TSD-2c 

PM2.5 modeling using the SMOKE/CMAQ system over the 

Ozone Transport Region (OTR) 

Bureau of Air Quality Analysis and Research 

Division of Air Resources 

New York State Department of Environmental Conservation 

Albany, NY 12233 

February 1, 2006 
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Air Quality Modeling Domain 

The modeling domain utilized in this application represented a sub-set of the inter-RPO’s 

continental modeling domain that covered the entire 48-state region with emphasis on the 

Ozone Transport Region. The OTC modeling domain at 12km horizontal mesh is 

displayed in Figure 1 is part of the 36km continental domain that is designed to provide 

boundary conditions (BCs). The particulars of the two modeling domains are: 

 The 36km domain covered the continental US by a 149 by 129 mesh in the east-west and 

north-south directions, respectively. The domain is based on Lambert Conformal 

Projection with the center at (97oW 40oN) and parallels at 33oN and 45oN. As evident 

from Figure 1, the 12km domain utilized in this analysis covers most areas of the eastern 

US and has 172 by 172 mesh in the horizontal. Both domains utilize 22 layers in the 

vertical extending to about 16km with 16 layers placed within the lower 3km. 

Photochemical Modeling -- CMAQ

The CMAQ (version 4.5.1) with CB4 chemistry, aerosol module for PM2.5 and RADM 

cloud scheme was utilized in this study. Photochemical modeling was performed with the 

CCTM software that is part of the CMAQ modeling package. Version 4.5.1 of this 

modeling software was obtained from the CMAS modeling center at 

http://www.cmascenter.org. The following module options were used in compiling the 

CCTM executable: 

• Horizontal advection: yamo 

• Vertical advection: yamo 

• Horizontal diffusion: multiscale 

• Vertical diffusion: eddy 

• Plume-in-Grid: non operational 

• Gas phase chemical mechanism: CB-4 

• Chemical solver: EBI 

• Aerosol module: aero3 

• Process analysis: non operational 

The following computational choices were made during compilation: 

• Compiler version: PGI 6.0 

• Fortran compiler flags:-Mfixed -Mextend -Bstatic -O2 -module ${MODLOC} -I. 

• C compiler flags: -v -O2 -I${MPICH}/include 

• IOAPI library: version 3.0 

• NETCDF library: version 3.6.0 

• Parallel processing library version: mpich 1.2.6 

• Static compilation on 32-bit system 
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The following choices were made for running the executable: 

• Number of processors: 8 

• Domain decomposition for parallel processing: 4 columns, 2 rows 

• Number of species written to the layer-1 hourly-average concentration output 

(ACONC) file: 39 (O3, NO, CO, NO2, HNO3, N2O5, HONO, PNA, PAN, NTR, 

NH3, SO2, FORM, ALD2, PAR, OLE, ETH, TOL, XYL, ISOP, ASO4I, ASO4J, 

ANO3I, ANO3J, ANH4I, ANH4J, AORGAI, AORGAJ, AORGPAI, AORGPAJ, 

AORGBI, AORGBJ, AECI, AECJ, A25I, A25J, ACORS, ASEAS, ASOIL) 

• Each daily simulation was performed for 24 hours starting at 05:00 GMT (00:00 

EST) 

The following postprocessing steps were performed using utility tools from the “ioapi” 

software package obtained from 

http://www.baronams.com/products/ioapi/AA.html#tools: 

• Extract and combine the following species for each hour for the first 16 model 

layers from the full 3-D instantaneous concentration output file: O3, CO, NO, 

NO2, NOY_1 (=NO + NO2 + PAN + HNO3), NOY_2 (=NO + NO2 + PAN + 

HNO3 + HONO + N2O5 + NO3 + PNA + NTR), HOX (=OH + HO2), VOC 

(=2*ALD2 + 2*ETH + FORM + 5*ISOP + 2*OLE + PAR + 7*TOL + 8*XYL), 

ISOP, PM2.5 (=ASO4I + ASO4J + ANO3I + ANO3J + ANH4I + ANH4J + 

AORGAI + AORGAJ + 1.167*AORGPAI + 1.167*AORGPAJ + AORGBI + 

AORGBJ + AECI + AECJ + A25I + A25J), PM_SULF (=ASO4I + ASO4J), 

PM_NITR (=ANO3I + ANO3J), PM_AMM (=ANH4I + ANH4J), PM_ORG_SA 

(=AORGAI + AORGAJ), PM_ORG_PA (=1.167*AORGPAI + 

1.167*AORGPAJ), PM_ORG_SB(=AORGBI + AORGBJ), PM_ORG_TOT 

(=AORGAI + AORGAJ + 1.167*AORGPAI + 1.167*AORGPAJ + AORGBI + 

AORGBJ), PM_EC (=AECI + AECJ), PM_OTH (=A25I + A25J), PM_COARS 

(=ACORS + ASEAS + ASOIL), SO2, HNO3, NH3, H2O2 

• Extract all species for all model layers for the last hour of each daily 

instantaneous concentration output file to enable “hot” restarts of modeling 

simulations 

• Create daily files of hourly running-average 8-hr ozone concentrations with time 

stamps assigned to the first hour of the averaging interval 

The following files are archived on LTO2 computer tapes (each tape holds approximately 

200 Gb of data) for each day: 

• Aerosol/visibility file 

• Layer-1 hourly-average concentration output file (contains 39 species) 

• Dry deposition file 

• Wet deposition file 

• Extracted 16-layer species file 

• Restart file (last hour of full 3-D instantaneous concentration file) 

• Hourly 8-hr concentration file 
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Photolysis Rates

One of the inputs to CMAQ is the photolysis rates. In this study, photolysis rate lookup 

tables were generated for each day of 2002 with the JPROC software that is part of the 

CMAQ modeling package. This software was obtained from the CMAS modeling center 

at http://www.cmascenter.org. Rather than using climatological ozone column data, daily 

ozone column measurements from the NASA Earthprobe TOMS instrument were 

downloaded from ftp://toms.gsfc.nasa.gov/pub/eptoms/data/ozone/Y2002/ and used as 

input to the JPROC processor. It should be noted that TOMS data were missing for the 

time period from August 3 – 11, 2002. The missing period was filled as follows-- TOMS 

data file for August 2 was used as JPROC input for August 3rd through August 7th, and 

the TOMS data file for August 12th was used as JPROC input for August 8th through 

August 11th. 

