RELEASE NOTES for CAMx v6.11, 12/15/14

The Comprehensive Air Quality Model with extensions (CAMx) is 

available at

http://www.camx.com. 

Overview of Version 6.11

------------------------

V6.11 includes a minor modification and several bug fixes from the 

previous

release (v6.10).

* Use the chemistry parameters files specifically labeled for v6.10.

* There are no changes to I/O file formats from v6.10.

* There are no changes to the CAMx control file namelist from v6.10.

v6.11 Modifications

-------------------

1. Added a TREESUM algorithm for time-averaging concentrations.

 Implications: TREESUM improves the fidelity of single-precision 

end-of-hour

 sums used to time-average concentrations for output. 

This

 helps reduce output concentration differences between 

MPI and

 non-MPI runs.

v6.11 Bug Fixes

---------------

1. Two improvements to PiG when using MPI parallelization:

 a) Fixed MPI pass of PiG puff location data at first hour of a 

model restart.

 b) Fixed MPI pass of gridded concentration data at first hour of 

restart when

 the LVISPIG option is invoked

 Implications: Both bugs were leading to small concentration 

differences

 between MPI and non-MPI runs at each model restart.

2. Fixed an MPI bug that was not passing ozone column maps to slave 

nodes when

 a simulation crosses through midnight.
 Implications: This bug was revealed only when CAMx was run across 

midnight,

 as opposed to running CAMx from midnight to midnight 

(as is 

 usual). It led to concentration differences between 

MPI and non-MPI runs.

3. Fixed MPI bug that was passing gridded snow code only at start of 

simulation,

 not when updated hourly.

 Implications: No effect in cases where snow is absent or when snow 

cover is

 static during a single run. It led to minor 

concentration 

 differences between MPI and non-MPI runs due to 

differences in

 surface albedo and possibly dry deposition.

4. Removed reading of dummy variables in UAM-formatted input files.

 Implications: The NSEG header variable is left over from UAM and 

has never 

 been used for CAMx. The NSEG slot is now used for 

simulation

 time zone in meteorological input files, but ignored 

in other

 files (emissions, IC/BC).

5. Improved internal checks for optional plume rise/distribution 

parameters.

 Implications: A recent CAMx modification allows for point source 

plume depth

 override by setting a negative value for the timedependent 

 "flowrate" variable. SMOKE has historically set 

flowrate

 to -9 (missing value), which led to model crashes now 

that

 negative values are not ignored. This fix allows 

SMOKE files

 to continue to operate correctly while still allowing 

the

 optional plume depth override to be invoked.

6. Fixed a bug in the argument list for Zhang dry deposition routine 

when called

 from RTRAC.

 Implications: The Zhang dry deposition routine was recently updated 

to
 receive species-dependent parameters via an argument 

list, but

 this change was not carried over to RTRAC, leading to 

model

 crashes with a segmentation fault.

7. Added rounding of time stamp in met input files to handle small 

increments

 of numerical fuzz.

 Implications: Some users complained that CAMx was missing met input 

times 

 because of imprecision in the file timestamps. This 

fix

 should alleviate the problem.

8. Removed trap to stop a simulation using RTRAC with Mechanism 2 

(CB6r2).

 Implications: This left-over trap was inadvertently included in the 

last

 distribution.

======================================================================

==========

RELEASE NOTES for CAMx v6.10, 04/02/14

The Comprehensive Air Quality Model with extensions (CAMx) is 

available at

http://www.camx.com. 

Overview of Version 6.10

------------------------

V6.10 includes new features, modifications, and bug fixes from the 

previous

release (v6.00).

* Use the chemistry parameters files specifically labeled for v6.10.

* There are no changes to I/O file formats from v6.00.

* The CAMx control file namelist has changed to support certain 

modifications.

The CAMx makefile has been streamlined and updated to support a 

variety of MPI

systems. It's functionality and execution syntax has changed; see the 

README

file, User's Guide, or type "make help" or "make" for instructions.
v6.10 Major Updates and New Capabilities

----------------------------------------

1. Gas-phase chemistry mechanism 2 has been updated from CB6r1 to 

CB6r2 and

 includes the capability to run with emitted methane (ECH4).

 Implications: CB6r2 differentiates organic nitrates (ON) between 

simple 

 alkyl nitrates that remain in the gas-phase 

(providing a 

 reservoir of NO2) and multi-functional ONs that can 

partition

 into organic aerosols (OA). ON present in OA are 

then assumed

 to undergo hydrolysis to nitric acid. These changes 

tend to

 reduce regional concentrations of ozone and ON, and 

increase

 nitric acid. Regional CAMx simulations with CB6r2 

show that 

 accounting for ON hydrolysis in aerosols improved 

performance 

 for ozone and the partitioning of NOy between ON and 

nitric 

 acid. CB6r2 will run with CF or CMU aerosol 

chemistry and

 works with all Probing Tools except Process Analysis.

 ECH4 represents emitted methane over and above the 

global 

 background for methane, which continues to be set 

internally 

 at 1.75 ppm for all mechansisms. ECH4 decays by 

oxidation and

 has the same OH rate constant and products as global 

background

 methane.

2. The Plume-in-Grid (PiG) submodel has been extensively updated to 

include a

 condensed gas-phase chemical mechanism for GREASD PiG, reduced 

nocturnal 

 puff growth rates, and other minor updates to improve performance 

and

 diagnostic output.

 Implications: GREASD PiG chemistry now runs much faster. Reduced 

nocturnal

 growth rates lead to puff sizes in better agreement 

with in
 situ aircraft measurements, and prolonged puff life 

for both

 GREASD and IRON PiG. These updates can result in a 

wide range

 of ozone, precursor, and PM impacts on the grid, 

especially

 for coarser grids that allow for extended puff 

lifetimes.

3. PM-DDM has been added to the model. This change includes an update 

of 

 ISORROPIA from v1.6 to v1.7. The "short" names of DDM sensitivity 

tracers

 have been changed to accomodate 3-digit chemical species pointers.

 Implications: DDM sensitivity analysis is now available for PM. 

Only first

 order sensitivities are calculated with PM-DDM, but 

they can

 be calculated for all PM species. PM-DDM works only 

with the

 CF aerosol option. See the User's Guide for more 

information.

 The short names of DDM output sensitivities written 

to output

 files support up to 999 species, compared to 99 

species in

 previous versions.

4. The RTRAC probing tool has been expanded to allow tracers to 

directly use

 photolysis and deposition rates calculated for any core model 

species.

 Implications: This update allows RTRAC to be used to emulate any 

core

 model species. For example, RTRAC could track the 

transport

 and decay/removal of ozone boundary conditions for 

any 

 spatial stratification designed by the user. See the 

User's

 Guide to see how to use RTRAC to point to specific 

core

 species.

5. A surface model has been added that performs chemical reactions on

 deposited material and re-emits those species and chemical products 

back

 to the atmosphere.
 Implications: Heterogeneous reactions can be simulated at the 

surface and

 chemical products can be released to the air. The 

algorithm

 includes irreversible loss to soil leaching and 

vegetation

 penetration, and removal by precipitation. The 

surface

 model currently works with the Wesely deposition 

option.

v6.10 Modifications

-------------------

1. The treatment of aqueous chemistry (RADM-AQ) has been modified:

 a) Bi-section solver was reverted from H+ back to pH;

 b) Check on high SO2 > 1 ppm (low pH) added to skip aqueous 

chemistry 

 c) Minimum cloud water content was reverted from 0.01 back to 0.05 

g/m3.

 Implications: Changes to aquous chemistry implemented in v5.41 and 

v6.00

 are reverted back to pre-v5.41 code, with the added 

safety of

 checking for high SO2 leading to low pH. Many user's 

complained of model crashes in RADM-AQ due to 

excessive looping

 in the pH solver. Expect minor changes to sulfate 

and nitrate

 concentrations and wet deposition.

2. A single output species labelled "ALL" can be set in the namelist, 

which

 will trigger the output of all gas and PM species for the chosen 

chemical

 mechanism.

 Implications: Saves time typing long lists of species names, 

ensures every

 species is included, and alleviates typographical 

errors. Use

 this in cases when all state species (radicals 

excluded)

 are needed for output, such as generating boundary 

conditions

 in successive 1-way nesting applications.

3. The HDF5 output option has been disabled.
 Implications: Only the default Fortran binary output files are 

generated.

 If conversion to a common self-describing file format 

is

 needed, use the tool "camx2ioapi" to convert fortran 

output

 files to netCDF/IO-API. 

v6.10 Bug Fixes

---------------

1. An MPI bug in passing the variable "depsp" was fixed.

 Implications: Corrects occasional MPI+OMP segmentation faults using

 MVAPICH.

2. Point source HRVOC tracking was reinstated in DDM.

 Implications: HRVOC emissions can now be tracked by DDM for 

sensitivity

 analsis. Previously added to developmental versions 

of CAMx

 v4.5, it was erroneosly dropped from the code. 

3. The passing of layer 1 height to MICROMET.F was corrected from 

deltaz to 

 deltaz/2 in calls from ACM2 and PiG.

 Implications: This fixes an inconsistency that can lead to minor 

differences

 in surface layer stability parameters. It negligibly 

affects

 only ACM2 diffusion and PiG growth rates.

4. An RTRAC indexing bug loading boundary conditions for NOx was 

fixed.

 Implications: This correction properly maps RTRAC boundary 

conditions for NOx

 species.

5. Mapping indices were added for new Hg species for DDM and IEH 

chemistry.

 Implications: These pointer mappings were erroneously left out when 

Hg

 chemistry was updated in v6.00.

6. Point source mapping bug in nested grid boundary cells was fixed. 
 Implications: This error led to the improper indexing of point 

sources

 located in nested grid boundary (buffer) cells, such 

that these

 sources were dropped from the simulation. 
CAMx User’s Guide Version 6.1

User’s Guide

COMPREHENSIVE AIR QUALITY MODEL 

WITH EXTENSIONS

Version 6.1

ENVIRON International Corporation

773 San Marin Drive, Suite 2115

Novato, California, 94945

www.environcorp.com

P-415-899-0700

F-415-899-0707

April 2014

0

200

400

600

800

1000

0

20

40

60

80

100

0

40

80

120

160

200

240

Maximum

Ozone (ppb)

Initial

VOC (ppbC)

Initial

NOx (ppb)

Stack

CAMx Ozone

Particulates

Toxics
April 2014 CAMx User’s Guide Version 6.1

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION www.camx.com

Copyright: ENVIRON International Corporation,

1997 – 2014

This publication may be reproduced for

non-commercial purposes with appropriate attribution.
April 2014 CAMx User’s Guide Version 6.1

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION i www.camx.com

ACKNOWLEDGMENTS

ENVIRON acknowledges the following groups for their contributions to the development of 

CAMx:

• The Texas Commission on Environmental Quality (TCEQ), for sponsoring the development, 

testing, and review of numerous components of the model;

• The Lake Michigan Air Directors Consortium (LADCo), for sponsoring the development, 

testing and review of numerous components of the model;

• The Coordinating Research Council (CRC), for sponsoring the development, testing, and 

review of numerous components of the model;

• The Carnegie-Mellon University, Department of Chemical Engineering, for providing fullscience PM algorithms, assistance in incorporating them into CAMx, and testing the 

implementation;

• The University of Texas, Center for Energy and Environmental Resources, for assistance in 

developing and testing the Open-MP multi-processor capability;

• Atmospheric, Meteorological, and Environmental Technologies (ATMET), for providing 

libraries and implementation support for the MPI parallel processing capability;

• The Midwest Ozone Group (MOG), for sponsoring the development and testing of the MPI 

parallel processing capability;

• The U.S. Environmental Protection Agency (EPA), for sponsoring the development, testing, 

and review of the MPI parallel processing capability and numerous other components of 

the model. Special thanks to Dr. Jon Pleim for assistance with our implementation of 

ACM2;

• The San Francisco Bay Area Air Quality Management District (BAAQMD), for supporting 

and testing the coupling of SAPRC99 gas-phase chemistry to the PM chemistry algorithm;

• The American Petroleum Institute (API), for sponsoring the development and testing of 

improvements to the vertical advection algorithm;

• Atmospheric and Environmental Research (AER), for developing the mercury chemistry 

algorithm.
April 2014 CAMx User’s Guide Version 6.1

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION ii www.camx.com

CONTENTS

ACKNOWLEDGMENTS.......................................................................................................... I

1. OVERVIEW......................................................................................................................1

1.1 CAMX FEATURES......................................................................................................2

1.2 CAMX EXTENSIONS AND PROBING TOOLS................................................................4

1.3 UPDATES IN CAMX VERSION 6.1...............................................................................4

2. THE CAMX MODELING SYSTEM .......................................................................................6

2.1 CAMX PROGRAM STRUCTURE..................................................................................7

2.1.1 Memory Management .......................................................................................... 8

2.1.2 Parallel Processing................................................................................................. 9

2.2 COMPILING CAMX .................................................................................................10

2.2.1 A Note on Fortan Binary Input/Output Files....................................................... 11

2.3 RUNNING CAMX ....................................................................................................12

2.3.1 Control File Namelist Input.................................................................................. 12

2.3.2 Using Scripts to Run CAMx .................................................................................. 20

2.4 BENCHMARKING MODEL RUN TIMES .....................................................................24

2.5 CAMX PRE- AND POST-PROCESSORS ......................................................................25

2.5.1 Emissions............................................................................................................. 25

2.5.2 Meteorology ........................................................................................................ 26

2.5.3 Photolysis Rates................................................................................................... 27

2.5.4 Air Quality............................................................................................................ 28

2.5.5 Landuse................................................................................................................ 28

2.5.6 Post-processors ................................................................................................... 29

3. CORE MODEL INPUT/OUTPUT STRUCTURES ..................................................................30

3.1 CAMX CHEMISTRY PARAMETERS FILE.....................................................................31

3.2 PHOTOLYSIS RATES FILE .........................................................................................39

3.3 OZONE COLUMN FILE.............................................................................................41

3.4 FORTRAN BINARY INPUT/OUTPUT FILES.................................................................44

3.4.1 What is a Fortran Binary File? ............................................................................. 44

3.4.2 CAMx Binary File Headers ................................................................................... 45

3.4.3 Input Files ............................................................................................................ 46

3.4.4 Output Files ......................................................................................................... 58

4. CORE MODEL FORMULATION........................................................................................63

4.1 NUMERICAL APPROACH.........................................................................................63

4.2 CAMX GRID CONFIGURATION ................................................................................65

4.2.1 Grid Cell Arrangement......................................................................................... 65

4.2.2 Grid Nesting......................................................................................................... 66

4.2.3 Flexi-Nesting ........................................................................................................ 68

4.3 TREATMENT OF EMISSIONS....................................................................................68

4.3.1 Gridded Emissions............................................................................................... 69

4.3.2 Elevated Point Emissions..................................................................................... 69

4.4 THREE-DIMENSIONAL TRANSPORT.........................................................................73

4.4.1 Fundamentals....................................................................................................... 73

4.4.2 Transport Algorithms........................................................................................... 75
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4.4.3 ACM2 Vertical Diffusion ...................................................................................... 76

4.5 WET DEPOSITION...................................................................................................78

4.5.1 Precipitation Parameters..................................................................................... 80

4.5.2 Gas Scavenging .................................................................................................... 81

4.5.3 Aerosol Scavenging.............................................................................................. 84

4.6 DRY DEPOSITION ...................................................................................................85

4.6.1 The Wesely/Slinn Model...................................................................................... 86

4.6.2 The Zhang Model................................................................................................. 90

4.7 SURFACE MODEL FOR CHEMISTRY AND RE-EMISSION ............................................95

4.7.1 Surface Model Algorithms................................................................................... 95

4.7.2 Running CAMx With the Surface Model.............................................................. 99

5. CHEMISTRY MECHANISMS ..........................................................................................100

5.1 GAS-PHASE CHEMISTRY .......................................................................................101

5.1.1 Carbon Bond 2005............................................................................................. 101

5.1.2 Carbon Bond Version 6...................................................................................... 101

5.1.3 Carbon Bond Version 6 with Iodine Chemistry ................................................. 102

5.1.4 Carbon Bond Version 6, Revision 2 ................................................................... 103

5.1.5 SAPRC 1999........................................................................................................ 103

