Appendix D 

Modeling Analysis Protocol and 

Quality Assurance Project Plan
 Appendix C - 1
 Appendix C - 2

1. Introduction 

The regional haze modeling was coordinated by the Southeast Regional Planning Organization, 

Visibility Improvement State and Tribal Association of the Southeast (VISTAS), which is 

comprised of the ten Southeast States (Alabama, Florida, Georgia, Kentucky, Mississippi, North 

Carolina, South Carolina, Tennessee, Virginia and West Virginia) and the local programs and 

tribal agencies located within these states. VISTAS contracted with Environ International Corp, 

Alpine Geophysics, LLC and the University of California Riverside to perform the emissions and 

air quality modeling for this regional haze state and tribal implementation plans implementation 

plans. 

Attachment C.1 contains modeling protocol submitted by the contractors entitled Modeling 

Protocol for the VISTAS Phase II Regional Haze Modeling. The modeling protocol documents 

the meteorological model, emissions model and air quality model that will be used for this 

project. It discusses details about the configuration of the models, modeling domains, quality 

assurance objectives, etc. 

Attachment C.2 contains the quality assurance project plan that was developed by the modeling 

contractors to outline the quality assurance procedures to be used in the modeling process. 

Attachment C3 contains an article from Atmospheric Environment published in 2006. The article 

contains details of modifications made to the secondary organic aerosols (SOA) module in 

CMAQ, by ENVIRON, to better quantify SOA. This was necessary as preliminary modeling 

runs showed organic carbon was significantly under-predicted in the summer and this under 

prediction was determined to be unacceptable because organic carbon is a major contributor to 

PM mass and visibility impairment in the southeastern US. The modified SOA module in 

CMAQ incorporates additional SOA formation based on emissions data from pine forests in 

Durham, NC. Full details of the SOA module are included in section 4 of the article. 
Appendix C.1 

VISTAS Modeling Protocol 
 May 2003 

Second Draft Report 

VISTAS Emissions and 

Air Quality Modeling— 

Phase I Task 6 Report: 

Modeling Protocol for the VISTAS Phase II 

Regional Haze Modeling 

Prepared by: 

Ralph E. Morris 

Bonyoung Koo 

ENVIRON International Corporation 

101 Rowland Way 

Novato, California 94945 

T.W. Tesche 

Cyndi Loomis 

Gregory Stella 

Alpine Geophysics LLC 

3479 Reeves Drive 

Ft. Wright, Kentucky 41017 

Gail Tonnesen 

Zion Wang 

UC Riverside 

CE-CERT 

1084 Columbia Avenue 

Riverside, California 92507 

May 6, 2004 

 101 Rowland Way, Suite 220, Novato, CA 94945 415.899.0700 

Appendix C.1 - 1
May 2004 

i 

TABLE OF CONTENTS 

Page 

EXECUTIVE SUMMARY ...........................................................................ES-1 

Background...........................................................................................ES-1 

Top-Down Evaluation Methodology .............................................................ES-1 

Results ............................................................................................ES-3 

Conclusions ..........................................................................................ES-6 

Recommendations...................................................................................ES-7 

1. INTRODUCTION ...................................................................................1-1 

2. MODELING METHODOLOGY.................................................................2-1 

Modeling Databases ..................................................................................2-1 

Emission Inventories..................................................................................2-3 

DDM Sensitivity Coefficients.......................................................................2-6 

Ambient Data ........................................................................................ 2-15 

3. RESULTS..............................................................................................3-1 

Aircraft Data...........................................................................................3-1 

Summary of Model Performance for Aircraft Measurements .................................3-4 

Top-Down Evaluation of Emissions by Source Category ......................................3-8 

Model Performance Evaluation with Surface Precursor Data ............................... 3-46 

Top-Down Evaluation of Emissions by Geographic Region ................................. 3-50 

4. VOC RELATIVE REACTIVITY FACTORS.................................................4-1 

5. SUMMARY AND CONCLUSIONS .............................................................5-1 

 Top-Down Evaluation Methodology ...............................................................5-1 

 Results ..............................................................................................5-2 

 Conclusions ............................................................................................5-5 

 Recommendations.....................................................................................5-6 

REFERENCES........................................................................................... R-1 

APPENDICES 

Appendix A: Comparisons of Modeled and Observed Ozone 

 Concentrations for TexAQS Aircraft Flights on August 27-31, 2000 

Appendix C.1 - 2
May 2004 

ii 

TABLES 

Tables ES-1. Summary of emissions scenarios....................................................ES-3 

Table 2-1. Summary of MM5 and CAMx layer heights........................................2-1 

Table 2-2. Model-ready emissions (tons/day) for the HGBPA 11 county area. ............2-5 

Table 2-3. Average OH-reactivity (kOH, ppm-1 min-1) for VOC emissions. ..............2-6 

Table 3-1. Regression coefficients from least squares fits to single term models......... 3-15 

Table 3-2. Sensitivity of least squares fits to HCHO errors.................................. 3-16 

Table 3-3. Regression coefficients from least squares fits to combinations 

 of NOx emission categories under the PT_O2N2 emissions scenario......... 3-17 

Table 3-4. Summary of VOC emissions scenarios............................................. 3-18 

Table 3-5a. Summary of model performance statistics for emission 

 scenarios described in the text. .................................................... 3-20 

Table 3-5b. Summary of model performance statistics for emission 

 scenarios described in the text....................................................... 3-21 

Table 3-6a. Summary of model performance statistics for emission 

 scenarios described in the text....................................................... 3-23 

Table 3-6b. Summary of model performance statistics for emission 

 scenarios described in the text....................................................... 3-24 

Table 3-7. Model performance summary statistics based on 

 aircraft observations for O3, NOy, and HCOH .................................. 3-25 

Table 3-8. Regression coefficients from least squares fits to combinations of 

 VOC emission categories under the MABVOC emissions scenario........... 3-38 

Table 3-9. Summary of ozone model performance statistics for the 

 NOxMAP emission scenario relative to the PT_O2N2 scenario............... 3-39 

Table 3-10. Summary of CAMx model performance for formaldehyde 

 at the La Porte and Williams Tower monitoring sites ........................... 3-46 

Table 3-11. Summary of CAMx model performance for NOy at the 47 

Table 3-12. Emission totals (episode average tons/day) for sub-regions 

 identified in Figure 3-21 (“Other” refers to the entire 

 modeling domain outside the six sub-regions). ................................... 3-51 

Table 3-13. Single term least squares fit results based on sub-regional 

 sensitivities (highlighted rows indicates statistically 

 significant fits at 98% confidence level). .......................................... 3-58 

Table 3-14. Least squares fit results based on sub-regional VOC sensitivities 

 for all species (five term model; highlighted rows indicates statistically 

 significant regression coefficients at 98% confidence level).................... 3-58 

Table 3-15. Least squares fit results based on sub-regional VOC sensitivities 

 for ozone and formaldehyde only (five term model; 

 highlighted rows indicates statistically significant regression 

 coefficients at 98% confidence level)............................................... 3-59 

Table 3-16. Least squares fit results based on sub-regional VOC sensitivities 

 for ozone only (five term model; highlighted rows indicates 

 statistically significant regression coefficients at 98% confidence level) ..... 3-59 

Appendix C.1 - 3
May 2004 

iii 

Table 3-17. Least squares fit results based on sub-regional NOx sensitivities 

 for all species (five term model; highlighted rows indicates 

 statistically significant regression coefficients at 98% confidence level). .... 3-59 

Table 3-18. Least squares fit results based on sub-regional NOx sensitivities 

 for NOy only (five term model; highlighted rows indicates statistically 

 significant regression coefficients at 98% confidence level).................... 3-60 

Table 3-19. Least squares fit results based on sub-regional NOx sensitivities 

 for ozone only (five term model; highlighted rows indicates statistically 

 significant regression coefficients at 98% confidence level).................... 3-60 

Table 4-1. Reactivities for CB4-VOCs relative to ethylene for the Houston 

 points source emissions and the EKMA box model MIR scenario ..............4-2 

Table 5-1. Summary of emissions scenarios......................................................5-2 

FIGURES 

Figure 2-1. The CAMx modeling domain showing the 

 nested 36, 12 and 4 km grids. .........................................................2-2 

Figure 2-2. Detail of the CAMx 4 km grid and the flexi- 

 nested 1 km grid used on selected days. .............................................2-2 

Figure 2-3. Mask defining 4 km grid cells in the 11 County 

 HGBPA nonattainment area............................................................2-4 

Figure 2-5. Sensitivity of ozone (ppb) to emissions in the 

 11 county HGBPA area for 13:00 on August 29, 2000 under 

 the PT_O2N2 emissions and the 070PBLmeteorology: 

 on-road mobile VOC; b) area and low-level point VOC; 

 c) biogenic VOC; d) elevated point VOC; e) on-road 

 mobile NOx; f) area and low-level point NOx; g) biogenic 

 NOx; h) elevated point NOx......................................................... 2-10 

Figure 2-6. Sensitivity of ozone (ppb) to area and low-level point VOC 

 emissions in the 11 county HGBPA area for 13:00 on 

 August 29, 2000: a) Base4a emissions with standard meteorology; 

 b) Base4a emissions with the 070PBL meteorology; c) PT_O2N2 

 emissions with 070PBL meteorology............................................... 2-12 

Figure 2-7. Comparison of modeled (filled contours) and aircraft observed 

 (filled circles) ozone at 13:00 on August 29, 2000 for: a) Base4a 

 emissions with 070_PBL meteorology, and; b) PT_O2N2 emissions 

 with 070_PBL meteorology. ......................................................... 2-13 

Figure 2-8. Surface ozone monitoring site locations and codes in the 1 km grid. ......... 2-16 

Figure 3-1. Example aircraft/model ozone comparisons for: a) August 27; b) 

 August 28; c) August 29; d) August 30 and e) August 31, 2000. ...............3-2 

Figure 3-2. Scatter plot of aircraft ozone observations and corresponding 

 CAMx predictions under the Base4a emissions scenario (red stars 

 indicate observed/predicted pairs for which observed ozone is greater 

 than 125 ppb).............................................................................3-5 

Appendix C.1 - 4
May 2004 

iv 

Figure 3-3. Scatter plot of aircraft ozone observations and corresponding CAMx 

 predictions under the PtO2N2 emissions scenario (red stars indicate 

 observed/predicted pairs for which observed ozone is greater 

 than 125 ppb).............................................................................3-5 

Figure 3-4. Scatter plot of aircraft formaldehyde observations and corresponding 

 CAMx predictions under the Base4a emissions scenario (red stars 

 indicate observed/predicted pairs for which observed ozone is greater 

 than 125 ppb).............................................................................3-6 

Figure 3-5. Scatter plot of aircraft formaldehyde observations and corresponding 

 CAMx predictions under the PtO2N2 emissions scenario (red stars 

 indicate observed/predicted pairs for which observed ozone is greater 

 than 125 ppb).............................................................................3-6 

Figure 3-6. Scatter plot of aircraft NOy observations and corresponding 

 CAMx predictions under the Base4a emissions scenario (red stars 

 indicate observed/predicted pairs for which observed ozone is greater 

 than 125 ppb).............................................................................3-7 

Figure 3-7. Scatter plot of aircraft NOy observations and corresponding CAMx 

 predictions under the PtO2N2 emissions scenario (red stars indicate 

 observed/predicted pairs for which observed ozone is greater than 125 ppb ..3-7 

Figure 3-8. Percentile box plot displays of DDM O3 sensitivity coefficient 

 distributions under the PtO2N2 emissions scenario for low and high 

 O3 aircraft observations (high O3 defined as O3 > 125 ppb). ................ 3-10 

Figure 3-9. Percentile box plot displays of DDM NOy sensitivity coefficient 

 distributions under the PtO2N2 emissions scenario for low and high 

 O3 aircraft observations (high O3 defined as O3 > 125 ppb). ................ 3-11 

Figure 3-10. Percentile box plot displays of DDM HCOH sensitivity coefficient 

 distributions under the PtO2N2 emissions scenario for low and high 12 

Figure 3-11. Scatter plot matrix for DDM sensitivity coefficients under the PtO2N2 

emissions scenario. .................................................................... 3-12 

Figure 3-12. Time series of predicted and observed ozone at surface monitoring 

 sites under three emissions scenarios described in the text. .................... 3-13 

Figure 3-13. Contour map (light gray contours at 20 ppb intervals) of 

 predicted surface layer daily maximum ozone concentrations 

 for 25 August 2000 under the four emissions scenarios described 

 in the text. Predicted maximum shown in red; observed daily 

 maximum ozone concentrations shown in blue at monitor site 

 locations. County boundaries and coast line shown in orange................. 3-26 

Figure 3-14. Contour map (light gray contours at 20 ppb intervals) of 

 predicted surface layer daily maximum ozone concentrations 

 for 29 August 2000 under the four emissions scenarios described 

 in the text. Predicted maximum shown in red; observed daily 

 maximum ozone concentrations shown in blue at monitor site locations. 

 County boundaries and coast line shown in orange .............................. 3-33 

Appendix C.1 - 5
May 2004 

v 

Figure 3-15. Contour map (light gray contours at 20 ppb intervals) of 

 predicted surface layer daily maximum ozone concentrations 

 for 30 August 2000 under the four emissions scenarios described 

 in the text. Predicted maximum shown in red; observed daily 

 maximum ozone concentrations shown in blue at monitor site locations. 

 County boundaries and coast line shown in orange. ............................. 3-35 

Figure 3-16. Contour map (light gray contours at 20 ppb intervals) of 

 predicted surface layer daily maximum ozone concentrations 

 for 31 August 2000 under the four emissions scenarios described 

 in the text. Predicted maximum shown in red; observed daily 

 maximum ozone concentrations shown in blue at monitor site 

 locations. County boundaries and coast line shown in orange................. 3-36 

Figure 3-17. Locations of surface (fixed site) ozone monitoring network in Houston...... 3-37 

Figure 3-18. Time series of observed ozone at surface observing sites along 

 corresponding predicted values under the PT_O2N2 and 

 AP scenarios............................................................................ 3-40 

Figure 3-19. Comparison of predicted and observed formaldehyde 

 concentrations at La Porte and Williams Tower monitoring sites 

 under the PT_O2N2 and VOCMAB emission scenarios. ....................... 3-48 

Figure 3-20. Comparison of predicted and observed NOy concentrations 

 at La Porte and Williams Tower monitoring sites under the 

 PT_O2N2 and VOCMAB emission scenarios .................................... 3-49 

Figure 3-21. Spatial distribution of emissions in the Houston modeling 

 domain for 28 August 2000 under the PT_O2N2 scenario: 

 elevated and low point source NOx (top) and on-road mobile 

 VOC (bottom); black boxes indicate sub-region boundaries; 

 sub-regions are numbered 1 to 6 as shown in top panel......................... 3-52 

Figure 3-22. Relationship of low-level to elevated source VOC DDM 

 sensitivities for ozone ................................................................. 3-53 

Figure 3-23. Scatter plot matrix of low-level VOC and elevated point 

 NOx DDM coefficients from the sub-region sensitivity analysis 

 (E0n01VOC and E0n02NOx refer to the low-level VOC and 

 elevated point NOx DDM sensitivities for sub-region 

 1, 2 ... 5 as defined in Figure 3-21) ................................................ 3-54 

Figure 3-24. Percentile box plot displays of sub-region (Reg. 1 – Reg. 5) 

 low plus elevated source O3 sensitivity coefficient distributions 

 low (right panel) and high (left panel) O3 aircraft observations 

 h O3 defined as O3 > 125 ppb)...................................................... 3-55 

Figure 3-25. Percentile box plot displays of sub-region (Reg. 1 – Reg. 5) 

 low plus elevated source NOy sensitivity coefficient distributions 

 low (right panel) and high (left panel) O3 aircraft 

 observations (high O3 defined as O3 > 125 ppb)................................. 3-56 

Figure 3-26. Percentile box plot displays of sub-region (Reg. 1 – Reg. 5) 

 low plus elevated source formaldehyde sensitivity coefficient 

 contributions for low (right panel) and high (left panel) O3 aircraft 

 observations (high O3 defined as O3 > 125 ppb)................................. 3-57 

Figure 3-27. Mean ozone prediction errors (ppb) from aircraft data: PT_O2N2 scenario. 3-61 

Figure 3-28. Mean NOy prediction errors (ppb) from aircraft data: PT_O2N2 scenario .. 3-62 

Appendix C.1 - 6
May 2004 

vi 

Figure 3-29. Mean formaldehyde prediction errors (ppb) from 

 aircraft data: PT_O2N2 scenario.................................................... 3-63 

Figure 4-1. Ozone sensitivity to OLE (olefins) compared to ETH 

 (ethylene) for O3 > 80ppb and VOC sensitive conditions........................4-3 

Figure 4-2. Ozone sensitivity to PAR (paraffins) compared to ETH 

 (ethylene) for O3 > 80ppb and VOC sensitive conditions........................4-3 

Figure 4-3. Ozone sensitivity to TOL (toluenes) compared to ETH 

 (ethylene) for O3 > 80ppb and VOC sensitive conditions........................4-4 

Figure 4-4. Ozone sensitivity to XYL (xylenes) compared to ETH 

 (ethylene) for O3 > 80ppb and VOC sensitive conditions........................4-4 

Figure 4-5. Ozone sensitivity to MEOH (methanol) compared to ETH 

 (ethylene) for O3 > 80ppb and VOC sensitive conditions........................4-5 

Figure 4-6. Ozone sensitivity to ETOH (ethanol) compared to ETH 

 (ethylene) for O3 > 80ppb and VOC sensitive conditions........................4-5 

Figure 4-7. Ozone sensitivity to FORM (formaldehyde) compared to ETH 

 (ethylene) for O3 > 80ppb and VOC sensitive conditions........................4-6 

Figure 4-8. Ozone sensitivity to ALD2 (aldehydes) compared to ETH 

 (ethylene) for O3 > 80ppb and VOC sensitive conditions........................4-6 

Figure 4-9. Ozone sensitivity to ISOP (isoprene) compared to ETH 

 (ethylene) for O3 > 80ppb and VOC sensitive conditions........................4-7 

Figure 4-10. Ozone sensitivity to PT_O2N2 point source VOC emissions compared 

 to ETH (ethylene) for O3 > 80ppb and VOC sensitive conditions..............4-7 

Figure 4-11. Comparison of relative reactivities for CB4-VOCs from 

 Houston point sources and the EMKA MIR scenario..............................4-8 

Appendix C.1 - 7
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-1 

EXECUTIVE SUMMARY 

INTRODUCTION 

The Visibility Improvement State and Tribal Association of the Southeast (VISTAS) is a 

collaborative effort of state governments, tribal governments, and various federal agencies 

established to initiate and coordinate activities associated with the management of regional haze, 

visibility and other air quality issues in the Southeastern United States. It is one of five Regional 

Planning Organizations (RPOs) covering the U.S. that are developing a regional approach for 

addressing regional haze, fine particulate matter (PM) and ozone issues. VISTAS is comprised 

of the states of Alabama, Florida, Georgia, Kentucky, Mississippi, North Carolina, South 

Carolina, Tennessee, Virginia, and West Virginia as well as the Eastern Band of Cherokee 

Indians. The agencies participating in VISTAS are committed to a sound and thorough scientific 

analysis of regional haze problems, impacts from natural and man-made pollutants, and potential 

solutions. Stakeholders are encouraged to participate at the workgroup level in order that all 

aspects of the problem and possible strategies may be given consideration. 

The Clean Air Act establishes goals for visibility in many national parks, wilderness 

areas, and international parks as “the prevention of any future, and the remedying of any 

existing, impairment of visibility in mandatory Class I Federal areas which impairment results 

from manmade air pollution” (40 CFR 51.300). States are required to develop State 

Implementation Plans (SIPs) to attain visibility standards, and Tribes also may opt to assume 

responsibility for visibility programs under 40 CFR Part 49 by developing Tribal Implementation 

Plans (TIPs). The goal of the Regional Haze Rule (RHR) is to achieve natural visibility 

conditions at the Federally mandated Class I areas by 2064. To achieve this goal, the RHR has 

set up several milestone years of 2018, 2028, 2038, 2048, 2058 and 2064 to monitor progress 

toward natural visibility conditions. Section 308 requires the first visibility SIP/TIP be submitted 

to EPA by 2007 - 2008 that demonstrates progress to natural visibility conditions in 2018 using 

the 2000-2004 five-year baseline. 

VISTAS has embarked on a multi-year effort to address the RHR requirements for the 

southeastern U.S. One of the components of VISTAS is the use of meteorological, emissions 

and regional particulate matter (PM)/ ozone models to project visibility at VISTAS Class I areas 

in future-years. The VISTAS modeling effort has been split into two Phases. Under Phase I, 

which was performed primarily in 2003, VISTAS tested and evaluated meteorological, emissions 

and PM/ozone models for three episodes to identify the optimal configuration for regional fine 

particulate, ozone and visibility modeling in the southeastern U.S. In Phase II, which was 

initiated in 2004, VISTAS is setting up and applying the selected models, with the optimal 

configuration identified by Phase I work, for an annual cycle and possibly additional periods. 

The short-term objectives of the Phase II activities are to achieve a satisfactory base year base 

case simulation and model performance evaluation, as well as initial future-year simulations, by 

the end of 2004 so that control strategy evaluation can begin in 2005. This document is the 

second draft Modeling Protocol for the VISTAS Phase II work efforts that has incorporated 

comments from the VISTAS Technical Analysis workgroup that was dated March 12, 2004 

(Morris et. al., 2004). 

 In order to meet the VISTAS Phase II schedule, that VISTAS Phase II emissions and air 

quality modeling is dependent on receiving data from other VISTAS contractors. Figure ES-1 

Appendix C.1 - 8
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-2 

displays key milestone dates of the VISTAS Phase II activities including the emissions and air 

quality modeling work elements that are the shaded boxes in Figure ES-1. The Phase II 

emissions and air quality modeling is dependent upon receiving data in a timely fashion from 

other VISTAS contractors in order to meet the deliverable deadlines. 

Figure ES-1. VISTAS Phase II emissions meteorological and air quality modeling activities to 

be carried out in 2004 and early 2005. 

PRELIMINARY CONCEPTUAL MODEL OF VISIBILITY IMPAIRMENT IN THE 

VISTAS REGION 

VISTAS is currently developing a comprehensive conceptual model of visibility 

impairment in the southeastern US. Brewer, Holman and Hornback (2003) have reported a 

preliminary analysis to characterize the components of PM2.5 and their contributions to visibility 

impairment in the VISTAS region. The analyses was based on monitoring data from the 

Interagency Monitoring of Protected Visual Environments (IMPROVE) network for the period 

1998 to 2001 and from the Southeast Aerosol Research Characterization Study (SEARCH) 

network for the period 1999 to 2001. 

Jan 2004

Revised 2002 

VISTAS Em Inv

Feb 2004

MM5 Met runs

6 mo 2002 

Apr 2004

Draft “2018” 

National Inv 

Sep 2004

Revised 2002

National Inv

Mar-Sep 2004

Annual 2002 

CMAQ model

performance

Dec 04 ?

“2018” Base 

Run 

Apr 2004:

DDM in 

CMAQ

May-Oct 2004

“2018” Emissions 

Sensitivity Runs 

Sep 2004

“Typical” 2002

Modeling Inv

Oct-Dec 2004:

Control Strategy 

Inventories

Jan 2005

Phase II “2018”

Sensitivity Runs 

Jan-Jun 2005

“2018” Control 

Strategy Runs

Apr 2004

CART:select

episodes

July-Dec 2005:

Observations

Conclusions

Recommendations

Jan 2005

Interim Future 

Year Model Runs

Dec 2004

Interim Future 

Year Inventories

Emissions, Meteorological, Air Quality Modeling Deliverables

State Regulatory 

Activities

Jan-Jun 2004

Define BART sources

Jun 2004

Identify BART controls

Draft 1/16/04

EPA- approved

Modeling 

Protocol

June 2005

Economic Analyses

Feb 2004

Em Modeling 

QA + Fill Gaps

Jan 2004

Met modeling

protocol 

Feb 2004

AQ modeling

protocol 

Jan 2004

AQ Phase I 

wrapup 

Jan-Mar 2004

Define inv growth and 

control assumptions 

Dec 2004

Revised 2002

Base Run 

(model 

performance)

Oct 2004:

Revised “2018”

Em Inv

Sept 2004

MM5 Met 

Final Report Dec 2004

“Typical” 

2002 Run 

(compare to 

“2018” runs)

Aug 2004

Natural Background and Reasonable Progress Goals

Appendix C.1 - 9
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-3 

Fine particle composition and contribution to light extinction were evaluated for days with the 

20% highest and 20% lowest total light extinction (on annual basis) for 1998 to 2001 in the 

IMPROVE network and for 1999 to 2001 in the SEARCH network. For the IMPROVE sites, on 

the 20% haziest days (highest extinction), light extinction (i.e., visibility impairment) is greater 

at the Southern Appalachian, Mammoth Cave, and Sipsey sites than at the coastal and coastal 

plain sites (Figure ES-2). Visual range on the 20% haziest days varies from 18 -25 km at the 

northern IMPROVE sites and 27-48 km at the coastal and coastal plain sites. 

Figure ES-2. Components of average light extinction (Mm-1) at southeastern US IMPROVE 

monitors for the 20% best visibility days from 1998-2001). 

Light extinction for the 20% haziest days is generally higher at the northern SEARCH 

sites than the coastal SEARCH sites. Visual range on the 20% haziest days at the SEARCH sites 

varies from 15-24 km. For the 20% clearest days (lowest extinction), there is less spatial 

variation in extinction than is observed for the 20% haziest days. Visual range on the 20% 

clearest days varies from 75-131 km at the IMPROVE sites and 57-91 km at the SEARCH sites. Extinction (Mm-1)

 Coarse

Soil

Organics

EC

NH3NO3

(NH4)2SO4

Rayleigh

Dolly Sods, WV

Shenandoah, VA

James Rvier Face, VA

Mammoth Cave, KY

Sipsey, AL

Great Smoky Mtns, TN

Linville Gorge, NC

Swan Quarter, NC

Cape Romain, SC

Okefenokee, GA

Chassahowitzka, FL

Everglades, FL

Shining Rock, NC

Figure 3. Light Extinction on 20% Poorest Visibility Days - IMPROVE 1998 - 2001

50

100

150

200

250

0

Appendix C.1 - 10
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-4 

Figure ES-3. Components of average light extinction (Mm-1) at southeastern US IMPROVE 

monitors for the 20% best visibility days from 1998-2001). 

In both the IMPROVE and SEARCH networks, the 20% haziest days in the year occur 

most frequently in the summer and spring quarters and least frequently in the winter quarters. 

Variation in sulfate concentrations is the greatest contributor to seasonal variation in extinction 

in the VISTAS region. Ammonium sulfate, (NH4)2SO4, fine particles are the largest contributors 

to light extinction for both the 20% clearest and 20% haziest days at all IMPROVE and all 

SEARCH sites in all years and all quarters. (NH4)2SO4 fine particles are also the largest 

contributors to reconstructed fine particle mass at all IMPROVE and SEARCH sites for the 20% 

haziest days and at all IMPROVE sites for the 20% clearest days. On the 20% clearest days at 

the SEARCH sites, organic carbon (OC) mass can be greater than (NH4)2SO4 mass. 

Ammonium nitrate, NH4NO3, typically contributes 0-15% of the fine particle mass and 

fine mass light extinction at the SEARCH and IMPROVE sites. NH4NO3 has the highest 

contributions at the urban Birmingham and Atlanta SEARCH sites and less contribution at the 

more rural SEARCH and IMPROVE sites. Available NH4 measurements for the SEARCH and 

IMPROVE sites indicate that SO4 is not fully neutralized, particularly during the summer 

quarter. Modeling analyses suggest that NH4NO3 formation in the southeastern U.S. is limited 

by NH4 availability in the atmosphere 

Organic carbon, OC, has the second largest contribution to fine particle mass and fine 

mass light extinction for the 20% haziest days at all sites (see Figure ES-2). On the 20% clearest 

days at IMPROVE sites, NH4NO3 has an equal or sometimes larger contribution to fine mass 

extinction than OC (Figure ES-3). The contribution of OC to fine mass extinction is relatively 

constant across the quarters of the year. Analysis indicates that OC fine mass in the fall and 

winter periods is predominantly from primary sources (e.g. gasoline, diesel, wood burning) and Extinction (Mm-1)

 Coarse

Soil

Organics

EC

NH3NO3

(NH4)2SO4

Rayleigh

Dolly Sods, WV

Shenandoah, VA

James Rvier Face, VA

Mammoth Cave, KY

Sipsey, AL

Great Smoky Mtns, TN

Linville Gorge, NC

Swan Quarter, NC

Cape Romain, SC

Okefenokee, GA

Chassahowitzka, FL

Everglades, FL

Shining Rock, NC

Figure 5. Extinction on 20% Best Visibility Days - IMPROVE 1998 - 2001

0

10

20

30

40

50

60

Appendix C.1 - 11
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-5 

that secondary organic aerosols (e.g. from biogenic emissions) have small contributions to total 

OC fine mass in the fall and winter months and larger contributions in the spring and summer 

months. 

Elemental carbon, EC, typically contributes 3-15% to fine particle mass and fine mass 

light extinction at the IMPROVE and SEARCH sites. The highest levels of EC are at the urban 

Birmingham and Atlanta SEARCH sites. Elevated levels of OC, EC, and non-soil potassium can 

be used as indicators of episodes where emissions from fires impacted the monitoring sites. In 

particular, poor visibility conditions in October 2000 and November 2001 at several sites 

throughout the southeastern U.S. have been attributed to impacts due to emissions from fires. 

Further analyses is needed to separate the relative contributions of different types of combustion 

sources (e.g. forest fire, prescribed forest burning, land clearing, agricultural burning, residential 

wood combustion, or industrial wood combustion) to elevated OC and EC measures. 

Fine Soil generally contributes 0-3 % of the fine mass extinction and 5-20% of the fine 

particle mass at the southeastern U.S. SEARCH and IMPROVE sites. Soil has a higher 

percentage contribution to fine mass and fine mass extinction at Chassahowitzka and Everglades 

IMPROVE monitors in Florida than at the other IMPROVE and SEARCH sites in the 

southeastern U.S. Coarse mass generally contributes less than 5% to total extinction at the 

IMPROVE sites and at those SEARCH sites where coarse mass is measured. There is 

considerable inter-annual variability in all of the above measures of fine particle mass and 

extinction. 

Fine particle mass and composition are also measured by the state agencies at several 

sites throughout the VISTAS region. The national ambient air quality standard for PM2.5 for an 

annual average (15 μg/m3

) is measured to be exceeded in several urban areas in the southeastern. 

SUMMARY OF PHASE I FINDINGS 

The Phase I program entailed systematic meteorological, emissions, and air quality model 

testing and evaluation to identify the most reliable, scientifically valid, and operational efficient 

modeling configuration for visibility assessment in the Southeastern U.S. VISTAS selected three 

episodes to serve as the foundation for model testing and evaluation: (a) 1-20 January 2002, (b) 

13-27 July 2001, and (c) 13-21 July 1999. A brief summary of the Phase I findings is given 

below. 

Meteorological Modeling Findings 

The VISTAS meteorological modeling contractor, Baron Advanced Meteorological 

Systems (BAMS), applied the PSU/NCAR Mesoscale Model (MM5) to the three Phase I 

episodes in multiple configurations and evaluated its performance against surface and aloft 

meteorological observations (see: http://www.baronams.com/projects/VISTAS/). Several 

different Land Surface Model (LSM) and Planetary Boundary Layer (PBL) configurations were 

evaluated (LSM_PBL): 

Appendix C.1 - 12
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-6 

> px_acm: Pleim-Xiu land surface model, asymmetric convective mixing 

(ACM) Planetary Boundary Layer (PBL), interppx to link LSM 

run segments. 

> px_acm2: Similar to px_acm, except no iterppx linkage across run 

segments of LSM data. 

> noah_mrf: Noah land surface scheme with the medium range forecast 

(MRF) PBL. 

> multi_blkdr: Multi-layer soil scheme with Blackadar PBL and Zilitinkevich 

thermal roughness length. 

> noah_eta-my: Noah land-surface scheme with the ETA Mellor-Yamada PBL 

(IMDVDIF = 0). 

One of the key findings from the Phase I MM5 meteorological modeling was that the 

px_acm2 configuration was judged “best” overall, in part because it did not exhibit significant 

instances of very poor statistical performance for any quantity. Thus, a variant the px_acm2 

configuration (px_acm8) was selected for the Phase II modeling (further details can be found at 

the BAMS VISTAS website listed above). 

Emissions Modeling Findings

The emissions modeling under VISTAS Phase I was performed using the Sparse Matrix 

Operator Kernal Emissions (SMOKE) modeling system. Key findings in the Phase I emissions 

processing with the SMOKE system include: 

3⁄4 Although the SMOKE computational methodology provides quick executions 

times, the large number and sizes of input, output and intermediate data files 

require substantial time and disk space for file management activities. 

3⁄4 Data input and output review, process monitoring and data management, and QA 

reporting and evaluation activities substantially increase the calendar time 

required for each production episode. 

Computer runtimes for the SMOKE emissions processing were significant, 

notwithstanding the computational efficiencies inherent in the sparse matrix solution technique. 

Based on the SMOKE processing time requirements encountered with all three Phase I episodes, 

we project that the processing time for a full 365 day annual 36 km and 12 km grid will require 

approximately 20 days of dedicated CPU time and 60 calendar days to complete. This amount of 

processing time would limit the number of emission scenarios that could be examined potentially 

compromising the Phase II schedule. Accordingly, the VISTAS modeling team has developed 

an emissions processing approach that models a representative week (on-road mobile sources) or 

days for each month of the year in order to make the SMOKE processing time more manageable 

and consistent with the Phase II schedule. Day and hourly specific emissions for the base year 

base case are still modeled for biogenic, Electrical Generating Unit (EGU) point and fire sources. 

Appendix C.1 - 13
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-7 

Air Quality Modeling Findings

One of the main objectives of the Phase I modeling was the identification of the optimal 

model configuration(s) for simulating fine particulate and visibility in the Southeastern U.S. 

Details of the emissions and air quality modeling activities, publications, and modeling results 

under Phase I may be found at: http://pah.cert.ucr.edu/vistas/. The identification of the optimal 

Phase II model configuration considered three main, and often competing, issues: 

(1) Science: Preferable to use better science options in the Phase II model configuration; 

 

(2) Model Performance: Preferable to use model options that produce better model 

performance. 

(3) Run Time: Faster run times are preferable. 

Key findings from the Phase I air quality model testing include: 

3⁄4 Duration of CMAQ Spin-up Initialization Period: A 10-15 day spin up period 

is needed to initialize the model for modeling domains the size of the continental 

US. For the VISTAS Phase II annual modeling, the 2002 annual run will be 

performed in four quarters. The first quarter (January – March, 2002) will be 

initialized with ~13 spin up days (starting 00Z on December 18, 2001) with the 

other three quarters initialized with 15 spin up days.

3⁄4 Number of Vertical Layers: Comparisons between the CMAQ modeling results 

for the base configuration of 19 vertical layers with 34 vertical layers that exactly 

matched the MM5 layer structure revealed small changes in modeled 

concentrations, but essentially no change in the basic attributes of model 

performance. The 34 layer version takes almost twice the CPU time of the 19 

layer version. Thus, the 19 vertical layer model configuration is adopted for the 

Phase II modeling. 

3⁄4 36 km vs. 12 km Horizontal Grid Size: Similar overall model performance was 

exhibited by CMAQ using a 36 km versus a 12 km grid. However, at specific 

times and locations there could be substantial differences in estimated 

concentrations due to different precipitation and transport patterns. Although the 

12 km runs require significantly more computer resources, they do represent 

better science for photochemical and PM grid modeling so will be retained in 

Phase II. However, more sensitivity tests will be performed using the 36 km 

model configuration than with the 12 km configuration. 

3⁄4 Minimum Vertical Kz: The VISTAS Phase I modeling tested minimum vertical 

turbulent exchange coefficients (Kz) of 1.0 m2

/s and 0.1 m2/s. Model 

performance using the two minimum Kz values was mixed, with no one 

configuration consistently producing superior model performance over the other 

across all species, locations and periods when analyzing the 24-hour fine particle 

measurements. However, when analyzing the hourly carbon measurements the 

0.1 m2

/s Kz_min sensitivity test exhibited spikes in the diurnal variations that was 

Appendix C.1 - 14
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-8 

not present in the observations and use a 1.0 M2/s Kz_min reduced this 

undersizable attribute. Thus, a 1.0 Kz_min value was selected for the initial Phase 

II model configuration. 

3⁄4 Fine Dust Transportable Fraction: For the Phase I modeling, the application of 

a fugitive dust transport fraction of 0.25 was recommended by EPA and 

minimized the bias for the Coarse Matter (CM) species over the other factors 

studied (1.00 and 0.05). For the Phase II modeling, county-specific fugitive dust 

emission adjustment factors, based on land-use categories, are applied to the 

fugitive dust emissions within the base inventories prior to SMOKE emissions 

modeling, so no additional adjustment will be made in the emissions modeling. 

3⁄4 Adjustment to NH3 Mass Emissions Estimates: Ammonia emissions were 

reduced 50% for the January 2002 Phase I episode and no adjustments were made 

for the two summer Phase I episodes (July 1999 and July 2001). For the Phase II 

modeling, the ammonia emissions inventory has been updated using the CMU 

ammonia emissions model and state submissions so additional adjustments may 

not be needed. Thus, the initial Phase II simulations would be performed without 

any additional ammonia emission adjustments. However, the Phase I sensitivity 

analysis indicated that the fine particulate and visibility estimates were very 

sensitive to ammonia emissions so they will likely be a subject of sensitivity tests 

in Phase II. 

3⁄4 Adjustment to NH3 Emissions Temporal Profile: An ammonia emissions 

temporal adjustment sensitivity test was performed that reduced ammonia 

emissions more at night. Although some marginal improvements in model 

performance were seen, the new diurnal profile could not be justified so that 

Phase II modeling will use the current EPA recommended diurnal profile for 

ammonia emissions. 

3⁄4 Significance of Mexico and Canadian Emissions: CMAQ PM estimates in the 

VISTAS states appear to be not substantially affect by emissions from Canada 

and Mexico for the three Phase I episodes. Use of Canadian and Mexican 

emissions is more technically justifiable, so they will be included in the Phase II 

modeling. 

3⁄4 Minimum PBL Depth: There are some concerns that MM5 px_acm may 

sometimes estimate a too low a PBL depth under some conditions (e.g., clouds). 

In Phase I, minimum PBL depth sensitivity tests were performed, but they did not 

substantially improve model performance and were difficult to technically justify. 

Thus, for Phase II the MM5 PBL depth estimates will be used as is. 

3⁄4 Use of Global Chemistry Transport Model Output for Boundary Conditions: 

Boundary condition (BC) sensitivity tests were conducted using CMAQ default 

and seasonal, monthly and 3-hourly values from a 2001 simulation of the GEOSCHEM global model. Use of the GEOS-CHEM results produced more realist 

spatial and temporal changes in BCs so will be used in Phase II. 

Appendix C.1 - 15
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-9 

3⁄4 Wesely Dry Deposition Scheme: Comparison of CMAQ model performance 

using MM5 Pleim-Xiu (PX) and Wesely algorithms saw that the PX dry 

deposition scheme produced better model performance and represents scientific 

improvements over the Wesely scheme so will be used in Phase II. 

3⁄4 Eta-Mellor-Yamada MM5 PBL Scheme: The MM5 simulation using the EtaMY PBL scheme sometimes produced negative PBL heights and when used with 

CMAQ produced degraded PM model performance. Thus, based on better 

science and improved model performance, the MM5 using the px_acm LSM_PBL 

configuration was selected for VISTAS Phase II modeling. 

3⁄4 Aerosol Mass Conservation Patch: A mass conservation patch that was 

developed by the Georgia Institute of Technology was added to CMAQ to assure 

the conservation of sulfur, reactive nitrogen and reduced nitrogen in the CMAQ 

aerosol modules. Model performance with and without the mass conservation 

patch was essentially identical. Therefore, based on better science, the mass 

conservation patch was adopted for the Phase II modeling. 

3⁄4 CB4-2002 Chemistry: Comparisons of CMAQ model performance using the 

CB4 and CB4-2002 revealed almost identical, or slightly degraded (nitrate for 

CB4-2002) model performance. Although the CB4-2002 chemical mechanism is 

more scientifically correct than CB4, it runs substantially slower since it is only 

implemented in the slower SMVGEAR solver. Given the much slower run times 

and little change or degraded model performance, CB4-2002 was not selected for 

the VISTAS Phase II modeling. This decision will be reconsidered if CB4-2002 

is implemented in the faster EBI chemistry solver. 

3⁄4 SAPRC99 Chemistry: The CMAQ simulations using the CB4 and SAPRC99 

chemical mechanisms produced different model performance, but both exhibited 

similar skill such that no one simulation was clearly performing better than the 

other across all species, locations and periods. Not tested, however, was whether 

the chemical mechanisms responded differently in response to emission 

reductions. SAPRC99 chemistry represents more current science than CB4 

chemistry. However, CMAQ using SAPRC99 chemistry takes twice the CPU 

time as CMAQ/CB4 and also requires more memory and disk space. Thus, for 

Phase II modeling it was decided to use the CB4 chemistry for the initial CMAQ 

2002 base case simulations and evaluate the sensitivity of SAPRC99 and CB4 to 

emissions reductions using the Phase I databases. Depending on the results of the 

Phase II emission reduction sensitivity tests, the SAPRC99 chemistry may be 

used in the revised 2002 CMAQ base case simulation starting in September 2004. 

3⁄4 AIM Aerosol Chemistry: The AIM sectional aerosol module did not produce 

any improvements in model performance over the standard CMAQ modal AE3 

approach and required substantially more computing time. Thus, the standard 

CMAQ model was adopted for Phase II modeling. 

3⁄4 Alternative Model: The CAMx model was exercised for the July 1999 and July 

2001 Phase I episodes. In general model performance was similar, but there were 

Appendix C.1 - 16
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-10 

some differences. CMAQ performed better for sulfate, whereas CAMx 

performed better for carbon (EC and OC). Both models performed poorly for 

nitrate. As neither model performed significantly better than the other across all 

species and periods, the CMAQ model was retained as the lead model for the 

Phase II modeling with CAMx an optional corroborative model.

Note that there are two parameters in the Phase I CMAQ base configuration that differ 

from the default recommendations: (1) use of a 0.1 m2

/s over a 1.0 m2/s minimum Kz; and (2) 

use of the mass conservation patch. Regarding the 0.1 m2

/s minimum Kz, the VISTAS science 

team believes it is more technically correct and produces better nighttime ozone performance, 

whereas PM performance was mixed. The conservation of sulfur and nitrogen is a fundamental 

property of the real atmosphere so we believe that justifies the use of the mass conservation 

patch. 

PHASE II MODELING APPROACH 

The Phase II modeling will include annual PM/regional haze simulations for an annual 

period plus additional shorter duration episodes. 

Overview of Approach 

The Phase II modeling will perform a detailed performance testing of the modeling 

system followed by exercising the model for a variety of emissions control scenarios aimed at 

enabling VISTAS to assess the effects of future year emission control strategies on visibility and 

other air quality issues. The modeling system will also allow VISTAS to track reasonable 

progress toward regional haze goals. More specifically, the VISTAS Phase II program will focus 

on the use of the CMAQ modeling system for calendar year 2002 over the same 36/12 km 

horizontal grid system used in Phase I. In addition, the modeling of episodes from 2003 or other 

non-2002 years is being considered to capture conditions not present in the b2002 year. A 

potentially large number of annual (and episodic) model simulations will be performed, the list 

below reflects current short-term (i.e., 2004) plans: 

3⁄4 2002 Annual Run. The initial annual model simulations and performance 

evaluations will be performed in early 2004 using the initial 2002 inventory for 

VISTAS and non-VISTAS states, Canada and Mexico. Multiple iterations of the 

2002 annual simulation will be required to confirm the appropriateness of the 

model science configuration(s) recommended by the Phase I work, to evaluate 

updates to the model and model inputs, and to refine model performance. 

3⁄4 2002 Revised Annual Run. A subsequent annual 2002 simulation using revised 

2002 modeling inventory for VISTAS and non-VISTAS states, Canada and 

Mexico would be performed in Fall 2004. The primary objective of this run is 

model performance demonstration using updated emissions inventories and best 

science model configurations. Additional model sensitivity simulations would be 

carried out using the revised 2002 emissions. 

Appendix C.1 - 17
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-11 

3⁄4 2002 Annual Run with “Typical Year” EGU/Fire Inventory. An annual 2002 

simulation representing the 2000-2004 baseline period for EGU and fire 

emissions and using 2002 revised inventory for all other source sectors. The 

primary objective of this inventory is to provide the base line modeled air quality 

condition against which future year modeling runs will be compared to develop 

relative reduction factors for each pollutant species. 

3⁄4 Future Year Annual Runs. Future year simulations involving a base case 

inventory of typical EGU and fire emissions for VISTAS-selected future period. 

Additional future year inventories may also be modeled. The objective of these 

future year model runs is to establish the modeled air quality basis against which 

the effectiveness of emissions control strategies will be evaluated. 

3⁄4 Future year emission control strategies. Prescription of the future year 

emissions control strategies to be performed later in Phase II (e.g., 2005) and will 

be defined after the foregoing simulations and analyses have been completed. A 

combination of annual and episodic runs is anticipated. 

Closely integrated with the annual (and possibly episodic) meteorological, emissions and 

air quality modeling will be ongoing project management, technical review, and quality 

assurance activities performed under the guidance of the VISTAS Contracting Officer and the 

VISTAS Technical Analysis Workgroup (TAWG). The modeling team members will participate 

with VISTAS management in regular monthly conference calls, as well as ad hoc topical 

conference calls as needed, and will attend periodic meetings with the TAWG members 

throughout Phase II. 

Episode Selection 

EPA’s current draft guidance on PM2.5/Regional Haze modeling (EPA, 2001) identifies 

specific goals to consider when selecting one or more episodes for use in demonstrating 

reasonable progress in attaining the regional haze NAAQS. EPA recommends that episode 

selection derive from three principal criteria: 

3⁄4 A variety of meteorological conditions should be covered; 

 

3⁄4 To the extend possible, the modeling data base should include days for which 

extensive data bases (i.e. beyond routine aerometric and emissions monitoring) 

are available; and 

3⁄4 Sufficient days should be available such that relative reduction factors (RRFs) can 

be based on several (i.e., > 15) days. 

 

For regional haze modeling, the guidance goes further by suggesting that the preferred 

approach is to model a full, representative year. Moreover, the required RRF values should be 

based on model results averaged over the 20% worst and 20% best visibility days determined for 

each Class I are based on monitoring data from the 2000 – 2004 baseline period. More recent 

EPA guidance (Timin, 2002) suggests that states should model at least 10 worst and 10 best 

visibility days at each Class 1 area. EPA also lists several ‘other considerations’ to bear in mind 

when choosing potential PM/regional haze episodes including: (a) choose periods which have 

Appendix C.1 - 18
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-12 

already been modeled, (b) choose periods which are drawn from the years upon which the 

current design values are based, (c) include weekend days among those chosen, and (d) choose 

modeling periods that meet as many episode selection criteria as possible in the maximum 

number of nonattainment or Class I areas as possible. 

 VISTAS adopted a logical, stepwise approach in implementing the EPA guidance in 

order to identify the most preferable, representative year for PM/regional haze modeling. These 

steps include the following: 

Representativeness of Meteorological Conditions: The VISTAS meteorological 

contractor (BAMS) identified important meteorological characteristics and data sets in 

the VISTAS region directly relevant to the evaluation of candidate annual modeling 

episodes. 

Initial Episode Typing: A separate detailed aerometric analysis and pattern recognition 

study was carried out by ICF Consulting to characterize the extent to which days from 

January-March 2002 and January-March 2003 represent the type of meteorological 

conditions that are most frequently associated with high and low values of a haze index 

and PM2.5 concentrations using the standard Classification and Regression Tree (CART) 

analysis software. 

Data Availability: In parallel with the CART analysis, episode characterization analyses, 

collaborative investigations by VISTAS states (e.g., NCDAQ, Georgia DNR, FL DEP) 

intensively studied the availability of PM2.5, meteorological, and emissions data and 

representativeness of alternative Baseline modeling periods from a regulatory standpoint. 

Years to be used by Other RPOs: VISTAS also considered what years other RPO would 

be modeling, several had already chosen CY-2002 as the modeling year. 

After a lengthy process of integrated studies, the episode selection process culminated in 

the selection of calendar year 2002 (1 January through 31 December) as the most current, 

representative, and pragmatic choice for VISTAS Phase II modeling. All of the EPA criteria for 

PM/regional haze episode selection were directly considered in this process together with many 

other pragmatic considerations (e.g., timing of new emissions or aerometric data deliveries by 

EPA or the states to the modeling teams). In addition to selecting CY-2002 as the base year, the 

merits of selecting one or more other shorter duration episode periods (say 2-4 weeks or more in 

duration) was thoroughly considered. Such additional episodes were believed to add potentially 

valuable insights into the various source-receptor relationships influencing PM2.5 and regional 

haze air quality at Class I sites and other locations of interest and have the potential to capture 

important meteorological conditions not covered in the CY-2002 period. Work on identifying 

potentially attractive candidate episodes to include with the annual 2002 modeling is ongoing 

and will be summarize in a subsequent updates to this protocol. In particular, ICF Consulting 

has been funded to determine whether any key meteorological conditions are not captured by the 

2002 model year and identify additional modeling episodes. Additional modeling periods from 

2003 would be ideal due to the presence of continuous PM monitoring data at the FOCUS sites 

that were not in operation during CY-2002. 

Appendix C.1 - 19
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-13 

Model Selection 

Based on the Phase I findings, VISTAS selected the following models for use in 

modeling particulate matter (PM) and regional haze in the Southeast under Phase II: 

3⁄4 MM5: The Pennsylvania State University/National Center for Atmospheric Research 

(PSU/NCAR) Mesoscale Meteorological Model (MM5) is a nonhydrostatic, 

prognostic meteorological model routinely used for urban- and regional-scale 

photochemical, fine particulate, and regional haze regulatory modeling studies. 

 

3⁄4 SMOKE: The Sparse Matrix Operator Kernel Emissions (SMOKE) modeling system 

is an emissions modeling system that generates hourly gridded speciated emission 

inputs of mobile, nonroad, area, point, fire and biogenic emission sources for 

photochemical grid models. 

3⁄4 CMAQ: EPA’s Models-3/Community Multiscale Air Quality (CMAQ) modeling 

system is a ‘One-Atmosphere’ photochemical grid model capable of addressing 

ozone, particulate matter (PM), visibility and acid deposition at regional scale for 

periods up to one year. 

In addition, EPA’s fine particulate and regional haze modeling guidance encourages the 

use of alternative models to corroborate the findings of the primary model. The VISTAS Phase II 

modeling currently has an optional task to apply alternative models. The following are the 

alternative models identified in the Phase I work effort. 

3⁄4 CAMx: ENVIRON’s Comprehensive Air Quality Model with Extensions (CAMx) 

modeling system is also a state-of-science ‘One-Atmosphere’ photochemical grid 

model capable of addressing ozone, particulate matter (PM), visibility and acid 

deposition at regional scales for periods up to one year. 

3⁄4 CMAQ – AIM or CMAQ-MADRID: These two models are variations of CMAQ 

that utilize a sectional treatment of PM size distribution and have alternative science 

options for some aerosol processes. They could also be used in Phase II as 

corroborative diagnostic tools. 

MM5 Configuration for Phase II Modeling

Based on the extensive sensitivity testing carried out under VISTAS Phase I, the MM5 

(Version 3.6, MMP) configuration to be used the Phase II modeling will consist of the following: 

3⁄4 Nested 108/36/12 km grids, with 34 vertical layers; 

3⁄4 Two way nesting, no feedback; 

3⁄4 Initialization and boundary conditions from Eta analysis fields; 

3⁄4 Pleim-Xiu (P-X) soil model; 

3⁄4 Asymmetric Convective Mixing (ACM) PBL model; 

3⁄4 Kain-Fritsch 2 cumulus parameterization; 

3⁄4 Mixed phase (Reisner 1) cloud microphysics; 

3⁄4 Raptid Radiative Transfer Model (RRTM) radiation; 

Appendix C.1 - 20
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-14 

3⁄4 Snow effect turned on; 

3⁄4 ETA model sea surface temperature; 

3⁄4 24-category USGS vegetation data sets; 

3⁄4 Thermal roughness by the Garratt method; and 

3⁄4 Standard FDDA analysis nudging on 36 km and 12 km grid nests. 

MM5 will be operated in 5 day segments starting at 12Z on December 17, 2001. Each 

segment would overlap by 12 hours the previous segment and would be initialized off of the 

input analysis fields (i.e., no linking of the LSM or PBL variables between run segments). 

SMOKE Configuration

SMOKE will be run on the same grid and configured in the same manner as was 

performed in the Phase I modeling, only SMOKE Version 2.0 will be used instead of Version 

1.5beta that was used in Phase I. As an emissions processor, there are far less science options in 

SMOKE than in MM5 or CMAQ. The number of days SMOKE will be used to process 

emissions for the annual modeling period has been optimized to maximize the temporal 

variations in emissions while minimize the number of days to be processed. For many source 

categories (i.e., area, non-road and non-EGU point sources) temporal adjustments of the annual 

emissions are made by month and by day of week, Thursday, Friday, Saturday, Sunday and 

Monday, with Tuesday and Wednesday assumed to be the same as Thursday (i.e., 5 days). For 

biogenic, fire and EGU point sources, day-specific hourly emissions will be used for the whole 

year. The most computationally limiting step in emissions modeling is the generation of on-road 

mobile sources. Accordingly, on-road mobile sources will be generated for one week (7 days) 

per month to obtain monthly and day-of-week variations in the mobile sources emissions. This 

results in the following number of days SMOKE will be applied for the annual simulation: 

3⁄4 365 biogenic days; 

3⁄4 365 CEM days for EGU point sources; 

3⁄4 All days with fires (365 maximum); 

3⁄4 5 x 12 = 60 “other” point days; 

3⁄4 5 x 12 = 60 area source days; 

3⁄4 5 x 12 = 60 nonroad mobile sources days; and 

3⁄4 7 x 12 = 84 on-road mobile source days. 

CMAQ Configuration

The CMAQ modeling system would be set up and exercised on the same nested 36/12 

km grid domain used in Phase I, employing one-way grid nesting. A total of 19 vertical layers 

would be implemented, extending up to a region top of 100 mb (approximately 15 km AGL). 

The PPM advection solver would be used along with the spatially varying (Smagorinsky) 

horizontal diffusion approach and K-theory for vertical diffusion. MM5 meteorological output 

based on the Pleim-Xiu Land-Surface Model (LSM) and the ACM planetary boundary layer 

(PBL) scheme will be used and the recently updated CMAQ Meteorological-Chemistry Interface 

Processor (MCIP2.2) would process the MM5 data using the “pass through” option. The CB4 

gas-phase, RADM aqueous-phase, and AERO3/ISORROPIA aerosol chemistry schemes will be 

used in the initial CMAQ 2002 modeling. Treatment of reversible secondary organic aerosols 

Appendix C.1 - 21
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-15 

would be simulated by the SORGAM implementation in CMAQ (ver 4.3). Under the Phase I 

modeling, VISTAS evaluated three photochemical mechanisms: CB4, CB4-2002 and SAPRC99. 

CB4-2002 produced nearly identical results as CB4 but took much longer to run since it is only 

implemented in the slower SMVGEAR chemistry solver. Thus, CB4-2002 was dropped from 

consideration in Phase II. The Phase I comparisons of CB4 and SAPRC99 found they produced 

somewhat similar but different model performance. However, one mechanism was not 

performing better than the other across all species, sites and periods. The Phase I testing only 

evaluated the mechanism’s base case performance, not their response to emission reductions. 

Given that CB4 runs twice as fast as SAPRC99, for Phase II it was decided to perform initial 

2002 CMAQ modeling using CB4 and evaluate CB4 and SAPRC99 responses to emission 

reductions using the Phase I episodes. If SAPRC99 is deemed to be performing better than CB4 

it would be used for the revised 2002 CMAQ base case simulation in September 2004. 

Quality Assurance 

 Effective and extensive Quality Assurance (QA) and Quality Control (QC) are main 

components of the VISTAS Phase II modeling activities. In December 2002, the USEPA 

publish extensive guidance on developing a Quality Assurance Project Plan (QAPP) for 

modeling studies (EPA, 2002). The objective of a QAPP is to ensure that a modeling study is 

scientifically sound, robust, and defensible. The new EPA guidance suggests that a QAPP should 

include the following elements: 

• a systematic planning process including identification of assessments and related 

performance criteria; 

• peer reviewed theory and equations; 

• a carefully designed life-cycle development process that minimizes errors; 

• clear documentation of assumptions, theory, and parameterization that is detailed enough 

so others can fully understand the model output; 

• input data and parameters that are accurate and appropriate for the problem; 

• output data that can be used to help inform decision making. 

• documentation of any changes from the original quality assurance plan; 

 Moreover, the EPA guidance specifies that different levels of QAPP may be required 

depending on the intended application of the model, with a modeling study designed for 

regulatory purposes requiring the highest level of quality assurance. The QAPP also provides a 

valuable resource for project management. It can be used to document data sources and 

assumptions used in the modeling study, and it can be used to guide project personnel through 

the data processing and model application process to ensure that choices are consistent with the 

project objectives. The modeling team has already developed QA documents and procedures in 

the Phase I effort. For the Phase II effort these will be enhanced and modified to assure that it 

conforms to the EPA QAPP guidance. 

Complementing the data acquisition, modeling input development activities, and project 

management activities, four other Phase II activities will be performed, consistent with the 

Appendix C.1 - 22
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-16 

Quality Assurance (QA) plan: 

Data Gatekeepers

The VISTAS Phase II emissions and air quality modeling team are receiving emissions, 

meteorological and air quality data from other VISTAS contractors or other sources and as a first 

line of QA, we have defined a Gatekeeper function to assure the data have been received 

correctly, evaluate the quality of the data, and document the data received. Separate air quality, 

meteorological and emissions Gatekeepers have been identified whose roles are defined below. 

In addition, a Data Management Gatekeeper has been defined who will post data, reports and 

results to the project website and archive all key data generated in the project. 

3⁄4 Air Quality Data Gatekeeper. Obtain air quality data as appropriate for 

model input development and model performance evaluation and assure 

quality of all air quality data obtained, consistent with approved QA plan. 

This gatekeeper will also provide documentation of evaluation and generate 

IC/BC inputs for CMAQ for all modeling runs. 

3⁄4 Meteorological Gatekeeper. Obtain meteorological data, as MM5 or MCIP 

files, as appropriate for annual 2002 modeling runs and other episode periods 

and perform data quality checks as approved in QA plan together with 

appropriate documentation of model performance evaluation activities. 

3⁄4 Emissions Gatekeeper. Obtain emissions inventory data necessary to 

support annual 2002 and future year modeling and recommend source of 

emissions data to be used for Canada and Mexico. Assure quality of all 

emissions data received, consistent with approved QA plan and develop all 

emissions modeling files to support modeling runs for 2002. This gatekeeper 

will also develop the chemical speciation files and temporal and spatial 

allocation files necessary to convert annual inventories into hourly and daily 

emissions modeling files, as appropriate. The Emissions Gatekeeper will also 

develop all emissions modeling files for non-VISTAS states to support 

modeling runs for future year base case and emissions strategies as defined by 

VISTAS. 

3⁄4 Data Management Gatekeeper: This gatekeeper will maintain the VISTAS 

Modeling Website including posting modeling input and output files, reports, 

interpretation of results, and other documents as requested by VISTAS to 

support all Phase II tasks. This includes, for example, the storage of model 

inputs and outputs for annual (and episodic) runs and the transfer (via fire 

wire or alternative media) of electronic files to VISTAS states, other regional 

planning organizations, EPA, other contractors, and stakeholders. 

Emissions QA/QC

Emissions Quality Assurance (QA) and Quality Control (QC) are the single most critical 

steps in performing air quality modeling studies. Because emissions processing is tedious, time 

consuming and involves complex manipulation of many different types of large data sets, errors 

Appendix C.1 - 23
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-17 

are frequently made in emissions processing and, if rigorous QA measures are not in place, these 

errors may remain undetected. In Phase II we will continue with multistep emissions the QA/QC 

approach applied in the Phase I modeling. This includes the initial emissions QA/QC by the 

Emissions Gatekeeper described above, as well as QA/AC by the Emissions Modeler during the 

processing of emissions and then additional QA/QC by the air quality modeler of the processed 

model ready emission files. This multistep process with three separate groups involved in the 

QA/QC of the emissions is much more likely to catch any errors prior to the air quality model 

simulations. 

Emissions QA/QC that would be performed as part of the emissions modeling will include: 

EMS and EPA Input Screening Error Checking Algorithms: Although the SMOKE 

emissions model will be used for emissions processing, some of the more advanced EMS 

input error checking algorithms will be used to screen the data and identify potential 

emission input errors. Additionally, EPA has issued a revised stack QA and augmentation 

procedures memorandum that will be used to identify and augment any outlying stacks. 

SMOKE error messages: SMOKE provides various cautionary or warning messages 

during the emissions processing. We will redirect the SMOKE output to log files and 

review the log files for serious error messages. An archive of the log files will be 

maintained so that the error messages can be reviewed at a later date if necessary. 

SMOKE emissions summaries: We will use QA functions built into the SMOKE 

processing system to provide summaries of processed emissions as daily totals according 

to species, source category and county and state boundaries. These summaries will then 

be compared with summary data prepared for the pre-processed emissions, e.g., state and 

county totals for emissions from the augmented emissions data. 

Once the CMAQ-ready emission inputs have been prepared, we will perform additional 

emissions QA/QC as follows: 

Spatial Summary: We will sum the emissions for all layers and for all 24 hours that is 

used to prepare a PAVE plot showing the daily total emissions spatial distribution. For a 

20 day simulation this produces approximately 20 days x 20 species x 5 emissions 

categories = 2,000 plots. In our base case simulations these plots will be presented as tons 

per day. The objective of this step is to identify errors in spatial distribution of emissions. 

Vertical Profile: For point sources the emissions total for each layer will be summed and 

plotted to show the vertical distribution of emissions. These plots show the emissions on 

the x-axis for each model layer on the y-axis. The objective of this step is to identify 

possible errors in vertical distribution of emissions. 

Short Term Temporal Summary: The total domain emissions for each hour will be 

accumulated and time series plots prepared that display the diurnal variation in total 

hourly emissions. The objective of this step is to identify errors in temporal profiles. 

Long Term Temporal Summary: The total domain emissions for each day will be 

accumulated and displayed as time series plots that show the daily total emissions across 

Appendix C.1 - 24
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-18 

the domain as a function of time. The objective of this step is to identify particular days 

for which emissions appear to be inconsistent with other days for no reason (e.g., not a 

weekend) and compare against the general trend. 

Control Strategy Spatial Displays: Spatial summary plots of the daily total emissions 

differences between a control strategy and base case emissions scenarios will be 

generated. These plots can be used to immediately identify a problem in a control 

strategy. For example, if a VISTAS states SO2 control strategy is being analyzed and 

there are changes in emissions for other pollutants or for SO2 outside of the VISTAS 

states problems in emissions processing can be identified prior to the air quality model 

simulation. 

Meteorology QA/QC

The VISTAS meteorological modeling contractor (BAMS) will have primary 

responsibility in the QA/QC of the MM5 meteorological fields. However, the emissions and air 

quality modeling team will also perform some QA/QC of the meteorological data to assure that it 

has transferred correctly, to obtain an assessment of the quality of the data and to assist in the 

interpretation of the air quality modeling results. 

The VISTAS Phase II Meteorological Gatekeeper will perform the following: 

3⁄4 Analyze the MM5 data to assure it has been transferred correctly; 

 

3⁄4 Evaluate the MM5 using METSTAT and the surface meteorological network; 

3⁄4 Evaluate upper-air MM5 meteorological estimates by comparison them to upper-air 

observations and satellite images; and 

3⁄4 Compare the VISTAS 2002 MM5 simulation with the one generated by WRAP. 

3⁄4 Generate the CMAQ-ready meteorological inputs using the MCIP2.2 processor. 

Air Quality Modeling QA/QC

Key aspects of QA for the CMAQ input and output data include the following: 

• Verification that correct configuration and science options are used in compiling and 

running each model in the CMAQ modeling system, where these include the MCIP, 

JPROC, ICON, BCOM and the CCTM. 

• Verification that correct input data sets are used when running each model. 

• Evaluation of CCTM results to verify that model output is reasonable and consistent with 

general expectations. 

• Processing of ambient monitoring data for use in the model performance evaluation. 

Appendix C.1 - 25
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-19 

• Evaluation of the CCTM results against concurrent observations. 

• Backup and archiving of critical model input data. 

 The most critical element in the QA plan for CMAQ simulations is the QA/QC of the 

meteorological and emissions input files, which is discussed above. The major QA issue 

specifically associated with the air quality model simulations is verification that the correct 

science options were specified in the model itself and that the correct input files were used when 

running the model. For the CMAQ model we employ a system of naming conventions using 

environment variables in the compile and run scripts that guarantee that correct inputs and 

science options are used. We also employ a redundant naming system so that the name of key 

science options or inputs are included in the name of CMAQ executable program, in the name of 

the CMAQ output files, and in the name of the directory in which the files are located. This is 

accomplished by using the environment variables in the scripts to specify the names and 

locations of key input files. 

 A second key QA procedure is to never “recycle” run scripts, i.e., we always preserve the 

original runs scripts and directory structure that were used in performing a model simulation. 

 We will also perform a post-processing QA of the CMAQ output files similar to that 

described for the emissions processing. We will generate animated gif files using PAVE that can 

be viewed to search for unexpected patterns in the CMAQ output files. In the case of model 

sensitivity studies, the animated gifs will be prepared as difference plots for the sensitivity case 

minus the base case. Often, errors in the emissions inputs can be discovered by viewing the 

animated GIFs. Finally, we will produce 24 hour average plots for each day of the CMAQ 

simulations. This provides a summary that can be useful for more quickly comparing various 

model simulations. 

 Another important component of the air quality modeling QA/QC is the model 

performance evaluation, which is discussed next. 

Model Performance Evaluation 

The model performance evaluation methodology to be used is an extension of that used in 

Phase I and is fully consistent with current EPA guidance and science community consensus on 

how Eulerian fine particulate/regional haze and ozone models should be evaluated with 

contemporary surface and aloft monitoring databases. Key to this evaluation is that the model is 

evaluated separately for each component of particulate matter (PM), including sulfate, nitrate, 

elemental carbon, organic carbon, other fine particulate and coarse particulate, as well as 

important gaseous species (e.g., ozone, NOx, CO, ammonia and nitric acid). 

EPA’s “Draft Guidance for Demonstrating Attainment of Air Quality Goals for PM2.5 and 

Regional Haze” (EPA, 2001) recommends a comprehensive, multi-layered approach to model 

performance testing should be performed, consisting of the following four components: 

> Operational Evaluation: Tests the ability of the model to estimate PM 

concentrations (both fine and coarse) and the components at PM10 and PM2.5

Appendix C.1 - 26
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-20 

including the quantities used to characterize visibility (i.e., sulfate, nitrate, 

ammonium, organic carbon, elemental carbon, PM2.5, and PM10); 

> Diagnostic Evaluation: Tests the ability of the model to predict visibility and 

extinction, PM chemical composition including PM precursors (e.g., SOx, NOx, and 

NH3) and associated oxidants (e.g., ozone and nitric acid); PM size distribution; 

temporal variation; spatial variation; mass fluxes; and components of light extinction 

(i.e., scattering and absorption); 

> Mechanistic Evaluation: Tests the ability of the model to predict the response of PM 

and visibility to changes in variables such as emissions and meteorology; and 

> Probabilistic Evaluation: Takes into account the uncertainties associated with the 

model predictions and observations of PM and visibility. 

Given the scope of the VISTAS Phase II effort and with consideration of the type and 

amount of measurement data available to support the various evaluations, the CMAQ model 

evaluation will included elements of each of these components. Obviously, the operational and 

diagnostic evaluations will receive the greatest attention, mechanistic tests (with probing tools 

such as DDM) will also be considered along with potentially probabilistic evaluations, through 

the use of traditional sensitivity and uncertainty simulations as well as through the use of an 

alternative science platforms such as CAMx (optional). 

An important consideration is that different PM monitoring networks may use different 

measurement approaches that “measure” different amounts of the same species that are also 

different from the modeled species. For example, the IMPROVE network only speciates PM2.5

so any sulfate or nitrate in the coarse mode (PM2.5-10) is included in the CM species. Like was 

done in Phase I, the model will be evaluated separately for each network in addition to a 

composite evaluation using all data. The mapping of the modeled species to the monitored data 

will also have to be performed in a consistent fashion. 

We will compare the model outputs to observational data obtained from the IMPROVE, 

SEARCH, CASTNet, EPA-FRM, EPA-STN and other monitoring networks. These monitoring 

data will be obtained from AIRS, VIEWS, and other appropriate organizations. These 

comparisons will be performed as follows: 

3⁄4 Compare both daily averages and longer-term (e.g., monthly, seasonal and annual) 

averages for SO2, SO4, NO3, EC, OC, PM2.5, and PM10, taking care to exclude 

periods of sampling interference in the observational data. We will look for 

systematic biases between the model results and IMPROVE observations, and if 

biases are found, identify possible sources of error in the model inputs. 

 

3⁄4 Compare hourly/high resolution PM species and gaseous species concentrations at 

sites where available (e.g., SEARCH, AIRS and EPA-Supersites). 

3⁄4 At sites with contrasting aerosol mass loadings (i.e. differing major components of 

fine particulate), we will analyze the temporal behavior of the major scattering and 

Appendix C.1 - 27
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-21 

absorbing aerosol constituents along with the visibility trends, to establish 

correlations. 

The model evaluation will also include the following analyses: 

3⁄4 Evaluate seasonal trends in observations of organic and inorganic aerosol precursors 

and their effects on PM composition and visibility, and evaluate the ability of the 

model to capture these seasonal trends. 

3⁄4 Evaluate how well the model predicts the relative roles and budgets of various 

processes by (1) examining observed and modeled correlations between various 

species pairs, and (2) comparing model-predicted ratios of various species (individual 

or families) with observations to evaluate gas/particle partitioning (e.g., nitrate/total 

nitrate, SO4/SOx). 

3⁄4 Investigate the performance of the model at selected observational sites characterized 

by different chemical regimes that may be encountered either spatially or during 

different seasons to help identify any inadequacies in the model and to provide a 

better understanding of conditions under which model inferences may be weak. 

3⁄4 Compare hourly 24-hour average, and episode averages of the PM constituents for the 

2002 Phase I VISTAS annual modeling period as well as the 2003 episodes across all 

sites. 

3⁄4 Create scatter plots of modeled vs. observed data and hourly and 24-hour averages by 

site and subregion to help identify any site-specific biases. 

3⁄4 Create time series plots of predicted and observed concentrations as appropriate. 

3⁄4 Evaluate for total sulfur (SO2 + SO4), nitrate (HNO3 + NO3) and ammonia (NH3 + 

NH4). 

3⁄4 Compare observed versus modeled mass fractions of PM constituents at various sites 

that are characterized by their proximity or remoteness relative to sources, or by 

specific meteorological conditions (e.g., frontal passage, stagnation, precipitation); 

these will enable identification of trends in the model of over- or under-prediction of 

specific PM constituents under these conditions. 

3⁄4 Pay particular close attention to the model performance at the Class I areas for SO4

NO3 EC OC and CM on the 20% best and 20% worst days to document whether 

certain of these days should be eliminated from the visibility projections due to 

inadequate model performance. 

A suite of statistical metrics and graphical tools will be employed to identify performance 

problems with the CMAQ simulations should they exist and to and highlight differences between 

model runs. Experience in ozone/PM modeling is the best basis upon which to identify 

obviously flawed simulation results. Efforts to improve the CMAQ model’s base case 

performance will be made if needed (i.e., to reduce the discrepancies between model estimates 

Appendix C.1 - 28
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-22 

and observations), and consistent with the project resources and schedule; however, these model 

performance improvements efforts must be based on sound scientific principles. “Curve-fitting” 

exercises will be avoided. 

Current draft EPA’s guidance suggests an interim set of fine particulate modeling 

performance goals for aggregated mean normalized gross error and mean normalized bias as 

follows: 

Pollutant Gross Error Normalized Bias 

PM2.5 ~30-50% ~"10% 

Sulfate ~30-50% ~"20-30% 

Nitrate ~20-70% ~"15-50% 

EC ~15-60% NA 

OC ~40-50% ~"38% 

Because regional-scale fine particulate and regional haze modeling is an evolving science, 

these performance goals are not fully established and certainly not universally endorsed by the 

scientific community. Indeed, EPA recognizes this and sponsored a 2-day national model 

performance evaluation workshop in February 2004 to address current science in PM model 

performance evaluation. 

Model sensitivity experiments are useful in three distinct phases or ‘levels’ of an air quality 

modeling study and all will be used as appropriate in the VISTAS Phase II modeling with 

CMAQ. These levels are 

 Level I. Model algorithm evaluation and configuration testing; 

Level II. Model performance testing, uncertainty analysis and compensatory error 

diagnosis, and 

Level III. Investigation of model output response (e.g., ozone, aerosol, deposition) to 

changes in precursors as part of emissions control scenario analyses. 

Many of the Level I sensitivity tests with CMAQ have already been completed in the 

Phase I configuration and diagnostic analyses. However, given that open community nature of 

CMAQ and the frequent science updates to the model and supporting data bases, it is possible 

that some additional configuration sensitivity testing will be necessary in Phase II. 

