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

# CMAQ version 5.0 (February 2012 release) Technical Documentation
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## Contents

• 1 Summary ofFeatures 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 ofAmmonia and Mercury: I • 1.10 Two-way Coupled WRF-CMAQ • 2 RELEASE

_NOTES for CMAQv5.0- February 2012 • 2.1 Changes and newfeatures • 2.2 Two-way Coupled WRF 3.3 and CMAQ 5.0 • 2
.3 Known Issues • 2.4 Other Documentation 

## Summary ofFeatures and Enhancements in CMAQvS.O Page 1 of8

The release version ofCMAQ 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 ofa more robust model. Summarized below are the main enhancements to the modeling system. Gas-phase Chemistry: CMAQv5.0 includes a new version ofthe SAPRC gas-phase chemical mechanism, namely SAPRC07TB (Carter, Development ofthe SAPRC-07 chemical mechanism, Atrnos. Environ., 44, 5324

- 5335, 201Oa; Carter, Development ofa condensed SAPRC-07 chemical mechanism, Atmos. Environ. , 44, 5336-5345, 201Ob; 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 oforganic 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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... 611/2015CMAQ version 5.0 (February 2012 release) Technical Documentation- cmaqwiki Page 2 of8 201 Oa,b ). The mechanism also explicitly repre sents organic species with either high emiss ion s, 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 Mechan i sm and Emissions Assignment Files**(http://www.cert.ucr.edu/~carter/SAPRC/fi es.htm)**  ). Add iti ona lly , the CB05 mechanism has been updated to include the updated toluene chemistry recommended by Whitten et al. (A new condensed toluene mechan i sm for Carbon Bond: CB05 - T U, 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 smal l (Sarwar et al. , Impact of a new condensed toluene mechanism on a i r quality model predictions in the US, Geosci. Model Dev., 4, 183 - 193, 2011). Photolysis Rates:

Previous versions of CMAQ relied on l ook-up tab l es for estimat i o n of photolysis rates . The on- lin e photolysis rate module, which incorporates the radiative impacts of aeroso l lo ading simulated by the model, has been further enhanced in CMAQv5.0. This treatment allows for inclusion of the effects of scattering and absorbing aeroso l s 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 enhancemen t enables the model to more accurately represent the increase in photolysis due to re flection 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 leve l s ofF e and Mn are us ed in the catalysis reactions instead of the previous background values, which would help in improved representation of spatial and seasonal variability in t he rel ative 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 specia t ion. 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 Nat ional Emission In ventory (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 spec ia t ion now allows for detailed characterization of the species, processes, and emission sector contributions to the model bias in primary and consequently total PM. The explici t treatment of Fe and Mn also allows for explicit representation oftheir catalysis effects on S(IV) to S(VI) http://www.airqualitymodeling.org /c maqwiki/index.php?title=CMAQ _ version _ 5.0 _ %28Feb ... 6 / 1/2015CMAQ version 5.0 (February 2012 release) Technical Documentation- cmaqwiki Page 3 of8
conversion through aqueous chemistry, and consequently more consistent treatment ofsulfate production pathways inthe model. The representation ofgas/particle partitioning ofinorganic species was also improved through the incorporation ofiSORROPIA version 2.0. Many ofthe 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 ofCa 2+

, K+, and Mg2+,

. species abundant in sea-sC).lt and soil dust. In previous versions ofCMAQ, contributions ofnatural

windblown dust on airborne PM mass were not explicitly represented. CMAQv5.0 includes a module that dynamically estimates natural emissions offine 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 ofdust emission and PM composition simulated by CMAQv5.0. Finally, a scheme to represent the oxidation ofprimary organic aerosol has been included. The oxidation oforganic carbon increases the non-carbon organic matter, thereby increasing PM2.5 mass concentrations. Comparison ofmodeled OM/OC ratios with those inferred from the IMPROVE measurements, show improved representation ofboth spatial and seasona l variability in the predicted OM/OC ratio. 

### LightningNOx 

### emissions: The application ofthe 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 ofatmospheric 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 ofreactive 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 overthe Continental U.S., the algorithm uses lightning flash totals from the National Lightning DetectionNetwork (NLDN). For cases, where such data is not available, an alternate algorithm which estimates the number oflightning flashes based on the modeled convective precipitation canbe invoked. Besides impacting ambient concentrations ofreactive nitrogen species and 

### 0 3 in the troposphere, initial simulations also show large improvements in nitrogen wet deposition simulations as a result ofincluding lightning NOx emissions in

.the model. 

### TransportProcesses: Physical process changes to CMAQv5.0 include updates to the representation ofturbulent 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 ofthe 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 ofa concerted effort to review and update the model systems code structure and architectural design. As the complexity ofthe model system has increased since its initial release in 1998, some ofthe 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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... 611/2015CMAQ version 5.0 (February 2012 release) Techn ic al Documentation- cmaqwiki Page 4 of8 CMAQv5.0. First, a complete redesign of the aerosol module was implemen ted w hi ch eliminated numerous dependencies and duplication across modules; the improved modularity has and will continue to further enhance the aerosol module and red uce 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 spec ifi cation of various attributes of the modeled chemical species and enables users to more easily modify and customize the modeled species set fo r 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 wit h OAQPS and includes the 33 HAPs iden t ified under t he Integrated Urban Air Toxic s Strategy as posing the grea t est 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 a llow s 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 contro l strategies can be more robustly examined. Bi -d irectional Exchange of Ammonia and Mercury: Unlike most gas phase po llu tants, 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 e l emental 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 Mul t isca l e 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 co ll aborated 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, 1683-1 689, 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 evalua ted against field observations (Cooter et al. Estimation ofNH 3 bi-directional flux from managed agricultural soils, Atmos. Environ. 44,2107-2115, 2010) and coupled to CMAQ linking agric ultural management practices to regional transportation and deposition of gaseous NH 3 and ammonium aerosols. This parameterization was applied on a regional scale by representing bi-directional exchange ofNH3 and Hg based on varying land -u se, soil, and plant compensation points and is included in CMAQv5.0. The inclusion ofNH3 bidirectional exchange in CMAQ significantly reduces t he 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 http://www.airqualitymodeling.org/cmaqwiki/index.php?title = CMAQ _ version _ 5.0 _ %28Feb ... 611/2015CMAQ version 5.0 (February 2012 release) Technical Documentation