5.1.6 Implicit Gas-Phase Species................................................................................ 103

5.1.7 Photolysis Rates................................................................................................. 104

5.1.8 Gas-Phase Chemistry Solvers ............................................................................ 108

5.1.9 Chemical Mechanism Compiler......................................................................... 109

5.2 AEROSOL CHEMISTRY...........................................................................................110

5.2.1 Additional Gas-Phase Species............................................................................ 110

5.2.2 Aerosol Processes.............................................................................................. 112

5.2.3 Aerosol Sectional Approach .............................................................................. 113

5.3 MERCURY CHEMISTRY .........................................................................................115

5.3.1 Gas-Phase Chemistry......................................................................................... 116

5.3.2 Adsorption of Hg(II) on PM................................................................................ 117

5.3.3 Aqueous-Phase Chemistry................................................................................. 118

5.3.4 Implementation Approach ................................................................................ 119

5.3.5 Chemistry Parameters for Mercury................................................................... 120

5.4 SIMPLE CHEMISTRY VIA MECHANISM 10..............................................................121

6. PLUME-IN-GRID SUBMODEL........................................................................................123

6.1 CAMX PIG FORMULATION....................................................................................124

6.1.1 Basic Puff Structure and Diffusive Growth........................................................ 124

6.1.2 Puff Transport.................................................................................................... 128

6.2 GREASD PIG.........................................................................................................129

6.3 PARTICULATE MATTER IN PIG...............................................................................132

6.4 IRON PIG..............................................................................................................132

6.5 PIG FEATURES......................................................................................................133

6.5.1 Puff Layer Spanning (IRON and GREASD).......................................................... 133

6.5.2 Puff Overlap and the Idea of Virtual Dumping (IRON only) .............................. 133

6.5.3 Multiple Puff Reactors (IRON only) ................................................................... 134

6.5.4 Puff Dumping (IRON and GREASD).................................................................... 135

6.5.5 PiG Rendering (IRON and GREASD)................................................................... 135

6.5.6 High Resolution Puff Sampling (IRON and GREASD) ......................................... 136

6.6 DEPOSITION.........................................................................................................136

6.6.1 Dry Deposition................................................................................................... 137

6.6.2 Wet Deposition.................................................................................................. 138
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6.7 PIG CONFIGURATION ...........................................................................................139

6.7.1 Guidance on the Use of CAMx PiG.................................................................... 140

7. OZONE SOURCE APPORTIONMENT TECHNOLOGY........................................................144

7.1 INTRODUCTION ...................................................................................................144

7.2 OSAT FORMULATION...........................................................................................148

7.2.1 Mass Consistency with CAMx............................................................................ 149

7.2.2 Emissions........................................................................................................... 149

7.2.3 Deposition.......................................................................................................... 150

7.2.4 Transport and Diffusion..................................................................................... 150

7.2.5 Chemical Change ............................................................................................... 151

7.2.6 Alternative Chemical Apportionment Techniques............................................ 160

7.3 RUNNING CAMX WITH OSAT................................................................................163

7.3.1 CAMx Control File.............................................................................................. 163

7.3.2 Specifying Emission Groups............................................................................... 164

7.4 INPUT FILE FORMATS ...........................................................................................170

7.4.1 Source Area Mapping ........................................................................................ 170

7.4.2 Receptor Definition ........................................................................................... 170

7.5 OUTPUT FILE FORMATS........................................................................................172

7.5.1 Tracer Species Names........................................................................................ 173

7.5.2 Receptor Concentration File.............................................................................. 173

7.6 POSTPROCESSING................................................................................................175

7.7 STEPS IN DEVELOPING INPUTS AND RUNNING OSAT ............................................175

8. PARTICULATE SOURCE APPORTIONMENT TECHNOLOGY..............................................177

8.1 PSAT METHODOLOGY ..........................................................................................178

8.2 RUNNING CAMX WITH PSAT ................................................................................181

8.2.1 CAMx Control File.............................................................................................. 181

8.3 STEPS IN DEVELOPING INPUTS AND RUNNING PSAT.............................................184

9. DECOUPLED DIRECT METHOD FOR SENSITIVITY ANALYSIS ...........................................186

9.1 IMPLEMENTATION...............................................................................................187

9.1.1 Tracking Sensitivity Coefficients Within CAMx.................................................. 190

9.1.2 Flexi-DDM .......................................................................................................... 191

9.2 RUNNING CAMX WITH DDM AND HDDM .............................................................191

9.3 APPROACHES TO DEFINE IC, BC AND EMISSIONS SENSITIVITIES ............................196

9.4 DDM OUTPUT FILES .............................................................................................196

9.5 DDM SENSITIVITY COEFFICIENT NAMES................................................................197

9.5.1 Initial Condition Sensitivity Names.................................................................... 198

9.6 STEPS IN DEVELOPING INPUTS AND RUNNING DDM.............................................201

10. PROCESS ANALYSIS ...................................................................................................203

10.1 PROCESS ANALYSIS IN CAMX..............................................................................203

10.1.1 Integrated Process Rate Analysis .................................................................... 204

10.1.2 Integrated Reaction Rate Analysis................................................................... 205

10.1.3 Chemical Process Analysis............................................................................... 205

10.2 RUNNING PROCESS ANALYSIS ............................................................................208

10.2.1 Setting CAMx Parameters................................................................................ 210

10.2.2 Output File Formats......................................................................................... 211

10.3 POSTPROCESSING ..............................................................................................211
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10.3.1 IPR Output Files............................................................................................... 211

10.3.2 IRR Output Files............................................................................................... 212

10.3.3 CPA Output Files.............................................................................................. 216

11. REACTIVE TRACERS ...................................................................................................217

11.1 DESCRIPTION OF RTRAC .....................................................................................217

11.1.1 RTRAC Gas-Phase Chemistry ........................................................................... 220

11.1.2 RTRAC Source-Receptor Relationships and Double Counting......................... 222

11.2 DESCRIPTION OF RTCMC ....................................................................................223

11.2.1 RTCMC Gas-Phase Chemistry .......................................................................... 223

11.3 REACTIVE TRACERS IN IRON PIG.........................................................................230

11.3.1 Integration of RTRAC Puff Sampling................................................................ 232

11.4 RUNNING CAMX WITH REACTIVE TRACERS.........................................................232

11.4.1 CAMx Control File............................................................................................ 232

11.4.2 User Adjustable Parameters............................................................................ 235

12. REFERENCES..............................................................................................................236

APPENDIX A ....................................................................................................................248

CAMX MECHANISM 2 .................................................................................................248

CB6R2 GAS-PHASE CHEMISTRY ...................................................................................248

APPENDIX B.....................................................................................................................259

CAMX MECHANISM 7 .................................................................................................259

CB6 GAS-PHASE CHEMISTRY .......................................................................................259

APPENDIX C.....................................................................................................................270

CAMX MECHANISM 1 .................................................................................................270

CB6 WITH IODINE CHEMISTRY ....................................................................................270

References................................................................................................................... 273

APPENDIX D ....................................................................................................................274

CAMX MECHANISM 6 .................................................................................................274

CB05 GAS-PHASE CHEMISTRY .....................................................................................274

APPENDIX E.....................................................................................................................281

CAMX MECHANISM 5 .................................................................................................281

SAPRC99 GAS-PHASE CHEMISTRY ...............................................................................281

TABLES

Table 2-1. Parameters and their defaults in Includes/camx.prm used to 

statically dimension local arrays in low-level subroutines. ....................................8

Table 2-2. CAMx output file suffixes and their corresponding file types. ..................................20

Table 2-3. CAMx v5.00 speed performance with MPI and OMP for the 

distribution test case available at www.camx.com (processed on 

2.83 Ghz Intel Xeon chipsets). ................................................................................24
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Table 2-4. CAMx v5.00 speed performance with MPI and OMP for the 

EPA/OAQPS test case (processed on 2.83 Ghz Intel Xeon chipsets). .....................25

Table 3-1. Data requirements of CAMx. .....................................................................................30

Table 3-2. Description of the CAMx chemistry parameters file. The record labels 

exist in columns 1-20, and where given, the input data for that 

record start in column 21. The format denoted “list” indicates a 

free-format list of numbers (comma or space-delimited). ....................................32

Table 3-3a. Rate constant expression types supported in CAMx and order of 

expression parameters for the chemistry parameters file.....................................40

Table 3-3b. List of parameters that must be provided in the CAMx chemistry 

parameter file for each of the seven types of rate constant 

expressions. Use ppm/minute units for A and Kelvin for Ea and TR. 

The variable O is the order of the reaction (1 to 3)................................................41

Table 3-4. The 11 WESELY89 landuse categories, their default UV surface 

albedos, and their surface roughness values (m) by season. Winter 

is defined for conditions where there is snow present; winter 

months with no snow are assigned to the Fall category. Roughness 

for water is calculated from the function 6 2.5

0 z 2 10 w− = × , where w

is surface wind speed (m/s)....................................................................................47

Table 3-5. The 26 ZHANG03 landuse categories, their UV albedos, and their 

default annual minimum and maximum LAI and surface roughness 

(m) ranges. Roughness for water is calculated from the function 

6 2.5

0 z 2 10 w− = × , where w is surface wind speed (m/s)........................................48

Table 4-1. Summary of the CAMx models and methods for key physical 

processes. ...............................................................................................................63

Table 4-2. Relationships between season and month/latitude used in the CAMx 

Wesely/Slinn dry deposition model. Exception: seasons for the area 

within 50N-75N and 15W-15E are internally set to those of latitude 

band 35-50 to account for regions of Europe in which the climate is 

influenced by the Gulf Stream................................................................................90

Table 4-3. Description of CAMx surface model variables shown in Figure 1. ............................97

Table 4-4. CAMx landuse categories and associated default annual-averaged 

soil/ vegetation split factors and shade factors. ....................................................98

Table 5-1. Gas-phase chemical mechanisms currently implemented in CAMx. ........................100

Table 5-2. Default dry extinction efficiency and single-scattering albedo at 350 

nm (Takemura et al., 2002) in the distributed CAMx chemistry 

parameters file........................................................................................................106

Table 5-3. SOA precursor reactions included in CAMx...............................................................111
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Table 5-4. Properties of CG/SOA pairs........................................................................................112

Table 5-5. List of PM species for the CAMx CF aerosol option...................................................114

Table 7-1. Numbers of emission file sets (i.e., low level files and point source file) 

needed for different model configurations............................................................165

Table 7-2. Format for the receptor definition file. .....................................................................172

Table 9-1. DDM output file suffix names....................................................................................197

Table 10-1. Process information reported by the IPR option.....................................................205

Table 10-2. Chemical Process Analysis (CPA) variables calculated in CAMx for the 

CB6, CB05 and SAPRC99 mechanisms. Concentrations are ppb; 

production and destruction are ppb/hr; photolysis rates are hr-1, 

ratios are unitless....................................................................................................206

Table 10-3. Process analysis keywords and associated CAMx output files................................208

Table 11-1. Keywords, options and default values for the Control section of the 

IMC file....................................................................................................................225

Table 11-2a. Recommended SCICHEM rate constant expression types for use in 

CAMx.......................................................................................................................230

Table 11-2b. Parameters required by SCICHEM rate constant expression types. .....................231

Table 11-3. Determining the reaction order and consequent unit dimensions for 

rate constants. ........................................................................................................231

Table 11-4. RTCMC parameters default settings in the 

Includes/rtcmcchm.inc include file. ..........................................................235

Table A-1. Reactions and rate constants/parameters for the CB6r2 mechanism......................248

Table A-2. Explicit species in the CB6r2 mechanism...................................................................256

Table A-3. Properties of VOC species in the CB6r2 mechanism: carbon numbers, 

kOH values (ppm-1min-1) and maximum incremental reactivity (MIR) 

values (mole O3/mole VOC)....................................................................................258

Table B-1. Reactions and rate constants/parameters for the CB6 mechanism. ........................259

Table B-2. Explicit species in the CB6 mechanism. .....................................................................268

Table B-3. Properties of VOC species in the CB6 mechanism: carbon numbers, 

kOH values (ppm-1min-1) and maximum incremental reactivity (MIR) 

values (mole O3/mole VOC)....................................................................................269

Table C-1. Listing of the chemical mechanism for iodine and ozone. ........................................270

Table C-2. Model species names and properties in the chemical mechanism for 

iodine and ozone. ...................................................................................................271

Table C-3. Photolysis rates (s-1) for iodine-containing species and reference 

reactions. ................................................................................................................272
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Table D-1. Reactions and rate constants for the CB05 mechanism. ..........................................274

Table D-2. Explicit species in the CB05 mechanism....................................................................279

Table D-3. Properties of VOC species in the CB05 mechanism: carbon numbers, 

kOH values (ppm-1min-1) and maximum incremental reactivity (MIR) 

values (mole O3/mole VOC)....................................................................................280

Table E-1. Reactions and rate constants for the SAPRC99 mechanism......................................281

Table E-2. Explicit species in the SAPRC99 mechanism. .............................................................289

Table E-3. Properties of VOC species in the SAPRC99 mechanism: molecular 

weights, average carbon numbers, kOH values (ppm-1min-1) and 

maximum incremental reactivity (MIR) values (mole O3/mole VOC)....................291

FIGURES

Figure 2-1. Schematic diagram of the CAMx modeling system. See Table 3-1 for a detailed 

list of specific model input requirements for the five major data classes shown 

at the top of the figure. Certain pre- and post-processor programs shown in 

the figure are described in this section. Third-party models, processors, and 

visualization software are not described in this User’s Guide and are not 

distributed with CAMx. .........................................................................................................6

Figure 2-2. A sample CAMx job script that generates a “CAMx.in” file and runs the model 

with OMP parallelization.....................................................................................................21

Figure 2-3. An example of global ozone column from the Ozone Monitoring Instrument 

(OMI) platform. White areas denote missing data. From 

http://ozoneaq.gsfc.nasa.gov/OMIOzone.md....................................................................27

Figure 3-1a. Example CAMx chemistry parameters file for Mechanism 6 (CF scheme), 

including the mercury species HG0, HG2, and HGP............................................................34

Figure 3-1b. Example inert chemistry parameters file (requires chemistry flag to be set false 

– see the description of the CAMx control file). .................................................................38

Figure 3-2. Example of the first several panels of lookup data in the photolysis rates input 

file........................................................................................................................................42

Figure 3-3. Example structure of a single-grid ozone column input file showing panels for 

the optional time-invariant land-ocean mask and time-varying ozone column 

field. ....................................................................................................................................44

Figure 4-1. A horizontal representation of the Arakawa C variable configuration used in 

CAMx...................................................................................................................................66

Figure 4-2. An example of horizontal grid nesting, showing two telescoping nested grids 

within a 10×10 cell master grid. The outer nest contains 10×12 cells (including 

buffer cells to hold internal boundary conditions), and the inner nest contains 

6×10 cells (including buffer cells)........................................................................................67
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Figure 4-3. Schematic representation of the turbulent exchange among layers within a 

vertical grid column during convective adjustment in the ACM2 (taken from 

Pleim [2007]).......................................................................................................................78

Figure 4-4. Comparison of monthly LAI data embedded in the Zhang dry deposition scheme 

against episode-specific LAI for June 2005. ........................................................................93

Figure 4-5. Comparison of particle dry deposition velocities as a function of size and wind 

speeds (m/s) for three models: black – Zhang et al. (2001); blue – Slinn and 

Slinn (1980); orange – AERMOD (EPA, 1998). Results are shown for a forest 

landuse category during daytime neutral stability. Particle density was set at 

1.5 g/cm3

. ............................................................................................................................94

Figure 4-6 Comparison of particle dry deposition velocities determined by the Zhang et al.