Boundary Conditions (BCs)

The boundary conditions for the 12km grid were extracted from the 36km CMAQ 

simulation. The 36km simulation utilized boundary conditions that were based on a oneway nest approach to GEOS-CHEM global model outputs (Moon and Byun 2004, Baker 

2005). As stated above, the intent of the 36km CMAQ simulation was to provide the 

BCs for the 12km model that would be more reflective of the emissions and meteorology 

rather than to use either clean or arbitrary pollutant fields. Also, in this study the CMAQ 

simulations utilized a 15-day ramp-up period, thereby minimizing the propagation of the 

boundary fields into the areas of concern. A report on the setup and application of the 

36km CMAQ and the extraction of the BCs is available from NYSDEC. 

Meteorological data

The meteorological data for this study was based on MM5 modeling (see Meteorological 

Modeling, 2007). The MM5 fields are then processed by MCIP version 3.0, a utility 

available as part of the CCTM software from CMAS Modeling Center (see 

http://www.cmascenter.org) to provide CMAQ model-ready inputs. 

Emissions

 

The emissions data for 2002 were generated by individual states within the OTR and 

were assembled and processed through the Mid Atlantic Northeast Visibility Union 

(MANE-VU), a Regional Planning Organization (RPO). These emissions were then 

processed by NYSDEC using SMOKE processor to provide CMAQ compatible inputs 

(Anthro-Emissions 2006). The 2002 emissions for the non-OTR areas within the 

modeling domain were obtained from the corresponding RPOs and were processed using 

SMOKE, in a manner similar to that of the OTR.emissions. Details of this processing are 

outlined in the report (Pechan 2007), and the hourly biogenic emissions (Bio-Emissions, 

2006) 
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CMAQ simulations

CMAQ simulations were performed using the one-way nesting approach in which we 

perform the continental CMAQ simulation at 36km grid spacing. For this simulation we 

utilized clean initial conditions with boundary conditions extracted from the simulation of 

GEOS-CHEM global chemical model. The interface program used in this application was 

developed by University of Huston (Moon and Byun 2004), which was applied to obtain 

hourly 36km boundary concentrations from GEOS-CHEM outputs. The CMAQ 36km 

simulation was initiated from December 15, 2001 with the first 15 days as spin up period 

and terminated on December 31, 2002. The simulation utilized the 2002 emissions data 

available from the RPOs and 2002 MM5 meteorological fields developed by the 

University of Maryland (TSD-1a). The hourly boundary fields for the 12km CMAQ 

domain were obtained by application of BCON program to the 3-D concentration fields 

generated by the 36km CMAQ simulation. 

The 12km simulations for both base and future year were assigned the boundary 

conditions based on the 36km CMAQ simulation and clean initial conditions. The annual 

simulation was parsed out between different member states or their contractors of the 

OTR, so as to expedite the process of completing the simulation in a limited time. The 

approach used is as follows: The annual simulation was parsed out into five parts and 

each modeling center identified below initiated and completed the simulation, extracted 

the outputs which were then combined to provide the annual simulation. There was 

considerable exchange of information in the setup and execution of the modeling system 

between the centers using benchmark runs to ensure consistency and uniformity between 

the centers. The process was followed both for the base year 2002 and for the future year 

2009. Details on CMAQ setup and run scripts are available from NYSDEC. 

Modeling Center Simulation period Analysis period 

MDE/UMD Dec 15, 2001 to Feb 28, 2002 Jan 01, 2002 to Feb 28, 2002 

NJDEP/Rutgers Feb 15, 2002 to May 14, 2002 Mar 01, 2002 to May 14, 2002 

NYSDEC May 01, 2002 to Sep 30, 2002 May 15, 2002 to Sep 30, 2002 

VA DEQ Sep 15, 2002 to Oct 30, 2002 Oct 01, 2002 to Oct 30, 2002 

NESCAUM Oct 15, 2002 to Dec 31, 2002 Nov 01, 2002 to Dec 31, 2002 

References 

Baker, K.: (2005) http://www.ladco.org/tech/photo/present/ozone.pdf

Moon, N. and D. Byun: (2004) A simple user’s guide for “geos2cmaq”code: Linking 

CMAQ with GEOS-CHEM. Version 1.0. Institute for Multidimensional Air quality 

Studies (IMAQS), University of Houston, Houston TX. 
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Meteorological Modeling: (2007) Meteorological Modeling of 2002 using Penn 

State/NCAR 5th Generation Mesoscale Model (MM5). TSD-1a 

Pechan: (2006) Technical Support document for 2002 MANE-VU SIP Modeling 

inventories, version 3. Prepared by E. H. Pechan & Associates, Inc. 3622 Lyckan 

Parkway, Suite 2005, Durham, NC 27707. 

Bio-Emissions: (2006) Processing of Biogenic Emissions for OTC/MANE-VU 

Modeling. TSD-1b 

Anthro-Emissions: (2006) Emission Processing for the Revised 2002 OTC Regional and 

Urban 12 km Base Case Simulations. TSD-1c 

 Figure 1 Display of 36- and 12km air quality modeling domains.