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field intensive data and has also beenrigorously evaluated against NH3 flux measurements as well as thoroughly assessed as to its impact on model performance ofambient nitrogen levels and wet deposition amounts. Two-way Coupled WRF-CMAQ Previous versions ofCMAQ were run in a sequential off-line manner, wherein, archived output on the dynamical state ofthe 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 ofthe 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 ofCMAQ at sma ller 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 ofpollutant 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. Inthe on-line mode, the WRF and CMAQ modeling systems are coupled through the use ofmemory-resident buffer data files, which provide flexibility both in the frequency ofdata 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 ofthe two modeling systems. This approach also mitigates the need to maintain separate versions ofthe 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 ofthe 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 ofdata 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 ofaerosols which are then used in the radiation calculations in WRF. Thus, direct radiative effects ofabsorbing 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 ofthe impacts of atmospheric loading ofradiatively importanttrace 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

http:/ /www.airqualitymodeling.org/cmaqwiki/index.php?title=CMAQ_ version_ 5.0 _%28Feb
... 6/1/2015CMAQ version 5.0 (February 2012 release) Technical Documentation- cmaqwiki 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, AS IJ , ATIJ, ACA J , AMG J , AKJ, AMN J • Anthropogenic emissions of 4 existing PM2.s species: ANA J , ACLJ, A H20J , 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 spec i es. CMAQ will crash if any emitted PM species is not included in the emissions input files. See PM emitted species li st for details on naming species in the emissions file . Emission Changes for this release of CMAQ

includ ing changes needed fo r AER06 are summarized in Emission Changes for CMAQv5.0 • POA aging • Oxidative aging ofPOC le ads 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 h ydrolysis in CB05 based on the la test recommendation of IUPAC • Added re act ions oftoluene and xylene with chlorine radical (CL) • SAPRC07(TB & TC) • Fully u pdated organic and inorganic reactions . • Updated photolysis r ates • Use operator species to better repre sent chemica l reactions in low-NOx conditions • Additional species with high emission, high tox ici ty, or high SOA formation are treated explicitly • In-line Option for Photolysis Rates • Moved opacity and photolysis data (absorption cross sections and quant u m yield data) to an ASCII input file, that is created by a p re -p rocessor and depends only on

the mechanism for gas chemistry (not time). • Allows more flexibility to change/ in troduce data for photolysis rates or create/modify a chemical mechanism.**http:/ www.airq~alitymodeling.org/cmaqwiki/index.php?title=CMAQ_**  version_ 5.0 _ %28Feb .. . 6 /1/ 2015CMAQ version 5.0 (February 2012 release) Technical Documentation- cmaqwiki Page 7 of8

• The ASCII file also defines the number ofwavelength and temperature interpolation points, allowing for adjustments to improve the accuracy ofthe 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 seaice coverage. 3. Vertical Diffusion (ACM2) • Defaultread 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 m 2

s- 1to 0.01 m2 s- 1and from 2.0 m 2

s- 1to 1.0 m2 s- 1for urban areas. Minimum eddy diffusivity in WRF/ACM2 is 0.01 m2 s- 1 everywhere. 4. Vertical Advection • A new method for computing the vertical velocity has beenimplemented 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 getthe change in column mass and then solve for omega layer-by-layer using the horizontal mass divergence. See equat ion 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 ofnitrogen 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 impacton summer nitrogen deposition, minor impact on surface concentrations 6. Dry Deposition • Bidirectional Exchange ofNH3 • Has a substantial impact on the wet and dry deposition ofreduced nitrogen and in ambientreduced nitrogen concentrations • Bidirectional Exchange ofHg0 • In-line processing ofdirect natural and recycled Hg0 emissions • Mesophyll resistance in m3dry • Added runtime option (CTM_MOSAIC) for output ofland use specific deposition velocity and flux • If this option is selected, user may also optto output a separate file ofstomatal flux (CTM

_FST). • N02 deposition velocity • Deposition velocity output in previous versions included th e effects ofthe HONO heterogeneous chemistry. In CMAQv5.0, these effects are no longer included. • Mesophyll resis.tance is now calculated as a function ofthe Henry's Law constant 7. Structural Updates • Namelist redesign ofCGRID model species implementation
http://www.airqualitymodeling.org/cmaqwiki/index.php?title=CMAQ_ version

_5.0

_%28Feb
... 6/1/2015CMAQ version 5.0 (February 2012 release) Technical Documentation- cmaqwiki Page 8 of8 • 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 Hg 0 • In-line processing of direct natural and recyc l ed Hg 0 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 Retrieved from "http: / /www .airqualitymodeling.org/cmaqwiki/index. php?t it le = CMAQ_ version _ 5 . 0 _ (February_2012_release)_Technical_Documentation&oldid=ll" ------------------------------- • This page was last modified on 15 November 2012, at 07 : 25. • This page has been accessed 11, 160 times. http://www.airqualitymodeling.org/cmaqwikilindex.php?title=CMAQ_version_5.0_%28Feb ... 6/1/2015