(2001) and Slinn and Slinn (1980) models, as a function of landuse and wind 

speed during daytime neutrally stable conditions. Particle density was set at 

1.5 g/cm3

. ............................................................................................................................95

Figure 4-7. Schematic of the CAMx surface model...................................................................................97

Figure 4-8. The portions of the CAMx chemistry parameters file (highlighted) to support the 

surface model. In this example, 3 gases are treated, and NO2 and HNO3 react 

to form HONO. All three are subject to decay by soil leaching and plant 

penetration. ........................................................................................................................99

Figure 5-1. Relative humidity adjustment factor applied to the dry extinction efficiency for 

hygroscopic aerosols (FLAG, 2000). ..................................................................................107

Figure 5-2. Impact of chemical decay on the concentration of the donor species PMT........................122

Figure 5-3. Impact of chemical production on the concentration of the recipient species 

PM2. ..................................................................................................................................122

Figure 6-1. Schematic representation of CAMx PiG puff shape in the horizontal plane. 

Directional orientation of the puff is arbitrary, and evolves according to wind 

direction, shears and diffusive growth along its trajectory. .............................................125

Figure 6-2. Plan-view schematic representation of a chain of PiG puffs emitted from a point 

source into an evolving gridded wind field. The red line connected by dots 

represents puff centerlines, with dots representing leading and trailing points 

of each puff. The CAMx computational grid is denoted by the blue lines.......................129

Figure 6-3. Example of a single point source PiG plume as depicted by a sampling grid with 

200 m resolution (shown by the extent of the plot; 40 km by 32 km total 

extent). This sampling grid was set within a CAMx computational grid with 4-

km resolution. The source location is arbitrary and is emitting an inert tracer. .............137

Figure 7-1. Example of the sub-division of a CAMx domain into separate areas for 

geographic source apportionment. ..................................................................................145

Figure 7-2. Example display of ozone source apportionment information provided by OSAT 

for a run with 17 source areas and 1 emission group.......................................................146
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Figure 7-3. Daytime reactions of ozone with HOx (OH and HO2) showing potential for 

reformation of ozone or ozone destruction via peroxide formation................................153

Figure 7-4. Box model simulation to evaluate PH202/PHNO3 indicator for VOC vs. NOx limited 

ozone formation (see text). Ozone is plotted against the left axis, PH202/PHNO3

is plotted against the right axis. For PH202/PHN03 below 0.35 ozone formation is 

VOC limited. Thus, the transition from VOC to NOx limited ozone formation is 

predicted to occur about 12 noon. Initial VOC/NOx = 10:1.............................................157

Figure 7-5. Effect on ozone of controlling VOC and NOx by 30 percent for the base scenario 

shown in Figure 7-4. The vertical dashed line shows the transition from VOC 

to NOx limited ozone formation for the base case derived in Figure 7-4. Initial 

base case VOC/NOx = 10:1................................................................................................157

Figure 7-6. Change in ozone (control-base) for the VOC and NOx control scenarios shown in 

Figure 7-5. The vertical dashed line shows the transition from VOC to NOx 

limited ozone formation for the base case derived in Figure 7-4. Initial base 

case VOC/NOx = 10:1. .......................................................................................................158

Figure 7-7a. As Figure 7-4, but for an Initial VOC/NOx = 20:1. ...............................................................158

Figure 7-7b. As in Figure 7-6, but for an Initial VOC/NOx = 20:1. ...........................................................159

Figure 7-8a. As Figure 7-4, but for an Initial VOC/NOx = 5:1. .................................................................159

Figure 7-8b. As Figure 7-6, but for an Initial VOC/NOx = 5:1..................................................................160

Figure 7-9a. An example of OSAT input records in the CAMx run control file. The options for 

this run are as follows: this is a two-grid run, master and nested grid surface 

concentrations are written to file, a single tracer type is to be used for all 

boundaries, 19 source regions, and one emission group (i.e., zero additional 

emission files and no leftover group). This is the first day of the simulation 

(i.e., restart is false), so no OSAT restart files are supplied. .............................................166

Figure 7-9b. As in Figure 7-9(a), but in this case the run is a continuation, and so the restart 

flag is set to TRUE and a “Tracer Restart” files are supplied. ...........................................167

Figure 7-9c. As in Figure 7-9(a), but in this case the run is a continuation day of a run with 

three emission groups. The three emission groups are defined by supplying 

two pairs of extra emission files for each grid (AREA group 1, AREA group 2, 

and POINT group 2), and setting the “Use_Leftover_Group” flag to TRUE for 

the model to calculate the third group internally. The POINT group 1 filename 

is blank because group 1 is a category with no point source emissions (e.g., 

biogenics). .........................................................................................................................168

Figure 7-9d. As in Figure 7-9(c) (i.e. a continuation day of a run with three emission groups), 

but in this case all three emission groups are defined explicitly by supplying 

extra emission files (AREA group 1, AREA group 2, POINT group 2, AREA group 

3, and POINT group 3). Therefore, the “Use_Leftover_Group” flag is set to 

FALSE. The POINT group 1 filename is blank because group 1 is a category 

with no point source emissions (e.g., biogenics). .............................................................169
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Figure 7-10. Example source area mapping file for the domain and source areas shown in 

Figure 7-1. .........................................................................................................................171

Figure 7-11. Example Receptor Concentration File. Lines ending with “..” are truncated to 

fit the page, and the file would continue with data for additional receptors 

and hours in the same format...........................................................................................174

Figure 8-1. This figure follows from Figure 7-9(d): it is a continuation day of a 2-grid run with 

three emission groups, and all three emission groups are defined explicitly by 

supplying extra emission files (AREA group 1, AREA group 2, POINT group 2, 

AREA group 3, and POINT group 3). Therefore, the “Use_Leftover_Group” flag 

is set to FALSE. The POINT group 1 filename is blank because group 1 is a 

category with no point source emissions (e.g., biogenics). PSAT will trace PM 

sulfate and nitrate species only. .......................................................................................183

Figure 9-1. Example input of DDM options and filenames via the CAMx control file. In this 

case, CAMx is run with two grids, and DDM is configured to track emissions 

from four source regions and two source groups (biogenic and 

anthropogenic). Initial and boundary conditions are tracked as a single 

sensitivity called “ALL”, while emissions are tracked with two sensitivities 

called “NOX” and “VOC”. Sensitivity for a single rate constant group will be 

calculated involving mechanism reaction numbers 120, 121, and 122. Three 

groups of second-order sensitivities to anthropogenic NOx and VOC emissions 

(emissions group 2) from source region 1 will be computed (d2

/dNOx2, 

d2

/dVOC2 and d2/dNOxdVOC). No source region map is provided for the 

nested grid (the region assignments on the nest are defined by the master 

grid). Initial condition file is not provided (a restart day), and only the group 2 

point sources are tracked (no biogenic point sources are available). ..............................195

Figure 9-2. Example concordance of long and short sensitivity coefficient names from the 

CAMx diagnostic output file..............................................................................................198

Figure 10-1. Example section of a CAMx control file specifying options for Process Analysis. ..............210

Figure 10-2. Time-averaged IPR analysis for PSO4 and PNO3 on June 13 and 14, 2002; all of

the processes are plotted individually. .............................................................................213

Figure 10-3. IPR time series analysis for PSO4 and PNO3; Lateral boundary/Chemistry terms 

are not aggregated............................................................................................................214

Figure 10-4. IPR time series analysis for PSO4 and PNO3; Lateral boundary/Chemistry terms 

are aggregated to a single net term, in contrast to Figure 10-3.......................................215

Figure 11-1. Example RTRAC chemistry input file for modeling the MATES toxic species using 

CB4 as the host chemical mechanism (CB4 is no longer available in CAMx)....................218

Figure 11-2. Example RTRAC chemistry input file for modeling toxic species with SAPRC99 as 

the host chemical mechanism. .........................................................................................219
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Figure 11-3. Example RTRAC receptor input file identifying the grid cells with locations of 

point source complexes where hourly decay rates will be output for subgridscale point source modeling (see format for OSAT receptor file in Table 7-2).................222

Figure 11-4. Example free-format RTCMC IMC chemistry input file. .....................................................224

Figure 11-5. Example RTRAC tracer plume emanating from a large point source and 

displayed on a surface sampling grid with 1-km grid spacing. The figure 

illustrates the entire extent of the sampling grid. ............................................................232

Figure 11-6. Example input of RTRAC options and filenames within the CAMx control file. .................234
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1. Overview

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 1 www.camx.com

1. OVERVIEW

The Comprehensive Air quality Model with extensions (CAMx) is an Eulerian photochemical 

dispersion model that allows for integrated “one-atmosphere” assessments of tropospheric air 

pollution (ozone, particulates, air toxics, and mercury) over spatial scales ranging from 

neighborhoods to continents. It is designed to unify all of the technical features required of 

“state-of-the-science” air quality models into a single open-source system that is 

computationally efficient, flexible, and publicly available. The model’s FORTRAN source code is 

modular and well-documented. The FORTRAN binary input/output file formats are based on 

the Urban Airshed Model (UAM) convention and are compatible with many existing pre- and 

post-processing tools. Meteorological fields are supplied to CAMx from separate weather 

prediction models.

CAMx simulates the emission, dispersion, chemical reaction, and removal of pollutants by 

marching the Eulerian continuity equation forward in time (t) for each chemical species (l) on a 

system of nested three-dimensional grids. The continuity equation specifically describes the 

time dependency of volume-average species concentration within each grid cell as a sum of all

physical and chemical processes operating on that volume. This equation is expressed 

mathematically in terrain-following height (z) coordinates as follows:

where cl is species concentration (mass/volume), VH is the horizontal wind vector, η is the net 

vertical transport rate, h is the layer interface height, ρ is atmospheric density, and K is the 

turbulent exchange (diffusion) coefficient. The first term on the right-hand side represents 

horizontal advection, the second term represents net resolved vertical transport across an 

arbitrary space- and time-varying height grid, and the third term represents sub-grid scale 

turbulent diffusion. Chemistry is treated by simultaneously solving a set of reaction equations 

defined by specific chemical mechanisms. Pollutant removal includes both dry surface uptake 

(deposition) and wet scavenging by precipitation.

CAMx can perform simulations on three types of Cartesian map projections: Universal 

Transverse Mercator, Rotated Polar Stereographic, and Lambert Conic Conformal. CAMx also 

offers the option of operating on a geodetic latitude/longitude grid system. The vertical grid 

structure is defined externally, so layer interface heights may be specified as any arbitrary 

function of space and/or time. This flexibility in defining the horizontal and vertical grid 

structures allows CAMx to be configured to match the grid of any meteorological model that is 

used to provide environmental input fields.

( ) ( )

Removal

l

Chemistry

l

Emission

l

l l

l

H H l

l

t

c

t

c

t

c

K c

z t

h

c

z

c V c

t

c

∂

∂

+

∂

∂

+

∂

∂

+

+ ∇ ⋅ ∇

















∂ ∂

∂ − ∂

∂ = − ∇ ⋅ +

∂

∂

ρ ρ η /

2
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1.1 CAMx Features

Two-Way Nested Grid Structure: Run CAMx with variable grid spacing. Use a coarse grid for 

regional domains where high spatial resolution is not particularly needed, while in the same 

run, nest finer grids in specific areas of interest. Two-way nesting propagates information both 

up- and down-scale across all grids. Nests may possess different meshing factors from their 

parent grids, as long as they are common denominators of parent resolution.

Flexi-Nesting: Arbitrarily introduce and/or remove nested grids at any point during a 

simulation. Upon model restart, CAMx automatically diagnoses any changes to the grid system. 

You can supply complete information for new grids (emissions, meteorology, surface

characteristics) or allow CAMx to interpolate any or all of these inputs from parent grids. 

Multiple Photochemical Gas Phase Chemistry Mechanisms: CAMx offers several versions of 

Carbon Bond chemistry (CB05 and CB6 variants; CAMx Mechanisms 1, 2, 6, and 7) and the 1999 

version of the Statewide Air Pollution Research Center chemistry (SAPRC99; CAMx Mechanism 5).

Multiple Gas Phase Chemical Solvers: The Euler-Backward Iterative (EBI) solver is fast and 

accurate, and we recommended its use for any application. The Implicit-Explicit Hybrid (IEH) 

solver is highly accurate and comparable to reference methods such as LSODE but is several 

times slower than EBI. The fully explicit Gear-type Livermore Solver for Ordinary Differential 

Equations (LSODE) can be used to "benchmark" a simulation to evaluate the performance of EBI

or IEH. We do not recommend LSODE for typical applications as the model will run much more 

slowly.

Particulate Matter (PM) Chemistry: CAMx includes algorithms for aqueous chemistry (RADMAQ), inorganic aerosols (ISORROPIA), and secondary organic aerosols (SOAP). These algorithms 

use products from the gas-phase photochemistry for the production of sulfate, nitrate, 

condensable organic gases, and chloride. CAMx provides two options to represent the particle 

size distribution: a static two-mode coarse/fine (CF) scheme, and an evolving multi-section 

(CMU) scheme.

Mercury Chemistry: CAMx optionally treats the chemistry of five mercury species (two gases 

and three particulates) via gas-phase and aqueous pathways, including Hg(II) adsorption to PM. 

The mercury chemistry module requires PM concentrations, so mercury must be modeled with 

the “CF” two-mode PM mechanism by including mercury species among the list of modeled 

species. All of the rate and equilibrium constants for the mercury mechanism are hard-coded 

within the chemistry module.

User-Defined Chemistry Mechanism: “Mechanism 10” provides a simple way to define your 

own chemistry mechanism. This option is intended to define simple chemical decay or 

transformations between gas and/or aerosol species. You must develop your own Mechanism 

10 subroutine and chemistry parameters file.

Plume-in-Grid (PiG) Module: PiG treats the chemistry and dispersion of point source emission 

plumes at sub-grid scales using a Lagrangian puff model, until such time as the pollutant mass 
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can be adequately represented within the grid model framework. Both gas-phase and PM 

chemistry can be treated. PiG includes a “sampling grid” capability to passively sample plume 

surface concentrations at any resolution, which is particularly useful to visualize near-source 

sub-grid scale impacts.

Horizontal Advection Solver Options: CAMx offers the Piecewise Parabolic Method (PPM) of 

Colella and Woodward (1984), and the area-preserving advection solver of Bott (1989). Both 

possess high-order accuracy, little numerical diffusion, and are sufficiently quick for applications

on very large grids.

Vertical Diffusion (Mixing) Options: By default, CAMx employs a standard “K-theory” approach 

for vertical diffusion to account for sub-grid scale mixing layer-to-layer. Version 2 of the 

Asymmetric Convective Model (ACM2; Pleim, 2007) is available as an alternative to the Ktheory approach. ACM2 is a hybrid of local K-theory and non-local convective transport 

between the surface and layers aloft. ACM2 can increase CAMx runtime considerably relative 

to the default K-theory. ACM2 does not work with the Integrated Process Rate (IPR) 

component of the Process Analysis (PA) tool.

Dry Deposition Options: CAMx offers two dry deposition options: an older approach based on 

the models of Wesely (1989) and Slinn and Slinn (1980); and an updated approach based on the 

algorithms of Zhang et al. (2001; 2003). The Wesely/Slinn model is formulated for 11 landuse 

categories, while the Zhang model uses 26 landuse categories.

Surface Chemistry/Re-emission Model: CAMx includes a simple surface sub-model that treats 

sorption and penetration of deposited pollutant mass into soils and vegetation, chemical 

degradation and transformation, and volatilization back into the air (re-emission). The surface 

model treats any subset of species listed in the core model’s chemical mechanism. The surface 

model can only be used with the Wesely (1989) dry deposition option; it cannot be used with 

the Plume-in-Grid treatment.

Advanced Photolysis Model: The TUV radiative transfer and photolysis model, developed and 

distributed by the National Center of Atmospheric Research (NCAR, 2011), is used as a CAMx 

preprocessor to provide the air quality model with a multi-dimensional lookup table of clear-sky 

photolysis rates. CAMx internally adjusts clear-sky rates for the presence of clouds and aerosols 

using a fast in-line version of TUV.