 

 Level II sensitivity analyses are an integral part of the Phase II CMAQ model 

performance evaluation activity. Level II sensitivity analyses will be performed, as necessary, to 

accomplish the following objectives: 

3⁄4 To reveal internal inconsistencies in the model; 

3⁄4 To provide a basis for compensatory error analysis; 

3⁄4 To reveal the parameters (or inputs) that dominate (or do not dominate) the model’s 

operation; 

3⁄4 To reveal propagation of errors through the model; and 

3⁄4 To provide guidance for model refinement and data collection programs. 

Appendix C.1 - 29
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-23 

 At this time, it is not possible to compile a specific listing of the types of Level II 

sensitivity runs that might be needed to establish a reliable annual 2002 CMAQ base case. 

Noteworthy in EPA’s new ozone, PM, and regional haze guidance documents is the 

encouragement of the use of alternative modeling methods to corroborate the performance 

findings and control strategy response of the primary air quality simulation model. Mindful of 

EPA’s endorsement of corroborative modeling methods and the rigorous use of ‘weight of 

evidence’ investigations, we recommend that the most recent version of CAMx be used in 

supportive, corroborative role to CMAQ in Phase II. Among other things, this will permit us to 

more explicitly identify the expected range of model uncertainty and to corroborate the general 

effectiveness of the Phase II CMAQ regional haze control strategies. Other corroborative 

modeling methods such as the CMAQ-AIM and CMAQ-MADRID should also be considered. 

However, as these models are derivatives of CMAQ they would not provide as robust 

independent corroboration as CAMx. Although at this time VISTAS does not plan to use 

alternative models to corroborate the CMAQ findings, this option is available to VISTAS at a 

later date if desired. 

Visibility Assessment and Comparisons 

One of the primary purposes of the VISTAS Phase II work effort is to develop the 

modeling tools necessary to project future-year visibility estimates at Class I areas to 

demonstrate progress toward clean natural background visibility levels in 2064. The Regional 

Haze Rule (RHR) requires that progress toward natural background visibility be demonstrated 

every 10 years. The 2000-2004 five-year period is used to define baseline conditions and the 

first future progress period is 2018, that has been interpreted as either the 2013-2017 or 2014-

2018 five year periods. A State is required to set progress goals for each Class I area in the State 

for two visibility metrics: 

• Provide for an improvement in visibility for the most impaired (i.e., 20% worst) 

visibility days; and 

 

• Ensure no degradation in visibility for the least impaired (i.e., 20% best) visibility 

days. 

EPA guidance recommends using the model in a relative sense to project future-year 

visibility conditions. This is done through the use of Relative Reduction Factors (RRFs) that are 

defined as the ratio of the future-year to the current-year modeling results. The RRFs are applied 

to the baseline visibility conditions to project future-year visibility. The major features of EPA’s 

recommended visibility projections are as follows: 

• Monitored data should be used to define current air quality. 

• Monitored concentrations of PM10 are divided into six major components, the first 

five of which are assumed to be PM2.5 and the sixth is PM2.5-10. 

3⁄4 SO4 (sulfate); 

3⁄4 NO3 (particulate nitrate); 

3⁄4 OC (organic carbon); 

3⁄4 EC (elemental carbon); 

Appendix C.1 - 30
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-24 

3⁄4 OF (other fine particulate); and 

3⁄4 CM (coarse matter). 

• Models are used in a relative sense to develop relative reduction factors (RRFs) 

between future and current predicted concentrations of each component. 

• Component-specific relative reduction factors are multiplied by current monitored 

values to estimate future component concentrations. 

• Estimates of future component concentrations are consolidated to provide an 

estimate of future air quality, which can be related to a goal for regional haze. 

• Future estimated air quality is compared with the goal to see if the simulated 

control strategy results in the goal being met. 

• It is acceptable to assume that all measured sulfate is in the form of ammonium 

sulfate [(NH4)2SO4] and all particulate nitrate is in the form of ammonium nitrate 

[NH4NO3]. 

Associated with each PM species is an extinction coefficient that converts concentrations (in 

g/m3

) to light extinction (in inverse mega meters, Mm-1). Sulfate and nitrate are hygroscopic so 

relative humidity adjustment factors [f(RH)] are used to modify the extinction coefficients that 

increase the particle’s extinction efficiency with increasing RH to account for the particles taking 

on water and having higher light scattering properties. EPA has defined site-specific monthly 

average f(RH) values that will be used in the visibility projections. Note that some Organic 

Matter (OM) compounds may also have hygroscopic properties, but the IMPROVE 

reconstructed mass extinction equations assume OM is non-hygroscopic. 

bSulfate = 3 x f(RH) x [SO4] 

bNitrate = 3 x f(RH) x [NO3] 

bEC = 10 x [EC] 

bOM = 4 x [OM] 

bSoil = 1 x [Soil] 

bCM = 0.6 x [CM] 

The total light extinction (bext) is assumed to be the sum of the light extinction due to the six PM 

species listed above plus Rayleigh (blue sky) background (bRay) that is assumed to be 10 Mm-1. 

 bext = bRay + bSulfate + bNitrate + bEC +bOM + bSoil + bCM

The total light extinction (bext) in Mm-1 is related to visual range (VR) in km using the following 

relationship: 

 VR = 3912 / bext

The Regional Haze Rule requires that visibility be expressed in terms of deciview (dv) 

that uses natural logarithms of the extinction as follows: 

Appendix C.1 - 31
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-25 

 dv = 10 ln(bext/10) 

Modeling results are used in a relative fashion to project future-year visibility through 

relative reduction factors (RRFs). RRFs are expressed as the ratio of the modeling results for the 

future-year to the results of the base year and are Class I area and PM species specific. RRFs are 

applied to the Baseline Conditions observed PM species to project future-year PM levels from 

which visibility can be assessed using the IMPROVE RCM extinction equations listed above. 

EPA has identified the following six steps to project future-year visibility for the 20% best and 

20% worst days: 

1. For each Class I area visibility is ranked using IMPROVE reconstructed PM mass (RCM) 

extinction equation for each year that comprises the five-year Baseline Conditions (i.e., 

2000-2004). 

2. Calculate the arithmetic average of the 20% best and 20% worst visibility days, in 

deciview (dv), for each year of the five-year baseline period and then calculate the fiveyear average of the 20% best and 20% worst days. Document which days during the 

five-year baseline period comprise the 20% best and 20% worst observed visibility days. 

3. Use an air quality model to simulate the baseline period emissions and future-year 

emissions. Extract 24-hour average PM species concentrations “near” each Class I area. 

Calculate the average PM species concentration estimates in the current and future-year 

simulation across the 20% best and 20% worst observed visibility days for each year in 

the five-year baseline period. Average across the five-years the average PM species 

concentrations for the 20% best and 20% worst days and for each year in the five-year 

baseline period. Calculate Class I area and best/worst 20% days RRFs for each of the six 

PM components as the ratio of the five-year average estimated PM species concentration 

in the future-year to current year. 

4. Multiple PM species dependent RRFs for the 20% best/worst days by the observed 24-

hour PM species concentrations for each day from the 20% best/worst days to obtain 

future-year daily average PM species concentrations for each day from the 20% best and 

20% worst visibility days from the five-year baseline period. 

5. Using the future-year estimated 24-hour PM species concentrations for the best/worst 

20% observed days, calculate extinction using the IMPROVE reconstructed mass 

extinction equation and daily deciview, perform annual averaging of the visibility (dv) 

estimates for the 20% best/worst days for each year and then obtain the five-year average 

visibility (dv) for the future-year. 

When selecting model estimated PM species concentrations “near” the monitor, EPA 

recommends taking a spatial average of PM concentrations across a grid cell resolution 

dependent NX by NY array of cells centered on the grid containing the monitor. For the 

VISTAS Phase II 36 km modeling, just the model estimates for the grid cell containing the 

monitor will be used (i.e., NX=NY=1). For the VISTAS Phase II 12 km modeling, EPA 

recommends that NX=NY=3, that is the model estimated PM species concentrations are 

averaged across 9 grid cells centered on the IMPROVE monitor (EPA, 2001). 

Appendix C.1 - 32
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Exec_Sum.doc ES-26 

VISTAS Phase II Future-Year Modeling

The VISTAS Phase II future-year modeling will use the 2002 MM5 meteorological 

conditions. That is, we will assume that the meteorological conditions for the future-year are the 

same as for 2002. This will allow for the comparison of the changes in visibility at Class I areas 

from the current (2002) to future-year due to changes in air emissions. This means that the 

effects of climate change and climatic variations will not be accounted for. 

Future-Year Emissions

The VISTAS emissions projection contractor will provide future-year emissions to the 

emissions and air quality modeling team. They would be processed into the gridded speciated 

hourly three-dimensional emissions inputs for photochemical grid modeling using the SMOKE 

emissions model. The same biogenic emissions as used in the 2002 Base Case modeling will be 

used for the future-year modeling. This assume that the same land use and biomass distribution 

as used in the 2002 Base Case emissions would exit in the future-year emission scenarios. The 

same Typical Year fire emissions that were used in the 2002 Typical Year emissions scenario 

would be used in the future-year. Future-year Typical Year emissions for Electrical Generating 

Units (EGUs) would also be used for the future-year scenarios, however for EGUs these would 

not be identical to the 2002 Typical Year EGU emissions. 

Visibility Projections

 The CMAQ modeling system would be used to estimate 2002 and future-year PM 

estimates for Base Case emission scenarios that include “typical” fire and EGU emissions. 

Future-year visibility estimates for the best 20% and worst 20% days would be projected using 

the latest observed current conditions and the model derived RRFs. The future-year visibility 

estimates for the worst 20% days would be compared against the visibility goal at each Class I 

area and the projected visibility for the best 20% days would be compared to the current 

conditions to assure there is no worsening of air quality. As an initial future-year visibility target 

or goal we will assume a linear glide path slope (in dV) from the current conditions to the EPA 

default natural conditions for each Class I area. Refinements to this approach are likely (e.g., 

updated natural conditions). These calculations are repeated for each future-year emissions 

scenario. 

Appendix C.1 - 33
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-1 

1.0 INTRODUCTION 

This report constitutes the first draft of the Air Quality Modeling Protocol and Quality 

Assurance (QA) plan for the VISTAS Phase II emissions and air quality modeling activities to be 

performed by the contractor team of ENVIRON International Corp, the University of California 

at Riverside, and Alpine Geophysics, LLC. Development of this first draft protocol governing 

the VISTAS Phase II emissions and air quality modeling and model evaluation was performed as 

Task 6 in the Phase I study. 

1.1 Background 

The Visibility Improvement State and Tribal Association of the Southeast (VISTAS) is a 

collaborative effort of state governments, tribal governments, and various federal agencies 

established to initiate and coordinate activities associated with the management of regional haze, 

visibility and other air quality issues in the Southeastern United States. Figure 1-1 identifies the 

various Regional Planning Organizations in the U.S, including VISTAS. Figure 1-2 depicts the 

key Class I areas within the study domain. As shown in these figures, VISTAS is comprised of 

the states of Alabama, Florida, Georgia, Kentucky, Mississippi, North Carolina, South Carolina, 

Tennessee, Virginia, and West Virginia as well as the Eastern Band of Cherokee Indians. The 

agencies participating in VISTAS are committed to a sound and thorough scientific analysis of 

regional haze problems, impacts from natural and man-made pollutants, and potential solutions. 

Stakeholders are encouraged to participate at the workgroup level in order that all aspects of the 

problem and possible strategies may be given consideration. 

The Clean Air Act establishes special goals for visibility in many national parks, 

wilderness areas, and international parks. Through the 1977 amendments to the Clean Air Act, 

Congress set a national goal for visibility as “the prevention of any future, and the remedying of 

any existing, impairment of visibility in mandatory Class I Federal areas which impairment 

results from manmade air pollution” (40 CFR 51.300). States are required to develop State 

Implementation Plans (SIPs) to attain visibility standards, and Tribes also may opt to assume 

responsibility for visibility programs under 40 CFR Part 49 by developing Tribal Implementation 

Plans (TIPs). The goal of the Regional Haze Rule (RHR) is to achieve natural visibility 

conditions at the Federally mandated Class I areas by 2064. To achieve this goal, the RHR has 

set up several milestone years of 2018, 2028, 2038, 2048, 2058 and 2064 to monitor progress 

toward natural visibility conditions. Section 308 requires the first visibility SIP/TIP be submitted 

to EPA by 2007 - 2008 to demonstrate progress toward natural visibility conditions in 2018 

using the 2000-2004 five-year baseline. The VISTAS “game plan” is to have an evaluation of 

initial strategies by 2005 so that States and Tribes can start their planning process for submitting 

their plans to EPA that were originally due by 2008. 

Regional haze is linked to fine particulate (PM2.5) for which EPA has a new standard. 

PM2.5 SIPS are to be submitted 3 years after designation of PM2.5 nonattainment areas. EPA 

intends to perform the final designations of the PM2.5 nonattainment areas by December 2004, 

which would make the PM2.5 SIP due by December 2007. As regional haze is intricately linked 

to PM2.5, the PM2.5 and regional haze SIPs are in the process of being aligned so they would both 

be due by December 2007, if the PM2.5 final designations occur as planned. EPA also intends to 

designate 8-hour nonattainment areas by April 2004 that would make 8-hour ozone SIPs also due 

Appendix C.1 - 34
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-2 

Figure 1-1. Regional Planning Organizations Engaged in Regional Haze Modeling.

in 2007. States are considering whether to use the integrated one-atmosphere VISTAS base year 

modeling for ozone modeling in addition to PM2.5 and regional haze. Those decisions will be 

based on schedule constraints, model performance, appropriateness of the episodes and 

feasibility. These regulatory drivers emphasize the importance of completing the VISTAS Phase 

I modeling to test and evaluate model configurations in 2003 and starting the annual modeling in 

2004. These issues also emphasize the importance in testing the models for ozone as well as 

PM2.5 and visibility. 

VISTAS is one of five Regional Planning Organizations (RPOs) in the United States that 

are implementing the requirements of the RHR. The purposes of VISTAS are: 

> To promote the coordinated efforts of State, Local, and Tribal air agencies to meet 

federal regional haze and visibility requirements; 

> To identify regional or common air management issues; 

Appendix C.1 - 35
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-3 

Figure 1-2. VISTAS Study Region Showing the Class 1 Areas.

> To conduct research and undertake other activities to provide the membership 

with scientific and technological information which may be of value in the 

development of agency strategies; and 

> To develop strategies on regional haze for use by member states and tribes, where 

appropriate, in developing their implementation programs. 

Appendix C.1 - 36
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-4 

The Southeastern States Air Resource Managers (SESARM) has been designated by the 

US Environmental Protection Agency as the entity responsible for coordinating and 

implementing regional planning for the states in the VISTAS region. 

1.2 VISTAS Two-Phased Approach 

1.2.1 Phase I 

The objective of VISTAS Phase I was to determine the optimal modeling configuration 

for use in the subsequent Phase II visibility assessment. Accordingly, Phase I entailed a 

comprehensive literature review of recent relevant visibility studies using various 

photochemical/aerosol modeling platforms in order to assess and identify appropriate model 

configurations, data bases, and model testing methodologies that were appropriate for use in 

conducting the VISTAS Phase I emissions and PM modeling assessment. Key elements of 

Phase I included: 

3⁄4 Review all relevant air quality model simulations that have been completed related to 

regional haze and PM2.5 modeling and document the relevant sensitivity analyses, model 

configuration testing, and performance evaluations that have been performed 

(ENVIRON, 2003d); 

 

3⁄4 Review the current science in regional emissions modeling (e.g., EPS, EMS and 

SMOKE) and PM air quality modeling (e.g., CMAQ, CMAQ-MADRID, CMAQ-AIM, 

REMSAD, UAM-V/PM, CAMx4 and PMCAMx) to determine the most appropriate 

model(s) for use by VISTAS (ENVIRON, 2003b); 

3⁄4 Review available ambient data for evaluating one-atmosphere PM/ozone models 

(ENVIRON, 2003c);

3⁄4 Develop and implement a plan for testing and evaluating alternative science 

configurations of the recommended Phase I model(s) and document the results 

(ENVIRON, 2003d); 

3⁄4 Prepare a Task 6 report prescribing the model set-up, data base development, 

performance testing, and control strategy evaluation procedures to be implemented in 

VISTAS Phase II (this protocol document). 

VISTAS formed three standing workgroups to plan and direct. These included (a) the 

Technical Analysis (emissions and modeling) Workgroup; (b) the Data (monitoring) Workgroup; 

and (c) the Planning Workgroup. Under Phase I, the VISTAS Technical Analysis Workgroup 

(TAWG) managed the comprehensive model configuration testing program aimed, as noted 

above, at evaluating the capabilities of current state-of-science regional emissions, prognostic 

meteorological and PM/visibility models. The resultant modeling system (models and databases) 

identified and tested in Phase I were intended to be applied in Phase II (discussed below) 

following the procedures set forth in this protocol. 

For the meteorological component of the Phase I modeling, SESARM contracted with 

Baron Advanced Meteorological Systems (BAMS) to apply the PSU/NCAR Mesoscale Model 

Appendix C.1 - 37
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-5 

(MM5) in multiple configurations and to evaluate its performance against surface and aloft 

meteorological observations. The emissions modeling component of VISTAS Phase I was 

carried out by the research team of ENVIRON/UC/Alpine with staff at Alpine Geophysics taking 

the lead role in setting up, testing, and applying the emissions modeling system. The air quality 

modeling component was performed by the team at the ENVIRON/UC/Alpine modeling centers. 

A dominant theme during Phase I was the exchange of modeling codes, databases, and 

evaluation software between the three modeling centers as the air quality modeling was carried 

out. 

1.2.2 Phase II 

The Phase II modeling will include annual PM/regional haze simulations plus additional 

shorter duration episodes. After detailed performance testing, the modeling system will then be 

exercised with a variety of emissions control scenarios aimed at enabling VISTAS to assess the 

effects of future year emission control strategies on visibility and other air quality issues. The 

modeling system will also allow VISTAS to track reasonable progress toward regional haze 

goals. More specifically, the VISTAS Phase II program will focus on the use of the CMAQ 

modeling system for calendar year 2002 over the same 36/12 km horizontal grid system used in 

Phase I. A potentially large number of annual (and episodic) model simulations will be 

performed; the list below reflects current plans: 

3⁄4 2002 Initial Annual Run. The initial annual model simulations and performance 

evaluations using the 2002 inventory for VISTAS and non-VISTAS states, Canada and 

Mexico. Multiple iterations of the 2002 annual simulation will be required to confirm the 

appropriateness of the model science configuration(s) recommended by the Phase I work, 

to evaluate updates to the model and model inputs and to refine model performance. 

 

3⁄4 2002 Revised Annual Run. A subsequent annual 2002 simulation using revised 2002 

modeling inventory for VISTAS and non-VISTAS states, Canada and Mexico. The 

primary objective of this run is model performance demonstration using updated 

emissions inventories and best science model configurations. Additional sensitivity tests 

will be conducted using the revised base case year annual run. 

3⁄4 2002 Annual Run with “Typical Year” EGU/Fire Inventory. An annual 2002 

simulation representing the 2000-2004 baseline period for EGU and fire emissions and 

using 2002 revised inventory for all other source sectors. The primary objective of this 

inventory is to provide the base line modeled air quality condition against which future 

year modeling runs will be compared to develop relative reduction factors for each 

pollutant species. 

3⁄4 Future Year Annual Runs. Future year simulations involving a base case inventory of 

typical EGU and fire emissions for VISTAS-selected future period. Additional future 

year inventories may also be modeled. The objective of these future year model runs is 

to establish the modeled air quality basis against which the effectiveness of emissions 

control strategies will be evaluated. 

3⁄4 Future year emission control strategies. Prescription of the future year emissions 

control strategies to be performed later in Phase II (e.g., 2005) will be defined after the 

Appendix C.1 - 38
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-6 

foregoing simulations and analyses have been completed. A combination of annual and 

episodic runs is anticipated. 

Closely integrated with the annual (and possibly episodic) meteorological, emissions and 

air quality modeling will be ongoing project management, technical review, and quality 

assurance activities performed under the guidance of the VISTAS Contracting Officer and the 

TAWG. The modeling team members will participate with VISTAS management in regular 

monthly conference calls, as well as ad hoc topical conference calls as needed, and will attend 

periodic meetings with the TAWG members throughout Phase II. 

Complementing the data acquisition, modeling input development activities, and project 

management activities, four other Phase II activities will be performed, consistent with the 

Quality Assurance (QA) plan: 

Data Gatekeepers

The VISTAS Phase II emissions and air quality modeling team are receiving emissions, 

meteorological and air quality data from other VISTAS contractors or other sources and as a first 

line of QA, we have defined a Gatekeeper function to assure the data have been received 

correctly, evaluate the quality of the data, and document the data received. Separate air quality, 

meteorological and emissions Gatekeepers have been identified whose roles are defined below. 

In addition, a Data Management Gatekeeper has been defined who will post data, reports and 

results to the project website and archive all key data generated in the project. 

3⁄4 Air Quality Data Gatekeeper. Obtain air quality data as appropriate for 

model input development and model performance evaluation and assure 

quality of all air quality data obtained, consistent with approved QA plan. 

This gatekeeper will also provide documentation of evaluation and generate 

IC/BC inputs for CMAQ for all modeling runs. 

3⁄4 Meteorological Gatekeeper. Obtain meteorological data, as MM5 or MCIP 

files, as appropriate for annual 2002 modeling runs and other episode periods 

and perform data quality checks as approved in QA plan together with 

appropriate documentation of model performance evaluation activities. 

3⁄4 Emissions Gatekeeper. Obtain emissions inventory data necessary to 

support annual 2002 and future year modeling and recommend source of 

emissions data to be used for Canada and Mexico. Assure quality of all 

emissions data received, consistent with approved QA plan and develop all 

emissions modeling files to support modeling runs for 2002. This gatekeeper 

will also develop the chemical speciation files and temporal and spatial 

allocation files necessary to convert annual inventories into hourly and daily 

emissions modeling files, as appropriate. The Emissions Gatekeeper will also 

develop all emissions modeling files for non-VISTAS states to support 

modeling runs for future year base case and emissions strategies as defined by 

VISTAS. 

Appendix C.1 - 39
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-7 

3⁄4 Data Management Gatekeeper: This gatekeeper will maintain the VISTAS 

Modeling Website including posting modeling input and output files, reports, 

interpretation of results, and other documents as requested by VISTAS to 

support all Phase II tasks. This includes, for example, the storage of model 

inputs and outputs for annual (and episodic) runs and the transfer (via fire 

wire or alternative media) of electronic files to VISTAS states, other regional 

planning organizations, EPA, other contractors, and stakeholders. 

Emissions QA/QC 

Emissions Quality Assurance (QA) and Quality Control (QC) are the single most critical 

steps in performing air quality modeling studies. Because emissions processing is tedious, time 

consuming and involves complex manipulation of many different types of large data sets, errors 

are frequently made in emissions processing and, if rigorous QA measures are not in place, these 

errors may remain undetected. In Phase II we will continue with multistep emissions the QA/QC 

approach applied in the Phase I modeling. This includes the initial emissions QA/QC by the 

Emissions Gatekeeper described above, as well as QA/AC by the Emissions Modeler during the 

processing of emissions and then additional QA/QC by the air quality modeler of the processed 

model ready emission files. This multistep process with three separate groups involved in the 

QA/QC of the emissions is much more likely to catch any errors prior to the air quality model 

simulations. 

Emissions QA/QC that would be performed as part of the emissions modeling will include: 

EMS and EPA Input Screening Error Checking Algorithms: Although the SMOKE 

emissions model will be used for emissions processing, some of the more advanced EMS 

input error checking algorithms will be used to screen the data and identify potential 

emission input errors. Additionally, EPA has issued a revised stack QA and augmentation 

procedures memorandum that will be used to identify and augment any outlying stacks. 

SMOKE error messages: SMOKE provides various cautionary or warning messages 

during the emissions processing. We will redirect the SMOKE output to log files and 

review the log files for serious error messages. An archive of the log files will be 

maintained so that the error messages can be reviewed at a later date if necessary. 

SMOKE emissions summaries: We will use QA functions built into the SMOKE 

processing system to provide summaries of processed emissions as daily totals according 

to species, source category and county and state boundaries. These summaries will then 

be compared with summary data prepared for the pre-processed emissions, e.g., state and 

county totals for emissions from the augmented emissions data. 

Appendix C.1 - 40
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-8 

Once the CMAQ-ready emission inputs have been prepared, we will perform additional 

emissions QA/QC as follows: 

Spatial Summary: We will sum the emissions for all layers and for all 24 hours that is 

used to prepare a PAVE plot showing the daily total emissions spatial distribution. For a 

20 day simulation this produces approximately 20 days x 20 species x 5 emissions 

categories = 2,000 plots. In our base case simulations these plots will be presented as tons 

per day. The objective of this step is to identify errors in spatial distribution of emissions. 

Vertical Profile: For point sources the emissions total for each layer will be summed and 

plotted to show the vertical distribution of emissions. These plots show the emissions on 

the x-axis for each model layer on the y-axis. The objective of this step is to identify 

possible errors in vertical distribution of emissions. 

Short Term Temporal Summary: The total domain emissions for each hour will be 

accumulated and time series plots prepared that display the diurnal variation in total 

hourly emissions. The objective of this step is to identify errors in temporal profiles. 

Long Term Temporal Summary: The total domain emissions for each day will be 

accumulated and displayed as time series plots that show the daily total emissions across 

the domain as a function of time. The objective of this step is to identify particular days 

for which emissions appear to be inconsistent with other days for no reason (e.g., not a 

weekend) and compare against the general trend. 

Control Strategy Spatial Displays: Spatial summary plots of the daily total emissions 

differences between a control strategy and base case emissions scenarios will be 

generated. These plots can be used to immediately identify a problem in a control 

strategy. For example, if a VISTAS states SO2 control strategy is being analyzed and 

there are changes in emissions for other pollutants or for SO2 outside of the VISTAS 

states problems in emissions processing can be identified prior to the air quality model 

simulation. 

Meteorology QA/QC 

The VISTAS meteorological modeling contractor (BAMS) will have primary 

responsibility in the QA/QC of the MM5 meteorological fields. However, the emissions and air 

quality modeling team will also perform some QA/QC of the meteorological data to assure that it 

has transferred correctly, to obtain an assessment of the quality of the data and to assist in the 

interpretation of the air quality modeling results. 

The VISTAS Phase II Meteorological Gatekeeper will perform the following: 

3⁄4 Analyze the MM5 data to assure it has been transferred correctly; 

 

3⁄4 Evaluate the MM5 using METSTAT and the surface meteorological network; 

Appendix C.1 - 41
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-9 

3⁄4 Evaluate upper-air MM5 meteorological estimates by comparison them to upper-air 

observations and satellite images; and 

3⁄4 Compare the VISTAS 2002 MM5 simulation with the one generated by WRAP. 

3⁄4 Generate the CMAQ-ready meteorological inputs using the MCIP2.2 processor. 

Air Quality Modeling QA/QC 

Key aspects of QA for the CMAQ input and output data include the following: 

• Verification that correct configuration and science options are used in compiling and 

running each model of the in the CMAQ modeling system, where these include the 

MCIP, JPROC, ICON, BCOM and the CCTM. 

• Verification that correct input data sets are used when running each model. 

• Evaluation of CCTM results to verify that model output is reasonable and consistent with 

general expectations. 

• Processing of ambient monitoring data for use in the model performance evaluation. 

• Evaluation of the CCTM results against concurrent observations. 

• Backup and archiving of critical model input data. 

 The most critical element in the QA plan for CMAQ simulations is the QA/QC of the 

meteorological and emissions input files, which is discussed above. The major QA issue 

specifically associated with the air quality model simulations is verification that the correct 

science options were specified in the model itself and that the correct input files were used when 

running the model. For the CMAQ model we employ a system of naming conventions using 

environment variables in the compile and run scripts that guarantee that correct inputs and 

science options are used. We also employ a redundant naming system so that the name of key 

science options or inputs are included in the name of CMAQ executable program, in the name of 

the CMAQ output files, and in the name of the directory in which the files are located. This is 

accomplished by using the environment variables in the scripts to specify the names and 

locations of key input files. 

 A second key QA procedure is to never “recycle” run scripts, i.e., we always preserve the 

original runs scripts and directory structure that were used in performing a model simulation. 

 We will also perform a post-processing QA of the CMAQ output files similar to that 

described for the emissions processing. We will generate animated gif files using PAVE that can 

be viewed to search for unexpected patterns in the CMAQ output files. In the case of model 

sensitivity studies, the animated gifs will be prepared as difference plots for the sensitivity case 

minus the base case. Often, errors in the emissions inputs can be discovered by viewing the 

Appendix C.1 - 42
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-10 

animated GIFs. Finally, we will produce 24 hour average plots for each day of the CMAQ 

simulations. This provides a summary that can be useful for more quickly comparing various 

model simulations. 

1.3 Preliminary Conceptual Model of Visibility Impairment in the VISTAS Region 

VISTAS is currently developing a comprehensive conceptual model of visibility impairment in 

the southeastern US. Brewer, Holman and Hornback (2003) have reported a preliminary 

analysis to characterize the components of PM2.5 and their contributions to visibility impairment 

in the VISTAS region. The analyses was based on monitoring data from the Interagency 

Monitoring of Protected Visual Environments (IMPROVE) network (Malm et. al., 2003) for the 

period 1998 to 2001 and from the Southeast Aerosol Research Characterization Study 

(SEARCH) network (Hansen et al., 2004)for the period 1999 to 2001. IMPROVE monitors are 

located in 15 of the 18 Class I areas (national parks greater than 6,000 acres and wilderness areas 

greater than 5,000 acres) in the in the VISTAS region (Figure 1-3). These areas represent a 

broad geographic range from the Atlantic and Gulf Coasts and coastal plains to the Southern 

Appalachian Mountains and western Kentucky. The SEARCH network consists of four urban 

sites (Atlanta, GA, Birmingham, AL, Gulfport, MS, and Pensacola, FL) paired with a nearby 

rural site (or suburban in the case of Pensacola) for a total of 8 sites (Figure 1-3). 

Figure 1-3. Locations of IMPROVE and SEARCH fine particulate monitoring sites used to 

characterize visibility impairment in the southeastern U.S. 

Similar multi-filter systems and analytical methods are used in the two networks. The 

IMPROVE network collects 24-hour samples every third day. The SEARCH network collects 

24-hour samples either daily or every third day. Light extinction was calculated as described in 

SEARCH (urban)

SEARCH (rural)

IMPROVE (limited data)

IMPROVE (5+ years)

Sipsey

Chassahowitzka

Okefenokee

Mammoth Cave

Shining Rock

Great Smoky Mtns.

Shenandoah

James River Face

Dolly Sods

Cape Romain

Jefferson St 

(Atlanta)

Birmingham

Pensacola

Old Fort

Gulfport

Yorkville

Centerville

Oak Grove

Saint Marks

Cohutta

Linville Gorge

Swan Quarter

Everglades

Figure 2. IMPROVE and SEARCH Sites in VISTAS region

Appendix C.1 - 43
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-11 

the draft Guidance for Tracking Progress under the Regional Haze Rule (EPA, 2001), except 

that relative humidity was not allowed to exceed.95%. Coarse mass measurements were not 

available for the SEARCH sites in Gulfport and Oak Grove, Mississippi. 

EPA’s guidance (EPA, 2001) calculates visibility impairment through fine mass light extinction 

that is attributable to light scattering due to air molecules (Rayleigh scattering), scattering by 

ammonium sulfate, (NH4)2SO4; ammonium nitrate, NH4NO3; organic carbon (OC), and fine Soil, 

and absorption by elemental carbon, EC. Coarse mass (fine particles with diameters between 2.5 

and 10 microns) also contributes to total light extinction. Fine particle composition and 

contribution to light extinction were evaluated for days with the 20% highest and 20% lowest 

total light extinction (on annual basis) for 1998 to 2001 in the IMPROVE network and for 1999 

to 2001 in the SEARCH network (ARS, 2002). For the IMPROVE sites, on the 20% haziest 

days (highest extinction), light extinction (i.e., visibility impairment) is greater at the Southern 

Appalachian, Mammoth Cave, and Sipsey sites than at the coastal and coastal plain sites (Figure 

1-4). Visual range on the 20% haziest days varies from 18 -25 km at the northern IMPROVE 

sites and 27-48 km at the coastal and coastal plain sites. 

Light extinction for the 20% haziest days is generally higher at the northern SEARCH 

sites than the coastal SEARCH sites (Figure 1-5). Visual range on the 20% haziest days at the 

SEARCH sites varies from 15-24 km. For the 20% clearest days (lowest extinction), there is less 

spatial variation in extinction than is observed for the 20% haziest days (see Figures 1-4 and 1-

5). Visual range on the 20% clearest days varies from 75-131 km at the IMPROVE sites and 57-

91 km at the SEARCH sites. 

Figure 1-4. Components of average light extinction (Mm-1) at southeastern US IMPROVE 

monitors for the 20% worst visibility days from 1998-2001. Extinction (Mm-1)

 Coarse

Soil

Organics

EC

NH3NO3

(NH4)2SO4

Rayleigh

Dolly Sods, WV

Shenandoah, VA

James Rvier Face, VA

Mammoth Cave, KY

Sipsey, AL

Great Smoky Mtns, TN

Linville Gorge, NC

Swan Quarter, NC

Cape Romain, SC

Okefenokee, GA

Chassahowitzka, FL

Everglades, FL

Shining Rock, NC

Figure 3. Light Extinction on 20% Poorest Visibility Days - IMPROVE 1998 - 2001

50

100

150

200

250

0

Appendix C.1 - 44
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-12 

Figure 1-5. Components of average light extinction (Mm-1) at southeastern US 

SEARCH monitors for the 20% worst visibility days from 1999-2001. 

Figure 1-6. Components of average light extinction (Mm-1) at southeastern US 

IMPROVE monitors for the 20% best visibility days from 1998-2001). Atlanta, GA Yorkville, GA Birmingham, AL Centerville, AL Gulfport, MS* Oak Grove, MS* Pensacola, FL Old Fort, FL

50

100

150

200

250

300

Extinction (Mm-1)

 Coarse*

 Soil

 Organics

 EC

 NH4NO3

 (NH4)2 SO4

 Rayleigh

Figure 4. Light Extinction on 20% Poorest Visibility Days - SEARCH 1999 - 2001

*coarse not measured at 2 MS sites 

Extinction (Mm-1)

 Coarse

Soil

Organics

EC

NH3NO3

(NH4)2SO4

Rayleigh

Dolly Sods, WV

Shenandoah, VA

James Rvier Face, VA

Mammoth Cave, KY

Sipsey, AL

Great Smoky Mtns, TN

Linville Gorge, NC

Swan Quarter, NC

Cape Romain, SC

Okefenokee, GA

Chassahowitzka, FL

Everglades, FL

Shining Rock, NC

Figure 5. Extinction on 20% Best Visibility Days - IMPROVE 1998 - 2001

0

10

20

30

40

50

60

Appendix C.1 - 45
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-13 

Figure 1-7. Components of average light extinction (Mm-1) at southeastern US SEARCH 

monitors for the 20% best visibility days from 1999-2001. 

In both the IMPROVE and SEARCH networks, the 20% haziest days in the year occur 

most frequently in the summer and spring quarters and least frequently in the winter quarters. 

Variation in sulfate concentrations is the greatest contributor to seasonal variation in extinction 

in the VISTAS region. 

Ammonium sulfate, (NH4)2SO4, fine particles are the largest contributors to light 

extinction for both the 20% clearest and 20% haziest days at all IMPROVE and all SEARCH 

sites in all years and all quarters. (NH4)2SO4 fine particles are also the largest contributors to 

reconstructed fine particle mass at all IMPROVE and SEARCH sites for the 20% haziest days 

and at all IMPROVE sites for the 20% clearest days. On the 20% clearest days at the SEARCH 

sites, organic carbon (OC) mass can be greater than (NH4)2SO4 mass. 

Ammonium nitrate, NH4NO3, typically contributes 0-15% of the fine particle mass and 

fine mass light extinction at the SEARCH and IMPROVE sites. NH4NO3 has the highest 

contributions at the urban Birmingham and Atlanta SEARCH sites and less contribution at the 

more rural SEARCH and IMPROVE sites. Available NH4 measurements for the SEARCH and 

IMPROVE sites indicate that SO4 is not fully neutralized, particularly during the summer quarter 

(ARS, 2002b). NH4 will preferentially neutralize SO4 particles before reacting with nitric acid to 

form NH4NO3. Modeling analyses suggest that NH4NO3 formation in the southeastern U.S. is 

limited by NH4 availability in the atmosphere (Odman et al., 2002). NH4NO3 volatizes at higher 

temperatures, and therefore NH4NO3 particle concentrations are higher in the fall and winter 

months than in the warmer months. On a daily basis, NH4NO3 is most likely to be formed early Atlanta, GA Yorkville, GA Birmingham, AL Centerville, AL Gulfport, MS* Oak Grove, MS* Pensacola, FL Old Fort, FL Extinction (Mm-1)

 Coarse*

 Soil

 Organics

 EC

 NH4NO3

 (NH4)2 SO4

 Rayleigh

Figure 6. Light Extinction on 20% Best Visibility Days - SEARCH 1999 - 2001

*coarse not measured at 2 MS sites 

10

20

30

40

50

60

70

0

Appendix C.1 - 46
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-14 

in the morning when temperatures are generally cooler and relative humidity higher than later in 

the day when conditions are hotter and drier. 

Organic carbon, OC, has the second largest contribution to fine particle mass and fine 

mass light extinction for the 20% haziest days at all sites (see Figures 1-4 and 1-5). On the 20% 

clearest days at IMPROVE sites, NH4NO3 has an equal or sometimes larger contribution to fine 

mass extinction than OC (Figures 1-6 and 1-7). The contribution of OC to fine mass extinction is 

relatively constant across the quarters of the year. The IMPROVE and SEARCH 24-hr samples 

do not allow separation of primary OC from secondary OC sources nor anthropogenic sources 

from biogenic sources. However, chemical mass balance receptor model analysis (Zheng et al., 

2002) and carbon-14 analyses of OC samples for the SEARCH sites (Edgerton, 2003) suggest 

that OC fine mass in the fall and winter is predominantly from primary sources (e.g. gasoline, 

diesel, wood burning). These analyses suggest that secondary organic aerosols (e.g. from 

biogenic emissions) have small contributions to total OC fine mass in the fall and winter months 

and larger contributions in the spring and summer months. 

Elemental carbon, EC, typically contributes 3-15% to fine particle mass and fine mass 

light extinction at the IMPROVE and SEARCH sites. The highest levels of EC are at the urban 

Birmingham and Atlanta SEARCH sites. Elevated levels of OC, EC, and non-soil potassium can 

be used as indicators of episodes where emissions from fires impacted the monitoring sites 

(ARS, 2002c). In particular, poor visibility conditions in October 2000 and November 2001 at 

several sites throughout the southeastern U.S. have been attributed to impacts due to emissions 

from fires. Further analyses is needed to separate the relative contributions of different types of 

combustion sources (e.g. forest fire, prescribed forest burning, land clearing, agricultural 

burning, residential wood combustion, or industrial wood combustion) to elevated OC and EC 

measures. 

Fine Soil generally contributes 0-3 % of the fine mass extinction and 5-20% of the fine 

particle mass at the southeastern U.S. SEARCH and IMPROVE sites. Soil has a higher 

percentage contribution to fine mass and fine mass extinction at Chassahowitzka and Everglades 

IMPROVE monitors in Florida than at the other IMPROVE and SEARCH sites in the 

southeastern U.S. Coarse mass generally contributes less than 5% to total extinction at the 

IMPROVE sites and at those SEARCH sites where coarse mass is measured. There is 

considerable inter-annual variability in all of the above measures of fine particle mass and 

extinction. 

Fine particle mass and composition are also measured by the state agencies at several 

sites throughout the VISTAS region. The national ambient air quality standard for PM2.5 for an 

annual average (15 μg/m3

) is measured to be exceeded in several urban areas in the southeastern 

states (see Figure 1-8). The annual PM2.5 standard is not exceeded at any of the IMPROVE sites. 

No exceedances of the 24-hour standard (65 μg/m3) have been reported through 2002, except 

those related to forest fire events. 

Appendix C.1 - 47
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-15 

Figure 1-8. Counties in the southeastern U.S. with 1999-2001 annual PM2.5 Design Values that 

exceed the fine particulate annual standard. 

1.4 Summary of Phase I Findings 

The Phase I program entailed systematic meteorological, emissions, and air quality model 

testing and evaluation to identify the most reliable, scientifically valid, and operational efficient 

modeling configuration for visibility assessment in the Southeastern U.S. Collaboratively, the 

VISTAS TAWG and modeling contractors selected three episodes to serve as the foundation for 

model testing and evaluation: (a) 1-20 January 2002, (b) 13-27 July 2001, and (c) 13-21 July 

1999. A brief summary of the Phase I findings is given below. 

1.4.1 Meteorological Modeling Findings 

As noted above, SESARM contracted with Baron Advanced Meteorological Systems 

(BAMS) to apply the PSU/NCAR Mesoscale Model (MM5) in multiple configurations and to 

evaluate its performance against surface and aloft meteorological observations. Moreover, 

BAMS scientists participated with the emissions and air quality modeling team in assessing how 

the air quality modeling system responded to sensitivity features of the meteorological model. 

Significant findings of the Phase I MM5 meteorological modeling are presented in a series of 

reports (Olerud, 2003a,b; Olerud and Sims, 2003) and meeting presentations (e.g., Olerud, 

2003c; Abraczinskas, 2003; Appel, 2003). Further details and a compendium of meteorological 

modeling results may be found at the following website: 

http://www.baronams.com/projects/VISTAS/. 

Figure 7. Counties with 1999-01 design values above PM2.5 annual standard

Appendix C.1 - 48
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-16 

 Following the Phase I MM5 modeling protocol (Olerud, 2003a), BAMS generated a 

prodigious array of results that helped elucidate several key questions, namely: 

3⁄4 Are the synoptic patterns captured? 

 

3⁄4 Are the modeled meteorological fields reasonable? 

3⁄4 Does the model properly show diurnal evolution in key state fields including mixing 

heights, temperatures, and winds? 

3⁄4 Are cloud cover and precipitation fields unbiased and reasonably accurate? 

3⁄4 Do the fields lead to acceptable air quality results? 

The MM5 (Version 3.6; Grell et al., 1994, MPP version) was exercised for all three 

VISTAS episodes. The specific MM5 modeling periods were: (a) 00Z 26 Dec ’01 to 12Z 21 Jan 

’02, (b) 00Z 6 Jul to 12Z 28 Jul ’01, and (c) 00Z 9 Jul to 12Z 22 Jul ’99. The MM5 sensitivity 

matrix focused on five model configurations: 

px_acm: Pleim-Xiu land surface model (LSM), asymmetric convective 

mixing (ACM) Planetary Boundary Layer (PBL) (Xiu and Pleim, 

2000), interppx to link LSM run segments. 

px_acm2: Similar to px_acm, except no iterppx linkage across run segments 

of LSM data. 

noah_mrf: Noah land surface scheme (Chen and Dudhia, 2001) with the 

medium range forecast (MRF) PBL (Hong and Pan, 1996). 

multi_blkdr: Multi-layer soil scheme with Blackadar PBL and Zilitinkevich 

thermal roughness length. 

noah_eta-my: Noah land-surface scheme with the Eta Mellor-Yamada PBL 

(IMDVDIF = 0). 

Common MM5 physics options underlying the Phase I sensitivity tests included: (a) 

Kain-Fritsch 2 cumulus parameterization, (b) mixed phase (Reisner 1) microphysics, (c) Rapid 

Radiative Transfer Model (RRTM) radiation, (d) snow effects turned on, and (e) analysis 

nudging of surface and aloft winds, temperature, and moisture on the 36 km and 12 km grids. A 

variety of statistical time series plots, statistical tables, and spatial plots were generated to 

quantify and display the modeling results, both at the ground and aloft. 

Key findings distilled from the work of Olerud (2003d,e) included: 

Appendix C.1 - 49
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-17 

o The MM5 (ver 3.6) is most sensitive to the choice of planetary boundary layer 

(PBL) and soil (LSM) schemes1

; 

 

o There was no ‘definite winner’ among the five model configurations tested; 

o The noah_mrf and noah_eta-my exhibit markedly different PBL behavior; 

o The noah_mrf wind performance was poorer than the other configurations, while 

the temperature and precipitation of the noah_eta-my was also poorer than the 

others; 

o Negative PBL heights were generated by the noah_eta-my scheme under some 

situations; 

o The px_acm2 was judged “probably best overall” in part because it did not 

exhibit significant instances of very poor statistical performance for any quantity; 

 

o The PBL behavior produced by both px_acm and px_acm2 was a concern in some 

situations; and 

o There was some residual uncertainty as to whether the px_acm or px_acm2 

scheme was preferable, based on the available results. 

Further details and interpretation of the MM5 configuration analyses are described in the 

citations mentioned above and are also available on the BAMS project website. Reflecting 

Olerud’s findings and the collective judgments of the Emissions and Air Quality Modeling Team 

and the VISTAS TAWG, a slight modification of the px_acm2 scheme (pc_acm8) was chosen as 

the final MM5 configuration for the Phase II modeling. The pc_acm8 MM5 configuration 

differs from pc_acm2 in that the MM5 program little_r is used instead of regrid to generate the 

analysis fields used in the MM5 data assimilation. 

1.4.2 Emissions Modeling Findings 

The emissions and air quality modeling activities of VISTAS Phase I were carried out as 

a joint effort by the research team of ENVIRON/UC/Alpine. For the emissions processing with 

SMOKE, day-to-day emissions modeling tasks were performed principally by staff at Alpine, 

although all team members participated in emissions-related tasks in a number of ways, 

including quality assurance (QA). Key findings in the Phase I emissions processing with the 

SMOKE system include: 

 

1

 This judgment, proffered by Olerud (2003d; page 1) in the VISTAS Task2e meteorological 

modeling review and assessment report, was not derived from the Phase I meteorological 

modeling sensitivity analyses since the latter were not designed to test model physics options 

beyond PBL and LSM schemes. Nonetheless, we agree with Olerud’s assessment based on the 

Emissions and Air Quality Modeling teams experience in literally dozens of MM5 modeling 

studies throughout the U.S. 

Appendix C.1 - 50
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-18 

3⁄4 Although the SMOKE computational methodology provides quick executions 

times, the large number and sizes of input, output and intermediate data files 

require substantial time and disk space for file management activities. 

3⁄4 Data input and output review, process monitoring and data management, and QA 

reporting and evaluation activities substantially increase the calendar time 

required for each production episode. 

Computer runtimes for the SMOKE emissions processing were significant, 

notwithstanding the computational efficiencies inherent in the sparse matrix solution technique. 

After the initial system configuration and setup process, the following runtimes were required for 

a production run of the 2-20 January 2002 episode for the 12K and 36K domains: 

 30 CPU hours 

 4 calendar days 

 40.3 Gigabytes (Gb) output file storage

These times were produced on a dual Athlon 2600+ system utilizing a local Ultra 320 RAID 5 

disk array. 

Based on the SMOKE processing time requirements encountered with all three Phase I 

episodes, we project that the processing time for an annual (365 days) 36 km and 12 km will be 

approximately: 

 19 CPU days of dedicated machine time 

 60 calendar days, and 

1,398 Gb (1.4 Terabytes, Tb) output file storage space.

SMOKE processing also requires approximately 3 times the output file storage space for 

intermediate file handling. These extreme file size requirements will significantly affect the 

amount of time required for emissions generation, file handling and data transfers. 

1.4.3 Air Quality Modeling Findings 

The air quality modeling component was also performed as a joint effort by the 

ENVIRON/UC/Alpine research team. Details of the emissions and air quality modeling 

activities, publications, and modeling results under Phase I may be found at: 

http://pah.cert.ucr.edu/vistas/. The Final Report on the Phase I modeling, including an 

evaluation of CMAQ and CAMx model performance together with results of pertinent modeling 

sensitivity experiments is expected to be delivered to VISTAS in early May 2004. 

The identification of the Phase II model configuration considered three main, and often 

competing, issues: 

(1) Science: Preferable to use better science options in the Phase II model configuration; 

 

(2) Model Performance: Preferable to use model options that produce better model 

performance. 

Appendix C.1 - 51
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-19 

(3) Run Time: Faster run times are preferable. 

Key findings from the Phase I CMAQ configuration testing include: 

3⁄4 Duration of CMAQ Spin-up Initialization Period: Our experience with the 

VISTAS Phase I and Western Regional Air Partnership (WRAP) regional 

modeling was that a minimum 10-15 day spin up period is needed to initialize the 

model for modeling domains the size of the continental US. Even with a 10-15 

day spin up, small differences in concentrations are seen versus a continuous run. 

However, these differences are small enough that they do not affect model 

performance. In general, longer spin up periods are needed for summer than 

winter periods due to more stagnation, higher photochemical oxidant levels and 

weaker synoptic forcing. Just as important as the length of the spin up period is 

the need to operate the model in a consistent fashion across scenarios. For the 

VISTAS Phase II annual modeling, the 2002 annual run will be performed in four 

quarters. The first quarter (January – March, 2002) will be initialized with ~13 

spin up days (starting 00Z on December 18, 2001) with the other three quarters 

initialized with 15 spin up days.

3⁄4 Number of Vertical Layers: Comparisons between the CMAQ modeling results 

for the base configuration of 19 vertical layers with 34 vertical layers that exactly 

matched the MM5 layer structure revealed small changes in modeled 

concentrations, but essentially no change in the basic attributes of model 

performance. The concentration changes were greater for those species that are 

emitted mainly aloft (e.g., SO2 and sulfate), whereas the estimated concentrations 

for primarily surface emitted species (e.g., EC) were essentially identical using 

the two vertical layer structures. Model run time is almost linearly proportional to 

the number of vertical layers, thus the 34 layer CMAQ run requires approximately 

80% more CPU time than the 19 layer run. Based on these results, the 19 vertical 

layer model configuration with a 100 mb (~15 km) region top is adopted for the 

Phase II modeling. 

3⁄4 36 km vs. 12 km Horizontal Grid Size: Similar overall model performance was 

exhibited by CMAQ using a 36 km versus a 12 km grid. However, at specific 

times and locations there could be substantial differences in estimated 

concentrations due to different precipitation and transport patterns. With some 

exceptions, the general trend was a slight degradation in the model performance 

measures using a 12km verses 36km grid. However, the basic model performance 

features remained unchanged using the two grid resolutions. The 12 km CMAQ 

runs required approximately 2 times more CPU time than the 36 km runs. 

Although the 12 km runs require significantly more computer resources, they do 

represent better science for photochemical and PM grid modeling so will be 

retained in Phase II. However, more sensitivity tests can be performed using the 

36 km model configuration. 

3⁄4 Minimum Vertical Kz: The VISTAS Phase I modeling tested minimum vertical 

turbulent exchange coefficients (Kz) of 1.0 m2

/s and 0.1 m2/s. Model 

Appendix C.1 - 52
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-20 

performance using the two minimum Kz values was mixed, with no one 

configuration consistently producing superior model performance over the other 

across all species, locations and periods. Although EPA recommends using a 1.0 

m2

/s minimum Kz, the consensus of the VISTAS modeling group was that a 0.1 

m

2

/s was more technically correct because use of a 1 m2/s minimum Kz would 

result in complete mixing between layers 1 and 2 so could not simulate a stable 

inversion layer near the surface that traps pollutants. Thus, a 0.1 m2

/s minimum 

Kz values was selected for the Phase II modeling. 

3⁄4 Fine Dust Transportable Fraction: For the Phase I modeling, the application of 

a fugitive dust transport fraction of 0.25 was recommended by EPA and 

minimized the bias for the Coarse Matter (CM) species over the other factors 

studied (1.00 and 0.05). For the Phase II modeling, county-specific fugitive dust 

emission adjustment factors based on land-use categories are applied to the 

fugitive dust emissions within the base inventories prior to SMOKE emissions 

modeling (Pace, 2003). Thus, no additional fugitive dust transport fraction factor 

will be applied in the emissions modeling step. 

3⁄4 Adjustment to NH3 Mass Emissions Estimates: Current ammonia emission 

inventories (e.g., NEI99) are believed to overstate ammonia emissions during 

colder months. EPA has performed inverse modeling to estimate the level of 

ammonia emissions needed to match measurements and developed monthly 

ammonia emission adjustment factors that resulted in an approximately 50% 

reduction in ammonia emissions for the January 2002 and no adjustments for the 

July 1999 and July 2001 Phase I episodes. The VISTAS Phase I modeling 

produced much better model performance for the January 2002 episode using the 

50% ammonia emissions adjustment factor. For the Phase II modeling, the 

ammonia emissions inventory has been updated using the CMU ammonia model 

and state submissions so additional adjustments may not be needed. 

3⁄4 Adjustment to NH3 Emissions Temporal Profile: An ammonia emissions 

temporal adjustment sensitivity test was performed that reduced ammonia 

emissions by 50% with more reductions occurring at night and less during the 

day. Model performance was marginally improved over the across-the-board 

50% adjustment. However, as we could not justify the arbitrarily selected 

ammonia emissions diurnal profile, Phase II modeling will use the default diurnal 

profile for ammonia emissions. 

3⁄4 Significance of Mexico and Canadian Emissions: CMAQ runs with and without 

emissions from Canada and Mexico produced nearly identical model performance 

in the VISTAS Southeast US region. Use of Canadian and Mexican emissions is 

more technically justifiable, so they will be included in the Phase II modeling. 

3⁄4 Minimum PBL Depth: There are some concerns that MM5 may sometimes 

estimate a PBL depth that is too low under some conditions (e.g., clouds). In 

Phase I, minimum PBL depth sensitivity tests were performed, but they did not 

substantially improve model performance and were difficult to technically justify. 

Thus, for Phase II the MM5 PBL depth estimates will be used as is. 

Appendix C.1 - 53
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-21 

3⁄4 Use of Global Chemistry Transport Model Output for Boundary Conditions: 

Three boundary condition (BC) sensitivity tests were carried out using the July 

2001 VISTAS Phase I episode: EPA CMAQ default BCs; monthly average July 

2001 GEOS-CHEM values; and 3-hour specific GEOS-CHEM results. Although 

model performance in the VISTAS domain was only marginally affected by the 

different BCs for the July 2001 episode, BCs could have more effect under 

cleaner conditions and for other episodes with higher wind speeds. VISTAS is 

currently evaluating whether a 2002 GEOS-CHEM simulation should be 

performed to provide BCs for the 2002 CMAQ run, although it would not be 

ready until later in 2004. Thus, in the mean time the initial 2002 CMAQ 

modeling would use monthly average GEOS-CHEM BCs based on the 2001 

GEOS-CHEM values. 

3⁄4 Wesely Dry Deposition Scheme: CMAQ has two dry deposition options, one 

that uses data from the MM5 Pleim-Xiu (PX) LSM model (M3Dry), and one 

based on the Wesely scheme from RADM. In order to evaluate alternative MM5 

simulations that cannot use the PX dry deposition scheme, a dry deposition 

sensitivity test was performed using the Wesely dry deposition scheme. The 

Wesely dry deposition sensitivity test produced degraded model performance 

compared to when the PX scheme was used. Thus, based on better science and 

better model performance, the PX dry deposition scheme was selected for Phase 

II CMAQ modeling. 

3⁄4 Eta-Mellor-Yamada MM5 Scheme: The MM5 simulation using the Eta-MY 

PBL scheme produced some negative PBL heights. Thus, a patch was added to 

the CMAQ MCIP processor to correct the negative PBL heights. CMAQ model 

performance using the MM5_Eta-MY PBL scheme (with the MCIP PBL patch) 

was not as good as the performance using the MM5 with the Pleim-Xiu LSM and 

ACM PBL (PX_ACM) configuration (no MCIP PBL patch needed). Thus, based 

on better science and improved model performance, the MM5 using the PX_ACM 

LSM_PBL configuration was selected for VISTAS Phase II modeling. 

3⁄4 Aerosol Mass Conservation Patch: Georgia Institute of Technology noted that 

sulfur and nitrogen mass was not being conserved on calls to the CMAQ aerosol 

algorithms subroutines. Thus a mass conservation patch was added to CMAQ 

that assured the conservation of sulfur, reactive nitrogen and reduced nitrogen. 

Model performance with and without the mass conservation patch was essentially 

identical. Therefore, based on better science, CMAQ using the mass conservation 

patch was adopted for the Phase II modeling. 

3⁄4 CB4-2002 Chemistry: The CB4-2002 chemical mechanism was implemented in 

the SMVGEAR chemistry solver in CMAQ. The CB4 and SAPRC99 chemical 

mechanisms are implemented in the much faster EBI chemistry solver that 

requires some hard coding. For most species, the CMAQ model performance 

using CB4 and CB4-2002 are nearly identical. For nitrate, CB4-2002 produced 

degraded model performance for the January 2002 episode. Given the much 

Appendix C.1 - 54
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-22 

slower run times and little changed or degraded model performance, CB4-2002 

was not selected for the VISTAS Phase II modeling. 

3⁄4 SAPRC99 Chemistry: The CMAQ simulations using the CB4 and SAPRC99 

chemistries produced different model performance, but both exhibited similar 

skill so that one simulation was not clearly performing better than the other across 

all species, locations and periods. Not tested, however, was whether one chemical 

mechanism behaved differently in response to emission reductions over another. 

SAPRC99 chemistry represents more current science than CB4 chemistry. 

However, CMAQ using SAPRC99 chemistry takes twice the CPU time as 

CMAQ/CB4 and requires more memory and disk space also. Thus, for Phase II 

modeling it was decided to use the CB4 chemistry for the initial CMAQ 2002 

base case simulations and evaluate the sensitivity of SAPRC99 and CB4 to 

emissions reductions using the January 2002 and July 2001 Phase I databases. 

Depending on the results of the Phase II emission reduction sensitivity tests, the 

SAPRC99 chemistry may be used in the revised 2002 CMAQ base case 

simulation starting in September 2004. 

3⁄4 AIM Aerosol Chemistry: The AIM sectional aerosol module did not produce 

any improvements in model performance over the standard CMAQ modal AE3 

approach and required significantly more computer time and disk storage. Thus, 

the standard CMAQ model was adopted for Phase II modeling. 

3⁄4 Alternative Model: The CAMx model was exercised for the July 1999 and July 

2001 Phase I episodes. In general model performance between the two models 

was similar, but there were some differences. CMAQ performed better for 

sulfate, whereas CAMx performed better for carbon (EC and OC). Both models 

performed poorly for nitrate. As neither model performed significantly better 

than the other across all species and periods, the CMAQ model was retained as 

the lead model for the Phase II modeling with CAMx an optional corroborative 

model.

Note that there are two parameters in the Phase I CMAQ base configuration that differ 

from the default recommendations: (1) use of a 0.1 m2

/s over a 1.0 m2/s minimum vertical 

diffusion coefficient (Kz); and (2) use of the mass conservation patch. Regarding the 0.1 m2

/s 

minimum Kz, the VISTAS science team believes it is more technically correct and, as described 

by Morris and co-workers (2004), it produced better nighttime ozone performance, whereas PM 

performance was mixed. The conservation of sulfur and nitrogen is a fundamental property of 

the real atmosphere so we believe that justifies the use of the mass conservation patch. 

 The CMAQ run times are highly dependent on the number of CPUs used and the network 

loading as well as vary for CB4 vs. SAPRC99 chemistry and 12 km vs. 36 km grid. Using 6 

Athlon 2600+ CPUs, the following are the elapsed times for several CMAQ configurations: 

 CB4 36 km – 1.9 hrs/day 

 CB4 12 km – 3.9 hrs/day 

 SAPRC99 36 km – 2.8 hrs/day 

 SAPRC 12 km – 8.0 hrs/day 

Appendix C.1 - 55
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-23 

Thus an annual CMAQ/CB4 run on the 36 km and 12 km grid using 6 Athlon 2600+ 

processors would require approximately 30 and 60 days to complete if run sequentially from 

January to December. 

1.5 Modeling Protocol 

Based on the model configuration decisions made in Phase I, the Phase II emissions and 

air quality modeling protocol is intended to specify the procedures for performing the base year 

modeling and the evaluation of emission control strategies for future years. The protocol will 

prescribe model set up methods, procedures for performance evaluation, sensitivity analysis, 

uncertainty examination, and the various statistical metrics and graphical tools to be used in the 

interpretation of base case and future year control simulations. Included as part of the Phase II 

protocol is the Quality Assurance Plan. The QA plan defined how quality assurance tasks will 

be performed and sets forth guidelines for accountability in correcting errors identified through 

the various review activities. Although completed at the outset of Phase II, the modeling 

protocol is expected to evolve as the project proceeds and will likely be revised as the knowledge 

base expands. 

As discussed later in this report, particular emphasis in the Modeling Protocol has been 

given to: (a) general and specific emissions and air quality model configurations; (b) 

configurations of all key interface and processor programs; (c) emissions processing 

methodologies and data sources to be used; (d) air quality model input preparation procedures 

and data sources to be used; (e) application procedures for the historical year base case, typical 

base year, future year, and strategies; (f) procedures for model evaluation, sensitivity analyses, 

and uncertainty examination; (g) documentation; (h), data transfer, backup and archiving; (i) 

design and maintenance of project website, (j) quality assurance plans for each element of the 

Phase II modeling including accountability for correcting errors found through review and 

quality assurance activities and, (k) schedule and deliverables. 

1.6 Phase II Study Participants and Responsibilities 

The VISTAS Phase II Emissions and Air Quality Modeling Study is being carried out by 

ENVIRON, Alpine and UCR under contract to SESARM. Table 1-1 lists the contact 

information of the key participants. Their roles in the work are as follows: 

3⁄4 Pat Brewer, VISTAS Technical Coordinator is the Contracting Officer for the 

study; 

 

3⁄4 James Boylan of the Georgia Environmental Protection Division is the Technical 

Contact for the VISTAS Emissions and Air Quality Modeling; 

3⁄4 Michael Abraczinskas of the North Carolina Department of Environment and 

Natural Resources is the Technical Contact for the VISTAS MM5 Meteorological 

Modeling; 

3⁄4 Laura Boothe of the North Carolina Department of Environmental and Natural 

Resources is the Technical contact for the VISTAS Emissions Inventory; 

Appendix C.1 - 56
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-24 

3⁄4 Sheila Holman of the North Carolina Department of Environment and Natural 

Resources is the chair of the VISTAS Technical Analysis Work Group (TAWG); 

3⁄4 Ralph Morris of ENVIRON is the Project Manager for the VISTAS Emissions 

and Air Quality Modeling ENVIRON/Alpine/UCR/UCD Team; 

3⁄4 Ralph Morris of ENVIRON, T.W. Tesche of Alpine, and Gail Tonnesen of UCR 

will lead the efforts of their respective institutions; 

3⁄4 Cyndi Loomis, Greg Stella and Jim Wilkinson of Alpine are leading the emissions 

modeling efforts; 

3⁄4 Dennis McNally of Alpine, Chris Emery of ENVIRON and Zion Wang of UCR 

will lead the meteorological data processing; and 

1.7 Communications and Issue Resolution 

The ENVIRON/UC/Alpine Team will maintain regular contact with the VISTAS 

Contracting Office, Technical Contacts, key members of the TAWG and other VISTAS 

Contractors through regular conference calls and emails. Four list servers have been set up to 

facilitate communications among the groups to address specific air quality, emissions, and 

meteorologist issues as well as all issues as follows: 

Vistas-modeling@cert.ucr.edu

Vistas-emissions@cert.ucr.edu

Vistas-met@cert.ucr.edu

Vistas-all@cert.ucr.edu

The modeling team will take direction from the VISTAS TAWG through the VISTAS 

Contracting Officer and the VISTAS Technical Contact for the Emissions and Air Quality 

Modeling Study. Issues that need to be resolved among the TAWG will follow VISTAS 

resolution principles. 

1.8 VISTAS Phase II SOW 

A preliminary Scope of Work (SOW) for the VISTAS Phase II emissions and air quality 

modeling has been developed and is provided in Appendix A. The Phase II SOW delineates the 

tasks, approach and schedule for carrying out the work identified in this modeling protocol. The 

SOW is broken down into a base effort that focuses on annual modeling of 2002 and several 

optional tasks. The ultimate objective of the Phase II work effort in 2004 is to obtain a fully 

evaluated and operational emissions and air quality modeling system for the 2002 and 2018 

annual calendar years so that control strategy evaluation can begin in 2005. 

1.9 Organization of Phase II Emissions and Air Quality Modeling Protocol 

Following this introduction, Chapters 2 and 3 identify the models and modeling period(s) 

selected by the VISTAS TAWG for use in Phase II. Chapter 2 also identifies the Phase I 

recommendations concerning the optimal configurations and science options to be used in the 

Appendix C.1 - 57
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-25 

SMOKE emissions and CMAQ air quality models. Details of the modeling domain specification 

for annual modeling and the data sets to be used in developing model inputs and in support of the 

model performance evaluation and strategy application are presented in Chapter 4. Subsequent, 

in Chapter 5, the procedures for preparing emissions and air quality inputs are specified. Chapter 

6 discusses the Phase II Quality Assurance Plan while Chapters 7 and 8 address the model 

performance evaluation and model application activities, respectively. In Chapter 9, we outline 

the procedures to be used in utilizing the annual (and potentially episodic) air quality modeling 

results to develop future year visibility estimates and to make pertinent comparisons with the 

reasonable progress goals. Issues related to data management and security (Chapter 10), 

documentation (Chapter 11), and the Phase II schedule (Chapter 12) are discussed in turn. The 

VISTAS Phase II SOW is provided in Appendix A. The core procedures to be used in 

conducting the operational and scientific performance evaluation of the air quality model for key 

gas-phase and primary and secondary aerosol species is discussed in the VISTAS Phase I Task 2 

Modeling Protocol (Morris et al. 2003) and is not repeated here. 

Table 1-1. Summary of Key Participants and Contact Information for the VISTAS Phase II 

Emissions and Air Quality Modeling Study.

Person & Role Affiliation/Address Contact Information 

Patricia Brewer 

(Contracting Officer) 

VISTAS Technical Coordinator 

59 Woodfin Place 

Asheville, NC 28801 

(828) 251-6208 

(Fax) (828) 251-6452 

pat.brewer@ncmail.net

James Boylan 

(Technical Contact 

for Emissions and 

Air Quality 

Modeling) 

Georgia DNR 

Air Protection Branch 

4244 International Pkwy, Suite 

120 

Atlanta, GA 30354-3906 

(404) 362-4851 

(Fax) (404) 363-7100 

James_Boylan@mail.dnr.state.ga.us

Michael 

Abraczinskas 

(Technical Contact 

for MM5 Modeling) 

North Carolina DENR 

1641 Mail Service Center 

Raleigh, NC 27699-1641

(919) 715-3743 

Michael.Abraczinskas@ncmail.net

Ralph Morris 

(Project Manager 

and Co-Principal 

Investigator) 

ENVIRON 

101 Rowland Way 

Novato, CA 94945 

(415) 899-0708 

(Fax) (415) 899-0707 

rmorris@environcorp.com

T.W Tesche 

(Co-Principal 

Investigator) 

Alpine Geophysics, LLC 

3479 Reeves Drive 

Ft. Wright, KY 41017 

(859) 341-7502 

(Fax) (859) 341-7502 

twt@iac.net

Gail Tonnesen 

(Co-Principal 

Investigator) 

UC Riverside 

CE-CERT 

1084 Columbia Avenue 

Riverside, CA 92507 

(909) 781-5676 

(Fax) (909) 781-5790 

tonnesen@cert.ucr.edu

Key ENVIRON Participants 

Greg Yarwood ENVIRON 

101 Rowland Way 

Novato, CA 94945 

(415) 899-0704 

gyarwood@environcorp.com

Chris Emery ENVIRON 

101 Rowland Way 

Novato, CA 94945 

(415) 899-0740 

cemery@environcorp.com

Bonyoung Koo ENVIRON 

101 Rowland Way 

(415) 899-0727 

bkoo@environcorp.com

Appendix C.1 - 58
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 1.doc 1-26 

Person & Role Affiliation/Address Contact Information 

Novato, CA 94945 

Edward Tai ENVIRON 

101 Rowland Way 

Novato, CA 94945 

(415) 899-0725 

etai@environcorp.com

Steven Lau ENVIRON 

101 Rowland Way 

Novato, CA 94945 

(415) 899-0739 

slau@environcorp.com

Key Alpine Geophysics Participants 

Dennis McNally Alpine Geophysics, LLC 

7341 Poppy Way 

Arvada, CO 80007 

(303) 421-2211 

(Fax) (303) 421-9553 

dem@alpinegeophysics.com

Cyndi Loomis Alpine Geophysics, LLC 

7341 Poppy Way 

Arvada, CO 80007 

(303) 421-2211 

(Fax) (303) 421-9553 

cfl@alpinegeophysics.com

Greg Stella Alpine Geophysics, LLC 

387 Pollard Mine Road 

Burnsville, NC 28714 

(828) 675-9045 

gms@alpinegeophysics.com

UCR CE-CERT Participants 

Zion Wang UC Riverside 

CE-CERT 

1084 Columbia Avenue 

Riverside, CA 92507 

(909) 781-5655 

zsw@cert.ucr.edu

Bill Carter UC Riverside 

CE-CERT 

1084 Columbia Avenue 

Riverside, CA 92507 

(909) 781-5797 

carter@cert.ucr.edu

Bo Wang UC Riverside 

CE-CERT 

1084 Columbia Avenue 

Riverside, CA 92507 

(909) 781-5680 

bwang@cert.ucr.edu

Chao-Jung Chien UC Riverside 

CE-CERT 

1084 Columbia Avenue 

Riverside, CA 92507 

(909) 781-5666 

chien@cert.ucr.edu

Glen Kaukola UC Riverside 

CE-CERT 

1084 Columbia Avenue 

Riverside, CA 92507 

(909) 781-5630 

glen@cert.ucr.edu

Appendix C.1 - 59
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-1 

2.0 MODEL SELECTION 

This chapter introduces the regional meteorological, emissions and air quality models to 

be used in the annual PM/regional haze modeling for VISTAS Phase II. The specific science 

configurations for each modeling system are identified and discussed briefly, where necessary. 

Although the configurations of each modeling system have been selected as the culmination of 

the Phase I modeling, there remains the possibility that certain algorithms and parameter settings 

may still be updated in the establishment of the final annual 2002 base case simulation and 

model performance testing—the first major modeling activity in Phase II to be completed in 

early 2004. The Phase II modeling team will remain alert to progressive model code 

improvements, data base refinements, and emergent analysis procedures throughout the entire 

activity. For example a major update in the CMAQ code is expected to be released around June 

2004 that would require a rerunning of the initial CMAQ 2002 base case and reanalysis of the 

model performance evaluation. Notable limitations of the models relevant to their intended 

purpose in VISTAS are identified. We conclude with a general overview of the input 

requirements for each system with more details provided in chapter 5. 

2.1 Recommended Models 

Based on the Phase I findings, VISTAS selected the following models for use in 

modeling particulate matter (PM) and regional haze in the Southeast under Phase II: 

3⁄4 MM5: The Pennsylvania State University/National Center for Atmospheric Research 

(PSU/NCAR) Mesoscale Meteorological Model (MM5) is a nonhydrostatic, 

prognostic meteorological model routinely used for urban- and regional-scale 

photochemical, fine particulate, and regional haze regulatory modeling studies. 

 

3⁄4 SMOKE: The Sparse Matrix Operator Kernel Emissions (SMOKE) modeling system 

is an emissions modeling system that generates hourly gridded speciated emission 

inputs of mobile, nonroad, area, point, fire and biogenic emission sources for 

photochemical grid models. 

3⁄4 CMAQ: EPA’s Models-3/Community Multiscale Air Quality (CMAQ) modeling 

system is a ‘One-Atmosphere’ photochemical grid model capable of addressing 

ozone, particulate matter (PM), visibility and acid deposition at regional scale for 

periods up to one year. 

In addition, alternative models may also be applied as part of Phase II modeling to corroborate 

the CMAQ analyses such as: 

3⁄4 CAMx: ENVIRON’s Comprehensive Air Quality Model with Extensions (CAMx) 

modeling system is also a state-of-science ‘One-Atmosphere’ photochemical grid 

model capable of addressing ozone, particulate matter (PM), visibility and acid 

deposition at regional scale for periods up to one year. Its use in Phase II will likely 

be as a corroborative, diagnostic tool and is currently an optional task (see Appendix 

A). 

Appendix C.1 - 60
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-2 

3⁄4 CMAQ – AIM or CMAQ-MADRID: These two models are variations of CMAQ 

that utilize a sectional treatment of PM size distribution and have alternative science 

options for some aerosol processes. They could also be used in Phase II as 

corroborative diagnostic tools. 

Application of the MM5 in Phase II is being performed by BAMS under contract to SESARM. 

Details of the model application and evaluation procedures being carried out by BAMS may be 

found at http://www.baronams.com/projects/VISTAS/. For completeness, in this chapter we 

describe all four regional modeling systems and their intended use in the Phase II annual 

modeling. 

2.2 MM5 Mesoscale Prognostic Model 

Over the past decade, researchers at the Pennsylvania State University (PSU) and the 

National Center for Atmospheric Research (PSU/NCAR) have collaborated in the refinement 

and extension of the PSU Mesoscale Meteorological Model leading to the current version of the 

system, MM5 (ver 3.6, MPP). Originally developed in the 1970s at PSU and first documented 

by Anthes and Warner (1978), the MM5 modeling system maintains its status as a state-of-thescience model through enhancements provided by a broad user community (e.g., Chen and 

Dudhia, 2001; Stauffer and Seaman, 1990, 1991; Xiu and Pleim, 2000). The MM5 modeling 

system is routinely employed in forecasting projects as well as refined investigations of severe 

weather. Utilization of MM5 within air quality applications is also a common practice. In recent 

years, the MM5 modeling system has been successfully applied in continental scale annual 

simulations for the years 1996 (Olerud et al., 2000), 2001 (McNally and Tesche, 2003), and 2002 

(Johnson, 2003). Due to its ongoing scientific development worldwide, extensive historical 

applications, broad user community support, public availability, and established performance 

record compared with other applications-oriented prognostic models, VISTAS selected the MM5 

as the preferred meteorological model. This section provides an overview of the MM5 and its 

data input requirements. 

