, 201 0). 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 

ofNH3 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 ofNH3 and Hg based on varying land-use, soil, and plant 

compensation points and is included in CMAQv5.0. The inclusion ofNH3 bidirectional exchange in 

CMAQ significantly reduces the models annual bias in NHx wet deposition (Appel et al., A multiresolution 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 

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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 CMAQvS.O- February 2012 

Changes and new features 

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1. Aerosol Module 

• Redesign 

• Eliminated dependencies and duplication across modules 

• AER06 

• PMother speciation 

Page 6 of8 

• Addition of9 new PM2.s species: APNCOMI/J, AFEJ, AALJ, ASIJ, ATIJ, 

ACAJ, AMGJ, AKJ, AMNJ 

• Anthropogenic emissions of 4 existing PM2.s species: ANAJ, ACLJ, AH20J, 

ANH4J 

• Changed names of2 species: AORGPAl/J --> APOCI/J and A25I/J --> 

AOTHRI/J 

• Note: When preparing emissions for AER06, 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 AER06 are summarized in Emission Changes for 

CMAQv5.0 

• POA aging 

• Oxidative aging ofPOC 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 ofPOC minus moles of primary 

organic oxygen). 

• ISORROPIA2 

• Sulfur Chemistry 

• Windblown dust 

• Updates to SOA yield parametrization (AER05 and AER06) 

2. Chemistry 

• CB05 

• Replaced existing toluene chemistry in CB05 with updated toluene chemistry (CB05-

TU, Whitten et al., 2010) 

• Revised rate constants for N20s hydrolysis in CB05 based on the latest 

recommendation of IUPAC 

• Added reactions oftoluene 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. 

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• 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 ofC-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 ofWRF (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 m2

s- 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: http://www.mmm.ucar.edu/wrf/users/docs/arw_v3.pdfThe 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 

• Bidirectional Exchange ofNH3 

• Has a substantial impact on the wet and dry deposition of reduced nitrogen and in 

ambient reduced nitrogen concentrations 

• Bidirectional Exchange of Hg0 

• In-line processing of direct natural and recycled Hg0 emissions 

• Mesophyll resistance in m3dry 

• Added runtime option (CTM_MOSAIC) for output of land use specific deposition velocity 

and flux 

• If this option is selected, user may also opt to output a separate file of stomatal flux 

(CTM_FST). 

• N02 deposition velocity 

• Deposition velocity output in previous versions included the effects of the HONO 

heterogeneous chemistry. In CMAQv5.0, these effects are no longer included. 

• Mesophyll resis.tance is now calculated as a function of the Henry's Law constant 

7. Structural Updates 

• Namelist redesign of CGRID model species implementation 

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• CMAQ Updates to comply with Models-3/EDSS I/0 API version 3.1 

• CMAQv5.0 requires I/O-API version 3.1 

• Removed usage of deprecated include files (PARMS3.EXT, FDESC3.EXT, and 

IODECL3.EXT) 

• Removed usage of deprecated TRIMLEN 

• Utilize M3UTILIO 

8. Multi-Pollutant Modeling 

• Mechanism and Species 

• Bidirectional Exchange of Hg0 

• In-line processing of direct natural and recycled Hg0 emissions 

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 

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