Parallel Processing: CAMx supports two types of parallelization: (1) OpenMP (OMP), which 

allows parallel processing on shared-memory (e.g., multi-core) computers; and (2) Message 

Passing Interface (MPI), which allows parallel processing across distributed memory 

(networked) computer cluster environments. Both OMP and MPI can be used in combination 

to maximize speed performance. To use OMP, your FORTRAN compiler must include libraries 

to enable in-code directives. To use MPI, you must have external MPI libraries installed on your 

system. 
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1.2 CAMx Extensions and Probing Tools

Ozone and Particulate Source Apportionment Technology (OSAT/PSAT): Source apportionment 

technology tracks emission contributions to predicted ozone and/or PM species concentrations

by source region and/or category. OSAT also reports information to determine whether each 

ozone component formed in NOx or VOC sensitive conditions. OSAT/PSAT provides ozone/PM

attribution to source regions and categories for a given emissions matrix, but does not provide 

quantitative information as to how ozone/PM contributions would change as emissions are 

altered because chemical interactions are non-linear.

Decoupled Direct Method (DDM) and High-Order DDM (HDDM) Source Sensitivity: This tool 

calculates first-order (DDM) and second-order (HDDM) concentration sensitivity to changes in 

emissions, initial conditions and boundary conditions. PM sensitivity is limited to first-order

DDM. (H)DDM estimates how pollutant concentrations respond to region- and categoryspecific emission changes, but does not provide information on source attribution.

Process Analysis (PA): This probing tool provides in-depth information on the physical and 

chemical processes occurring during a CAMx run. Through PA, one can more fully understand 

the complex interactions of the different processes, explain simulation results within the 

context of model formulation, and improve the design of control strategies. PA is available for 

CB05, CB6 variants, and SAPRC99 chemical mechanisms, and for EBI, IEH, and LSODE chemistry 

solvers. Three components of PA are implemented in CAMx:

1) Integrated Processes Rate (IPR): Provides detailed process rate information for each bulk 

process in CAMx (i.e., advection, diffusion, deposition, emissions, chemistry, etc.) for 

selected grid cells and selected species;

2) Integrated Reaction Rate (IRR): Provides detailed reaction rate information for all 

reactions in the chemical mechanism for selected grid cells; and

3) Chemical Process Analysis (CPA): Closely related to the IRR method, it is designed to be 

more user friendly and accessible. 

Reactive Tracers (RTRAC): RTRAC provides a flexible add-on to simulate the emission, 

dispersion, chemistry, and deposition of multiple gas and particle tracers (such as specific 

toxics) that are not included in the model’s core gas/PM chemistry mechanisms. Gas-phase 

chemistry can be simply defined as a set of decay rates by species (via user-defined photolysis 

and oxidation rates), or as a complex non-linear system defined by the user through the RTRAC 

Chemical Mechanism Compiler (RTCMC).

1.3 Updates In CAMx Version 6.1

Updated CB6 Mechanism: CB6 “revision 2” (CB6r2) is now available as chemistry mechanism 2, 

and it includes the capability to run with emitted methane (ECH4). CB6r2 differentiates organic 

nitrates (ON) between simple alkyl nitrates that remain in the gas-phase (providing a reservoir 

of NO2) and multi-functional ONs that can partition into organic aerosols (OA). ON present in 

OA are then assumed to undergo hydrolysis to nitric acid. These changes tend to reduce 

regional concentrations of ozone and ON, and increase nitric acid. Regional CAMx simulations 
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with CB6r2 show that accounting for ON hydrolysis in aerosols improves performance for ozone 

and the partitioning of NOy between ON and nitric acid. CB6r2 runs with CF or CMU aerosol 

chemistry and works with all Probing Tools except Process Analysis. ECH4 represents emitted 

methane over and above the global background for methane, which continues to be set 

internally at 1.75 ppm for all mechanisms. ECH4 decays by oxidation and has the same OH rate 

constant and products as global background methane.

Extension of DDM to Particulates: The Decoupled Direct Method has been extended to 

calculate and track first-order (linear) sensitivity coefficients for any particulate species listed in 

the core model’s chemistry parameters file. Chemical sensitivities are determined for inorganic 

(ISORROPIA), organic (SOAP), and aqueous (RADM-AQ) processes. PM-DDM is applicable only 

for the C-F aerosol chemistry option. 

New Surface Chemistry and Re-Emission Model: CAMx includes a surface sub-model that treats 

sorption and penetration of deposited pollutant mass into soils and vegetation, chemical 

degradation and transformation, and volatilization back into the air (re-emission). The surface 

model treats any subset of species listed in the core model’s chemical mechanism. The surface 

model can only be used with the Wesely (1989) dry deposition option; it cannot be used with 

the Plume-in-Grid treatment.

Updates to Plume-in-Grid: An efficient condensed inorganic chemistry mechanism was added 

to treat NOx and ozone chemistry within large NOx point source plumes. The new mechanism 

improves PiG speed and NOy mass budget accuracy. The nocturnal minima set for certain 

turbulence parameters were reduced, leading to improved PiG puff growth rates in agreement 

with in situ aircraft measurements. Reduced nocturnal growth rates affect all PiG options and 

can extend puff lifetimes significantly, particularly in coarse resolution grids. 

Extension of RTRAC: The Reactive Tracer tool was extended to allow user-defined tracers to 

better emulate chemical destruction and removal of core model species such as ozone: (1) the 

dry deposition velocity of an RTRAC species can now be set equal to the time/space-varying 

deposition velocity of a particular core model species, and (2) the photolysis rate of an RTRAC 

species can now be set equal to the time/space-varying photolysis rate of a particular core 

model species.
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2. THE CAMX MODELING SYSTEM

CAMx comprises the core component of an overall air quality modeling system, as illustrated in 

Figure 2-1. CAMx inputs are developed using independent third-party models and processing 

tools that characterize meteorology, emissions, and various other environmental conditions

(land cover, radiative/photolysis properties, and initial/boundary conditions). Interface 

programs are needed to translate the products of each of these models/processors into the 

specific input fields and formats required by CAMx. After the air quality simulation is 

completed, additional programs are used to post-process the concentration fields, develop 

model performance statistics and measures, manipulate Probing Tool output into various 

reportable formats, and further translate raw results into forms necessary for regulatory 

purposes. While third-party visualization software, meteorological models, and emission 

processors are not distributed with CAMx, ENVIRON does provide many of the necessary 

interface programs and post-processors on the CAMx web site (www.camx.com). A brief 

description of each of these is provided at the end of this section. 

Figure 2-1. Schematic diagram of the CAMx modeling system. See Table 3-1 for a detailed list 

of specific model input requirements for the five major data classes shown at the top of the 

figure. Certain pre- and post-processor programs shown in the figure are described in this 

section. Third-party models, processors, and visualization software are not described in this 

User’s Guide and are not distributed with CAMx. 

SMOKE,

CONCEPT,

EPS3

WRF,

MM5,

RAMS TUV

CAMx

PiGSET,

WINDOW,

MRGUAM

WRFCAMx,

MM5CAMx,

RAMSCAMx,

KVPATCH

Total 

Atmospheric

Ozone Column

Landcover

Emission Inventory,

Fire Activity

Analyses,

Observations,

Topography,

Landcover

ICBCPREP

BNDEXT

O3MAP

CAMxTRCT,

CAMx2IOAPI,

BIN2ASC

AVGDIF,

CAMxPOST,

EPASTAT

MATS PA Tools,

User-Developed Post-Processors

Land/Ocean Mask

Global Models

(GEOS-CHEM,

MOZART, AM3)

GEOS2CAMx,

MOZART2CAMx

Leaf Area Index

Data

Models &

Pre-Processors

Interface

Programs

Core Model

Post-Processors 

File Formatting Performance Regulatory Probing Tools

Emissions Meteorology Photolysis Geographic Air Quality

MERGE_LULAI 

GIS Processing

Biogenic Models

SEASALT

Vegetative

Cover
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2.1 CAMx Program Structure

The core CAMx model is written in Fortran90, but includes some utilities written in C to 

interface with MPI. The program is highly modular and well documented to ease code review, 

modifications and substitution of alternate routines. The source code is arranged in several 

directories, grouped according to function. The main source directory contains version release 

notes, the GNU user license, the “Makefile” compile utility, and a control file namelist template. 

Sub-directories contain source code for the core model and ancillary routines according to the 

following:

CAMx/ Source code for the main driver routine CAMx.f and core model 

routines.

CF_AERO/ Source code for inorganic aerosol chemistry (aqueous and 

thermodynamic partitioning) for the 2-mode CF scheme.

CMC/ Source code for the gas-phase chemical mechanism routines.

CMU_AERO/ Source code for inorganic aerosol chemistry (aqueous and 

thermodynamic partitioning) for the multi-section CMU scheme.

DDM/ Source code for the (H)DDM Probing Tool, consisting of I/O and core 

routines that are unique to (H)DDM.

HG/ Source code for the mercury chemistry routines.

Includes/ FORTRAN “include” files, consisting of program parameters and memory 

management code.

IO_bin/ Source code for FORTRAN binary (unformatted) I/O.

Mod_src/ Source code for F90 memory management modules.

MPI/ Source code for routines specific to MPI parallelization.

OSAT/ Source code for the OSAT/PSAT Probing Tools, consisting of I/O and core 

routines that are unique to OSAT/PSAT.

PA/ Source code for the Process Analysis Probing Tool, consisting of I/O and 

core routines that are unique to PA.

PiG/ Source code for the Plume-in-Grid sub-model, consisting of I/O and core 

routines that are unique to PiG.

RTRAC/ Source code for the Reactive Tracer Probing Tool, consisting of I/O and 

core routines that are unique to RTRAC/RTCMC.

SOAP/ Source code for secondary organic aerosol thermodynamic partitioning.
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2.1.1 Memory Management

All of the model’s global data structures are dynamically allocated when the model starts. The 

data necessary to allocate memory space for a given model run are read from the CAMx control 

file developed by the user (see Section 2.3). However, to alleviate compiler dependency on 

speed performance, CAMx utilizes some hard-coded FORTRAN parameters to statically allocate 

local arrays in low-level subroutines. All of these parameters are defined in the 

Includes/camx.prm file. The distribution version of this “include” file sets key array 

parameters to default values that should be sufficiently large to accommodate most 

applications: see Table 2-1 for a description of parameters and their default values. However, 

you may want to customize these values to ensure that they are large enough to accommodate 

all of your model configurations, or to exactly match your specific application, thus preventing 

wasted memory.

If any parameter is set to a value that is too small to support your application the model will 

stop, displaying an informative error message. To conserve memory, default values of 1 are 

set for Probing Tool tracers, PiG sampling grids, and sampling grid dimensions. These must be 

increased accordingly if Probing Tools or sampling grids are to be used.

Table 2-1. Parameters and their defaults in Includes/camx.prm used to statically 

dimension local arrays in low-level subroutines.

Parameter Name Description

Default 

Value

MXCELLS Number of cells in X/Y direction for any grid 200

MXLAYER Number of layers 30

MXSPEC Number of species (could be number of radicals, number of input 

species, or total number of model species) 138

MXREACT Number of reactions (depends on the mechanism; see the user's 

guide for the value for each mechanism) 288

MXGRID Number of grids 10

MXPTSRC Number of point sources 100000

MXTRSP Number of Probing Tool tracer species 1

MXPIG Number of PiG puffs 50000

MXSAMPLE Number of PiG sampling grids 1

MXCOLSMP Number of PiG sampling grid columns 1

MXROWSMP Number of PiG sampling grid rows 1

All of the parameters in the table above can be determined before starting a simulation except 

for MXPIG. A value of 50,000 is usually sufficient for most applications in which PiG is used; set 

this parameter to 1 if PiG is not used to conserve memory. If this parameter is exceeded during 

a simulation, the model will stop with an informative error message. If this happens, simply 

increase MXPIG, recompile the model executable, and restart the simulation. The other 

parameters in camx.prm beyond those listed in Table 2-1 will not normally need to be 

changed and are not discussed further.
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2.1.2 Parallel Processing

Parallel processing refers to distributing a model application to multiple processors (CPUs) that 

share the computational load. CAMx supports two types of parallelization: (1) OpenMP (OMP), 

which allows parallel processing on shared-memory (e.g., multi-core) computers; and (2) 

Message Passing Interface (MPI), which allows parallel processing across distributed memory 

(networked) computer cluster environments. Both OMP and MPI can be used in combination 

to maximize speed performance. 

To use OMP, your FORTRAN compiler must include libraries to enable the in-code 

parallelization directives. OMP distributes calculations for individual processes, such as 

chemistry within a single grid cell or advection/diffusion along a single row of cells, to a number 

of CPUs defined by the user. Once each CPU has completed its calculations, it works on the 

next individual process until all processes over the entire grid are completed. 

To use MPI, you must have an external MPI library installed on your system. MPICH is a specific 

open source MPI library widely used in the numerical modeling community; CAMx has been 

specifically developed and tested using MPICH. With MPI, the CAMx modeling grid is divided 

into sub-regions and each is assigned to a CPU on the user-defined network. Each CPU 

operates the entire model on its assigned sub-region and passes common information needed 

by other CPUs via large data “messages”. 

MPI in CAMx is designed using a “master/slave” parallel processing approach. The CPU on 

which the program is launched serves as the master node and will not conduct any model 

computations on any part of the modeling domain. This process will perform all of the model 

setup, the vast majority of I/O, and manage the communication between the slave or compute

nodes. Since the master node handles the important I/O it is the only CPU that needs access to 

the disk volume containing the input files and the location of the output directory. This 

approach allows for a minimal amount of network traffic to/among the compute nodes by 

eliminating the need for them to manage NFS mounts. The master node may need access to 

the LAN for data access, but the compute nodes only need access to the internal cluster 

network. However, the compute nodes will need access to a copy of the executable program. 

This can be accomplished in a number of ways: (1) have an NFS mount on the master node 

accessible to the internal cluster network and launch the model from that location; or (2) port a 

copy of the executable program, using rcp or scp, to the user’s home directory on each 

compute node and launch the model from the user’s home directory on the master node.

During each model time step, when computations are performed by the compute nodes, some 

information is written to the diagnostic and message output files. Rather than just eliminate 

this information altogether, we decided to create node-specific versions of each of these two 

files and have each compute node write the information to its own version. However, in order 

to prevent the need to have the output directory available to the compute node across the 

network, we have designed the model so that the node-specific files are created in the current 

working directory. This means that if the model is launched from an NFS-mounted directory, all 

of the node-specific files will all be created in that location. On the other hand, if the model is 
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launched from a user's home directory on the compute nodes, you will have to log in to the 

specific compute node to view the files.

When using a hybrid MPI/OMP approach, the domain will be divided into slices in the usual way 

as part of MPI, but when operating on a particular slice, the host will spawn multiple OMP 

threads to parallelize the portions of the code where OMP directives have been included.

2.2 Compiling CAMx

A “Makefile” script is provided in the main source directory. The Makefile will compile all CAMx 

source code, link with necessary libraries, and build an executable program. It supports 

platforms running Linux (Portland Group and Intel compilers) and Macintosh OSX (Absoft

compiler); it does not currently support compilers on platforms running Windows.

The choice for OMP and MPI parallelization, and the memory configuration for probing tools,

are set during model compilation. All other CAMx choices for chemical mechanism, model 

algorithms, Probing Tools, and other options are selected at run time. 

CAMx is compiled by issuing the following command at a shell prompt within the main source 

directory:

make COMPILER=my_compiler <CONFIG=my_app> <MPI=mpi_option>

where the text within the brackets “<>” is optional. To display an interactive help message, 

you may type

make help

The mandatory COMPILER argument should be set to one of the following:

pgf or pgfomp (Portland Group compiler for Linux)

ifort or ifortomp (Intel compiler for Linux)

absoft or absoftomp (Absoft compiler for Macintosh OSX)

These keywords inform the Makefile of the compiler being used to compile and run the model, 

so that the Makefile can invoke the proper compiler-specific commands and flags. If OMP is not 

specified as part of the keyword then CAMx will not be able to run with OMP parallelization.

The optional CONFIG argument allows the CAMx executable program to be labeled for a 

specific memory configuration as defined within the CAMx parameters file 

(Includes/camx.prm) described above. You may want to customize some applications, for 

example to configure the Probing Tool extensions, and it is convenient to be able to distinguish 

between these executables. The Makefile will search for a CAMx parameters file called:

Includes/camx.prm.my_app
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If CONFIG is not set on the make command line, the Makefile will compile CAMx using the 

default parameters file, Includes/camx.prm.v6.10. 