2.2.1 MM5 Overview 

The non-hydrostatic MM5 model (Dudhia, 1993; Grell et al., 1994) is a threedimensional, limited-area, primitive equation, prognostic model that has been used widely in 

regional air quality model applications (Seaman, 2000). The basic model has been under 

continuous development, improvement, testing and open peer-review for more than 20 years 

(Anthes and Warner, 1978; Anthes et al., 1987) and has been used world-wide by hundreds of 

scientists for a variety of mesoscale studies, including cyclogenesis, polar lows, cold-air 

damming, coastal fronts, severe thunderstorms, tropical storms, subtropical easterly jets, 

mesoscale convective complexes, desert mixed layers, urban-scale modeling, air quality studies, 

frontal weather, lake-effect snows, sea-breezes, orographically induced flows, and operational 

mesoscale forecasting. 

MM5 is based on the prognostic equations for three-dimensional wind components (u, v, 

and w), temperature (T), water vapor mixing ratio (qv), and the perturbation pressure (p'). Use of 

a constant reference-state pressure increases the accuracy of the calculations in the vicinity of 

steep terrain. The model uses an efficient semi-implicit temporal integration scheme and has a 

nested-grid capability that can use up to ten different domains of arbitrary horizontal and vertical 

Appendix C.1 - 61
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-3 

resolution. The interfaces of the nested grids can be either one-way or two-way interactive. The 

model is also capable of using a hydrostatic option, if desired, for coarse-grid applications. 

 

MM5 uses a terrain-following non-dimensionalized pressure, or "sigma", vertical 

coordinate similar to that used in many operational and research models. In the non-hydrostatic 

MM5 (Dudhia, 1993), the sigma levels are defined according to the initial hydrostaticallybalanced reference state so that the sigma levels are also time-invariant. The gridded 

meteorological fields produced by MM5 are directly compatible with the input requirements of 

‘one atmosphere’ air-quality models using this coordinate (e.g., CMAQ). MM5 fields can be 

easily used in other regional air quality models with different coordinate systems (e.g., CAMx) 

by performing a vertical interpolation, followed by a mass-conservation re-adjustment. 

Distinct planetary boundary layer (PBL) parameterizations are available for air-quality 

applications, both of which represent sub-grid-scale turbulent fluxes of heat, moisture and 

momentum. These parameterizations employ various surface energy budget equations to 

estimate ground temperature (Tg), based on the insolation, atmospheric path length, water vapor, 

cloud cover and longwave radiation. The surface physical properties of albedo, roughness 

length, moisture availability, emissivity and thermal inertia are defined as functions of land-use 

for numerous categories via a look-up table. One scheme uses a first-order eddy diffusivity 

formulation for stable and neutral environments and a modified first-order scheme for unstable 

regimes. The other uses a prognostic equation for the second-order turbulent kinetic energy, 

while diagnosing the other key boundary layer terms. 

Initial and lateral boundary conditions are specified from mesoscale three-dimensional 

analyses performed at 12-hour intervals on the outermost grid mesh selected by the user. 

Additional surface fields are analyzed at three-hour intervals. A Cressman-based technique is 

used to analyze standard surface and radiosonde observations, using the National Meteorological 

Center's (NMC) spectral analysis as a first guess. The lateral boundary data are introduced into 

MM5 using a relaxation technique applied in the outermost five rows and columns of the most 

coarse grid domain. 

A major feature of the MM5 is its use of state-of-science methods for Four Dimensional 

Data Assimilation (FDDA). The theory underlying this approach and details on how it has been 

applied in a variety of applications throughout the country are described in depth elsewhere 

(Stauffer and Seaman, 1990, 1991; Seaman et al., 1992, 1997). 

 Results of detailed performance evaluations of the MM5 modeling system in regulatory 

air quality application studies have been widely reported in the literature (e.g., Emery et al., 

1999; Tesche et al., 2000, 2003) and many have involved comparisons with other prognostic 

models such as RAMS and SAIMM. The MM5 enjoys a far richer application history in 

regulatory modeling studies compared with RAMS or other models. Furthermore, in evaluations 

of these models in over 60 recent regional scale air quality application studies since 1995, we 

have generally found that MM5 model tends to produce somewhat better photochemical model 

inputs than alternative models. For these and other reasons set forth in the MM5 modeling 

protocol developed by BAMS (Olerud and Sims, 2003), MM5 was selected as the 

meteorological modeling system for the VISTAS study. 

Appendix C.1 - 62
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-4 

2.2.2 MM5 Configuration for Phase II Modeling 

 Based on the extensive sensitivity testing carried out by Olerud and Sims (2003), the 

MM5 (ver 3.6, MMP) configuration to be used by BAMS modelers in the Phase II modeling will 

consist of the following (see Table 2-1 for more details): 

 > Nested 36/12 km grids, with 34 vertical layers; 

 > Two way nesting, no feedback; 

 > Initialization and boundary conditions from Eta analysis fields; 

 > Pleim-Xiu (P-X) soil model; 

 > Asymmetric Convective Mixing (ACM) PBL model; 

 > Kain-Fritsch 2 cumulus parameterization; 

 > Mixed phase (Reisner 1) cloud microphysics; 

 > Raptid Radiative Transfer Model (RRTM) radiation; 

 > Snow effect turned on; 

> ETA model sea surface temperature; 

 > 24-category USGS vegetation data sets; 

 > Thermal roughness by the Garratt method; and 

 > Standard FDDA analysis nudging on 36 km and 12 km grid nests. 

2.3 SMOKE Emissions Modeling System 

2.3.1 SMOKE Overview 

The Sparse Matrix Operator Kernel Emissions (SMOKE) Emissions Processing System 

Prototype was originally developed at MCNC (Coats, 1995; Houyoux and Vukovich, 1999). As 

with most ‘emissions models’, SMOKE is principally an emission processing system and not a 

true emissions modeling system in which emissions estimates are simulated from ‘first 

principles’. This means that, with the exception of mobile and biogenic sources, its purpose is to 

provide an efficient, modern tool for converting emissions inventory data into the formatted 

emission files required by an air quality simulation model. For mobile sources, SMOKE actually 

simulates emissions rates based on input mobile-source activity data, emission factors and 

outputs from transportation travel-demand models. 

SMOKE was originally designed to allow emissions data processing methods to utilize 

emergent high-performance-computing (HPC) as applied to sparse-matrix algorithms. Indeed, 

SMOKE is the fastest emissions processing tool currently available to the air quality modeling 

community. The sparse matrix approach utilized throughout SMOKE permits both rapid and 

flexible processing of emissions data. The processing is rapid because SMOKE utilizes a series 

of matrix calculations instead of less efficient algorithms used in previous systems. The 

processing is flexible because the processing steps of temporal projection, controls, chemical 

speciation, temporal allocation, and spatial allocation have been separated into independent 

operations wherever possible. The results from these steps are merged together at a final stage of 

processing. 

SMOKE supports area, mobile, fire and point source emission processing and also 

includes biogenic emissions modeling through a rewrite of the Biogenic Emission Inventory 

System, version 3 (BEIS3) (see, http://www.epa.gov/ttn/chief/software.html#pcbeis). SMOKE 

Appendix C.1 - 63
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-5 

has been available since 1996, and it has been used for emissions processing in a number of 

regional air quality modeling applications. In 1998 and 1999, SMOKE was redesigned and 

improved with the support of the U.S. Environmental Protection Agency (EPA), for use with 

EPA's Models-3/CMAQ (http://www.epa.gov/asmdnerl/models3). The primary purposes of the 

SMOKE redesign were support of: (a) emissions processing with user-selected chemical 

mechanisms and (b) emissions processing for reactivity assessments. 

SMOKE contains a number of major features that make it an attractive component of the 

VISTAS modeling system (Seppanen, 2003). The model supports a variety of input formats from 

other emissions processing systems and models including the Inventory Data Analyzer (IDA), 

Emissions Modeling System—2003 (EMS-2003), and the Emissions Preprocessor System 2.x 

(EPS2.x). It supports both gridded and county total land use scheme for biogenic emissions 

modeling. Although not necessary in VISTAS, SMOKE can accommodate emissions files from 

up to 10 countries and any pollutant can be processed by the system. 

Recent computational improvements to SMOKE include: (a) enhanced disk space 

requirements compared with other emissions processing software, (b) run-time memory 

allocation, eliminating any need to recompile the programs for different inventories, grids, or 

chemical mechanisms, and (c) updated I/O API libraries. A number of science features have 

been incorporated into the latest version of SMOKE (ver. 2.0) including: (a) any chemical 

mechanism can be used to partition pollutants to model species, as long as the appropriate input 

data are supplied, (b) integration with the MOBILE6.2 on-road mobile source emissions model 

including link based processing, (c) support of plume-in-grid (PiG) processing, (d) integration of 

the BEIS3 emissions factors in SMOKE. 

Notable features of SMOKE from an applications standpoint include: (a) improved 

control strategy input formats and designs, (b) control strategies can include changes in the 

reactivity of emitted pollutants, a useful capability, for example, when a solvent is changed in an 

industrial process, (c) no third party software is required to run SMOKE, although some input 

file preparation may require other software, (d) fewer SMOKE programs than the SMOKE 

prototype because programs were combined where possible to be used for multiple source 

categories, (e) integration with Models-3 file formats and settings, (f) improved data file formats, 

(g) support of various air quality model emissions input formats (e.g., CMAQ, MAQSIP, UAMIV, UAM-V, REMSAD and CAMx), (h) enhanced quality assurance pre- and post-processing, 

(h) fully integrated with Models-3, which will provide the SMOKE Tool for SMOKE input file 

preparation, (i) enhanced treatment of growth and control factors, (j) improved emissions 

reporting and QA capabilities, and (k) improved temporal allocation. 

Continuing model development activities with SMOKE now occur out of the University 

of North Carolina (UNC) Carolina Environmental Program (CEP). SMOKE beta Version 1.5b 

was released 17 March 2003 and this is the version employed in Phase I. Several patches to the 

model were provided during the summer of 2003, and SMOKE ver2.0 was released on 30 Sept 

’03. Barring unanticipated difficulties with this release, the Phase II modeling will employ the 

SMOKE Ver 2.0. The SMOKE executables, scripts and databases may be downloaded through 

the Community Modeling and Analysis (CMAS) center’s Model Clearinghouse at 

http://www.cmascenter.org/modelclear.shtml. The SMOKE user’s guide is available online at 

the main SMOKE website, http://www.cep.unc.edu/empd/products/smoke. 

Appendix C.1 - 64
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-6 

2.3.2 SMOKE Configuration for Phase II Modeling 

As an emissions processing system, SMOKE has far fewer ‘science configuration’ 

options compared with the MM5 and CMAQ models. For a thorough characterization of the 

methods that will be used to exercise the SMOKE system for the annual 2002 emissions 

processing, see section 5.2, “Development of Emissions Model Inputs and Resultant 

Inventories”. Table 2-1 summarizes the version of the SMOKE system to be used and the 

sources of data to be employed in constructing the required modeling inventories. 

2.4 CMAQ Modeling System 

2.4.1 CMAQ Overview 

For more than a decade, EPA has been developing the Models-3 Community Multiscale 

Air Quality (CMAQ) modeling system with the overarching aim of producing a ‘OneAtmosphere’ air quality modeling system capable of addressing ozone, particulate matter (PM), 

visibility and acid deposition within a common platform (Dennis, et al., 1996; Byun et al., 1998a; 

Byun and Ching, 1999, Pleim et al., 2003). The original justification for the Models-3 

development emerged from the challenges posed by the 1990 Clean Air Act Amendments and 

EPA’s desire to develop an advanced modeling framework for ‘holistic’ environmental modeling 

utilizing state-of-science representations of atmospheric processes in a high performance 

computing environment (Ching, et al., 1998). EPA completed the initial stage of development 

with Models-3 and released the Community Multi-Scale Air Quality model (CMAQ) in mid1999 as the initial operating science model under the Models-3 framework (Byun et al., 1998b). 

The most recent rendition is CMAQ version 4.3, publicly released late-summer 2003 and is the 

version used in the VISTAS Phase I modeling (Although the initial Phase I modeling runs used 

CMAQ version 4.3beta). A major update to CMAQ is expected around summer of 2004. 

CMAQ consists of a core Chemical Transport Model (CTM) and several pre-processors 

including the Meteorological-Chemistry Interface Processor (MCIP), initial and boundary 

conditions processors (ICON and BCON) and a photolysis rates processor (JPROC). EPA is 

continuing to improve and develop new modules for the CMAQ model and typically provides a 

new release each year. In the past EPA has also provides patches for CMAQ as errors are 

discovered and corrected. More recently EPA has funded the Community Modeling and 

Analysis Systems (CMAS) center to support the coordination, update and distribution of the 

Models-3 system. 

A number of features in CMAQ’s theoretical formulation and technical implementation 

make the model well-suited for annual PM modeling. In CMAQ, the modal approach has been 

adapted to dynamically represent the PM size distribution using three log-normal modes (2 fine 

and 1 coarse). Transfer of mass between the aerosol and gas phases is assumed to be in 

equilibrium and all secondary aerosol (sulfate, nitrate, SOA) is assumed to be in the fine modes. 

The thermodynamics of inorganic aerosol composition are treated using the ISORROPIA 

module. Aerosol composition is coupled to mass transfer between the aerosol and gas phases. 

For aqueous phase chemistry, the RADM model is currently employed. This scheme includes 

oxidation of SO2 to sulfate by ozone, hydrogen peroxide, oxygen catalyzed by metals and 

radicals. The impact of clouds on the PM size distribution is treated empirically. For wet 

deposition processes, CMAQ uses the RADM/RPM approach. Particle dry deposition is 

Appendix C.1 - 65
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-7 

included as well. CMAQ contains three options for treating secondary organic aerosol (SOA), 

latest being the Secondary Organic Aerosol Model (SORGAM) that was updated in August 2003 

to be an reversible semi-volatile scheme whereby VOCs can be converted to condensable gases 

that can then form SOA and then evaporate back into condensable gases depending on 

atmospheric conditions. 

 Pleim et al., (2003) describe the newest features implemented in CMAQ ver 4.3 (released 

August 2003). Many of these features are mentioned above; others pertain to details in the 

model’s chemistry, transport, computer implementation, and model operation. Table 2-3 

highlights the major options in CMAQ (ver 4.3) for different processes and compares them with 

the recently released CAMx (ver 4.3) model in Table 2-4, which is discussed later in this chapter. 

2.4.2 CMAQ Configuration for Phase II Modeling 

 One of the principal accomplishments in the Phase I modeling was the identification and 

justification of the CMAQ science options recommended for Phase II modeling. We 

summarized the Phase I findings briefly in the introduction. In this section we identify the main 

science options we recommend for annual PM modeling with CMAQ. In particular, we propose 

to run CMAQ (ver 4.3) with the base configuration as shown in Table 2-3. The model would be 

set up and exercised on the same nested 36/12 km grid domain used in Phase I, employing oneway grid nesting. That is, boundary conditions for the 12 km grid simulation are extracted from 

the 36 km run using the CMAQ BCON processor. A total of 19 vertical layers would be 

implemented, extending up to a region top of 100 mb (approximately 15 km AGL). 

The PPM advection solver would be used along with the spatially varying (Smagorinsky) 

horizontal diffusion approach and K-theory for vertical diffusion. MM5 meteorological output 

based on the Pleim-Xiu Land-Surface Model (LSM) and the ACM planetary boundary layer 

(PBL) scheme will be used (see Table 2-1) and the recently updated CMAQ MeteorologicalChemistry Interface Processor (MCIP2.2) would process the MM5 data using the “pass through” 

option. The CB4 gas-phase, RADM aqueous-phase, and AERO3/ISORROPIA aerosol 

chemistry schemes are recommended for use in the initial CMAQ 2002 modeling. Treatment of 

reversible secondary organic aerosols would be simulated by the SORGAM implementation in 

CMAQ (ver 4.3). Under the Phase I modeling, VISTAS evaluated three photochemical 

mechanisms: CB4, CB4-2002 and SAPRC99. CB4-2002 produced nearly identical results as 

CB4 but took much longer to run since it is only implemented in the slower SMVGEAR 

chemistry solver, compared to CB4 that is also implemented in the faster EBI chemistry solver. 

Thus, CB4-2002 was dropped from consideration in Phase II. The Phase I comparisons of CB4 

and SAPRC99 found they produced mostly similar but different model performance. However, 

one mechanism was not performing better than the other across all species, sites and periods. 

The Phase I testing only evaluated the mechanism’s base case performance, not their response to 

emission reductions. Given that CB4 runs twice as fast as SAPRC99, for Phase II it was decided 

to perform initial 2002 CMAQ modeling using CB4 and evaluate CB4 and SAPRC99 responses 

to emission reductions using the Phase I episodes. If SAPRC99 is deemed to be performing 

better than CB4 it would be used for the revised 2002 CMAQ base case simulation in September 

2004. 

Appendix C.1 - 66
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-8 

2.5 Alternative Models 

 EPA’s guidance on model selection for PM2.5 SIPs and Regional Haze “reasonable 

progress demonstrations” do not identify a preferred photochemical grid modeling system, 

recognizing that at present there is “no single model which has been extensively tested and 

shown to be clearly superior or easier to use than several alternatives” (EPA, 2001, pg. 169.) 

The agency recommends that models used for PM2.5 SIPS or RH reasonable progress 

requirements should meet the requirements for alternative models. The CMAQ, CMAQ-AIM 

and CAMx modeling systems all meet these requirements. 

 We believe that there is potentially significant value in including an alternative regional 

modeling system or multiple systems as an adjunct to the SMOKE/MM5/CMAQ system 

proposed as the mainstay of the Phase II analyses. Our testing of the CAMx model in Phase I 

and other recent PM2.5/regional haze applications demonstrates that the model is capable of 

producing results of comparable accuracy and reliability as CMAQ, given similar effort in 

preparing model inputs, diagnosing and improving model performance and in conducting 

weight-of-evidence investigations. The Phase I testing of CMAQ-AIM model raised questions 

on whether it was performing correctly, the differences with CMAQ could not be explained 

based on their differences in formulation with CMAQ-AIM performing poorer than CMAQ. 

Accordingly, at this time we cannot recommend adopting CMAQ-AIM in Phase II and 

recommend VISTAS consider the parallel use of CAMx in the Phase II program for seven 

specific purposes: 

3⁄4 Diagnosis: To serve as an efficient diagnostic tool addressing model performance 

issues that may arise in the establishment of the CMAQ annual 2002 and episodic 

base cases. CAMx’s suite of diagnostic probing tools plus it’s flexi-nesting 

algorithms make it an attractive tool for assisting in the diagnosis of CMAQ 

performance should unexpected situation arise; 

3⁄4 Model Evaluation Corroboration: To provide corroboration of the base case model 

performance evaluation exercises to be performed with CMAQ and help identify any 

compensatory errors in the MM5/SMOKE/CMAQ modeling system; 

3⁄4 Emissions Control Response Corroboration: To provide corroboration of the 

response of the CMAQ modeling system to generic and specific future year emissions 

changes on modeled gas-phase and particulate aerosol concentrations and resultant 

regional haze impacts; 

3⁄4 Quantification of Model Uncertainty: To provide one estimate of the range of 

uncertainty that attends statements of CMAQ model performance in the annual and 

episodic base case simulations, and in the estimate of PM2.5 and visibility reductions 

associated with future emissions change scenarios; 

3⁄4 Alternative Science: CAMx contains alternative science algorithms that may 

elucidate model performance issues with CMAQ or provide an alternative approach 

for simulating aerosols. 

Appendix C.1 - 67
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-9 

3⁄4 Consistency with Other RPOs: The Midwest RPO (MWRPO) may end up using 

CAMx for their regional haze modeling. As sources in the MWRPO likely influence 

visibility at Class I areas in VISTAS and vice versa, having results from a common 

model would be useful for reconciling any differences. 

3⁄4 Backup Contingency: To provide a ‘backstop’ model to CMAQ in the event that 

unforeseen difficulties with the primary model make it necessary to switch to an 

alternative ‘One-Atmosphere’ model at some point during Phase II. 

The benefits of employing a pair of complimentary state-of-science air quality models are thus 

quite significant and well worth considering. Especially considering that the same MM5 output 

(through MM5CAMx) and SMOKE output and CMAQ IC/BC files (through CMAQ-to-CAMx 

emissions and IC/BC converters) can be used to operate CAMx without performing any 

additional meteorological or emissions modeling. Accordingly, below we provide an overview 

of the CAMx regional photochemical/PM modeling system and the science options 

recommended for use in Phase II. 

2.5.1 CAMx Overview 

The Comprehensive Model with Extensions (CAMx) modeling system is a publicly 

available (www.camx.com) three-dimensional multi-scale photochemical/aerosol grid modeling 

system that is developed and maintained by ENVIRON International Corporation. CAMx was 

developed with all new code during the late 1990s using modern and modular coding practices. 

This has made the model an ideal platform for the extension to treat a variety of air quality issues 

including ozone, particulate matter (PM), visibility, acid deposition, and air toxics. The flexible 

CAMx framework has also made it a convenient and robust host model for the implementation 

of a variety of mass balance and sensitivity analysis techniques including Process Analysis (IRR 

and IPR), Decoupled Direct Method (DDM), and the Ozone Source Apportionment Technology 

(OSAT). Designed originally to address multiscale ozone issues from the urban- to regionalscale, CAMx has been widely used in recent years by a variety regulatory agencies for 1-hr and 

8-hr ozone SIP modeling studies. Key attributes of the CAMx model for simulating gas-phase 

chemistry include the following: 

3⁄4 Two-way grid nesting that supports multi-levels of fully interactive grid nesting (e.g., 

36/12/4/1.33 km); 

 

3⁄4 CB4 or SAPRC99 Chemical Mechanisms; 

3⁄4 Two chemical solvers, the CAMx Chemical Mechanism Compiler (CMC) Fast 

Solver or the highly accurate Implicit Explicit Hybrid (IEH) solver; 

3⁄4 Multiple numerical algorithms for horizontal transport including the Piecewise 

Parabolic Method (PPM), Bott, and Smolarkiewicz advection solvers; 

3⁄4 Subgrid-scale Plume-in-Grid (PiG) algorithm to treat the near-source plume dynamics 

and chemistry from large NOx point source plumes; 

Appendix C.1 - 68
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-10 

3⁄4 Ability to interface with a variety of meteorological models including the MM5 and 

RAMS prognostic hydrostatic meteorological models and the CALMET diagnostic 

meteorological model (others also compatible); 

3⁄4 The Ozone Source Apportionment Technology (OSAT) ozone apportionment 

technique that identifies the ozone contribution due to geographic source regions and 

source categories (e.g., mobile, point, biogenic, etc.); and 

3⁄4 The Decoupled Direct Method (DDM) sensitivity method is implemented for 

emissions and IC/BC to obtain first-order sensitivity coefficients for all gas-phase 

species. 

3⁄4 Treatment of particulate matter (PM) using an empirical aerosol thermodynamics 

algorithm. 

Culminating extensive model development efforts at ENVIRON and other participating groups, 

the CAMx (ver 4.3+) code was released in the autumn of 2003 as a truly “One-Atmosphere’ 

models that rigorously integrates the gas-phase ozone chemistry with the simulation of primary 

and secondary fine and course particulate aerosols. This extension of CAMx to treat PM 

involved the addition of several science modules to represent important physical processes for 

aerosols. Noteworthy among these are: 

3⁄4 Two separate treatments of particulate matter (PM), Mechanism 4 (M4) “oneatmosphere” treatment uses two size sections and science modules comparable to 

CMAQ (e.g., RADM aqueous-phase chemistry and ISORROPIA equilibrium) and a 

multi-section “full-science” approach using aerosol modules developed at Carnegie 

Mellon University (CMU). 

 

3⁄4 Size distribution is represented using the Multi-component Aerosol Dynamics Model 

(MADM), which uses a sectional approach to represent the aerosol particle size 

distribution (Pilinis et al., 2000). MADM treats the effects of 

condensation/evaporation, coagulation and nucleation upon the particle size 

distribution. 

3⁄4 Inorganic aerosol thermodynamics can be represented using ISORROPIA (Nenes et 

al, 1998; 1999) equilibrium approach within MADM, or a fully dynamic or hybrid 

approach can also be used. 

3⁄4 Secondary organic aerosol thermodynamics are represented using the semi-volatile 

scheme of Strader and co-workers (1999). 

3⁄4 Aqueous-phase chemical reactions are modeled either using the RADM module (like 

CMAQ) or the Variable Size-Resolution Model (VRSM) of Fahey and Pandis (2001), 

which automatically determine whether water droplets can be represented by a single 

‘bulk’ droplet-size mode or whether it is necessary to use fine and coarse droplet-size 

modes to account for the different pH effects on sulfate formation. 

Appendix C.1 - 69
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-11 

CAMx (ver 4.3+) provides two key options to users interested in simulating PM. For CPUefficient annual PM modeling applications, CAMx may be run using Mechanism 4 (M4) with 

only two size sections (fine and coarse) and the efficient RADM bulk aqueous-phase module (as 

used in CMAQ). Alternatively, more rigorous aerosol simulations (perhaps for shorter episode) 

may be addressed using the version that treats N-size sections (N is typically 10) and the 

rigorous, but computationally-extensive CMU multi-section aqueous-phase chemistry module. 

2.5.2 CAMx Configuration for Phase II Modeling 

We recommend exercising CAMx (ver 4.3) as a companion model to CMAQ using as 

many similar science options and input data sets as possible. However, in some instances, the 

CMAQ and CAMx model development teams chose different options for characterizing physical 

and chemical processes, or for implementing the governing equations on modern parallel 

computers. In these cases, we will utilize the science configurations embodied in the current 

release of CAMx. At this time VISTAS has not budgeted any resources in Phase II for CAMx 

modeling, however it remains an option if desired at a later date. 

Table 2-4 lists the main CAMx configurations recommended for Phase II. The latest 

version of CAMx (ver 4.3) will be employed and the model will be set up and exercised on the 

same 36/12 km grid as CMAQ. However, CAMx would be run using two-way grid nesting. The 

base configuration of CAMx would use 19 vertical layers that exactly match those used by 

CMAQ. The PPM advection solver would be used along with the spatially varying 

(Smagorinsky) horizontal diffusion approach. Vertical diffusion in CAMx would be modeled by 

K-theory. The MM5 simulation using the Pleim-Xiu Land-Surface Model (LSM) and the ACM 

Planetary Boundary Layer (PBL) scheme would be used in the CAMx base configuration using 

the MM5CAMx processor that is similar to the CMAQ MCIP2.2 “pass through” option of the 

MM5 data invoked. CAMx would be exercised with the CB4 gas-phase, RADM aqueous-phase, 

and CMU/ISORROPIA aerosol chemistry schemes. The SOAP secondary organic aerosol 

scheme would be used for the base configuration in CAMx. 

Note that it may be desirable to exercise CAMx using its “full-science” configuration for 

selected periods to investigative scientific issues that may be of interest that can not be simulated 

by CMAQ, such as: 

3⁄4 The full sectional approach could be used to determine whether allowing secondary 

PM to grow into the coarse mode affects the model estimates; 

 

3⁄4 Model could be exercised with chemical active Sea Salt emissions, this could be 

important for fine particulate and visibility at key coastal sites in the VISTAS 

domain, especially when looking at clean days or natural background; and 

3⁄4 The full sectional aqueous-phase chemistry module may be important for sulfate 

formation. 

Appendix C.1 - 70
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-12 

2.6 Model Limitations 

All mathematical models possess inherent limitations owing to the necessary 

simplifications and approximations made in formulating the governing equations, implementing 

them for numerical solution on fast computers, and in supplying them with input data sets and 

parameters that are themselves approximations of the full state of the atmosphere and emissions 

processes. Below, we list the more important limitations of the various modeling systems to be 

employed in VISTAS Phase II 

2.6.1 MM5 

In Phase I, four different configurations of the MM5 Land Soil Model (LSM) and 

Planetary Boundary Layer (PBL) were evaluated. Depending on the meteorological variable 

(e.g., winds, temperature, moisture) and location (e.g., mountains, coastal, east, west) different 

LSM_PBL configurations performed better. The PX_ACM LSM_PBL configuration was 

selected because it consistency was near the top performing configuration in the VISTAS region 

across variables and locations and was never the worst performing configuration. However, 

there are numerous limitations in the MM5 with the LSM and PBL treatment being some of the 

most important. The MM5 PX_ACM frequently predicts very low PBL heights that can appear 

as “holes” in the spatial distribution of PBL heights that don’t appear physically realistic and 

may affect air quality modeling. Although the MM5 P_ACM configuration model performance 

in the VISTAS region mostly met performance benchmarks, the performance was much worst in 

the western U.S. In addition, there is a stochastic component of real world meteorology that is 

not captured by MM5. For example, for some ozone episodes stagnation is an important 

attribute that MM5 fails to simulate well as it tries to organize the flow fields. The MM5 model 

represents approximately 20 years of development by various researchers and is showing its age. 

The many limitations in MM5 have spawned the development of a new meteorological model, 

the Weather Research Forecast (WRF) model. However, the WRF model will not be used or 

tested in the VISTAS Phase II modeling. 

2.6.2 SMOKE 

In Phase I a number of undocumented features of the SMOKE 1.5b version necessitated 

re-runs of the emissions processing software to overcome errors and/or ambiguities in source 

documentation and QA reporting. It is unclear whether similar conditions will be encountered 

with the SMOKE 2.0 release. As a full software release, rather than a “beta” version, we expect 

the SMOKE 2.0 to be more robust and fully documented than the SMOKE 1.5b release. 

However, as a newly released software system, there is the potential for errors and/or ambiguities 

to affect the emissions modeling schedule. Should problems arise or issues be encountered 

which would require additional SMOKE runs or potential SMOKE modifications or alternate 

modeling methods, we will immediately notify VISTAS and make recommendations for 

resolving the issues. Upon receipt of technical direction from VISTAS, appropriate corrective 

action will be taken. 

Features are continuing to be developed in the SMOKE emissions model. As it is not as mature 

as some other emission models (e.g., EMS, EPS, etc.) it does not include as many features. We 

Appendix C.1 - 71
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-13 

will keep abreast of SMOKE development activities to identify new features that will assist in 

the VISTAS emissions modeling.

2.6.3 CMAQ 

 

Like all air quality models, a major limitation of CMAQ is the emissions, meteorological 

and IC/BC inputs. Key science limitations in the model itself include the nitrate formation 

chemistry. The Phase I testing found the CMAQ nitrate performance suspect with winter 

overestimations and summer underestimations. Other science limitations in the current version 

of CMAQ include inadequate treatment of sea salt and the assumption that all secondary PM is 

in the fine mode. Lack of any two-way grid nesting limits the ability of the model to properly 

resolve point source plumes or urban photochemistry and their effects on more distant Class I 

areas without a prohibitive number of grid cells. Another limitation of CMAQ is the 

computational requirements, including the need of excessive disk space. 

2.6.4 CAMx 

The model inputs are also a major limitation in CAMx. Nitrate formation chemistry is 

also a major limitation, as evident by the Phase I performance. Although CAMx has some more 

advanced science modules available, such as the VSRM aqueous-phase and MADM dynamic 

aerosol modules, for annual modeling these modules are too computationally expensive to use. 

Treatment of clouds and wet deposition is an area of current research that needs to be updated. 

2.7 Model Input Requirements 

Each of the VISTAS modeling system components have significant data base 

requirements. These data needs fall into two categories: those required for model setup and 

operation, and those required for model evaluation testing. Below, we identify the main input 

data base requirements for the meteorological, emissions, and air quality models. 

2.7.1 MM5 

 The databases required to set up, exercise, and evaluate the MM5 model for the annual 

2002 episode consist of various fixed and variable inputs. 

3⁄4 Topography: High resolution (e.g., 30 sec to 5 min) topographic information derived 

from the Geophysical Data Center global data sets from the National Center for 

Atmospheric Research (NCAR) terrain databases are available for prescribing terrain 

elevations throughout the 36 km and 12 km grid domain. 

3⁄4 

> Vegetation Type and Land Use: Vegetation type and land use information on the 36 km 

grid may be developed using the NCAR/PSU 10 min. (~18.5 km) databases while for the 

12 km grids, the United States Geological Survey (USGS) data are available. 

> Atmospheric Data: Initial and boundary conditions to the MM5 may be developed from 

operationally analyzed fields derived from the National Center for Environmental 

Predictions (NCEP) ETA (40 km resolution) following the procedures outlined by 

Stauffer and Seaman (1990). These 3-hr synoptic-scale initialization data the horizontal 

Appendix C.1 - 72
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-14 

wind components (u and v), temperature (T), and relative humidity (RH) at the standard 

pressure levels, plus sea-level pressure (SLP) and ground temperature (Tg). Here, Tg 

represents surface temperature over land and sea-surface temperature over water. 

> Water Temperature: Water temperatures required on both 36 km and 12 km grids can be 

derived from the ETA skin temperature variable. These temperatures are bi-linearly 

interpolated to each model domain and, where necessary, filtered to smooth out 

irregularities. 

> Clouds and Precipitation: While the non-hydrostatic MM5 treats cloud formation and 

precipitation directly through explicit resolved-scale and parameterized sub-grid scale 

processes, the model does not require precipitation or cloud input. The potential for 

precipitation and cloud formation enters through the thermodynamic and cloud processes 

formulations in the model. The only precipitation-related input required is the initial 

mixing ratio field that is developed from the NWS and NMC data sets previously 

discussed. 

> Multi-Scale FDDA: The standard “multi-scale” data assimilation strategy to be used on 

the 36 km and 12 km grids will objectively analyzed three-dimensional fields produced 

every 3-hr from the NWS rawinsonde wind, temperature, and mixing ratio data, and 

similar analyses generated every three hours from the available NWS surface data. 

2.7.2 SMOKE

 

The databases required to set up and operate SMOKE for the 2002 annual simulation are as 

follows: 

 Area Source emissions in IDA format 

 NonRoad source emissions in IDA format 

 Stationary Point Source emissions in IDA format 

 CEM emissions, day specific for 2002 

 Wildfire emissions, day specific for 2002 

 On-road Motor Vehicle VMT and activity data 

 MOBILE6.2 input parameters 

 

Also required for annual modeling are data files specific for: 

 Temporal allocation 

 Spatial allocation 

 Speciation 

Chapter 5 discusses the data input requirements and data sources in detail.

2.7.3 CMAQ 

 

As described in more detail in Chapter 5, the CMAQ Chemical Transport Model (CTM) requires 

the following inputs: 

Appendix C.1 - 73
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-15 

3⁄4 Three-dimensional hourly meteorological fields that will be generated by the CMAQ 

MCIP2.2 processing of the BAMS MM5 output; 

3⁄4 Three-dimensional hourly emissions generated by SMOKE; 

3⁄4 Initial conditions and boundary conditions (IC/BC); 

3⁄4 Topographic information; 

3⁄4 Land use categories; and 

3⁄4 Photolysis rates generated by the CMAQ JPROC processor. 

2.7.4 CAMx 

CAMx model inputs include: 

3⁄4 Three-dimensional hourly meteorological fields generated by MM5CAMx processing 

of the BAMS MM5 output; 

3⁄4 Two-dimensional low-level (surface layer) emissions and elevated point source 

emissions generated by the CMAQ-to-CAMx emissions processor. 

3⁄4 IC/BC inputs generated by the CMAQ-to-CAMx IC/BC processors; 

3⁄4 Photolysis rates look up table; 

3⁄4 Albedo/Haze/Ozone Column input file; 

3⁄4 Land use and topography 

Appendix C.1 - 74
May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-16 Table 2-1. MM5 Meteorological Model Configuration for VISTAS Phase II 

Science Options Configuration Details/Comments 

Model Code MM5 version 3.6 (MPP) Grell et al., 1994 Horizontal Grid Mesh 36/12 km  36 km grid 164 x 128 cells  12 km grid 180 x 189 cells Vertical Grid Mesh 34 layers Vertically varying; sigma pressure coord. Grid Interaction No Feedback IFEED=0 Initialization Eta first guess fields/LittleR Boundary Conditions Eta first guess fields/LittleR Microphysics Reisner I Mixed Ice Look up table Cumulus Scheme Kain-Fritsch 2 On 36/12 Grids Planetary Boundary Layer ACM PBL Radiation RRTM Vegetation Data USGS 24 Category Scheme Land Surface Model P-X Land Surface Model (LSM) Shallow Convection None Sea Surface Temperature Eta Skin Spatially varying Thermal Roughness Garratt Snow Cover Effects None 4D Data Assimilation Analysis Nudging on 36/12 Integration Time Step 90 seconds Simulation Periods Annual 2002 Other episodic periods to be defined Platform Linux Cluster Done at BAMS Run-Time (expected) 10% Real Time Platform Dependent 

Appendix C.1 - 75
May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-17 Table 2-2. SMOKE Emissions Model Configuration for VISTAS Phase II 

Emissions Component Configuration Details/Comments 

Emissions Model SMOKE ver 2.0 Oct '03 release w/ latest updates Horizontal Grid Mesh 36/12 km  36 km grid 148 x 112 cells RPO Unified Grid  12 km grid 168 x 177 cells Area Source Emissions VISTAS Domain: VISTAS State 2002 EI Updated '02 developed by VISTAS states 

Other States: EPA '02 NEI augmented with other 2002 Generated from EPA NEI02 v.1 and RPO interaction Mexico/Canada Emissions: Same as Phase I w/ revisions based on available updates 

On-Road Mobile Sources VISTAS Domain: VISTAS State 2002 EI Updated '02 developed by VISTAS states 

Other States: EPA '02 NEI augmented with other 2002 Generated from EPA NEI02 v.1 and RPO interaction Mexico/Canada Emissions: Same as Phase I w/ revisions based on available updates 

Point Sources VISTAS Domain: VISTAS State 2002 EI Updated '02 developed by VISTAS states and stakeholders 

Other States: EPA '02 NEI augmented with other 2002 Generated from EPA NEI02 v.1 and RPO interaction Mexico/Canada Emissions: Same as Phase I w/ revisions based on available updates 

Off-Road Mobile Sources VISTAS Domain: VISTAS State 2002 EI Updated '02 developed by VISTAS states 

Other States: EPA '02 NEI augmented with other 2002 Generated from EPA NEI02 v.1 and RPO interaction Mexico/Canada Emissions: Same as Phase I w/ revisions based on available updates 

Biogenic Sources VISTAS Domain: VISTAS State 2002 EI Updated '02 developed by VISTAS states 

Other States: EPA '02 NEI augmented with other 2002 Generated from EPA NEI02 v.1 and RPO interaction Mexico/Canada Emissions: Same as Phase I w/ revisions based on available updates 

Temporal Adjustments Seasonal, day, hour Based on latest collected information and CEM-based profiles Chemical Speciation Revised CB4 Chemical Speciation Expected EPA release in Jan '04 Gridding Revised EPA Spatial Surrogates Used Gridding of surrogates from http://www.epa.gov/ttn/chief/emch/spatial/ Growth and Controls VISTAS Special Interest Team Generated Data Base Cases defined by VISTAS Planning Workgroup Quality Assurance QA Tools in SMOKE 2.0 Independent QA with AG's Established Protocol Simulation Periods Annual 2002 Other episodic periods to be defined Platform Dual Athelon 2600 \+ Local 1.8 terabyte Ultra 320 RAID 5 system processing and storage 

Appendix C.1 - 76
May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-18 Table 2-3. CMAQ Air Quality Model Configuration for VISTAS Phase II 

Science Options Configuration Details/Comments 

Model Code CMAQ (ver 4.3) Pleim et al., (2003) Horizontal Grid Mesh 36/12 km 

36 km covering cont. U.S; 12 km covering all VISTAS states 

 36 km grid 148 x 112 cells RPO National Grid  12 km grid 168 x 177 cells Vertical Grid Mesh 19 Layers First 17 layers sync'd w/ MM5 Grid Interaction One-way nesting Initial Conditions 15 days full spin-up Separately run 4 quarters of 2002 Boundary Conditions GEOS-CHEM annual run 

 Initially use 2001 GEOS-CHEM seasonal values; Will be replaced with 2002 GEOSCHEM run. 

Emissions  Baseline Emissions Processing See SMOKE (Ver 2.0) model configuration MM5 Meteorology input to SMOKE, CMAQ  Dust Transport Fraction Applied in emissions before SMOKE Tom Pace updates  NH3 Inventory Adjustment Applied in emissions before SMOKE  Sub-grid-scale Plumes No Plume-in-Grid (PinG) PinG for PM not available yet Chemistry  Gas Phase Chemistry CBM-IV SAPRC99 may be considered in Fall 2004  Aerosol Chemistry AE3/ISORROPIA  Secondary Organic Aerosols Secondary Organic Aerosol Model (SORGAM) Schell et al., (2001)  Aerosol Mass Conservation Patch Yes  Cloud Chemistry RADM-type aqueous chemistry Includes subgrid cloud processes N2O5 Reaction Probability 0.01 – 0.001 Meteorological Processor MCIP ver 2.2 

Includes dry deposition and snow cover updates 

Horizontal Transport  Eddy Diffusivity Scheme K-theory with Kh grid size dependence Multiscale Smagorinsky (1963) approach Vertical Transport  Eddy Diffusivity Scheme K-theory  Diffusivity Lower Limit Kzmin = 1.0 Planetary Boundary Layer No Patch Deposition Scheme M3dry Directly linked to Pleim-Xiu Land Surface Model 

Appendix C.1 - 77
May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-19 Table 2-3. CMAQ Air Quality Model Configuration for VISTAS Phase II 

Science Options Configuration Details/Comments 

parameters 

Numerics  Gas Phase Chemistry Solver Euler Backward Iterative (EBI) solver 

Hertel et al (1993) EBI solver ~ 2x faster than MEBI 

 Horizontal Advection Scheme Piecewise Parabolic Method (PPM) scheme Simulation Periods Annual 2002 Other episodic periods to be defined Integration Time Step TBD 15 minute coupling time step Platform Athlon MP 2600+ Run-Time (expected) 30-60 days Platform Dependent Table 2-4 CAMx Air Quality Model Configuration for VISTAS Phase II 

Science Options Configuration Details 

Model Code CAMx (ver 4.3+) ENVIRON (2003) Horizontal Grid Mesh 36/12 km 

36 km covering cont. U.S; 12 km covering all VISTAS states 

 36 km grid 148 x 112 cells  12 km grid 168 x 177 cells Vertical Grid Mesh 19 Layers 17 Layers sync'd w/ MM5 Grid Interaction Two-way nesting Initial Conditions 15 days full spin-up Separately run 4 quarters of 2002 Boundary Conditions GEOS-CHEM annual run 

 Initially use 2001 GEOS-CHEM seasonal values; revised run will use 2002 GEOS-CHEM run. 

Emissions  Baseline Emissions Processing See SMOKE (Ver 2.0) model configuraton MM5 Meteorology input to SMOKE, CAMx  Dust Transport Fraction Applied in emissions before SMOKE  NH3 Inventory Adjustment Applied in emissions before SMOKE  Sub-grid-scale Plumes No Plume-in-Grid (PinG) PinG for PM not available yet Chemistry  Gas Phase Chemistry CBM-IV with Isoprene updates  Aerosol Chemistry ISORROPIA equilbrium Dynamic and hybrid also available 

Appendix C.1 - 78
May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 2.doc 2-20 Table 2-4 CAMx Air Quality Model Configuration for VISTAS Phase II 

Science Options Configuration Details 

 Secondary Organic Aerosols SOAP  Aerosol Mass Conservation Patch Not identified as needed  Cloud Chemistry RADM-type aqueous chemistry 

Alternative is CMU multi-section aqueous chemistry 

N2O5 Reaction Probability None Meteorological Processor MM5CAMx Horizontal Transport  Eddy Diffusivity Scheme K-theory with Kh grid size dependence Vertical Transport  Eddy Diffusivity Scheme K-Theory  Diffusivity Lower Limit Kzmin = 1.0 Planetary Boundary Layer No Patch Deposition Scheme Wesely Numerics  Gas Phase Chemistry Solver CMC Fast Solver  Horizontal Advection Scheme Piecewise Parabolic Method (PPM) scheme Simulation Periods Annual 2002 Other episodic periods to be defined Integration Time Step Wind speed dependent Platform Athlon MP 2600+ processors Run-Time (expected) 30-60 days Dual Processor 

Appendix C.1 - 79
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 3.doc 3-1 

3.0 EPISODE SELECTION 

This chapter provides a brief overview of the process followed by the VISTAS Technical 

Analysis Workgroup (TAWG) and contractors (including the ENVIRON/UC/Alpine team) in 

determining the most appropriate modeling periods to be used in the Phase II regional haze modeling 

with CMAQ. While the TAWG plans to prepare a formal report documenting these activities, this 

work was not available at the time of this writing. However, much of the technical work 

underpinning the VISTAS episode selection process has been published and peer-reviewed over the 

later stages of Phase I and it is this body of information that we have distilled in preparing the brief 

episode selection summary that follows. 

3.1 Overview of EPA Guidance 

EPA’s current draft guidance on PM2.5/Regional Haze modeling (EPA, 2001) identifies 

specific goals to consider when selecting one or more episodes for use in demonstrating reasonable 

progress in attaining the regional haze NAAQS. However, since there is much in common with the 

goals for selecting episodes for annual and episodic PM2.5 attainment demonstrations as well as 

regional haze, EPA’s guidance addresses all three in a common document. More recently, EPA has 

published an updated summary of PM2.5 and Regional Haze Modeling Guidance (Timin, 2002) that 

serves, in some respects, as in interim placeholder until the final guidance is issued as part of the 

PM2.5/regional haze NAAQS implementation process that is expected during 2004. 

 EPA recommends that episode selection derive from three principal criteria: 

 > A variety of meteorological conditions should be covered; 

> To the extend possible, the modeling data base should include days for which 

extensive data bases (i.e. beyond routine aerometric and emissions monitoring) are 

available; and 

> Sufficient days should be available such that relative reduction factors (RRFs) can be 

based on several (i.e., > 15) days. 

 

For regional haze modeling, the guidance goes further by suggesting that the preferred 

approach is to model a full, representative year (EPA, 2001, pg. 188). Moreover, the required RRF 

values should be based on model results averaged over the 20% worst and 20% best visibility days 

determined for each Class I are based on monitoring data from the 2000 – 2004 baseline period. 

More recent EPA guidance (Timin, 2002) suggests that states should model at least 10 worst and 10 

best visibility days at each Class 1 area. EPA also lists several ‘other considerations’ to bear in 

mind when choosing potential PM/regional haze episodes including: (a) choose periods which have 

already been modeled, (b) choose periods which are drawn from the years upon which the current 

design values are based, (c) include weekend days among those chosen, and (d) choose modeling 

periods that meet as many episode selection criteria as possible in the maximum number of 

nonattainment or Class I areas as possible. 

 VISTAS adopted a logical, stepwise approach in implementing the EPA guidance in order to 

identify the most preferable, representative year for PM/regional haze modeling. These steps are 

Appendix C.1 - 80
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 3.doc 3-2 

summarized briefly in this chapter. 

3.2 Episode Selection Methodology 

 The episode selection methodology entailed coordinated investigations by VISTAS 

contractors and members of the Technical Analysis Workgroup (TAWG). To begin, Olerud (2003b) 

identified important meteorological characteristics and data sets in the VISTAS region directly 

relevant to the evaluation of candidate annual modeling episodes. A separate detailed aerometric 

analysis and pattern recognition study was carried out by ICF (Douglas et al., 2003) to characterize 

the extent to which days from January-March 2002 and January-March 2003 represent the type of 

meteorological conditions that are most frequently associated with high and low values of a haze 

index and PM2.5 concentrations. Using the standard Classification and Regression Tree (CART) 

analysis software, these researchers characterized each of the days within these two three-month 

periods relative to haze and PM2.5 observations as well as other relevant meteorological factors. 

This work was based on previous episode characterization work carried out in support of the 

SEARCH and MARAMA research projects (Douglas et al., 2003). The analysis was also supported 

by climate summaries provided by the North Carolina Division of Air Quality (NCDAQ). 

 In parallel with the CART episode characterization analyses, collaborative investigations by 

VISTAS TAWG participants (e.g., NCDAQ, Georgia DNR, FL DEP) intensively studied the 

availability of PM2.5, meteorological, and emissions data and representativeness of alternative 

Baseline modeling periods from a regulatory standpoint (Boylan et al., Brewer et al., 2003). Daily 

average speciated PM 2.5 monitoring data in the VISTAS region were review intensively, by site 

and by monitoring network (e.g., IMPROVE, SEARCH, STN). In addition to analyzing data 

representativeness, consideration was given to the timeliness with which new data could be obtained 

for Phase II modeling. Also, data availability from parallel meteorological and emissions database 

acquisition efforts were considered both for the VISTAS states as well as for other states and 

countries in the 36 km domain. 

 To assess the representativeness of the regional haze rule five year baseline 2000-2004 

period, temperature and precipitation records were examined over the 108 yr period of record and 

additional high-resolution meteorological analyses were considered (e.g., CART analyses for 

SEARCH and MARAMA sites). For each PM2.5 monitoring site in the VISTAS domain, and for 

each component of PM 2.5, monthly means and deviations (from the monthly mean) were calculated 

for the months within the 2002-2003 period of record. Daily, monthly, and annual trends of PM 2.5 

concentrations across the three year period were subsequently analyzed (Boylan et al., 2003). 

Equally as important, the methodologies and decisions underpinning the episode selection processes 

carried out by other RPOs were also considered (several had already chosen CY-2002 as the 

modeling year). 

3.3 Selection of CY 2002 For VISTAS Phase II 

After a lengthy process of integrated studies, the episode selection process culminated in the 

selection of calendar year (CY) 2002 (1 January through 31 December) as the most current, 

representative, and pragmatic choice for VISTAS Phase II modeling. All of the EPA criteria for 

PM/regional haze episode selection were directly considered in this process together with many 

other pragmatic considerations (e.g., timing of new emissions or aerometric data deliveries by EPA 

Appendix C.1 - 81
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 3.doc 3-3 

or the states to the modeling teams). In addition to selecting CY-2002 as the base year, the merits of 

selecting one or more other shorter duration episode periods (say 2-4 weeks or more in duration) was 

thoroughly considered. Such additional episodes were believed to add potentially valuable insights 

into the various source-receptor relationships influencing PM2.5 and regional haze air quality at 

Class I sites and other locations of interest. No specific decision was made regarding the exact 

number of shorter term episodes (falling outside CY 2002) nor on the duration or specific periods to 

be considered. Work on identifying potentially attractive candidate episodes to include with the 

annual 2002 modeling is ongoing and will be summarize in a subsequent updates to this protocol. In 

particular, ICF has been funded to determine whether any key meteorological conditions are not 

captured by the 2002 model year and if so identify additional modeling episodes outside of 2002 that 

would capture them. Additional modeling periods from 2003 would be ideal due to the presence of 

continuous PM monitoring data at the FOCUS sites (Millbrook, NC; Cape Romain, SC; and GRSM, 

TN) not available in previous years. 

Appendix C.1 - 82
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-1 

4.0 MODELING DOMAINS AND DATA AVAILABILITY 

This chapter summarizes the model domain definitions including the model domain, 

resolution, map projections and nesting schemes for high resolution sub-domains. 

4.1 Horizontal Modeling Domain 

The horizontal domains for each of the models will be identical to those used in the 

Phase I modeling. As in Phase I, a coarse grid continental United States (US) domain with a 36 

km horizontal grid resolution will be used. The CMAQ domain is nested in the MM5 domain. 

The selection of the MM5 domain is described in the VISTAS MM5 modeling protocol (Olerud, 

2003). Figure 4-1 shows the MM5 horizontal domain as the outer most, blue grid. Also shown in 

Figure 4-1 is the CMAQ 36 km domain nested in the MM5 domain. To achieve finer spatial 

resolution in the VISTAS states we will also use a one-way nested high resolution grid with a 12 

km grid resolution. Figure 4-2 shows the 36 km CMAQ continental grid and the high resolution, 

nested 12-km grid in the VISTAS states. Figure 4-3 shows in more detail the 12 km grid for the 

VISTAS region. 

Both MM5 and CMAQ employ the Regional Planning Organization (RPO) unified grid 

definition for the 36 km continental domain. The RPO unified grid consists of a LambertConformal map projection using the map projections parameters listed in Table 4-1. 

Table 4-1. RPO Unified Grid Definition. 

PARAMETER VALUE 

projection Lambert-conformal 

alpha 33 degrees 

beta 45 degrees 

x center 97 degrees 

y center 40 degrees 

The MM5 36 km grid include 164 cells in the east-west dimension and by 128 cells in the 

north-south dimension. The CMAQ 36 km grid include 148 cells in the east-west dimension and 

112 cells in the north-south dimension. Because the MM5 model is also nested in the Eta model, 

there is a possibility of boundary effects near the MM5 boundary that occur as the Eta 

meteorological variables are being simulated by MM5 and must come into dynamic balance with 

MM5’s algorithms. Thus, a larger MM5 domain was selected to provide a buffer of 8 to 9 grid 

cells around each boundary of the CMAQ 36 km domain. This is designed to eliminate any 

errors in the meteorology from boundary effects in the MM5 simulation at the interface of the 

MM5 and Eta models. The buffer region used here exceeds the EPA suggestion of at least 5 grid 

cell buffer at each boundary. 

Table 4-2 lists the number of rows and columns and the definition of the X and Y origin 

(i.e., the southwest corner) for the 36 km and 12 km grids for both MM5 and CMAQ. Note that 

the CMAQ grid is rotated 90 degrees relative to the MM5 grid, so rows and columns are 

reversed. In Table 4-2 “Dot” refers to the grid mesh defined at the vertices of the grid cells while 

“cross” refers to the grid mesh defined by the grid cell centers. Thus, the dimension of the dot 

mesh is equal to the cross mesh plus one. Finally, we note that the grid definition for the CMAQ 

Appendix C.1 - 83
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-2 

Meteorology Chemistry Interface Processor (MCIP) and CMAQ Chemical Transport Model 

(CCTM) are identical. 

Table 4-2. Grid Definitions For MM5 and CMAQ. 

MODEL COLUMNS 

DOT(CROSS) 

ROWS 

DOT(CROSS)

XORIGIN YORIGIN 

MM5 36km 129 (128) 165 (164) -2952000 -2304000 

CMAQ 36km 149 (148) 113 (112) -2736000 -2088000 

MM5 12km 190 (189) 181 (180) 7200 -1656000 

CMAQ 12km 169 (168) 178 (177) 108000 -1620000 

4.2 Vertical Modeling Domain 

The CMAQ vertical structure is primarily defined by the vertical grid used in the MM5 

modeling. The MM5 model employed a terrain following coordinate system defined by pressure, 

using 34 layers that extend from the surface to the 100 mb. Table 4-3 list the layer definitions for 

both MM5 and for CMAQ. As in Phase 1, a layer averaging scheme is adopted for CMAQ to 

reduce the computational cost of the CMAQ simulations. The effects of layer averaging were 

evaluated in the Phase 1 modeling effort and found to have a relatively minor effect on the model 

performance metrics when both the 34 layer and a 19 layer CMAQ models were compared to 

ambient monitoring data. 

Appendix C.1 - 84
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-3 

Figure 4-1. Nesting of 36-km CMAQ Grid in the MM5 36-km Grid. 

Appendix C.1 - 85
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-4 

Figure 4-2. Nesting of 12-km Grid in the CMAQ 36-km Grid. 

Appendix C.1 - 86
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-5 

Figure 4-3. Domain Definition for High Resolution 12-km Grid.

Appendix C.1 - 87
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-6 

Table 4-3. Vertical Layer Definition For MM5 Simulations (Left Most Columns), And 

Approach For Reducing CMAQ Layers By Collapsing Multiple MM5 Layers (Right Columns). 

MM5 CMAQ 19L

Layer Sigma Pres(mb) Height(m Depth(m) Layer Sigma Pres(mb) Height(m) Depth(m)

34 0.000 100 14662 1841 19 0.000 100 14662 6536

33 0.050 145 12822 1466 0.050 145

32 0.100 190 11356 1228 0.100 190

31 0.150 235 10127 1062 0.150 235

30 0.200 280 9066 939 0.200 280

29 0.250 325 8127 843 18 0.250 325 8127 2966

28 0.300 370 7284 767 0.300 370

27 0.350 415 6517 704 0.350 415

26 0.400 460 5812 652 0.400 460

25 0.450 505 5160 607 17 0.450 505 5160 1712

24 0.500 550 4553 569 0.500 550

23 0.550 595 3984 536 0.550 595

22 0.600 640 3448 506 16 0.600 640 3448 986

21 0.650 685 2942 480 0.650 685

20 0.700 730 2462 367 15 0.700 730 2462 633

19 0.740 766 2095 266 0.740 766

18 0.770 793 1828 259 14 0.770 793 1828 428

17 0.800 820 1569 169 0.800 820

16 0.820 838 1400 166 13 0.820 838 1400 329

15 0.840 856 1235 163 0.840 856

14 0.860 874 1071 160 12 0.860 874 1071 160

13 0.880 892 911 158 11 0.880 892 911 158

12 0.900 910 753 78 10 0.900 910 753 155

11 0.910 919 675 77 0.910 919

10 0.920 928 598 77 9 0.920 928 598 153

9 0.930 937 521 76 0.930 937

8 0.940 946 445 76 8 0.940 946 445 76

7 0.950 955 369 75 7 0.950 955 369 75

6 0.960 964 294 74 6 0.960 964 294 74

5 0.970 973 220 74 5 0.970 973 220 74

4 0.980 982 146 37 4 0.980 982 146 37

3 0.985 986.5 109 37 3 0.985 986.5 109 37

2 0.990 991 73 36 2 0.990 991 73 36

1 0.995 995.5 36 36 1 0.995 995.5 36 36

0 1.000 1000 0 0 0 0 1.000 1000 0 0

Appendix C.1 - 88
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-7 

4.3 Data Availability 

The CMAQ modeling system requires emissions, meteorological, initial and boundary 

condition (IC/BC) and ozone column data for defining the inputs to operate the CMAQ Chemical 

Transport Model and air quality data with which to evaluate the CMAQ CTM concentrations and 

deposition estimates. 

4.3.1 Emissions Data 

The base year emissions inventory for Phase II of the VISTAS modeling will be founded 

on revised 2002 emissions developed by VISTAS emission inventory contractors in NEI Input 

Format (NIF) 3.0. These revised emissions were reviewed by VISTAS stakeholders and 

considered complete in January of 2004. Non-VISTAS state emissions will be based on 

inventories obtained by the Study Team and determined to be representative of the 2002 episode 

year. Mexican and Canadian emissions will be based on the latest available inventories 

obtainable by the Study Team in formats lending themselves to emissions modeling. For 

purposes of air quality model validation, actual 2002 calendar year emissions for EGU and fire 

activity will be used. Whereas for strategy and future year emission runs, “typical year” 

emissions for these categories will be processed for 2002 and the future years. 

A final revised 2002 VISTAS state emission inventory is expected by September 2004 

and will be used in the final model performance demonstration and configuration expected to 

begin in October 2004. Non-VISTAS state emissions are expected to be based on State 

submittals to EPA under the CERR and will be augmented with additional data provided by 

RPO, State, and international sources. As in the initial revised modeling, actual 2002 calendar 

year emissions will be modeled for EGU and fires for base case model performance evaluation, 

while “typical year” emissions for these categories for 2002 and the future years will be 

processed during the strategy runs. 

All emissions will be converted to Inventory Data Analyzer (IDA) formatted versions and 

the data will be processed for air quality modeling using Version 2.0 of the Sparse Matrix 

Operating Kernel Emissions (SMOKE) model. Included in these runs will be the temporal and 

speciation profiles and cross-reference data provided with the version 2.0 release of the model 

augmented with any recommended and approved emission profile data provided by the 

emissions inventory contractor, obtained from EPA, or prepared by the Study Team prior to 

initial emissions modeling. Spatial allocation of the emissions will be based on profiles and 

spatial allocation factors developed for the National RPO grid. Additional description of 

emissions processing is described in Chapter 5 and emissions QA is described in Chapter 6. 

4.3.2 Air Quality 

Data from ambient monitoring networks for both gas and aerosol species are used in the 

model performance evaluation. Ambient monitoring data are described in detail in the Phase I 

Task 3 Report: “Review and Assessment of Available Ambient Air Quality Data to Support 

Modeling and Modeling Performance Evaluation for the Three VISTAS Phase I Episodes” 

(ENVIRON, UCR and Alpine 2003) so are not repeated here. Table 4-4 summarizes ambient 

monitoring networks. Data have been compiled for all networks except the PAMS and PM 

Supersites. 

Appendix C.1 - 89
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-8 

If optional modeling of episode periods from 2003 is performed under VISTAS Phase II, 

then data from the new FOCUS sites will be available. As the FOCUS sites were not in 

operation during the 1999-2002 period that included the three Phase I episodes, they are not 

described in the Phase I Task 3 report so are discussed here (the reader can refer to the Phase I 

Task 3 report for information on the other networks). There are four focus sites in the VISTAS 

region: 

• Look Rock south of the Great Smoky Mountains National Park; 

• Raleigh, North Carolina; 

• Cape Romain, South Carolina; and 

• Atlanta , Georgia. 

Each Focus sites collects continuous PM mass, speciated PM (sulfate, nitrate and carbon) 

and gaseous pollutant concentrations (SO2, NOy, CO and O3). Each site also collects visibility 

(nephelometers), surface meteorology and athalometers (light absorption). 

Appendix C.1 - 90
May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-9 Table 4-4. Overview of Ambient Data Monitoring Networks. 

Monitoring Network Chemical Species Measured Sampling Period Data Availability/Source The Interagency Monitoring of Protected Visual Environments (IMPROVE) 

Speciated PM25 and PM10 (see species mappings) 

1 in 3 days; 24 hr average 

http://vista.cira.colostate.edu/improve/Data/IMPRO

VE/improve_data.htm

Clean Air Status and Trends Network (CASTNET) 

Speciated PM25, Ozone (see species mappings) 

Approximately 1-week average 

http://www.epa.gov/castnet/data.html

National Atmospheric Deposition Program (NADP) 

Wet deposition (hydrogen (acidity as pH), sulfate, nitrate, ammonium, chloride, and base cations (such as calcium, magnesium, potassium and sodium)), Mercury 

1-week average http://nadp.sws.uiuc.edu/

Air Quality System (AQS) Aka 

Aerometric Information Retrieval System (AIRS) 

CO, NO2, O3, SO2, PM25, PM10, Pb 

Typically hourly average 

http://www.epa.gov/air/data/

Speciation Trends Network (STN) Speciated PM 24-hour average http://www.epa.gov/ttn/amtic/amticpm.html Southeastern Aerosol Research and Characterization (SEARCH) 

24-hr PM25 (FRM Mass, OC, BC, SO4, NO3, NH4, Elem.); 24-hr PM coarse (SO4, NO3, NH4, elements); Hourly PM2.5 (Mass, SO4, NO3, NH4, EC, TC); and Hourly gases (O3, NO, NO2, NOy, HNO3, SO2, CO) 

Hourly or 24-hour average, depending on parameter. 

Electric Power Research Institute (EPRI), Southern Company, and other companies. http://www.atmospheric-research.com

EPA Particulate Matter Supersites Speciated PM25 http://www.epa.gov/ttn/amtic/supersites.htmlPhotochemical Assessment Monitoring Stations (PAMS) 

Varies for each of 4 station types. http://www.epa.gov/ttn/amtic/pamsmain.html

National Park Service Gaseous Pollutant Monitoring Network 

Acid deposition (Dry; SO4, NO3, HNO3, NH4, SO2), O3, meteorological data 

Hourly http://www2.nature.nps.gov/ard/gas/netdata1.htm

Appendix C.1 - 91
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 4.doc 4-10 

4.3.3 Ozone Column Data 

Additional data used in the air quality modeling include the Total Ozone Mapping 

Spectrometer (TOMS). TOMS data is available for 24-hour average and is obtained from 

http://toms.gsfc.nasa.gov/eptoms/ep.html. The TOMS data is used in the CMAQ radiation 

model (JPROC) to calculate photolysis rates. 

4.3.4 Meteorological Data 

Meteorological data are being generated using the MM5 prognostic meteorological model 

by Baron Advanced Meteorological Systems (BAMS). BAMS is operating the MM5 at 5-day 

increments for 2002 on the 36 km and 12 km grid with a 14 day spin up period for the end of 

December 2001. Details on the VISTAS Phase II 2002 MM5 modeling can be found at the 

BAMS VISTAS website: http://www.baronams.com/projects/VISTAS/. 

4.3.5 Initial and Boundary Conditions Data 

The CMAQ default Initial Concentrations (ICs) will be used along with a ~15 day spin 

up period to eliminate any significant influence of the ICs. 

The CMAQ Boundary Conditions (BCs) for the initial simulations will be based on 

seasonal averages of 3-hour 2001 GEOS-CHEM global simulation model output. VISTAS and 

other RPOs are finding a 2002 GEOS-CHEM simulation that would be used to define days 

specific high time resolved (e.g., 3-hourly) CMAQ BCs. 

Appendix C.1 - 92
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-1

5.0 MODEL INPUT PREPARATION PROCEDURES 

In this section we describe the procedures to be used to develop the CMAQ model inputs 

for the Phase II 2002 annual and potentially additional ~60 days episodic simulations. We also 

discuss how the CAMx model inputs will be generated if the optional task to run an alternative 

model to corroborate the CMAQ results is selected. The development of the CMAQ 

meteorological and emissions inputs are discussed first followed by the science options to be 

used by CMAQ. The procedures for developing the initial and boundary conditions and 

photolysis rates inputs are then discussed along with the model application procedures. 

5.1 Meteorological Inputs to Emissions and Air Quality Models 

The emissions and air quality models require certain meteorological input data including 

wind fields, estimates of turbulent eddy dispersion, humidity, temperature, clouds, and actinic 

flux. Spatially gridded and hourly varying meteorological data are needed to estimate biogenic, 

mobile source emissions, and plume-rise for large, elevated point sources. Meteorological data 

are needed to drive chemical transport models for solving atmospheric diffusion and chemistry 

equations for model species. Because observed data are not available for the full gridded model 

domain, numerical meteorological models are used to provide these inputs. 

The National Center for Atmospheric Research (NCAR)/Pennsylvania State University 

(PSU) Fifth-Generation Mesoscale Model (MM5) (v3.6) is being used by the VISTAS 

meteorological modeling contactor, Baron Advanced Meteorological Systems (BAMS) (Olerud, 

2004) to simulate meteorology at a 36-km resolution for calendar year 2002 over the entire 

continental United States and including portions of Canada, Mexico, and the Atlantic and Pacific 

Oceans. MM5 is also being applied over the southeastern U.S. using a 12 km resolution grid. 

The MM5 is a three-dimensional prognostic meteorological model that is used not only for 

meteorology studies but also for air quality studies. Some of the physics used in the simulation 

include one-way nesting; nonhydrostatic dynamics; four-dimensional data assimilation of wind, 

temperature, and mixing ratio; explicit treatment of moisture; cumulus cloud parameterization; 

vertical mixing of momentum in the mixed layer; PBL process parameterization; atmospheric 

radiation; sea ice treatment; and snow cover (see Chapter 2 for more details). 

After the MM5 simulation is completed, the MM5 output files are transferred to the 

emissions and air quality modeling team and analyzed by the Meteorological Gatekeeper. The 

Meteorological Gatekeeper performs two main roles. To provide an independent evaluation of 

the 2002 MM5 simulation that also serves to determine whether the MM5 data have been 

transferred correctly from the VISTAS meteorological modeling contractor. And to process the 

2002 MM5 output using Version 2.2 of the Models-3 CMAQ Meteorological-Chemical Interface 

Processor (MCIP) to generate meteorological fields that will be used for emissions processing 

and air quality simulation. 

5.1.1 MCIP Reformatting Methodology 

 

The Models-3 Community Multiscale Air Quality (CMAQ) modeling system is designed 

to simulate multiscale (urban and regional) and multi-pollutant (oxidants, acid deposition, and 

particles) air quality problems. But before running the CMAQ Chemical Transport Model 

(CCTM), the MM5 generated meteorological data must be pre-processed and converted to 

Appendix C.1 - 93
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-2

Models-3 consistent data structures. MCIP version 2.2 will be used to preprocess the MM5 

meteorological output. The “pass through” option in MCIP will be used in the VISTAS Phase II 

modeling. One of MCIP’s functions is to translate meteorological parameters from the output of 

the Pennsylvania State University/National Center for Atmospheric Research (PSU/NCAR) 

Mesoscale Modeling System Generation 5 (MM5) to the Models-3 input/output applications 

program interface (I/O API format) which is required for operation of Models-3 CMAQ 

processors. Some other necessary parameters not available from the meteorological model are 

estimated with appropriate diagnostic algorithms in the program. The key functions of MCIP 

include: 

1. Reading in meteorological model output files 

2. Extraction of meteorological data for CTM window domain 

3. Interpolation of coarse meteorological model output for finer grid 

4. Collapsing of meteorological profile data if coarser vertical resolution data is requested 

5. Computation or passing through surface and PBL parameters 

6. Diagnosing of cloud parameters 

7. Computation of species-specific dry deposition velocities 

8. Generation of coordinate dependent meteorological data for the generalized coordinate 

CCTM simulation 

9. Output meteorological data in Models-3 I/O API format 

The MCIP processor transforms the data into I/O API format while also calculating several 

new data fields (e.g. low, middle, and high cloud fractions) that are not readily available in the 

raw MM5 output. It also interpolates temperature and wind speed to observation height (1.5m 

and 10m, respectively). The MCIP processor culls a minimum of six cells about the domain 

periphery to minimize edge effects in the MM5 simulation. MCIP can be used to further reduce 

the rows or columns in the MM5 data so that the domain definition for the MCIP output files 

precisely matches the domain used in the air quality modeling. MCIP also allows MM5 layers to 

be “collapsed” (i.e., some layers can be aggregated). When feasible it is desirable to use the same 

layer structure in the air quality model as in the MM5 to prevent errors associated with 

aggregating layer data and to maintain consistency between data produced by the meteorological 

model and those used by the chemistry-transport model. However, due to computational costs 

associated with using large number of vertical layers, vertical layer collapsing is typically used to 

reduce the total number of layers used by the CCTM. In the VISTAS Phase II modeling we will 

collapse from 34 layers in MM5 output into 19 layers for the CMAQ air quality simulations. The 

first 8 layers of CMAQ, up to approximately 450 m AGL, will match the MM5 vertical layer 

structure exactly. The MM5 layers are then “doubled up” in CMAQ, up to a height of 

approximately 3,500 m AGL. The region top for CMAQ is the same as used by MM5, 100mb 

(approximately 15 km AGL). The 36 km analysis domain contains 148 columns, 112 rows, and 

19 layers. The 12 km analysis domain covers 168 columns, 177 rows, and 19 layers. More 

details on the CMAQ modeling domain definitions are provided in Chapter 4 with the vertical 

layer structure of MM5 and MCIP/CMAQ shown at Table 4-3. 

5.1.2 Products of the Meteorological Input Development Process 

The meteorological input development process produces three two-dimensional and four 

three-dimensional daily meteorological and geophysical output data in the Models-3 I/O API 

format. These CCTM-ready meteorological input files are used in both emissions processing and 

Appendix C.1 - 94
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-3

the CCTM simulations. The met fields are 36 km and 12 km horizontal resolution on a Lambert 

Conformal Projection (LCP) coordinate system with 19 vertical sigma layers extending from the 

surface to the 100 mb pressure level. The data files include three-dimensional gridded fields of 

u- and v-wind components, vertical velocity, temperatures, Jacobian, Jacobian weighted air 

density, total air density, water vapor, cloud water content, rain water content, ice and snow 

mixing ratio, layer heights, and vertical exchange coefficients. Two-dimensional gridded fields 

of latitude and longitude, squared map-scaled factor, surface temperatures and pressures, 1.5 and 

10 meter temperature, planetary boundary heights, rainfall, total cloud fraction, snow cover, 

deposition velocities, u* and w*, surface roughness length, as well as dominant land use 

category are also developed. 

Table 5-1 shows the configuration to be used in MCIP version 2.2 for processing the 

2002 MM5 output to produce CCTM-ready meteorology input files. 

Table 5-1. MCIP V2.2 Configuration used In the VISTAS Phase II Modeling. 

Module or option Values or 

setting 

Additional Information 

PBL value computation option 1 Use PBL value from input meteorology 

Radiation fields 1 Use radiation fields from input 

meteorology 

Dry deposition option 2 Use Models-3 (Pleim) dry deposition 

routine 

Output interval 60 Unit is in minutes 

Vertical layer structure 19 layers See Chapter 4 

5.2 Development of Emissions Model Inputs and Resultant Inventories 

 The base year emissions inventory for Phase II of the VISTAS modeling will be founded 

on revised 2002 emissions developed by VISTAS emission inventory contractors in NEI Input 

Format (NIF) 3.0. These revised emissions were reviewed by VISTAS stakeholders and 

considered complete in March of 2004. 

Non-VISTAS state emissions are based on inventories obtained by the Study Team and 

determined to be representative of the 2002 episode year. Western State base year point and area 

source emissions for 2002 were provided by the WRAP RPO. Additionally, an inventory of 

point source resolved agricultural fire emissions were provided by WRAP and utilized in the 

modeling. The CENRAP RPO provided VISTAS with an inventory of 2002 area source 

ammonia emissions which were also used in developing the remaining non-VISTAS emissions. 