The optional MPI argument will enable MPI parallel processing. This requires that third-party 

MPI libraries have been built and installed on the machine that is running this Makefile script 

and compiling CAMx. If MPI is not set on the command line, the Makefile script will ignore the 

MPI libraries and CAMx will not be able to run with MPI parallelization. The optional MPI

argument should be set to one of the following:

mpich (MPICH versions 1 or 2)

mpich3 (MPICH version 3)

mvapch

openmpi (PGF and IFORT compilers only)

You should check that the variable “MPI_INST” in the CAMx Makefile, and in the MPI 

utilities Makefile (located in the MPI/util sub-directory), are correctly set to your system's 

MPI installation path.

CAMx supports the use of both OMP and MPI parallelization in a single run using PGF and IFORT 

compilers. To utilize OMP in your MPI application, be sure to specify the appropriate OMP

compiler keyword. 

The Makefile will generate a CAMx executable program named

CAMx.my_app.MPI_option.my_compiler

which will reside in the main source directory. For example, a default compilation using the 

Portland Group compiler will result in an executable named

CAMx.v6.10.noMPI.pgf.

If you need to rebuild CAMx using different Makefile arguments we recommend typing “make 

clean” between builds. Make clean will delete all existing object files and force a complete 

re-build.

2.2.1 A Note on FORTRAN Binary Input/Output Files

Large CAMx input and output data fields are contained within Fortran “unformatted” (binary) 

files. This means that the data are read and written as represented in memory, without 

translation between binary and ASCII character sets as is performed for “text” files. Binary files 

reduce file volume and improve program read/write speed, but the user cannot directly view or 

manually edit them. There are two ways to represent binary information in memory: “big 

endian” and “little endian.” The difference between these is essentially the order of bits in a 

word, and which order is used depends on the computer chipset. Historically, big endian has 

been used in many Unix workstations (Sun, SGI, HP, and IBM). The x86 processors on personal 

computer platforms (e.g., Intel and AMD) use little endian, while PowerPC chips are big endian.
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CAMx can be compiled and run on machines that use either big or little endian binary

representations, as long as the model and all of its pre- and post-processors are consistently 

compiled and run on the same type of platform. If any component of the modeling system is 

compiled on a different platform using the opposite binary representation, I/O files will not be 

properly read and will likely lead to a program crash. 

A typical run-time error message from trying to read the wrong binary format is “input record 

too long,” so if you get this error message, check for big endian / little endian consistency 

between your binary files and Fortran compiler options.

Compilers for little endian machines (e.g., x86 PC chipsets) provide compile-time switches that 

allow binary files to be read and written as big endian. The Portland Group compiler option is

“-byteswapio”, whereas the Intel compiler option is “-convert big_endian.” The 

CAMx Makefile sets compiler flags to consistently use big endian to maximize platform 

portability. Therefore, use of the CAMx Makefile will by default result in the model reading and 

writing big endian binary files. In practice, users should use the default binary format that is 

built into the CAMx Makefile and that is used for the CAMx distribution test case. 

2.3 Running CAMx

2.3.1 Control File Namelist Input

CAMx reads a text (ASCII) run control file named “CAMx.in” that must exist locally in the 

directory from which the model is run. This file must be in the Fortran “namelist” format, and 

contains all user-specified control parameters for a given simulation, including model 

configuration, option-specific inputs, and I/O filenames. The run control file must contain the 

primary namelist module labeled “&CAMx_Control”, which provides all of the information to 

configure the core model. Additional namelist modules may be provided in the run control file 

to configure the various CAMx Probing Tool extensions. These optional namelist modules are 

ignored if no Probing Tools are selected in the primary namelist. 

Each record in the CAMx control file contains a variable name that is explicitly set to a 

numerical, logical, or character value. The variable names are used by the program directly, 

and therefore cannot be changed without source code modifications. Character strings must 

be enclosed by single quotes, and all variable assignments must be delimited with commas. 

The order of the records may be arranged in any fashion that the user prefers. Any number of 

comment statements may be included anywhere within the namelists, provided that they do 

not interrupt variable assignments (variable_name = value,). The “!” character is the 

Fortran namelist comment delimiter.

Certain variables are multi-dimension arrays; the user may provide a comma-delimited list of 

values to fill the array or assign values to specific array elements. Certain other variables are 

optional or associated with option flags; these do not need to appear in the namelist if their 

associated options are not invoked, and they will be ignored if they remain in the file. 

If the user does not provide necessary inputs, the model will stop with a descriptive error 

message. 
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2.3.1.1 Common Errors When Creating a Namelist

Fortran programs ingest the entire contents of namelist modules using a single READ 

statement. If the program experiences an error reading the namelist, it echoes a simple error 

message like “error reading namelist” and the program stops. It is therefore difficult to 

determine the cause of the read error, especially if the namelist is lengthy and contains a 

variety of data types. When experiencing an error reading the CAMx control file namelist, you 

must carefully inspect the file for any syntax errors. These errors can be subtle and difficult to 

spot. Here are a few of the common reasons an error occurs when reading a namelist:

• Mistyped variable name:

All variables to be assigned within a namelist must be recognized as a declared namelist 

variable within the reading program. If a variable is misspelled or an unknown variable 

is assigned a value, a read error will occur.

• Incorrect data type for the assigned variable:

If the data type of the value assigned to a namelist variable does not match the 

variable’s declared data type within the reading program, an error will occur. Some 

compilers will allow real type variables to be assigned to integer values, but not the 

converse.

• Missing period around a logical value:

The logical values .true. and .false. must be surrounded by a period.

• Missing quotes around a character variable:

Any character data type must be surrounded by quotes.

• Overflow when assigning values to an array:

The values in an array can be assigned using array index notation. If the index used to 

assign an array value exceeds the declared dimension of the array, a read error occurs. 

Check the “MXNAM” parameter in the Includes/namelist.inc include file to see 

if this value needs to be increased. Alternatively, check your namelist file to be sure all 

of your array indices are correct.

• Wrong number of dimensions when assigning values to a multi-dimensional array:

When assigning values to an array using array index notation, the number of subscripts 

in the assignment must match the declared dimensions of the array (e.g., assignments 

to an array dimensioned var(i,j) must be referenced using two indices).

• Missing comma following a variable definition:

A comma must be the last character in a variable assignment (variable = value,). 

A comment may be placed after the comma (delimited using the “!” symbol, see below) 

on the same file record. This restriction on the use of commas is ignored on some 

compilers.

• Too many commas following a scalar variable definition:

More than one comma following a scalar variable assignment will result in a read error.

• Too many commas following the variable assignment list for an array:
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The entire contents of an array can be assigned using a single statement by listing the 

values of each element separated by commas. The read will fail if there are more 

commas than the dimension of the array.

• Comment does not begin with !:

The character that delimits a comment in a namelist is the exclamation point. 

Comments can appear anywhere within the namelist. However, all text in the namelist 

must either be part of a namelist variable assignment or part of an identified comment.

We suggest that new CAMx users start with the “CAMx.namelist.template” that is 

provided with the source code.

2.3.1.2 The Primary Namelist Module

This section describes the primary namelist module; detailed descriptions of each of the 

Probing Tool modules are provided in their respective sections (Sections 7 through 11). A listing

of all namelist variables necessary to run the core model is presented on the following pages. 
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Description of CAMx Run Control File Variables

&CAMx_Control Label for the primary namelist module that configures the core 

model; it must begin in column 2

& Flag ending a namelist module; it must be in column 2

Run_Message 60-character simulation message, written to output files to label 

the run

The short simulation “run message” is written to all output files to describe and label the run. 

Model Clock Control

Time_Zone Integer time zone (0=UTC, 5=EST, 6=CST, 7=MST, 8=PST)

Restart Logical model restart flag (TRUE=read restart file, FALSE=read 

initial conditions file)

Start_Date_Hour Integer array start time (YYYY, MM, DD, HHmm)

End_Date_Hour Integer array end time (YYYY, MM, DD, HHmm)

Maximum_Timestep Real maximum allowable timestep (minutes)

Met_Input_Frequency Real input frequency of environmental fields (minutes)

Ems_Input_Frequency Real input frequency of emissions (minutes)

Output_Frequency Real output frequency (minutes)

The user specifies the simulation start/end year, month, day, and hour; the model uses Julian

dates internally. All times must be given in military format (e.g., 1:30 PM must be given as 

1330). The simulation time zone must match the time zone in which the emission and 

environmental inputs are developed. 

Map Projection Parameters

Map_Projection Character mapping projection keyword (LAMBERT, POLAR, 

UTM, LATLON)

UTM_Zone Integer UTM zone

POLAR_Longitude_Pole Real longitude of projection pole (degrees, west<0)

POLAR_Latitude_Pole Real latitude of projection pole (degrees, south<0)

LAMBERT_Center_Longitude Real central longitude of modeling domain (degrees, west<0)

LAMBERT_Center_Latitude Real central latitude of modeling domain (degrees, south<0)

LAMBERT_True_Latitude1 Real first true latitude of projection (degrees, south<0)

LAMBERT_True_Latitude2 Real second true latitude of projection (degrees, south<0)

The grid projection may be selected as Cartesian (fixed physical distance coordinates on a flat 

plane) or curvi-linear geodetic (following the curved surface of the Earth). The Cartesian 

options include Universal Transverse Mercator (UTM), Lambert Conic Conformal (LAMBERT), 

and Rotated Polar Stereographic (POLAR). The geodetic option performs the simulation on a 

latitude/longitude grid (LATLON). All gridded input files must be defined on the grid projection 

specified for the CAMx simulation. 
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Parameters For The Master (First) Grid

Number_of_Grids Integer number of grids in simulation

Master_Origin_XCoord Real x-coordinate of domain southwest corner (km, or degrees 

for LATLON)

Master_Origin_YCoord Real y-coordinate of domain southwest corner (km, or degrees 

for LATLON)

Master_Cell_XSize Real cell size in x (km, or degrees for LATLON)

Master_Cell_Ysize Real cell size in y (km, or degrees for LATLON)

Master_Grid_Columns Integer number of master grid columns (E-W grid cells)

Master_Grid_Rows Integer number of master grid rows (N-S grid cells)

Number_of_Layers Integer number of grid layers (applies to all grids)

The master grid is defined by its location (southwest corner point in the chosen projection 

space), number of grid cells (east-west, north-south, vertically), and horizontal resolution. 

Vertical resolution is defined by the layer structure specified in the input 3D meteorological file.

Parameters For The Nested Grids

Nest_Meshing_Factor Integer array (by grid) nested grid cell size relative to master 

grid

Nest_Beg_I_Index Integer array (by grid) master grid column containing western 

edge of nest

Nest_End_I_Index Integer array (by grid) master grid column containing eastern 

edge of nest

Nest_Beg_J_Index Integer array (by grid) master grid row containing southern edge 

of nest

Nest_End_J_Index Integer array (by grid) master grid row containing northern edge 

of nest

The definition of nested grids is specified in the CAMx.in file in terms of the range of master 

grid cells that each nested grid spans (see Section 4). The “meshing factor” sets the resolution 

or cell size of the nested grids relative to the master grid. The CAMx diagnostic output file 

provides information on the location and size of each nested grid to help ensure proper setup.

Model Options

Diagnostic_Error_Check Logical model startup diagnostic flag (TRUE=stops before first 

timestep indicating successful model initialization, 

FALSE=continues with simulation after model initialization)

Flexi_Nest Logical flexi-nesting flag (TRUE=allow some/all nested input 

fields to be interpolated from the parent grid, FALSE=all data 

must be provided for all nests)

Advection_Solver Character horizontal advection solver keyword (PPM, BOTT)

Chemistry_Solver Character chemistry solver keyword (EBI, IEH, LSODE)

PiG_Submodel Character PiG submodel keyword (NONE, GREASD, IRON)
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Probing_Tool Character Probing Tool keyword (NONE, OSAT, GOAT, APCA, 

PSAT, DDM, HDDM, PA, IPR, IRR, RTRAC, RTCMC)

Chemistry Logical chemistry flag (TRUE=chemistry on, FALSE=chemistry 

off)

Drydep_Model Character dry deposition model keyword (NONE, WESELY89, 

ZHANG03)

Wet_Deposition Logical wet deposition flag (TRUE=deposition on, 

FALSE=deposition off)

ACM2_Diffusion Logical ACM2 vertical diffusion flag (TRUE=ACM2 on, 

FALSE=standard K-theory diffusion)

Super_Stepping Logical super-stepping flag (TRUE=use super-stepping for 

horizontal advection to maximize model speed, FALSE=do not 

use super-stepping).

Gridded_Emissions Logical gridded emissions flag (TRUE=gridded emissions will be 

used, FALSE=gridded emissions will be ignored)

Point_Emissions Logical elevated point source flag (TRUE=point emissions will be 

used, FALSE=point emissions will be ignored)

Ignore_Emission_Dates Logical date-insensitive emission flag (TRUE=dates on emission 

files will be ignored, FALSE=dates on emission files will be 

checked against simulation date)

The user has the option of selecting among the Bott or Piecewise Parabolic Method horizontal 

advection solvers by specifying “BOTT” or “PPM” as keywords in the run control file. The user 

also has the option to use the EBI, IEH, or LSODE chemistry solvers for gas-phase chemistry by 

specifying these respective keywords. Probing Tools are selected by specifying one of the 

allowed keywords; no Probing Tool will be run if this keyword is set to “None”. The description 

of the PiG submodel is provided in Section 6. 

Super stepping maximizes the model’s speed performance by setting the largest grid-specific 

driving time steps possible. This results in the need for potentially many sub-steps to be 

applied in horizontal advection on a layer-by-layer basis to maintain a stable solution. While 

super stepping has little impact on surface concentrations in non-MPI mode, larger differences 

are seen using MPI. A “super-stepping” flag was added to the control namelist that allows 

users to specifically turn off super stepping when they wish to compare concentrations 

between MPI and non-MPI runs in the most consistent manner possible. Super stepping can 

reduce the accuracy of the vertical transport solution, especially in high wind conditions over 

complex terrain. Turning super stepping off will cause the model to run much more slowly.

Output Specifications

Root_Output_Name Character root output path/filename (see Table 2-2 for 

description of file suffixes)

Average_Output_3D Logical 3-D average output file flag (TRUE=output full 3-D 

concentration fields, FALSE=output surface layer concentration 

fields)
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Output_3D_Grid Logical array (by grid) 3-D average output file flag (TRUE=output 

full 3-D concentration fields for specified grid, FALSE=output 

surface layer concentration fields)

Output_Species_Names Character array (by output species) species names to be written 

to average and deposition output files, or the single name “ALL” 

to output all state gas and PM species (excluding radicals)

PiG_Sampling_Grid Logical sampling grid flag for IRON PiG output (TRUE=sampling 

grids are specified, FALSE=sampling grids will not be generated)

Sample_Background Logical flag to include background concentrations 

(TRUE=background concentrations from the host computational 

grid will be added to puff increments, FALSE=only puff 

increments will be shown)

Number_of_Sampling_Grids Integer number of sampling grids

SG_Beg_I_Index Integer array (by sampling grid) master grid column containing 

western edge of sampling grid

SG_End_I_Index Integer array (by sampling grid) master grid column containing 

eastern edge of sampling grid

SG_Beg_J_Index Integer array (by sampling grid) master grid row containing 

southern edge of sampling grid

SG_End_J_Index Integer array (by sampling grid) master grid row containing 

northern edge of sampling grid

SG_Mesh_Factor Integer array (by sampling grid) cell size relative to master grid

The user specifies a “root” path and filename that will be used for all standard CAMx core 

model output files. The model appends suffixes to these root names according to the file type 

generated. 