For the remaining U.S. domain, point source projections were based on EPA’s 2001 

modeling platform inventories and area source, nonroad mobile, and fire emissions were based 

on EPA’s preliminary 2002 NEI. VMT and MOBILE input files were taken from EPA’s 

preliminary 2002 FTP site and used in running MOBILE6 nationally. 

Appendix C.1 - 95
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-4

Mexican and Canadian emissions are be based on the latest available inventories 

obtainable by the Study Team in formats lending themselves to emissions modeling. At this time, 

these inventories are the same as in Phase I. 

For purposes of air quality model validation, actual 2002 calendar year emissions for 

EGU and fire activity will be used, while during strategy and future year emission runs, “typical 

year” emissions for these categories will be processed. 

A final revised 2002 VISTAS state emission inventory is expected by September 2004 

and will be used in the final model performance demonstration and configuration expected to 

begin in October 2004. Non-VISTAS state emissions are expected to be based on State 

submittals to EPA under the CERR and will be augmented with additional data provided by 

RPO, State, and international sources. As in the initial modeling, the revised modeling will use 

actual 2002 calendar year emissions for EGU and fires, while “typical year” emissions for these 

categories will be processed during the strategy runs. 

 These emissions will then be converted to Inventory Data Analyzer (IDA) formatted 

versions and the data will be processed for air quality modeling using Version 2.0 of the Sparse 

Matrix Operating Kernel Emissions (SMOKE) model. Included in these runs will be the 

temporal, spatial, and speciation profiles and cross-reference data currently provided with the 2.0 

release of the model augmented with any recommended and approved emission profile data 

provided by the emissions inventory contractor or obtained from EPA prior to initial emissions 

modeling. The processing will be adjusted for each run to account for the specific air quality 

model (AQM) input required by CMAQ. 

5.2.1 Emissions Modeling Methodology

Emissions inventory development for photochemical modeling must address several 

source categories including: (a) stationary point sources, (b) area sources, (c) on-road mobile 

sources, (d) non-road mobile sources, and (e) biogenic sources. For this analysis, these estimates 

must be developed to support the episode that is being modeled (i.e., the historical base year 

when the episode actually occurred; 2002). 

Development of an emissions inventory customized for the VISTAS region requires a 

merging of: (a) the most recent pertinent regional inventory and (b) available high-resolution, 

locale-specific emissions estimated by local, state, and regional agencies in the VISTAS region. 

Local air regulatory and transportation planning agencies are generally the best sources of 

domain specific activity and control factors to use in developing the base year emissions. Often, 

these local emissions data sets come from a variety of sources, frequently in different formats. 

 The study team will acquire emissions estimate data from Emissions Inventory 

Contractor, in the NIF 3.0 format for purposes of generating the emission inventory base year 

files necessary for Phase II of the VISTAS contract. These data will be augmented with highway 

mobile source data submitted to the VISTAS emission inventory contractors from the VISTAS 

participating States. 

Contacts with VISTAS’ emission inventory contractors and the U.S. EPA will be 

established and formal requests made for inventory corrections, updates and ancillary data 

Appendix C.1 - 96
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-5

pertinent to the modeling of emissions in their jurisdictions. Where feasible and consistent with 

project resources and schedule, these updated data sets will be acquired and will be used to 

create day-specific modeling inventories specific to the VISTAS domain for the base year 

episodes to be modeled. 

5.2.2 Set-up of SMOKE Over the VISTAS Domain 

 SMOKE will be configured to generate point, area, nonroad, highway, and biogenic 

source emissions. In addition, certain subcategories, such as fires and EGUs will be maintained 

in separate source category files in order to allow maximum flexibility in producing alternate 

strategies. Settings for each of the source categories are discussed in relevant sections below. 

With the exception of biogenic and highway mobile source emissions that are generated using 

the, respectively, BEIS and MOBILE6 modules in SMOKE, pre-computed annual emissions will 

be processed using the month, day, and hour specific temporal profiles of the SMOKE model. 

 To produce an emissions inventory to support annual modeling, representative time 

periods will be selected and modeled. Area, nonroad, and point sources will be modeled as a 

block of Thursday, Friday, Saturday, Sunday, Monday one per month (total of 60 days modeled). 

On-Road motor vehicles will be represented by a entire single week for each month. This 

selection criteria allows for the representation of day-of-the-week variability in the on-road 

motor vehicles, and models a representation of the meteorological variability in each month. 

Holidays will be modeled as Sundays. A list of modeled holidays is provided in Table 5-2. The 

biogenic emissions will be modeled on a day specific basis (365 days). 

Table 5-2. SMOKE Modeled Holidays. 

Date Julian Day Holiday Description 

January 1, 2002 2002001 New Year's Day 

March 29, 2002 2002089 Good Friday 

May 27, 2002 2002147 Memorial Day 

July 4, 2002 2002185 July 4th 

September 2, 2002 2002245 Labor Day 

November 28, 2002 2002332 Thanksgiving Thurs 

November 29, 2002 2002333 Thanksgiving Fri 

December 24, 2002 2002358 Christmas Eve 

December 25, 2002 2002359 Christmas Day 

 Population will be used as a gridding default for all source categories when the assigned 

surrogate would cause SMOKE to drop emissions. This can be a case when the county-level 

emission inventories are prepared using surrogates other than those available for modeling 

purposes. 

 The domain for the Phase II episode will be identical to the Phase I domain, which is 

based on the EPA’s 36-km national CMAQ domain, illustrated in Figure 5-1 below (details on 

the modeling domains are provided in Chapter 4). 

Appendix C.1 - 97
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-6

Figure 5-1. EPA 36-km National CMAQ Domain. 

The parameters for the SMOKE runs are as follows: 

Episodes: 2002 Calendar Base Year. Optional tasks for episodic modeling of up to 60 

days that will likely be from 2003. 

Future Years: To be determined. 

Output Time Zone: Greenwich Mean Time (zone 0) 

Projection: Lambert Conformal with Alpha=33, Beta=45, Gamma=-97, and center at (-

97,40). 

Domain: 

• 36 Kilometer Grid: Origin at (-2736, -2088) kilometers with 148 rows by 112 

columns and 36-km square grid cells. 

• 12 Kilometer Grid: Origin at (108, -1620) kilometers with 168 rows by 177 columns 

and 12-km square grid cells. 

Layer Structure: The CMAQ layer structure will be 19 layers, with specific layer 

positions defined in the meteorology files (see Chapter 4). 

CMAQ Model Species: The CMAQ initial configuration will be for the CB-IV chemical 

mechanism with PM. The model species in the emission input files will be: CO, NO, 

Appendix C.1 - 98
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-7

NO2, ALD2, ETH, FORM, ISOP, NR, OLE, PAR, TERPB, TOL, XYL, NH3, SO2, 

SULF, PEC, PMFINE, PNO3, POA, PSO4, and PMC. 

Meteorology Data: Daily (25-hour). SMOKE requires the following five types of MCIP 

outputs: (1) Grid cross 2-d, (2) Grid cross 3-d, (3) Met cross 2-d, (4) Met cross 3-d, and 

(5), Met dot 3-d. These files need to match the grid projection and overlap with the 

emissions modeling region but can be larger in the horizontal directions than the 

modeling region shown in Figure 1. Therefore, the data files for the 36 Kilometer grid 

domain will be at least 90 columns by 132 rows 

Elevated Sources: All sources will be treated by SMOKE as potentially elevated. No 

plume-in-grid sources will be modeled. Wildfire emissions will be handled as point 

sources. 

Producing 365 day-specific input files for all source categories places a burden on 

available computing facilities, data management systems, and would adversely affect the Phase 

II schedule. Selecting representative model days for some or all of the source categories reduces 

the processing and file handling requirements to a more manageable level, and in most cases 

does not compromise the accuracy of the emissions files. 

Other current or recent projects undertaken by EPA, WRAP and LADCo have used a 

selection approach for all of the source categories (except biogenics) that use a representative 

weekday/Saturday/Sunday either for each month or each season to model all of the emissions 

files. In an attempt to better represent the level of temporal and spatial detail available for each 

source category, we have developed a more detailed strategy. 

Biogenic emissions will be modeled for each episode day, using the daily meteorology. 

Point sources, including CEM and fire emissions will be modeled for each episode day to take 

advantage of the available day-specific emissions and meteorology. Area sources, including 

non-road mobile and dust emissions do not utilize meteorological data, and are temporally 

allocated by monthly, daily and hourly profiles. Reviewing these profiles indicate that maximum 

temporal definition can be achieved by selecting representative Thursday, Friday, Saturday, 

Sunday, and Monday profiles for each month. 

Motor vehicle emissions are influenced by meteorological variability, but the processing 

requirements for daily motor vehicle emissions were determined to be prohibitive under the 

current schedule. Rather than utilizing averaged meteorological data or pre-calculated motor 

vehicle emissions, a single week per month was selected for modeling. This week was selected 

from mid-month, to try to best represent the average temperature ranges for the month, and also 

adjusted to exclude holidays that would require atypical processing. The area source modeling 

dates were also selected from these ranges to simplify data handling procedures. 

2002 On-Road Mobile Sources Represented by the Following Weeks: 

 January 13-19 

 February 10-16 

 March 10-16 

 April14-20 

 May 12-18 

Appendix C.1 - 99
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-8

 June 9-15 

 July 14-20 

August 11-17 

September 15-21 

October 13-19 

November 10-16 

December 15-21 

5.2.3 Development of Point Source Emissions 

 Stack parameters are often more important to the reliability of the air quality modeling 

results than the emissions rates themselves. Stack parameter data are frequently incorrect, 

especially in some of the current regional modeling inventories and careful QA is required to 

assure that the point source emissions are properly located both horizontally and vertically on the 

modeling grid. To screen for simple, but potentially serious inventory errors such as these, the 

study team has modified procedures originally developed by EPA to quality assure, augment, 

and where necessary, revise, stack parameters to examine the accuracy of the point source 

emissions, as well as standardize procedures to identify and correct stack data errors. These 

procedures will be implemented in the NIF to IDA conversion step of the inventory 

development. Additionally, SMOKE has a number of built-in QA procedures designed to catch 

missing or out-of-range stack parameters. These procedures will also be invoked in the 

processing of the point source data. 

For the Phase II initial baseline modeling, we will be separating the point source 

emissions into EGU and non-EGU categories. The non-EGU category will not be using any day 

or hour-specific emissions. All non-EGU point source emissions will be temporally allocated to 

month, day, and hours using annual emissions and source category code (SCC) based allocation 

factors. These factors will be based on the cross-reference and profile data supplied with the 

SMOKE 2.0 version and will be supplemented with relevant data provided to the study team by 

VISTAS or its contractors. 

For EGU sources with EPA reported CEM data or with hourly emissions provided by 

stakeholders, actual hourly data will be used. For those sources where EPA CEM data are 

utilized, NOx, SO2, and heat input-based hour-specific profiles were developed and applied to 

NOx, SO2, and all other emissions, respectively. This ensured that the annual emission values 

provided by the EI contractor were maintained, but distributed using hourly to annual profiles. 

For sources providing hour-specific data and where they were approved by the State in which 

they operated, those data were substituted for EPA CEM-based emissions and distributions. 

To temporally allocate the remaining EGU point sources, the NOx, SO2, and heat input 

data were collected from the 2002 Continuous Emissions Monitoring (CEM) datasets, and used 

to develop unit-level temporal distributions. The hour, day of week, and monthly specific 

temporal profiles will be used in conjunction with the EI supplied emissions data to calculate 

hourly EGU emissions by unit. 

Appendix C.1 - 100
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-9

All point sources will be spatially allocated in the domain based on the stationary source 

geographic coordinates. If a point source is missing its latitude/longitude coordinates, the source 

will be placed in the center of its respective county. 

5.2.4 Development of Area and Non-Road Source Emissions 

All area and non-road source emissions will be temporally allocated to month, day, and 

hours using annual emissions and source category code (SCC) based allocation factors. These 

factors will be based on the cross-reference and profile data supplied with the SMOKE 2.0 beta 

version and will be supplemented with relevant data provided to the study team by VISTAS or 

its contractors. Area and non-road sources will be spatially allocated in the domain based on 

SCC-based spatial allocation factor files. If an area or non-road source SCC does not have an 

existing cross-reference profile assigned to it, the county-level emissions will be allocated by 

population density in the respective county. 

A crustal PM transport factor will be applied to fugitive dust emission sources that have 

been identified in U.S. EPA modeling to have only a portion of its mass transportable from the 

source of the emission generation. The EPA’s studies indicate that 60 to 90 percent of PM 

emissions from fugitive dust sources do not reach an elevated level necessary to be transported 

or modeled in an episodic simulation. For this reason, the VISTAS emissions contractor will 

apply county-specific fugitive dust emissions transport factors to these sources to adjust PM 

emissions accordingly. The fugitive dust emissions adjustment is done by the VISTAS 

emissions contractor prior to receipt by the emissions and air quality modeling Team. Thus, no 

additional adjustment will be made in the emissions modeling. (for adjustment factors see: 

http://www.epa.gov/ttn/chief/emch/invent/statusfugdustemissions_082203.pdf). 

5.2.5 Development of On-Road Mobile Source Emissions 

The MOBILE6 module of SMOKE will be used to develop the base year on-road mobile 

source emissions estimates for CO, NOx, PM, and VOC emissions. The MOBILE6 parameters, 

vehicle fleet descriptions, and VMT estimates will be combined with gridded, episode-specific 

temperature data to calculate the gridded, temporalized emission estimates. Of note, whereas the 

on-network emissions estimates are spatially allocated based on link location and subsequently 

summed to the grid cell level, the off-network emissions estimates are spatially allocated based 

on a combination of the FHWA version 2.0 highway networks and population. For the VISTAS 

36/12 km modeling, no link based data will be used. The MOBILE6 emissions factors are based 

on episode-specific temperatures predicted by the meteorological model. Further, the MOBILE6 

emissions factors model accounts for the following: 

• Hourly and daily minimum/maximum temperatures; 

• Facility speeds; 

• Locale-specific inspection/maintenance (I/M) control programs, if any; 

• Adjustments for running losses; 

• Splitting of evaporative and exhaust emissions into separate source categories; 

• VMT, fleet turnover, and changes in fuel composition and Reid vapor pressure 

(RVP). 

Appendix C.1 - 101
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-10

The primary input to MOBILE6 is the MOBILE shell file. The MOBILE shell contains the 

various options (e.g. type of inspection and maintenance program in effect, type of oxygenated 

fuel program in effect, alternative vehicle mix profiles, RVP of in-use fuel, operating mode) that 

direct the calculation of the MOBILE6 emissions factors. 

 

5.2.6 Development of Biogenic Source Emissions 

 A revised version of a commonly used biogenic emissions model, the Biogenic 

Emissions Inventory System (BEIS), has recently been developed and tested by EPA over two 

separate modeling domains/episodes. This version of the model (BEIS-3, v0.9) contains several 

changes over BEIS-2, including the following: 

• Vegetation input data -- are now based on a 1-km Biogenic Emissions Landuse 

Database (BELD3) vegetation data base, 

• Emission factors – many updates including some recent NARSTO modifications, 

• Environmental algorithm -- includes a sunlit/shaded leaf solar radiation model. 

A series of sensitivity modeling simulations has been completed and concluded that the more 

recent BEIS-3 methodology will impact base case model ozone predictions in most parts of the 

U.S. The preliminary tests have also shown that the newer biogenic emissions do not appear to 

have a large effect on: 1) the control signal response, 2) relative reduction factors resulting from 

a projected emissions change, or 3) overall regional model performance in the eastern U.S. 

For this particular application of BEIS-3, version 0.9 as currently incorporated in the 

SMOKE processor will be used. This means that: 1) soil NO emissions shall be prepared 

without the input of specific soil moisture and precipitation data and 2) MEOH emissions will 

not be modeled explicitly. Otherwise, the modeling should be identical to a BEIS-3 (v1.0) 

application. 

The BELD-3 landuse data on a Lambert conformal grid at 1-km resolution have already 

been developed, are available, and will be used to estimate biogenic emissions in this study. The 

BEIS model also requires as input hourly, gridded temperature and solar radiation data to 

estimate biogenic emissions, and these data will be derived from the MM5 predictions. 

 5.2.7 Wildfires, Prescribed Burns, Wind Blown Dust and Sea 

 Salt Source Emissions 

Wildfires and Prescribed Burns

Wildfire and prescribed burn emissions will be handled separately from the standard area 

source input files. The study team expects to receive monthly estimates of fire emissions from 

the EI contractor, which include burn acreage and biomass loading information for the VISTAS 

states. Depending on the completeness and quality of the data received, attempts will be made to 

calculate spatial and temporal distributions of the fire emissions, rather than relying on standard 

distribution profiles. Also, the study team will attempt to calculate vertical distribution of the 

fire emissions, based on fire size and biomass involvement. The SMOKE 2.0 can model fire 

plume rise if provided with the following variables: 

Appendix C.1 - 102
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-11

PTOP – Top of the fire plume profile (meters above ground level) 

PBOT – Bottom of the fire plume profile (meters above ground level) 

Lay1 – The percent of the emissions entrained in the first modeling layer 

The WRAP Fire Emissions Joint Forum Emissions Inventory Report (FEJF,2002) has 

documented an approach to calculating these plume descriptors. In this method, the fires are 

assigned to one of 5 size categories, based on the total burn acreage, and the biomass fuel 

loading. These categories are then used to calculate representative hourly plume profiles. These 

profiles are then used by SMOKE2.0 to distribute the vertical emissions for the fires. To 

successfully model fires as elevated point sources, the data provided by the EI contractor will 

need to include both the day or days on which the fire occurs, and a spatial identifier of the fire 

location. At a minimum, a latitude and longitude of the fire location can be used, while a 

polygon coverage would be preferable. 

 In addition, wildfire and prescribed burn data, including emissions estimates and plume 

rise distributions, will be obtained from the WRAP contractor and used to supplement the 

inventory for the WRAP states. 

Windblown Dust

PM10 and PM2.5 emissions from wind erosion of natural geogenic sources (SCCs 

2730100000 [total] and 2730100001 [dust devils]) will be excluded from the resulting modeling 

files using a 100 percent reduction in the control packets. 

Sea Salt

CMAQ currently treats sea salt as an inert PM species. That is, the sea salt is not allowed 

to chemically interact with other species, such as producing particulate sodium nitrate. There are 

plans to update CMAQ to have chemically active sea salt, but it is unclear whether such an 

update will occur during the Phase II modeling. Accordingly, the initial Phase II modeling will 

be conducted without any sea salt emissions. If CMAQ is updated to treat chemically active Sea 

Salt, or if CAMx is run using its full-science options, then Sea Salt emissions will be generated 

using appropriate procedures (e.g., as was done in Phase I). 

5.2.8 Speciation and Reformatting of Emissions 

SMOKE will be run to speciate the emissions estimates according to the requirements of 

the Carbon Bond Mechanism version four (CBM-IV, CB-IV or CB4). Note that VISTAS is 

evaluating whether the CB-IV or SAPRC99 photochemical mechanisms are more appropriate for 

the Phase II modeling and may switch to the SAPRC99 mechanism for the revised base case 

modeling that will be initiated in September 2004. The SMOKE model will also reformat the 

emissions estimates for use in CMAQ modeling. For each model-ready emissions inventory, 

SMOKE will produce at a minimum five (5) separate air quality model-ready files: low-level 

point source, area source, elevated point source, mobile source, and biogenics. Other source 

categories, such as EGU and fire emissions may also be handled as separate air quality modelready files.

 

Appendix C.1 - 103
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-12

5.2.9 Development of Modeling Inventories 

 The emissions inventories modeled for the VISTAS Phase II can be grouped into three 

distinct types: 1) 2002 annual inventories, 2) Future Year episodic inventories, using Phase I 

definitions, and 3) Alternate Base Year Episodic Inventories. In all cases, the Study Team 

expects to receive the emissions inventory data for the VISTAS states from the Emissions 

Inventory contractor, add non-VISTAS states and Canadian and Mexican data acquired from 

alternate EPA and/or RPO sources, and produce the CMAQ ready emissions files. 

 5.2.9.1 2002 Annual Inventories 

 The initial 2002 annual base inventory will be produced in two phases, coinciding with 

the delivery of the MM5 model results for the first 8 months and last 4 months of the 2002 

calendar year. The initial inventory will consist of all of the required source categories: area, 

nonroad, point, motor vehicle and biogenics. 

 A revised 2002 annual inventory will be modeled later in the project, using updated 

emissions as supplied by the EI contractor. This may require re-production of all or some of the 

source categories. A “typical” inventory will be produced, based on the revised 2002, and 

replacing the revised actual emissions for EGUs and fires with “typical” EGU and fire emissions, 

as provided by the EI contractor. The Study Team will also produce up to 3 future year scenario 

annual runs, based on the 2002 meteorology. The composition of these future year runs is yet to 

be determined. 

5.2.9.2 Future Year Phase I Episodic Inventories 

 Utilizing emissions data provided by the EI contractors, the Study Team will model up to 

2 alternate future-year scenarios, using 2 of the Phase I episodes and the accompanying MM5 

meteorological data: (1) January 2- January 21, 2002, and (2) July 7 to July 28, 2001. This may 

require re-modeling of all of the source categories, with the exception of the biogenics. 

 5.2.9.3 Alternate Year Episodic Inventories 

To capture visibility conditions that are not otherwise represented by 2002 conditions, we 

may perform episodic air quality modeling for up to 60 additional episode days selected from 

2003 or another year. Emissions inventories for these additional days will be prepared by the 

Study Team and the requisite meteorological modeling results would be provided prior to any 

modeling. The additional episode days will be modeled for a single base case inventory. 

5.2.10 Products of the Emissions Inventory Development Process

 In addition to the CMAQ-ready input files generated for each hour of the days modeled 

in the Phase II annual run, a number of quality assurance (QA) files will be prepared and used to 

check for gross errors in the emissions inputs. Importing the model-ready emissions into PAVE 

and looking at both the spatial and temporal distribution of the emission provides insight into the 

quality and accuracy of the emissions inputs. 

Appendix C.1 - 104
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-13

C Visualizing the model-ready emissions with the scale of the plots set to a very low value, 

we can determine whether there are areas omitted from the raw inventory or if emissions 

sources are erroneously located in water cells. 

C Spot-check the holiday emissions files to confirm that they are temporally allocated like 

Sundays. 

C Producing pie charts emission summaries that highlight the contribution of each 

emissions source component (e.g. nonroad mobile). 

C Normalizing the emissions by population for each state will illustrate where the 

inventories may be deficient and provide a reality check of the inventories. 

C Spot check vertical allocation of point sources using PAVE. 

We will use state inventory summaries prepared prior to the emissions processing to compare 

against SMOKE output report totals generated after each major step of the emissions generation 

process. 

 To check the chemical speciation of the emissions to CB-IV terms and the vertical 

allocation of the emissions, we will compare reports generated with SMOKE reports to target 

these specific areas of the processing. For speciation, we will compare the inventory import state 

totals versus the same state totals with the speciation matrix applied. 

 For checking the vertical allocation of the emissions, we will create reports by source, 

hour, and layer for randomly selected states in the domain. We will create these reports for a 

representative weekday in each of the episodes for each of these selected states. 

 The quantitative QA analyses often reveal significant deficiencies in the input data or the 

model setup. It may become necessary to tailor these procedures to track down the source of 

each major problem. As such, we can only outline the basic quantitative QA steps that we will 

perform in an attempt to reveal the underlying problems with the inventories or processing. 

Following are some of the reports that may be generated to review the processed emissions: 

C State and county totals from inventory for each source category 

C State and county totals after spatial allocation for each source category 

C State and county totals by day after temporal allocation for each source category for 

representative days 

C State and county totals by model species after chemical speciation for each source 

category 

C State and county model-ready totals (after spatial allocation, temporal allocation, and 

chemical speciation) for each source category and for all source categories combined 

C If elevated source selection is chosen by user, the report indicating which sources have 

been selected as elevated and plume-in-grid will be included. 

Appendix C.1 - 105
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-14

C Totals by source category code (SCC) from the inventory for area, mobile, and point 

sources 

C Totals by state and SCC from the inventory for area, mobile, and point sources 

C Totals by county and SCC from the inventory for area, mobile, and point sources 

C Totals by SCC and spatial surrogates code for area and mobile sources 

C Totals by speciation profile code for area, mobile, and point sources 

C Totals by speciation profile code and SCC for area, mobile, and point sources 

C Totals by monthly temporal profile code for area, mobile, and point sources 

C Totals by monthly temporal profile code and SCC for area, mobile, and point sources 

C Totals by weekly temporal profile code for area, mobile, and point sources 

C Totals by weekly temporal profile code and SCC for area, mobile, and point sources 

C Totals by diurnal temporal profile code for area, mobile, and point sources 

C Totals by diurnal temporal profile code and SCC for area, mobile, and point sources 

C PAVE plots of gridded inventory pollutants for all pollutants for area, mobile, and point 

sources 

5.3 Quality Model Configuration and Input Preparation 

5.3.1 CMAQ Science Configuration 

This section described the model configuration and science options to be used in the 

Phase II modeling effort. The recommendations are based on testing and model evaluations of 

several models or model configurations carried out in the VISTAS Phase I study. Table 5-3 

summarizes the proposed configuration for CMAQ. The latest version of CMAQ is currently 

Version 4.3 that was released October 2003. However, EPA is expected to release an updated 

version of CMAQ in mid 2004, and this version will likely be used in the Phase II modeling. In 

addition, we will perform simulations for at least January and July using the CMAQ 4.3 and the 

new versions of CMAQ to determine if the CMAQ updates substantially change the model 

predictions or performance. 

In the CMAQ base configuration we will run both the 36 km and 12 km grids using oneway grid nesting where the boundary conditions for the 12 km grid simulation are extracted from 

the 36 km run using the CMAQ BCON processor. The base configuration of CMAQ will use 19 

vertical layers up to a region top of 100 mb (approximately 15 km AGL). 

Appendix C.1 - 106
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-15

The PPM advection solver would be used along with the spatially varying (Smagorinsky) 

horizontal diffusion approach. K-theory will be used for vertical diffusion with a minimum 

eddy diffusion constant (Kz) of 0.1 m2

/s. Note that the CMAQ default minimum Kz value is 1.0 

m

2

/s. However, based on theoretical considerations and the Phase I testing and evaluation a 0.1 

m

2

/s minimum Kz values was selected for Phase II modeling. 

The MCIP2.2 will be used to process the MM5 data using the “pass through” option. 

The AERO3/ISORROPIA aerosol chemistry scheme will be used for inorganic aerosol 

thermodynamics. During the Phase I testing of the CMAQ model it was noted that the 

AERO3/ISORROPIA aerosol modules failed to conserve sulfur and nitrogen mass. A mass 

conservation patch developed by the Georgia Institute of Technology was added to the model 

that renormalized the total sulfur, reactive nitrogen and reduced nitrogen species after the call to 

the aerosol modules to conserve sulfur and nitrogen mass in the model. Sensitivity simulations 

were performed with and without the mass conservation patch. Although the mass conservation 

patch did not affect model performance, the VISTAS science team believes that mass 

conservation is a fundamental characteristic of the real-world atmosphere so have retained the 

mass conservation patch for the Phase II modeling. The SORGAM scheme, which includes a 

reversible thermal equilibrium, will be used for secondary organic aerosols. 

Phase I testing included comparisons of the three gas phase chemistry mechanisms: the 

Carbon Bond Mechanism version 4 (CB4, Gery et al., 1989), a recent update of CB4 (CB4-2002, 

Jeffries et al., 2002), and the SAPRC99 (Carter, 1999). Although Phase I testing did not show 

notably better performance for any one mechanism, the use of either CB4-2002 or SAPRC99 

chemistry in the Phase II modeling is desirable because these mechanisms employ the most 

recent available chemical kinetics data and are more scientifically defensible than the older CB4 

mechanism. The computational cost of the SAPRC99 chemistry is nearly twice that of the CB4. 

Since CB4-2002 is only implemented in the slower SMVGEAR chemistry solver, the 

computational penalty of using CB4-2002 chemistry over using CB4 with the EBI chemistry 

solver is even greater than that for SAPRC99. Given that the initial testing of the CMAQ model 

in the first half of 2004 will be more of a shakedown of the modeling system, including the 2002 

MM5 data and initial 2002 emission estimates, and the three chemical mechanisms produce 

similar model performance, then we propose to use the CB4 chemical mechanism for the initial 

2002 base case modeling. In the mean time, under Task 7 of the Phase II work effort the 

sensitivity of the CMAQ model to emission reductions using the CB4 and SAPRC99 chemistries 

will be evaluated using the January 2002 and July 2001 Phase I episodes to determine whether 

the two mechanisms have different responses. Based on this evaluation, and considerations of 

whether CB4-2002 has been implemented in CMAQ using the faster EBI chemistry solver, a 

decision will be made on the choice of the gas-phase photochemical mechanism for the revised 

2002 base case modeling to be initiated in September 2002. 

Finally, recent environmental chamber experiments at UCR suggest that both CB4-2002 

and SAPRC99 may underestimate the reactivity of aromatic compounds. UCR and others expect 

to test new versions of CB4 and SAPRC chemistry during 2004 independently of the VISTAS 

work effort. Although updates in aromatic chemistry will primarily affect urban areas, it is 

desirable to perform Phase II modeling using the most up-to-date version of the chemistry 

possible. We will report any pertinent findings or new chemical mechanisms to VISTAS as they 

become available. 

Appendix C.1 - 107
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-16

Table 5-3. Proposed Phase II Model Configuration for the CMAQ.

Model Option CMAQ 

Model Version Version 4.4 (April 2004) 

Horizontal Resolution 36/12 km 

No. Vertical Layers NZ = 19 

Horizontal Advection PPM 

Vertical Advection PPM 

Horizontal Diffusion Spatially Varying 

Vertical Diffusion KV (Eddy Diffusion) 

MM5 Configuration Pleim-Xiu/ACM 

MM5 Processing MCIP2.2 Pass Through 

Gas-Phase Chemistry CB4 

Gas-Phase Chemistry Solver MEBI/Hertel 

Secondary Organic Aerosol SORGAM 

Aqueous-Phase Chemistry RADM 

Aerosol Chemistry AE3/ISORROPIA 

Dry Deposition Pleim-Xiu 

Plume-in-Grid Off 

Initial Concentrations CMAQ Default 

Boundary Conditions Initial: Seasonal 2001 GEOS-CHEM 

Revised: 3-Hourly 2002 GEOS-CHEM 

Emissions NEI 1999 v2 

CMU NH3 Adjustments 

5.3.2 Spin-Up Initialization 

For the 2002 annual CMAQ modeling, the model will be exercised separately for four 

quarters. The 2002 MM5 modeling started on December 17, 2001 at 12Z. Thus, allowing for 12 

hours of spin up of the MM5 model, CMAQ will be initialized at 00Z on December 18, 2001. 

This results in a 13 day spin up period for CMAQ and the first quarter run segment of 2002. For 

the other quarter run segments of 2002, CMAQ will be initialized with a 15 day spin up period. 

5.3.3 Boundary Conditions 

The Phase I modeling included comparisons of several schemes for producing boundary 

conditions for the 36-km domain, including the following: 

• Fixed, default values at each edge, with vertical variation based on CMAQ default data. 

• Clean boundary conditions. 

• Seasonal mean output from the GEOS-CHEM model for a 2001 simulation 

In addition, for the July 2001 episode we examined the following three boundary conditions: 

• Fixed CMAQ default values; 

• 3-hourly temporally and spatially varying BCs based on the 2001 GEOS-CHEM output 

• Monthly average GEOS-CHEM output for July 2001 

Appendix C.1 - 108
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-17

Sensitivity experiments showed that model performance in the VISTAS states during conditions 

of high visibility impairment was relatively insensitive to variations in the boundary conditions, 

although differences in concentrations did occur. However, it is likely that boundary conditions 

will have a larger effect on visibility for clean days and for future conditions as visibility begins 

to improve. Moreover, boundary conditions will have a more significant effect on natural 

background visibility. In fact the BCs had a larger effect on the cleaner January 2002 model 

estimates than the dirtier July 1999 and 2001 episodes. Therefore, as a long-term effort we 

recommend that boundary conditions for the 36 km continental US domain be obtained from a 

global model such as GEOS-CHEM. However, because global model results are not yet 

available for 2002, in the initial Phase II modeling we will use seasonal average diurnally 

varying data from a 2001 GEOS-CHEM data to provide boundary conditions for the 36 km 

domain. If 2002 GEOS-CHEM results become available, the BCs will be updated with high 

temporal resolution (e.g., 3-hourly) day-specific GEOS-CHEM output. Boundary conditions for 

the 12 km nest will be obtained from the CMAQ 36-km simulation. 

5.3.4 Photolysis Rates 

Several chemical reactions in the atmosphere are initiated by the photodissociation of 

various trace gases. To accurately represent the complex chemical transformations in the 

atmosphere, accurate estimates of these photodissociation rates must be made. The Models-3 

CMAQ system includes the JPROC processor, which calculates a table of clear-sky photolysis 

rates (or J-values) for a specific date. JPROC uses default values for total aerosol loading and 

provides the option to use default column O3 data or to use TOMS data for total column O3. 

Previously, in the Phase I modeling we used TOMS data, and we will continue to use TOMS 

data for Phase II. There are a few days in 2002 for which TOMS data is not available, and we 

will used default column O3 data or previous days data for those days. 

JPROC produces a "look-up" table provides the photolysis rates as a function of latitude, 

altitude, and time (in terms of the number of hours of deviation from local noon, or hour angle). 

In the current CMAQ implementation, the J-values are calculated for six latitudinal bands (10o, 

20o, 30o, 40o, 50o, and 60o N), seven altitudes (0 km, 1 km, 2 km, 3 km, 4 km, 5 km, and 10 km), 

and hourly values up to "8 hours of deviation from local noon. During model calculations, 

photolysis rates for each model grid cell are estimated by first interpolating the clear-sky 

photolysis rates from the look-up table using the grid cell latitude, altitude, and hour angle, 

followed by applying a cloud correction factor. 

The photolysis rates input file must be prepared as separate look-up tables for each 

simulation day. The modeling team has already prepared scripts to automate the production of 

photolysis rate files for each day of the annual simulation. Photolysis files are ASCII files, and 

these will be visually checked for selected days to verify that photolysis are within the expected 

ranges. 

5.4 CAMx Model Inputs 

If the optional task to apply the CAMx model to corroborative the CMAQ results were 

selected, then the model inputs would be prepared in a manner consistent with the CMAQ inputs. 

The same modeling domain and grid structure as used for the CMAQ modeling of 2002 would 

Appendix C.1 - 109
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 5.doc 5-18

be used for CAMx (see Chapter 4). Meteorological inputs would be generated using the 

MM5CAMx processor using options similar to the MCIP “pass through” option and with a 0.1 

m2

/s minimum Kz. The CAMx initial and boundary conditions (IC/BC) inputs would be 

generated from the CMAQ IC/BC inputs using the CMAQ-to-CAMx IC/BC processors. The 

CAMx emission inputs would be generated using the CMAQ-ready emission inputs and the 

CMAQ-to-CAMx emission processor. 

Appendix C.1 - 110
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 6.doc 6-1 

6.0 QUALITY ASSURANCE PLAN

In this section we discuss the quality assurance procedures that will be used in the Phase 

II modeling. More details are provided in the VISTAS Phase II Quality Assurance Project Plan 

(QAPP) that is under preparation. 

6.1 Quality Assurance Objectives 

 In December 2002, the USEPA publish extensive guidance on developing a Quality 

Assurance Project Plan (QAPP) for modeling studies (EPA, 2002). The objective of a QAPP is 

to ensure that a modeling study is scientifically sound, robust, and defensible. The new EPA 

guidance suggests that a QAPP should include the following elements : 

• a systematic planning process including identification of assessments and related 

performance criteria; 

• peer reviewed theory and equations; 

• a carefully designed life-cycle development process that minimizes errors; 

• clear documentation of assumptions, theory, and parameterization that is detailed enough 

so others can fully understand the model output; 

• input data and parameters that are accurate and appropriate for the problem; 

• output data that can be used to help inform decision making. 

• documentation of any changes from the original quality assurance plan; 

 Moreover, the EPA guidance specifies that different levels of QAPP may be required 

depending on the intended application of the model, with a modeling study designed for 

regulatory purposes requiring the highest level of quality assurance. 

 The QAPP also provides a valuable resource for project management. It can be used to 

document data sources and assumptions used in the modeling study, and it can be used to guide 

project personnel through the data processing and model application process to ensure that 

choices are consistent with the project objectives. 

 The modeling team has already developed QA documents and procedures in the Phase I 

effort. For the Phase II effort these will be enhanced and modified to assure that it conforms to 

the EPA QAPP guidance. 

 The guidance document also addresses model development, coding and selection of 

models, and model performance requirements. For the Phase II modeling we are using an 

existing EPA sponsored model. Thus, our QAPP will focus primarily on documenting data 

sources and QA of data processing performed by the model team. In addition, because no official 

EPA guidance currently exists for visibility model performance, a major objective of our QAPP 

will be to propose and define model performance evaluation procedures. QA objectives for 

specific aspects of the project are discussed below, and these will be incorporated into a QAPP 

that conforms to the EPA guidance document for modeling studies. 

Appendix C.1 - 111
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 6.doc 6-2 

6.2 Emissions Model Inputs and Outputs 

Emissions Quality Assurance (QA) and Quality Control (QC) are the single most critical 

step in performing air quality modeling studies. Because emissions processing is tedious, time 

consuming and involves complex manipulation of many different types of large data sets, errors 

are frequently made in emissions processing and, if rigorous QA measures are not in place, these 

errors may remain undetected. 

As part of the VISTAS Phase II QA effort, an “Emissions Gatekeeper” function will be 

implemented similar to that used effectively in Phase I. The Study Team envisions the role of 

this Gatekeeper as one to perform quality assurance activities on the following emission 

inventory (EI) data: 

(1) EI data obtained from the VISTAS emissions inventory contractors; and 

(2) The emission inventory to be used for modeling outside of the States in the VISTAS 

region. 

Specifically, the Emissions Gatekeeper will review the content and format of the provided 

emission inventories ensuring an appropriate appraisal of the emissions data and estimates for 

the VISTAS States. Other tasks will include any additional translation from mass emissions files 

into the emissions modeling input file structure necessary for modeling. The Study Team will 

supplement these activities with QA checks on the intermediate and model output files using 

internal and public domain visualization and diagnostic packages. 

We propose to continue with multistep emissions the QA/QC approach applied in the 

Phase I modeling. This includes the initial emissions QA/QC by the Emissions Gatekeeper 

described above, as well as QA/QC by the Emissions Modeler during the processing of 

emissions and then additional QA/QC by the air quality modeler of the processed model ready 

emission files. This multistep process with three separate groups involved in the QA/QC of the 

emissions is much more likely to catch any errors prior to the air quality model simulations. 

6.2.1 Emissions Modeling QA/QC 

EMS and EPA Input Screening Error Checking Algorithms: Although the SMOKE emissions 

model will be used for emissions processing, some of the more advanced EMS input error 

checking algorithms will be used to screen the data and identify potential emission input errors. 

Additionally, EPA has issued a revised stack QA and augmentation procedures memorandum 

that will be used to identify and augment any outlying stacks. 

SMOKE error messages: SMOKE provides various cautionary or warning messages during the 

emissions processing. We will redirect the SMOKE output to log files and review the log files 

for serious error messages. An archive of the log files will be maintained so that the error 

messages can be reviewed at a later date if necessary. 

SMOKE emissions summaries: We will use QA functions built into the SMOKE processing 

system to provide summaries of processed emissions as daily totals according to species, source 

category and county and state boundaries. These summaries will then be compared with 

Appendix C.1 - 112
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 6.doc 6-3 

summary data prepared for the pre-processed emissions, e.g., state and county totals for 

emissions from the augmented emissions data. 

6.2.2 QA of the Model-Ready Emissions Impacts 

The goal of the post-processed emissions summary QA is to detect possible errors in the 

final, model-ready binary emissions files by preparing summary plots that characterize spatial 

and temporal patterns in the emissions data. This step is designed to catch errors that may be 

missed in the internal SMOKE QA procedures. We will use a QA/QC post-processing program 

that read the CMAQ-ready I/O API emissions file formats for each of the major source 

categories (mobile, area, point, biogenic, fire) and produce the following plots. 

Spatial Summary: We will sum the emissions for all layers and for all 24 hours that is used to 

prepare a PAVE plot showing the daily total emissions spatial distribution. For a 20 day 

simulation this produces approximately 20 days x 20 species x 5 emissions categories = 2,000 

plots. In our base case simulations these plots will be presented as tons per day. The objective of 

this step is to identify errors in spatial distribution of emissions. 

Vertical Profile: For point sources the emissions total for each layer will be summed and plotted 

to show the vertical distribution of emissions. These plots show the emissions on the x-axis for 

each model layer on the y-axis. The objective of this step is to identify possible errors in vertical 

distribution of emissions. 

Short Term Temporal Summary: The total domain emissions for each hour will be accumulated 

and time series plots prepared that display the diurnal variation in total hourly emissions. The 

objective of this step is to identify errors in temporal profiles. 

Long Term Temporal Summary: The total domain emissions for each day will be accumulated 

and displayed as time series plots that show the daily total emissions across the domain as a 

function of time. The objective of this step is to identify particular days for which emissions 

appear to be inconsistent with other days for no reason (e.g., not a weekend) and compare against 

the general trend. 

Control Strategy Spatial Displays: Spatial summary plots of the daily total emissions differences 

between a control strategy and base case emissions scenarios will be generated. These plots can 

be used to immediately identify a problem in a control strategy. For example, if a VISTAS states 

SO2 control strategy is being analyzed and there are changes in emissions for other pollutants or 

for SO2 outside of the VISTAS states problems in emissions processing can be identified prior to 

the air quality model simulation. 

6.3 Meteorological Model Outputs 

As part of the VISTAS Phase II QA effort, a “Meteorological Gatekeeper” function will 

be implemented similar to that used effectively in Phase I (Tesche and McNally, 2002a,b,c). The 

task of the Gatekeeper is to provide an independent review and quality assurance of the 

meteorological modeling and related data sets developed by the VISTAS meteorological 

modeling contractor (BAMS) and used subsequently by the emissions and air quality modeling 

teams. This Gatekeeper QA review serves two specific purposes: (a) to ensure that any potential 

Appendix C.1 - 113
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 6.doc 6-4 

problems with the data sets (should they exist) are identified and corrected in a timely manner, 

and (b) to provide the study team with information to support ongoing CMAQ model 

performance testing and sensitivity analyses. In the case of meteorology, the Gatekeeper’s 

independent QA analysis of the MM5 meteorological data sets serves to provide direct assistance 

to the emissions and air quality modeling team as it undertakes to ratify the SMOKE model 

outputs and to diagnose CMAQ model performance and sensitivity analyses. 

In addition to having personal responsibility for the quality and chain of custody of the 

meteorological data sets supplied by other VISTAS contractors, the Meteorological Gatekeeper 

will be responsible for ensuring and maintaining the integrity of the data files uploaded to the 

project website. This website, hosted by UCR, serves as the repository of data for the 

ENVIRON/UCR/Alpine modeling centers and for the VISTAS TAWG participants. In 

performing the Gatekeeper quality assurance activity, one of the first steps is to conduct an 

independent operational evaluation on the MM5 model results at 36 km and 12 km grid scale. 

This evaluation covers surface and aloft wind direction, temperature, mixing ratio, precipitation, 

and planetary boundary layer (PBL) depths on a continental scale (36 km) and subregional scale 

(12 km) basis. The specific techniques to be used are described in the MM5 model performance 

protocol prepared for EPA for annual modeling (McNally and Tesche, 2002). The Gatekeeper 

will also perform supplemental, ad hoc analysis of pertinent MM5 fields (e.g., PBL depths) 

where that might be useful to the emissions and air quality modeling teams. Another task of the 

Gatekeeper will be to exercise the Meteorological Chemistry Interface Processor (MCIP) version 

2.2 is to read the MM5 outputs from BAMS and produce binary input files for the CMAQ 

Chemical Transport Model (CCTM) to provide the complete set of parameters necessary in the 

emissions processing and air quality modeling. 

In summary, the quality assurance plan for the meteorological data will include the 

following elements: 

3⁄4 Upon receiving the MM5 and MCIP 2.2 output files from BAMS, we will verify the 

integrity of the file transfer (e.g., no missing and/or corrupted files); 

 

3⁄4 Since the CMAQ modeling domain is a subset of the MM5 domain, we will verify 

that the modeling domain and vertical layer structures in the MCIP files are identical 

to the CMAQ modeling domain; 

3⁄4 We will select several days of the MM5 output and reprocess the MM5 files with 

MCIP v2.2 using the predetermined MCIP options. We will then compare the MCIP 

files with those provided by BAMS to verify that we obtain identical results from the 

MCIP processing. 

3⁄4 We will create horizontal and vertical plots of temperature, pressure, precipitation, 

modeled flow patterns, PBL heights, etc. to assess whether the MCIP output fields are 

reasonable; 

Appendix C.1 - 114
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 6.doc 6-5 

3⁄4 The VISTAS 2002 MM5 simulation will be evaluated using the same surface 

observations, subdomains and procedures as used to evaluate the WRAP 2002 MM5 

simulation as an independent QA and evaluation of the database. 

3⁄4 We will make the plots available on the VISTAS website for viewing and download. 

6.4 Air Quality Model Inputs and Outputs 

Key aspects of QA for the CMAQ input and output data include the following: 

• Verification that correct configuration and science options are used in compiling and 

running each model of the in the CMAQ modeling system, where these include the 

MCIP, JPROC, ICON, BCON and the CCTM. 

• Verification that correct input data sets are used when running each model. 

• Evaluation of CCTM results to verify that model output is reasonable and consistent with 

general expectations. 

• Processing of ambient monitoring data for use in the model performance evaluation. 

• Evaluation of the CCTM results against concurrent observations. 

• Backup and archiving of critical model input data. 

 The most critical element in the QA plan for CMAQ simulations is the QA/QC of the 

meteorological and emissions input files. The major QA issue specifically associated with the air 

quality model simulations is verification that the correct science options were specified in the 

model itself and that the correct input files were used when running the model. For the CMAQ 

model we employ a system of naming conventions using environment variables in the compile 

and run scripts that guarantee that correct inputs and science options are used. We also employ a 

redundant naming system so that the name of key science options or inputs are included in the 

name of CMAQ executable program, in the name of the CMAQ output files, and in the name of 

the directory in which the files are located. This is accomplished by using the environment 

variables in the scripts to specify the names and locations of key input files. For example, if a 

model simulation is performed using the CB4 mechanism, all compile and run scripts contain the 

variable definition “$MECH = CB4”, and this variable is hard coded into the script for the 

executable name, the output file name, and the output directory name. This procedure produces 

long file/directory names but it effectively prevents mistakes or makes mistakes readily apparent 

if they do occur. 

 

 A second key QA procedure is to never “recycle” run scripts, i.e., we always preserve the 

original runs scripts and directory structure that were used in performing a model simulation. For 

example, if we perform simulation with the SAPRC mechanism, instead of editing the original 

scripts to specify “$MECH = SAPRC” we will create a parallel directory structure with a new set 

of scripts to perform the SAPRC simulations. This provides a permanent archive of the scripts 

that were used in performing model simulations. In addition, output from the model simulation 

Appendix C.1 - 115
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 6.doc 6-6 

will be directed to a log file that provides a record of input file names, warning messages etc that 

will be archived. 

 We will also perform a post-processing QA of the CMAQ output files similar to that 

described for the emissions processing. We will generate animated gif files using PAVE that can 

be viewed to search for unexpected patterns in the CMAQ output files. In the case of model 

sensitivity studies, the animated gifs will be prepared as difference plots for the sensitivity case 

minus the base case. Often, errors in the emissions inputs can be discovered by viewing the 

animated GIFs. Finally, we will produce 24 hour average plots for each day of the CMAQ 

simulations. This provides a summary that can be useful for more quickly comparing various 

model simulations. 

Appendix C.1 - 116
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-1 

7.0 MODEL PERFORMANCE EVALUATION 

7.1 OVERVIEW

As noted in Chapter 1, Appendix A presents a summary of the Scope of Work (SOW) for the 

VISTAS Phase II Emissions and Air Quality Modeling activities. This Phase II SOW delineates the 

tasks, approach and schedule for carrying out the various technical activities described in greater 

detail in this modeling protocol. The SOW in Appendix A is broken down into a base effort that 

focuses on annual modeling of 2002 and several optional tasks to be evaluated by VISTAS. The 

ultimate objective of the Phase II work effort in 2004 is to obtain a properly evaluated operational 

emissions and air quality modeling system for the 2002 annual calendar year so that control strategy 

evaluation can begin in 2005. Given the formal contractual role that the SOW plays in guiding the 

work products of the Emissions and Air Quality Modeling Team in Phase II, where ambiguities 

might arise regarding the Task 4a/4b model evaluation effort, the SOW takes precedence over this 

Protocol Document. Consistent with the spirit of a modeling protocol for regulatory decisionmaking, this document lays out the ‘roadmap’ for achieving an adequately tested modeling system 

for regulatory usage. But, obviously, this does not mean that every analysis identified in this chapter 

will be carried out or is indeed even possible given the Phase II schedule and resources, the existing 

aerometric data bases, and present technology constraints. The roadmap guides the way to the 

desired destination – in this case, an evaluated, operational PM/regional haze modeling system – but 

does not commit the driver to exploring every side street and back country road along the way. 

Indeed, one expectation of the VISTAS TAWG is a close working relationship with the modeling 

team to ensure that the available resources and schedule are applied most efficiently in reaching the 

aforementioned goal. 

 This chapter describes a range of model testing methodologies potentially available to the 

Emissions and Air Quality Modeling study team in its efforts to adequately evaluate the performance 

of the CMAQ air quality modeling system for the 2002 annual period. Since one cannot know at 

this juncture the specific performance problems that may arise in the initial 2002 CMAQ testing 

(Task 4a) or the final year 2002 evaluation (Task 4b), we set forth in this chapter a broad range of 

methods and techniques that may be brought to bear in examining CMAQ model performance. We 

identify the core operational evaluation procedures, recommended in EPA (2001) guidance, that will 

be performed in Tasks 4a and 4b. We also describe a broad range of additional performance testing 

methods that may be worth considering, if necessary. Implementation of one or several of these 

various techniques would fall under Optional Task 14 (Enhanced Model Performance Evaluation). 

The Optional Task 14 represents a means for marshalling additional VISTAS funding, or perhaps 

supplemental funding from other stakeholder groups, for the purpose of enhancing the core 

operational evaluation presently budgeted for Tasks 4a and 4b. Should portions or all of Optional 

Task 14 be invoked, we strongly recommend that this be guided by a cooperative effort by the 

modeling team and the TAWG to ensure that the highest priority “supplemental evaluations” be 

selected and properly carried out. 

 Clearly, not all of the supplemental evaluative techniques identified in this chapter will 

ultimately be performed. There are three reasons for this: 

3⁄4 The Phase II SOW places clear limits on the resources available to perform model 

evaluation analyses. Accordingly, some evaluation steps, while desirable, simply 

Appendix C.1 - 117
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-2 

may not be possible given current funding levels; 

3⁄4 The Phase II SOW places stringent schedule demands on the model evaluation. A 

number of the model performance evaluation methods introduced in this chapter (e.g. 

Weight of Evidence analyses, diagnostic testing with individual measurement 

networks, PM indicator species and ratios analyses, use of the alternative CAMx 

model) could very likely require more time to carry out given their quasi-research 

nature. Since VISTAS Phase II is not a model research and development effort, but 

rather an operational evaluation of existing modeling systems for regulatory 

decision-making, some interesting, but time consuming analyses simply may not be 

possible given the present schedule; and 

3⁄4 To conform to the EPA PM guidance documents requirements for PM model testing, 

it may not be necessary to conduct many of the diagnostic and Weight of Evidence 

tests identified in this protocol. Indeed, an adequate evaluation of the Phase II 

modeling system may be possible through straightforward application of the core 

operational performance evaluation procedures identified in EPA’s 2001 draft 

guidance. 

 At a minimum, the evaluation of the CMAQ modeling system for the Phase II annual 2002 

simulation (and for any additional episodes that might be chosen by VISTAS) will be consistent with 

EPA’s draft guidance on PM model testing. This guidance essentially calls for an operational 

evaluation of the model focusing on a specific set of gas phase and aerosol chemical species and a 

suite of statistical metrics for quantifying model response over the annual cycle. The emphasis is on 

assessing: (a) How accurately the model predicts observed concentrations? and, (b) How accurately 

does the model predict responses of predicted air quality to changes in inputs? States are 

encouraged to utilize the evaluation procedures set forth in the earlier 1991 guidance document 

(EPA, 1991) for gas phase species and the newer (2001) guidance of PM species. Thus, in carrying 

out the initial Task 4a operational evaluation and the subsequent Task 4b final evaluation, we will 

implement the suggested EPA performance testing methodologies for the key gas phase and aerosol 

species. Since these methods are explicitly presented in EPA’s guidance document, there is no need 

to repeat them here. 

 Subject to the availability of time and Optional Task 14 resources, the Phase II evaluation 

will also attempt to employ other testing methods beyond those in the EPA guidance document. In 

addition, if the initial Task 4a evaluation evolves smoothly without problems arising in the early 

performance testing efforts, resources and/or time conserved in such a situation might then be used 

to underwrite on or more scientifically rigorous model performance investigations (e.g., those 

afforded by the rich observational networks such as the continuous speciation SEARCH 

measurements and the EPA Supersite data). To this end, we discuss in this chapter various 

supplemental performance testing methods that might be worth pursuing given adequate, additional 

resources and time. 

 We conclude by again emphasizing that most important goal of the Phase II CMAQ 

evaluation is to determine whether the aggregate modeling system (model codes plus input data sets 

and observational data for testing) offers sufficiently reliable and accurate results that public 

decision-makers may have reasonable confidence in using the model to help choose between 

Appendix C.1 - 118
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-3 

alternative regional haze reduction scenarios. If the CMAQ model evaluation, as outlined in this 

chapter, provides sufficient evidence that the modeling system is operating reliably and in 

conformance with measurements and scientific expectations, then specific justifications explaining 

why the model is acceptable for developing regional haze strategies will be offered in the 2002 

CMAQ Modeling Summary Report. Conversely, should the evaluation determine that the modeling 

system suffers from important flaws or errors that undermine its reliability or use, these findings will 

also be documented, together with recommendations regarding the use of alternate methods, steps to 

improve the model and/or data base, or other approaches. 

7.2 Context for the VISTAS Phase II Model Evaluation 

 We begin the discussion of the Phase II modeling evaluation methodology by reviewing how 

the CMAQ model output is used in regional haze applications to project changes in visibility1

. 

When designing a model performance evaluation, it is important to understand how the modeling 

results will ultimately be used. EPA has published two versions of draft guidance for fine particulate 

and regional haze modeling (EPA, 2000; 2001), utilizing a Fine Particulate Guidance Workgroup to 

provide technical input in the development of both documents2

. More recently, EPA has provided 

an informal update on the PM/regional haze modeling guidance (Timin, 2002) and conducted a PM 

model evaluation workshop (see, for example, Timin, 2004; Boylan, 2004) shedding additional light 

on what the final guidance document might contain. 

A key concept in EPA’s guidance for addressing regional haze issues is that the modeling 

results should be used in a relative sense to scale or roll back the observed particulate matter (PM) 

concentrations from which light extinction is estimated. Adopting the recommendations from the 

Federal Land Managers’ Air Quality Related Values Workgroup (FLAG), estimates of visibility are 

obtained from observed fine particulate concentrations using the following IMPROVE reconstructed 

mass extinction equation (FLAG, 2000): 

bext = 3{f(RH)[(NH4)2SO4]} + 3{f(RH)[NH4NO3]} 

 + 4{f’(RH)[OC]} + 10[EC] + 1[IP] 

+ 0.6[CM] + brayleigh 

where: 

 bext is the estimated extinction coefficient (Mm-1); 

 [SO4] is the sulfate concentration assumed to be ammonium sulfate; 

 [NO3] is the particulate nitrate concentration assumed to be ammonium nitrate; 

 [OC] is the organic carbon concentration; 

 [EC] is the elemental carbon concentration; 

 

1

 Details on the definitions of model performance evaluation statistical measures and graphical 

displays in three reports to VISTAS: (a) the Phase I Task 2 model configuration report (ENVIRON, 

2003b), (b) the Task 4a/b model sensitivity and CMAQ configuration report (ENVIRON, 2003d), 

and (c) the Final Phase I Evaluation and Model Sensitivity Analysis report (ENVIRON, 2004). 

Additional details are also presented in Table 7-4. 

2 Members of the VISTAS modeling team participated on this work group over the two-year span of 

its activities. 

Appendix C.1 - 119
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-4 

[IP] is the inorganic primary fine particulate (< 2.5 :) concentration excluding primary 

sulfates and nitrates; 

[CM] is the coarse particulate (> 2.5 : and < 10 :) concentration; 

brayleigh is the light-scattering due to Rayleigh scattering (assumed to be 10 Mm-1); 

f(RH) is a relative humidity adjustment factor for the sulfate and nitrates; and 

f’(RH) is a relative humidity adjustment factor for OC that is assumed to be 1.0. 

The relative humidity (RH) values used in the above equation are monthly- specific and 

Class I area-specific values based on a long term average (EPA, 2003a). 

The regional haze rule expresses reasonable progress in terms of changes in the deciview 

()dV) from the current to future year conditions. Deciview (dV) is expressed as the natural 

logarithm of the extinction coefficient (bext) to Rayleigh scattering: 

Deciview = 10 ln(bext/10) 

)dV = 10 ln[(bext)future / (bext)base] 

In this framework, changes in visibility in terms of percentage changes in extinction over a 

natural “clean” background visibility rather than changes in deciview. Changes in deciview or 

extinction are essentially mathematically identical with a 1% change in deciview being 

approximately equivalent to a 10% change in extinction. Both visibility parameters will be 

calculated in the Phase II model applications. 

The VISTAS Phase II model testing will concentrate on an operational evaluation of those 

model predictions that are most necessary for estimating visibility (i.e., NH4, SO4, NO3, OC, EC, IP 

and CM). Where feasible and supported by sufficient measurement data, we will also evaluate the 

modeling system for its ability to accurately estimate gas-phase oxidant and precursor/product 

species since correct, unbiased simulation of gas-phase photochemistry is a necessary element of 

reliable regional haze predictions. This evaluation will be carried out across the full VISTAS 

domain for the entire year and also on subdomains and month-by-month basis to help build 

confidence that the modeling system is operating correctly. With this context in mind, we next turn 

to the philosophy of the model evaluation process. 

7.3 Multi-Layered Model Testing Process 

EPA’s “Draft Guidance for Demonstrating Attainment of Air Quality Goals for PM2.5 and 

Regional Haze” (EPA, 2001) affirms the recommendations of numerous modeling scientists over the 

past decade (see, for example, Dennis et al., 1990; Tesche et al., 1990, 1994; Seigneur et al., 1998, 

2000; Russell and Dennis, 2000; Arnold et al., 2003; Boylan et al., 2003; Tonnesen, 2003) that a 

comprehensive, multi-layered approach to model performance testing should be performed, 

consisting of the four components: operational, diagnostic, mechanistic (or scientific) and 

probabilistic. As applied to regional PM/visibility models, this multi-layered framework may be 

viewed conceptually as follows: 

> Operational Evaluation: Tests the ability of the model to estimate PM concentrations 

(both fine and coarse) and the components at PM10 and PM2.5 including the quantities 

Appendix C.1 - 120
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-5 

used to characterize visibility (i.e., sulfate, nitrate, ammonium, organic carbon, elemental 

carbon, PM2.5, and PM10). This evaluation examines whether the measurements are 

properly represented by the model predictions but does not necessarily ensure that the 

model is getting “the right answer for the right reason”; 

> Diagnostic Evaluation: Tests the ability of the model to predict visibility and extinction, 

PM chemical composition including PM precursors (e.g., SOx, NOx, and NH3) and 

associated oxidants (e.g., ozone and nitric acid); PM size distribution; temporal variation; 

spatial variation; mass fluxes; and components of light extinction (i.e., scattering and 

absorption); 

> Mechanistic Evaluation: Tests the ability of the model to predict the response of PM 

and visibility to changes in variables such as emissions and meteorology; and 

> Probabilistic Evaluation: Takes into account the uncertainties associated with the 

model predictions and observations of PM and visibility. 

Within the constraints of the Phase II schedule and budget resources the VISTAS Phase II effort will 

attempt to include elements of each of these components. The operational evaluation will obviously 

receive the greatest attention since this is the primarily thrust of EPA’s 2001 PM guidance. 

However, we will consider, where feasible and appropriate, diagnostic and mechanistic tests (e.g., 

use of probing tools, indicator species and ratios, aloft model evaluations, urban vs. rural 

performance analyses), traditional sensitivity simulations to explore uncertainty, and the use of 

alternative science platforms (e.g., CAMx). The scope of these additional diagnostic and 

mechanistic tests will be shaped by the resources available in Optional Task 14 and the timing of 

when such analyses are commissioned relative to the Phase II schedule and resources. 

Before discussing the types of testing procedures available for the above evaluation 

components, we first identify the surface and aloft data sets that are available to support these 

comparisons. 

7.4 Development of Consistent Evaluation Data Sets 

 7.4.1 Surface Measurements 

 The ground-level model evaluation database will be developed using several routine and 

research-grade databases. The first is the routine gas-phase concentration measurements for ozone, 

NO, NO2 and CO archived in EPA’s Aerometric Information Retrieval System (AIRS/AQS) 

database. Other sources of information come from the various PM monitoring networks in the U.S., 

with particular emphasis in the central and eastern U.S. These include the: (a) Interagency 

Monitoring of Protected Visual Environments (IMPROVE), (b) Clean Air Status and Trends 

Network (CASTNET), (c) Southeastern Aerosol Research and Characterization (SEARCH), (d) EPA 

PM2.5 and PM10 Mass Networks (EPA-FRM), (e) EPA Speciation Trends Network (STN); (f) 

National Acid Deposition Network (NADP) and (g) EPA Supersites (EPA-SPEC) networks. 

Typically, these networks provide ozone, other gas phase precursors and product species, PM, and 

visibility measurements. Noteworthy is the continuous speciated PM2.5 measurements available 

Appendix C.1 - 121
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-6 

from the SEARCH network for 2002 modeling period. For 2003 episode modeling, additional 

continuous PM speciated data will be available from the FOCUS network. 

 As an example, the IMPROVE network gives daily (24-hour) average mass concentrations 

every 3 days for SO4, NO3, organic carbon (OC), elemental carbon (EC), soil (IP), CM, PM2.5 and 

PM10. These data are available at approximately 38 sites in the VISTAS 12 km domain. In addition, 

hourly values of light extinction and deciview are available at several of these sites. The SEARCH 

network provides 24-hour as well as continuous (hourly) speciated measurements of PM2.5

components and other specifics from 8 stations, depending on the time period (Hansen et al., 2003). 

We will use data from these and the other observational databases listed in Table 7-1, supplemented 

with the routine AIRS/AQS data, as appropriate, for CMAQ model performance testing. 

 Care must be taken in selecting data that are representative of regional concentrations and the 

prediction of regional haze at the sensitive Class I areas within the VISTAS (see Table 7-3). For 

example, the criteria and other pollutants in the AIRS/AQS database are typically urban-oriented. 

Thus, would not expect CMAQ predictions for these species using a 36/12 km grid mesh to be 

ideally suited to simulating urban-scale concentrations. With other data sets (e.g., SEARCH) it may 

be possible to reproduce the urban-to-rural gradients in PM2.5 components. While finer grid meshes 

(e.g., 4 km) might be more appropriate, high-resolution modeling at 4 km scale on an annual time 

frame for the VISTAS region is prohibitive given current computer technology and model run times. 

 Accordingly, some selectivity is needed in assembling pertinent measurement sites for comparisons 

with regional-scale model predictions and the interpretation of the modeled and measured 

comparisons must be made with care. 

 

 Another important consideration is that different PM monitoring networks may use different 

measurement approaches that “measure” different amounts of the same species that are also different 

from the modeled species. For example, the IMPROVE network only speciates PM2.5 so any sulfate 

or nitrate in the coarse mode (PM2.5-10) is included in the CM species. As was done in Phase I, the 

model will be evaluated separately for each network. While Phase II is clearly not aimed at new 

model development or algorithm refinement, information discerned from model performance across 

the various networks should be useful in later model refinement activities and network design 

improvements. Finally, the mapping of the modeled species to the monitored data will also have to 

be performed in a consistent fashion. 

 The VISTAS Phase I air quality data assessment report (ENVIRON, 2003c) provides more 

details on the ambient monitoring data available for Phase II modeling. 

 7.4.2 Aloft Measurements 

In recent years, the use of instrument aircraft in support of regulatory monitoring and research 

programs has become much more commonplace. Indeed, in the upper Midwest, the Lake Michigan 

Air Directors Consortium (LADCo) has been centrally involved in aircraft programs to support 

model development and applications studies for seventeen (17) years, beginning with pioneering 

flights in 1987. Supplementing the long-term sampling performed by LADCo in the Midwest, there 

have been other occasional intensive airborne sampling campaigns throughout the eastern U.S. (e.g., 

the 1999 SOS field program which provided aloft data for our evaluation of CMAQ for the July ’99 

episode), that have produced very useful information for air quality model performance testing. 

Appendix C.1 - 122
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-7 

Fortunately, during CY-2002, there were at least two mature airborne field programs underway in 

the eastern U.S. One was centered over the Midwest, the other on the mid-Atlantic coast. A brief 

characterization of these potentially valuable CMAQ model evaluation data sets is given here. Note 

that the advanced modeling evaluation using non-routine data sets like aircraft data, would be 

covered under Optional Task 14 (see Appendix A). 

During 2002, the Wisconsin Department of Natural Resources (WDNR) and the Midwest 

RPO (MRPO) (who funded the Jacko aircraft) collaborated on the support of airborne sampling 

using two aircraft that, along with ground-based measurements, provided a 3-dimensional 

representation of air pollution concentrations across the upper Midwest with some flight paths 

extending south to include the Mammoth Cave, KY and Dolly Sods, WV Class I areas in the 

VISTAS domain. The goal of the WDNR/MRPO flights was to collect aloft air quality and 

meteorological data to support model evaluation and data analyses. The aircraft flights were aimed 

at: (1) characterizing high fine particle and ozone episodes, (2) characterizing air quality over the 

Class I areas in the upper Midwest (Isle Royale National Park and Seney National Wildlife Refuge 

in northern Michigan) on both clean and hazy days, and (3) characterizing urban areas in the 

Midwest. 

As indicated in Table 7-2, airborne sampling was performed over a broad region of the 

Midwest (including portions of the VISTAS states) from 1 June to 22 November. Lasting 3-5 hours, 

the WDNR and Jacko aircraft sampled a variety of aerometric parameters (depending upon the flight 

and aircraft) including wind speed, wind direction temperature, dew point, relative humidity, 

pressure, O3, NO, NO2, NOx, NOy, speciated VOCs, carbonyls, HNO3, NH3, Hg, SO4, OC, EC, 

PM2.5, and light scattering (Neph). Still photographs documenting visibility were also collected. 

Presently, the full WDNR/MRPO aircraft database, from the first flights in 1987 to the recent 

sampling in 2003 is being aggregated into a master data base archive. 

 At the University of Maryland, researchers have been using ground-based monitors, 

radiosondes, profilers, and instrumented aircraft to make observations each year since 1992. 

Parameters measured included meteorology; selected trace gases; fine particulate chemistry, 

microphysics and optical properties across broad regions of the middle Atlantic coast. During 2002, 

the University Research Foundation’s Aztec-F aircraft instrument suite included O3, NO, CO, SO2 

samplers, as well as a NO2 closed-path tunable diode laser system, and a differential GPS-based 

meteorology (T, RH) and horizontal wind (u and v horizontal components) data system. Aztec-F 

flights were made from 23 May to 3 October, typically lasting 3 hours. 

The volume of aircraft information available for CMAQ performance testing during 2002 is 

quite significant and, as discussed later, this data set will be used as extensively as possible. 

Historically, aircraft data sets have been used only sporadically in evaluating model performance 

aloft. To our knowledge, the VISTA Phase II evaluation under optional Task 14 could represent the 

most thorough utilization of aircraft data for regional model ozone/PM model evaluation yet 

attempted. 

7.5 Model Evaluation Tools 

This section introduces the various statistical measures, graphical tools, and related analytical 

procedures that have proven useful over the years in evaluating grid-based chemical transport 

Appendix C.1 - 123
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-8 

models. Many of the methodologies mentioned below were utilized to one degree or another in 

Phase I. Where appropriate, they will also be used in the 2002 annual and episodic evaluation of the 

CMAQ modeling system. However, as with Phase I, while we plan on calculating a rich variety of 

statistical performance metrics, only a very limited subset of these measures will actually be relied 

upon to form judgments concerning model acceptability and in the final reporting. 

 The current methodologies and statistical metrics may be augmented, as necessary and 

appropriate, by new measures that may become available during the course of the Phase II modeling. 

Definitions of the statistical measures for gas-phase species such as ozone are provided in the Phase 

I Task 4 report (ENVIRON, 2003d); measures geared more toward fine particulate aerosol species 

are identified later in this chapter. In sum, the Phase II evaluation will employ similar methods and 

evaluation tools used in Phase I but the evaluation will remain open to emergent methods for testing 

model performance where necessary and consistent with the project schedule and resources.

 7.5.1 Statistical Performance Metrics 

EPA’s 2001 PM and regional haze guidance suggests a suite of metrics for use in evaluating 

model performance. The standard set of statistical performance measures suggested by EPA for 

evaluating fine particulate models include: (a) normalized bias; (b) normalized gross (unsigned) 

error; (c) fractional bias; (d) fractional gross error; and (e) fractional bias in standard deviations. 

These measures are subsumed within the list of metrics that were calculated on a routine basis in 

Phase I using the UCR analysis package. (These are identified in Table 7-4). The UCR evaluation 

software will generate these statistical measures for each model simulation performed for each 

analysis region (see below). In parallel, the AG MAPS software will be used to generate 

complimentary statistical measures which combine the methods recommended in the EPA ozone 

guidance (EPA, 1991; 1999) and the newer 2001 PM guidance. From past regional PM model 

evaluations we have found the fractional bias and fractional error to be the most useful summary 

measures and we will focus mainly upon them in Phase II, but not to the exclusion of others that are 

found to yield discriminating power. For ozone and other gas phase species (NO, NO2, SO2) we will 

include use the traditional statistical measures (Tesche et al., 1990; EPA, 1991, 1999) develop with 

MAPS as an adjunct to the UCR analysis measures. 

Typically, the statistical metrics are calculated at each monitoring site across the full 

computational domain for all simulation days. In the Phase II CMAQ evaluation, we will stratify the 

performance statistics across relevant space and time scales. As part of the Task 4a/b operational 

evaluation, the gas-phase and aerosol statistical measures shown in Table 7-4 will be computed for 

the full 36 km and 12 km domains, as well as for the individual RPOs (including VISTAS of 

course) and on other subdomains as appropriate. Temporally, we will compute the statistical 

measures for the appropriate averaging times: 1 hr for ozone, and gas-phase precursors such as NO, 

NO2, CO, SO2; 8-hr for ozone, and 24 hr for sulfate, nitrate, PM and other aerosol species. These 

results will then be averaged over annual, monthly, and seasonal periods for display, further 

analysis, and reporting. Should it become necessary as part of model performance diagnosis, we 

will consider aggregating the statistics in other ways, e.g., (a) day vs. night, (b) weekday vs. 

weekend, (c) precipitation vs. non-precipitation days, (d) month of the year, and (e) the 20% 

haziest/cleanest days, in order to help elucidate model performance problems. Absent performance 

difficulties, these supplemental time/space analyses would only be considered if supported under 

directed Optional Task 14 funding. In subregional performance testing, the focus would likely be on 

Appendix C.1 - 124
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-9 

the Class I areas and sites where enhanced monitoring (EPA STN locations, the hourly/daily 

SEARCH sites) within the VISTAS 12 km domain (Hansen et al., 2003) is available. 

As part of the operational evaluation, the metrics defined in Table 7-4 will be calculated for 

each gas phase species and each fine particulate species in the extinction equation as well as 

separately for SO4, NO3 and ammonium (NH4) on both the 36 km and 12 km domains. In any 

diagnostic evaluations that are performed, we will examine the model’s ability to estimate the 

gaseous species listed above from EPA’s guidance (EPA, 2001). However, in reality ambient 

gaseous species in 2002 are principally available for ozone, NO2, SO2, and CO. Since most of the 

gaseous air quality monitors are located in urban settings, these data sets will be of somewhat 

restricted value in evaluating the 36/12 km regional-scale CMAQ predictions. Under Optional Task 

14, we would consider the merits of assembling a rural-oriented gaseous species observational 

model performance evaluation database for use with CMAQ. This database could be composited 

with measurement from rural sites from the AQS, CASTNet, NPS, STN, and SEARCH networks. If 

commissioned under Optional Task 14 by VISTAS, this rural vs. urban scale operational evaluation 

would be conducted to augment the more traditional operational evaluation using all valid data sets. 

 

 7.5.2 Graphical Representations 

The Task 4a/b core operational air quality model evaluation will utilize numerous graphical 

displays to facilitate quantitative and qualitative comparisons between CMAQ predictions and 

measurements, many of which were used in the Phase I Final Report (ENVIRON, 2004). Together 

with the statistical metrics listed in Table 7-4, the graphical procedures are intended to help: (a) 

identify obviously flawed model simulations, (b) guide the implementation of Task 4a/4b 

performance improvements in the 2002 model input files in a logical, defensible manner, and (c) to 

help elucidate the similarities and differences between the alternative CMAQ simulations. These 

graphical tools are intended to depict the model’s ability to predict the observed fine particulate and 

gaseous species concentrations. 

The Phase I modeling helped to refine the suite of graphical tools most effectively in 

assessing model performance and the differences between the baseline CMAQ runs and sensitivity 

experiments. The core graphical displays to be considered for use in Phase II include the following: 

> Spatial mean concentration time series plots; 

> Time series plots at monitoring locations; 

> Ground-level gas-phase and particulate concentration maps (i.e., tile plots); 

> Concentration scatterplots stratified by station, by time, and by network; 

> Bias and error stratified by concentration; 

> Bias and error stratified by time; 

> Histogram plots of the statistical metrics, stratified by day, by pollutant, by subregion 

(e.g., 12 km vs. 36 km, by RPO), and by monitoring network; and 

> Quantile-Quantile (Q-Q) plots. 

These graphical displays will be generated, were appropriate for the full annual cycle as well as for 

monthly and seasonal periods. The displays will be generated with a consistent suite of products 

including the UCR analysis tools, Alpine MAPS software and ENVIRON evaluation software. 

Appendix C.1 - 125
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-10 

 

Appendix C.1 - 126
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-11 

7.5.3 MAPS/Flying Data Grabber Routines 

This section describes the procedures we would implement for the aloft gas phase and PM 

model evaluation with CMAQ using aircraft data should Optional Task 14 be commissioned by 

VISTAS. This aloft performance evaluation would employ aircraft data sets from various sampling 

programs carried out over the Midwest and eastern U.S. during 2002. Details on how these data are 

used to evaluate CMAQ performance aloft together with findings from our aloft model evaluations 

with the 10-21 July 1999 episode are described in the Phase I Final Report (ENVIRON, 2004). 

The principal challenge in using the aircraft data for meteorological and photochemical 

model evaluations relates to the ‘incommensurability’ of Lagrangian aircraft observations with 

Eulerian (i.e., fixed location) volume-averaged model estimates (see, for example, Hanna, 1994). 

Aircraft data are essentially continuous, high frequency Lagrangian samples having response times 

on the order of 30 seconds or less. In contrast, CMAQ model estimates represent hourly-averaged 

values. Thus, the aircraft data must be averaged in some manner to yield quantities that are at least 

qualitatively comparable to the air quality fields estimated by CMAQ in the grid volume(s) through 

which the aircraft passes. The objective is to develop hourly-average time series of measurements 

and model estimates that are as nearly comparable as possible. 

The procedures proposed for processing the aloft meteorological and air quality observations 

and CMAQ model predictions have been described in several science reports prepared in connection 

with the Lake Michigan Ozone Study (Tesche and McNally, 1993a-d, 2001) and more recently the 

Houston-Galveston 1-hr ozone SIP modeling that utilized the TexAQS 2000 data base (Tesche and 

Jeffries, 2002). These methods, formalized within AG’s Flying Data Grabber (FDG) model, were 

employed in Phase I for the 13-21 July 1999 episode. The methods used are substantial extensions 

of the techniques pioneered a decade ago by Schere and Wayland (1989) for the Regional Oxidant 

Model (ROM2.0) evaluation against the NEROS database and by Barchet and Dennis (1990) for the 

RADM/ADOM evaluation (Dennis et al., 1990). 

For a typical aircraft (or helicopter flight), the Flying Data Grabber first identifies the 

specific time interval during which the aircraft was located in a given CMAQ model grid cell along 

the flight path. The observations are then integrated to produce mean, standard deviation, bias and 

error estimates for the variable measured within each grid cell of the flight path. This averaging 

process produces an observed, averaged time series for the above statistical quantities along the 

flight path. Note, that these time intervals are characteristically much smaller than the one-hour 

model averaging time. Flight path statistics, together with the mean modeled and observed 

horizontal winds along the flight paths are also produced by the FDG. The maximum and minimum 

values during each time segment within a grid cell are also recorded. 

The FDG methodology further assumes that the air quality model estimates vary 

approximately linearly during each hour. It is then straightforward to construct an estimated time 

series of the modeled values that corresponds to the above-described observed time series derived 

from the aircraft data. The measurements and model estimates, now on roughly comparable time 

and space scales, are subsequently processed with the MAPS statistical/graphical software tools 

described in the Phase I Task 4a report (ENVIRON, 2003d). The statistics of principal interest are 

the mean values of the observed and modeled concentrations together with estimates of bias and 

Appendix C.1 - 127
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-12 

imprecision (i.e., gross error). A variety of graphical representations are also produced to facilitate 

evaluation an intercomparison. 

7.5.4 Use of Multiple Evaluation Packages

In Phase I model evaluation (ENVIRON, 2004) relied principally on the UCR evaluation 

package that was originally developed for WRAP and then enhanced by VISTAS. This package 

produce scatter plots by site, day or all sites and days, time series plots and statistical measures. In 

Phase I modeling an error was introduced in the extension of the package to treat 12 km grids that 

caused some delays as we attempted to resolve the 36 km and 12 km performance issues. In Phase II 

we will attempt to prevent such a reoccurrence by using additional software evaluation packages 

specifically, the Alpine MAPS package will be used to not only corroborate the UCR results but also 

provide some additional model evaluation measures and displays (e.g. spatial average time series 

plots). In addition; ENVIRON’s evaluation software that focuses on the evaluation of the model at 

Class I areas for the 20% best and 20% worst days will be employed to identify how the model is 

predicting PM species on these key days and identify any days from the 20% worst and 20% best 

days3

 where model performance is so suspect that use of the modeling results on these days to 

project visibility improvements may not be desirable. 

 7.5.5 Probing Tools and Allied Methods 

 The CMAQ model evaluation in Tasks 4a and 4b will employ routine operational evaluation 

methods and standard statistical metrics (Table 7-4) and graphical displays to support the assessment 

of whether the model is shown to perform with sufficient accuracy and reliably for its intended 

purpose. Ideally, this operational evaluation will confirm that the modeling system is performing 

consistent with its scientific formulation, technical implementation, and at a level that is at least as 

reliable as other current state-of-science methods. Should unforeseen model performance problems 

arise in the initial or refined year 2002 model simulations, it may be necessary to draw into the 

evaluation supplemental diagnostic tools to aid in model testing. These diagnostic techniques are 

loosely referred to as “probing tools”. The actual need for their use, if any, can only be determined 

once the initial 2002 CMAQ operational evaluation is completed. Should such diagnostic methods 

actually be needed, their usage would be funded by Optional Task 14 and/or Optional Task 15 

(Contingency). The scope of these additional analyses into the Task 4a/b evaluation process will be 

closely coordinated with the VISTAS TAWG, with due consideration being given to the Phase II 

schedule and resources. Below, we identify the types of probing tools that could be brought to bear 

under Optional Tasks 14 and/or 15 should their use become necessary at some later time. 

Current ‘One-Atmosphere” models such as CMAQ and CAMx have been outfitted with a 

number of “probing tools” that have proven to be very useful in testing and improving model 

performance and in evaluating emissions control strategies. Among the probing tools available in 

one or both models are: (a) ozone source apportionment technology (OSAT) algorithms, (b) process 

analysis (PA), and (c) the direct decoupled method (DDM) for sensitivity analysis. In addition, the 

 

3

 Mention here and elsewhere in this protocol of evaluation efforts for the 20% best and worst days 

is in addition to the planned evaluation of all days in the annual cycle. While EPA visibility 

guidance addresses the 20% days, and our evaluation is tailored to follow the guidance, the overall 

CMAQ evaluation will address all days in the year. 

Appendix C.1 - 128
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-13 

project team is implementing PM Sour apportionment techniques in CMAQ and CAMx. VISTAS 

may choose to evaluate these tools as part of the Phase II modeling exercise. It is currently unclear 

what funding will be available under Optional Tasks 14 and/or 15 for these options. 

Source Apportionment Technology: CAMx contains a suite of “source attribution” 

methods. One such method is Ozone Source Apportionment Technology (OSAT). OSAT tracks 

ozone formation based on how groups of ozone precursors contributed to ozone formation. Thus, 

OSAT decides whether ozone formation is NOx or VOC limited in each grid cell at each time step, 

and bases ozone attributions on the relative amounts of the limiting precursor from different sources 

that are present in that grid cell at that time step. These incremental ozone attributions are integrated 

throughout the model run. The method is generally applicable and has been widely used to aid 

model diagnosis in the performance testing phase and to guide control strategy formulations as well. 

 

A new PM Source Apportionment Technology (PSAT) is being implemented in CAMx funded by 

the MRPO that is in its final stages of testing. A Tagged Species Source Apportionment (TSSA) 

approach has also been implemented in CMAQ and tested for nitrate (Tonneson, 2004, personal 

communication). 

Decoupled Direct Method (DDM): Various forms of the Decoupled Direct Method (DDM) 

have been installed in CMAQ and CAMx, based on the original work of Dunker and co-workers 

(Dunker, 1981; 1984; Dunker et al., 2002) and researchers at Georgia Institute of Technology (GIT). 

 In general, the DDM method: (a) calculates first order sensitivities dC/dP where C is a 

concentration output and P an input parameter4

, (b) promotes accuracy by using consistent numerical 

methods and the same time steps for concentrations and sensitivities, (c) optimizes the code for 

efficiency, but not at expense of accuracy, and (d) calculates sensitivities with respect to parameters 

representing pollutant sources – emissions, BCs and ICs. Finally, the DDM provides a flexible and 

powerful user interface for defining various sensitivities including: 

> Emissions resolved by geographic area. 

> Emissions resolved by source category. 

> BCs optionally resolved by boundary edge (N, S, E, W, Top). 

> All sensitivities available relative to sources of individual species (NO, PAR, etc.) or 

species group (VOC, NOx or ALL). 

> Simultaneously calculate sensitivities to many initial condition, boundary condition 

and emissions parameters. 

In recent comparisons between CAMx DDM sensitivities and brute-force sensitivities 

(calculated from +/- 20% perturbations) Dunker et al., (2002a,b) reported that sensitivities of ozone 

with respect to area source NOx and VOC emissions were calculated and results indicated that the 

agreement between DDM and brute force sensitivities is excellent. DDM implementation into 

CMAQ is reported by Kumar (2003). 

Process Analysis (PA): Photochemical air quality model simulations are usually evaluated 

primarily in terms of their ability to simulate observed O3 data. There is an increasing awareness that 

 

4 Recent research by Prof. Russell and coworkers at GIT has led to the extension of the CMAQ 

DDM method to include second order sensitivity coefficients (see, Hakami et al., 2003). 

Appendix C.1 - 129
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-14 

chemical mechanisms, and air quality models must also be evaluated in terms of their ability to 

simulate the fundamental chemical processes that control O3 formation and the sensitivity of O3 to 

emissions reductions (Arnold et al., 1998). Process analysis is a method for explaining model 

simulations by adding algorithms to the AQM to store the integrated rates of species changes due to 

individual chemical reactions and other sink and source processes (Jeffries and Tonnesen, 1994; 

Tonnesen, 1995). By integrating these rates over time and outputting them at hourly intervals, 

process analysis provides diagnostic outputs that can be used to explain a model simulation in terms 

of the budgets of free radicals, production and loss of odd oxygen and O3, and conversion of NOx to 

inert forms, as well as the effects of transport and other sink and source terms. Of particular 

importance to the VISTAS modeling, process analysis can also improve model diagnosis and 

performance evaluation efforts by identifying processes that are ‘out of balance’ (Tesche and 

Jeffries, 2002), by identifying situations for which the model formulation and/or implementation 

should not be expected to apply and by suggesting how ambient data can be used to evaluate model 

accuracy for key terms in the chemical processing of VOC and NOx (e.g., Imre et al., 1998). 

Process Analysis (PA) is implemented in both CMAQ and CAMx and each model supports 

three complementary aspects of the method: (a) the integrated process rate (IPR), (b) integrated 

reaction rate (IRR) and (c) chemical process analysis (CPA). Several versions of process analysis 

(PA) have been implemented in air quality models (AQMs) including both trajectory models 

(Tonnesen, 1990, 1995) and grid models (Jang et al., 1995, Tonnesen and Dennis, 2000; Arnold et 

al., 1998; and Wang, 1997). 

The fundamental approach in all versions of PA is similar: The AQM is modified to 

calculate the integral over time of the individual sink and source processes and each chemical 

reaction. These integrated sink/source process rates (IPR) and integrated reaction rates (IRR) can 

then be stored to a file and analyzed using a post-processor, or some processing can be performed 

internally in the model and a more limited set of process diagnostic information is output directly by 

the AQM. Chemical process analysis (CPA) is an improvement on the IRR method whereby some 

of the processing of IRR information is internalized within the AQM to output chemically 

meaningful parameters directly (e.g., budget terms for O3, NOx and odd oxygen). 

 Process analysis measures for aerosol chemistry have not been analyzed as much as for 

ozone chemistry. Although the ozone chemistry process analysis is directly related to secondary 

sulfate and nitrate formation, there is additional process analysis information available in the aerosol 

modules that are not extracted in either CMAQ or CAMx. In particular, information on sulfate 

formation and oxidants from the aqueous-phase module and on the sulfate/nitrate equilibrium from 

the aerosol thermodynamics module would be a useful addition to the current process analysis 

output. 

Because application of all three of these probing tools--source apportionment, DDM, and 

Process Analysis—are computational intensive and require a fair amount of analysis time to reap the 

benefits of using the methods, they do not lend themselves directly to annual simulations. However, 

each method has potential for use in addressing key episodic periods or geographical locations in the 

VISTAS domain where performance in the 2002 simulation may present a problem or where 

particular attention needs to be focused on emissions controls (a specific Class 1 area for example). 

In such focused applications, one or more of these probing tools may indeed serve a purpose and 

will be considered where appropriate.

Appendix C.1 - 130
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-15 

Appendix C.1 - 131
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-16 

7.6 Phase II Model Evaluation Procedures 

EPA guidance (EPA, 2001, pg. 227) suggests that the performance evaluation focus on two 

aspects: 

 > How well is the model able to replicate observed concentrations of components of 

PM2.5, and total observed mass of PM2.5? and 

 > How accurately does the model characterize the sensitivity of changes in component 

concentrations to changes in emissions? 

Recognizing that the former is much easier to accomplish than the latter, EPA goes on to declare that 

testing of a model’s reliability in estimating the actual effects of emissions changes is the more 

important. Over the past 20 years, a substantial body of information and analytical techniques has 

been developed to address the first aspect. Unfortunately, even today there are little rigorous 

methods available for quantifying the accuracy and precision of a model’s predictions of ozone, PM 

or visibility changes as the result of emissions changes. In this section we explain how the VISTAS 

Phase II testing will address the first aspect of the performance evaluation, i.e., how does the model 

compare against observed data. In section 7.9 we consider the second performance consideration. 

 7.6.1 Assessment of Ground-Level Gas-Phase and Aerosol Species 

Given that visibility is expressed in terms of extinction built off of individual components of 

fine particulate matter, the model should be evaluated separately for each of the key fine particulate 

matter components that make up the extinction coefficient. Current EPA guidance suggests that the 

model should also be evaluated for ammonium as well as several key gas-phase species that are 

important for fine particulate modeling. For particulate species this includes SO4 and/or S, NH4, 

NO3, mass associated with SO4, mass associated with NO3, elemental carbon (EC), organic carbon 

(OC), IP, mass of individual constituents of IP, and coarse matter (CM). The gaseous species

include ozone (O3), HNO3, NO2, PAN, NH3, NOy, SO2, CO, and H2O2. 

As indicated above, for some of the VISTAS subregions there are very few measurements, if 

any, for most of the gaseous species. But ozone measurements are available and should be 

integrated into the model performance evaluation. Given the importance of the photochemistry and 

the radical cycle in forming secondary fine particulate matter, the ozone evaluation will provide 

some insight into the model’s ability in this area. However, given the coarse grid resolution to be 

used (36 km and 12 km) perhaps greater weight should be given to the model evaluation results at 

the more rural ozone monitors (e.g., CASTNet) compared to urban ozone monitors. In addition to 

the list of PM and gaseous species from EPA’s guidance document listed above, the Task 4a/4b 

evaluation will also examine model’s ability to estimate PM2.5 mass, PM10 mass, extinction (bext) and 

deciview (dV) using the equation above to obtain extinction from fine particulate concentrations. 

At some of the IMPROVE sites there are also direct measurements of hourly extinction using 

transmissometer or nephelometer instruments.5

 Thus, it would be scientifically interesting to 

 

5 The Phase I modeling did not utilize the hourly extinction data in the operational evaluation of the 

CMAQ and CAMx models due to schedule and resource constraints and because the models 

Appendix C.1 - 132
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-17 

evaluate the model estimated extinction with the hourly measured values at these sites. If such a 

comparison were to be made, day-specific hourly and site-specific RH and f(RH) values could be 

used to convert model estimated fine particulate matter to extinction rather than the monthly f(RH) 

EPA recommends for projecting visibility improvements (EPA, 2003a). Furthermore, there have 

been some discrepancies reported in the past between the extinction calculated using the 

reconstructed mass data and the hourly measurements. Thus, it would be interesting to calculate 

day-specific extinction using day-specific f(RH) values and the reconstructed mass data for 

comparison with the direct measurements and the model estimates. Whether and to what extend this 

more detailed investigation into light extinction is pursued would depend upon the availability of 

Optional Task 14 authorization. 

As part of the CMAQ operational evaluation, model outputs will be compared statistically 

and graphically to observational data obtained from the IMPROVE, SEARCH, CASTNet, EPAFRM, EPA-STN, and other monitoring networks. These monitoring data will be obtained from 

AIRS, VIEWS, and other appropriate organizations. These comparisons will likely include: 

> Daily monthly, seasonal and annual averages for SO2, SO4, NO3, EC, OC, PM2.5, and 

PM10, taking care to exclude periods of sampling interference in the observational data. 

We will look for systematic biases between the model results and IMPROVE 

observations, and if biases are found, identify possible sources of error in the model 

inputs. 

> Hourly, high resolution PM species and gaseous species concentrations at sites where 

available (e.g., SEARCH, AIRS and EPA-Supersites). 

> At sites with contrasting aerosol mass loadings, analysis of the temporal behavior of the 

major scattering and absorbing aerosol constituents along with the visibility trends, to 

establish correlations. 

 The optional Phase II CMAQ diagnostic model evaluations may entail several components, 

many of which can be identified presently. Of course, the actual diagnostic analyses to be 

performed and the scope of such analyses can only be determined once the initial Task 4a model 

testing is underway. These diagnostics analyses – to be funded through Optional Task 14 (Enhanced 

Model Performance Evaluation)-- will need to be carefully defined and rank-ordered in terms of 

their priority to ensure that they can be accommodated within available resources and schedule. 

Among the diagnostic model evaluation analyses that could be considered are: 

> Evaluate seasonal trends in observations of organic and inorganic aerosol precursors and 

their effects on PM composition and visibility, and evaluate the ability of the model to 

capture these seasonal trends. 

> Evaluate how well the model simulates various physicochemical processes by: 

(a) examining observed and modeled correlations between various species pairs, and 

 

performance for the major PM components was deemed more important in terms of evaluating 

alternative model science configurations. 

Appendix C.1 - 133
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-18 

(b) comparing model-predicted ratios of various species (individual or families) with 

observations to evaluate gas/particle partitioning (e.g., nitrate/total nitrate, SO4/SOx). 

> Investigate the performance of the model at selected observational sites characterized by 

different chemical regimes that may be encountered either spatially or during different 

seasons to help identify any inadequacies in the model and to provide a better 

understanding of conditions under which model inferences may be weak. 

> Compare hourly 24-hour average, and episode averages of the PM constituents for the 

2002 Phase I VISTAS annual modeling period as well as the 2003 episodes across all 

sites. 

> Create scatter plots of modeled vs. observed data and hourly and 24-hour averages by 

site and subregion to help identify any site-specific biases. 

> Create time series plots of predicted and observed concentrations as appropriate. 

> Evaluate for total sulfur (SO2 + SO4), nitrate (HNO3 + NO3) and ammonia (NH3 + NH4). 

> Compare observed versus modeled mass fractions of PM constituents at various sites that 

are characterized by their proximity or remoteness relative to sources, or by specific 

meteorological conditions (e.g., frontal passage, stagnation, precipitation); these will 

enable identification of trends in the model of over- or under-prediction of specific PM 

constituents under these conditions. 

 > Calculate the measured and predicted relative abundance of key PM components and 

compare with EPA guideline recommendations and emergent alternative science 

recommendations (e.g., removing the soil component from the calculations, use of 

alternative relative importance equations [i.e., Boylan, 2004]). 

> Pay particular close attention to the model performance at the Class I areas for SO4, NO3, 

EC, OC, IP and CM on the 20% best and 20% worst days to document whether certain of 

these days should be eliminated from the visibility projections due to inadequate model 

performance. 

The suite of statistical metrics and graphical tools identified in the previous section for the 

core operational evaluation efforts under Task 4a/4b would likely also be used to diagnose 

performance problems with the CMAQ simulations should they exist and to highlight differences 

between model runs. Experience in ozone/PM modeling is the best basis upon which to identify 

obviously flawed simulation results. Efforts to improve the CMAQ model’s base case performance 

will be made, where necessary, warranted (i.e., to reduce the discrepancies between model estimates 

and observations), and consistent with the project resources and schedule; however, these model 

performance improvements efforts must be based on sound scientific principles. “Curve-fitting” 

exercises will be avoided. 

Appendix C.1 - 134
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-19 

 7.6.2 Assessment of Aloft Gas-Phase and Aerosol Species 

 A substantial number of aircraft flights were conducted during 2002 over the Midwest and 

Eastern U.S. Should VISTAS elect to fund the optional aloft model performance evaluation, we will 

endeavor to obtain this information and use it in a scientific performance evaluations of aloft gasphase and aerosol species (see section 7.3.2). 

7.7 Performance Goals and Benchmarks 

 Establishment of performance goals and benchmarks for regulatory modeling is a necessary 

but difficult activity. Here, performance goals refer to targets that we believe a good performing 

model should achieve, where as performance benchmarks are based on historical model performance 

measures for the best performing simulations. Performance goals are necessary in order to provide 

consistency in model applications and expectations across the country and to provide standardization 

in how much weight may be accorded modeling study results in the decision-making process. It is a 

problematic activity, though, because many areas present unique challenges (e.g., Houston, San 

Joaquin Valley, Los Angeles) and no one set of performance goals is likely to fit all needs. Equally 

concerning is the very real danger that modeling studies will be truncated when the ‘statistics look 

right’ before full assessment of the model’s reliability is made. This has the potential from breeding 

built-in compensating errors (Reynolds et al., 1996) as modelers strive to get good statistics as 

opposed to searching for the explanations for poor performance and then rectifying them. A 

NARSTO review of more than two-dozen urban-scale ozone SIP applications found this tendency to 

be all too prevalent in the regulatory modeling of the 1990s. (Roth et al, 1997). 

Nearly 15 years ago, research sponsored by the California Air Resources Board (Tesche et 

al., 1990) led to the agency’s adoption of three performance goals for 1-hour ozone modeling in the 

state: 

> Unpaired (in time and space) peak prediction accuracy (≤ ± 20%); 

> Mean normalized bias in hourly averaged concentrations (≤ ± 15%); and 

> Mean normalized gross error in hourly concentrations (≤ 35%). 

These performance goals for 1-hr ozone concentrations were adapted from previous surveys of 

several dozen urban-scale photochemical grid modeling studies (principally in California) focusing 

on ozone episodes of 1 to at most 3 days in duration. A surprising number of these studies did not 

include biogenic VOC emissions in the inventory under the then prevailing belief that biogenics 

were a negligibly small source category compared to automobile emissions. Most of the studies 

(Tesche, 1985, 1988; Tesche et al., 1985; 1990) comprising the data base from which the California 

ozone performance goals were derived entailed hourly ozone concentrations well above background 

levels (~40-50 ppb). As a result, it was common practice to use a “cutoff values” ranging between 

40 ppb to 60ppb to eliminate prediction-observations pairs that would cause these bias and error 

residual statistics to become extraordinarily large when measured concentrations were low.) 

Accordingly, normalized statistics such as bias and error proved to be suitable in most applications 

since the observed concentrations were generally high. These three California ozone model 

performance goals were adopted by EPA (1991) as part of the nationwide photochemical modeling 

guidelines and have been heavily used since. 

Appendix C.1 - 135
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-20 

However, when these evaluation metrics and goals were later adapted to PM and PM species, 

difficulties arose because performance statistics that divide by low concentration observations 

become much less useful. Indeed, some PM species may approach zero (e.g., NO3). In time, this 

has led to the introduction of the fractional and normalized mean bias and error metrics in addition to 

the mean normalized metrics and related performance expectations based on these alternative 

measures. 

While the 1-hr metrics and goals still have value in interpreting ozone and some gas-phase 

species performance, it has been necessary to develop new performance metrics and goals for fine 

particulates. EPA’s PM guidance document (EPA, 2001) guidance document identifies particulate 

matter components of interest to include: SO4 and/or S, NH4, NO3, mass associated with SO4, mass 

associated with NO3, EC, OC, IP, and mass of individual constituents of inorganic primary 

particulate matter (i.e., IP). Gaseous pollutants of interest include ozone, HNO3, NO2, PAN, NH3, 

NOy, SO2, CO, and H2O2. In addition, EPA guidance identifies several potentially useful statistical 

measures including: (a) accuracy of spatially averaged concentrations near a monitor, (b) fractional 

bias in means and standard deviations of predictions and observations, (c) normalized bias, (d) 

normalized gross error, (e) unpaired comparisons between predicted and observed peak 

concentrations. (Interested readers are referred to the EPA guidance document on the details of 

these metrics including mathematical formulae and implementation methods.) 

As with ozone in the 1980s, actual experience with PM models has led to the development of 

the current performance expectations for these models. For example, PM10 SIP model performance 

goals for mean normalized gross error of < 30% for southern California (SCAQMD, 1997; 2003) 

and < 50% for Phoenix (ENVIRON, 1998) have been used. As correctly pointed out by Seigneur 

and co-workers (2003), the current ability of regional PM models to predicting regional PM and 

visibility is an area of research with improvements needed for characterizing meteorology and 

emissions as well as PM models themselves. To this list we would add the need for improvements 

in model evaluation methodologies as well. 

When EPA’s draft guidance was developed nearly four (4) years ago, an interim set of fine 

particulate modeling performance goals were suggested for aggregated mean normalized gross error 

and mean normalized bias as follows: 

Pollutant Gross Error Normalized Bias 

PM2.5 ~30-50% ~"10% 

Sulfate ~30-50% ~"20-30% 

Nitrate ~20-70% ~"15-50% 

EC ~15-60% NA 

OC ~40-50% ~"38% 

Because regional-scale fine particulate and regional haze modeling is an evolving science, and 

considerable practical application and performance testing has transpired in the intervening years 

since these goals were postulated, we consider them general guidelines. As part of the Phase II 

model evaluation effort, we will compare the EPA goals in the 2001 guidance document with the 

results of the CMAQ/CAMx Phase I modeling, together with other recent PM modeling studies 

(e.g., WRAP, MRPO) to advance a proposed set of performance goals most relevant to the VISTAS 

Appendix C.1 - 136
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-21 

study. Results of the Phase I model evaluation together with recommendations from science 

workshops (e.g., EPA’s PM Model Performance Evaluation Workshop in February 2004) and 

recently published scientific studies (e.g., Boylan, 2004) will be used to provide support to these 

recommendations. 

We regard the above goals as simply general interim guidance. Certainly, more information 

on likely performance expectations will be available once the Phase I CMAQ/CAMx ozone and PM 

performance evaluation and sensitivity results are fully analyzed. In the VISTAS Phase II 

modeling, we will generate the model performance statistics listed in Table 7-4 and make 

comparisons with EPA’s interim goals as one means for: 

> Establishing a benchmark on the annual 2002 VISTAS modeling episode, and 

> Guiding the interpretation of the CMAQ modeling results. 

Equally as useful, we will endeavour to compare the results of the Phase II multi-species evaluations 

of CMAQ with the Phase I results for the Jan ’02, Jul ’99 and Jul ’01 episodes as well as modeling 

results from other studies (e.g., BRAVO, EPA, CRC, etc.), other RPOs, and the modeling research 

community in general. This will allow judgments about the adequacy of the Phase II modeling 

results to be placed in the most current perspective possible. 

7-8. Diagnostic and Sensitivity Testing 

Rarely does a modeling team find that the first simulation satisfactorily meets all (or even 

most) model performance expectations. Indeed, our experience has been that initial simulations that 

‘look very good’, usually do so as the result of compensating errors. The norm is to engage in a 

logical, documented process of model performance improvement wherein a variety of diagnostic 

probing tools and sensitivity testing methods are used to identify, analyze, and then attempt to 

remove the causes of inadequate model performance. This is invariably the most technically 

challenging and time consuming phase of a modeling study. We anticipate that the annual CMAQ 

model base case simulations will present some performance challenges that may necessitate focused 

diagnostic and sensitivity testing in order for them to be resolved. Hopefully, these diagnostic and/or 

sensitivity tests can be adequately carried out within the resources and schedule of Tasks 4a/4b. If 

not, then it may be necessary to draw upon the Optional Task 14 (Enhanced Model Performance 

Evaluation) and/or Optional Task 15 (Contingency) resources to conduct the necessary work. 

Where practical, diagnostic or sensitivity analyses, if needed, could be performed on selected 

episodes within the annual cycle, thereby avoiding the time-consuming task of running CMAQ for 

the fully 2002 period. Below we identify the types of diagnostic and sensitivity testing methods that 

might be employed in diagnosing inadequate model performance and devising appropriate methods 

for improving the model response. 

 7.8.1 Traditional Sensitivity Testing 

Model sensitivity experiments are useful in three distinct phases or ‘levels’ of an air quality 

modeling study and all will be used as appropriate in the VISTAS Phase II modeling with CMAQ. 

These levels are: 

Appendix C.1 - 137
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-22 

> Level I. Model algorithm evaluation and configuration testing; 

> Level II. Model performance testing, uncertainty analysis and compensatory error 

diagnosis, and 

> Level III. Investigation of model output response (e.g., ozone, aerosol, deposition) to 

changes in precursors as part of emissions control scenario analyses. 

Most of the Level I sensitivity tests with CMAQ have already been completed in the Phase I 

configuration and diagnostic analyses. However, given that open community nature of CMAQ and 

the frequent science updates to the model and supporting data abases, it is possible that some 

additional configuration sensitivity testing will be necessary in the early months of Phase II 

Potential Level I sensitivity runs would be carried out at one or more of the Team’s three modeling 

centers. 

Potential Level II sensitivity analyses might be helpful in accomplishing the following tasks: 

> To reveal internal inconsistencies in the model; 

> To provide a basis for compensatory error analysis; 

> To reveal the parameters (or inputs) that dominate (or do not dominate) the model’s 

operation; 

 > To reveal propagation of errors through the model; and 

 > To provide guidance for model refinement and data collection programs. 

At this time, it is not possible to identify one or more Level II sensitivity runs that might be needed 

to establish a reliable annual 2002 CMAQ base case. The merits of performing Level II sensitivity 

testing will depend upon whether performance problems are encountered in Tasks 4a/4b. Also, the 

number of tests possible, should performance difficulties arise, will be limited by the available 

schedule and Phase II resources under Optional Task 14 (Extended Model Performance Evaluation). 

 Thus, at this juncture, one cannot be overly prescriptive on the number and emphasis of sensitivity 

runs that may ultimately be desirable in Phase II. However, from past experience with CMAQ and 

other models, experience it is possible to identify examples of sensitivity runs could be useful in 

model performance improvement exercises with the annual 2002 CMAQ simulation. These include: 

> Modified biogenic emissions estimates; 

 > Modified on-road motor vehicle emissions; 

 > Modified air quality model vertical grid structure; 

 > Modified boundary conditions; 

 > Modified fire emissions; 

 > Modified EGU emissions; 

 > Modified ammonia emission estimates. 

 > Modified aerosol/N2O5/HNO3 chemistry; and 

 > Modified NH3 and HNO3 deposition velocities. 

Note that in a few cases (e.g., vertical grid structure, NH4 emissions estimates), some sensitivity 

experimentation has already been carried out in Phase I with the Jan ’02, Jul ’01 and Jul ’99 

episodes. To the extent that this Phase I information can help guide the Phase II diagnostics 

analyses, we will capitalize on this earlier work. 

Appendix C.1 - 138
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-23 

If necessary, Process Analysis extraction outputs can be included in these Level II diagnostic 

sensitivity simulations in order to provide insight into why the model responds in a particular way to 

each input modification. Again, the number, complexity, and importance of these types of 

traditional sensitivity simulations can only be determined once the initial CMAQ annual 2002 

simulation(s) are executed. 

 Level III sensitivity analyses have two main purposes. First, they facilitate the emissions 

control scenario identification and evaluation processes. Today, four complimentary sensitivity 

“tools” can be used in regional photochemical models depending upon the platform being used. 

These methods include: (a) traditional or ‘brute force’ testing, (b) the direct decoupled method 

(DDM), (c) Ozone Source Apportionment Technology (OSAT) and PM Source Apportionment 

Technology (PSAT), and (d) Process Analysis (PA). Each method has its strong points and they will 

be employed in Phase II where needed. The second purpose of Level III sensitivity analyses is to 

help quantify the estimated reliability of the air quality model in simulating the atmosphere’s 

response to significant emissions changes. This important model evaluation need is addressed in 

further detail in section 7.9 below. 

 Based on experience in other regional studies, examples of Level III monthly or annual 

sensitivity runs for Phase II might include: 

> Ozone, sulfate, nitrate, ammonium and other aerosol sensitivities to SO2 emissions; 

> Ozone, sulfate, nitrate, ammonium and other aerosol sensitivities to elevated point 

source NOx emissions; 

> Ozone, sulfate, nitrate, ammonium and other aerosol sensitivities to ground level 

NOx emissions; and 

> Sulfate, nitrate, ammonium and other aerosol sensitivities to ammonia. 

 

 Of course, traditional ‘brute force’ sensitivity experiments is just one way of quantifying 

these or other Level III sensitivities. Other methods that can be applies include DDM, OSAT, or 

PSAT simulations. 

 The need to perform sensitivity experimentation (Levels I, II, or III) will depend on the 

outcome of the Task 4a/4b operational performance evaluations. If such a need arises, the ability to 

actually carry out selected sensitivity and/or diagnostic experiments will hinge on the availability of 

Optional Task 14 and/or 15 resources and sufficient time to carry out the analyses. Clearly, 

selection of the specific analysis method will depend upon the nature of the technical question(s) 

being addressed at the time. Note that as part of VISTAS Phase II modeling, Georgia Institute of 

Technology will be performing emissions sensitivities with CMAQ using the Phase I databases. 

 7.8.2 Diagnostic Tests 

A rich variety of diagnostic probing tools are available for investigating model performance 

issues and devising appropriate means for improving the model and/or its inputs. Previously, in 

section 7.4.4 we introduced the suite of ‘probing tools’ available for use in the CMAQ and CAMx 

modeling system for use in Phase II. Where the need exists (i.e., if performance problems are 

encountered) and assuming VISTAS elects to fund the use of the probing tool applications (under 

Optional Task 14 or elsewhere), these techniques could be employed as appropriate to assist in the 

Appendix C.1 - 139
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-24 

model performance improvement efforts associated with the annual 2002 CMAQ basecase 

development. Here we describe an additional diagnostic method – indicator species and species 

ratios -- that is potentially useful not only in model performance improvement activities but also in 

judging the models reliability in estimating the impacts on air quality from future emissions. This 

method involves the use of so-called ‘indicator species’ and species ratios. If, during the conduct of 

Phase II, we determine that application of indicator species and species ratio techniques would be 

beneficial to the study (and if existing project resources allow), we will discuss with the TAWG the 

merits of including this additional probing tool as part of Optional Task 14. 

Beginning in the mid 1990s, considerable interest arose in the calculation of indicator species 

and species ratios as a means of diagnosing photochemical model performance and in assessing 

model credibility in estimating the effects of emissions changes. Major contributions to the 

development and refinement of this general diagnostic method over the past decade have been made 

many scientists including Milford et al., (1994), Sillman (1995, 1999), Sillman et al., (1997), 

Blanchard (2000), Blanchard and Fairley (2001), and Arnold et al., (2003). Indeed, a recent 

evaluation of CMAQ using indicator species ratios such as O3/NOx, NOz/NOy (a measure of 

chemical aging), and O3/NOz (a measure of the ozone production efficiency per NOx converted), 

showed not only good agreement with measurements (Arnold et al., 2003) but also convincingly 

demonstrated the utility of the method for diagnosing model performance in a variety of ways. 

 Traditionally, indicator species analyses have focused on ozone and its precursor and product 

species. However the method is equally applicable to PM species and species ratios given sufficient 

measurement data for comparisons. With some of the high-resolutions monitoring data available 

from the SEARCH program and the EPA Supersites, it is indeed feasible to compute relevant 

indicator species and ratios for PM and its component species. For example, Ansara and Pandis 

(1998) demonstrated how indicator species ratios could be applied to show how the modeled mass of 

PM might respond to sulfate, nitrate and ammonia emissions-related reductions.

7.9 Corroborative and Weight of Evidence Modeling Analyses 

This section identifies additional modeling analyses that might be worth pursuing under 

Optional Task 14 (Extended Model Performance Evaluation) to add strength to the core model 

evaluation efforts already planned as part of Tasks 4a and 4b. 

 7.9.1 Corroborative Models 

Noteworthy in EPA’s new ozone, PM, and regional haze guidance documents is the 

encouragement of the use of alternative modeling methods to corroborate the performance findings 

and control strategy response of the primary air quality simulation model. This endorsement of the 

use of corroborative methodologies, stems from the common understanding that no single 

photochemical modeling system can be expected to provide exact predictions of the observed ozone 

and PM species concentrations in a region the size of VISTAS, especially over time scales spanning 

1-hr to 1 year. Although the photochemical/PM models identified in EPA’s PM/regional haze 

guidance document possess many up-to-date science and computational features, there still can be 

important differences in modeled gas-phase and aerosol predictions when alternative models are 

exercised with identical inputs. 

Appendix C.1 - 140
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-25 

As we discovered in the Phase I CMAQ/CAMx inter-comparisons, the general levels of 

difference revealed between the two model’s ozone and PM predictions is typical of what one 

encounters when inter-comparing alternative state-of-science regional models. These differences 

provide some insight into the current limits of predictability and reproducibility of today’s best 

photochemical/PM models. In light of these understandable differences in modeling results between 

state-of-science “One Atmosphere” models, not only is the issue of model selection for VISTAS 

Phase II critical6, but the procedures for the selected model (CMAQ in this instance) and interpreting 

its output are important as well. Thus, recognizing the uncertainty that attends even the most 

sophisticated models, the EPA’s draft PM/regional haze modeling guidance explicitly addresses the 

issue of modeling uncertainty by recommending that alternative models (photochemical and 

observation-based) be considered in the attainment demonstration ‘weight of evidence’ analyses. 

Indeed, the Relative Reduction Factor (RRF) approach in the formal attainment demonstration 

process is designed to address the fact that no model is fully capable of giving precise predictions. 

In fact the RRF approach was developed in response to the findings of many modelers (as we have 

also demonstrated in Phase I) that alternative, comparable models give somewhat divergent ozone 

and secondary aerosol predictions. 

Mindful of EPA’s endorsement of corroborative modeling methods and the rigorous use of 

‘weight of evidence’ investigations, we recommend that the most recent version of CAMx may be 

used in supportive, corroborative role to CMAQ in Phase II . Among other things, this will permit us 

to more explicitly identify the expected range of model uncertainty and to corroborate the general 

effectiveness of the Phase II CMAQ regional haze control strategies. Other corroborative modeling 

methods such as the CMAQ-AIM and CMAQ-MADRID should also be considered. However, as 

these models are derivatives of CMAQ they would not provide as robust independent corroboration 

as CAMx. 

Thus, we recommend CMAQ as the primary photochemical model for use in VISTAS Phase 

II and CAMx as a supportive model to be used for corroboration and are in the identification of 

compensation errors in the MM5/SMOKE/CMAQ modeling system. The use of CAMx is under 

Optional Task 11 in the Phase II SOW that is currently not funded (see Appendix A). Additional 

corroborative models should also be considered. 

 7.9.2 Weight of Evidence Analyses 

 EPA’s guidance recommends three general types of ‘weight of evidence’ analyses in support 

of the attainment demonstration: (a) use of air quality model output, (b) examination of air quality 

and emissions trends, and (c) the use of corroborative modeling such as observation-based (OBM) or 

observation-driven (OBD) models. We will consider the use of one or more methods in conducting 

the Phase II CMAQ modeling because it could significantly strengthen the credibility and reliability 

of the modeling available to the states for their subsequent use. The exact details of the ‘weight of 

evidence’ analyses must wait until Phase II evolves further. It is premature to prescribe which, if 

any of the WOE analyses would be performed since the model’s level of performance with the 2002 

episode is obviously not known at this time and the time and remaining project resources available 

to support WOE analyses is unknown as well. Nonetheless, we outline below our thoughts 

 

6 Model selection is a key issue that all RPOs have addressed and some such as WRAP and VISTAS have chosen 

CMAQ. Others, such as the MRPO have adopted CAMx instead. Still other RPO’s have yet to decide between these 

two or another model. Clearly, there does not appear to be any one ‘right’ selection at the present time. 

Appendix C.1 - 141
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-26 

regarding what would likely be considered should the operational CMAQ model evaluation need to 

be bolstered with WOE analyses. 

Use of Air Quality Models. As just discussed, we recommend augmenting the CMAQ 

annual 2002 and episodic simulations with the use of CAMx to provide additional information on 

model uncertainty and sensitivity. More specifically, we propose to exercise CAMx on a somewhat 

limited basis to corroborate the key model performance evaluation results and emissions control 

findings of the primary model, CMAQ. Second, we propose to apply the DDM and OSAT/PSAT 

methods to develop corroborative information on source-receptor relationships and model 

sensitivities. These supplemental calculations would be performed with one or both models 

(CMAQ does not contain OSAT/PSAT presently) for one or more key episodes within the annual 

2002 cycle. The results of this additional modeling would be used directly in the ‘weight of 

evidence’ analyses to quantify the degree of modeling uncertainty and to corroborate 

appropriateness of the subsequent PM emissions reductions scenarios. 

Use of Emissions and Air Quality Trends. A limited scope emissions and trend analysis 

could be employed in Phase II to support the ‘weight of evidence’ determinations. However, 

traditionally, these types of analyses are performed by the lead agency’s own staff. With this 

expectation, we would coordinate our efforts with the VISTAS TAWG to develop a trends analysis 

supporting the future year applications of CMAQ. 

Use of Corroborative Observational Modeling. While regulatory modeling studies for 

ozone attainment demonstrations have traditionally relied upon photochemical models to evaluate 

ozone control strategies, there has recently been growing emphasis on the use of data-driven models 

to corroborate the findings of air quality models. As noted, EPA’s guidance now encourages the use 

of such observation-based or observation-driven models (OBMs/ODMs). As part of Phase II, we 

will consider the merits of using these techniques as supportive weight of evidence. While the 

OBD/OBM models cannot predict future year air quality levels, they do provide useful corroborative 

information on the extent to which specific subregions may be VOC-limited or NOx-limited, for 

example, or where controls on ammonia or SO2 emissions might be most influential in reducing 

PM2.5. Information of this type, together with results of DDM and traditional ‘brute-force’ 

sensitivity simulations, can be extremely helpful in postulating emissions control scenarios since it 

helps focus on which pollutant(s) to control. 

7.10 Assessing Model Reliability in Estimating the Effects of Emissions Changes 

 EPA identifies three methods (EPA, 2001, pg. 228) potentially useful in quantifying a 

model’s reliability in predicting air quality response to changes in model inputs, e.g., emissions. 

These include: 

> Examination of conditions for which substantial changes in (accurately estimated) 

emissions occur; 

> Retrospective modeling, that is, modeling before and after historical significant 

changes in emissions to assess whether the observed air pollution changes are 

adequately simulated; and 

 

Appendix C.1 - 142
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-27 

3⁄4 Use of predicted and observed ratios of ‘chemical indicator species’. 

We note that in some urban-scale analyses, the use of weekday/weekend information has been 

helpful in assessing the model’s response to emissions changes. However, we suspect that this 

approach would not prove feasible with an annual episode over geographic domain as large as 

VISTAS. 

The first two methods have actually been considered for over 15 years and were the subject 

of intensive investigations in the early 1990s in Southern California in studies sponsored by the 

South Coast Air Quality Management District (Tesche, 1991) and the American Petroleum Institute 

(Reynolds et al., 1996). To date, neither method has proven useful largely because of the great 

difficulty in developing historical emissions inventories of sufficient quality to make such an 

analysis credible and the difficulties in removing the influences of different meteorological 

conditions such that the modeling signal reflects only the model’s response to emissions changes. It 

is difficult enough to construct reliable emissions inventories using today’s modeling technology let 

alone construct retrospective inventories 5-10 years ago prior to the implementation of significant 

emissions control programs or major land use changes. The use of indicator species, however, offers 

some promise. 

However, recent analytical and numerical modeling studies have demonstrated how the use of 

ambient data and indicator species ratios can be used to corroborate the future year control strategy 

estimates of Eulerian air quality models. Blanchard et al., (1999), for example used data from 

environmental (i.e., smog) chambers and photochemical models to devise a method for evaluating 

the 1-hr ozone predictions of models due to changes in precursor NOx and VOC emissions. 

Reynolds et al., (2003) followed up this analysis, augmented with process analysis, to assess the 

reliability of SAQM photochemical model estimate of 8-hr ozone to precursor emissions cutbacks. 

With respect to secondary aerosol PM, the recent CMAQ evaluation by Arnold et al. (2003) clearly 

demonstrated how the use of indicator species analysis could be use to develop insight into the 

expected reliability and adequacy of a photochemical/PM model for simulating the effects of 

emissions control scenarios. These researchers used three indicator ratios (or diagnostic ‘probes’) to 

quantify the model’s response to input changes: 

 > The ozone response surface probe [O3/NOx]; 

 > The chemical aging probe [NOz/NOy ]; and 

 > The ozone production efficiency probe [O3/NOz ]. 

 By closely examining CMAQ’s response to key input changes, properly focused in time and 

spatial location, Arnold et al., (2003) were able to conclude that the photochemical processing in 

CMAQ was substantially similar to that in the atmosphere 

 Thus, the extension of these techniques to address CMAQ predictions for secondary aerosols 

will doubtless be quite challenging, but the use of indicator species (e.g., ammonia or HNO3

limitation for nitrate particle formation) and species ratios appears to offer, at this time, the only real 

opportunity to quantify the expected reliability of the air quality model to correctly simulate the 

effects of emissions changes. In the Phase II CMAQ model evaluation, we will remain alert to 

opportunities to extend the indicator species ratio analyses to the problem of fine particulate and 

regional haze. This is one area where technical collaboration between the Emissions and Air Quality 

Appendix C.1 - 143
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-28 

Modeling team and the VISTAS TAWG can be especially fruitful in terms of identifying and testing 

emergent methods for challenging the model’s ability to correctly simulate the effects of future year 

emissions changes. Finally, we note that this is truly a current research area and as such falls outside 

the scope of the Phase II modeling effort. However, given its importance, we will remain alert to 

opportunities to utilize newly available methods should this prove feasible within the Phase II 

resources and schedule. 

Table 7-1. Ground-Level Ambient Data Monitoring Networks and Stations Available in VISTAS 12 

Km Domain for CY-2002. 

Monitoring 

Network 

Chemical Species Measured Sampling 

Frequency; 

Duration 

Approximate 

Number of 

Monitors 

IMPROVE Speciated PM2.5 and PM10 1 in 3 days; 24 hr 38 

CASTNET Speciated PM2.5, Ozone Hourly, Weekly; 

1 hr, Week 

74 

SEARCH 24.hr PM25 (FRM Mass, OC, BC, 

SO4, NO3, NH4, Elem.); 24-hr PM 

coarse (SO4, NO3, NH4, elements); 

Hourly PM2.5 (Mass, SO4, NO3, 

NH4, EC, TC); and Hourly gases 

(O3, NO, NO2, NOy, HNO3, SO2, 

CO) 

Daily, Hourly; 8 

NADP WSO4, WNO3, WNH4 Weekly 100 

EPA-FRM Only total fine mass (PM2.5) 1 in 3 days; 24 hr 313 (?)

EPA-SPEC Speciated PM2.5 Varies; Varies 43 (?)

AIRS/AQS CO, NO, NO2, NOx, O3 Hourly; Hourly 6,407 

Table 7-2. Aircraft Sampling Programs Performed in the VISTAS 12 Km Domain for CY-2002.

Aircraft Program Meteorological Parameters & 

Chemical Species Measured 

Sampling 

Program & 

Flight Duration 

Approximate 

Number of 

Flights; Days; 

Aircraft 

University of 

Maryland (UMD); 

Univ. Research 

Foundation (URF) 

Meteorology: WS, WD, Temp, 

RH, 

Air Quality: O3, NO, NO2, CO, 

SO2, aerosol absorption, 

aerosol scattering. 

23 May to 3 Oct; 

Typically 3 hrs 

54 flights, 

54 days, 

1 aircraft 

Midwest RPO & 

Wisconsin DNR

Meteorology: WS, WD, Temp, 

RH, dew point, pressure 

Air Quality: O3, NO, NO2, NOx, 

NOy, speciated VOCs, 

carbonyls, HNO3, NH3, Hg, 

SO4, OC, EC, PM2.5, light 

scattering (Neph), visibility 

pictures. 

1 June to 22 Nov; 

Typically 3-5 hrs 

133 flights; 

29 days; 

2 aircraft 

(WDNR and 

Jacko Aircraft) 

Appendix C.1 - 144
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-30 

Table 7-3. Federal Mandated Class I Areas in the VISTAS States.

State Acreage Federal Land Manager Public Law 

Alabama

Sipsey Wilderness Area 12,646 USDA-FS 93-622 

Arkansas 

Caney Creek Wilderness Area 7,344 USDA-FS 93-622 

Upper Buffalo Wilderness Area 9,912 USDA-FS 93-622 

Florida

Chassahowitzka Wilderness Area 23,360 USDI-FWS 94-557 

Everglades NP 1,397,429 USDI-NPS 73-267 

St. Marks Wilderness Area 17,745 USDI-FWS 93-632 

Georgia

Cohotta Wilderness Area 33,776 USDA-FS 93-622 

Okefenokee Wilderness Area 343,850 USDI-FWS 93-429 

Wolf Island Wilderness Area 5,126 USDI-FWS 93-632 

Kentucky 

Mammoth Cave NP 51,303 USDI-NPS 69-283 

Louisiana 

Breton Wilderness Area 5,000+ USDI-FWS 93-632 

 

North Carolina

Great Smoky Mountains NP{1} 273,551 USDI-NPS 69-268 

Joyce Kilmer-Slickrock Wilderness Area{2} 10,201 USDA-FS 93-622 

Linville Gorge Wilderness Area 7,575 USDA-FS 88-577 

Shining Rock Wilderness Area 13,350 USDA-FS 88-577 

Swanquarter Wilderness Area 9,000 USDI-FWS 94-557 

{1}Great Smoky Mountains National Park, 514,758 acres overall, of which 273,551 acres are in North Carolina, and 241,207 

acres are in Tennessee. 

{2}Joyce Kilmer-Slickrock Wilderness, 14,033 acres overall, of which 10,201 acres are in North Carolina, and 3,832 acres are 

in Tennessee. 

South Carolina

Cape Romain Wilderness 28,000 USDI-FWS 93-632 

Tennessee

Great Smoky Mountains NP{1} 241,207 USDI-NPS 69-268 

Joyce Kilmer-Slickrock Wilderness{2} 3,832 USDA-FS 93-622 

{1} Great Smoky Mountains National Park, 514,758 acres overall, of which 273,551 acres are in North Carolina, and 241,207 

acres are in Tennessee. 

{2} Joyce Kilmer Slickrock Wilderness, 14,033 acres overall, of which 10,201 acres are in North Carolina, and 3,832 acres are 

in Tennessee. 

Appendix C.1 - 145
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-31 

Virginia

James River Face Wilderness 8,703 USDA-FS 93-622 

Shenandoah NP 190,535 USDI-NPS 69-268 

West Virginia

Dolly Sods Wilderness 10,215 USDA-FS 93-622 

Otter Creek Wilderness 20,000 USDA-FS 93-622 

Table 7-4. Core Statistical Measures to be used in the VISTAS Phase II Air Quality Model 

Evaluation with Ground-Level Data (see ENVIEON, 2003b,d for details).

Statistical 

Measure 

Shorthand 

Notation 

Mathematical 

Expression Notes 

Accuracy of 

paired peak (Ap) 

Paired_Peak 

peak

peak

O

− OP Ppeak = paired (in 

both time 

 and 

space) peak 

 prediction 

Coefficient of 

determination (r

2

) 

Coef_Determ 

∑ ∑

∑

= =

=

− −





 



 −−

N

i

N

i

i i

N

i

i i

OOPP

OOPP

1 1

2 2

2

1

)()(

))((

Pi = prediction at 

time and 

 location i; 

Oi = observation 

at time 

 and location 

i; 

P = arithmetic 

average of Pi, 

i=1,2,..., N; 

O = arithmetic 

average of Oi, 

i=1,2,...,N 

Normalized Mean 

Error (NME) 

Norm_Mean_Err 

∑

∑

=

=

−

N

i

i

N

i

ii

O

OP

1

1

Reported as % 

Root Mean 

Square Error 

(RMSE) 

Rt_Mean_Sqr_Err 

( )

2

1

1

1 2





 



 ∑ − =

N

i

OP ii N

Reported as % 

Fractional Gross 

Error (FE) 

Frac_Gross_Err 

∑= +

− N

i ii

ii

OP

OP

N 1

2 Reported as % 

Appendix C.1 - 146
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 7.doc 7-32 

Mean Absolute 

Gross Error 

(MAGE) 

Mean_Abs_G_Err 

∑=

−

N

i

OP ii N 1

1

Mean Normalized 

Gross Error 

(MNGE) 

Mean_Norm_G_Err

∑=

− N

i i

ii

O

OP

N 1

1 Reported as % 

Mean Bias (MB) Mean_Bias 

∑( ) =

−

N

i

OP ii N 1

1 Reported as 

concentration 

(e.g., μg/m3

) 

Mean Normalized 

Bias (MNB) 

Mean_Norm_Bias ( ) ∑=

− N

i i

ii

O

OP

N 1

1 Reported as % 

Mean 

Fractionalized 

Bias (Fractional 

Bias, MFB) 

Mean_Fract_Bias 

∑= 















+

− N

i ii

ii

OP

OP

N 1

2 Reported as % 

Normalized Mean 

Bias (NMB)

Norm_Mean_Bias 

∑

∑

=

=

−

N

i

i

N

i

ii

O

OP

1

1

)(

Reported as % 

Bias Factor (BF) Bias Factor 

1

1 N

i

i i

P

N O =

      ∑

Reported as 

BF:1 or 1: BF or 

in fractional 

notation (BF/1 or 

1/BF). 

Appendix C.1 - 147
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-1

8.0 VISIBILITY ASSESSMENT AND COMPARISON 

 

 This chapter provides a summary of how the modeling results will be used to satisfy the 

requirements of the Regional Haze Rule (RHR) as part of the Section 308 visibility State 

Implementation Plans (SIPs) and Tribal Implementation Plans (TIPs) due in 2007. Note that the 

VISTAS Phase II modeling results will also likely be used in some capacity as the regional 

component in some State’s fine particulate (PM2.5) and 8-hour ozone SIPs that are also due in 

2007. However, how the modeling results will be used to address PM2.5 and 8-hour ozone issues is 

not discussed in this chapter and will be addressed by the pertinent States at a later time. The 

Phase II modeling results generated in 2004 will likely not be the final basis for the Section 308 

SIPs as the results will be updated and refined. However, it is important to start planning how the 

modeling results will be used to project visibility changes, optimize the presentation of results and 

identify any potential pitfalls early on. 

8.1 Regional Haze Rule Requirements 

The Regional Haze Rule (RHR) regulations were published by EPA in 1999 (Federal 

Register 35769, July 1, 1999) and are designed to address the requirements of Section 169A and 

169B of the Clean Air Act (CAA). The CAA and RHR call for the protection of visibility at the 

156 “mandatory Federal Class I areas.”1

 Section 169A of the Clean Air Act Amendments 

(CAAA) established a national visibility goal to remedy existing impairment due to air pollution at 

the Class I areas. This is accomplished by defining a visibility goal of “natural conditions” to be 

achieved at each Class I area by 2064. The RHR requires States with Class I areas to develop SIPs 

that include reasonable progress goals for improving visibility in each Class I area and emission 

reduction measures to meet those goals. For the initial control strategy SIPs due in 2007, States 

are required to adopt progress goals for improving visibility from baseline conditions. The 2000-

2004 five-year period is used to define baseline conditions and the first future progress period is 

2018, that has been interpreted as the 2013-2017 or 2014-2018 five year periods. A State is 

required to set progress goals for each Class I area in the State for two visibility metrics: 

• Provide for an improvement in visibility for the most impaired (i.e., 20% worst) 

visibility days; and 

 

• Ensure no degradation in visibility for the least impaired (i.e., 20% best) visibility 

days. 

The reasonable progress goals must provide for a rate of improvement sufficient to attain “natural 

conditions” by 2064, or justify any alternative rate. States are to define controls to meet progress 

goals every 10 years, starting in 2018, that defines progress periods ending in 2018, 2028, 2038, 

2048, 2058 and finally 2064. States will determine whether they are meeting their goals by 

comparing visibility conditions from one five-year period to another (e.g., 2000-2004 to 2013-

2017). As stated in 40 CFR 51.308 (d) (1), baseline visibility conditions, progress goals, and 

 

1

 Areas designated as mandatory Class I areas are those National Parks exceeding 6,000 acres, wilderness areas 

and national memorial parks exceeding 5,000 acres, and all international parks that were in existence on August 7, 

1977. Since then some new Class I areas have been defined and some existing Class I areas have been expanded. 

However, these areas are not included as part of the 156 “Federal mandated Class I areas” for which the RHR 

applies. In this document the term “Class I area” refers to the 156 “Federal mandated” Class I Areas. 

Appendix C.1 - 148
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-2

changes in visibility must be expressed in terms of deciview (dv) units. The deciview unit of 

visibility impairment is derived from light extinction (bext) as follows: 

dv = 10 ln (bext/10) 

 Where light extinction (bext) is expressed in terms of inverse megameters (Mm-1 = 10-6 m

-1). 

Section 8.2.1.1 below discusses how bext is calculated using the observed fine particulate 

concentrations from the IMPROVE monitors and Section 8.2.1.2 below defines how the modeling 

results will be mapped to the IMPROVE measurements for the purpose of projecting visibility 

improvements. 

8.2 EPA Guidance for Complying with Regional Haze Rule 

EPA has published three guidance documents that relate to how modeling results should be 

used to demonstrate compliance with the RHR: 

“Guidance for Demonstrating Attainment of Air Quality Goals for PM 2.5 and Regional 

Haze, Draft 2.1 (EPA, 2001). 

“Guidance for Tracking Progress Under the Regional Haze Rule” (EPA, 2003a). 

“Guidance for Estimating Natural Visibility Conditions Under the Regional Haze Rule” 

(EPA, 2003b). 

The first EPA modeling guidance document listed above (EPA, 2001) discusses the use of 

modeling results to demonstrate progress toward the RHR goals. This is a draft document that will 

be updated during 2004. When the draft modeling guidance is updated that may necessitate an 

update of this Modeling Protocol to keep it consistent with current EPA guidance. The second 

document (EPA, 2003a) focuses on monitored visibility and how to define the visibility baseline 

and how to track visibility goals. The third EPA guidance document discusses procedures for 

defining “natural conditions” for a Class I area that is the visibility goal in 2064. In the discussion 

below we are assuming that other VISTAS participants would define the “natural conditions” for 

each VISTAS Class I area. In this Chapter we address the use of the modeled and monitored fine 

particulate concentrations at the Class I areas for projecting visibility changes from the current to 

future years. 

VISTAS is currently evaluating EPA’s assumptions for projecting visibility improvements 

in their guidance documents (EPA, 2001; 2003a,b). If technically justified, VISTAS may make 

modifications to EPA’s procedures based on their analysis. For example, recent measurements 

suggest that, at least for the VISTAS region, sulfate is not always fully neutralized by ammonium 

and that ammonium bisulfate and sulfuric acid can exist, especially in the summer. Thus, the EPA 

approach assuming that sulfate is always completely neutralized by ammonium may have to be 

updated. The current EPA approach also does not account for sea salt that can be a contributor to 

visibility impairment, especially at coastal sites. VISTAS is also evaluating EPA’s default “natural 

conditions” and its appropriateness for the VISTAS region. Below we describe EPA’s approach 

for projecting visibility improvements, but be aware they may be modified by VISTAS at a later 

date. 

Appendix C.1 - 149
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-3

8.2.1 Procedures for Projecting Visibility Changes 

EPA guidance recommends using the model in a relative sense to project future-year 

visibility conditions (EPA, 2001; 2003a). This is done through the use of Relative Reduction 

Factors (RRFs) that are defined as the ratio of the future-year to the current-year modeling results. 

The RRFs are applied to the baseline visibility conditions to project future-year visibility. The 

major features of EPA’s recommended visibility projections are as follows (EPA, 2003a,b): 

• Monitored data should be used to define current air quality. 

• Monitored concentrations of PM10 are divided into six major components, the first 

five of which are assumed to be PM2.5 and the sixth is PM2.5-10. 

3⁄4 SO4 (sulfate); 

3⁄4 NO3 (particulate nitrate); 

3⁄4 OC (organic carbon); 

3⁄4 EC (elemental carbon); 

3⁄4 OF (other fine particulate); and 

3⁄4 CM (coarse matter). 

• Models are used in a relative sense to develop relative reduction factors (RRFs) 

between future and current predicted concentrations of each component. 

• Component-specific relative reduction factors are multiplied by current monitored 

values to estimate future component concentrations. 

• Estimates of future component concentrations are consolidated to provide an 

estimate of future air quality, which can be related to a goal for regional haze. 

• Future estimated air quality is compared with the goal to see if the simulated control 

strategy results in the goal being met. 

• It is acceptable to assume that all measured sulfate is in the form of ammonium 

sulfate [(NH4)2SO4] and all particulate nitrate is in the form of ammonium nitrate 

[NH4NO3]. 

In order to facilitate tracking visibility progress, three important visibility parameters are required 

for each Class I area: 

Baseline Conditions: Baseline Conditions represent visibility for the 20% best and 20% 

worst days for the initial five-year baseline period of the regional haze program. Baseline 

Conditions are calculated using monitor data collected during the 2000-2004 five-year 

period. 

Current Conditions: Current Conditions for the best and worst visibility days are calculated 

from the latest five-year average based on the latest five-years of monitored data (which is 

currently 1998-2002, but expected to be 1999-2003 by the time the initial future-year Phase 

II visibility projections will be made in late 2004).. 

Appendix C.1 - 150
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-4

Natural Conditions: Estimates of natural visibility conditions for the 20% best and 20% 

worst days at a Class I area that is the goal of the RHR is 2064 that has been defined as 

visibility conditions that would be experienced in the absence of human-caused 

impairment” (EPA, 2003b). 

8.2.1.1 Calculation of Baseline Conditions 

Baseline and Current Conditions for Class I areas are calculated using fine and coarse 

particulate concentration measured at Interagency Monitoring of Protected Visual Environments 

(IMPROVE) monitors. Currently, each Class I area in the VISTAS domain has an associated 

IMPROVE PM monitor. The IMPROVE monitors do not directly measure visibility, but instead 

measure speciated fine particulate (PM2.5) and total PM2.5 and PM10 mass concentrations from 

which visibility is obtained through the IMPROVE reconstructed mass extinction equation. 

Visibility conditions are estimated starting with the IMPROVE reconstructed 24-hour 

average particulate matter (PM) mass measurements for six PM species: 

• Sulfate [SO4]; 

• Particulate Nitrate [NO3]; 

• Organic Matter [OM]; 

• Elemental Carbon [EC]; 

• Other Fine Particulate [Soil]; and 

• Coarse Matter [CM]. 

The IMPROVE monitors do not directly monitor some of these species so assumptions are 

made as to how the IMPROVE measurements can be adjusted and combined to obtain these six 

components of light extinction. For example, sulfate and particulate nitrate are assumed to be 

completely neutralized by ammonium and are assume to occur solely in the fine particulate mode 

(that is any coarse mode sulfate and nitrate in the real atmosphere may be present in the CM 

IMPROVE measurement). Concentrations for the above six components of light extinction in the 

IMPROVE reconstructed mass (RCM) extinction equation are obtained from the IMPROVE 

measured species as follows: 

Table 8-1. Definition of IMPROVE Reconstructed Mass (RCM) Species from Measured 

IMPROVE Species. 

IMPROVE RCM IMPROVE Measured Species 

SO4 1.375 x ( 3 x S) 

NO3 1.29 x NO3_ 

OM 1.4*OC1 + 1.4*OC2 + 1.4*OC3 + 1.4*OC4 + 1.4*OP 

EC EC1 + EC2 + EC3 – OP 

Soil 2.2*AL + 2.49*SI + 1.63*CA + 2.42*FE + 1.94*TI 

CM MT – MF 

Where: 

• S is elemental sulfur as determined from proton induced x-ray emissions (PIXE) 

analysis of the IMPROVE Module A that is multiplied by 3 to account the presence of 

oxygen, if S is missing then the sulfate (SO4) measured by ion chromatography 

analysis of the Module B is used to replace (3 x S). It is assumed to be completely 

neutralized by ammonium (1.375 x SO4). 

Appendix C.1 - 151
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-5

• NO3_ is the particulate nitrate measured by ion chromatography analysis of the Module 

B. It is assumed to be completely neutralized by ammonium (1.29 x). 

• The IMPROVE Organic Carbon (OC) measurements are multiplied by 1.4 to obtain 

Organic Matter (OM) to adjust the OC mass for other elements assumed to be 

associated with OC. 

• Elemental Carbon (EC), which is also referred to as Light Absorbing Carbon (LAC) is 

determined by TOR analysis and is the sum of EC fractions minus the pyrolized 

fraction. 

• Soil is determined as a sum of the mass of those elements (measured by PIXE) 

predominately associated with soil, whose mass is adjusted for oxygen in the common 

compounds. 

• MT and MF are total PM10 and PM2.5 mass, respectively. 

Associated with each PM species is an extinction coefficient that converts concentrations (in 

g/m3

) to light extinction (in inverse mega meters, Mm-1). Sulfate and nitrate are hygroscopic so 

relative humidity adjustment factors [f(RH)] are used to modify the extinction coefficients that 

increase the particle’s extinction efficiency with increasing RH to account for the particles taking 

on water and having higher light scattering properties. Note that some Organic Matter (OM) 

compounds may also have hygroscopic properties, but the IMPROVE reconstructed mass 

extinction equations assume OM is non-hygroscopic. 

BSulfate = 3 x f(RH) x [SO4] 

bNitrate = 3 x f(RH) x [NO3] 

bEC = 10 x [EC] 

bOM = 4 x [OM] 

bSoil = 1 x [Soil] 

bCM = 0.6 x [CM] 

Monthly average f(RH) factors are used as recommended in EPA’s guidance (EPA, 2003a). 

These values have been recently updated (SAIC, 2003) and are available at: 

ftp://ftp.saic.com/raleigh/RegionalHaze_2002FRHcurve/fRH_analysis/. 

The total light extinction (bext) is assumed to be the sum of the light extinction due to the 

six PM species listed above plus Rayleigh (blue sky) background (bRay) that is assumed to be 10 

Mm-1. 

 Bext = bRay + bSulfate + bNitrate + bEC +bOM + bSoil + bCM

The total light extinction (bext) in Mm-1 is related to visual range (VR) in km using the 

following relationship: 

 VR = 3912 / bext

The Regional Haze Rule requires that visibility be expressed in terms of deciview (dv) that 

uses natural logarithms of the extinction as follows: 

 dv = 10 ln(bext/10) 

Appendix C.1 - 152
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-6

 The equations above using data from the associated IMPROVE monitor are used to 

estimate the daily average visibility at each Class I area. For each year from the 2000-2004 

baseline these daily average visibility values, in terms of deciview (dv), are then ranked from 

highest to lowest. The 20% worst days visibility for each given year is given as the average 

visibility across the 20% highest visibility days in deciview. Similarly, the 20% best days are 

given as the average visibility across the 20% lowest visibility days in terms of deciview. The 

Baseline Conditions is the average of the 20% best and 20% worst days across the five-years of 

2000-2004. The Current Conditions is the average of the 20% best and 20% worst days based on 

the latest five-years of available data, which would be 1999-2003 for the VISTAS Phase II 

analysis being conducted in late 2004. 

8.2.1.2 Mapping of Modeling Results to the IMPROVE Measurements

As noted above, to project future-year visibility at Class I areas the modeling results are 

used in a relative sense to scale current observed visibility for the 20% best and 20% worst 

visibility days using RRFs that are the ratio of modeling results for the future-year to current-year. 

This scaling is done separately for each of the six components of light extinction in the IMPROVE 

reconstructed mass extinction equations. The modeled species do not necessarily exactly match up 

with the IMPROVE reconstructed mass species, thus assumptions must be made to map the 

modeled species to the IMPROVE reconstructed mass species for the purpose of projecting 

visibility improvements. For example, the models explicitly simulates ammonium and sulfate may 

or may not be fully neutralized in the model, whereas the IMPROVE reconstructed mass equations 

assume sulfate is fully neutralized by ammonium. For the CMAQ Version 4.3 model that was 

used in VISTAS Phase I modeling, the mapping of modeled species to IMPROVE reconstructed 

mass (RCM) species listed in Table 8-2 is proposed to be used in the VISTAS Phase II modeling. 

Table 8-2. Proposed Mapping of CMAQ V4.3 Modeled Species Concentrations to IMPROVE 

Reconstructed Mass (RCM) Species. 

IMPROVE RCM CMAQ V4.3 Species 

SO4 1.375 x (ASO4J + ASO4I) 

NO3 1.29 x (ANO3J + ANO3I) 

EC AECJ + AECI 

OM AORGAJ + AORGAI + AORGPAJ + AORGPAI + AORGBJ + AORGBI 

Soil A25J + A25I 

CM ACORS + ASEAS + ASOIL 

If a different model is used (e.g., CAMx or CMAQ-AIM) or updates to CMAQ change its 

species definitions, then the species mappings would have to be defined specific for that model. 

Note that in the above species mapping it is assumed that all of the CMAQ estimated sulfate and 

particulate nitrate are in the fine mode. If a fully sectional model was used (e.g., CMAQ-AIM or 

CAMx), then a decision would have to be made whether to map the coarse mode sulfate and 

nitrate to the IMPROVE fine SO4 and NO3 species (as implicitly assumed for CMAQ) using 

mappings in Table 8-2) or to include it in the IMPROVE CM species. In fact this is also an issue 

for the CMAQ V4.3 modal approach in which the lognormal size distribution for sulfate and 

nitrate in the accumulation mode (i.e., ASO4J and ANO3J) may have some mass greater than 2.5 

:m, however the current usual convention for CMAQ is to assume all the sulfate and nitrate are in 

the fine mode. 

Appendix C.1 - 153
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-7

8.2.1.3 Using Modeling Results to Project Changes in Visibility 

Modeling results are used in a relative fashion to project future-year visibility using relative 

reduction factors (RRFs). RRFs are expressed of the ratio of the modeling results for the futureyear to the results of the base year and are Class I area and PM species specific. RRFs are applied 

to the Baseline Conditions observed PM species to project future-year PM levels from which 

visibility can be assessed using the IMPROVE RCM extinction equations listed above. EPA has 

identified the following six steps to project future-year visibility for the 20% best and 20% worst 

days (EPA, 2001;2003a): 

1. For each Class I area visibility is ranked using IMPROVE reconstructed PM mass (RCM) 

extinction equation for each year that comprises the five-year Baseline Conditions (i.e., 

2000-2004). 

2. Calculate the arithmetic average of the 20% best and 20% worst visibility days, in deciview 

(dv), for each year of the five-year baseline period and then calculate the five-year average 

of the 20% best and 20% worst days. Document which days during the five-year baseline 

period comprise the 20% best and 20% worst observed visibility days. 

3. Use an air quality model to simulate the baseline period emissions and future-year 

emissions. Extract 24-hour average PM species concentrations “near” each Class I area. 

Calculate the average PM species concentration estimates in the current and future-year 

simulation across the 20% best and 20% worst observed visibility days for each year in the 

five-year baseline period. Average across the five-years the average PM species 

concentrations for the 20% best and 20% worst days and for each year in the five-year 

baseline period. Calculate Class I area and best/worst 20% days RRFs for each of the six 

PM components as the ratio of the five-year average estimated PM species concentration in 

the future-year to current year. 

4. Multiply the 20% best/worst days and PM species dependent RRFs by the observed 24-

hour PM species concentrations for each day from the 20% best/worst days to obtain 

future-year daily average PM species concentrations for each day from the 20% best and 

20% worst visibility days from the five-year baseline period. 

5. Using the future-year estimated 24-hour PM species concentrations for the best/worst 20% 

observed days, calculate extinction using the IMPROVE reconstructed mass extinction 

equation and daily deciview, perform annual averaging of the visibility (dv) estimates for 

the 20% best/worst days for each year and then obtain the five-year average visibility (dv) 

for the future-year. 

When selecting model estimated PM species concentrations “near” the monitor, EPA (2001) 

recommends taking a spatial average of PM concentrations across a grid cell resolution dependent 

NX by NY array of cells centered on the grid containing the monitor. For the VISTAS Phase II 36 

km modeling, just the model estimates for the grid cell containing the monitor will be used (i.e., 

NX=NY=1). For the VISTAS Phase II 12 km modeling, EPA recommends that NX=NY=3, that is 

the model estimated PM species concentrations are averaged across 9 grid cells centered on the 

IMPROVE monitor (EPA, 2001). 