The types of CAMx output files are listed in Table 2-2. A subset of state (gas or PM) and radical 

species may be output to the average concentration output files; see the description of output 

file formats in Section 3. By specifying a single output name “ALL”, the model will automatically 

output fields for all state gas and PM species listed in the input chemistry parameters file, 

excluding radicals. If “ALL” is specified, it must be the only name listed; no species names may 

be listed before or after “ALL”. There are two flags that control whether 3-D average output 

files are generated. The first (original) flag will toggle 3-D output for all grids in the run. The 

second is the “Output_3D_Grid” flag array, which allows 3-D average output to be set for 

specific grids. The original flag supersedes the grid-specific flag.

PiG sampling grids are set identically to the way nested grids are specified for the host model, 

with one exception: there are no vertical levels to define (sampling grids are currently only 2-D 

surface fields). The same rules that apply for the specification of nested grids holds for the 

specification of all sampling grids (see Section 4).
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Input Files

Chemistry_Parameters Character input chemistry parameters path/filename

Photolyis_Rates Character input photolysis rates path/filename (optional 

according to Chemistry flag and Chemistry_Parameters file)

Ozone_Column Character input ozone column path/filename (ignored if 

Chemistry=FALSE)

Initial_Conditions Character input master grid initial conditions path/filename 

(ignored if Restart=TRUE)

Boundary_Conditions Character input master grid boundary conditions path/filename

Point_Sources Character input elevated point source emissions path/filename 

(ignored if Point_Emissions=FALSE)

Master_Grid_Restart Character input master grid restart path/filename (ignored if 

Restart=FALSE)

Nested_Grid_Restart Character input nested grid restart path/filename (ignored if 

Restart=FALSE or Number_of_Grids=1)

PiG_Restart Character input PiG restart path/filename (ignored if 

Restart=FALSE or PiG_Submodel=FALSE)

Surface_Grid Character array (by grid) input static 2D surface path/filename 

(optional for nested grids)

Met2D_Grid Character array (by grid) input time-variant 2D surface

meteorology path/filename (optional for nested grids)

Met3D_Grid Character array (by grid) input time-variant 3D meteorology

path/filename (optional for nested grids)

Vdiff_Grid Character array (by grid) input time-variant 3D vertical 

diffusivity path/filename (optional for nested grids)

Cloud_Grid Character array (by grid) input time-variant 3D cloud/rain 

path/filename (optional but required if Wet_Deposition=TRUE, 

optional for nested grids)

Emiss_Grid Character array (by grid) input gridded emissions path/filename 

(ignored if Gridded_Emissions=FALSE, optional for nested grids)

If CAMx cannot find or open a non-blank input filename provided in the run control file, the 

model will stop with an error. CAMx will accept blank input filenames for only those files that 

are optional.
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Table 2-2. CAMx output file suffixes and their corresponding file types.

Suffix CAMx File Type

.out Text simulation tracking file (CPU, input files read, error/warning messages) 

.diag Text simulation diagnostic file (repeat of run control inputs, PiG diagnostics, 

miscellaneous diagnostic output) 

.mass Text mass budget file for subsequent postprocessing

.inst Fortran binary master grid instantaneous concentration file at the end of 

the simulation (used for restarts) 

.finst Fortran binary nested grid instantaneous concentration file at the end of the 

simulation (used for restarts) 

.pig Fortran binary PiG sub-model file (used for restarts)

Standard CAMx Output Option

.avrg.grdnn Fortran binary average concentration file for grid nn; optionally contains 2-D 

layer 1 concentration field or full 3-D concentration field

.depn.grdnn Fortran binary surface deposition file for grid nn

.smpnn Fortran binary average surface concentration file for PiG sampling grid nn

(optional)

2.3.2 Using Scripts to Run CAMx

The generation of the run control file is most easily accomplished in the job script that actually 

runs the model; Figure 2-2 shows an example of a CAMx job script that builds a “CAMx.in” file 

and runs the model for each day to be simulated. Alternatively, the run control file could be 

written separately with a name specific to a given simulation, then linked or copied to the 

standard “CAMx.in” filename before the model is executed at a command line or in a job 

script.
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#!/bin/csh

#

# CAMx 6.10

#

setenv OMP_NUM_THREADS 4

setenv MPSTKZ 128M

limit stacksize unlimited

#

set EXEC = "../../src/CAMx.v6.10.noMPI.pg_linuxomp"

#

set RUN = "v6.10.midwest.36.12.noMPI"

set INPUT = "../inputs"

set MET = "../inputs/met"

set EMIS = "../emiss"

set PTSRCE = "../ptsrce"

set OUTPUT = "../outputs"

#

mkdir -p $OUTPUT

#

# --- set the dates and times ----

#

set RESTART = "NO"

foreach today (03.154 04.155)

set JUL = $today:e

set CAL = $today:r

set YESTERDAY = `echo ${CAL} | awk '{printf("%2.2d",$1-1)}'`

#

if( ${RESTART} == "NO" ) then

 set RESTART = "false"

else

 set RESTART = "true"

endif

#

# --- Create the input file (always called CAMx.in)

#

cat << ieof > CAMx.in

&CAMx_Control

Run_Message = 'CAMx 6.10 Test Problem -- Mech6 CF CB05 $RUN',

!--- Model clock control ---

Time_Zone = 0, ! (0=UTC,5=EST,6=CST,7=MST,8=PST)

Restart = .${RESTART}.,

Start_Date_Hour = 2002,06,${CAL},0000, ! (YYYY,MM,DD,HHmm)

End_Date_Hour = 2002,06,${CAL},2400, ! (YYYY,MM,DD,HHmm)

Maximum_Timestep = 15., ! minutes

Met_Input_Frequency = 60., ! minutes

Ems_Input_Frequency = 60., ! minutes

Output_Frequency = 60., ! minutes

Figure 2-2. A sample CAMx job script that generates a “CAMx.in” file and runs the model

with OMP parallelization. 
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!--- Map projection parameters ---

Map_Projection = 'LAMBERT', ! (LAMBERT,POLAR,UTM,LATLON)

LAMBERT_Center_Longitude = -97., ! deg (west<0,south<0)

LAMBERT_Center_Latitude = 40., ! deg (west<0,south<0)

LAMBERT_True_Latitude1 = 45., ! deg (west<0,south<0)

LAMBERT_True_Latitude2 = 33., ! deg (west<0,south<0)

!--- Parameters for the master (first) grid ---

Number_of_Grids = 2,

Master_Origin_XCoord = -792., ! km or deg, SW corner of cell(1,1)

Master_Origin_YCoord = -1656., ! km or deg, SW corner of cell (1,1)

Master_Cell_XSize = 36., ! km or deg

Master_Cell_YSize = 36., ! km or deg

Master_Grid_Columns = 68,

Master_Grid_Rows = 68,

Number_of_Layers = 16,

!--- Parameters for the second grid ---

Nest_Meshing_Factor(2) = 3, ! Cell size relative to master grid

Nest_Beg_I_Index(2) = 22, ! Relative to master grid

Nest_End_I_Index(2) = 51, ! Relative to master grid

Nest_Beg_J_Index(2) = 22, ! Relative to master grid

Nest_End_J_Index(2) = 58, ! Relative to master grid

!--- Model options ---

Diagnostic_Error_Check = .false., ! True = will stop after 1st timestep

Advection_Solver = 'PPM', ! (PPM,BOTT)

Chemistry_Solver = 'EBI', ! (EBI,IEH,LSODE)

PiG_Submodel = 'None', ! (None,GREASD,IRON)

Probing_Tool = 'None', ! (None,OSAT,GOAT,APCA,PSAT,DDM,

! HDDM,PA,IPR,IRR,RTRAC,RTCMC)

Chemistry = .true.,

Drydep_Model = ‘WESELY89’, ! (NONE, WESELY89, ZHANG03)

Wet_Deposition = .true.,

ACM2_Diffusion = .false.,

Super_Stepping = .true.,

Gridded_Emissions = .true.,

Point_Emissions = .true.,

Ignore_Emission_Dates = .true.,

!--- Output specifications ---

Root_Output_Name = '$OUTPUT/CAMx.$RUN.200206${CAL}',

Average_Output_3D = .false.,

Output_Species_Names(1) = 'NO',

Output_Species_Names(2) = 'NO2',

Output_Species_Names(3) = 'O3',

Output_Species_Names(4) = 'SO2',

Output_Species_Names(5) = 'H2O2',

Output_Species_Names(6) = 'HNO3',

Output_Species_Names(7) = 'NH3',

Output_Species_Names(8) = 'PNO3',

Output_Species_Names(9) = 'PSO4',

Output_Species_Names(10) = 'PNH4',

Output_Species_Names(11) = 'POA',

Figure 2-2 (continued).
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Output_Species_Names(12) = 'PEC',

Output_Species_Names(13) = 'FPRM',

Output_Species_Names(14) = 'CPRM',

Output_Species_Names(15) = 'CCRS',

Output_Species_Names(16) = 'FCRS',

Output_Species_Names(17) = 'SOA1',

Output_Species_Names(18) = 'SOA2',

Output_Species_Names(19) = 'SOA3',

Output_Species_Names(20) = 'SOA4',

Output_Species_Names(21) = 'SOA5',

!--- Input files ---

Chemistry_Parameters = '$INPUT/CAMx6.1.chemparam.6_CF',

Photolyis_Rates = '$INPUT/tuv.200206.STL.txt',

Ozone_Column = '$INPUT/o3col.200206.STL_36_68X68_12_92X113.txt',

Initial_Conditions = '$INPUT/IC.vistas_2002gt2a_STL_36_68X68_16L.2002081',

Boundary_Conditions = '$INPUT/BC.vistas_2002gt2a_STL_36_68X68_16L.2002${JUL}',

Point_Sources = '$PTSRCE/ptsrce.stl.36km.2002${JUL}.a0.bin',

Master_Grid_Restart = '$OUTPUT/CAMx.$RUN.200206${YESTERDAY}.inst',

Nested_Grid_Restart = '$OUTPUT/CAMx.$RUN.200206${YESTERDAY}.finst',

PiG_Restart = ' ',

Flexi_Nest = .false.

Emiss_Grid(1) = '$EMIS/emiss.stl.36km.200206${CAL}.a1.bin',

Surface_Grid(1) = '$INPUT/met/camx.lu.36k.bin',

Met2D_Grid(1) = '$INPUT/met/camx.2d.200206${CAL}.36k.bin',

Met3D_Grid(1) = '$INPUT/met/camx.3d.200206${CAL}.36k.bin',

Vdiff_Grid(1) = '$INPUT/met/camx.kv.200206${CAL}.36k.bin',

Cloud_Grid(1) = '$INPUT/met/camx.cr.200206${CAL}.36k.bin',

Emiss_Grid(2) = '$EMIS/emiss.stl.12kmsmall.200206${CAL}.a1.bin',

Surface_Grid(2) = '$INPUT/met/camx.lu.12ksmall.bin',

Met2D_Grid(2) = '$INPUT/met/camx.2d.200206${CAL}.12ksmall.bin',

Met3D_Grid(2) = '$INPUT/met/camx.3d.200206${CAL}.12ksmall.bin',

Vdiff_Grid(2) = '$INPUT/met/camx.kv.200206${CAL}.12ksmall.bin',

Cloud_Grid(2) = '$INPUT/met/camx.cr.200206${CAL}.12ksmall.bin',

/

!-------------------------------------------------------------------------------

ieof

#

# --- Execute the model ---

#

if( ! { $EXEC } ) then

 exit

endif

end

Figure 2-2 (concluded).
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2.4 Benchmarking Model Run Times

Two cases with very different model configurations were used to test CAMx v5.00 with 

MPI/OMP. Note that runtimes and parallelization scalability for the current version of CAMx 

have been improved according to updates to the MPI implementation since v5.00 – however, 

conclusions drawn from these test remain valid. The first model configuration is the standard 

CAMx test case available for download from www.camx.com: it employs two relatively small 

grids at 36 and 12 km resolution, centered over St Louis, Missouri:

• Grids: 68×68 and 92×115

• 16 layers

• No PiG

• Mechanism 6 (CB05, no PM)

The second configuration was provided by the EPA/OAQPS, and employs two larger grids, the 

36-km RPO domain covering most of North America and a 12-km grid covering the entire 

eastern U.S.:

• Grids: 148×112 and 281×242

• 14 layers

• No PiG

• Mechanism 4 CF (CB4, with PM)

Results from both test cases are shown in Tables 2-3 and 2-4, respectively. These results 

consistently show that MPI is most advantageous for larger applications in which overhead 

processes (e.g., model setup, I/O, etc.) are a much smaller fraction of total model run time. In 

other words, CAMx applications on expansive multiple grids, employing extensive chemistry 

(PM and RTRAC), and/or including Probing Tools (OSAT, PSAT, DDM) would benefit most from 

MPI parallelization.

Table 2-3. CAMx v5.00 speed performance with MPI and OMP for the distribution test case 

available at www.camx.com (processed on 2.83 GHz Intel Xeon chipsets).

MPI Slices OMP threads / Slice Total CPU Minutes /Sim Day Equivalent Processors

1 1 1 106

2 1 2 57 1.9

4 1 4 32 3.3

8 1 8 21 5.0

16 1 16 18 5.9

1 4 4 43 2.5

2 4 8 25 4.3

4 4 16 17 6.2

*Equivalent Processors is defined as the ratio of runtime for multiple processors to the runtime for a single processor.
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Table 2-4. CAMx v5.00 speed performance with MPI and OMP for the EPA/OAQPS test case 

(processed on 2.83 GHz Intel Xeon chipsets).

MPI Slices OMP threads / Slice Total CPU Minutes / Sim Day Equivalent Processors*

1 1 1 503

2 1 2 266 1.9

4 1 4 138 3.6

8 1 8 81 6.2

12 1 12 76 7.0

16 1 16 61 8.2

24 1 24 49 10.3

1 8 8 111 4.5

2 8 16 79 6.4

4 4 16 71 7.1

3 8 24 52 9.7

*Equivalent Processors is defined as the ratio of runtime for multiple processors to the runtime for a single processor.

2.5 CAMx Pre- And Post-Processors

This section describes a variety of CAMx pre- and post-processors that we have made available 

to the user community. Since they support CAMx I/O, these programs are written in Fortran77 

and Fortran90 and distributed by ENVIRON as free software. As such, they contain notices like 

this in the source code:

 ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

c Copyright (C) 2003 ENVIRON

c 

c This program is free software; you can redistribute it and/or

c modify it under the terms of the GNU General Public License

c as published by the Free Software Foundation; either version 2

c of the License, or (at your option) any later version.

c 

c This program is distributed in the hope that it will be useful,

c but WITHOUT ANY WARRANTY; without even the implied warranty of

c MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

c GNU General Public License for more details.

c

c To obtain a copy of the GNU General Public License

c write to the Free Software Foundation, Inc., 

c 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

ENVIRON occasionally posts updates for certain widely-used programs when necessary, but 

does not actively support or maintain every one. Users can e-mail questions, comments, 

suggestions or improvements to ask-camx@environ.org. A few of the more important pre- and 

post-processors are briefly described below. Each come with README files, makefiles, and 

sample job scripts that document their purpose and usage.

2.5.1 Emissions

Most emission models (those shown in Figure 2-1) can provide speciated, temporally-allocated, 

gridded and point source emission input files in the CAMx-ready format. Further processing 

may be required, however, to select point sources for the PiG treatment, translate the point 
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source files from a common ASCII text format to CAMx-ready binary files, or to refine the 

domain size/resolution for gridded emissions.

PIGSET: This program allows the user to select and set certain point sources for the Plume-inGrid (PiG) treatment in a CAMx simulation. It also converts ASCII point source files 

commonly generated by emission models such as SMOKE, CONCEPT, and EPS3 to 

CAMx-ready binary format. See the source code for more information, and the sample 

job for usage. Also see Section 6 for guidance in selecting PiG point sources and 

manipulating day-specific point source files.

WINDOW: This program is used to “window” out a sub-section of the surface emissions grid for 

use on a smaller CAMx grid. It can also be used to aggregate or interpolate surface 

emissions to coarser or finer resolution, respectively. See the sample job for usage.

SEASALT: This program generates aerosol emissions of sodium and chloride, and gaseous 

emissions of chlorine and halo-methane compounds, using CAMx-ready meteorological 

and landuse files. A separate merging program is included that allows sea salt 

emissions to be merged in with pre-existing CAMx-ready gridded emission files.