Appendix C.1 - 154
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-8

8.2.1.4. Exclusion of Days from 20% Best/Worst Conditions

As discussed in Chapter 7, the model performance evaluation will pay particular close 

attention to the model’s PM performance at each Class I area for the 20% Best and 20% Worst 

days. If the model performance is extremely poor for one or more of these days at a Class I area, it 

may be desirable to exclude that day when calculating the RRFs for visibility projections. For 

example, if a day is one of the Worst 20% days at a Class I area and the model estimates clean 

background concentrations then it would be inappropriate to use the modeling results, even in a 

relative fashion through the RRFs, to project future-year visibility. The modeling Team would 

identify such suspect days and work with the VISTAS TAWG on whether they should be excluded 

from the visibility projections on a case-by-case basis. 

8.3 VISTAS Phase II Future-Year Modeling 

The VISTAS Phase II future-year modeling will use the 2002 MM5 meteorological 

conditions. That is, we will assume that the meteorological conditions for the future-year are the 

same as for 2002. This will allow for the comparison of the changes in visibility at Class I areas 

from the current (2002) to future-year due to changes in emissions. This means that the effects of 

climate change and climatic variations will not be accounted for. Several other decisions 

concerning the future-year to be modeled, model(s) to be used and modifications to the model 

inputs to reflect future years do need to be made such as: 

8.3.1 Future-Year to be Modeled 

Visibility projects are needed for the 20% best and 20% worst days from the five-year 

baseline period of 2000-2004 to 2018, which has been interpreted as the five-year future-year 

periods of 2013-2017 or 2014-2018. The EPA guidance documents are inconsistent on what 

future-year should be used for the assessment. The 2001 modeling guidance says that the mid-year 

from the 2013-2017 five-year projection period should be used, which would be 2015 (EPA, 2001, 

pg. 221). The 2003 guidance for tracking progress doesn’t discuss the future-year that should be 

modeled, but does mention that goals should be compared across 5-year planning periods “(e.g., 

2000-2004 to 2013-2017) and progress should be measured as improvement from 2004 to “2018” 

(EPA, 2003, pg. 1-6). VISTAS and other RPOs will be looking to EPA for providing more 

definitive guidance as to which future-year should be used for modeling visibility progress and this 

Modeling Protocol will be updated when such information is available. Thus, in the discussion 

below we just refer to the “future-year” with the actual year to be determined during 2004. There 

may also be some benefits to projecting visibility improvements for an interim future-year between 

2002 and 2018 to help track progress to the 2018 visibility targets. 

8.3.2 Future-Year Emissions 

The future-year emissions will be provided to the emissions and air quality modeling team 

(ENVIRON/Alpine/UCR) by the VISTAS emissions projection contractor (MacTec). They would 

be processed into the gridded speciated hourly three-dimensional emissions inputs for 

photochemical grid modeling using the SMOKE emissions model and the procedures discussed in 

Section 5.2. The same biogenic emissions as used in the 2002 Base Case modeling will be used 

for the future-year modeling. This assumes that the same land use and biomass distribution as 

used in the 2002 Base Case emissions would exist in the future-year emission scenarios. The 

Appendix C.1 - 155
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-9

effects of urban sprawl, increased agricultural, deforestation, locations of new roads, etc. between 

the current (2002) and future-year would not be accounted for. The same Typical Year fire 

emissions that were used in the 2002 Typical Year emissions scenario would be used in the futureyear. Future-year Typical Year emissions for Electrical Generating Units (EGUs) would also be 

used for the future-year scenarios, however for EGUs these would not be identical to the 2002 

Typical Year EGU emissions. 

8.3.3 Future-Year Initial and Boundary Conditions 

The same Initial Conditions (ICs) as used in the 2002 Base Case would be used in the 

future-year modeling. Because a ~15 day spin up period is being used, ICs will have minimal if 

any influence on the model estimated concentrations. 

As discussed in Section 5.3, the source of the boundary conditions (BCs) to be used along 

the lateral edges of the continental US national RPO 36 km modeling domain for current (2002) 

and future-year modeling is being studied by VISTAS. The VISTAS Phase I modeling analyzed 

several different types of boundary conditions, including the CMAQ default values and seasonal, 

monthly and 3-hour average values estimated by the GEOS-CHEM global model for a 2001 

annual simulation. 

The effects of using time varying (3-hourly) BCs produced by the 2001 GEOS-CHEM 

global model simulation versus the seasonal GEO-CHEM BCs were analyzed using the CMAQ 

model and the VISTAS Phase I July 2001 episode. These results support the notion that a 2002 

GEOS-CHEM simulation would be beneficial to support regional air quality modeling of the 2002 

calendar year. Accordingly, VISTAS is pursuing performing a 2002 GEOS-CHEM simulation, 

whose results would be used to define BCs for the CMAQ revised basecase simulation in the fall 

of 2004. 

Initially, BCs based on seasonal average results from the GEOS-CHEM 2001 simulation 

will be used for the VISTAS Phase II CMAQ modeling of the initial 2002 base case. If a 2002 

GEOS-CHEM simulation is ready in time, then the Phase II modeling 2002 BCs would be updated 

with that data. If a 2002 GEOS-CHEM simulation is performed, there is the possibility that 

GEOS-CHEM would also be run for the future-year emissions scenario in which case the futureyear CMAQ BCs would be based on the future-year GEOS-CHEM simulation. In the absence of a 

future-year emissions scenario GEOS-CHEM simulation, we recommend that the same CMAQ 

BCs be used in the future-year as used in the 2002 base year as any adjustments to them would be 

arbitrary and speculative. 

8.3.4 Other Future-Year Modeling Inputs 

All other future-year CMAQ modeling inputs would be identical to the 2002 Base Case 

simulation including meteorology, photolysis rates, geophysical, and other inputs. 

Appendix C.1 - 156
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-10

8.4 Presentation of Results 

There are various ways that the future-year modeling results can be presented to display the 

visibility projections and convey the key findings. Although the projection of visibility 

improvements at the Class I areas is a key element of the Regional Haze Rule (RHR), analyzing 

the results solely at the Class I areas is a very narrow view of them, thus we intend to present the 

future-year modeling results in other forms to convey a more complete picture. 

8.4.1 Projection of Visibility Improvements at Class I Areas 

The results of the visibility projections at each Class I area in and around the VISTAS 

domain would be displayed graphically as well as in tabular summaries. Spread sheets of the 

results would be generated ordered by state and provided to VISTAS. The visibility projections at 

each Class I area would be compared with the 2018 visibility progress goal calculated following 

EPA’s “Guidance for Tracking Progress Under the Regional Haze Rule (EPA, 2003a). 

Figure 8-1 displays a sample plot of a visibility progress goal prepared for the Grand 

Canyon National Park as part of the WRAP Section 309 SIP work effort. The modeled projected 

visibility could be plotted on the same figure as a graphical way of presenting the results. Shown 

as a straight line near the bottom of Figure 8-1 is the EPA default “natural conditions” for the 20% 

worst visibility days as the green line with green triangles that represents the visibility goal at 

Grand Canyon of 6.97 dv in 2064. The black diamonds on the left side of the plot are the “current 

conditions” that are based on IMPROVE observations for the 20% worst days for five-year periods 

ending in 1993 (i.e., 1989-1993) to 2001 (i.e., 1997-2001). The “current conditions” for the latest 

five years of data, which is 1997-2001 in this graph (the Section 309 SIP analysis was performed 

in 2003 before the 2002 IMPROVE data were available), is assumed as the “baseline conditions” 

(i.e., 2000-2004) that is the starting point in 2004 (12.00 dv) for the glide path or linear uniform 

rate of progress to natural conditions in 2064 (purple line with squares). In this example, the 

visibility progress goal in 2018 would be 10.83 dv so that a 1.17 dv reduction in visibility is 

needed by 2018 to meet the visibility progress target in 2018 at the Grand Canyon National Park 

(GMNP). Note that we would expect higher observed visibility levels for the 20% worst days at 

Class I areas in VISTAS due to higher density population and higher sulfate concentrations in the 

eastern US, but Figure 8-1 illustrates the types of graphs that can be utilized to display visibility 

progress goals combined with visibility progress projections. 

Tabular summaries could list for each Class I area, in terms of deciview, the observed 

Baseline Conditions, the 2018 Progress Goal, the difference (i.e., visibility progress target) and 

then the modeled difference for each future-year emissions scenario. Such a table would clearly 

state which future-year emission scenarios met the RHR 2018 Progress Goals at which Class I 

areas. 

Another useful display of the projected visibility improvements are stacked bar charts of 

extinction showing the contributions of each of the six major PM components to light extinction 

for the IMPROVE measured current period to the future-year period and the 20% best and 20% 

worst days. These side–by-side current to future-year extinction comparisons can graphically 

display which extinction components are getting better and which are getting worse. They can 

also be used to identify why the emission controls may not have had the desired effect. For 

Appendix C.1 - 157
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-11

example, an SO2 emissions control strategy may have had the desired effect in reducing sulfate 

concentrations but the visibility estimates remain relatively unchanged as the lower sulfate 

concentrations frees up ammonia that then forms particulate nitrate that compensates for the lower 

sulfate in the visibility equations. Such a chemical shift in the extinction budget would be readily 

apparent in the stacked bar charts. The most useful forms to convey the modeling results will 

evolve over the project. 

Figure 8-1. Example Calculation Of Visibility Progress Goals Using IMPROVE Data Collected 

At The Grand Canyon National Park For The 20% Worst Days Showing EPA Default “Natural 

Conditions” (Green Triangles) For The 20% Worst Days That Is The 2064 Goal (6.97 dv), 

“Current Conditions” Observed Visibility (dv) As Black Triangles Whose Latest Value (12.00 dv) 

Is Assumed As The Starting Point For The 2000-2004 Baseline (First Purple Square), And The 

Glide Path From 2004 Baseline To “Natural Conditions” In 2064 Assuming Linear Uniform Rate 

Of Progress. 

Uniform Rate of Reasonable Progress Glide Path

Grand Canyon NP - 20% Worst Days

12.0011.66 10.83 9.99 9.15 8.31 7.47 6.97

0

5

10

15

20

25

30

1993 1998 2003 2008 2013 2018 2023 2028 2033 2038 2043 2048 2053 2058 2063

Year

Haziness Index Unit:Deciviews 

Glide Path Natural Visibility Conditions Observation

Appendix C.1 - 158
 May 2004

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 8.doc 8-12

8.4.2 Spatial Maps of Results 

Spatial maps of changes in individual species, total PM mass, extinction and deciview from 

the 2002 Typical Year to future-year simulations would be used to provide a big picture view of 

the changes in regional air quality and visibility from 2002 to the future–year. The display of 

hourly and 24-hour animations as well as longer-term averages (e.g., monthly, seasonal and 

annual) may provide more insight into the modeling results. 

8.4.3 Time Series Plots 

Time series plots of concentrations extinction and deciview at key receptor locations, such 

as Class I areas, may also provide additional insight into the modeling results. Hourly time series 

for selected periods and locations may provide insight into short-term changes, whereas changes in 

24-hour concentrations for the year provides information for all days, not just the ~40 days that 

constitute the 20% best/worst days of the year. 

8.4.4 Box Plots and Q-Q Plots 

Box and whisker plots of the projected extinction and deciview at Class I areas as well as 

absolute modeled extinction and deciview at all sites can be used to see changes in visibility across 

all concentrations, not just the 20% best/worst days. Quantile-Quantile plots of the changes in 

frequency distribution projected using RRFs and absolute results from the model would also 

provide an indication of the changes in visibility from the current to future-year across all days. 

Appendix C.1 - 159
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 9.doc 9-1

9.0 DATA MANAGEMENT 

Data management and data security procedures are critical components of the VISTAS 

regional fine particulate and haze modeling. Very large data files are used in each component of 

the modeling process, including processing of the meteorology data, emissions processing, and 

visibility modeling with CMAQ. An annual simulation on the VISTAS 36-km domain requires 

approximately 2 Terabytes (Tb) of disk storage while an annual simulation on the VISTAS 12-

km domain requires over 3 Tb of disk storage. This chapter describes data management 

practices. 

For all critical files we will maintain backup copies either on tapes or redundant disk 

systems. In addition, because model simulations will be performed separately by ENVIRON, 

UCR and AG, each institution will maintain its own copy and backup of critical input and output 

files. Because there are differences in system configurations at each of the 3 modeling centers 

(ENVIRON, UCR, and Alpine Geophysics) the data backup and archiving are discussed 

separately for each center, below. 

CMAQ generates large output files of which most information is rarely used (for 

example, model output for layers other than the surface layer). Under Phase I, we extracted layer 

1 data for analysis and then deleted the 3-dimensional CMAQ instantaneous concentration 

CONC output files. However, we permanently saved the script, executables and input data so 

that 3-D files can be regenerated if needed. During Phase I a new version of CMAQ was 

released that outputs hourly average layer 1 concentrations for selected species (ACONC) in 

addition to the 3-D instantaneous concentration CONC files. For Phase II we propose to output 

and archive all species on the layer 1 ACONC file and extract and archive 3-D CONC files just 

for the last hour of each month so that monthly sensitivity tests could be performed. In the event 

the Optional Task 14 is funded to evaluate CMAQ estimates aloft, we will save the 3-D CONC 

files for periods with aircraft flights. We do not plan redundant archiving for model output files 

(including output from MCIP and SMOKE) because these files can be regenerated by repeating 

model simulations, and this is approach more efficient and more cost effective than redundant 

archiving. 

 To promote efficient, reliable communication among project participants, the modeling 

team has created 4 different listservs to aid in dissemination of information and as a primary 

means for distributing emissions and air quality modeling information to the VISTAS TAWG. 

The listservs are: 

• vistas-all@cert.ucr.edu: general project information for all interested persons. 

• vistas-modeling@cert.ucr.edu: private list for the VISTAS project management team and 

modeling contractors. 

• vistas-emissions@cert.ucr.edu: list for sharing information on emissions processing and 

QA. 

• vistas-met@cert.ucr.edu: list for sharing information on meteorology modeling and 

processing of MM5 data using MCIP. 

Appendix C.1 - 160
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 9.doc 9-2

These separate listservs are aimed at providing better organization of communications and 

allowing for detailed discussions of specific topics such as emissions QA. 

9.1 Project Website 

For the VISTAS Phase I modeling effort, a project webpage at UCR has been used to 

publish and disseminate all project results. The webpage address is: www.cert.ucr.edu/vistas and 

it includes sections on model input data, emissions QA, visibility modeling results, and project 

reports and presentations. Because the Phase I webpage already contains results for a very large 

number of model simulations, we propose to establish a new, parallel webpage for Phase II 

using the address www.cert.ucr.edu/aqm/vistas2 that will be identical in design to the Phase I 

webpage. The advantages of establishing a new webpage include the following: 

• Separating Phase I and Phase II results will avoid confusion in presenting or interpreting. 

Results. 

• The Phase II results will be simpler and more accessible. 

• All Phase I results will continue to be available at the previously published web page 

addresses. 

 

As in Phase I, the project webpage will be the primary mechanism for communicating results of 

model simulations and analysis to funding agencies and other interested parties. 

9.2 Data Transfer 

Data transfer among the 3 modeling centers and between other VISTAS participants or 

contractors will be accomplished using a combination of email, ftp downloads and portable disk 

drives depending on the size of the data transfer. For data files smaller than a few MB email 

typically works well and is most efficient. For data files of less than about 500 MB file transfer 

protocol (ftp) is typically the fastest and most efficient method. ENVIRON, UCR and AG each 

maintain webpages and ftp pages that can be used for exchanging data. In addition, each 

modeling center has several portable disk drives with both USB2 and firewire interfaces that can 

be FedEx among project participants to exchange large data sets. Portable disk drives range in 

size from 80 to 300 GB and are adequate for all large files data transfers. The approach 

described here has been used throughout the VISTAS Phase I project and has proven to be 

economical and efficient. 

9.3 Data Backup and Archiving 

Data backup and archiving will be performed at each of the modeling centers. Copies of 

critical project data will be maintained at each modeling center to provide redundant backup of 

key project data. In addition, each modeling center will perform backups of key project data to 

tape or redundant disk storage systems. Data storage and back up resources at each modeling 

center are described next. 

ENVIRON 

Over 10,000 Gigabytes (>10 Terabytes, Tb) of disk storage are available to the 

UNIX/Linux workstations. All of the workstations are networked together and are accessible 

Appendix C.1 - 161
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 9.doc 9-3

from each employee’s desktop PC. All workstations have CD-ROM drives and can access DLT, 

4mm DAT and 8mm Exabyte tape drives for data backup and data transfer. ENVIRON can also 

create CDs (CD-R and CD-RW) and DVDs (DVD+ and DVD-) for data backup and distribution. 

For Phase II modeling, most CMAQ simulations would be performed on a new 9 node Beowulf 

Linux Cluster that included one master node and 8 processing nodes. Each node consists of two 

AMD Athlon 2600+ processors. The master node has 2 Gb of memory and is connected to a 2.8 

Tb RAID disk system. Each secondary processing node includes 1 Gb of memory. The 

ENVIRON Novato computing center also includes approximately 10 dual processor Linux 

workstations with processing speeds of 1700+ to 3000+. Three older Unix workstations are also 

available, SUN, DEC and SGI. The Linux computer systems are located in their own room with 

their own dedicated air conditioning (AC) system. The room includes a temperature sensitive 

power shut off device that will shut off the power to all computers in case the AC breaks down 

so that catastrophic failure due to too high temperatures does not occur. Backups are made on 

IDE disk drives that are removed from the computer and stored on a shelf to protect against 

power surges destroying the backup data. 

UC Riverside 

 Data storage systems at UCR include more than 22 TB of disk space configured as 

RAID5 disk systems. All computers and disk systems are connected using high speed Gigabit 

Ethernet for efficient simulation and analysis of large datasets. To provide maximum data 

security the systems are located behind the UCR firewall and an additional firewall internally 

within the laboratory. A separate system is used for the project websites and ftp site to allow 

project data to be accessed thought the UCR T1 internet connection. The data backup/archiving 

system include 8mm tape drives and DLT and Super DLT auto loading cartridge system capable 

of performing unattended archive/backups of over 1 Tb (uncompressed). Key disk systems have 

hot-swappable hard drives with stand-by spare drives and redundant power supplies. Copies of 

critical project data are backed up to tape and to a redundant RAID5 disk system. The compute 

clusters and disk systems are located in a locked, secure room with a dedicated climate control 

system and with backup air conditioning. The laboratory has a full time systems administrator to 

perform system backups, maintenance and updates and Dr. Tonnesen’s group includes a second 

full time systems administrator who performs weekly backups of critical data to tape.

Alpine Geophysics 

 Alpine Geophysics' computing facilities consist of SUN Microsystems SPARCstation 

computers and a very powerful array of 19 multiprocessor Linux-based workstations. Disk 

storage systems include 12 Tb of aggregate disk space and over 8 Tb of SCSI and IDE Raid-5 

protected space. All client data is stored on at least one RAID-5 protected disk array. To further 

protect client data, two of our main servers backup their disk drives on a weekly basis to a 

second server that is physically disconnected from the power supply when not doing an active 

transfer. This way a catastrophic power failure will not compromise the ability for Alpine 

Geophysics to deliver. 

Appendix C.1 - 162
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 10.doc 10-1 

10.0 DOCUMENTATION 

 This section describes the documentation that be provided during VISTAS Phase II and the 

potential for modifications to this Modeling Protocol and QA Plan that might become necessary as 

this phase of the study unfolds. 

10.1 Planned Documentation 

Documentation associated with the emissions and air quality modeling performed during 

Phase II will include all relevant input data bases and scripts associated with the pre- and postprocessing associated with model input development, model application, sensitivity and diagnostic 

analyses, and performance evaluations. Interim reports describing the methodologies and results of 

the model performance evaluation, model intercomparison, and visibility assessment will be 

provided. As shown in Appendix A, the interim reports for many of the subtasks will consist of 

PowerPoint presentations and/or results posted to the project website. For the major tasks, however, 

we do intend to document the work activities in more formal reports. Such planned reports for the 

base effort include: 

• Phase II Modeling Protocol (this document) 

• Phase II Quality Assurance Project Plan (QAPP) 

• 2002 emissions modeling draft and final reports 

• Initial 2002 CMAQ modeling summary report 

• Revised 2002 CMAQ modeling summary report 

• Future-year visibility projections modeling report 

• Draft and final Executive Summary report 

• Optional Journal Article(s) 

In addition, copies of all scripts, reports and documentation provided to the VISTAS TAWG 

will be maintained on the project website. A final report summarizing all aspects of the project will 

also be provided. The list of deliverables for this project is described in a summary of the Phase II 

scope of work provided in Appendix A. 

 Reporting on each task in Phase II will consist of documentation of the data sources, 

methods, results, and findings. Individual task deliverables shall reflect any changes and revisions 

that occur over duration of Phase II. At the completion of Phase II, a draft final Executive 

Summary report will be prepared that details, documents and summarizes the results. This 

documentation will conform to the recommendations set forth in EPA’s "Draft Guidance for 

Demonstrating Attainment of Air Quality Goals for PM2.5 and Regional Haze (Jan ‘01)” and any 

subsequent versions. The final Executive Summary report will contain: (a) an executive summary 

abstract that provides a brief overview and summary of the modeling effort, emissions and air 

quality models used, model configuration, model performance evaluation overview and results, and 

rationale for the selected configuration, (b) technical detail covering all relevant aspects of the Phase 

II emissions and PM grid modeling, and (c) a discussion on data accessibility and availability for 

review by the public. The report will be provided in electronic form, (e.g., Word 2000 and pdf 

formats) and shall be submitted to the VISTAS Project Officer and also posted on the project web 

site. 

Appendix C.1 - 163
 May 2004 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\Chapter 10.doc 10-2 

10.2 Procedures for Updating Modeling Protocol and QA Plan

One of the underlying realizations stemming from the Phase I activities was the awareness 

that the science of ‘One-Atmosphere’ PM/regional haze modeling is advancing very rapidly. Part of 

this stems from the parallel activities being carried out by the RPOs; some if it is due to other 

ongoing 8-hr ozone and PM modeling studies being performed by various states. In addition, EPA 

is in the process of revising its PM2.5 and regional haze guidance documents. Collectively, it is quite 

likely that there will be new opportunities to strengthen the modeling algorithms, input data sets, and 

evaluation procedures throughout the duration of Phase II. Moreover, the Phase II emissions and air 

quality modeling activities involve the collaboration with the TAWG as well as other VISTAS 

contractors who will provide the required emissions and meteorological inputs to the SMOKE and 

CMAQ models. Given the ongoing model refinement activities and the need for strong coordination 

with other VISTAS contractors, it may be necessary to modify certain aspects of this modeling 

protocol. In this event, modification will be made in consultation with the VISTAS TAWG and the 

revised protocol will be submitted to the workgroup for approval. 

Appendix C.1 - 164
 May 2003 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\References.doc R-1 

REFERENCES 

Alpine Geophysics, 2003a. “VISTAS Emissions and Air Quality Modeling – Phase I Subtask 3c1 Report: MM5 Meteorology QA/QC Summary Report for Episode 1: 2-20 January 

2002.” Alpine Geophysics LLC, ENVIRON International Corporation and University of 

California at Riverside. Ft. Wright, Kentucky (available at: 

http://pah.cert.ucr.edu/vistas/docs.shtml). September 10. 

Alpine Geophysics, 2003b. “VISTAS Emissions and Air Quality Modeling – Phase I Subtask 3c1 Report: MM5 Meteorology QA/QC Summary Report for Episode 1: 13-22 July 1999.” 

Alpine Geophysics LLC, ENVIRON International Corporation and University of 

California at Riverside. Ft. Wright, Kentucky (available at: 

http://pah.cert.ucr.edu/vistas/docs.shtml). September 15. 

Alpine Geophysics, 2003c. “VISTAS Emissions and Air Quality Modeling – Phase I Subtask 3c1 Report: MM5 Meteorology QA/QC Summary Report for Episode 1: 11-27 July 2001.” 

Alpine Geophysics LLC, ENVIRON International Corporation and University of 

California at Riverside. Ft. Wright, Kentucky (available at: 

http://pah.cert.ucr.edu/vistas/docs.shtml). September 16. 

Anthes, R.A. 1977. “A Cumulus Parameterization Scheme Utilizing a One-Dimensional Cloud 

Model”, Mon. Wea. Rev., Vol. 105, pp. 270-286. 

Anthes, R.A. and T.T. Warner. 1978. “The Development of Mesoscale Models Suitable for Air 

Pollution and Other Mesometeorological Studies”, Mon. Wea. Rev., Vol. 106, pp, 1045-

1078. 

Arnold, J.R.; R.L. Dennis, and G.S. Tonnesen. 1998. Advanced techniques for evaluating 

Eulerian air quality models: background and methodology. In: Preprints of the 10th Joint 

Conference on the Applications of Air Pollution Meteorology with the Air & Waste 

Management Association, January 11-16, 1998, Phoenix, Arizona. American 

Meteorological Society, Boston, Massachusetts, paper no. 1.1, pp. 1-5. 

Arnold, J.R., R.L. Dennis, and G.S. Tonnesen. 2003. “Diagnostic Evaluation of Numerical Air 

Quality Models with Specialized Ambient Observations: Testing the Community 

Multiscale Air Quality Modeling System (CMAQ) at Selected SOS 95 Ground Sites”, 

Atmos. Environ., Vol. 37, pp. 1185-1198. 

ARS. 2002a. Analysis of IMPROVE and SEARCH Speciated PM2.5 Data. Air Resource Specialists, 

Inc. Report to VISTAS, August 28, 2002. http://www.vistas-sesarm.org. 

ARS. 2002b. Analysis of Alternative Methods. Air Resource Specialists, Inc. Report to VISTAS, 

August 28, 2002. http://www.vistas-sesarm.org.

ARS. 2002c. Review of Selected Factors Responsible for High and Low Extinction. Air Resource 

Specialists, Inc. Report to VISTAS, October 14, 2002. http://www.vistas-sesarm.org.

Appendix C.1 - 165
 May 2003 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\References.doc R-2 

Barchet, W.R., and R.L. Dennis. 1990. “ANAPAP Model Evaluation, Volume 1: Protocol”, 

prepared for the U.S. Environmental Protection Agency, prepared by Battelle Pacific 

Northwest Laboratories, Richland, WA. 

Boylan, J. W., 2004. “Calculationg Statistics: Concentration Related Performance Goals”, paper 

presented at the EPA PM Model Performance Workshop, Chapel Hill, NC. 11 February. 

Brewer, P., S. Holman and J. Hornback. 2003. “Vistas Analyses of Regional Haze in the 

Southeastern United States.” Presented at Annual Air and Waste Management Association 

Meeting and Exhibition, San Diego, CA. June. 

Byun, D.W., and J.K.S. Ching. 1999. “Science Algorithms of the EPA Models-3 Community 

Multiscale Air Quality (CMAQ) Modeling System”, EPA/600/R-99/030. 

Carter, W.P.L. 1999. Documentation of the SAPRC-99 Chemical Mechanism for VOC 

Reactivity Assessment, Draft report to the California Air Resources Board, Contracts 92-

329 and 95-308, 9/13/99. 

Chang, J.S., R.A. Brost, I.S.A. Isakson, S. Madronic, P. Middleton, W.R. Stockwell and C.J. 

Walcek. 1987. A three-dimensional Eulerian acid deposition model: Physical concepts 

and formulation. J. Geophys. Res., 92, 14681-14700. 

Chang, J. S., et al. 1997. “The SARMAP Air Quality Model", prepared for the California Air 

Resources Board, prepared by the State University of New York, Albany, New York. 

Coella, P., and P. L., Woodward. 1984. “The Piecewise Parabolic Method (PPM) for GasDynamical Simulations”, J. Comp. Physics, Vol. 54, pp. 174-201. 

Dennis, R. L., et al. 1990. "Evaluation of Regional Acid Deposition Models", State-ofScience/Technology Report No. 5, National Acid Precipitation Assessment Program, 

Washington, D.C. 

Dentener, F. J., and P. J. Crutzen. 1993. Reaction of N2O5 on tropospheric aerosols: Impact on 

global distributions of NOx, O3, and OH, J. Geophys. Res., 98, 7149-7163. 

Donahue, N.M., M.K. Dubey, R. Mohrschladt, K.L. Demerjian, and J.G. Anderson. 1997. 

High-pressure flow study of the reactions OH+NOx → HONOx: Errors in the falloff 

region. J. Geophys. Res. 102, 6159-6168. 

Dudhia, J. 1993. "A Non-hydrostatic Version of the Penn State/NCAR Mesoscale Model: 

Validation Tests and Simulation of an Atlantic Cyclone and Cold Front", Mon. Wea. Rev., 

Vol. 121. pp. 1493-1513. 

Edgerton, E. S., Sources of PM2.5 Carbon in the Southeast US, presentation at the MARAMA 

Science Meeting, Baltimore, MD, January 22, 2003. http://www.marama.org.

Appendix C.1 - 166
 May 2003 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\References.doc R-3 

ENVIRON, Alpine Geophysics, UC Riverside and UC Davis. 2003a. “VISTAS Emissions and 

Air Quality Modeling – Phase I Task 4a/b Report: Review of Model Sensitivity 

Simulations and Recommendations of Initial CMAQ Model Configurations and Sensitivity 

Tests.” Revised Draft July 25. 

ENVIRON, Alpine Geophysics , UC Riverside and UC Davis. 2003b. “VISTAS Emissions and 

Air Quality Modeling – Phase I Task 3 Report: Review and Assessment of Available 

Ambient Air Quality Data to Support Modeling and Modeling Performance Evaluation for 

the Three VISTAS Phase I Episodes.” Revised Draft July 22. 

ENVIRON. 2002. “User’s Guide Comprehensive Air Quality Model With Extensions (CAMx) 

Version 3.10.” ENVIRON International Corporation, Novato, California (available at 

www.camx.com) April. 

ENVIRON. 2003a. “Development of an Advanced Photochemical Model for Particulate Matter: 

PMCAMx.” ENVIRON International Corporation, Novato, CA. Prepared for 

Coordinating Research Council, Inc. Project A-30 (available at www.crcao.com). 

ENVIRON, 2003b. “VISTAS Emissions and Air Quality Modeling – Phase I Task 2 Report: 

Recommended Model Configurations and Evaluation Methodology for Phase I Modeling.” 

 Prepared by ENVIRON International Corporation, Alpine Geophysics, LLC and 

University of California at Riverside. Novato, California. (available at: 

http://pah.cert.ucr.edu/vistas/docs.shtml). August 4. 

ENVIRON, 2003c. “VISTAS Emissions and Air Quality Modeling – Phase I Task 3 Report: 

Review and Assessment of Availablre Ambient Air Quality Modeling and Performance 

Evaluation for the Three VISTAS Phase I Episoides.” Prepared by ENVIRON 

International Corporation, Alpine Geophysics, LLC and University of California at 

Riverside. Novato, California. (available at: http://pah.cert.ucr.edu/vistas/docs.shtml). 

July 22. 

ENVIRON, 2003d. “VISTAS Emissions and Air Quality Modeling – Phase I Task 4a/b Report: 

Review of Model Sensitivity Simulations and Recommendations of Initial CMAQ Model 

Configurations and Sensitivity Tests.” Prepared by ENVIRON International Corporation, 

Alpine Geophysics, LLC and University of California at Riverside. Novato, California. 

(available at: http://pah.cert.ucr.edu/vistas/docs.shtml). July 25. 

EPA, 1991. "Guidance for Regulatory Application of the Urban Airshed Model (UAM), "Office 

of Air Quality Planning and Standards, U.S. Environmental Protection Agency, Research 

Triangle Park, N.C. 

EPA, 1999. “Draft Guidance on the Use of Models and Other Analyses in Attainment 

Demonstrations for the 8-hr Ozone NAAQS”. Draft (May 1999), U.S. Environmental 

Protection Agency, Office of Air Quality Planning and Standards, Research Triangle 

Park, N.C 

Appendix C.1 - 167
 May 2003 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\References.doc R-4 

EPA. 2000. “Guidance for Demonstrating Attainment of Air Quality Goals for PM2.5 and 

Regional Haze”, Preliminary Draft Report, U.S. Environmental Protection Agency, 

Research Triangle Park, NC. 

EPA. 2001. “Guidance for Demonstrating Attainment of Air Quality Goals for PM2.5 and 

Regional Haze”, Draft Report, U.S. Environmental Protection Agency, Research Triangle 

Park, NC. 

EPA. 2003a. “Guidance for Tracking Progress Under the Regional Haze Rule”, U.S. 

Environmental Protection Agency, Research Triangle Park, NC. 

EPA. 2003b. “Guidance for Estimating Natural Visibility Conditions Under the Regional Haze 

Rule”, U.S. Environmental Protection Agency, Research Triangle Park, NC.

Fahey, K.M., and S.N. Pandis. 2001. Optimizing model performance: variable size reduction in 

cloud chemistry modeling. Atmos. Environ. Vol. 35, pp. 4471-4478. 

FLAG. 2000. Federal Land Manager’s Air Quality Related Values Workgroup (FLAG) Phase I 

Report. (http://www2.nature.nps.gov/ard/flagfiee/AL.doc). 

Gery, M. W., G.Z. Whitten, J.P. Killus, and M.C. Dodge. 1989. A photochemical mechanism 

for urban and regional-scale computer modeling. J. Geophys. Res. 94, 12925-12956. 

Gipson, G, and J. Young. 1999. Process Analysis, in Science Algorithms of the EPA Models-3 

Community Multiscale Air Quality (CMAQ) Modeling System, Chapter 16, U.S. EPA, 

Office of Research and Development, Washington, DC 20460. 

Grell, G. A., J. Dudhia, and D. R. Stauffer. 1994. "A Description of the Fifth Generation Penn 

State/NCAR Mesoscale Model (MM5). NCAR Tech. Note, NCAR TN-398-STR, 138 pp. 

Hanna, S.R., A.G. Russell, J. Wilkinson, and J. Vukovich. 2002. Review of BEIS3 

Formulation and Consequences Relative to Air Quality Standards: Estimation of 

Uncertainties in BEIS3 Emissions Outputs. EPRI Technical Report 1005159, EPRI, 3412 

Hillview Ave., Palo Alto, CA 94304. 

Hanna, S.R., A.G. Russell, J. Wilkinson, and J. Vukovich. 2003. Review of BEIS3 Formulation 

and Consequences Relative to Air Quality Standards: Estimation of Effects of 

Uncertainties in BEIS3 Emissions on Uncertainties in Ozone Predictions by Chemical 

Transport Models, EPRI, Palo Alto, CA: 2002 (report is currently under review by 

EPRI). 

Hanna, S. R. 1994. "Mesoscale Meteorological Model Evaluation Techniques with Emphasis on 

Needs of Air Quality Models", in Mesoscale Modeling of the Atmosphere, R. A. Pielke and 

R. P. Pierce (Eds.), American Meteorological Society, Boston, MA.

Hermann, H. et al., 2000. manuscript submitted to J. Geophys. Res.

Appendix C.1 - 168
 May 2003 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\References.doc R-5 

IPCC. 2001. "Climate Change 2001: The Scientific Basis -- Contribution of Working Group I to 

the Third Assessment Report of IPCC." Intergovernmental Panel on Climate Change. 

ISBN: 0521014956. 

Jacob, D. J. 1999. Heterogeneous chemistry and tropospheric ozone. Atmos. Environ., special 

issue, 1999 NARSTO Assessment. 

Khasibatla, P. et al. 1997. Impact of inert organic nitrate formation on ground-level ozone in a 

regional air quality model using the Carbon Bond Mechanism 4. Geophys. Res. Letters, 

24, 3205-3208. 

Liu, G., C. Hogrefe, and S.T. Rao. 2003. “Evaluating the Performance of Regional-Scale 

Meteorological Models: Effects of Clouds Simulation on Temperature Prediction”, Atmos. 

Environ., Vol. 36, pp. 1691-1705. 

Matthias-Maser, S. and R. Jaenicke. 1995. "The size distribution of primary biological aerosol 

particles with radii >0.2 mm in an urban-rural influenced region." Atmos. Res., 39, 279-

286. 

McNally, D.E., and T.W. Tesche. 1994. "MAPS2.3 User's Guide", Alpine Geophysics, LLC, 

Golden, CO. 

McNally, D. E. 1997. “Development of Methodology for Mapping MM5 Fields onto Arbitrary 

Eulerian Photochemical Air Quality Simulation Models (PAQSM)”, Alpine Geophysics, 

LLC, Arvada, CO. 

Odman, M. T.; Boylan, J.W.; Wilkinson, J.G.; and Russell, A.G. SAMI Air Quality Modeling Final 

Report. Southern Appalachian Mountains Initiative. 2002. http://www.saminet.org.

Olerud, D. 2003a. “Evaluation Methodologies for Meteorological Modeling in Support of 

VISTAS (Visibility Improvement – State and Tribal Association): Task 1 Deliverables” 

(Draft) Baron Advanced Meteorological Systems, LLC, Research Triangle Park, NC. 

(available at: http://www.baronams.com/projects/VISTAS/#reports). April 16. 

Olerud, D and A. Sims. 2004. “Episode Selection from a Meteorological Perspective for 

VISTAS (Visibility Improvement – State and Tribal Association): Task 3a Deliverable.” 

Baron Advanced Meteorological Systems, LLC, Research Triangle Park, NC. (available 

at: http://www.baronams.com/projects/VISTAS/#reports). February 9. 

Olerud, D. 2003c. “Protocol for Annual MM5 Modeling of VISTAS (Visibility Improvement – 

State and Tribal Association): Task 7c Deliverable.” Baron Advanced Meteorological 

Systems, LLC, Research Triangle Park, NC. (available at: 

http://www.baronams.com/projects/VISTAS/#reports). March 27. 

Olerud, D. 2003d. “MM5 Sensitivity Modeling in Support of VISTAS (Visibility Improvement 

– State and Tribal Association): Task 2e Deliverable” (Draft) Baron Advanced 

Meteorological Systems, LLC, Research Triangle Park, NC. 4 December 2003 

Appendix C.1 - 169
 May 2003 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\References.doc R-6 

Olerud, D. 2003e. “VISTAS Meteorological Modeling Sensitivity Results”, PowerPoint 

presentation at the 29-30 September 2003 VISTAS Technical Review Meeting (Research 

Triangle Park, NC), prepared by Baron Advanced Meteorological Systems, LLC, 

Research Triangle Park, NC. 29 September 2003 

Pielke, R. A., and M. Uliasz. 1998. “Use of Meteorological Models as Input to Regional and 

Mesoscale Air Quality Models C Limitations and Strengths”, Atmos. Environ. Vol. 32, 

No. 8, pp. 1455-1466. 

Pilinis, C. and J. H. Seinfeld. 1987. “Continued Development of a General Equilibrium Model 

for Inorganic Multicomponent Atmospheric Aerosols”, Atmos. Environ. Vol.21, pp.2453. 

Pilinis, C., K.P. Capaldo, A. Nenes, and S.N. Pandis. 2000. “MADM - A new multicomponent 

aerosol dynamics model.” Aerosol Sci. Tech., Vol. 32(5), pp. 482-502. 2000. 

Russell, A.G., and R.L. Dennis. 2000. “NARSTO Critical Review of Photochemical Models 

and Modeling”, Atmos. Environ., Vol. 34, No. 12-14, pp. 2283-2324. 

Schere, K.L., and R.A. Wayland. 1989. "EPA Regional Oxidant Model (ROM2.0): Evaluation 

on 1980 NEROS Data Bases", EPA/600/3-80/057, Atmospheric Research and Exposure 

Assessment Laboratory, Research Triangle Park, NC. 

Seaman, N.L. 1995. “Status of Meteorological Pre-Processors for Air Quality Modeling”, 

International Conf. On Particulate Matter, Air and Waste Mgt. Assn., Pittsburgh, PA. 

Seaman, N.L. 1995. “Status of Meteorological Pre-Processors for Air Quality Modeling”, 

International Conf. On Particulate Matter, Air and Waste Mgt. Assn., Pittsburgh, PA. 

Seaman, N.L. 1996. “Study of Meteorological Variables Needed in Air-Quality Modeling’, 

Annual Progress Report prepared for the Coordinating Research Council (CRC), Interim 

Report, Project A-11, prepared by the Department of Meteorology, Penn State University, 

State College, PA. 

Seaman, N.L. 2000. “Meteorological Modeling for Air Quality Assessments”, Atmos. Environ., 

Vol. 34, No. 12-14, 2231-2260. 

Seaman, N. L., and D. R. Stauffer. 1996. "SARMAP Meteorological Model Final Report", 

prepared for the San Joaquin Valleywide Air Pollution Study Agency, prepared by the 

Department of Meteorology, Pennsylvania State University, University Park, PA. 

Seaman, N.L., and S.A. Michelson. 1998. “Mesoscale Meteorological Structure of a HighOzone Episode During the 1995 NARSTO-Northeast Study”, J. Appl. Meteo., 

(submitted). 

Seaman, N.L., D.R. Stauffer, and T.W. Tesche. 1992. "The SARMAP Meteorological Model: 

A Four-Dimensional Data Assimilation Technique Used to Simulate Mesobeta-Scale 

Meteorology During a High-Ozone Episode in California", International Specialty 

Conference on Tropospheric Ozone Nonattainment and Design Value Issues, U.S. 

Appendix C.1 - 170
 May 2003 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\References.doc R-7 

EPA/AWMA, 27-30 October, Boston, MA. 

Seaman, N.L., D.R. Stauffer, and L.M. Lario. 1995. "A MultiScale Four-Dimensional Data 

Assimilation System Applied to the San Joaquin Valley During SARMAP. Part I: 

Modeling Design and Basic Performance Characteristics", J. Appl. Meteo., Vol. 34, pp. 

1739-1761. 

Seaman, N.L., D.R. Stauffer, and D.E. McNally. 1996a. "Application of the MM5-FDDA 

Meteorological Model to the Southern California SCAQS-1997 Domain: Preliminary Test 

Using the SCAQS August 1987 Case", Ninth Joint Conference on Applications of Air 

Pollution Meteorology, American Meteorological Society, 28 January-2 February, 

Atlanta, GA. 

Seinfeld, J.H. and S.N. Pandis. 1998. Atmospheric Chemistry and Physics: From Air Pollution 

to Global Change. Wiley, New York. 

Seigneur, C., et al. 2000. “Guidance for the Performance Evaluation of Three-Dimensional Air 

Quality Modeling Systems for Particulate Matter and Visibility”, J. Air & Wast Manage. 

Assoc. Vol. 50, pp. 588-599. 

Simoneit, B.R.T., J.N. Cardoso and N. Robinson. 1990. "An assessment of the origin and 

composition of higher molecular weight organic matter in aerosols over Amazonia." 

Chemosphere, 21, 1285-1301. 

Stockwell, W.R., P. Middleton, J.S. Chang, and X. Tang. 1990. The second generation 

Regional Acid Deposition Model chemical mechanism for regional air quality modeling. J. 

Geophys. Res., 95, 16,343-16,367. 

Stockwell, W.R., P. Middleton, J.S. Chang, and X. Tang, X. 1997. The second generation 

Regional Atmospheric Chemistry Mechanism regional air quality modeling. J. Geophys. 

Res., 102. 

Strader, R., F.W. Lurmann and S.N. Pandis. 1999. “Evaluation of secondary organic aerosol 

formation in winter.” Atmos. Environ. Vol. 33, pp. 4849-4864. 

Tang, Y. 2002, “A Case Study of Nesting Simulation for the Southern Oxidants Study 1999 at 

Nashville”, Atmos. Environ., Vol. 36, pp. 1691-1705. 

Tesche, T. W., et al., 1990. "Improved Treatment of Procedures for Evaluating Photochemical 

Models", prepared for the California Air Resources Board, prepared by Alpine 

Geophysics, Crested Butte, CO. Contract No. A832-103. 

Tesche, T.W., and D.E. McNally. 1993a. “Operational Evaluation of the CAL-RAMS 

Meteorological Model for LMOS Episode 1: 26-28 June 1991", prepared for the Lake 

Michigan Air Directors Consortium, prepared by Alpine Geophysics, LLC, Crested Butte, 

CO. 

Appendix C.1 - 171
 May 2003 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\References.doc R-8 

Tesche, T.W., and D.E. McNally. 1993b. "Operational Evaluation of the CAL-RAMS 

Meteorological Model for LMOS Episode 2: 17-19 July 1991", prepared for the Lake 

Michigan Air Directors Consortium, prepared by Alpine Geophysics, LLC, Crested Butte, 

CO. 

Tesche, T.W., and D.E. McNally. 1993c. "Operational Evaluation of the CAL-RAMS 

Meteorological Model for LMOS Episode 3: 25-26 August 1991", prepared for the Lake 

Michigan Air Directors Consortium, prepared by Alpine Geophysics, LLC, Crested Butte, 

CO. 

Tesche, T.W., and D.E. McNally. 1993d. "Operational Evaluation of the CAL-RAMS 

Meteorological Model for LMOS Episode 4: 20-21 June 1991", prepared for the Lake 

Michigan Air Directors Consortium, prepared by Alpine Geophysics, LLC, Crested Butte, 

CO. 

Tesche, T.W. and D.E. McNally. 1996a. “Superregional Ozone Modeling and Analysis Study 

C Phase I: Work Element 3: Assessment of the OTAG Data Sets -- Task 2 Technical 

Memorandum: Review of the OTAG Meteorological Inputs and Outputs”, prepared for the 

Midwest Ozone Group, prepared by Alpine Geophysics, LLC, Ft. Wright, KY. 

Tesche, T.W. and D.E. McNally. 1996b. “Superregional Ozone Modeling and Analysis Study 

C Phase II: Work Element 5 Technical Report: Comparative Evaluation of the MM5 and 

RAMS Models for the July 1991 OTAG Episode”, prepared for the Midwest Ozone 

Group, prepared by Alpine Geophysics, LLC, Ft. Wright, KY. 

Tesche, T.W., and D.E. McNally. 1997a. “Superregional Ozone Modeling and Analysis Study 

C Final Report: Assessment of the Reliability of the OTAG Modeling System”, prepared 

for the Midwest Ozone Group, prepared by Alpine Geophysics, LLC, Ft. Wright, KY. 

Tesche, T.W., and D.E. McNally. 1997b. “Methodology for Climatological Analysis of MultiYear Aerometric Data to Support the Development of the Breton Conceptual Model and 

Field Program Design”, prepared for Walk Heydel Environmental, prepared by Alpine 

Geophysics, LLC, Ft. Wright, KY. 

Tesche, T.W., and D.E. McNally. 1997c. “The Use of the San Joaquin Valley Meteorological 

Model in Preparation of a Field Program in the South Coast Air Basin and Surrounding 

Regions of Southern California: Volume I: Final MM5 Evaluation for the 3-6 August 1990 

SARMAP Episode”, prepared for the California Air Resources Board, prepared by Alpine 

Geophysics, LLC, Ft. Wright, KY. 

Tesche, T.W. and D.E. McNally. 1999. “Comparative Evaluation of the MM5 and RAMS3c 

Prognostic Meteorological Models Over the Midwestern U.S. for Two 1999 LMOS 

Intensive Measurement Episodes”, prepared for the Coordinating Research Council, 

Project A-25 draft Final Report, prepared by Alpine Geophysics, LLC, Ft. Wright, KY. 

Tesche, T.W., and D.E. McNally. 2001. “Evaluation of CAMx and Models-3/CMAQ Over the 

Lower Lake Michigan Region with Inputs from the RAMS3c and MM5 Models”, 

Appendix C.1 - 172
 May 2003 

G:\VISTAS Modeling\Task6 Modeling Protocol\Draft#3\References.doc R-9 

prepared for the Coordinating Research Council, prepared by Alpine Geophysics, LLC, 

Ft. Wright, KY. 

Tesche, T.W., and H.E. Jeffries. 2002. “Findings From BCCA-AG Science Studies”, prepared 

for the Business Coalition for Clean Air- Appeals Group, (2002), prepared by Alpine 

Geophysics, LLC, Ft. Wright, KY. 

Timin, B. 2002. “PM2.5 and Regional Haze Modeling Guidance”. Prepared by the U.S. 

EPA/OAQPS. April 24. 

Timin, B. 2004. “PM2.5 Model Performance Evaluation: Purpose and Goals”. Presented at PM 

Model Evaluation Workshop, Chapel Hill, NC. February. 

Tonnesen, G.S. 1999. Effects of uncertainty in the reaction of the hydroxyl radical with nitrogen 

dioxide on model simulated ozone control strategies. Atmos. Environ. 33:1587-1598. 

Tonnesen, G.S. and R.L. Dennis. 2000. Analysis of radical propagation efficiency to assess 

ozone sensitivity to hydrocarbons and NOx. Part 1: Local indicators of odd oxygen 

production sensitivity. J. Geophys. Res., 105, 9213–9225. 

Watson, J.G. and J.C. Chow. 1999. Reconciling Urban Fugitive Dust Emissions Inventory and 

Ambient Source Contribution Estimates: Summary of Current Knowledge and Needed 

Research. Document No. 61110.4D2, Desert Research Institute, Reno NV, September 3. 

Zaveri, R.A and L.K. Peters. 1999. A new lumped structure photochemical mechanism for 

large scale applications, J. Geophys. Res., 30,387-30,415 

Zheng,, M.; Cass, G.R.; Schauer, J.J.; Edgerton, E.S. Environ. Sci. Tech. 2002, 36, 2361-2371.

Appendix C.1 - 173
 

Appendix A 

Summary of VISTAS Phase II 

Emissions and Air Quality Modeling 

Scope of Work (SOW) 

(Updated May 6, 2004)

Appendix C.1 - 174
 

VISTAS Phase II 2004 Atmospheric Modeling Scope of Work 

ENVIRON/Alpine/UCR 

Draft Version#5: May 6, 2004 

INTRODUCTION 

ENVIRON International Corporation, Alpine Geophysics (Alpine) and the University of California 

at Riverside (UCR) propose to perform the VISTAS Phase II emissions and air quality modeling 

as described in the Scope of Work (SOW) given below. As was seen in the VISTAS Phase I 

modeling, the SOW will likely be refined and modified during the course of the project and the 

ENVIRON/Alpine/UCR team is flexible in achieving the ultimate objectives and requirements 

needed by VISTAS. In putting together the VISTAS Phase II SOW, the ENVIRON/Alpine/UCR 

team is dependent on receiving data and information from other participants. The following are 

our assumed dates for deliverables that we expect to receive key data sources in developing 

our SOW. 

• January 31, 2004 – Initial 2002 baseline emissions for VISTAS states delivered by 

VISTAS contractors. (Achieved February 9, 2004.) 

 

• January 31, 2004 – First 8 months of 2002 MM5 modeling results delivered by VISTAS 

contractors. (Achieved February 20, 2004) 

• March 30, 2004 – Last 4 months of 2002 MM5 modeling results. 

• April 15, 2004 -- Initial 2018 Future-Year VISTASA States emissions for one scenario 

and 2 of the Phase I episodes (Jan ’02 and Jul ’01) from VISTAS contractor. Second 

2018 scenario available April 30, 2004. 

• September 15, 2004 – Revised 2002 baseline emissions for VISTAS states. 

• September 15, 2004 – Revised 2002 base year using typical year EGU and fire 

inventory for VISTAS states. 

• September 15, 2004 – 2002 base year inventory and typical year EGU and fire inventory 

for non-VISTAS states, Mexico, Canada as available from non-VISTAS sources 

• October 15, 2004 – Revised Future-Year emissions for VISTAS states, three future year 

scenarios and the 2002 annual period. 

• October 31, 2004 – MM5 modeling results for ~60 episode days from 2003 (or other 

years as appropriate) for optional episode modeling task. 

Key deliverables for the modeling team are as follows: 

• Draft modeling protocol by March 5, 2004, final protocol 2 weeks after VISTAS review 

comments received. 

• Analysis of GEOS-CHEM 2001 hourly and monthly outputs for CMAQ initial and 

boundary conditions (IC/BC) and recommendation whether to use 2002 GEOS-CHEM 

Appendix C.1 - 175
 

for IC/BC in CMAQ revised 2002 modeling in fall 2004 – due March 2004. 

• 2002 initial inventory for Non-VISTAS States, Mexico, Canada by March 15, 2004. 

• 2018 initial emissions estimates for Non-VISTAS States, Canada, Mexico and 2 Phase I 

episodes (Jan 2002 and Jul 2001) by April 15, 2004. 

• 2018 CMAQ-ready emissions from SMOKE for 2 Phase I episodes (July 2001 and Jan 

2002) for one scenario by May 15, 2004 and the other scenario by June 15, 2004. 

• 2002 CMAQ-ready emissions from SMOKE for 2002 annual period by May 31, 2004 

• Quality Assurance Project Plan (QAPP) for Phase II modeling (June 2004) 

• CMAQ model performance evaluation for annual 2002 runs using initial 2002 inventory 

by August 30, 2004 

• Collection of available 2002 revised inventory and typical year EGU and fire for nonVISTAS states, Canada, Mexico by September 15, 2004 

• Future year revised inventory for non-VISTAS states, Canada, Mexico by October 15, 

2004 for 3 scenarios 

• 2002 revised CMAQ-ready SMOKE outputs using revised 2002 inventories by October 

15, 2004 

• 2002 revised plus typical EGU and fire CMAQ-ready SMOKE outputs by October 31, 

2004 

• 2002 revised CMAQ annual run and model performance evaluation by December 1, 

2004 

• 2002 revised plus typical EGU and fire CMAQ annual run and model performance 

evaluation by December 31, 2004 

• Future year CMAQ-ready SMOKE outputs using revised inventories for first scenario by 

November 15, 2004, for second and third by December 15, 2004 

• Future year revised emissions CMAQ annual modeling runs for 3 scenarios due by 

January 31, 2005. 

• Optional task CMAQ-ready SMOKE outputs for 2003 episodes after January 1, 2005 

Table 1 summarizes the task structure, task leader, schedule and deliverables for the VISTAS 

Phase II proposed SOW. Figure 1 displays the current proposed schedule for the VISTAS 

Phase II modeling based on the above assumptions on data deliverables to the Modeling Team. 

This schedule will likely be revised and updated as more refined delivery dates are developed.

Appendix C.1 - 176
 

Figure 1. Current proposed schedule for the VISTAS Phase II modeling (May 6, 2004).

Appendix C.1 - 177
Table 1. Summary of proposed VISTAS Phase II Tasks, Task Managers, Deliverables and Costs (shaded tasks are currently not funded, May 6, 

2004). 

Work Element Manager Deliverables (Date) Task 1: Management Ralph Morris • Monthly Conference Calls (2004) 

• 3 Meetings with 2 People in Southeast US (2004) • First Draft Modeling Protocol (03/05/04) • Second Draft Modeling Protocol (03/30/04) • Updated Modeling Protocol (as needed) • QAPP (June 2004) • Draft Final Executive Summary Report (01/15/05) • Final Executive Summary Report (01/31/05) 

Task 2: IC/BCs Analysis Gail Tonnesen • Initial analysis of the need for 3-hr vs. seasonal BCs for CMAQ 

modeling (02/12/04). 

• 2002 IC/BC recommendations PowerPoint presentation, which 

includes monthly average vs. 3-hr BC CMAQ comparisons for July 2001 episode (March 2004) 

Subtask3a: Air Quality Gatekeeper 

Gail Tonnesen • 2002 Air Quality MPE database, QA/QC and PowerPoint 

presentation (04/30/04) 

• 2002 initial CMAQ IC/BC inputs (04/30/04) • Review of 2002 special study (e.g., aircraft data) data 

availability that would be used in Optional Task 14 Enhanced model evaluation (05/30/04) 

Subtask 3b: Meteorological Gatekeeper 

Dennis McNally • First eight months 2002 MM5 QA/QC Gatekeeper PowerPoint 

presentation (03/26/04) 

• CMAQ-ready meteorological inputs for first six months of 2002 

(03/31/04) 

• Last four months 2002 MM5 QA/QC Gatekeeper PowerPoint 

presentation (04/15/04) 

• CMAQ-ready meteorological inputs for first six months of 2002 

(04/15/04) 

Subtask 3c: Emissions Gatekeeper 

Gregory Stella • Recommendation for Mexico and Canadian Emissions 

(02/29/04) 

• VISTAS States emissions QA/QC Gatekeeper PowerPoint 

presentation on initial 2002 emissions (03/31/04) 

• VISTAS States emissions QA/QC Gatekee

per PowerPoint 

Appendix C.1 - 178
Work Element Manager Deliverables (Date) 

presentation on initial future year emissions (5/15/04) 

• VISTAS States emissions QA/QC Gatekeeper PowerPoint 

presentation on revised 2002 and future year emissions (10/15/04) 

• Initial 2002 Base Case emissions inventory for non-VISTAS 

states (03/15/04) 

• Revised 2002 emissions inventory for non-VISTAS States 

(09/15/04) 

• Initial future-year inventory for non-VISTAS states (05/15/04) • Three future-year emission inventories for non-VISTAS states 

(09/15/04) 

Subtask 3d: Emissions Modeling 

Cyndi Loomis • 2002 CMAQ-ready emission input using initial emissions for all 

of 2002 (05/30/04) 

• Initial 2002 emissions PowerPoint presentation (05/30/04) • 2002 CMAQ-ready emission inputs using revised and typical 

emissions (10/15/04) 

• Revised and typical 2002 emissions modeling PowerPoint 

presentation (10/31/04) 

• Future-year CMAQ-ready emissions for two scenarios using 

revised emissions (11/15/04 and 12/15/04) 

• Draft emissions summary report (11/30/04) • Final Phase II emissions modeling report (12/31/04) 

Subtask 3e: Future-Year Emissions Modeling for 2 VISTAS Phase I Episodes 

Cyndi Loomis • CMAQ-ready initial future-year emission inputs for two VISTAS 

Phase I episodes (05/15/04) 

• CMAQ-ready future-year emission inputs for second scenario 

and two VISTAS Phase I episodes (06/15/04) 

• Summary PowerPoint presentation on VISTAS Phase I episode 

future-year emissions (06/15/04) 

Subtask 3f: Interim Future-Year Modeling for 2002 

Cyndi Loomis • CMAQ-ready future-year emissions for interim future-year and 

2002 meteorology (12/15/04) 

• Interim future-year emissions summary PowerPoint presentation 

(12/30/04) 

Subtask 4a: Initial 2002 CMAQ Modeling and MPE 

T.W. Tesche • PowerPoint presentation of the initial CMAQ model performance 

for 2002 annual period (06/30/04) 

Appendix C.1 - 179
Work Element Manager Deliverables (Date) 

• Summary report of CMAQ initial 2002 model performance 

evaluation and sensitivity analysis including recommendations for “best” configuration (08/30/04) 

Subtask 4b: Revised 2002 CMAQ Modeling and MPE 

Ralph Morris • Power Point presentations on the revised CMAQ base case 

simulation and sensitivity analysis (11/30/04) 

• Draft Report of revised CMAQ 2002 Base Case simulation and 

MPE (12/15/04) 

• Report on model sensitivity tests (01/15/05) 

Subtask 4c: Typical year 2002 CMAQ Modeling 

Ralph Morris • PowerPoint presentation on 2002 typical year CMAQ modeling 

(12/31/04) 

Subtask 4d: Future-Year CMAQ Modeling for Two Scenarios 

Gail Tonnesen • Draft Report on future-year base case modeling for two 

scenarios using 2002 and episodic databases (01/31/05) 

Subtask 4e. Interim Future-Year CMAQ Modeling 

Gail Tonnesen • PowerPoint presentation of Interim Future-Year modeling 

results (01/31/05) 

Optional Task 5: 2003 Episodes 

• Starts after completion of future-year emissions modeling (starts 

~01/01/05) 

Subtask 5a: Episodic Emissions Gatekeeper and Modeling 

Cyndi Loomis • Emissions Gatekeeper summary PowerPoint presentation for 

revised episodic modeling emissions (2005) 

• Revised Episodic CMAQ-ready revised 2003 Base Case and 

Typical Year emission inputs and summary (2005) 

• Future-year CMAQ-ready episodic inputs for three scenarios 

and summary report on the episodic emissions modeling (2005) 

Subtask 5b: Episodic Meteorological Gatekeeper 

Dennis McNally • CMAQ MCIP meteorological modeling inputs (2005) 

• MM5 Gatekeeper evaluation and QA/QC PowerPoint 

presentation (2005) 

Subtask 5c: Episodic AQ Data Gatekeeper 

Gail Tonnesen • MPE air quality data database for episodic modeling periods 

(2005) 

• AQ data summary presentation for episode periods (2005) • CMAQ IC/BC inputs for “2003” episode periods (2005) 

Subtask 5d: Episodic Emissions for non-VISTAS states 

Greg Stella • Revised “2003” Base Case, Typical Year and Future-Year 

emissions for episodic modeling (2005) 

Appendix C.1 - 180
Work Element Manager Deliverables (Date) 

Subtask 5e. Episodic Base Case and Typical Year CMAQ Modeling 

Gail Tonnesen • CMAQ Base Case and MPE and Typical Year modeling report 

for episode periods (2005) 

Subtask 5f: Episodic Future-Year Modeling for Three scenarios 

Ralph Morris • Summary Report on future-year base case modeling for three 

scenarios using the episodic databases (2005) 

Subtask 6a: VISTAS Modeling Website 

Gail Tonnesen • VISTAS modeling website will be maintained and updated 

continuously during 2004. 

Subtask 6b: Data Transfer, Storage and Retrieval 

Gail Tonnesen • Performed continuously during 2004 

o Archive (2004) o Data transfer drive (12/31/04) 

Optional Task 7 Evaluate Relative Reduction Response using CB-IV vs. SAPRC for 2 Phase I episodes 

Gail Tonnesen • PowerPoint presentation documenting the emissions reduction 

sensitivity tests for the January 2002 and July 2001 episodes using CB4 and SAPRC99 chemistry (06/30/04) 

Optional Task 8: Emissions Sensitivity Modeling using Phase I episodes 

Ralph Morris • PowerPoint presentation and model output files for the emission 

reduction sensitivity simulations using winter and summer Phase I episodes (TBD, ~09/30/04) 

Optional Task 9: Additional Sensitivity using VISTAS Phase I Episodes 

T.W. Tesche • Summary report of additional Phase I sensitivity tests (TBD, 

09/30/04???) 

Optional Task 10: Journal Paper on VISTAS Phase I Modeling 

Gail Tonnesen • Draft Journal paper (05/31/04) 

• Draft final Journal paper submitted to Journal; (06/30/04) • Final Manuscript (TBD, 10/31/04???) 

Optional Task 11: Corroborate Analysis using Alternative Models 

Ralph Morris • Summary presentation of corroborative modeling analysis using 

alternative models (01/31/05) 

Optional Task 12: Natural Conditions Modeling 

Gail Tonnesen • Natural conditions summary presentation (TBD???) 

Optional Task 13: 2002 GEOS-CHEM BCs 

Gail Tonnesen • 2002 CMAQ BCs based on 2002 GEOS-CHEM simulation. 

Appendix C.1 - 181
Work Element Manager Deliverables (Date) 

Optional Task 14: Enhanced Model Performance Evaluation 

T.W. Tesche • Summary presentation of the enhanced model performance 

evaluation using initial database (08/31/04) 

• Summary presentation of the enhanced model performance 

evaluation using the revised base case results (11/30/04) 

Optional Task 14: Contingency 

Ralph Morris • To be determined. 

Appendix C.1 - 182
Appendix C.2 

VISTAS Modeling 

Quality Assurance Project Plan 
Quality Assurance Project Plan (Draft) 

For 

Visibility Improvements for States and Tribal 

Associations for the Southeastern States (VISTAS) 

Emissions and Air Quality Modeling 

Revision 0 

November 17, 2004 

Prepared for: 

Ms. Patricia Brewer 

Technical Coordinator 

Western Governors’ Association 

Project Manager and Co-Principal Investigator: 

Mr. Ralph Morris 

ENVIRON International Corporation 

101 Rowland Way, Site 220 

Novato, CA 94945 

Contractors: 

Co-Principal Investigator: 

Dr. Tom Tesche 

Alpine Geophysics, LLC 

3479 Reeves Drive 

Ft. Wright, KY 41017 

Co-Principal Investigator: 

Dr. Gail Tonnesen 

College of Engineering 

Center for Environmental Research and Technology 

University of California at Riverside 

Riverside, CA 92507 

Appendix C.2 - 1
Approvals 

Title: Quality Assurance Project Plan for Visibility Improvements for States and Tribal 

Associations for the Southeastern States (VISTAS) Emissions and Air Quality Modeling, 

November 17, 2004. 

Ms. Patricia Brewer Date: 

Technical Coordinator 

Visibility Improvements for States and Tribal Associations for the Southeastern States

(Name here) Date: 

Project Officer 

U.S. Environmental Protection Agency 

Mr. Ralph Morris Date: 

Project Manager and Co-Principal Investigator 

ENVIRON International Corporation 

Dr. Tom Tesche Date: 

Co-Principal Investigator 

Alpine Geophysics, LLC 

Dr. Gail Tonnesen Date: 

Co-Principal Investigator 

University of California at Riverside 

EVIRON International Corporation 

101 Rowland Way, Suite 220 

Novato, California 94945

Appendix C.2 - 2
CONTENTS 

1.0 INTRODUCTION................................................................................................................... 1 

1.1 Problem Definition.................................................................................................................... 2 

2.0 PROJECT DESCRIPTION ................................................................................................... 2 

2.1 Background............................................................................................................................... 2 

2.2 VISTAS Two-Phased Approach............................................................................................... 3 

2.2.1 VISTAS Phase I............................................................................................................. 3 

2.2.2 VISTAS Phase II............................................................................................................ 4 

2.2.2.1 Data Gatekeepers ................................................................................................... 5 

2.2.2.2 Emissions QA/QC................................................................................................... 6 

2.2.2.3 Meteorology QA/QC .............................................................................................. 8 

2.2.2.4 Air Qualtiy Modeling QA/QC ................................................................................ 8 

2.2.2.5 Overview of Data Flow and Quality Assurance Process........................................ 9 

2.3 VISTAS Phase I and II Modeling Protocols........................................................................... 14 

2.4 VISTAS Phase I Activities ..................................................................................................... 14 

2.4.1 Phase I Task 1: Project Management........................................................................... 14 

2.4.2 Phase I Task 2: Develop Model Configuration Evaluation Plan ................................. 15 

2.4.3 Phase I Task 3: Acquisition and Development of Modeling Data Bases .................... 15 

2.4.4 Phase I Task 4: Develop Optimal VISTAS Modeling Configuration ......................... 17 

2.4.5 Phase I Task 6: Phase II Modeling Protocol................................................................ 18 

2.4.6 Phase I Task 7: Website Development ........................................................................ 19 

2.5 VISTAS Phase II Activities.................................................................................................... 19 

2.5.1 Phase II Task 1: Project Management ......................................................................... 19 

2.5.2 Phase II Task 2: Develop IC/BCs for 2002 Annual Run ............................................. 21 

2.5.3 Phase II Task 3: 12002 Data Preparation and Model Inputs ....................................... 22 

2.5.3.1 Subtask 3a: Air Quality Data Gatekeeper............................................................. 22 

2.5.3.2 Subtask 3b: MM5 Meteorological Model Gatekeeper.......................................... 22 

2.5.3.3 Subtask 3c: Emissions Gatekeeper and Emissions Development 

 for Non-VISTAS States, Canada, and Mexico ..................................................... 22 

2.5.3.4 Subtask 3d: Emissinos Modeling.......................................................................... 23 

2.5.3.5 Subtask 3e: Future-Year Emissions Modeling for 

 Three VISTAS Phase I Episodes .......................................................................... 25 

2.5.3.6 Subtask 3f: Interim Future-Year Emissions Modeling using 2002 Meteorology. 25 

2.5.3.7 Phase II Task 3 Deliverables................................................................................. 25 

2.5.4 Phase II Task 4: 2002 Annual CMAQ Modeling ........................................................ 26 

2.5.4.1 Subtask 4a: Initial Base Case and Model Performance Evaluation...................... 26 

2.5.4.2 Subtask 4b: Revised Base Case Simulation.......................................................... 27 

2.5.4.3 Subtask 4c: Typical Year Emissions Simulation.................................................. 27 

2.5.4.4 Subtask 4d: Future-Year Modeling for Two Scenarios ........................................ 28 

2.5.4.5 Subtask 4e: Interim Future-Year using 2002 Database ........................................ 28 

2.5.4.6 Summary of Phase II Task 4 Deliverables............................................................ 28 

2.5.5 Phase II Task 5: Episodic Modleing ............................................................................ 29 

2.5.6 Phase II Task 6: Data Management ............................................................................. 29 

2.5.6.1 Subtask 6a: VISTAS Modeling Website .............................................................. 29 

2.5.6.2 Subtask 6b: Data Transfer, Storage and Retrieval................................................ 29 

Appendix C.2 - 3
2.5.6.3 Phase II Task 6 Data Management Deliverables .................................................. 30 

2.5.7 Phase II Task 7: Emission Reduction Sensitivity Simulations using 

 CB4 and SAPRC Chemistry and 2 Phase I Episodes .................................................. 30 

2.5.8 Phase II Task 10: Journal Paper on VISTAS Phase I Modeling.................................. 31 

2.5.9 Phase II Task 13: Analysis and Processing of 2002 GEOS-CHEM Data ................... 31 

3.0 PROJECT MANAGEMENT............................................................................................... 32 

3.1 Project Organization ............................................................................................................... 32 

3.1.1 ENVIRON Project manager and Co-Principal Investigator ........................................ 35 

3.1.2 ENVIRON, Alpine and UCR Co-Principal Investigators............................................ 35 

3.1.3 VISTAS Contracting Officer ....................................................................................... 36 

3.1.4 VISTAS Technical Contact ........................................................................................ 36 

3.1.5 VISTAS Technical Analysis Workgroup (TAWG)..................................................... 37 

3.2 Project Schedule and Execution.............................................................................................. 37 

3.3 Personnel Qualifications and Training.................................................................................... 37 

3.4 Communications Plan ............................................................................................................. 38 

3.5 Documentation and Records................................................................................................... 39 

4.0 MEASUREMENT AND DATA ACQUISITION .............................................................. 39 

4.1 Computer Hardware/Systems Administration ........................................................................ 39 

4.1.1 ENVIRON Modeling Center Hardware....................................................................... 39 

4.1.2 Alpine Geophysics Modeling Center Hardware .......................................................... 40 

4.1.3 UCR Modeling Center Hardware ................................................................................ 40 

4.1.4 Backup Procedures....................................................................................................... 41 

4.2 Sources for Data Used in Modeling........................................................................................ 42

5.0 EMISSIONS MODELING................................................................................................... 42 

5.1. Quality Assurance Components of Emissions Modeling ...................................................... 44 

5.1.1 Modeling QA ............................................................................................................... 44 

5.1.2 System QA ................................................................................................................... 44 

5.1.3 Gatekeeping and Outside Review................................................................................ 44 

5.1.4 Documentation............................................................................................................. 45 

5.2 Implementation of the QA System ......................................................................................... 45 

5.2.1 The Emissions QA Team ............................................................................................. 45 

6.0 METEOROLOGICAL MODELING ................................................................................. 48 

7.0 CMAQ MODELING SYSTEM........................................................................................... 48 

7.1 CMAQ Overview.................................................................................................................... 49 

7.2 CMAQ Configuration for Phase II Modeling......................................................................... 50 

7.3 Alternative Models.................................................................................................................. 50 

7.3.1 CAMx Overview.......................................................................................................... 52

7.3.2 CAMx Configuration for Phase II Modeling............................................................... 54 

8.0 ASSESSMENTS AND OVERSIGHT................................................................................. 55 

8.1 Assessment Responsibilities ................................................................................................... 55 

8.2 Assessment Types and Usage ................................................................................................. 55 

8.3 Assessment Criteria ................................................................................................................ 56 

Appendix C.2 - 4
9.0 REFERENCES...................................................................................................................... 56 

Figures 

Figure 2-1a. Data flow and quality assurance steps in the VISTAS 

 Emissions and Air Quality Modeling ....................................................................12 

Figure 2-1b. Data flow and quality assurance steps in the VISTAS 

 Emissions and Air Quality Modeling ....................................................................13 

Figure 3-1. VISTAS Emissions and Air Quality Modeling Project Organizational Chart ......33 

Figure 5-1. Flow Diagram of Major SMOKE Processing Steps ..............................................43 

Figure 5-2. Diagram of VISTAS Modeling Team Approach to SMOKE Modeling ...............47 

Tables 

Table 2-1. Model performance goals used in Phase I to help interpret modeling results .......11 

Table 2-2. Phase I Task 1 Project Management task deliverables and due dates ...................15 

Table 2-3. Phase I Task 2 Modeling Plan task deliverables and due dates.............................15 

Table 2-4. Phase I Task 3 Phase I Acquisition and Development of Model 

 Databases task deliverables and due dates.............................................................17 

Table 2-5. Phase I Task 4 Develop Optimal VISTAS Modeling Configuration task 

deliverables and due dates .....................................................................................18 

Table 2-6. Phase I Task 6 Phase II Modeling Protocol task deliverables and due dates ........19 

Table 2-7. Phase I Task 6 Develop Website task deliverables and due dates.........................19 

Table 2-8. Phase II Task 1 Project Management task deliverables and due dates..................21 

Table 2-9. Phase II Task 2 GEOS-CHEM Boundary Condition Analysis 

 task deliverables and due dates..............................................................................21 

Table 2-10. Phase II Task 3 2002 Data Preparation and Model Inputs 

 task deliverables and due dates..............................................................................25 

Table 2-11. Phase II Task 4 2002 CMAQ Modeling task deliverables and due dates..............28 

Table 2-12. Phase II Task 6 Data Management task deliverables and due dates......................30 

Table 2-13. Phase II Task 7 CB4/SAPRC Sensitivity modeling task 

 deliverables and due dates .....................................................................................31 

Table 2-14. Phase II Task 10 Phase I Journal Article task deliverables and due dates.............31 

Table 2-15. Phase II Task 13 2002 GEOS-CHEM Boundary Condition 

 Processing task deliverables and due dates............................................................32 

Table 3-1. VISTAS Phase II Emissions and Air Quality Modeling 

 project participants and contacts............................................................................34 

Table 3-2. VISTAS listservs maintained by the Emissions and 

 Air Quality Modeling Team...................................................................................38

Appendix C.2 - 5
Quality Assurance Project Plan (Draft) Page 1 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

1.0 INTRODUCTION 

This Quality Assurance Project Plan (QAPP) describes the quality management functions and 

activities performed by the Visibility Improvements for States and Tribal Associations in the 

Southeast (VISTAS) Phases I and II Emissions and Air Quality Modeling performed by 

ENVIRON International Corporation (Prime Contractor), Alpine Geophysics, LLC 

(Subcontractor) and the University of California at Riverside College of Engineering – Center 

for Environmental Research and Technology (UCR/CE-CERT; Subcontractor). 