2.5.2 Meteorology

The recommended approach to develop meteorological inputs for CAMx is through the use of 

prognostic meteorological models. ENVIRON provides interface programs for three specific 

models: WRF, MM5, and RAMS; This does not necessarily preclude other meteorological 

models to be used, but users will need to develop interface programs on their own.

WRFCAMx: This program generates CAMx v6 meteorological input files from WRF (ARW core) 

v2 and v3 output files. See the README in the archive for a description of the program 

and how it is applied.

MM5CAMx: This program generates CAMx v6 meteorological input files from MM5 v3 output 

files. See the README in the archive for a description of the program and how it is 

applied.

RAMSCAMx: This program generates CAMx v6 meteorological input files from RAMS v4/5/6

output files. See the README in the archive for a description of the program and how it 

is applied.

METCONVERT: This program converts older meteorological files from CAMx v4 and v5 to the 

CAMx format introduced with CAMx v6.

KVPATCH: This program applies minimum Kv values within a user-defined surface layer depth 

based on an input landuse grid. It optionally allows Kv profiles to be extended into 

daytime boundary-layer capping convection as defined by input cloud/rain files. See 

the source code for more information. Use of this program to adjust Kv inputs is 

entirely optional.
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2.5.3 Photolysis Rates

The development of photolysis rate inputs for CAMx is crucial for the photochemical 

mechanisms, but is not needed for inert or simple chemistry (e.g., Mechanism 10) applications. 

Two programs are available to assist the user in developing photolysis and ozone column input 

files.

O3MAP: This program prepares ozone column input files for CAMx, and must be run prior to 

running the TUV model as it defines the atmospheric ozone column intervals based on 

input data. Ozone column data files (http://ozoneaq.gsfc.nasa.gov/OMIOzone.md

or ftp://toms.gsfc.nasa.gov/pub/omi/data/) in latitude/longitude format must be 

supplied as input. NOTE: gaps in day-specific ozone column data at low latitudes, and 

high latitudes during winter, may result in zero values over portions of the modeling 

grid (see Figure 2-3). This results from the inability of polar-orbiting satellite 

instruments to cover the entire globe on a daily basis. The user may instead use 

seasonal-average ozone column files (no data gaps); alternatively, O3MAP provides an 

option to fill these day-specific gaps with an average determined from valid data 

processed for the extraction domain. See the Readme file and job script in the archive 

for usage.

Figure 2-3. An example of global ozone column from the Ozone Monitoring Instrument (OMI) 

platform. White areas denote missing data. 

From http://ozoneaq.gsfc.nasa.gov/OMIOzone.md. 
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TUV: This is a radiative transfer model that develops clear-sky photolysis rate inputs for all 

CAMx photochemical mechanisms. TUV is developed and distributed by NCAR (2011). 

The program specifies default intervals for 5 surface UV albedos, 3 terrain heights, 11 

altitudes above ground, and 10 solar zenith angles. Five total atmospheric ozone

column intervals are defined from the O3MAP program. See the sample job in the 

archive for usage.

2.5.4 Air Quality

There are numerous approaches for defining initial and boundary concentration inputs for 

CAMx. The level of possible detail ranges from time- and space-constant values for all 

pollutants, to specific time and space profiles for each. The level of detail depends on available 

measurements or modeling datasets, the particular focus and detail of the modeling exercise, 

and scale considerations (e.g., local vs. continental domains). ENVIRON provides a simple 

program that generates space and time-constant initial and boundary conditions for use in 

simple CAMx applications and testing. The more common approach for regional applications is 

to extract initial and boundary conditions from the output of global-scale chemical transport 

models. Users will need to develop their own programs if they choose an alternative 

methodology to generate initial/boundary conditions.

ICBCPREP: This program prepares CAMx initial and boundary condition files. Values are 

constant in space and time, but unique values may be specified for each chemical 

species to be modeled; they are defined in a simple text file. See the sample job in the 

archive for usage.

GEOS2CAMx: This program generates CAMx initial and boundary condition input files from 

GEOS-Chem global model output. See the Release Notes and job scripts in the archive 

for a description of the program and how it is applied.

MOZART2CAMx: This program generates CAMx and CMAQ initial and boundary condition input 

files from MOZART4 output (using both GEOS5 and NCEP meteorology). This program 

will also process AM3 datasets if output is first translated to a geodetic (lat/lon) grid, 

concentrations are provided as volume mixing ratio, and all needed state variables are 

available. See the README in the archive for a description of the program and how it is 

applied. You will need I/O-API and NetCDF libraries to compile and run this program.

2.5.5 Landuse

Approaches for developing landuse/landcover inputs for CAMx are about as varied as they are 

for initial/boundary conditions. Popular approaches have included: (1) translating gridded 

spatial allocation surrogates developed during emissions processing into the CAMx categories 

described in Section 3; (2) translating the gridded landuse/landcover fields from the 

meteorological model; or (3) separately developing landuse input fields from raw data (such as 

from the USGS or NLCD) using GIS or other programs. The advantages of (1) are consistency 

with input emissions estimation methodologies, and the fact that land cover processing is done

just once. The advantages of (2) are similar consistency with the meteorological modeling and 

one-time processing, but most models assign a single dominant landuse to each grid cell, which 
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may not be representative for coarse-resolution grids (CAMx allows a distribution of multiple 

land cover types per cell). ENVIRON provides meteorological interface programs (described 

above) that translate the meteorological model landuse/landcover fields to the CAMx 

definitions and grid configuration.

MERGE_LULAI: This program merges independently-developed landuse and/or LAI fields (for 

example via GIS processing of common terrestrial datasets) with an existing CAMx 2D 

surface file generated by the meteorological interface programs. See the sample job 

and source code for a description of the program and how it is applied. 

2.5.6 Post-processors

Most of the CAMx post-processors provided by ENVIRON provide some manner of 

concentration file manipulation, either to extract certain information from the raw output files, 

to re-format for use in other programs and applications, to concatenate files, etc. A few others 

are provided to assist in evaluating Probing Tool output. As stated above, ENVIRON does not 

provide any visualization or graphics software.

AVGDIF: This program is used to compare two CAMx format output average files and print a 

table of differences. This is useful for checking differences between CAMx runs on 

different machines or different compile options for the test case. See the sample job in 

the archive for usage.

BNDEXTR: Use this program to extract boundary conditions for a nested grid when you apply 

CAMx in one-way nesting mode. One-way nesting means that CAMx is run successively 

for each grid, with BNDEXTR as the interface between each run. This program is not 

needed when CAMx is run in the more standard two-way nesting mode, where all grids 

are run in a single simulation. See the example job for usage.

CAMxPOST: This is a suite of post-processing utilities designed to facilitate the evaluation of 

model performance. It is used to combine observations and predictions, calculate 

statistics, and plot time series. See the README file in the archive for usage.

CAMxTRCT: This program extracts specified chemical species for specified grids from the 

output average concentration and deposition files, and from input emission files. 

Output from this program can be written in the standard CAMx format, or alternatively 

to a text (ASCII) format in Surfer® “GRD” format for subsequent plotting. It also has the 

capability to convert units. See the sample job in the archive for usage.

CAMx2IOAPI: This program converts CAMx output average concentration and deposition files 

to I/O-API format. You will need I/O-API and NetCDF libraries to compile and run this 

program. This program allows you to use various third-party manipulation and 

visualization software that handle I/O-API format.

PA_Tools: This is a suite of post-processing utilities designed to extract IPR, IRR, and CPA data 

from CAMx Process Analysis output files and reformat the data suitable for subsequent 

analysis (e.g. using spreadsheets).
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3. CORE MODEL INPUT/OUTPUT STRUCTURES

Most CAMx input/output (I/O) files are Fortran binary and based on the Urban Airshed Model 

(UAM) convention. This allows the user to employ widely available software designed 

specifically for these formats to develop the input files or to post-process and visualize the 

output files.

CAMx requires input files that define the chemical mechanism and describe the photochemical 

conditions, surface characteristics, initial/boundary conditions, emission rates, and various 

meteorological fields over the entire modeling domain. Table 3-1 summarizes the input data 

requirements of CAMx. Preparing this information requires several preprocessing steps to 

translate “raw” emissions, meteorological, air quality and other data into final input files for 

CAMx. We expect that most CAMx applications will utilize output from a prognostic 

meteorological model that can generate all of the required time varying three-dimensional 

meteorological fields. 

Table 3-1. Data requirements of CAMx.

Data Types Data Fields

Meteorology

Supplied by Prognostic Meteorological Models

• 3-Dimensional Gridded Fields:

- Vertical Grid Structure

- Horizontal Wind Components

- Temperature

- Pressure

- Water Vapor

- Vertical Diffusivity

- Clouds/Precipitation

- Snow Cover

Air Quality

Developed from Other Models or Measurement Data

• Gridded Initial Concentrations

• Gridded Boundary Concentrations

Emissions

Supplied by Emissions Models and Processors

• Elevated Point Sources

- Industrial Facilities

- Prescribed, Agricultural, Wild Fires

- Lightning NOx

• Combined Gridded Sources

- Low-Level Point

- On-Road and Non-Road Mobile

- Area

- Biogenic

- Oceanic

Geographic

Developed from Terrain, Landuse/Landcover, and 

Vegetation Density Datasets

• Gridded Surface Characteristics

- Landuse/LandCover

- Terrain Elevation

- Leaf Area Index (LAI)

- Land/Ocean Mask

Photolysis

Derived from Satellite Measurements and Radiative 

Transfer Models

• Atmospheric Radiative Properties

- Gridded Ozone Column Codes

- Photolysis Rates Lookup Table
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CAMx produces gridded time-averaged concentration output files; the user selects the time 

interval (usually hourly), the species to be output (both “state” and “radical” species), and 

whether the output contains just two-dimensional surface layer fields or entire threedimensional fields. A separate average output file is written for each grid employed in the 

simulation. Surface deposition fields for the same user-selected species are also written to 

output files with the same structure as the average concentration files. Gridded threedimensional instantaneous concentrations of all species on all grids are written at the end of 

the simulation to allow for a model restart. Commonly available graphical visualization and 

animation software can be used to view CAMx average and deposition output files. The CAMx 

Probing Tool options provide their own information in separate output files in the same CAMx 

output format that can be viewed directly or further post-processed for detailed analysis. 

Diagnostic output files include three files that track computer resources, echo input selections, 

provide mass budget and diagnostic summaries, and provide error/warning messages.

3.1 CAMx Chemistry Parameters File

Chemistry parameters are provided in a text (ASCII) file that specifies the chemical mechanism 

be used and associated details on species properties and reaction types and rates. The 

chemistry parameters file format is defined in Table 3-2, and samples are given in Figure 3-1. 

Some records in this file are labeled (columns 1-20) to indicate the type of information to 

supply on that line (starting in column 21). For records that are not labeled, data start in 

column 1. Some chemistry parameter records are optional, depending upon the logical flags 

indicated for such records, and are shown in Table 3-2 by a check in the third column; if the 

indicated option is not invoked these records should not appear in the file. The first record of 

the chemistry parameters file must contain the string “VERSION6.1”, which indicates that the

file is specific to this version of CAMx.

If the chemistry flag is set “true” on the CAMx.in file, CAMx checks that certain properties of 

the selected mechanism are consistent with parameters supplied on the input file (e.g., number 

of reactions, photolysis reactions and species). If any discrepancies are found, they are 

reported in the output message file and the simulation is halted. The user may also specify an 

inert simulation by setting the chemistry flag to “false”. In this case, any number of arbitrarily 

named species may be listed, and chemistry reaction parameters are ignored. 

Gas-phase chemistry is controlled by the Mechanism ID (5, 6, 7, or 2 for SAPRC99, CB05, CB6, or 

CB6r1, respectively). Aerosol chemistry is controlled by the keywords “NONE”, “INERT”, “CF” or 

“CMU”. In the “INERT” case, the user can define any number of arbitrary particulate names and 

sizes. The “CF” and “CMU” options invoke aerosol chemistry and treat aerosol size using either 

static coarse and fine modes (CF) or an evolving size section model (CMU). Both CF and CMU 

options require a minimum set of specific aerosol names with associated chemistry.

The chemistry parameters file controls how photolysis rates are calculated in CAMx. So-called 

“primary” photolysis rates are input to CAMx via the photolysis rates file. The primary 

photolysis reactions are identified by number in the chemistry parameters file and the 

photolysis rates file must match this declaration. So-called “secondary” photolysis rates are set 

by scaling factors to one of the primary reactions. Use of secondary rates requires at least one 

primary photolysis reaction.
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Table 3-2. Description of the CAMx chemistry parameters file. The record labels exist in columns 1-20, and where given, the 

input data for that record start in column 21. The format denoted “list” indicates a free-format list of numbers (comma or space- delimited).

Record Label

(columns 1-20)

Record

Optional

Format Description

CAMx version A Model version keyword (VERSION6.1)

Mechanism ID list ID number of chemical mechanism (see Table 5-1)

Aerosol Option A Keyword for aerosol scheme (NONE, INERT, CF, or CMU)

1

Description A Message record to describe this file

No of gas species list Number of radical and state gas species (NGAS ≥ 1)

No of aero species list

Number of aerosol species (NAERO ≥ 0)

Aerosol chemistry timestep (min) (if NAERO > 0)

Number of size bins (NBIN ≥ 1) (if NAERO > 0)

2

Aerosol diameter (μm) for NBIN+1 cut points (if NAERO > 0)

No of reactions list Number of reactions (NREACT ≥ 0)

Prim photo rxns list Number of primary photolysis reactions (NPHOT1 ≥ 0)

List of primary photolysis reaction ID numbers (must match the photolysis rates input file)

No of sec photo rxn list Number of secondary photolysis reactions (NPHOT2 ≥ 0)

ID, prim ID, scale √ list

If NPHOT2 > 0, repeat this record for each secondary photolysis reaction 

ID number of the secondary photolysis reaction

ID number of the primary photolysis reaction used for scaling

Secondary reaction scale factor

SrfMod #spc, #rxns list Number of Surface Model species and reactions (see Section 4.8)

Set to 0,0 if not using the Surface Model

Species Records Heading

Gas Spec ... Heading

5X,

A10, 

E10.0,

E10.0, 

F10.0,

F10.0,

F10.0

F10.0

Repeat this record for each gas species (start in column 1)

Gas species name (radicals first, followed by state species)

Lower bound concentration (ppm)

Henry’s law constant (M/atm)

Henry’s law temperature dependence (K)

Molecular weight (g/mol)

Wesley’s reactivity parameter

Surface resistance scaling factor for strong acids (0-1)
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Table 3-2 (continued). Description of the CAMx chemistry parameters file. The record labels exist in columns 1-20, and where 

given, the input data for that record start in column 21. The format denoted “list” indicates a free-format list of numbers (comma 

or space-delimited).

Record Label

(columns 1-20)

Record

Optional

Format Description

Aero Spec ... √ Heading (if NAERO > 0)

√

5X,

A10, 

E10.0,

F10.0

F10.0

I10

F10.0

I10

If NAERO > 0, repeat this record for each aerosol species (start in column 1)

Aerosol species name

Lower bound concentration (μg/m3

)

Species density (g/cm3

)

Dry extinction efficiency (m2

/μm)

Hygroscopic extinction adjustment (0 = no adjustment, 1 = RH-dependent)

Single-scattering albedo

Assigned size bin (INERT and CF aerosols only – references cut points in record 6)

Reaction Records √ Heading (if NREACT > 0)

Rxn Typ Param ... √ Heading (if NREACT > 0)

√ list

If NREACT > 0, repeat this record for each gas-phase reaction (start in column 1)

Reaction ID number

Rate constant expression ID number (1-7, as shown in Table 3-3)

Rate constant parameters (depending on expression type in Table 3-3). For reactions identified as 

photolysis reactions above, the rate constant is not used and is customarily set to zero.

1 NONE = gas-phase chemistry only; INERT = user-defined inert PM species; CF = Coarse/Fine aerosol chemistry scheme; CMU = multi-sectional aerosol chemistry scheme;.