VISTAS is one of five Regional Planning Organizations (RPOs) that have responsibility for 

coordinating development of State Implementation Plans (SIPs) and Tribal Implementation Plans 

(TIPs) in selected areas of the U.S. to address the requirements of the Regional Haze Rule (RHR) 

visibility SIPs/TIPs due in 2007/2008. VISTAS modeling results will also likely form the 

regional component for 8-hour ozone and fine particulate (PM2.5) SIPs/TIPs that are also 

expected to be due in 2007/2008. The VISTAS Emissions and Air Quality Modeling Team is 

comprised of staff from ENVIRON International Corporation (ENVIRON), Alpine Geophysics, 

LLC (Alpine) and the University of California, Riverside (UCR). The ENVIRON/Alpine/UCR 

Team performs the emissions and air quality modeling simulations for states and tribes within 

the VISTAS region, providing analytical results used in developing implementation plans under 

the EPA Regional Haze Rule. 

The quality assurance approach utilized herein is generally based on the national consensus 

standard (ANSI/ASQC, 1994). This standard describes the necessary management and technical 

elements for developing and implementing a quality system. It recommends a tiered approach to 

the design of the specific quality system used in each of the organization’s efforts. This approach 

has been adopted by the ENVIRON/Alpine/UCR Team and is documented in the VISTAS Phase 

I and II Modeling Protocols (ENVIRON, 2003; 2004a) and in UCR’s Quality Management Plan 

(QMP; UCR, 2003). The VISTAS Modeling Protocols and UCR’s QMP formed the basis for 

much of the content in this VISTAS Emissions and Air Quality Modeling QAPP. 

This QAPP was prepared in accordance with the EPA guidelines for quality assurance project 

plans for modeling (EPA, 2002), for QAPPs (EPA, 2001), and the North American Research 

Strategy for Tropospheric Ozone (NARSTO) Quality Handbook for modeling projects 

(NARSTO, 1998). The EPA and NARSTO guidance documents were developed particularly for 

modeling projects, which have different quality assurance concerns than environmental 

monitoring data collection projects. The work performed in this project involves modeling at the 

basic research level and for regulatory/policy applications. In order to utilize model outputs for 

these purposes, it must be established that each model is scientifically sound, robust, and 

defensible. This is accomplished by following a project planning process that incorporates the 

following elements as described in the EPA guidance document for modeling: 

• A systematic planning process including identification of assessments and related 

performance criteria; 

• Peer reviewed theory and equations; 

Appendix C.2 - 6
Quality Assurance Project Plan (Draft) Page 2 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

• A carefully designed life-cycle development process that minimizes errors; 

• Documentation of any changes from original plans; 

• Clear documentation of assumptions, theory, and parameterization that is detailed 

enough so others can understand the model output; 

• Input data and parameters that are accurate and appropriate for the problem; and 

• Output data that can be used to help inform decision making. 

The purpose of this QAPP is to establish and encourage a continuous improvement process that 

will result in clearly defined data quality objectives, documentation, procedures, and 

requirements for QA benchmarks and reports. A rigorous quality system will assist in ensuring 

that the quality of the project products are known, defensible, and meet the user’s data quality 

objectives. This system will also enable the modeling team to systematically plan to 

accommodate the additional work that will be required to ensure high-quality results. 

1.1 Problem Definition 

The 1990 Amendments to the Clean Air Act and the 1999 U.S. EPA Regional Haze Rule 

establishes special goals for visibility in 156 national parks, wilderness areas, and international 

parks. Through these amendments, Congress set a national goal for visibility as “the prevention 

of any future, and the remedying of any existing, impairment of visibility in mandatory Class I 

Federal areas which impairment results from manmade air pollution” (40 CFR 51.300). States 

are required to develop State Implementation Plans (SIPs) to attain visibility standards, and 

Tribes also may opt to assume responsibility for visibility programs under 40 CFR Part 49 by 

developing Tribal Implementation Plans (TIPs). States, and potentially Tribes, in the 

Southeastern US are required to submit visibility SIPs under Section 308 of the Regional Haze 

Rule (RHR). 

Through the Southeastern States Air Resource Managers (SESARM), the Visibility 

Improvement State and Tribal Association of the Southeast (VISTAS) has implemented a 

regional air quality planning process to provide the necessary technical and policy tools needed 

by states and tribes to comply with the Section 308 of the RHR requirements. As part of this 

effort, VISTAS has funded modeling studies to support the development of SIPs and TIPs. In 

March 2003, VISTAS contracted with ENVIRON International Corporation, with Alpine 

Geophysics, LLC (Alpine) and University of California at Riverside (UCR) as Subcontractors, to 

perform Emissions and Air Quality Modeling. 

The results of the modeling studies performed by VISTAS will help determine the proper 

mitigation measures that will be necessary to comply with Section 308 of the RHR. 

2.0 PROJECT DESCRIPTION 

2.1 Background 

The VISTAS Emissions and Air Quality Modeling Team performs regional haze analyses by 

operating regional scale, three-dimensional air quality models that simulate the emissions, 

Appendix C.2 - 7
Quality Assurance Project Plan (Draft) Page 3 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

chemical transformations, and transport of gaseous and particulate matter (PM) species and 

consequently effects on visibility in Class I Areas in the southeastern U.S. A key element of this 

work includes the integration of emissions inventories and models with regional transport 

models. The general services provided by the VISTAS Emissions and Air Quality Modeling 

Team include, but are not limited to: 

• Emissions processing and modeling; 

• Air quality and visibility modeling simulations; 

• Analysis, display, and reporting of modeling results; and 

• Storage/quality assurance of the modeling input and output files. 

2.2 VISTAS Two-Phased Approach 

The VISTAS Emissions and Air Quality Modeling activities are being performed in two Phases. 

Phase I, which occurred primarily during the 2003 calendar year, consisted of emissions and 

regional haze modeling for three episodes to identify the optimal model configuration(s) for 

simulating regional haze in the southeastern US. Phase II, initiated in 2004, consists of operating 

the emissions and air quality models for the 2002 calendar year to develop the regional haze 

modeling databases needed to address the requirements of the Section 308 RHR SIPs and TIPs. 

2.2.1 VISTAS Phase I 

The objective of VISTAS Phase I was to determine the optimal modeling configuration for use 

in the subsequent Phase II visibility assessment. Accordingly, Phase I entailed a comprehensive 

literature review of recent relevant visibility studies using various photochemical/aerosol 

modeling platforms in order to assess and identify appropriate model configurations, data bases, 

and model testing methodologies that were appropriate for use in conducting the VISTAS Phase 

I emissions and PM modeling assessment. Key elements of Phase I included: 

3⁄4 Review all relevant air quality model simulations that have been completed related to 

regional haze and PM2.5 modeling and document the relevant sensitivity analyses, model 

configuration testing, and performance evaluations that have been performed 

(ENVIRON, 2003b); 

 

3⁄4 Review the current science in regional emissions modeling (e.g., EPS, EMS and 

SMOKE) and PM air quality modeling (e.g., CMAQ, CMAQ-MADRID, CMAQ-AIM, 

REMSAD, UAM-V/PM, CAMx4 and PMCAMx) to determine the most appropriate 

model(s) for use by VISTAS (ENVIRON, 2003b); 

3⁄4 Review available ambient data for evaluating one-atmosphere PM/ozone models 

(ENVIRON, 2003c);

Appendix C.2 - 8
Quality Assurance Project Plan (Draft) Page 4 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

3⁄4 Develop and implement a plan or Modeling Protocol for testing and evaluating 

alternative science configurations of the recommended Phase I model(s) and document 

the results (ENVIRON, 2003a); and 

3⁄4 Prepare a Task 6 report prescribing the model set-up, data base development, 

performance testing, and control strategy evaluation procedures to be implemented in 

VISTAS Phase II (ENVIRON, 2004a). 

VISTAS formed three standing workgroups to plan and direct the project. These included: (a) the 

Technical Analysis (emissions and modeling) Workgroup; (b) the Data (monitoring) Workgroup; 

and (c) the Planning Workgroup. Under Phase I, the VISTAS Technical Analysis Workgroup 

(TAWG) managed the comprehensive model configuration testing program aimed, as noted 

above, at evaluating the capabilities of current state-of-science regional emissions, prognostic 

meteorological and PM/visibility models. The resultant modeling system (models and databases) 

identified and tested in Phase I were intended to be applied in Phase II (discussed below) 

following the procedures set forth in the Phase II Modeling Protocol (ENVIRON, 2004a). 

For the meteorological component of the Phase I modeling, SESARM contracted with Baron 

Advanced Meteorological Systems (BAMS) to apply the PSU/NCAR Mesoscale Model (MM5) 

in multiple configurations and to evaluate its performance against surface and aloft 

meteorological observations (Olerud, 2003a-f). The emissions modeling component of VISTAS 

Phase I was carried out by the research team of ENVIRON/Alpine/UCR with staff at Alpine 

Geophysics taking the lead role in setting up, testing, and applying the emissions modeling 

system. The air quality modeling component was performed by the team at the 

ENVIRON/Alpine/UCR modeling centers. A dominant theme during Phase I was the exchange 

of modeling codes, databases, and evaluation software between the three modeling centers as the 

air quality modeling was carried out. 

2.2.2 VISTAS Phase II 

The Phase II modeling includes annual PM/regional haze simulations plus potentially additional 

shorter duration episodes. After detailed performance testing, the modeling system will then be 

exercised with a variety of emissions control scenarios aimed at enabling VISTAS to assess the 

effects of future year emission control strategies on visibility and other air quality issues. The 

modeling system will also allow VISTAS to track reasonable progress toward regional haze 

goals. More specifically, the VISTAS Phase II program will focus on the use of the CMAQ 

modeling system for calendar year 2002 over the same 36/12 km horizontal grid system used in 

Phase I. A potentially large number of annual (and episodic) model simulations will be 

performed; the list below reflects current plans: 

3⁄4 2002 Initial Annual Run. The initial annual model simulations and performance 

evaluations using the 2002 inventory for VISTAS and non-VISTAS states, Canada and 

Mexico. Multiple iterations of the 2002 annual simulation will be required to confirm the 

appropriateness of the model science configuration(s) recommended by the Phase I work, 

to evaluate updates to the model and model inputs and to refine model performance. 

Appendix C.2 - 9
Quality Assurance Project Plan (Draft) Page 5 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

 

3⁄4 2002 Revised Annual Run. A subsequent annual 2002 simulation using revised 2002 

modeling inventory for VISTAS and non-VISTAS states, Canada and Mexico. The 

primary objective of this run is model performance demonstration using updated 

emissions inventories and best science model configurations. Additional sensitivity tests 

will be conducted using the revised base case year annual run. 

3⁄4 2002 Annual Run with “Typical Year” EGU/Fire Inventory. An annual 2002 

simulation representing the 2000-2004 baseline period for EGU and fire emissions and 

using 2002 revised inventory for all other source sectors. The primary objective of this 

inventory is to provide the base line modeled air quality condition against which future 

year modeling runs will be compared to develop relative reduction factors for each 

pollutant species. 

3⁄4 Future Year Annual Runs. Future year simulations involving a base case inventory of 

typical EGU and fire emissions for VISTAS-selected future period. Additional future 

year inventories may also be modeled. The objective of these future year model runs is 

to establish the modeled air quality basis against which the effectiveness of emissions 

control strategies will be evaluated. 

3⁄4 Future Year Emission Control Strategies. Prescription of the future year emissions 

control strategies to be performed later in Phase II (e.g., 2005) will be defined after the 

foregoing simulations and analyses have been completed. A combination of annual and 

episodic runs is anticipated. 

Closely integrated with the annual (and possibly episodic) meteorological, emissions and air 

quality modeling will be ongoing project management, technical review, and quality assurance 

activities performed under the guidance of the VISTAS Contracting Officer and the TAWG. 

The modeling team members will participate with VISTAS management in regular monthly 

conference calls, as well as ad hoc topical conference calls as needed, and will attend periodic 

meetings with the TAWG members throughout Phase II. 

Complementing the data acquisition, modeling input development activities, and project 

management activities, four other Phase II activities will be performed, consistent with the 

Quality Assurance Project Plan (QAPP): 

2.2.2.1 Data Gatekeepers 

The VISTAS Phase II emissions and air quality modeling team are receiving emissions, 

meteorological and air quality data from other VISTAS contractors or other sources. As a first 

line of QA, we have defined a Gatekeeper function to assure the data have been received 

correctly, the quality of the data has been evaluated, and that the data received have been 

documented. Separate air quality, meteorological and emissions Gatekeepers have been 

identified whose roles are defined below. In addition, a Data Management Gatekeeper has been 

defined who will post data, reports and results to the project website and archive all key data 

generated in the project. 

Appendix C.2 - 10
Quality Assurance Project Plan (Draft) Page 6 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

3⁄4 Air Quality Data Gatekeeper. Obtain air quality data as appropriate for 

model input development and model performance evaluation and assure that 

the quality of all air quality data obtained are consistent with the approved 

QAPP. Provide documentation of evaluation and generate IC/BC inputs for 

CMAQ for all modeling runs. 

3⁄4 Meteorological Gatekeeper. Obtain meteorological data, as MM5 or MCIP 

files, as appropriate for annual 2002 modeling runs and other episode periods 

and perform data quality checks as approved in the QAPP, together with 

appropriate documentation of model performance evaluation activities. 

3⁄4 Emissions Gatekeeper. Obtain emissions inventory data necessary to 

support annual 2002 and future year modeling and recommend source of 

emissions data to be used for Canada and Mexico. Assure quality of all 

emissions data received are consistent with the approved QAPP, and develop 

all emissions modeling files to support modeling runs for 2002. Develop the 

chemical speciation files and temporal and spatial allocation files necessary to 

convert annual inventories into hourly and daily emissions modeling files, as 

appropriate. Develop all emissions modeling files for non-VISTAS states to 

support modeling runs for future year base case and emissions strategies as 

defined by VISTAS. 

3⁄4 Data Management Gatekeeper: Maintain the VISTAS Modeling Website 

including posting modeling input and output files, reports, interpretation of 

results, and other documents as requested by VISTAS to support all Phase II 

tasks. This includes, for example, the storage of model inputs and outputs for 

annual (and episodic) runs and the transfer (via fire wire or alternative media) 

of electronic files to VISTAS states, other regional planning organizations, 

EPA, other contractors, and stakeholders. 

2.2.2.2 Emissions QA/QC 

Emissions Quality Assurance (QA) and Quality Control (QC) are the single most critical steps in 

performing air quality modeling studies. Because emissions processing is tedious, time 

consuming and involves complex manipulation of many different types of large data sets, errors 

are frequently made in emissions processing and, if rigorous QA measures are not in place, these 

errors may remain undetected. In Phase II we will continue with the multistep emissions QA/QC 

approach applied in the Phase I modeling. This includes the initial emissions QA/QC by the 

Emissions Gatekeeper described above, as well as QA/AC by the Emissions Modeler during the 

processing of emissions and then additional QA/QC by the air quality modeler of the processed 

model ready emission files. This multistep process with three separate groups involved in the 

QA/QC of the emissions is designed to detect and correct errors prior to the air quality model 

simulations. 

Appendix C.2 - 11
Quality Assurance Project Plan (Draft) Page 7 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

Emissions QA/QC performed as part of the emissions modeling includes: 

EMS and EPA Input Screening Error Checking Algorithms: Although the SMOKE 

emissions model will be used for emissions processing, some of the more advanced EMS 

input error checking algorithms will be used to screen the data and identify potential 

emission input errors. Additionally, EPA has issued a revised stack QA and augmentation 

procedures memorandum that will be used to identify and augment any outlying stacks. 

SMOKE Error Messages: SMOKE provides various cautionary or warning messages 

during the emissions processing. We will redirect the SMOKE output to log files and 

review the log files for serious error messages. An archive of the log files will be 

maintained so that the error messages can be reviewed at a later date if necessary. 

SMOKE Emissions Summaries: We will use QA functions built into the SMOKE 

processing system to provide summaries of processed emissions as daily totals according 

to species, source category and county and state boundaries. These summaries will then 

be compared with summary data prepared for the pre-processed emissions, e.g., state and 

county totals for emissions from the augmented emissions data. 

Once the CMAQ-ready emission inputs have been prepared, we will perform additional 

emissions QA/QC as follows: 

Spatial Summary: We will sum the emissions for all layers and for all 24 hours that is 

used to prepare a PAVE plot showing the daily total emissions spatial distribution. For a 

20 day simulation this produces approximately 20 days x 20 species x 5 emissions 

categories = 2,000 plots. In our base case simulations these plots will be presented as tons 

per day. The objective of this step is to identify errors in spatial distribution of emissions. 

Vertical Profile: For point sources the emissions total for each layer will be summed and 

plotted to show the vertical distribution of emissions. These plots show the emissions on 

the x-axis for each model layer on the y-axis. The objective of this step is to identify 

possible errors in vertical distribution of emissions. 

Short Term Temporal Summary: The total domain emissions for each hour will be 

accumulated and time series plots prepared that display the diurnal variation in total 

hourly emissions. The objective of this step is to identify errors in temporal profiles. 

Long Term Temporal Summary: The total domain emissions for each day will be 

accumulated and displayed as time series plots that show the daily total emissions across 

the domain as a function of time. The objective of this step is to identify particular days 

for which emissions appear to be inconsistent with other days for no reason (e.g., not a 

weekend) and compare against the general trend. 

Control Strategy Spatial Displays: Spatial summary plots of the daily total emissions 

differences between a control strategy and base case emissions scenarios will be 

generated. These plots can be used to immediately identify a problem in a control 

Appendix C.2 - 12
Quality Assurance Project Plan (Draft) Page 8 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

strategy. For example, if a VISTAS state’s SO2 control strategy is being analyzed and 

there are changes in emissions for other pollutants or for SO2 outside of the VISTAS 

states problems in emissions processing can be identified prior to the air quality model 

simulation. 

2.2.2.3 Meteorology QA/QC 

The VISTAS meteorological modeling contractor (BAMS) will have primary responsibility in 

the QA/QC of the MM5 meteorological fields. However, the emissions and air quality modeling 

team will also perform some QA/QC of the meteorological data to assure that it has transferred 

correctly, to obtain an assessment of the quality of the data and to assist in the interpretation of 

the air quality modeling results. 

The VISTAS Phase II Meteorological Gatekeeper will perform the following: 

3⁄4 Analyze the MM5 data to assure it has been transferred correctly. 

 

3⁄4 Evaluate the MM5 using METSTAT and the surface meteorological network. 

3⁄4 Evaluate upper-air MM5 meteorological estimates by comparison them to upper-air 

observations and satellite images. 

3⁄4 Compare the VISTAS 2002 MM5 simulation with the one generated by WRAP. 

3⁄4 Generate the CMAQ-ready meteorological inputs using the MCIP2.2 processor. 

2.2.2.4 Air Quality Modeling QA/QC 

Key aspects of QA for the CMAQ input and output data include the following: 

3⁄4 Verification that correct configuration and science options are used in compiling and 

running each model of the in the CMAQ modeling system, where these include the 

MCIP, JPROC, ICON, BCOM and the CCTM. 

3⁄4 Verification that correct input data sets are used when running each model. 

3⁄4 Evaluation of CCTM results to verify that model output is reasonable and consistent 

with general expectations. 

3⁄4 Processing of ambient monitoring data for use in the model performance evaluation. 

3⁄4 Evaluation of the CCTM results against concurrent observations. 

3⁄4 Backup and archiving of critical model input data. 

Appendix C.2 - 13
Quality Assurance Project Plan (Draft) Page 9 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

The most critical element for CMAQ simulations is the QA/QC of the meteorological and 

emissions input files, which is discussed above. The major QA issue specifically associated with 

the air quality model simulations is verification that the correct science options were specified in 

the model itself and that the correct input files were used when running the model. For the 

CMAQ model we employ a system of naming conventions using environment variables in the 

compile and run scripts that guarantee that correct inputs and science options are used. We also 

employ a redundant naming system so that the names of key science options or inputs are 

included in the name of the CMAQ executable program, in the name of the CMAQ output files, 

and in the name of the directory in which the files are located. This is accomplished by using the 

environment variables in the scripts to specify the names and locations of key input files. 

A second key QA procedure is to never “recycle” run scripts, i.e., we always preserve the 

original runs scripts and directory structure that were used in performing a model simulation. 

We will also perform a post-processing QA of the CMAQ output files similar to that described 

for the emissions processing. We will generate animated gif files using PAVE that can be viewed 

to search for unexpected patterns in the CMAQ output files. In the case of model sensitivity 

studies, the animated gifs will be prepared as difference plots for the sensitivity case minus the 

base case. Often, errors in the emissions inputs can be discovered by viewing the animated GIFs. 

Finally, we will produce 24 hour average plots for each day of the CMAQ simulations. This 

provides a summary that can be useful for quickly comparing various model simulations. 

2.2.2.5 Overview of Data Flow and Quality Assurance Process 

Figure 2-1 displays an overview of the data flow and quality assurance process in the VISTAS 

Emissions and Air Quality Modeling study. The VISTAS Modeling Team receives different 

types of data from various VISTAS contractors and other sources that have performed their own 

Quality Assurance (QA) and Quality Control (QC). Whenever data are received by the 

Modeling Team, it is first subjected to a QA check by a Gatekeeper who assess the accuracy and 

quality of the data and prepares a summary presentation on the QA check. Figure 2-1a lists the 

Gatekeepers in the Modeling Team for emissions, boundary conditions, meteorological, ozone 

column (TOMS) and air quality data. If the Gatekeeper identifies any problems with the data, 

the provider of the data is contacted and asked to correct the data. Once the Gatekeeper has 

conducted a QA check of the data it is passed on to the modeler who performs their QA of the 

data. The data are then used in the modeling and resultant output (e.g., model-ready emissions or 

meteorological files) are then subjected to another round of QA to assure the integrity of the data 

is retained. 

Once the model-ready inputs have been developed and subjected to QA/QC, the models (e.g., 

CMAQ and/or CAMx) are applied using Base Case emissions and the modeling results subjected 

to a model performance evaluation. The model performance evaluation (MPE) represents an 

extensive QA effort and is the most time consuming component of the study. EPA has 

developed draft guidance for evaluating regional PM and haze models that includes performance 

goals (EPA, 2001). In addition, the Modeling team has adapted EPA MPE approaches and goals 

for 1-hour (EPA, 1991) and 8-hour (EPA, 1999) ozone modeling. The VISTAS Modeling Team 

performs the MPE/QA process using as many different tools and analysis as possible in order to 

Appendix C.2 - 14
Quality Assurance Project Plan (Draft) Page 10 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

fully understand the accuracy and reliability of the model simulation. As seen in Figure 2-1b, the 

MPE process in VISTAS is a multistep process using several different techniques: 

UCR Analysis Tools: The University of California at Riverside (UCR) Analysis Tools 

were used extensively in Phase I and are run on a Linux platform separately for each 

network. Graphics are automatically generated using gnuplot and the software generates 

the following: 

• Tabular statistical measures; 

• Time Series Plots; and 

• Scatter Plots by allsite_allday, allday_onesite and allsite_oneday. 

MAPS Analysis Tools: Alpine Geophysics (Alpine) has a MAPS Analysis Tool that also 

runs under Linux and is based on Fortran and NCAR Graphics. It was originally 

developed for evaluating ozone models and has been extended to treat PM species as 

well. In addition to calculating similar statistics, scatter plots and time series plots as the 

UCR Analysis Tools, it also can generate spatially averaged time series plots of 

concentrations, bias and error, performs analysis of peak concentrations and includes a 

Flying Data Grabber (FDB) for comparing modeling results with aircraft data. 

ENVIRON Analysis Tools: ENVIRON has developed specialized evaluation tools to 

analyze visibility model performance for the Best and Worst 20% visibility days that are 

used in visibility projections for the Section 308 SIPs/TIPs. ENVIRON has also 

developed “Soccer Plots” that displays model performance across networks, episodes, 

species, models and sensitivity tests and compare them with performance goals. 

GA DNR Analysis Plots: Dr. James Boylan of the Georgia Department of Natural 

Resources has extended the concept in EPA’s draft PM fine particulate and regional haze 

modeling guidance that model performance for species that make up a major contribution 

to visibility impairment be subjected to more stringent goals than species that are minor 

contributors by developing concentration-dependent performance goals and “Bugle 

Plots” to display them. 

The evaluation of the VISTAS Phase II initial 2002 CMAQ Base Case simulation used each of 

the analysis tools listed above demonstrating their descriptive and complimentary nature. 

The issue of model performance goals for PM species is an area of ongoing research and debate. 

For ozone modeling, EPA has established performance goals for 1-hour ozone normalized mean 

bias and gross error of #±15% and #35%, respectively (EPA, 1991). EPA’s draft fine particulate 

modeling guidance notes that performance goals for ozone should be viewed as upper bounds of 

model performance, that PM models may not be able to always achieve and we should demand 

better model performance for PM components that make up a larger fraction of the PM mass 

than those that are minor contributors (EPA, 2001). Measuring PM species is not as precise as 

ozone monitoring. In fact, the differences in measurement techniques for some species likely 

exceed the more stringent performance goals, such as those for ozone. For example, recent 

comparisons of the PM species measurements using the IMPROVE and STN measurement 

Appendix C.2 - 15
Quality Assurance Project Plan (Draft) Page 11 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 17, 2004 

technologies found differences of approximately "20% (SO4) to "50% (EC) (Solomon et al., 

2004). 

In the VISTAS 2002 CMAQ Base Case modeling, we have adopted three levels of model 

performance goals for bias and gross error as listed in Table 2-1 that are used to help evaluate 

model performance. Note that we are not suggesting that these performance goals be generally 

adopted or that they are the most appropriate goals to use. Rather, we are just using them to 

frame and put the PM model performance into context and to facilitate model performance 

intercomparison across episodes, species, models and sensitivity tests. 

As noted in EPA’s draft PM modeling guidance, less abundant PM species should have less 

stringent performance goals. Accordingly, we are also using performance goals that are a 

continuous function of average observed concentrations proposed by Dr. James Boylan at the 

Georgia Department of Natural Resources that have the following features: 

• Asymptotically approaching proposed performance goals or criteria when the mean of the 

observed concentrations are greater than 2.5 ug/m3

. 

• Approaching 200% error and "200% bias when the mean of the observed concentrations 

are extremely small. 

Dr. Boylan uses bias/error goals and criteria of ±30%/50% and ±60%/75% and plots bias and 

error as a function of average observed concentrations. As the mean observed concentration 

approaches zero the bias performance goal and criteria flare out to ±200% creating a horn shape, 

hence the name “Bugle Plots”.

Table 2-1. Model performance goals used in Phase I to help interpret modeling results. 

Fractional 

Bias Fractional 

Error 

Comment 

#"15% #35% Ozone model performance goal8

 for which PM model 

performance would be considered good. 

#"30% #50% A level of model performance that we would hope each PM 

species could meet 

#"60% #75% At or above this level of performance indicates fundamental 

problems with the modeling system. 

Appendix C.2 - 16
Quality Assurance Project Plan (Draft) Page 12 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 ENVIRON International Corporation November 12, 2004 Figure 2-1a. Data flow and quality assurance steps in the VISTAS Emissions and Air Quality Modeling. 

Appendix C.2 - 17
Quality Assurance Project Plan (Draft) Page 13 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 ENVIRON International Corporation November 12, 2004 Figure 2-1b. Concluded. Data flow and quality assurance steps in the VISTAS Emissions and Air Quality Modeling.

Appendix C.2 - 18
Quality Assurance Project Plan (Draft) Page 14 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

2.3 VISTAS Phase I and II Modeling Protocols 

As recommended in EPA’s draft regional haze modeling guidance (EPA, 2001), the VISTAS 

Phase I and II modeling efforts were initiated by developing Modeling Protocols that described 

the procedures to be used to conduct, quality assure and quality control (QA/QC), evaluate and 

use the modeling results (ENVIRON, 2003a; ENVIRON, 2004a). These Modeling Protocols 

were reviewed and commented on by the VISTAS TAWG and others and are updated 

accordingly. 

2.4 VISTAS Phase I Activities 

The VISTAS Phase I Emissions and Air Quality Modeling work was carried out mainly during 

2003 with some final deliverables provided in early 2004. The Phase I activities formed the 

basis for the Phase II modeling and was the foundation of the Phase II quality assurance (QA) 

and quality control (QC). 

2.4.1 Phase I Task 1: Project Management 

There are three aspects of Project Management that were performed under this task: (a) Project 

Management of the project’s resources and technical progress keeping VISTAS informed of 

progress; (b) Technical Management of the day-to-day technical activities of the 

ENVIRON/Alpine/UCR Team keeping clear lines of communication, and (c) Communication 

Management of the data flow and expectations among the other VISTAS contractors. 

Project Management: The Project Manager, Co-Principal Investigators (Co-PIs), and Task 

Managers had frequent communications with the VISTAS technical and project management 

group through regular conference calls, e-mails and meetings as needed. The ENVIRON, Alpine 

and UCR Modeling Centers were headed by each of the three Co-PIs (Ralph Morris, T.W. 

Tesche and Gail Tonnesen, respectively) with clear lines of communication. 

Technical Management: The three Co-PIs are responsible for the management of the technical 

work within each of their respective research groups. With responsibility comes accountability. 

Communication Management: Key to the communications management will be weekly internal 

conference calls among the three Co-Principal Investigators and the regular conference calls 

between the three Co-PIs and the VISTAS TAWG and other VISTAS contractors. When data 

are received from VISTAS contractors, the Modeling Team’s meteorological or emissions 

Gatekeeper subjected the data to an extensive QA. Any problems identified will be reported to 

the three Co-PIs who will then relay immediately that information to the VISTAS TAWG and 

the relevant contractor with the issue addressed in a conference call so that it can be resolved. 

List servers related to emissions, meteorology, and modeling issues were set up for prompt 

communication among the Team, VISTAS, and other VISTAS contractors. 

Deliverables under this task were continuous project management and conference calls, plus two 

project meetings held in Research Triangle Park, North Carolina (see Table 2-2). The project 

Appendix C.2 - 19
Quality Assurance Project Plan (Draft) Page 15 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

meetings were attended by the three Co-PIs and additional staff from the Emissions and Air 

Quality Modeling Team. 

Table 2-2. Phase I Task 1 Project Management task deliverables and due dates. 

Item Description Due Date 

1 VISTAS TAWG Modeling Meeting September 29-30, 2003 

at the Solution Center in Research Triangle Park, North 

Carolina 

09/29-30/03

2 VISTAS TAWG Modeling Meeting February 12-13, 2004 in 

Research Triangle Park, North Carolina 

02/12-13/04

2.4.2 Phase I Task 2: Develop Model Configuration Evaluation Plan 

The first activity under the VISTAS Phase I Emissions and Modeling Study was the 

development a detailed plan, or Modeling Protocol (ENVIRON, 2003a), outlining the data 

analysis procedures and statistical/graphical tools to be used in evaluating the core and 

alternative CMAQ configurations in Task 4. This plan identified the procedures used in 

producing internally consistent observational and modeling data sets for individual particulate 

species and species groupings. The main purpose of this plan is to provide a consistent set of 

procedures to be used in the early portion of the Phase I activities when the various CMAQ 

model configurations are being tested. The draft plan was submitted to VISTAS TAWG who 

provided comments that were incorporated in the final Phase I modeling plan (see Table 2-3). 

Table 2-3. Phase I Task 2 Phase I Modeling Plan task deliverables and due dates. 

Item Description Due Date 

1 Draft Report “VISTAS Emissions and Air Quality Modeling— 

Phase I Task 2 Report: Recommended Model Configurations and 

Evaluation Methodology For Phase I Modeling” 

06/03/03 

2 Revised Draft Report “VISTAS Emissions and Air Quality 

Modeling— Phase I Task 2 Report: Recommended Model 

Configurations and Evaluation Methodology For Phase I 

Modeling” Available at: 

http://pah.cert.ucr.edu/vistas/reports/VISTAS_Task2-

REPORT.pdf

08/04/03 

2.4.3 Phase I Task 3: Acquisition and Development of Modeling Data Bases 

Under this task we assembled the databases needed to operate and evaluate the CMAQ model for 

the three Phase I episodes. 

 

Subtask 3a: Assemble/QA Air Quality Data. Under this Subtask we assembled a comprehensive 

database of ambient measurements to evaluate model performance. As part of the WRAP model 

performance evaluation our team had previously assembled data from the CASTNet (weekly wet 

Appendix C.2 - 20
Quality Assurance Project Plan (Draft) Page 16 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

and dry deposition of SO4, NO3, NH4, pH, base cations) and IMPROVE (daily fine particulate 

mass composition as SO4, NO3, NH4, OC, EC, and soils). Additional processing of data was 

needed to include ambient data from the SEARCH and STN networks in the analysis. Several 

issues must be addressed to use these data to evaluate model performance. In many cases there 

is not a 1-to-1 correspondence to model species. Accordingly, formulas must be developed to 

correctly map the data to the model species (for details, see the IMPROVE and CASTNET links 

at: http://pah.cert.ucr.edu/rmc/ambient/ambient.shtml. Moreover, model predictions are hourly 

while some ambient data are daily or weekly averages, so algorithms were developed to correctly 

treat averaging periods including correct representation of the time zone used for each 

monitoring site. QA of ambient data is a key step; we reviewed all data for reasonableness and 

completeness and flagged apparent outliers for exclusion from the model evaluation. We 

processed the AIRS data including O3, NOx and CO to convert it to the IO/API data format so 

that it can be used with PAVE for visualization of model and ambient data. For long term 

modeling (monthly to annual) it is essential that the QA’d ambient databases be designed to 

work with our model performance evaluation software. This will facilitate rapid model 

evaluation for multiple sensitivity simulations or repeats of base case simulations. 

Subtask 3b: Assemble/QA Emissions Data. CMAQ emissions inputs were prepared using data 

supplied by the VISTAS emissions contractors, the EPA NEI version 2 databases and the 

SMOKE emissions modeling system. The study team is currently working with the NEI formats 

and has developed the necessary QA tools to make effective use of these data. The NEI 

database, while the best available national inventory, must be examined for local modeling, 

particularly in point source locations and stack parameters. The QA tools developed as part of 

the EMS-2001 are a useful adjunct to the tools currently available in SMOKE. 

The study team has also developed a suite of tools designed to QA and evaluate episode specific 

emissions prior to inclusion into the modeling inventory. Since the magnitude of the dayspecific emissions for large stationary source is often significant in the modeling inventory, 

special attention is placed on the QA of these emissions data. The study team has processed the 

spatial surrogates and BELD-3/BEIS-3 databases over the Unified RPO grid under contract to 

the Midwest RPO. These data are currently under review and revision and the version most 

current will be used. 

Subtask 3c: Assemble/QA Meteorological Data. The meteorological model (MM5) output data 

was acquired from the VISTAS meteorological modeling contractor. While we recognize that 

the MM5 data will already have been validated by the meteorological modeling contractor, it has 

been our Team’s experience that an independent review is both time and cost effective. As part 

of our quality assurance activities, a full operational model evaluation was performed on the 

MM5 data sets. This operational evaluation covered surface and aloft wind direction, 

temperature, mixing ratio, and planetary boundary layer depths on both a domain-wide and 

subregional basis. The techniques used will follow the model performance protocol prepared for 

EPA for annual MM5 modeling (McNally and Tesche, 2002). 

Table 2-4 summarizes the VISTAS Phase I Task 3 deliverables. 

Appendix C.2 - 21
Quality Assurance Project Plan (Draft) Page 17 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

Table 2-4. Phase I Task 3 Phase I Acquisition and Development of Model Databases task 

deliverables and due dates. 

Item Description 

Due 

Date 

1 Draft Report “VISTAS Emissions and Air Quality Modeling— Phase I Task 

3a Report: Review and Assessment of Available Ambient Air Quality Data 

to Support Modeling and Model Performance Evaluation for the Three 

VISTAS Phase I Episodes” Available at: 

http://pah.cert.ucr.edu/vistas/reports/VISTAS_Task_3_072203.pdf

07/22/03 

2 Draft Report “VISTAS Emissions and Air Quality Modeling— Phase I Task 

3b Report: CMAQ Emissions Inventory Development and Emissions 

QA/QC Summary Report for Episodes 1, 2 and 3” Available at: 

 http://pah.cert.ucr.edu/vistas/reports/VISTAS_subtask_3b_QA_report.pdf

09/25/03 

3 Subtask 3c-1 Report: “VISTAS Emissions and Air Quality Modeling— 

Phase I Task 3c-1 Report: MM5 Meteorology QA/QC Summary Report for 

Episode 1: 2-20 January 2002” Available at: 

http://pah.cert.ucr.edu/vistas/reports/met_episode_1_report.pdf

09/10/03 

4 Subtask 3c-2 Report: “VISTAS Emissions and Air Quality Modeling— 

Phase I Task 3c-2 Report: MM5 Meteorology QA/QC Summary Report for 

Episode 2: 13-22 July 1999” Available at: 

 http://pah.cert.ucr.edu/vistas/reports/met_episode_2_report.pdf

09/15/03 

5 Subtask 3c-3 Report: “VISTAS Emissions and Air Quality Modeling— 

Phase I Task 3c-3 Report: MM5 Meteorology QA/QC Summary Report for 

Episode 3: 11-27 July 2001” Available at: 

 http://pah.cert.ucr.edu/vistas/reports/met_episode_3_report.pdf

09/16/03 

2.4.4 Phase I Task 4: Develop Optimal VISTAS Modeling Configuration 

Under VISTAS Phase I Task 4, we developed plans for the initial testing and sensitivity 

modeling of the SMOKE and CMAQ modeling systems in order to identify the optimal model 

configurations) for simulating regional PM, ozone and visibility in the eastern US. We first 

reviewed and assessed recent relevant regional modeling studies from which we identified an 

initial configuration and list of sensitivity tests. We then performed the sensitivity tests to 

identify the optimal model configuration(s). 

Subtask 4a: Recent Literature Review. Initiating Task 4 we performed a literature review to 

identify and critically evaluate recent relevant fine particulate/regional haze modeling studies, 

field programs and related scientific investigations that shed light on: (a) the selection and 

evaluation of CMAQ model configuration options, (b) the availability and adequacy of gas-phase 

and PM data sets for model set up and performance testing, (c) the suitability of operational and 

diagnostic procedures for evaluating the performance of CMAQ, and (d) any pertinent 

information of future year emissions control evaluations (ENVIRON, 2003b). 

Subtask 4b: Recommend Initial SMOKE/CMAQ Configurations. Drawing from the Team’s 

experience with SMOKE and CMAQ, we identified a suite of initial model configurations to be 

Appendix C.2 - 22
Quality Assurance Project Plan (Draft) Page 18 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

evaluated with the three test episodes. These alternative configurations included definition of: 

(a) vertical and horizontal grids, (b) gas-phase chemistry mechanism, (c) secondary aerosol 

mechanisms, (d) advection algorithms, (e) diffusion algorithms, (f) cloud and surface removal 

processes, (g) numerical integration scheme(s), and so on (ENVIRON, 2003b). 

Subtask 4c: Evaluate Approved SMOKE/CMAQ Configurations. The ENVIRON, Alpine, and 

UCR team collaboratively evaluated the various model configurations recommended in Subtask 

4b. These evaluations employed internally consistent statistical and graphical procedures and 

display software (Morris et al., 2004a). 

 

Subtask 4d: Perform Diagnostic/Sensitivity Experiments. Paralleling and supporting Subtask 4c, 

the study team conducted a series of diagnostic/sensitivity experiments aimed at identifying the 

most technically sound and reliable chemistry, transport, removal, and numerical algorithms 

available (Morris et al., 2004a). 

Subtask 4e: Recommend Optimal Model Configuration. The culmination of the literature 

review, CMAQ configuration testing and module sensitivity/diagnostic studies was the 

identification of a final, optimal configuration for the VISTAS modeling platform to be used in 

Phase II (Morris et al., 2004a).

Subtask 4f: Technical Documentation. Thorough documentation was performed for all aspects 

of Task 4 (Morris et al., 2004a). In addition, many of the findings in this task were relevant to 

VISTAS and other RPO’s and warranted publication of the technical findings at scientific 

conferences or in journals (Morris et al., 2004b,c,d; Tesche et al., 2004).

Table 2-5. Phase I Task 4 Develop Optimal VISTAS Modeling Configuration task deliverables 

and due dates.

Item Description 

Due 

Date 

1 “VISTAS Emissions and Air Quality Modeling— Phase I Task 4a/b Report: 

Review of Model Sensitivity Simulations and Recommendations of Initial 

CMAQ Model Configurations and Sensitivity Tests” Available at: 

http://pah.cert.ucr.edu/vistas/reports/VISTAS_Task4a_Report.pdf

07/25/03

2 Final Report “VISTAS Emissions and Air Quality Modeling— Phase I Task 

4cd Report: Model Performance Evaluation and Model Sensitivity Tests for 

Three Phase I Episodes” Available at: 

http://pah.cert.ucr.edu/vistas/reports/Final_Phase1/VISTAS_Task4cd_FinalRe

port_ExcSum-Sec3_only.pdf

09/07/04

2.4.5 Phase I Task 6: Phase II Modeling Protocol 

The VISTAS Phase II Modeling Protocol describes in detail the work to be performed and the 

specific quality assurance (QA) procedures to be used in performing, evaluating, and archiving the 

annual model simulations performed in Phase II. Particular emphasis in the protocol was given to: (a) 

model configurations, (b) specific science issues to be addressed, (c) model improvements, (d) model 

Appendix C.2 - 23
Quality Assurance Project Plan (Draft) Page 19 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

input preparation, (e) model applications (base year, future year, and strategies), (f) model evaluation 

and sensitivity analyses, (g) documentation, (h) data transfer, backup and archiving, and (i) schedule 

and deliverables. As shown in Table 2-6, under this task a First Draft Modeling Protocol was 

prepared and submitted to the VISTAS TAWG for review and comment. Based on these comments 

a Revised First Draft Modeling Protocol was prepared and distributed to the entire group for review 

and comment. 

Table 2-6. Phase I Task 6 Phase II Modeling Protocol task deliverables and due dates. 

Item Description Due Date 

1 First Draft Report “VISTAS Emissions and Air Quality Modeling — 

Phase I Task 6 Report: Modeling Protocol for the VISTAS Phase II

Regional Haze Modeling”

03/03/04 

2 Revised First Draft Report “VISTAS Emissions and Air Quality 

Modeling — Phase I Task 6 Report: Modeling Protocol for the VISTAS 

Phase II Regional Haze Modeling.” Available at: 

http://pah.cert.ucr.edu/vistas/reports/VISTAS_PhaseII_Protocol_Mar12

_2004.pdf

03/12/04 

2.4.6 Phase I Task 7: Website Development 

We developed a technical web site that served as the primary means for distributing emissions 

and air quality modeling to the VISTAS TAWG. The website included model results, analyses, 

presentations and reports. We maintained 4 list-servs (all participants, general project 

management, emissions QA, and modeling results) for the VISTAS project that can be accessed 

from the website that provides a permanent archive for all email communications for the project. 

Separate list-servs provides better organization of communications and allow for detailed 

discussions of specific topics such as emissions QA. 

Table 2-7. Phase I Task 6 Develop Website task deliverables and due dates. 

Item Description Due Date 

1 VISTAS Phase I Emissions and Air Quality Modeling Project 

Website: http://pah.cert.ucr.edu/vistas/index.shtml

2003-2004 

2.5 VISTAS Phase II Activities 

Below we discuss the project and QA activities for the currently planned VISTAS Phase II 

Modeling work effort. 

2.5.1 Phase II Task 1: Project Management 

The objective of this task is to manage project activities, participate in conference calls, attend 3 

VISTAS meetings in the southeastern United States (US), project management with VISTAS 

contacts, subcontractor management and general oversight, and overall quality assurance. 

Appendix C.2 - 24
Quality Assurance Project Plan (Draft) Page 20 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

The VISTAS Phase II management structure for Emissions and Air Quality Modeling is the 

same as used in Phase I with Ralph Morris of ENVIRON serving as Project Manager and Ralph 

Morris, T.W. Tesche and Gail Tonnesen serving as Co-Principal Investigators (Co-PIs) and 

managing the activities in each of the ENVIRON, Alpine and UCR modeling centers, 

respectively. Under this task we are performing all management activities for the VISTAS Phase 

II modeling study, including: 

• Attendance of two scientists of the ENVIRON/Alpine/UCR Team at 3 VISTAS 

meetings to be held in the southeastern US. 

• Participation in scheduled conference calls to be held approximately once per month 

as well as expected ad hoc conference calls to be held as needed. 

• Refine Draft Phase II annual modeling protocol due early March 2004. Final initial 

Phase II annual modeling protocol incorporating review comments as directed by 

Contract Officer due two weeks after direction received. The modeling protocol 

follows EPA guidance and includes the specific task descriptions, data quality and 

assurance plan, and model performance evaluation plan for VISTAS Phase II 2004 

work. The VISTAS Phase II modeling protocol is a living document that will be 

updated as tasks are added to project work scope and to document revisions in the 

technical approach. 

• Develop and refine the Scope of Work and conduct contract discussions with the 

VISTAS modeling team and the VISTAS technical and project representatives. 

• Preparation of subcontracts, invoicing and payments. 

• Internal project conference calls and discussions among the ENVIRON/Alpine/UCR 

project team. 

• Develop and implement the Quality Assurance Project Plan (QAPP). 

• Model performance evaluation report using revised 2002 inventories. Report of 

model response to changes in inventory from 2002 revised to 2002 base year with 

“typical” EGU and fire. 

• Executive Summary report summarizing key findings and results from the task 

summary reports. 

Appendix C.2 - 25
Quality Assurance Project Plan (Draft) Page 21 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

Table 2-8. Phase II Task 1 Project Management task deliverables and due dates. 

Item Description Due Date 

1 Second Draft Report “VISTAS Emissions and Air Quality Modeling — 

Phase I Task 6 Report: Modeling Protocol for the VISTAS Phase II 

Regional Haze Modeling.” Available at: 

http://pah.cert.ucr.edu/vistas/vistas2/reports/vistasII_Final_Protocol_05_1

0_2004.pdf 

05/06/04 

2 Conference Calls with VISTAS among Modeling Team and with TAWG 2004-2005 

3 National Inter-RPO Modeling Meeting in Denver, Colorado May 25-26, 

2004 

05/25-26/04 

4 VISTAS TAWG Meeting in Atlanta, Georgia September 22-23, 2004 09/22-23/04 

5 VISTAS TAWG meeting to be determined (TBD) TBD 

6 Quality Assurance Project Plan (QAPP) November 2004 

7 Draft VISTAS Phase II Executive Summary Report 12/31/04 

8 Final VISTAS Phase II Executive Summary Report 01/15/05 

2.5.2 Phase II Task 2: Develop IC/BCs for 2002 Annual Run 

The objective of this task is to analyze the need for a high time resolution (e.g., 3-hourly) global 

climate model (e.g., GEOS-CHEM) output for generating Boundary Conditions (BCs) for 2002 

annual modeling of the 36 km national RPO grid. 

Under this task we are recommending a source of initial and boundary conditions (IC/BC) for 

2002 annual and 2003 episodic CMAQ modeling. We would analyze in more detail the VISTAS 

Phase I July 2001 episode CMAQ simulations using the BCs generated from GEOS-CHEM 

2001 3-hour concentrations outputs. The CMAQ model performance and output for the July 

2001 episode using BCs generated from GEOS-CHEM seasonal/monthly vs. 3-hour output 

performed under Phase I would be analyzed and compared with a run using the EPA CMAQ 

default BCs. This is followed by interaction with investigators at Harvard University and 

University of Houston to evaluate temporal and spatial variability between BC based on 3-hour 

average and monthly average GEOS-CHEM outputs for 2001. Based on these results we would 

recommend whether GEOS-CHEM 2002 day-specific outputs are justified to capture daily 

variability in BC concentrations. 

Table 2-9. Phase II Task 2 GEOS-CHEM Boundary Conditions Analysis task deliverables and due 

dates. 

Item Description Due Date 

1 PowerPoint Presentation: “VISTAS Phase I and II Modeling 

Boundary Condition Sensitivity” presented at February 12-13, 2004 

VISTAS Modeling Meeting in RTP, NC 

02/12-13/04 

Appendix C.2 - 26
Quality Assurance Project Plan (Draft) Page 22 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

2.5.3 Phase II Task 3: 2002 Data Preparation and Model Inputs 

The development of the VISTAS Phase II 2002 annual CMAQ model inputs is being performed 

in several Subtasks as follows. 

2.5.3.1 Subtask 3a: Air Quality Data Gatekeeper 

The objective of Subtask 3a is to acquire, process and QA/QC air quality data, deposition data 

and other data that can be used to evaluate CMAQ and other air quality models for the 2002 

annual cycle and the 36 km national RPO grid with particular emphasis on the VISTAS 

southeastern US region. 

Under this Subtask the Air Quality Gatekeeper would perform the following activities: 

• Obtain air quality data as appropriate for model input development and model 

performance evaluation. At a minimum, the same data bases as used in Phase I should 

be used in Phase II. 

• Identify if any special aircraft (or other) measurements are available within the VISTAS 

12-km domain for the 2002 modeling year. 

• Assure quality of all air quality data obtained, are consistent with the approved QA/QC 

plan. 

• Provide documentation of evaluation. 

• Generate IC/BC inputs for CMAQ for all 2002 modeling runs described in Task 4 below. 

2.5.3.2 Subtask 3b: MM5 Meteorological Model Gatekeeper 

The objectives of this Subtask is to acquire the 2002 MM5 data from the VISTAS 

Meteorological Contractor (BAMS) and perform QA/QC, an independent evaluation, and 

process the data using MCIP for input into CMAQ. 

The Meteorological Gatekeeper’s function for the VISTAS Phase II 2002 MM5 modeling results 

would be the similar as was done in Phase I, only we would leverage off of the 2002 MM5 

model evaluation infrastructure set up at ENVIRON for WRAP. The MM5 output would be 

acquired from BAMS and subjected to an initial quality check. Any issues associated with the 

2002 MM5 output would be reported immediately back to BAMS and VISTAS. After an initial 

quality check is performed, a more thorough QA/QC and an independent evaluation would be 

conducted. Results would be compared with other 2002 MM5 simulations (e.g., WRAP). The 

CMAQ-ready meteorological inputs would also be generated under this subtask. The MM5 data 

would be provided in two installments of 8 months and 4 months, respectively. 

2.5.3.3 Subtask 3c: Emissions Gatekeeper and Emissions Development for Non-VISTAS 

States, Canada, and Mexico 

Under this Subtask we would coordinate activities with the VISTAS emissions contractor and 

perform initial QA/QC of emissions. We would also develop emissions for non-VISTAS States, 

Canada, and Mexico for the 2002 annual modeling period. The Emissions Gatekeeper would 

Appendix C.2 - 27
Quality Assurance Project Plan (Draft) Page 23 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

coordinate activities with the VISTAS emissions contractors and technical advisors to assure that 

data are provided in the correct format and that there are no holes in the emissions inventory. 

They would also coordinate with EPA and other RPOs to determine the best sources of data for 

non-VISTAS States as well as Canada and Mexico. Once data are received from the VISTAS 

emissions contractor the Emissions Gatekeeper would perform a preliminary QA/QC and 

immediately report back to VISTAS and the emissions contractor any issues that are uncovered. 

These results would be documented in the Emissions Gatekeeper report. 

Under this task we would also develop emissions inventories for non-VISTAS States, Canada, 

and Mexico consistent with the RPO data exchange protocol, using existing national or regional 

modeling inventories, state CERR submittals, EPA National Emissions Inventories, or other 

sources, as appropriate 

2.5.3.4 Subtask 3d: Emissions Modeling 

The objective of this Subtask is to generate base- and future-year CMAQ-ready gridded, hourly, 

speciated, three-dimensional emission inputs for 2002. The SMOKE emissions processing 

system would be used along with the 2002 MM5 data to process the 2002 emissions for VISTAS 

states from the VISTAS emissions contractor and emissions from the non-VISTAS states, 

Canada and Mexico provided under Subtask 3c Emissions Gatekeeper. CMAQ emission 

modeling files would be generated to support four rounds of emissions modeling runs using the 

2002 meteorological conditions: 

1. An initial 2002 Base Case run of CMAQ-ready emission inputs using VISTAS States 

emissions data received by January 31, 2004, and MM5 meteorological data received by 

March 31, 2002 would be ready by May 30, 2004. 

2. Revised 2002 Base Case and 2002 Typical Year emission runs using the emissions 

submitted by September 15, 2004 that would be ready by October 15, 2004. 

3. Future-year emission scenarios using 2002 meteorology and emissions data submitted by 

October 15, 2004 would be ready by November 15, 2004. 

The initial 2002 Base Case emissions modeling would use the existing Phase I SMOKE 

emissions modeling set up. For the revised 2002 Base Case, 2002 Typical Year and Future-Year 

emissions modeling, the existing Phase I SMOKE emissions modeling set up would be updated 

and enhanced as follows: 

• Process emissions with SMOKE version 2 

• Implement EPA’s new spatial surrogate distributions 

• Implement EPA’s revised PM speciation profiles and SCC cross-references 

• Implement revised temporal profiles as collected and converted from data provided 

by VISTAS’ emissions contractors or other sources 

Biogenic emissions will be processed using SMOKE and the 2002 MM5 day-specific 

temperatures and held constant for all the 2002 and future-year emission scenarios (i.e., the 

effects of climate change and land cover changes will not be accounted for in the future-year 

biogenic emission estimates). 

Appendix C.2 - 28
Quality Assurance Project Plan (Draft) Page 24 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

On-road mobile sources comprise a major computational component of the SMOKE emissions 

modeling. If day-specific adjustments are required using day-of-week and daily MM5 

temperature estimates that would increase the SMOKE processing time considerably and 

potentially impact the schedule. 

Currently, other RPOs are modeling the motor vehicle emissions using average monthly 

temperature data, or by modeling one weekday, Saturday and Sunday from each quarter. To 

better represent the day-of the-week variability typical to motor vehicle emissions, and to make 

the best possible use of the meteorological data available, we propose to model one full week 

from each month of the annual episode, for a total of 84 episode days modeled. Note that this 

approach will allow us to expand the number of motor vehicle days modeled, if particular 

periods of the annual episode warrant additional refinement in the modeling inventory. 

Area source and non-road mobile source emissions will also be modeled for one week per 

month, using seasonal, monthly and day-of-week adjustments available in the current SMOKE 

configuration. 

EGU emissions will be supplied by the VISTAS emissions contractor in an annual file. To 

temporally allocate the EGU point sources, heat input data from the 2002 CEM datasets will be 

used to develop facility or unit-level temporal distributions. The day-specific and facility-specific 

temporal profiles will be used in conjunction with the emissions contractor supplied emissions 

data to calculate hourly EGU emissions by facility. 

For the 2002 Typical Year and Future-Year emission scenarios the VISTAS emissions contractor 

would provide average emissions for EGUs for the current baseline (2000-2004) and the futureyear baseline (2014-2018) periods. 

Day-specific emissions for fires (wildfires, prescribed burns and agricultural fires) may be 

provided by the VISTAS emissions contractor and would be used in the 2002 Base Case 

emissions scenario. If other temporally allocated fire emissions are provided, we will generate a 

set of actual 2002 fire-based temporal profiles and cross-references to allocate emissions to hours 

in the modeled episodes. Typical year emissions for fires would be provided by the VISTAS 

emissions contractor and would be used in both the 2002 Typical Year and Future-Year emission 

scenarios. 

Ammonia emissions will be modeled as provided by the emissions contractor. Supplemental 

ammonia modeling is not expected during the emissions modeling phase. 

Wind blown dust emissions (i.e., PM10 and PM2.5 emissions from wind erosion of natural 

geogenic sources (SCCs 2730100000 [total] and 2730100001 [dust devils]), will be excluded 

from the modeling files consistent with Phase I. 

Each round of emissions modeling would be documented in emission summary tables and 

PowerPoint presentations that would contain tables and graphs of the emissions and QA/QC 

summaries. A final report on the VISTAS Phase II emissions modeling would be prepared that 

focuses on the differences in emissions in the different emissions scenarios including 

Appendix C.2 - 29
Quality Assurance Project Plan (Draft) Page 25 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

documentation of the changes in emissions from the 2002 Typical Year to Future-Year emissions 

scenario that would assist in the interpretation of the visibility projections. 

2.5.3.5 Subtask 3e: Future-Year Emissions Modeling for Three VISTAS Phase I Episodes 

Under this Subtask we would develop emissions modeling files for the initial future-year base 

case inventory for the July 2001 and Jan 2002 Phase I episodes. These inventories will be used 

in emissions sensitivity modeling analyses between May 2004 and September 2004. The same 

SMOKE emissions set up from the Phase II Subtask 3d would be used. 

2.5.3.6 Subtask 3f: Interim Future-Year Emissions Modeling using 2002 Meteorology 

Under this Subtask we would generate CMAQ-ready emission inputs for an interim future-year 

and the 2002 meteorological year. The VISTAS emissions contractors would provide interim 

future-year emissions estimates. 

2.5.3.7 Phase II Task 3 Deliverables

The VISTAS Phase II Task 3 deliverables are summarized in Table 2-10. 

Table 2-10. Phase II Task 3 2002 Data Preparation and Model Inputs task deliverables and due 

dates. 

Item Description Due Date 

1 Subtask 3a 2002 Air Quality and Deposition Database for Model 

Performance Evaluation 

04/30/04 

2 PowerPoint Presentation for Subtask 3b: “VISTAS 2002 MM5 Annual 

Run Meteorological Gatekeeper Evaluation.” Available at: 

http://pah.cert.ucr.edu/vistas/vistas2/ppt_files/Task3b_VISTAS_II%20_

met_gatekeeper_.ppt 

06/30/04 

3 PowerPoint Presentation for Subtask 3c VISTAS Initial Base Year 2002 

Emissions Inventory Preparation.” Available at: 

http://pah.cert.ucr.edu/vistas/vistas2/ppt_files/Task3c_Initial_Base_Year

_EI_Preparation.ppt 

08/08/04 

4 PowerPoint Presentation for Subtask 3c VISTAS Future Year Emissions 

Inventory Preparation.” Available at: 

http://pah.cert.ucr.edu/vistas/vistas2/ppt_files/Task3c_Initial_Future_Ye

ar_EI_Preparation.ppt 

08/08/04 

5 Subtask 3d Initial 2002 Base Case CMAQ-ready Emission Inputs 05/30/04 

6 Subtask 3d Revised and Typical 2002 CMAQ-ready Emission Inputs 10/15/04 

7 Subtask 3d Future-Year (2018) CMAQ-ready Emission Inputs for Two 

Scenarios 

12/15/04 

8 Subtask 3e Future-Year (2018) CMAQ-ready Emission Inputs for Two 

Phase I Episodes 

06/15/04 

9 Subtask 3f Interim Future-Year (2009) CMAQ-ready Emission Inputs 12/15/04 

Appendix C.2 - 30
Quality Assurance Project Plan (Draft) Page 26 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

2.5.4 Phase II Task 4: 2002 Annual CMAQ Modeling 

Under Phase II Task 4 we would apply the CMAQ model using Initial and Revised 2002 Actual 

Base Case emissions and other inputs and perform a model performance evaluation on the 

results. 

2.5.4.1 Subtask 4a: Initial Base Case and Model Performance Evaluation 

A preliminary 2002 CMAQ Actual Base Case simulation would be performed using the initial 

2002 inventory for VISTAS and Non-VISTAS states, Canada and Mexico that are to be 

delivered to modeling team by January 31, 2004. After subjecting the initial 2002 emissions to 

the Emissions Gatekeeper quality checks and QA/QC (Subtask 3c), CMAQ-ready emissions 

would be generated using the initial emissions for 2002 (Subtask 3d). The primary objective of 

this initial CMAQ run is to set up and streamline the modeling system and approach and obtain a 

preliminary model performance evaluation for the 2002 annual period. The focus of the analysis 

will be on model performance diagnostics and experience in running the annual simulations to 

optimize model performance both in terms of ability to estimate fine particulate matter in the 

southeastern US as well as optimize the ability of the modeling centers to perform 2002 annual 

CMAQ runs. 

Once the initial CMAQ base case simulation is generated, it will be subjected to a model 

performance evaluation. In Phase II multiple approaches will be utilized in the evaluation 

process: 

• Alpine will use their MAPS software to generate performance statistics and graphical 

displays by network and by subregion. The MAPS software generated some 

performance measures not supported by other software (e.g., spatial average time 

series) and once set up can easily generate performance measures and displays by 

subregion. 

• Alpine will also apply the UCR statistical performance package that was used in 

Phase I that includes model performance metrics, scatter plots and time series plots. 

This package has been extended to include PAVE spatial maps with superimposed 

observation to provide spatial information on model performance. 

• UCR will help analyze and interpret the model performance results and post them on 

the VISTAS modeling website. 

• ENVIRON will evaluate the results using techniques they developed for WRAP that 

focus on model performance at Class I areas for the 20% Best and 20% Worst 

visibility days that are the data used to project future-year visibility improvements. 

This performance would include predicted and observed stacked bar charts of 

extinction showing the contributions of each of the for the 7 components of extinction 

(SO4, NO3, EC, OC, Soil, CM and Rayleigh) of extinction averaged and separately 

for the 20% Best/Worst days. Days from then 20% Best/Worst days and Class I areas 

where the modeling results deviate greatly from the observed values would be flagged 

Appendix C.2 - 31
Quality Assurance Project Plan (Draft) Page 27 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

for further analysis into model performance and possible exclusion for use in the 

visibility projections (i.e., calculating RRFs). 

Use of multiple MPE approaches will allow the quick identification of potential problems in the 

model estimates or the model performance evaluation software. The results would be shared 

among the group and with VISTAS. The operational model performance evaluation would be 

conducted using the same “routine” ambient databases as used in Phase I (e.g., IMPROVE, 

CASTNet, AQS, SEARCH, STN and SEARCH). 

Because the initial emissions may undergo significant changes, limited diagnostic sensitivity 

tests would be conducted using the initial 2002 CMAQ database. The limited sensitivity tests 

would be aimed at identifying and rectifying specific performance issues of the model that we 

don’t believe will be corrected by updated emissions. As in the VISTAS Phase I modeling, the 

sensitivity tests will be flexible and opportunistic to quickly identify and resolve areas of highest 

importance. However, the number of sensitivity tests will be limited by available funding and 

time constraints. 

2.5.4.2 Subtask 4b: Revised Base Case Simulation 

A 2002 CMAQ simulation would be conducted using the revised 2002 Base Case emissions 

inventory that is expected to be received from the VISTAS emissions contractor by September 

15, 2004. Several components of 2002 initial CMAQ set up could change including, but not 

limited to, emissions, meteorology, boundary conditions, CMAQ update, CMAQ chemical 

module. For example, if a 2002 GEOS-CHEM simulation is performed, then the revised BCs 

from Optional Task 13 would be used in the revised base case simulation. The revised 2002 

CMAQ simulation would be run using the “best configuration” identified in Subtask 4a. The 

results would be transferred to each of the modeling centers that would conduct their own 

operational MPE as was done under Subtask 4a. We have budgeted 8 annual 36 km and 4 

annual 12 km sensitivity simulations under this task to investigate alternative configurations, 

options and updates on model performance. The results would be documented in a draft final 

report submitted to VISTAS. 

2.5.4.3 Subtask 4c: Typical Year Emissions Simulation 

EPA guidance recommends using models in a relative sense to project future year visibility 

through relative reduction factors (RRFs). Thus, for projecting changes in visibility, the currentyear base case and future-year scenarios must be consistent. Thus, in this task typical emissions 

for fires and EGUs will be used for the 2002 Typical Year emissions scenario, instead of the 

episodic specific emissions used in the 2002 Base Case simulation. The 2002 typical year 

emissions generated under Subtask 3d would be used in this simulation. The results would be 

subjected to a QA/QC, compared with the 2002 Base Case simulation and a cursory evaluation 

would be conducted. 

Appendix C.2 - 32
Quality Assurance Project Plan (Draft) Page 28 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

2.5.4.4 Subtask 4d: Future-Year Modeling for Two Scenarios 

Using the CMAQ-ready emissions for the two future-year emission scenarios prepared under 

Subtask 3d that would be ready by November 15, 2004 and December 15, 2004, we would 

perform the two future-year CMAQ simulations under this subtask. New future-year boundary 

conditions (BCs) may be used depending on the availability of data. The future-year CMAQ 

results for the two scenarios and the CMAQ results for the 2002 Typical Year scenario would be 

used to project visibility improvements at Class I areas using EPA guidance. 

2.5.4.5 Subtask 4e: Interim Future-Year using 2002 Database 

Using the CMAQ-ready emissions for the interim future-year emission scenario prepared under 

Subtask 3f that would be ready by December 15, 2004, we would perform the interim future-year 

CMAQ simulation under this subtask. New future-year boundary conditions (BCs) may be used 

depending on the availability of data. The future-year CMAQ results for the interim future-year 

scenario and the CMAQ results for the 2002 Typical Year scenario would be used to project 

visibility improvements at Class I areas using EPA guidance. 

2.5.4.6 Summary of Phase II Task 4 Deliverables 

Table 2-11 summarizes the VISTAS Phase II Task 4 deliverables and due dates. 

Table 2-11. Phase II Task 4 2002 CMAQ Modeling task deliverables and due dates. 

Item Description 

Due 

Date 

1 PowerPoint Presentation for Subtask 4a: “Initial Vistas 2002 CMAQ Run, 

Analysis of 36 km Performance for PM.” Presented at July 27, 2004 

VISTAS TAWG Conference Call. Available at: 

 http://pah.cert.ucr.edu/vistas/vistas2/reports/2002_CMAQ_initial.ppt 

07/27/04

2 PowerPoint Presentation for Subtask 4a: “Initial VISTAS 2002 CMAQ Run: 

36/12 km Diagnostic MPE” Presented at July 27, 2004 VISTAS TAWG 

Conference Call. Available at: 

 http://pah.cert.ucr.edu/vistas/vistas2/reports/2002_CMAQ_initial_AG.ppt 

07/27/04

3 Revised Draft Final Report for Subtask 4a: “VISTAS Phase II Emissions 

and Air Quality Modeling -- Task 4a Report: Evaluation of the Initial 

CMAQ 2002 Annual Simulation.” Dated September 27, 2004. 

09/27/04

4 PowerPoint Presentation for Subtask 4a: “Initial CMAQ Diagnostic MPE 

for 2002: VISTAS Task 4a Results.” Presented at VISTAS September 21-

22, 2004 TAWG meeting in Atlanta, Georgia. Available at: 

 files/Sept_2004_tawg/2002_CMAQ%20Diagnostic%20MPE_TWT.ppt 

09/21/04

5 PowerPoint Presentation for Subtask 4a: “Initial VISTAS Phase II 2002 

CMAQ Operational Model Performance Evaluation.” Presented at VISTAS 

September 21-22, 2004 TAWG meeting in Atlanta, Georgia. Available at: 

http://pah.cert.ucr.edu/vistas/vistas2/docs.shtml

09/21/04

6 PowerPoint Presentation for Subtask 4a on diagnostic analysis of the Initial 11/12/04

Appendix C.2 - 33
Quality Assurance Project Plan (Draft) Page 29 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

Item Description 

Due 

Date 

2002 CMAQ Base Case simulation to identify OC and NO3 performance 

issues. 

7 PowerPoint Presentation for Subtask 4b on Revised 2002 XCMAQ Base 

Case Simulation and Model Performance Evaluation 

11/30/04

8 Subtask 4b Draft Report on Revised 2002 CMAQ Base Case simulation and 

model performance evaluation 

12/15/04

9 Subtask 4b Report on Model Sensitivity Tests 01/15/05

10 PowerPoint Presentation on Subtask 4c 2002 Typical Base Case simulation 12/31/04

11 Subtask 4d Draft Report on Future-Year (2018) Base Case modeling 01/31/04

12 PowerPoint Presentation on Subtask 4e Interim Future-Year modeling 01/31/05

2.5.5 Phase II Task 5: Episodic Modeling 

The VISTAS Phase II plan includes potential provisions for performing episodic modeling if 

needed. In particular, additional episodic modeling may be carried out to: (1) capture 

meteorological conditions for Worst 20% or Best 20% visibility days at Class I areas that did not 

occur during the 2002 annual modeling period; and (2) to obtain modeling periods during 2003 

when the FOCUS sites were operating that contain enhanced speciated PM measurements. The 

Phase II Task 5 Episodic Modeling work effort is currently not funded. Given that the 2003 year 

was fairly wet and atypical and the 2002 annual modeling year appears to capture most of the 

meteorological conditions, additional episodic modeling may not be carried out so is not 

addressed in this QAPP. 

2.5.6 Phase II Task 6: Data Management 

2.5.6.1 Subtask 6a: VISTAS Modeling Website 

Under this Subtask we would maintain the VISTAS Modeling Website including posting 

modeling input and output files, reports, interpretation of results, and other documents including 

Task Reports and PowerPoint Presentations presented during meetings and conference calls. 

2.5.6.2 Subtask 6b: Data Transfer, Storage and Retrieval 

Under this Subtask we would archive and store key model inputs and outputs and make them 

available to others. Storage of model inputs and outputs for up to 6 annual runs plus episodic 

runs or optional tasks to be defined. A firewire or IDE drive(s) of the key model inputs would be 

provided to VISTAS who could distribute it to states, stakeholders and others as desired (i.e., 

technology transfer). We would also perform data requests as directed by VISTAS under this 

Subtask. 

Appendix C.2 - 34
Quality Assurance Project Plan (Draft) Page 30 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

2.5.6.3 Phase II Task 6 Data Management Deliverables 

Table 2-12 summarizes the deliverables and schedule for the Phase II Task 6 Data Management. 

The VISTAS Phase II modeling website would be operated and maintained continuously during 

the 2004-2005. We expect the Initial and Revised 2002 CMAQ databases to be delivered to 

VISTAS in October and December 2004, respectively. Finally, as directed by VISTAS we 

would provide additional data to others as requested. 

Table 2-12. Phase II Task 6 Data Management task deliverables and schedule. 

Item Description Due Date 

1 VISTAS Phase II Modeling Website. Available at: 

http://pah.cert.ucr.edu/vistas/vistas2/index.shtml

2004-2005 

2 Firewire disks of Initial 2002 CMAQ annual modeling databases 10/15/04 

3 Firewire disks of Revised 2002 CMAQ annual modeling databases 12/31/04 

4 Disks, CD, DVD, ftp files and e-mail files of data transfer as directed by 

VISTAS 

2004-2005 

2.5.7 Phase II Task 7: Emission Reduction Sensitivity Simulations using CB4 and SAPRC 

Chemistry and 2 Phase I Episodes

The objective of this optional task is to investigate the sensitivity of estimated PM concentrations 

to emissions reductions using the CB4 and SAPRC99 chemical mechanisms. If significant 

differences exist and there are reasons to believe that the SAPRC99 response may be more 

correct, then the revised 2002 Base Case modeling starting in September would be performed 

using the SAPRC99 chemistry. 

The CB4 and SAPRC99 emission reductions sensitivity tests would be performed using the 

January 2002 (winter) and July 2001 (summer) episodes. We would perform 30% emission 

reductions across all source categories and across the entire modeling domain for the 36 km grid 

for the following five precursors: 

• NOx 

• SO2 

• VOC 

• NH3 

• NOx+NH3 

With 2 episodes and 2 chemical mechanisms this results in 10 total CMAQ 36 km simulations. 

We would also perform two corroborative emissions reductions sensitivity simulations using the 

CAMx model for the July 2001 episode and 36 km grid. Table 2-13 summarizes the deliverables 

under Phase I Task 7. 

Appendix C.2 - 35
Quality Assurance Project Plan (Draft) Page 31 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

Table 2-13. Phase II Task 7 CB4/SAPRC Sensitivity Modeling task deliverables and due dates. 

Item Description Due Date 

1 PowerPoint Presentation for Task 7: “VISTAS Phase II Task 7 Update: 

CMAQ Version 4.4beta CB4/SAPRC99 Comparisons” presented at July 27, 

2004 TAWG Conference Call. Available at: 

 http://pah.cert.ucr.edu/vistas/vistas2/reports/PhaseII_Task7_Update.ppt 

07/27/04 

2 PowerPoint Presentation for Task 7: “VISTAS Phase II Task 7 Results: 

CMAQ Version 4.4beta CB4/SAPRC99 Comparisons” presented at 

September 2, 2004 TAWG Conference Call. Available at: 

http://pah.cert.ucr.edu/vistas/vistas2/ppt_files/Task7_VISTAS_PhaseII_Tas

k7_CB4-SAPRC_Sep02_2004.ppt 

09/02/04 

3 PowerPoint Presentation for Task 7: “VISTAS Phase II Task 7 Results: 

CB4/SAPRC99 Comparisons for Urban Sites” presented at September 14, 

2004 TAWG Conference Call. Available at: 

http://pah.cert.ucr.edu/vistas/vistas2/ppt_files/Task7_VISTAS_PhaseII_CB

4-SAPRC_Urban_Sep14_2004.ppt 

09/14/04 

2.5.8 Phase II Task 10: Journal Paper on VISTAS Phase I Modeling 

The objective of this task is to write and submit the results of the VISTAS Phase I modeling 

results to a peer-review journal. An outline for a journal article on the VISTAS Phase I 

modeling would be prepared and distributed to VISTAS. Based on comments the outline would 

be updated and a draft paper written documenting the VISTAS Phase I modeling results. The 

draft paper would be distributed to VISTAS and updated based on their comments. In 

consultation with VISTAS a Journal would be selected and the paper submitted to the Journal for 

publication. The paper would be updated as needed to address comments of the Journal peerreviewers and a final manuscript submitted to the Journal for publication. 

Table 2-14. Phase II Task 10 Phase I Journal Article task deliverables and due dates. 

Item Description Due Date 

1 Draft Journal Article on VISTAS Phase I Modeling for VISTAS review 11/30/04 

2 Journal Article for Submission 12/31/04 

2.5.9 Phase II Task 13: Analysis and Processing of 2002 GEOS-CHEM Data 

Under this task we would process output from a 2002 GEOS-CHEM global climate model 

simulation performed by Harvard University to generate 2002 day-specific 3-hourly CMAQ 

boundary condition (BC) inputs for 2002. 

Appendix C.2 - 36
Quality Assurance Project Plan (Draft) Page 32 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

Table 2-15. Phase II Task 13 2002 GEOS-CHEM Boundary Condition Processing task deliverables 

and due dates. 

Item Description Due Date 

1 PowerPoint Presentation: “Documentation and Evaluation of the 2002 

GEOS-CHEM Simulation.” Presented during VISTAS TAWG October 4, 

2004 conference call. Available at: 

http://pah.cert.ucr.edu/vistas/vistas2/ppt_files/2002_GEOS_CHEM_10040

4.ppt 

10/01/04 

2 CMAQ-ready Boundary Condition (BC) input files 10/15/04 

3.0 PROJECT MANAGEMENT 

3.1 Project Organization 

This project is conducted by the ENVIRON International Corporation, Alpine Geophysics, LLC 

(Alpine), and the University of California at Riverside (UCR), with input from the VISTAS 

Technical Analysis Workgroup (TAWG). Organizational commitment is an essential element for 

developing and implementing a successful research project. Ralph Morris of ENVIRON would 

be the VISTAS Emissions and Air Quality Modeling Project Manager (PM). The VISTAS 

Phase II Modeling Team has three Co-Principal Investigators that coordinate activities at each of 

the three modeling centers, Ralph Morris of ENVIRON, T.W. Tesche of Alpine and Gail 

Tonnesen at UCR. The PM and three Co-PIs are kept apprised of all project activities, from 

identifying the need to develop sound experimental and project designs to delivering reports. 

Commitments to research and project activities, such as those described in this QAPP are made 

only after the activities are thoroughly reviewed and approved by the PM and Co-PIs and 

VISTAS TAWG. Figure 3-1 presents the organizational chart that shows the lines of 

responsibility and information flow for activities under this project. Table 3-1 lists the project 

responsibilities for participants in the VISTAS Emissions and Air Quality Modeling study, with 

more details on their roles provided next. 

Appendix C.2 - 37
Quality Assurance Project Plan (Draft) Page 33 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

 Southeastern States Air 

Resources Managers, Inc. 

(Contracting Agency) 

VISTAS 

Technical Analysis 

Workgroup (TAWG) 

Chairperson: 

Sheila Holman, North 

Carolina 

VISTAS 

Contracting Officer: 

Patricia Brewer, VISTAS 

VISTAS 

Technical Contact: 

James Boylan, Georgia 

Subcontractor 

Alpine Geophysics 

Co-Principal Investigator 

T. W. Tesche 

Staff 

Prime Contractor 

ENVIRON 

Project Manager and CoPrincipal Investigator 

Ralph Morris 

Staff 

Subcontractor 

UC Riverside 

Co-Principal Investigator 

Gail Tonnesen 

Staff 

Figure 3-1. VISTAS Emissions and Air Quality Modeling Project Organizational Chart. 

Appendix C.2 - 38
Quality Assurance Project Plan (Draft) Page 34 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

Table 3-1. VISTAS Phase II Emissions and Air Quality Modeling project participants and 

contacts. 

Person & Role Affiliation/Address Contact Information 

Patricia Brewer 

(Contracting Officer) 

VISTAS Technical Coordinator 

2090 US Highway 70 

Asheville, NC 28778 

(828) 296-4500 

(Fax) (828) 299-7043 

pat.brewer@ncmail.net

James Boylan 

(Technical Contact for 

Emissions & AQ 

Modeling) 

Georgia DNR 

Air Protection Branch 

4244 International Pkwy, Ste 120 

Atlanta, GA 30354-3906 

(404) 362-4851 

(Fax) (404) 363-7100 

James_Boylan@mail.dnr.state.ga.us

Michael Abraczinskas 

(Technical Contact for 

MM5 Modeling) 

North Carolina DENR 

1641 Mail Service Center 

Raleigh, NC 27699-1641

(919) 715-3743 

Michael.Abraczinskas@ncmail.net

Ralph Morris 

(Project Manager and 

Co-Principal 

Investigator) 

ENVIRON 

101 Rowland Way 

Novato, CA 94945 

(415) 899-0708 

(Fax) (415) 899-0707 

rmorris@environcorp.com

T.W Tesche 

(Co-Principal 

Investigator) 

Alpine Geophysics, LLC 

3479 Reeves Drive 

Ft. Wright, KY 41017 

(859) 341-7502 

(Fax) (859) 341-7502 

twt@iac.net

Gail Tonnesen 

(Co-Principal 

Investigator) 

UC Riverside 

CE-CERT 

1084 Columbia Avenue 

Riverside, CA 92507 

(951) 781-5676 

(Fax) (909) 781-5790 

tonnesen@cert.ucr.edu

Key ENVIRON Participants 

Bonyoung Koo ENVIRON 

101 Rowland Way 

Novato, CA 94945 

(415) 899-0727 

bkoo@environcorp.com

 

Edward Tai ENVIRON (415) 899-0725 

etai@environcorp.com

Steven Lau ENVIRON (415) 899-0739 

slau@environcorp.com

Key Alpine Geophysics Participants 

Dennis McNally Alpine Geophysics, LLC 

7341 Poppy Way 

Arvada, CO 80007 

(303) 421-2211 

(Fax) (303) 421-9553 

dem@alpinegeophysics.com

Cyndi Loomis Alpine Geophysics, LLC 

7341 Poppy Way 

Arvada, CO 80007 

(303) 421-2211 

(Fax) (303) 421-9553 

cfl@alpinegeophysics.com

Greg Stella Alpine Geophysics, LLC 

387 Pollard Mine Road 

Burnsville, NC 28714 

(828) 675-9045 

gms@alpinegeophysics.com

Key UCR CE-CERT Participants 

Zion Wang UC Riverside 

CE-CERT 

1084 Columbia Avenue 

Riverside, CA 92507 

(951) 781-5655 

zsw@cert.ucr.edu

Chao-Jung Chien UC Riverside (951) 781-5666 

chien@cert.ucr.edu

Glen Kaukola UC Riverside (951) 781-5630 

glen@cert.ucr.edu

Appendix C.2 - 39
Quality Assurance Project Plan (Draft) Page 35 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

3.1.1 ENVIRON Project Manager and Co-Principal Investigator 

Mr. Ralph Morris of ENVIRON is the Project Manager (PM) and Co-Principal Investigator (CoPI) for the VISTAS Emissions and Air Quality Modeling Team. He provides overall direction to 

the project and establishes a policy relationship with the sponsor, ensuring that all issues of 

importance to the VISTAS TAWG are addressed. The PM is responsible for the overall conduct 

of the project, experimental design, reporting of the results, and interacting with the client, 

consultants, and project staff. The specific responsibilities of the PM include, but are not 

necessarily limited to, the following: 

• Directs and coordinates the activities of the project team and computer facilities to 

conduct the test program 

• Ensures that this QAPP and the Modeling Protocol are followed during the course of the 

project

• Guides the overall approach for performing modeling evaluations

• Keeps current on project status and delivers progress reports 

• Conducts initial modeling or analysis of experiments to determine if inconsistencies or 

unexpected results suggest possible experimental or measurement problems 

• Evaluates overall data quality, characterization results, and overall system performance 

with regard to meeting project objectives 

• Reviews and delivers modeling and assessment reports 

• Interacts with external scientific reviewers, collaborators and other external groups in 

their area of expertise in the development of study priorities, reporting of results, and 

obtaining external input 

• Oversees the project team in responding to any issues raised in assessment reports and 

initiates corrective actions as necessary 

• Serve as ENVIRON’s primary point of contact for contract issues 

• Establishes a project budget and monitors the effort to ensure that budget is not exceeded

• Establishes a Subcontracts with Alpine and UCR to perform the work, and adhere to the 

terms and conditions of that contract 

• Assists in the performance of the modeling program in accordance with its contract and 

the Work Plan 

• Provides information to assist the VISTAS TAWG in achieving its goals as stated in its 

Work Plan and Strategic Plan 

• Develops individual test protocols and reports as directed 

• Analyzes modeling data and provides assessment reports 

• Supports the Principal Investigator and VISTAS in responding to any issues raised in 

assessment reports 

3.1.2 ENVIRON, Alpine and UCR Co-Principal Investigators 

The three Co-Principal Investigators of Ralph Morris, T.W. Tesche and Gail Tonnesen perform 

the following functions: 

• Directs and coordinates the day-to-day project activities of the project team and computer 

facilities to conduct the test program 

Appendix C.2 - 40
Quality Assurance Project Plan (Draft) Page 36 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

• Ensures that this QAPP and Modeling Protocol are followed during the course of the 

project

• Manages the activities in each of the three modeling centers

• Direct supervises personnel working on this project 

• Guides the approach for performing modeling evaluations following the direction of the 

Project Manager

• Keeps current on project status and delivers information to Project Manager for progress 

reports 

• Conducts initial modeling or analysis of experiments to determine if inconsistencies or 

unexpected results suggest possible experimental or measurement problems 

• Evaluates overall data quality, characterization results, and overall system performance 

with regard to meeting project objectives 

• Reviews and delivers data and sections for integration into modeling and assessment 

reports 

• With the Project Manager, interacts with external scientific reviewers, collaborators and 

other external groups in their area of expertise in the development of study priorities, 

reporting of results, and obtaining external input 

• Oversees the project team in each modeling center responding to any issues raised in 

assessment reports and initiates corrective actions as necessary with the Project Manager 

• Monitors the effort to ensure that budget is not exceeded

• Assists in the performance of the modeling program in accordance with its contract and 

the Work Plan 

• Develops individual test protocols and reports as directed 

• Analyzes modeling data and provides assessment reports 

3.1.3 VISTAS Contracting Officer 

The VISTAS Contracting Officer (Patricia Brewer) serves as the primary contact between the 

Emissions and Air Quality Modeling Team and VISTAS and performs the following functions: 

• Provides day-to-day oversight of VISTAS Phase II Emissions and Air Quality Modeling 

Team activities 

• Works with the Project Manager, Co-Principal Investigators, TAWG, States, Tribes 

oversight groups, collaborators, Stakeholders, etc. in assuring that the interests and 

concerns of all of the VISTAS participants are appropriately represented as project 

priorities are developed or modified due to external input 

• Assists in organizing and conducting meetings, conference calls, and workshops where 

this and related projects are discussed 

3.1.4 VISTAS Technical Contact 

The VISTAS Technical Contact (James Boylan) for the Emissions and Air Quality Modeling 

Team works with the VISTAS Contacting Officer in the day-to-day oversight and management 

of the modeling analysis: 

Appendix C.2 - 41
Quality Assurance Project Plan (Draft) Page 37 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

• Provides day-to-day oversight of VISTAS Phase II Emissions and Air Quality Modeling 

Team activities 

• Works with the VISTAS Contracting Officer, Project Manager, and Co-Principal 

Investigators to assure that the study is being carried out in a technically correct fashion 

following the QAPP and Modeling Protocol 

• Prepares and gives presentations to VISTAS groups on the activities of the Modeling 

team. 

3.1.5 VISTAS Technical Analysis Workgroup (TAWG) 

The Technical Analysis Workgroup is responsible for overseeing the regional haze and fine 

particulate modeling that will be required for the State Implementation Plans (SIP's). This 

workgroup provides both emissions inventory and modeling technical support to VISTAS. 

Emissions Inventory efforts include the development of emissions inventories and forecasts to be 

utilized in VISTAS modeling efforts. Modeling efforts will include identification, evaluation, 

and application of air quality modeling tools (including meteorological and air quality models) to 

quantify the effects of emission management options upon air quality in Class I areas in the 

VISTAS region. Specific activities of the TAWG include:

• Oversees the activities of the VISTAS Emissions and Air Quality Modeling Team 

through the Contracting Officer, conference calls, and periodic in-person meetings and 

workshops 

• Provides the Contracting Officer, technical Contact, Project Manager and Co-Principal 

Investigators input on the research plans and their ability to meet the needs of the various 

stakeholders relevant to the overall objectives of the project 

• Provides input as needed to assure that the project has effective and appropriate peer 

review 

• Makes the Project Manager and Co-Principal Investigators aware of other projects that 

may be of relevance to this project 

• Reviews the QAPP and conducts critical project reviews 

3.2 Project Schedule and Execution 

The schedule for each of the VISTAS Phase I and II Tasks are presented at the end of each Task 

Description in Sections 2.4 and 2.5. 

3.3 Personnel Qualifications and Training 

General education of all project personnel lays the foundation for successful project 

implementation. It is not intended to provide detailed and specific knowledge of all components 

of the project, but it promotes an understanding of the nature of the overall project goals, 

ensuring that all personnel understand the part they are to play in the project. The members of 

this project team include resident experts in emissions, meteorological and air quality model 

development and operations. 

Appendix C.2 - 42
Quality Assurance Project Plan (Draft) Page 38 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

All project personnel must have extensive experience in their particular disciplines. Each team 

member must be familiar with the content of this QAPP and all documents presented in Section 

8.0, thus obtaining a project overview, including information on all functions of the modeling 

systems, from experimental design, objectives, and data validation and reporting. Where 

applicable, project personnel must be familiar with the SOPs applicable to their areas of 

responsibility. In addition, if major revisions or enhancements are made to the QAPP and/or 

SOPs, all affected individuals must review those revisions at that time. 

3.4 Communications Plan 

The VISTAS Emissions and Air Quality Modeling Team members, other VISTAS Contractors 

and VISTAS representatives are linked by e-mail correspondence, and also use this as a means to 

communicate and exchange data, either as e-mail attachments, website or by network-accessible 

files. A considerable amount of information is exchanged by e-mail within this project. The 

VISTAS Modeling Team maintains four listservs to distribute information to different VISTAS 

groups as indicated in Table 3-2. 

Table 3-2. VISTAS listservs maintained by the Emissions and Air Quality Modeling Team. 

Listserv Purpose 

Vistas-all@cert.ucr.edu Contacts all participants including Modeling Team, VISTAS 

TAWG and Stakeholders 

Vistas-modeling@cert.ucr.edu Contacts Modeling team and VISTAS TAWG Modeling 

Contacts 

Vistas-emissions@cert.ucr.edu Contacts emissions staff in the Modeling team and emissions 

people in the VISTAS TAWG 

Vistas-met@cert.ucr.edu Contacts meteorology staff in the Modeling team and 

meteorology people in the VISTAS TAWG 

The Modeling Team members and VISTAS TAWG hold periodic conference calls and meetings 

to report results, discuss project status, and modify work plans as necessary. Unscheduled 

meetings or conference calls are also held concerning specific issues as the needs arise. In 

addition, periodic project meetings and conference calls are held. In these meetings detailed 

technical information is exchanged, project status is discussed, and project direction is assessed. 

Written progress reports on the VISTAS Emissions and Air Quality Modeling Team activities 

are submitted to the VISTAS Contracting Officer on a monthly basis. These reports summarize 

project progress, results to date, problems encountered and necessary action items, and plans for 

the upcoming reporting period. 

All modeling results, quality assurance reports, and related documents are posted on the project 

web site, as described in Section 3.5. 

Appendix C.2 - 43
Quality Assurance Project Plan (Draft) Page 39 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

3.5 Documentation and Records 

After the project tasks in Sections 2.4 and 2.5 that require deliverables are completed, the 

ensuing documents are posted on the VISTAS Modeling Phase I and II project websites at: 

http://pah.cert.ucr.edu/vistas/

http://pah.cert.ucr.edu/vistas/vistas2/

In addition, during the project, VISTAS is provided updates by e-mail or telephone. 

Document control is the system that ensures that only the latest revisions of the defined 

documents are used by the Modeling Team personnel engaging in project activities. The system 

includes retention of the document with original signed page(s) in a limited access storage area, a 

unique numbering system for all documents (typically identified by revision number and/or 

date), and electronic storage of documents by date so that the latest versions is clearly 

identifiable. Such documents are controlled documents, and can be revised only by the 

personnel listed within each document or the project quality document. The following is a typical 

list of the controlled documents within the project folder: 

1. The quality documents for the project such as the Quality Management Plan, Quality 

Assurance Project Plan. 

2. All applicable and referenced or attached Standard Operating Procedures and/or 

Methods. 

3. Project proposals, contracts, Work Plans, experimental designs, software documentation, 

and/or similar documents. 

4.0 MEASUREMENT AND DATA ACQUISITION 

4.1 Computer Hardware/Systems Administration 

All emissions, meteorology and air quality modeling is performed on computer equipment 

located at either the ENVIRON, Alpine or UCR modeling centers. 

4.1.1 ENVIRON Modeling Center Hardware 

The computing facilities at the ENVIRON Novato, CA office are built on current state-of-the-art 

hardware and software. The networked configuration of personal computers, workstations and 

printers includes Linux and Window PCs, SGI, SUN and DEC Unix workstations and a Linux 

Cluster all connected by a fast network with disk access to RAID systems. The ENVIRON 

computer center includes the very latest computing technology including both OMP (shared 

memory) and MPI (cluster) multi-processing capability. All staff also have their own state-ofAppendix C.2 - 44
Quality Assurance Project Plan (Draft) Page 40 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

the-art PCs and have access to all workstations at all times, there are no problems with computer 

resource availability. ENVIRON’s high speed Linux and UNIX computing environment includes 

workstations from three top suppliers, Sun, Digital Equipment Corporation (DEC) and Silicon 

Graphics Incorporated (SGI). ENVIRON also uses Linux PC workstations with several different 

distributions of the Linux OS (e.g., Red Hat, Debian, Mandrake) and these exceed the 

performance of fast UNIX workstations. Using workstations from several suppliers allows us to 

develop and test model codes on multiple computer platforms and means that we are experienced 

with most of the workstations used by our clients. The latest addition to the ENVIRON 

computing facilities is a 16 node Linux cluster using the Athlon MP2200 chip set with gigabit 

Ethernet that is configured as two 8 node MPI multiprocessing platforms. 

4.1.2 Alpine Geophysics Modeling Center Hardware 

Alpine Geophysics' computing facilities consist of SUN Microsystems SPARCstation computers 

and a very powerful array 10 multiprocessor Linux-based workstations. The aggregate network 

has over 7.3 Gbytes of memory and 2500 Gbytes of aggregate disk space with over 2000 Gbytes 

of SCSI and IDE Raid-5 protected space. All client data is stored on at least one RAID-5 

protected disk array. To further protect client data, two of our main servers backup their disk 

drives on a weekly basis to a second server that is physically disconnected from the power 

supply when not doing an active transfer. This way a catastrophic power failure will not 

compromise the ability for Alpine Geophysics to deliver. 

To efficiently share network resources, 100-BaseT fast ethernet switches interconnect the 

computers within each office. Additionally, the Arvada based computers have both the Parallel 

Virtual Machine (PVM) software package for computation on multiple nodes on the network and 

Open MP capabilities for shared memory multiprocessing within each computer. For the 

majority of model simulations, using a job level parallelization, where individual periods of a 

simulation are put onto each computational node, maximizes network throughput. However, the 

computational network also has the ability to share the multi-Gbyte memory and 20 processors 

on a single MM5 model simulation. 

A key feature of the AG computer network is the ability for AG to add computational resources 

quickly and cost effectively. Alpine scientists have been using Linux and Unix for 

meteorological and air quality modeling for over 16 years. This knowledge base, along with 

existing relationships with hardware vendors, software vendors, and system specialists, enable 

AG to meet the computational requirements of the VISTAS modeling study. 

4.1.3 UCR Modeling Center Hardware

The UCR computer laboratory is designed to process large data sets for air quality modeling. It 

includes 30 high-performance, dual CPU Linux workstations configured as several small Linux 

clusters on a private network to facilitate parallel simulations. These systems include a 24 CPU 

Athlon 2000MP cluster, an 8 CPU Xeon 2.2GHz cluster and an 8 CPU 64-bit Opteron 2GHz 

cluster. The data storage system includes over 23 TB of disk space configured as RAID5 disk 

systems. All computers and disk systems are networked using high speed Gigabit Ethernet for 

efficient simulation and analysis of large datasets. To provide maximum data security the 

Appendix C.2 - 45
Quality Assurance Project Plan (Draft) Page 41 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

systems are located behind the UCR firewall and an additional firewall is used internally within 

the laboratory so that only project team members have access to project computers and data. 

Data are also routinely transferred from the UCR systems to other organizations using a variety 

of tape formats and portable hard drives. The data backup/archiving system include 8mm tape 

drives and DLT and Super DLT auto loading cartridge system capable of performing unattended 

archive/backups of over 1 TB (uncompressed). Key disk systems have hot-swappable hard drives 

with stand-by spare drives and redundant power supplies. The compute clusters and disk systems 

are located in a locked, secure room with a dedicated climate control system and with backup air 

conditioning. UCR also uses the computer laboratory for air pollution modeling classes for 

graduate students and for professional staff from State and Tribal air pollution agencies. The 

laboratory has a full time systems administrator to perform system backups, maintenance and 

updates and Dr. Tonnesen’s group includes a second full time systems administrator. 

4.1.4 Backup Procedures 

Different back-up procedures are applied to three different sets of computers that include (1) file 

servers; (2) user desktop Windows PCs; and (3) RAID5 disks storage systems. Several different 

File servers are used to host systems and user information, websites and ftp sites. 

1. Each server receives a full Level 0 backup at least once every 14 days, and an 

incremental backup at least three times per week to an independent computer. In addition, 

incremental backups are periodically made to tape. 

2. Windows based PC’s are used to for editing project documents and reports. Each PC on 

the LAN receives a full Level 0 backup at least once every 14 days and incremental 

backups every three days. 

3. Most of the project data are stored on RAID5 disk systems. Because of the large volume 

of data (over 23 TB) it cannot be routinely backed up. Moreover, most of the project data 

are output from model simulations, which can be regenerated more quickly by re-running 

the models than by restoring from tape. Therefore, only critical model input data are 

backed-up. One 2 TB RAID5 disk system is reserved for back up of critical project data. 

Back-ups are performed weekly. In addition, critical project input data is archived to IDE 

drives, firewire drives or DLT tape. 

All incoming electronic mail receives virus scanning using commercial software (Norton or 

McAffee Anti-Virus), which is updated routinely. Windows PC receives automated, weekly 

scans for viruses. 

Three types of software are used in the project: (1) commercial software for word processing, 

project management, communications, and commercial software compilers; (2) compilers and 

computer operating systems publicly available through the GNU Public License (GPL) 

distribution channels; and (3) custom software used in computer simulation modeling and data 

analysis. All commercial software used in the VISTAS modeling is purchased with licenses and 

is installed and tested as specified by the publisher. Commercial compilers include Portland 

Appendix C.2 - 46
Quality Assurance Project Plan (Draft) Page 42 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

Group compilers, and Intel and IBM FORTRAN compilers. All GPL software is obtained from 

official distribution centers, such as Redhat, and are regularly maintained and updated with each 

official release from the code developers. Custom software is developed by UCR, EPA and other 

researchers using commercial and GPL compilers for FORTRAN, C and C++. 

4.2 Sources for Data Used in Modeling 

Most of the data used in the VISTAS Emissions and Air Quality Modeling are provided by other 

VISTAS contractors with the data subjected to quality assurance and quality control (QA/QC) 

prior to delivery to the Modeling team. In addition the Modeling Team have formed data 

“Gatekeeper” functions to further QA/QC provided to the Modeling Team prior to its use. 

Below we discuss the data used in the modeling and the function of the Gatekeeper roles, which 

are described in detail in Section 2.2.2.1: 

Air Quality Gatekeeper: The Air Quality Gatekeeper downloads air quality data from the 

VIEWS, SEARCH and AIRS websites and subjects it to QA/QC. The data are 

reformatted and processed for use in the modeling. 

Meteorological Gatekeeper: The Meteorological Gatekeeper evaluates the MM5 data 

provided by the VISTAS Meteorological Modeling Contractor (BAMS), subjects it to 

QA/QC and processes it for input to the CMAQ/CAMx air quality models. 

Emissions Gatekeeper: The Emissions Gatekeeper receives emissions data from the 

VISTAS Emissions Contractor (MACTEC), subjects them to a comprehensive QA/QC 

and rejects data that doesn’t pass the QA/QC and reformats the data for input into the 

SMOKE emissions model. 

Data Management Gatekeeper: The Data Management Gatekeeper maintains the project 

website, keeps back ups of data, responds to data requests and updates reports and files 

on the website. 

5.0 EMISSIONS MODELING 

The project objective is to integrate mezoscale emissions and transport modeling efforts so that 

predictions of regional haze in Class I areas can be performed under different emissions and 

meteorological transport scenarios. Meeting this objective means that modeling outputs must be 

of known quality. This section addresses emissions modeling and Section 6.0 addresses 

meteorological modeling as they are applied to this project. 

The VISTAS Modeling Team uses the Sparse Matrix Operator Kernel Emissions (SMOKE) 

emissions model to model the anthropogenic and biogenic gas and particulate matter (PM) 

emissions needed for regional haze modeling. A detailed quality assurance protocol for utilizing 

SMOKE has been prepared as part of the Phase II Modeling Protocol (ENVIRON, 2004a) and is 

summarized in this section. 

Appendix C.2 - 47
Quality Assurance Project Plan (Draft) Page 43 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

The purpose of SMOKE is to convert the resolution of the emission inventory data to the 

resolution needed by an air quality model. Emission inventories are typically available with an 

annual total emissions value for each emissions source, or perhaps with an average-day 

emissions value. The air quality models, however, typically require emissions data on an hourly 

basis, for each model grid cell (and perhaps model layer), and for each model species. 

Consequently, emissions processing for this project involve transformation of emission inventory 

data by temporal allocation, chemical speciation, spatial allocation, and layer assignment, to 

achieve the input requirements of the air quality model. 

SMOKE formulates emissions modeling in terms of sparse matrix operations. Figure 5-1 shows 

an example of how the matrix approach organizes the emissions processing steps for 

anthropogenic emissions, with the final step in creating the model-ready emissions being the 

merge step. This example does not include all processing steps, which can be different for each 

source category in SMOKE, but does include the major processing steps listed above, except the 

layer assignment. Specifically, the inventory emissions are arranged as a vector of emissions, 

with associated vectors that include characteristics about the sources such as it’s state and county 

(SCC). SMOKE also creates matrices that will apply the gridding, speciation, and temporal 

factors to the vector of emissions. In many cases, these matrices are independent from one 

another, and can therefore be generated in parallel. The processing approach ends with the merge 

step, which combines the inventory emissions vector (now an hourly inventory file) with the 

control, speciation, and gridding matrices to create model-ready emissions. 

Merge Import

Inventory

Temporal

Allocation

Speciation

Gridding

Inventory

Vectors

Controls

Hourly

Emissions

Speciation

Matrix

Gridding

Matrix

Control

Matrix

Model-ready

Emissions

Program File Shows input or output

Merge Import

Inventory

Temporal

Allocation

Speciation

Gridding

Inventory

Vectors

Controls

Hourly

Emissions

Speciation

Matrix

Gridding

Matrix

Control

Matrix

Model-ready

Emissions

Program File Shows input or output

Figure 5-1. Flow Diagram of Major SMOKE Processing Steps.

Appendix C.2 - 48
Quality Assurance Project Plan (Draft) Page 44 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

5.1 Quality Assurance Components of Emissions Modeling 

The quality assurance (QA) steps for the emissions modeling process has been divided into the 

four major classifications defined in the sections below. 

5.1.1 Modeling QA 

Modeling QA involves performing data quality checks, assuring simulation accuracy, and 

recognizing and identifying problems as they happen; it is the process of looking for glaring 

faults in the model input and output data (I/O) and determining whether the input data are 

producing the desired results. Scrutiny of the I/O using standard statistical analyses can reveal 

problems in the data and/or the model setup. Using a standard approach for analyzing emissions 

model I/O establishes reference points to use when scrutinizing the data. Seeking these indicators 

of correct model performance allows project personnel to determine the accuracy of the 

simulations and whether faults in the data or model configuration exist. 

5.1.2 System QA 

System QA addresses model installation and configuration issues, data accounting, and ensures 

that the modeling systems are producing results that are reasonable and reproducible. The first 

step in this process is to properly benchmark the model and assuring that the installation is 

complete. Confirmation of configuration settings, compile options, and other system-related 

parameters must then occur and be documented prior to producing any model results. Archiving 

the model installation at set “freeze points” in the project is also required in order to keep 

accurate records of the modeling installation and run scripts. A key feature of system QA is 

facilitating the reproduction of model results in the future and the ability to revert back to a 

previous configuration or installation after the model has been revised or updated. In addition to 

thorough documentation, version control software is required for archiving model executables, 

run and configuration scripts, and important data files. Combining documentation of the 

modeling procedures with archives of the model installation and data files will ensure that the 

model installation and configuration are correct and that past simulations are sufficiently documented and archived to allow their reproduction. 

5.1.3 Gatekeeping and Outside Review 

Gatekeeping and outside review is the process of ensuring that the data entering and exiting the 

SMOKE modeling process meet a predetermined quality level. A gatekeeper screens model data 

before they pass from one major step of the modeling process to the next. In emissions QA, 

gatekeeping is applied to the emissions inventory and SMOKE input files on the front end of the 

modeling process, and to the SMOKE output files at the back end. A gatekeeper (or gatekeeping 

team) is responsible for performing a series of reasonableness checks on both the input and 

output data streams. Outside reviewers are emissions experts who are not part of the VISTAS 

Modeling Team. They periodically review the entire process—the emissions data, the modeling, 

Appendix C.2 - 49
Quality Assurance Project Plan (Draft) Page 45 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

and the QA steps taken—using their judgment as experts to decide what to review and how to 

review it. 

5.1.4 Documentation 

Documentation, a component that is common to all of the other three QA classifications, 

provides the record of the QA process. Establishing a detailed set of requirements for documenting every step in the QA process will ensure not only that the documentation is created as 

expected but that the processes recorded by the documentation are completed correctly. In addition to records or lists of completed QA steps, documentation refers to summaries and interpretations of emissions inventory reports and analyses. Covering the entire realm of the modeling 

process, QA documentation will include records of model configuration, details about data files, 

simulation records, and final report generation. 

5.2 Implementation of the QA System 

5.2.1 The Emissions QA Team 

The level of effort required to implement the VISTAS Emissions QA framework requires a team 

consisting of: a data gatekeeper(s), a production modeler(s), a QA manager, outside reviewers, 

and a project manager (See Section 2.2.2.5 and Figure 2-1 for data flow and QA overview). Each 

team member contributes a different critical perspective on the data and modeling. 

• The Gatekeeper (or gatekeeping team) is responsible for reviewing the SMOKE I/O data 

streams for correctness. Before new datasets are used in SMOKE modeling, or new SMOKE 

output emissions datasets are used in air quality modeling, they must be reviewed by the 

gatekeeper. For all SMOKE input and output files, the gatekeeper will ensure that the data 

are complete, are formatted correctly, and pass reasonableness checks. Checking 

completeness entails examining the files for the necessary data elements, spatial coverage, 

and temporal extent. Data formats will be confirmed using the SMOKE manual to check 

ASCII files and using PAVE to check binary netCDF files, such as the meteorology inputs. 

Reasonableness checks consist of looking for glaring errors in the file contents and ensuring 

that the data make sense in the context of how they will be used and relative to similar or 

reference datasets. Issues that arise during the gate keeping process are reported to the project 

manager for resolution. 

• The Production Modeler is responsible for receiving input data, maintaining the model run 

scripts, running the model per the work plan, producing default QA reports, delivering model 

output data, and assisting with compiling QA reports into summaries for documentation 

purposes. A Lead Modeler oversees the entire modeling process, performs the majority of the 

SMOKE modeling, and receives and archives input and output data. Secondary Modelers

organize the SMOKE QA reports into emissions summaries for data QA and reporting, and 

generate custom QA summaries and reports for troubleshooting any problems encountered 

during the modeling process. 

Appendix C.2 - 50
Quality Assurance Project Plan (Draft) Page 46 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 12, 2004 

• The QA Manager performs and documents all of the checks required for determining model 

accuracy and revealing errors. The QA Manager also ensures that the software is configured 

correctly and that the data and model are being archived consistently and correctly. 

Overseeing the production modelers, the QA Manager verifies that SMOKE is being applied 

correctly and that all QA summaries are consistent with the relevant input data. Leading the 

documentation efforts, the QA Manager ensures that all the necessary QA summaries are 

generated and certified and that they are compiled into the project report. 

• The Project Manager is ultimately responsible for the quality of the final products of the 

modeling process. Providing technical assistance to the production modelers and clarifying 

any uncertainties about model input, configuration, and operation for the QA Manager, the 

Project Manager addresses any questions in the modeling process. Working with the QA 

Manager, the Project Manager approves the results of all QA procedures, and thoroughly 

scrutinizes the QA summaries for problems to determine whether the data are ready to be 

sent to the gatekeepers and outside reviewers for final review before delivery to the air 

quality modelers. For the VISTAS work, the Project Manager is the liaison between the 

emissions modeling team and the VISTAS TAWG and in this role communicates any issues 

raised during the emissions QA process. 

Figure 5-2 presents the QA framework developed by the VISTAS Modeling Team for SMOKE 

modeling. Identifying the specific participants in the VISTAS Modeling Team for performing all 

of the tasks in the framework is the first step of the QA process for each new emissions modeling 

scenario. Two Production Modelers are shown in the diagram, with the Lead Modeler 

performing the SMOKE simulations and receiving the input data and the Secondary Modeler 

compiling the output of the SMOKE QA programs into the QA products for evaluating the 

quality of the simulations. Gatekeepers are positioned in the SMOKE input and output data 

streams to screen the data before they are used in either SMOKE or CMAQ modeling, 

respectively. Reviewers are solicited from outside the emissions modeling team on a volunteer 

basis to conduct periodic reviews/audits of the data and modeling process. 

Appendix C.2 - 51
Quality Assurance Project Plan (Draft) Page 47 of 67 

VISTAS Emissions and Air Quality Modeling Revision 0 ENVIRON International Corporation November 8, 2004 

Figure 5-2. Diagram of VISTAS Modeling Team Approach to SMOKE Modeling.

VISTAS TAWG

VISTAS

Modeling Team

VISTAS 

Appendix C.2 - 52
Quality Assurance Project Plan (Draft) Page 48 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

6.0 METEOROLOGICAL MODELING 

The EPA Models-3/CMAQ system is the primary regional ozone and particulate matter (PM) air 

quality model being used in VISTAS modeling. Meteorological inputs for CMAQ are being 

generated by the VISTAS Meteorological Modeling Contractor using the MM5 meteorological 

model. The model will be applied for the entire year of 2002 on two grids: a continental scale 

domain with 36 km grid spacing and a regional-scale domain with 12 km grid spacing covering 

the eastern United States. The CMAQ model requires inputs of three-dimensional gridded wind, 

temperature, humidity, cloud/precipitation, and boundary layer parameters. The current version 

of CMAQ can only utilize output fields from the Fifth Generation Mesoscale Model (MM5), 

developed and maintained by the Pennsylvania State University and National Center for 

Atmospheric Research (PSU/NCAR). MM5 is being used to develop hourly meteorological 

fields on the 36 km and 12 km grids. 

A detailed protocol for utilizing MM5 as part of VISTAS has been prepared. The procedures 

used for applying MM5 for VISTAS are based on an extensive evaluation of MM5 and a series 

of sensitivity tests. The MM5 protocol contains a detailed description of MM5, the VISTAS 

modeling domain, the MM5 physical configuration, and a model application approach. The 

protocol also presents a plan for evaluating the performance of the model in replicating the 

evolution of observed winds, temperature, humidity, and boundary layer morphology to the 

extent that resources and data availability allow; this will serve as the primary approach to assess 

the reliability of the meteorological fields to adequately characterize the state of the atmosphere 

for input to CMAQ. Details on the VISTAS MM5 modeling can be found on the VISTS 

Meteorological Modeling website: 

http://www.baronams.com/projects/VISTAS/

MM5 is an atmosphere model that has proven useful for air quality applications and has been 

used extensively in past local, state, regional, and national modeling efforts. MM5 has undergone 

extensive peer-review, with all of its components continually undergoing development and 

scrutiny by the modeling community. MM5 is the most widely used public-domain prognostic 

model. In-depth descriptions of MM5 can be found in Dudhia (1993) and Grell et al. (1994), and 

at the following web site: 

 http://www.mmm.ucar.edu/mm5. 

7.0 CMAQ MODELING SYSTEM 

EPA’s Models-3 CMAQ modeling system is the primary air quality modeling system used in the 

VISTAS Emissions and Air Quality Modeling activities. 

Appendix C.2 - 53
Quality Assurance Project Plan (Draft) Page 49 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

7.1 CMAQ Overview 

For more than a decade, EPA has been developing the Models-3 Community Multiscale Air 

Quality (CMAQ) modeling system with the overarching aim of producing a ‘One-Atmosphere’ 

air quality modeling system capable of addressing ozone, particulate matter (PM), visibility and 

acid deposition within a common platform (Dennis, et al., 1996; Byun et al., 1998a; Byun and 

Ching, 1999, Pleim et al., 2003). The original justification for the Models-3 development 

emerged from the challenges posed by the 1990 Clean Air Act Amendments and EPA’s desire to 

develop an advanced modeling framework for ‘holistic’ environmental modeling utilizing stateof-science representations of atmospheric processes in a high performance computing 

environment (Ching, et al., 1998). EPA completed the initial stage of development with Models3 and released the Community Multi-Scale Air Quality model (CMAQ) in mid-1999 as the initial 

operating science model under the Models-3 framework (Byun et al., 1998b). The most recent 

rendition is CMAQ version 4.4, publicly released October 2004 and is the version that will be 

used in the VISTAS Phase II Revised 2002 Base Case modeling (Although the Phase I modeling 

runs used CMAQ version 4.3). 

CMAQ consists of a core Chemical Transport Model (CTM) and several pre-processors 

including the Meteorological-Chemistry Interface Processor (MCIP), initial and boundary 

conditions processors (ICON and BCON) and a photolysis rates processor (JPROC). EPA is 

continuing to improve and develop new modules for the CMAQ model and typically provides a 

new release each year. In the past EPA has also provides patches for CMAQ as errors are 

discovered and corrected. More recently EPA has funded the Community Modeling and 

Analysis Systems (CMAS) center to support the coordination, update and distribution of the 

Models-3 system. 

A number of features in CMAQ’s theoretical formulation and technical implementation make the 

model well-suited for annual PM modeling. In CMAQ, the modal approach has been adapted to 

dynamically represent the PM size distribution using three log-normal modes (2 fine and 1 

coarse). Transfer of mass between the aerosol and gas phases is assumed to be in equilibrium 

and all secondary aerosols (sulfate, nitrate, SOA) is assumed to be in the fine modes. The 

thermodynamics of inorganic aerosol composition are treated using the ISORROPIA module. 

Aerosol composition is coupled to mass transfer between the aerosol and gas phases. For 

aqueous phase chemistry, the RADM model is currently employed. This scheme includes 

oxidation of SO2 to sulfate by ozone, hydrogen peroxide, oxygen catalyzed by metals and 

radicals. The impact of clouds on the PM size distribution is treated empirically. For wet 

deposition processes, CMAQ uses the RADM/RPM approach. Particle dry deposition is 

included as well. CMAQ contains three options for treating secondary organic aerosol (SOA), 

latest being the Secondary Organic Aerosol Model (SORGAM) that was updated in August 2003 

to be an reversible semi-volatile scheme whereby VOCs can be converted to condensable gases 

that can then form SOA and then evaporate back into condensable gases depending on 

atmospheric conditions. 

A description of the newest features implemented in CMAQ ver 4.4 (released October 2004) is 

available on the CMAS website (www.cmascenter.org). Many of these features are mentioned 

above; others pertain to details in the model’s chemistry, transport, computer implementation, 

Appendix C.2 - 54
Quality Assurance Project Plan (Draft) Page 50 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

and model operation. For the VISTAS Phase I modeling and the Phase II Initial 2002 CMAQ 

run version 4.3 (released August 2003) was used, whereas for the Phase II Task 7 CB4/SAPRC 

sensitivity tests and Phase II Revised 2002 CMAQ runs Version 4.4beta (released March 2004) 

and 4.4, respectively, were used. 

7.2 CMAQ Configuration for Phase II Modeling 

One of the principal accomplishments in the Phase I modeling was the identification and 

justification of the CMAQ science options recommended for Phase II modeling. We 

summarized the Phase I findings briefly in the introduction. In this section we briefly identify 

the main science options we recommend for annual PM modeling with CMAQ, more details ate 

provided in the Modeling Protocols (ENVIRON, 2003a; 2004a). The model would be set up and 

exercised on the same nested 36/12 km grid domain used in Phase I, employing one-way grid 

nesting. That is, boundary conditions for the 12 km grid simulation are extracted from the 36 km 

run using the CMAQ BCON processor. A total of 19 vertical layers would be implemented, 

extending up to a region top of 100 mb (approximately 15 km AGL). 

The PPM advection solver would be used along with the spatially varying (Smagorinsky) 

horizontal diffusion approach and K-theory for vertical diffusion. MM5 meteorological output 

based on the Pleim-Xiu Land-Surface Model (LSM) and the ACM planetary boundary layer 

(PBL) scheme will be used and the latest CMAQ Meteorological-Chemistry Interface Processor 

(MCIP2.2 for Phase I and MCIP2.3 for Phase II) would process the MM5 data using the “pass 

through” option. The CB4 gas-phase, RADM aqueous-phase, and AERO3/ISORROPIA aerosol 

chemistry schemes are recommended for use in the initial CMAQ 2002 modeling. Treatment of 

reversible secondary organic aerosols would be simulated by the SORGAM implementation in 

CMAQ (ver 4.3). Under the Phase I modeling, VISTAS evaluated three photochemical 

mechanisms: CB4, CB4-2002 and SAPRC99. CB4-2002 produced nearly identical results as 

CB4 but took much longer to run since it is only implemented in the slower SMVGEAR 

chemistry solver, compared to CB4 that is also implemented in the faster EBI chemistry solver. 

Thus, CB4-2002 was dropped from consideration in Phase II. The Phase I comparisons of CB4 

and SAPRC99 found they produced mostly similar but different model performance. However, 

one mechanism was not performing better than the other across all species, sites and periods. 

The Phase I testing only evaluated the mechanism’s base case performance, not their response to 

emission reductions. Given that CB4 runs twice as fast as SAPRC99, for Phase II it was decided 

to perform initial 2002 CMAQ modeling using CB4 and evaluate CB4 and SAPRC99 responses 

to emission reductions using the Phase I episodes. 

7.3 Alternative Models 

EPA’s guidance on model selection for PM2.5 SIPs and Regional Haze “reasonable progress 

demonstrations” do not identify a preferred photochemical grid modeling system, recognizing 

that at present there is “no single model which has been extensively tested and shown to be 

clearly superior or easier to use than several alternatives” (EPA, 2001, pg. 169.) The agency 

recommends that models used for PM2.5 SIPS or RH reasonable progress requirements should 

Appendix C.2 - 55
Quality Assurance Project Plan (Draft) Page 51 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

meet the requirements for alternative models. The CMAQ, CMAQ-AIM and CAMx modeling 

systems all meet these requirements. 

We believe that there is potentially significant value in including an alternative regional 

modeling system or multiple systems as an adjunct to the SMOKE/MM5/CMAQ system 

proposed as the mainstay of the Phase II analyses. Our testing of the CAMx model in Phase I 

and other recent PM2.5/regional haze applications demonstrates that the model is capable of 

producing results of comparable accuracy and reliability as CMAQ, given similar effort in 

preparing model inputs, diagnosing and improving model performance and in conducting 

weight-of-evidence investigations. The Phase I testing of CMAQ-AIM model raised questions 

on whether it was performing correctly; the differences with CMAQ could not be explained 

based on their differences in formulation with CMAQ-AIM performing poorer than CMAQ. 

Accordingly, at this time we cannot recommend adopting CMAQ-AIM in Phase II and 

recommend VISTAS consider the parallel use of CAMx in the Phase II program for seven 

specific purposes: 

• Diagnosis: To serve as an efficient diagnostic tool addressing model performance 

issues that may arise in the establishment of the CMAQ annual 2002 and episodic 

base cases. CAMx’s suite of diagnostic probing tools plus it’s flexi-nesting 

algorithms make it an attractive tool for assisting in the diagnosis of CMAQ 

performance should this unexpected situation arise. 

• Model Evaluation Corroboration: To provide corroboration of the base case model 

performance evaluation exercises to be performed with CMAQ and help identify any 

compensatory errors in the MM5/SMOKE/CMAQ modeling system. 

• Emissions Control Response Corroboration: To provide corroboration of the 

response of the CMAQ modeling system to generic and specific future year emissions 

changes on modeled gas-phase and particulate aerosol concentrations and resultant 

regional haze impacts. 

• Quantification of Model Uncertainty: To provide one estimate of the range of 

uncertainty that attends statements of CMAQ model performance in the annual and 

episodic base case simulations, and in the estimate of PM2.5 and visibility reductions 

associated with future emissions change scenarios. 

• Alternative Science: CAMx contains alternative science algorithms that may 

elucidate model performance issues with CMAQ or provide an alternative approach 

for simulating aerosols. 

• Consistency with Other RPOs: The Midwest RPO (MWRPO) may end up using 

CAMx for their regional haze modeling. As sources in the MWRPO likely influence 

visibility at Class I areas in VISTAS and vice versa, having results from a common 

model would be useful for reconciling any differences. 

Appendix C.2 - 56
Quality Assurance Project Plan (Draft) Page 52 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

• Backup Contingency: To provide a ‘backstop’ model to CMAQ in the event that 

unforeseen difficulties with the primary model make it necessary to switch to an 

alternative ‘One-Atmosphere’ model at some point during Phase II. 

The benefits of employing a pair of complimentary state-of-science air quality models are thus 

quite significant and well worth considering. Especially considering that the same MM5 output 

(through MM5CAMx) and SMOKE output and CMAQ IC/BC files (through CMAQ-to-CAMx 

emissions and IC/BC converters) can be used to operate CAMx without performing any 

additional meteorological or emissions modeling. Accordingly, below we provide an overview 

of the CAMx regional photochemical/PM modeling system and the science options 

recommended for use in Phase II. 

7.3.1 CAMx Overview 

The Comprehensive Model with Extensions (CAMx) modeling system is a publicly available 

(www.camx.com) three-dimensional multi-scale photochemical/aerosol grid modeling system 

that is developed and maintained by ENVIRON International Corporation. CAMx was 

developed with all new code during the late 1990s using modern and modular coding practices. 

This has made the model an ideal platform for the extension to treat a variety of air quality issues 

including ozone, particulate matter (PM), visibility, acid deposition, and air toxics. The flexible 

CAMx framework has also made it a convenient and robust host model for the implementation 

of a variety of mass balance and sensitivity analysis techniques including Process Analysis (IRR 

and IPR), Decoupled Direct Method (DDM), and the Ozone Source Apportionment Technology 

(OSAT). Designed originally to address multiscale ozone issues from the urban- to regionalscale, CAMx has been widely used in recent years by a variety regulatory agencies for 1-hr and 

8-hr ozone SIP modeling studies. Key attributes of the CAMx model for simulating gas-phase 

chemistry include the following: 

Two-way grid nesting that supports multi-levels of fully interactive grid nesting (e.g., 

36/12/4/1.33 km). 

• CB4 or SAPRC99 Chemical Mechanisms. 

• Two chemical solvers, the CAMx Chemical Mechanism Compiler (CMC) Fast Solver 

or the highly accurate Implicit Explicit Hybrid (IEH) solver. 

• Multiple numerical algorithms for horizontal transport including the Piecewise 

Parabolic Method (PPM), Bott, and Smolarkiewicz advection solvers. 

• Subgrid-scale Plume-in-Grid (PiG) algorithm to treat the near-source plume dynamics 

and chemistry from large NOx point source plumes. 

• Ability to interface with a variety of meteorological models including the MM5 and 

RAMS prognostic hydrostatic meteorological models and the CALMET diagnostic 

meteorological model (others also compatible). 

Appendix C.2 - 57
Quality Assurance Project Plan (Draft) Page 53 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

• The Ozone Source Apportionment Technology (OSAT) ozone apportionment 

technique that identifies the ozone contribution due to geographic source regions and 

source categories (e.g., mobile, point, biogenic, etc.). 

• The Decoupled Direct Method (DDM) sensitivity method is implemented for 

emissions and IC/BC to obtain first-order sensitivity coefficients for all gas-phase 

species. 

• Treatment of particulate matter (PM) using an empirical aerosol thermodynamics 

algorithm. 

Culminating extensive model development efforts at ENVIRON and other participating groups, 

the CAMx (ver 4.3+) code was released in the autumn of 2003 as a truly “One-Atmosphere’ 

models that rigorously integrates the gas-phase ozone chemistry with the simulation of primary 

and secondary fine and course particulate aerosols. This extension of CAMx to treat PM 

involved the addition of several science modules to represent important physical processes for 

aerosols. Noteworthy among these are: 

• Two separate treatments of particulate matter (PM), Mechanism 4 (M4) “oneatmosphere” treatment uses two size sections and science modules comparable to 

CMAQ (e.g., RADM aqueous-phase chemistry and ISORROPIA equilibrium) and a 

multi-section “full-science” approach using aerosol modules developed at Carnegie 

Mellon University (CMU). 

• Size distribution is represented using the Multi-component Aerosol Dynamics Model 

(MADM), which uses a sectional approach to represent the aerosol particle size 

distribution (Pilinis et al., 2000). MADM treats the effects of 

condensation/evaporation, coagulation and nucleation upon the particle size 

distribution. 

• Inorganic aerosol thermodynamics can be represented using ISORROPIA (Nenes et 

al, 1998; 1999) equilibrium approach within MADM, or a fully dynamic or hybrid 

approach can also be used. 

• Secondary organic aerosol thermodynamics are represented using the semi-volatile 

scheme of Strader and co-workers (1999). 

• Aqueous-phase chemical reactions are modeled either using the RADM module (like 

CMAQ) or the Variable Size-Resolution Model (VRSM) of Fahey and Pandis (2001), 

which automatically determine whether water droplets can be represented by a single 

‘bulk’ droplet-size mode or whether it is necessary to use fine and coarse droplet-size 

modes to account for the different pH effects on sulfate formation. 

CAMx (ver 4.3+) provides two key options to users interested in simulating PM. For CPUefficient annual PM modeling applications, CAMx may be run using Mechanism 4 (M4) with 

only two size sections (fine and coarse) and the efficient RADM bulk aqueous-phase module (as 

Appendix C.2 - 58
Quality Assurance Project Plan (Draft) Page 54 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

used in CMAQ). Alternatively, more rigorous aerosol simulations (perhaps for shorter episode) 

may be addressed using the version that treats N-size sections (N is typically 10) and the 

rigorous, but computationally-extensive CMU multi-section aqueous-phase chemistry module. 

7.3.2 CAMx Configuration for Phase II Modeling 

We recommend exercising CAMx (ver 4.10s) as a companion model to CMAQ using as many 

similar science options and input data sets as possible. However, in some instances, the CMAQ 

and CAMx model development teams chose different options for characterizing physical and 

chemical processes, or for implementing the governing equations on modern parallel computers. 

In these cases, we will utilize the science configurations embodied in the current release of 

CAMx. At this time VISTAS has not budgeted any resources in Phase II for CAMx modeling, 

however it remains an option if desired at a later date. 

The latest version of CAMx (ver 4.10s) will be employed and the model will be set up and 

exercised on the same 36/12 km grid as CMAQ. However, CAMx would be run using two-way 

grid nesting. The base configuration of CAMx would use 19 vertical layers that exactly match 

those used by CMAQ. The PPM advection solver would be used along with the spatially 

varying (Smagorinsky) horizontal diffusion approach. Vertical diffusion in CAMx would be 

modeled by K-theory. The MM5 simulation using the Pleim-Xiu Land-Surface Model (LSM) 

and the ACM Planetary Boundary Layer (PBL) scheme would be used in the CAMx base 

configuration using the MM5CAMx processor that is similar to the CMAQ MCIP2.2 “pass 

through” option of the MM5 data invoked. CAMx would be exercised with the CB4 gas-phase, 

RADM aqueous-phase, and CMU/ISORROPIA aerosol chemistry schemes. The SOAP 

secondary organic aerosol scheme would be used for the base configuration in CAMx. 

Note that it may be desirable to exercise CAMx using its “full-science” configuration for 

selected periods to investigative scientific issues that may be of interest that can not be simulated 

by CMAQ, such as: 

• The full sectional approach could be used to determine whether allowing secondary 

PM to grow into the coarse mode affects the model estimates; 

• The model could be exercised with chemical active Sea Salt emissions, this could be 

important for fine particulate and visibility at key coastal sites in the VISTAS 

domain, especially when looking at clean days or natural background; and 

• The full sectional aqueous-phase chemistry module may be important for sulfate 

formation. 

Appendix C.2 - 59
Quality Assurance Project Plan (Draft) Page 55 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

8.0 ASSESSMENTS AND OVERSIGHT 

8.1 Assessment Responsibilities 

The primary point of contact for VISTAS Modeling project assessment is that of the Project 

Manager (PM). This PM is available to the VISTAS Contracting Officer, Technical Contact, 

TAWG, external reviewers, and internal staff by direct contact through e-mail and phone and is 

linked to each of the four VISTAS listservs (see Table 3-2). These links provide timely reviews 

of the project experimental design, implementation, and interpretation of the experimental 

results. 

The assessments of overall project quality are provided from a number of different sources. 

Internal reviews of selected project components are periodically performed by the Project 

Manager and Co-Principal Investigators. The results of this and other routine (e.g., QC checks) 

and special reviews of project data quality are documented in the monthly reports. 

The project team is committed to achieving and maintaining the highest level of quality possible 

throughout the performance of this program. The modeling information generated will be both 

technically sound, and, where appropriate, legally defensible. The former is an obvious 

requirement but is not, in and of itself, sufficient to defend the data against an adversarial 

inquiry. The latter will address, through documentation, the level of quality achieved. The 

quality of the project data will be maintained not only through the development and use of data 

quality objectives (DQOs), which place numerical limits on the quality control indicators, but 

also through the use of subjective science quality objectives. 

Science quality objectives are used to provide evaluations of the quality of the research project 

and goals of the study. Evaluations of all research activities by internal and external peer review 

will assure that the methodology, experimental processes, conclusions and recommendations 

provided by this project are scientifically sound. 

8.2 Assessment Types and Usage 

Assessments of the quality of the products generated on this project will be made by: 

• Conducting internal performance reviews of the critical components of the experimental 

setup and data processing systems. Where applicable, adherence to SOPs will be 

evaluated. The results of these reviews will contain any suggested corrective actions, and 

be appended to the reports generated in this project. 

• Independent peer reviews of thesis materials, reports, and papers resulting from this 

project. 

The VISTAS TAWG provides external review of all reports and plays an active role in the 

development of experimental matrices and to review research progress and plans for future 

project tasks. 

Appendix C.2 - 60
Quality Assurance Project Plan (Draft) Page 56 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

8.3 Assessment Criteria 

The project assessment criteria address the extent to which the modeling runs and experiments 

provide the quality of data needed to satisfy the objectives of this project. A major objective of 

this project consists of providing the data and information needed for evaluating and improving 

models for predicting the effects of emissions on air quality. Therefore, the evaluation process 

includes assessments of model uncertainties, the extent to which the proposed actions or system 

improvements can reduce these uncertainties, and estimates of the certainty of this work in 

providing the data of the type and quality needed. Criteria for assessing data utility and quality 

will include the following: 

• Utility of the type of measurements for model evaluation. For example, are model 

predictions of the measurements sensitive to the uncertainties in the mechanism that are 

being evaluated? Are the available resources being applied to the highest priority types of 

measurements? 

• Degree of characterization of experimental conditions for modeling. For data to be useful 

for model evaluation, experimental conditions must be sufficiently well characterized, so 

that the data can be used for model evaluation without characterization uncertainties 

dominating the results. 

• Accuracy, precision, and sensitivity of the measurement data. The measurements in the 

concentration region of interest should be sufficiently accurate and precise to provide a 

meaningful test of model predictions. 

• Procedures used to assure data quality, identify data not meeting quality objectives, and 

to minimize errors and other data quality problems. 

• Degree to which the modeling appropriately incorporates the characterization results in 

the inputs, and the analysis of the modeling results appropriately take into account 

characterization and measurement uncertainties and biases. 

• Degree to which the experimental procedures, measurement methods, and data 

processing and analyses, and modeling methods are documented. 

9.0 REFERENCES 

Adelman, Z. (2004) Quality Assurance Protocol: WRAP RMC Emissions Modeling with 

SMOKE, Prepared for WRAP Modeling Forum, January. 

Alpine Geophysics. 2003a. “VISTAS Emissions and Air Quality Modeling – Phase I Subtask 

3c-1 Report: MM5 Meteorology QA/QC Summary Report for Episode 1: 2-20 January 

2002.” Alpine Geophysics LLC, ENVIRON International Corporation and University of 

Appendix C.2 - 61
Quality Assurance Project Plan (Draft) Page 57 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

California at Riverside. Ft. Wright, Kentucky (available at: 

http://pah.cert.ucr.edu/vistas/docs.shtml). September 10. 

Alpine Geophysics. 2003b. “VISTAS Emissions and Air Quality Modeling – Phase I Subtask 

3c-1 Report: MM5 Meteorology QA/QC Summary Report for Episode 1: 13-22 July 

1999.” Alpine Geophysics LLC, ENVIRON International Corporation and University of 

California at Riverside. Ft. Wright, Kentucky (available at: 

http://pah.cert.ucr.edu/vistas/docs.shtml). September 15. 

Alpine Geophysics. 2003c. “VISTAS Emissions and Air Quality Modeling – Phase I Subtask 

3c-1 Report: MM5 Meteorology QA/QC Summary Report for Episode 1: 11-27 July 

2001.” Alpine Geophysics LLC, ENVIRON International Corporation and University of 

California at Riverside. Ft. Wright, Kentucky (available at: 

http://pah.cert.ucr.edu/vistas/docs.shtml). September 16. 

Alpine Geophysics. 2003d. Initial Review for 2002 Inventory Development, memorandum 

prepared by Gregory Stella, Alpine Geophysics, LLC for Pat Brewer, VISTAS, June 13, 

2003. 

ANSI/ASQC Q9000-1-1994. 1994. Quality Management and Quality Assurance Standards – 

Guidelines for Selection and Use (revisions and redesignations) of ANSI/ASQC Q90-

1987. Available at: http://webstore.ansi.org/ansidocstore/dept.asp?dept_id=50. 

Arnold, J.R., R.L. Dennis, and G.S. Tonnesen. 2003. “Diagnostic Evaluation of Numerical Air 

Quality Models with Specialized Ambient Observations: Testing the Community 

Multiscale Air Quality Modeling System (CMAQ) at Selected SOS 95 Ground Sites”, 

Atmos. Environ., Vol. 37, pp. 1185-1198. 

ARS. 2002. Air Resource Specialists, Inc. Analysis of IMPROVE and SEARCH Speciated 

PM2.5 Data. Report to VISTAS, August 28, 2002. http://www.vistas-sesarm.org. 

Boylan, J. W. 2003. “Comparisons of 36 km and 12 km Grid Resolutions”, PowerPoint 

presentation prepared for December 19, 2003 VISTAS modeling conference call. 

Available at: http://pah.cert.ucr.edu/vistas/ppt_files/12_36.ppt. 

Boylan, J. W. 2004. “Calculating Statistics: Concentration Related Performance Goals”, paper 

presented at the EPA PM Model Performance Workshop, Chapel Hill, NC. 11 February. 

Brewer, P., S. Holman and J. Hornback. 2003. “Vistas Analyses of Regional Haze in the 

Southeastern United States.” Presented at Annual Air and Waste Management 

Association Meeting and Exhibition, San Diego, CA. June. 

Byun, D.W., and J.K.S. Ching. 1999. “Science Algorithms of the EPA Models-3 Community 

Multiscale Air Quality (CMAQ) Modeling System”, EPA/600/R-99/030. 

Appendix C.2 - 62
Quality Assurance Project Plan (Draft) Page 58 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

Dudhia, J. (1993) A non-hydrostatic version of the Penn State/NCAR Mesoscale Model: 

validation tests and simulation of an Atlantic cyclone and cold front. Mon. Wea. Rev. 

121, pp.1493-1513. 

Edgerton, E. S. 2003. Sources of PM2.5 Carbon in the Southeast US, presentation at the 

MARAMA Science Meeting, Baltimore, MD, January 22, 2003. http://www.marama.org. 

Emery, C., E. Tai, and G. Yarwood. 2001. “Enhanced Meteorological Modeling and 

Performance Evaluation for Two Texas Episodes”, report to the Texas Natural Resources 

Conservation Commission, prepared by ENVIRON, International Corp, Novato, CA. 

ENVIRON. 2002. “User’s Guide Comprehensive Air Quality Model With Extensions (CAMx) 

Version 3.10.” ENVIRON International Corporation, Novato, California (available at 

www.camx.com) April. 

ENVIRON. 2003a. “VISTAS Emissions and Air Quality Modeling – Phase I Task 2 Report: 

Recommended Model Configurations and Evaluation Methodology for Phase I 

Modeling.” Prepared by ENVIRON International Corporation, Alpine Geophysics, LLC 

and University of California at Riverside. Novato, California. (available at: 

http://pah.cert.ucr.edu/vistas/docs.shtml). August 4. 

ENVIRON, Alpine Geophysics, UC Riverside and UC Davis. 2003b. “VISTAS Emissions and 

Air Quality Modeling – Phase I Task 4a/b Report: Review of Model Sensitivity 

Simulations and Recommendations of Initial CMAQ Model Configurations and 

Sensitivity Tests.” Revised Draft July 25. 

ENVIRON, Alpine Geophysics , UC Riverside and UC Davis. 2003c. “VISTAS Emissions and 

Air Quality Modeling – Phase I Task 3 Report: Review and Assessment of Available 

Ambient Air Quality Data to Support Modeling and Modeling Performance Evaluation 

for the Three VISTAS Phase I Episodes.” Revised Draft July 22. 

ENVIRON. 2003d. “Development of an Advanced Photochemical Model for Particulate 

Matter: PMCAMx.” ENVIRON International Corporation, Novato, CA. Prepared for 

Coordinating Research Council, Inc. Project A-30 (available at www.crcao.com).

ENVIRON, Alpine Geophysics, UC Riverside and UC Davis. 2004. “VISTAS Emissions and 

Air Quality Modeling — Phase I Task 6 Report: Modeling Protocol for the VISTAS 

Phase II Regional Haze Modeling.” Second Draft May 6. 

EPA. 1991. "Guidance for Regulatory Application of the Urban Airshed Model (UAM), 

"Office of Air Quality Planning and Standards, U.S. Environmental Protection Agency, 

Research Triangle Park, N.C.

EPA. 1999. “Draft Guidance on the Use of Models and Other Analyses in Attainment 

Demonstrations for the 8-hr Ozone NAAQS”. Draft (May 1999), U.S. Environmental 

Appendix C.2 - 63
Quality Assurance Project Plan (Draft) Page 59 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

Protection Agency, Office of Air Quality Planning and Standards, Research Triangle 

Park, N.C 

EPA. 2001. “Guidance for Demonstrating Attainment of Air Quality Goals for PM2.5 and 

Regional Haze”, Draft Report, U.S. Environmental Protection Agency, Research Triangle 

Park, NC. 

EPA. 2002. Guidance for Quality Assurance Project Plans for Modeling. EPA QA/G-5M. 

Washington DC. December. 

EPA. 2001. Requirements for Quality Assurance Project Plans, EPA QA/R-5. Washington DC. 

March. 

EPA. 2003a. “Guidance for Tracking Progress Under the Regional Haze Rule”, U.S. 

Environmental Protection Agency, Research Triangle Park, NC. 

EPA. 2003b. “Guidance for Estimating Natural Visibility Conditions Under the Regional Haze 

Rule”, U.S. Environmental Protection Agency, Research Triangle Park, NC. 

EPA. 2003c. National Emission Inventory QA and Augmentation Memo, prepared by Anne 

Pope, U.S. EPA, June 2003. 

http://www.epa.gov/ttn/chief/emch/invent/qaaugmementationmemo_99nei_60603.pdf

EPA. 2003d. Final Summary of the Development and Results of a Methodology for Calculating 

Area Source Emissions from Residential Fuel Combustion, prepared by Pacific 

Environmental Services, Inc. for U.S. EPA, September 2002. 

EPA. 2003e. Related Spatial Allocation Files - "New" Surrogates, U.S. EPA website updated 

August 2003. http://www.epa.gov/ttn/chief/emch/spatial/newsurrogate.html

EPA. 2003f. A Conceptual Model to Adjust Fugitive Dust Emissions to Account for Near 

Source Particle Removal in Grid Model Applications, prepared by Tom Pace, U.S. EPA, 

August 22, 2003. 

 http://www.epa.gov/ttn/chief/emch/invent/statusfugdustemissions_082203.pdf. 

Fahey, K.M., and S.N. Pandis. 2001. Optimizing model performance: variable size 

reduction in cloud chemistry modeling. Atmos. Environ. Vol. 35, pp. 4471-4478.

FLAG. 2000. Federal Land Manager’s Air Quality Related Values Workgroup (FLAG) Phase I 

Report. (http://www2.nature.nps.gov/ard/flagfiee/AL.doc). 

Grell, G.A., J. Dudhia, and D.R. Stauffer (1994) A description of the Fifth Generation Penn 

State/NCAR Mesoscale Model (MM5). NCAR Technical Note, NCAR TN-398-STR, 

138 pp. 

Appendix C.2 - 64
Quality Assurance Project Plan (Draft) Page 60 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

Hanson, D.A.; Edgerton, E.S.; Hartsell, B. E.; Jansen, J.J.; Kandasamy, K.; Blanchard, C. 

Southeastern Aerosol Research and Characterization Study (SEARCH): 1. Overview. 

Submitted to JAWM for publication. 

Malm, W.C.; Pitchford, M.L; Scruggs, M.; Sisler, J.F.; Ames, R.; Cepeland, S.; Gebhart, K.; 

Day, D.E. 2000. Spatial and Seasonal Patterns and Temporal Variability of Haze and 

Its Constituents in the United States. Report III. Cooperative Institute for Research in 

the Atmosphere, May. 

McNally, D.E., and T.W. Tesche. 1994. "MAPS2.3 User's Guide", Alpine Geophysics, LLC, 

Golden, CO. 

Morris, R.E., B. Koo, S. Lau, T.W. Tesche, D. McNally, C. Loomis, G. Stella, G. Tonnesen and 

Z. Wang. 2004. “VISTAS Emissions and Air Quality Modeling – Phase I Task 4cd 

Report: Model Performance Evaluation and Model Sensitivity Tests for Three Phase I 

Episodes”, prepared for the VISTAS Technical Analysis Committee, prepared by 

ENVIRON International Corporation, Alpine Geophysics, LLC, and the University of 

California, Riverside (CE-CERT). 

NARSTO (1999) NARSTO Quality Planning Handbook, Appendix A: Quality Integrated Work 

Plan Template for Monitoring and Measurement Research and Development Projects. 

www.cgenv.com/Narsto. 

Odman, M. T.; Boylan, J.W.; Wilkinson, J.G.; and Russell, A.G. 2002. SAMI Air Quality 

Modeling Final Report. Southern Appalachian Mountains Initiative. 

http://www.saminet.org. 

Olerud, D. 2003a. “Evaluation Methodologies for Meteorological Modeling in Support of 

VISTAS (Visibility Improvement – State and Tribal Association): Task 1 Deliverables” 

(Draft) Baron Advanced Meteorological Systems, LLC, Research Triangle Park, NC. 

(available at: http://www.baronams.com/projects/VISTAS/#reports). April 16. 

Olerud, D. T. 2003b. “Summation of Relevant MM5 Sensitivity Modeling in Support of 

VISTAS (Visibility Improvement - State and Tribal Association): VISTAS Task 2a 

Report”, Available from Mike Abraczinskas, Meteorologist, NC Division of Air Quality, 

1641 Mail Service Center, Raleigh, NC 27699-1641. 

Olerud, D. 2003c. “Protocol for Annual MM5 Modeling of VISTAS (Visibility Improvement – 

State and Tribal Association): Task 7c Deliverable.” Baron Advanced Meteorological 

Systems, LLC, Research Triangle Park, NC. (available at: 

http://www.baronams.com/projects/VISTAS/#reports). March 27. 

Olerud, D. 2003d. “MM5 Sensitivity Modeling in Support of VISTAS (Visibility Improvement 

– State and Tribal Association): Task 2e Deliverable” (Draft) Baron Advanced 

Meteorological Systems, LLC, Research Triangle Park, NC. 4 December 2003 

Appendix C.2 - 65
Quality Assurance Project Plan (Draft) Page 61 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

Olerud, D. 2003e. “VISTAS Meteorological Modeling Sensitivity Results”, PowerPoint 

presentation at the 29-30 September 2003 VISTAS Technical Review Meeting (Research 

Triangle Park, NC), prepared by Baron Advanced Meteorological Systems, LLC, 

Research Triangle Park, NC. 29 September 2003 

Olerud, D. 2003f. “Episode Selection from a Meteorological Perspective for VISTAS 

(Visibility Improvement – State and Tribal Association): Task 3a Report”, Baron 

Advanced Meteorological Systems, LLC, Research Triangle Park, NC. 

(http://www.baronams.com/projects/VISTAS/#reports).

Olerud, D. 2003g “Protocol for Annual MM5 Modeling of VISTAS (Visibility Improvement – 

State and Tribal Association): Task 7c Report.” Baron Advanced Meteorological 

Systems, LLC, Research Triangle Park, NC. 

 (http://www.baronams.com/projects/VISTAS/#reports).

Pilinis, C., K.P. Capaldo, A. Nenes, and S.N. Pandis. 2000. “MADM - A new 

multicomponent aerosol dynamics model.” Aerosol Sci. Tech., Vol. 32(5), pp. 482-

502. 2000.

Pleim, J.E. and J.S. Chang (1992) A non-local closure model for vertical mixing in the 

convective boundary layer. Atmos. Env., 26A, pp. 965-981. 

Seigneur, C., et al. 2000. “Guidance for the Performance Evaluation of Three-Dimensional Air 

Quality Modeling Systems for Particulate Matter and Visibility”, J. Air & Waste Manage. 

Assoc. Vol. 50, pp. 588-599. 

Solomon, P.S., T. Klamser-Williams, P. Egeghy, D. Crumpler and J. Rice. 2004. 

"STN/IMPROVE Comparison Study Preliminary Results”. Presented at PM Model 

Performance Workshop. Chapel Hill, NC. February 10. 

Strader, R., F.W. Lurmann and S.N. Pandis. 1999. “Evaluation of secondary organic 

aerosol formation in winter.” Atmos. Environ. Vol. 33, pp. 4849-4864.

Tesche, T. (1994) Evaluation Procedures for Regional Emissions, Meteorological, and 

Photochemical Models. Presented at the 86th Annual Meeting for the Air and Waste 

Management Association, 14-18 June, Denver, CO. 

Timin, B. 2002. “PM2.5 and Regional Haze Modeling Guidance”. Prepared by the U.S. 

EPA/OAQPS. April 24. 

Timin, B. 2004. “PM2.5 Model Performance Evaluation: Purpose and Goals”. Presented at PM 

Model Evaluation Workshop, Chapel Hill, NC. February. 

UCR/CE-CERT (2003) Quality Management Plan, Revision 2, August 8. 

Appendix C.2 - 66
Quality Assurance Project Plan (Draft) Page 62 of 62 

VISTAS Emissions and Air Quality Modeling Revision 0 

ENVIRON International Corporation November 8, 2004 

Xiu, A., and J.E. Pleim. 2000. Development of a land surface model. Part I: Application in a 

mesoscale meteorology model. Journal of Applied Meteorology, 40, 192-209. 

U.S. EPA (2002) Guidance for Quality Assurance Project Plans for Modeling. EPA QA/G-5M, 

December. 

U.S. EPA (2001) Requirements for Quality Assurance Project Plans, EPA QA/R-5, March. 

Western Regional Air Partnership (2003) Western Regional Air Partnership 2004 Work Plan, 

October. 

Western Regional Air Partnership (2003a) Strategic Plan 2003-2008 of the Western Regional Air 

Partnership, September. 

Xiu, A. and J.E. Pleim (2000) Development of a land surface model. Part I: application in a 

mesoscale meteorology model. J. App. Met., 40, pp. 192-209. 

Appendix C.2 - 67
Appendix C.3 

Secondary Organic Aerosol Module 

Modifications in CMAQ 
Appendix C.3 - 1
Appendix C.3 - 2
Appendix C.3 - 3
Appendix C.3 - 4
Appendix C.3 - 5
Appendix C.3 - 6
Appendix C.3 - 7
Appendix C.3 - 8
Appendix C.3 - 9
Appendix C.3 - 10
Appendix C.3 - 11
Appendix C.3 - 12
Appendix C.3 - 13