2 For the CF scheme, NBIN must be set to 2, and the user specifies the coarse/fine size ranges.
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CAMx Version |VERSION6.1

Mechanism ID |6

Aerosol Option |CF

Description |CB05 plus PM (CF) with Hg: PNA rates set to 0; molecular units

No of gas species |67

#aero, dt, bins |24 15.0 2 0.039 2.5 10.0

No of reactions |156

Prim photo rxns |19 1 8 9 14 15 25 36 51 52 53 62 65 75 76 87 91 102 143 152

No of sec photo rxn|4

ID, prim ID, scale |72 65 1.0

 |97 65 0.0

|106 91 1.0

|138 75 9.0

SrfMod #spc, #rxns |0 0

Species Records

 Gas Spec lower bnd H-law T-fact Molwt Reactvty Rscale

 1 O1D 1.00E-25 1.00E+00 0. 0.00 0.0 0.

 2 O 1.00E-25 1.00E+00 0. 0.00 0.0 0.

 3 OH 1.00E-25 1.00E+00 0. 0.00 0.0 0.

 4 HO2 1.00E-25 1.00E+00 0. 0.00 0.0 0.

 5 C2O3 1.00E-25 1.00E+00 0. 0.00 0.0 0.

 6 XO2 1.00E-25 1.00E+00 0. 0.00 0.0 0.

 7 XO2N 1.00E-25 1.00E+00 0. 0.00 0.0 0.

 8 CXO3 1.00E-25 1.00E+00 0. 0.00 0.0 0.

 9 MEO2 1.00E-25 1.00E+00 0. 0.00 0.0 0.

10 TO2 1.00E-25 1.00E+00 0. 0.00 0.0 0.

11 ROR 1.00E-25 1.00E+00 0. 0.00 0.0 0.

12 HCO3 1.00E-25 1.00E+00 0. 0.00 0.0 0.

13 CRO 1.00E-25 1.00E+00 0. 0.00 0.0 0.

14 AACD 1.00E-12 5.00E+03 -4000. 60.03 1.0 1.

15 ALD2 1.00E-09 6.30E+03 -6492. 44.04 1.0 1.

16 ALDX 1.00E-12 6.30E+03 -6492. 58.06 1.0 1.

17 CO 1.00E-04 1.00E-10 0. 28.00 0.0 1.

18 CRES 1.00E-09 2.70E+03 -6492. 108.12 1.0 1.

19 ETH 1.00E-09 1.00E-02 -4000. 28.05 0.0 1.

20 ETHA 1.00E-04 1.73E-03 -4000. 30.06 0.0 1.

21 ETOH 1.00E-09 2.20E+02 -4932. 46.05 1.0 1.

22 FACD 1.00E-12 5.68E+03 -6060. 46.00 1.0 1.

23 FORM 1.00E-09 6.30E+03 -6492. 30.01 1.0 1.

24 H2O2 1.00E-09 7.40E+04 -6643. 33.99 1.0 0.

25 HNO3 1.00E-09 2.10E+05 -8707. 62.98 0.0 0.

26 HONO 1.00E-09 5.90E+01 -4781. 46.99 1.0 1.

27 IOLE 1.00E-12 5.00E-03 -4000. 56.10 0.0 1.

28 ISOP 1.00E-09 1.00E-02 -4000. 68.11 0.0 1.

29 ISPD 1.00E-09 6.30E+03 -6492. 70.07 1.0 1.

30 MEOH 1.00E-09 2.20E+02 -4932. 32.03 1.0 1.

31 MEPX 1.00E-12 3.05E+02 -5250. 48.02 0.8 0.

32 MGLY 1.00E-09 2.70E+03 -6492. 72.04 1.0 1.

33 N2O5 1.00E-12 1.00E+05 -4000. 107.95 0.1 0.

34 NO 1.00E-15 1.90E-03 -1480. 29.99 0.0 1.

35 NO2 1.00E-09 1.00E-02 -2516. 45.98 0.8 1.

36 NO3 1.00E-12 1.00E+05 -4000. 61.97 0.1 0.

37 NTR 1.00E-09 9.40E+03 -8706. 119.07 0.0 1.

38 O3 1.00E-09 1.10E-02 -2415. 47.97 1.0 1.

39 OLE 1.00E-09 5.00E-03 -4000. 42.07 0.0 1.

40 OPEN 1.00E-12 2.70E+03 -6492. 84.05 1.0 1.

41 PACD 1.00E-12 5.00E+03 -4000. 76.02 1.0 1.

42 PAN 1.00E-09 3.60E+00 -5910. 120.99 0.6 1.

43 PANX 1.00E-09 3.60E+00 -5910. 135.02 0.6 1.

44 PAR 1.00E-04 1.00E-03 -4000. 72.13 0.0 1.

 

Figure 3-1a. Example CAMx chemistry parameters file for Mechanism 6 (CF scheme), 

including the mercury species HG0, HG2, and HGP.
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45 PNA 1.00E-09 2.00E+04 -5910. 78.97 1.0 1.

46 ROOH 1.00E-12 1.00E+02 -4000. 90.09 0.8 0.

47 SO2 1.00E-09 1.22E+00 -3156. 64.04 0.0 1.

48 SULF 1.00E-12 1.00E+10 0. 98.03 0.0 0.

49 TERP 1.00E-12 4.90E-02 -4000. 136.21 0.0 1.

50 TOL 1.00E-09 1.20E+00 -4000. 92.13 0.0 1.

51 XYL 1.00E-09 1.40E+00 -4000. 106.15 0.0 1.

52 NH3 1.00E-09 5.76E+01 -4100. 16.94 0.0 0.

53 HCL 1.00E-12 1.00E+05 -4000. 36.30 0.0 0.

54 TOLA 1.00E-09 1.20E+00 -4000. 91.94 0.0 1.

55 XYLA 1.00E-09 1.40E+00 -4000. 106.29 0.0 1.

56 ISP 1.00E-09 1.00E-02 -4000. 67.74 0.0 1.

57 TRP 1.00E-12 4.90E-02 -4000. 136.13 0.0 1.

58 SQT 1.00E-12 4.90E-02 -4000. 204.42 0.0 1.

59 CG1 1.00E-12 1.00E+05 -4000. 150.34 0.0 1.

60 CG2 1.00E-12 1.00E+05 -4000. 150.34 0.0 1.

61 CG3 1.00E-12 1.00E+05 -4000. 130.25 0.0 1.

62 CG4 1.00E-12 1.00E+05 -4000. 130.25 0.0 1.

63 CG5 1.00E-12 1.00E+05 -4000. 179.74 0.0 1.

64 CG6 1.00E-12 1.00E+05 -4000. 179.74 0.0 1.

65 CG7 1.00E-12 1.00E+05 -4000. 210.54 0.0 1.

66 HG0 1.00E-12 1.11E-01 -4970. 200.80 0.0 1.

67 HG2 1.00E-12 2.00E+05 -4000. 254.48 0.0 0.

 Aero Spec lower bnd Density Dry Bext RH Adjust SSA SizeBin

 1 PNO3 1.00E-09 1.5 7.0 1 0.99 1

 2 PSO4 1.00E-09 1.5 7.0 1 0.99 1

 3 PNH4 1.00E-09 1.5 7.0 1 0.99 1

 4 POA 1.00E-09 1.0 7.0 0 0.80 1

 5 SOA1 1.00E-09 1.0 7.0 0 0.80 1

 6 SOA2 1.00E-09 1.0 7.0 0 0.80 1

 7 SOA3 1.00E-09 1.0 7.0 0 0.80 1

 8 SOA4 1.00E-09 1.0 7.0 0 0.80 1

 9 SOA5 1.00E-09 1.0 7.0 0 0.80 1

10 SOA6 1.00E-09 1.0 7.0 0 0.80 1

11 SOA7 1.00E-09 1.0 7.0 0 0.80 1

12 SOPA 1.00E-09 1.0 7.0 0 0.80 1

13 SOPB 1.00E-09 1.0 7.0 0 0.80 1

14 PEC 1.00E-09 2.0 18.0 0 0.25 1

15 FPRM 1.00E-09 3.0 0.4 0 0.70 1

16 FCRS 1.00E-09 3.0 0.4 0 0.70 1

17 CPRM 1.00E-09 3.0 0.4 0 0.70 2

18 CCRS 1.00E-09 3.0 0.4 0 0.70 2

19 NA 1.00E-09 2.0 1.5 1 0.99 1

20 PCL 1.00E-09 2.0 1.5 1 0.99 1

21 PH2O 1.00E-09 1.0 0.0 0 0.99 1

22 HGP 1.00E-15 8.0 0.0 0 0.99 1

23 HGIIP 1.00E-20 8.0 0.0 0 0.99 1

24 HGIIPC 1.00E-20 8.0 0.0 0 0.99 2

Reaction Records

Rxn Typ Order Parameters (1 to 12, depending upon Typ)

1 1 1 0.000E+00

2 3 3 6.000E-34 0.0 -2.40 300.0

3 3 2 3.000E-12 1500.0 0.00 300.0

4 3 2 5.600E-12 -180.0 0.00 300.0

5 4 2 2.500E-31 0.0 -1.80 300.0 2.200E-11 0.0 -

0.70 300.0 0.60 1.00

6 4 2 9.000E-32 0.0 -1.50 300.0 3.000E-11 0.0 0.00 

300.0 0.60 1.00

7 3 2 1.200E-13 2450.0 0.00 300.0

8 1 1 0.000E+00

9 1 1 0.000E+00

10 3 2 2.100E-11 -102.0 0.00 300.0

Figure 3-1a (continued).
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11 1 2 2.200E-10

12 3 2 1.700E-12 940.0 0.00 300.0

13 3 2 1.000E-14 490.0 0.00 300.0

14 1 1 0.000E+00

15 1 1 0.000E+00

16 3 2 1.500E-11 -170.0 0.00 300.0

17 3 2 4.500E-14 1260.0 0.00 300.0

18 4 2 2.000E-30 0.0 -4.40 300.0 1.400E-12 0.0 -

0.70 300.0 0.60 1.00

19 1 2 2.500E-22

20 1 3 1.800E-39

21 4 1 1.000E-03 11000.0 -3.50 300.0 9.700E+14 11080.0 0.10 

300.0 0.45 1.00

22 3 3 3.300E-39 -530.0 0.00 300.0

23 1 3 5.000E-40

24 4 2 7.000E-31 0.0 -2.60 300.0 3.600E-11 0.0 -

0.10 300.0 0.60 1.00

25 1 1 0.000E+00

26 3 2 1.800E-11 390.0 0.00 300.0

27 1 2 1.000E-20

28 4 2 2.000E-30 0.0 -3.00 300.0 2.500E-11 0.0 0.00 

300.0 0.60 1.00

29 6 2 2.400E-14 -460.0 0.00 300.0 2.700E-17 -2199.0 0.00 

300.0 6.500E-34 -1335.0 0.00 300.0

30 3 2 3.500E-12 -250.0 0.00 300.0

31 1 2 0.000E+00

32 1 1 0.000E+00

33 1 2 0.000E+00

34 7 2 2.300E-13 -600.0 0.00 300.0 1.700E-33 -1000.0 0.00 

300.0

35 7 3 3.220E-34 -2800.0 0.00 300.0 2.380E-54 -3200.0 0.00 

300.0

36 1 1 0.000E+00

37 3 2 2.900E-12 160.0 0.00 300.0

38 1 2 1.100E-10

39 3 2 5.500E-12 2000.0 0.00 300.0

40 3 2 2.200E-11 -120.0 0.00 300.0

41 3 2 4.200E-12 240.0 0.00 300.0

42 4 2 6.900E-31 0.0 -1.00 300.0 2.600E-11 0.0 0.00 

300.0 0.60 1.00

43 3 2 4.800E-11 -250.0 0.00 300.0

44 3 2 3.000E-11 -200.0 0.00 300.0

45 3 2 1.400E-12 2000.0 0.00 300.0

46 1 2 1.000E-11

47 1 2 2.200E-11

48 1 2 3.500E-12

49 1 2 1.000E-17

50 3 2 8.500E-13 2450.0 0.00 300.0

51 1 1 0.000E+00

52 1 1 0.000E+00

53 1 1 0.000E+00

54 3 2 2.600E-12 -365.0 0.00 300.0

55 3 2 2.600E-12 -365.0 0.00 300.0

56 3 2 7.500E-13 -700.0 0.00 300.0

57 3 2 7.500E-13 -700.0 0.00 300.0

58 1 2 6.800E-14

59 1 2 6.800E-14

60 1 2 6.800E-14

61 3 2 5.900E-13 360.0 0.00 300.0

62 1 1 0.000E+00

63 4 2 3.000E-31 0.0 -3.30 300.0 1.500E-12 0.0 0.00 

300.0 0.60 1.00

Figure 3-1a (continued).
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64 3 2 3.010E-12 -190.0 0.00 300.0

65 1 1 0.000E+00

66 7 2 1.440E-13 0.0 0.00 300.0 3.430E-33 0.0 0.00 

300.0

67 3 2 2.450E-12 1775.0 0.00 300.0

68 3 2 2.800E-12 -300.0 0.00 300.0

69 3 2 4.100E-13 -750.0 0.00 300.0

70 3 2 9.500E-14 -390.0 0.00 300.0

71 3 2 3.800E-12 -200.0 0.00 300.0

72 1 1 0.000E+00

73 3 2 7.300E-12 620.0 0.00 300.0

74 1 2 9.000E-12

75 1 1 0.000E+00

76 1 1 0.000E+00

77 3 2 3.400E-11 1600.0 0.00 300.0

78 1 2 5.800E-16

79 3 2 9.700E-15 -625.0 0.00 300.0

80 3 1 2.400E+12 7000.0 0.00 300.0

81 1 2 5.600E-12

82 3 2 5.600E-15 -2300.0 0.00 300.0

83 1 2 4.000E-13

84 3 2 1.800E-11 1100.0 0.00 300.0

85 3 2 5.600E-12 -270.0 0.00 300.0

86 3 2 1.400E-12 1900.0 0.00 300.0

87 1 1 0.000E+00

88 3 2 8.100E-12 -270.0 0.00 300.0

89 4 2 2.700E-28 0.0 -7.10 300.0 1.200E-11 0.0 -

0.90 300.0 0.30 1.00

90 4 1 4.900E-03 12100.0 0.00 300.0 5.400E+16 13830.0 0.00 

300.0 0.30 1.00

91 1 1 0.000E+00

92 3 2 4.300E-13 -1040.0 0.00 300.0

93 3 2 2.000E-12 -500.0 0.00 300.0

94 3 2 4.400E-13 -1070.0 0.00 300.0

95 3 2 2.900E-12 -500.0 0.00 300.0

96 3 2 4.000E-13 -200.0 0.00 300.0

97 1 1 0.000E+00

98 3 2 4.000E-13 -200.0 0.00 300.0

99 3 2 1.300E-11 870.0 0.00 300.0

100 3 2 5.100E-12 -405.0 0.00 300.0

101 1 2 6.500E-15

102 1 1 0.000E+00

103 3 2 6.700E-12 -340.0 0.00 300.0

104 4 2 2.700E-28 0.0 -7.10 300.0 1.200E-11 0.0 -

0.90 300.0 0.30 1.00

105 4 1 4.900E-03 12100.0 0.00 300.0 5.400E+16 13830.0 0.00 

300.0 0.30 1.00

106 1 1 0.000E+00

107 1 2 3.000E-13

108 3 2 4.300E-13 -1040.0 0.00 300.0

109 3 2 2.000E-12 -500.0 0.00 300.0

110 3 2 4.400E-13 -1070.0 0.00 300.0

111 3 2 2.900E-12 -500.0 0.00 300.0

112 3 2 2.900E-12 -500.0 0.00 300.0

113 3 2 8.700E-12 1070.0 0.00 300.0

114 3 2 6.900E-12 230.0 0.00 300.0

115 1 2 8.100E-13

116 3 1 1.000E+15 8000.0 0.00 300.0

117 1 1 1.600E+03

118 1 2 1.500E-11

119 3 2 1.000E-11 280.0 0.00 300.0

120 1 2 3.200E-11

Figure 3-1a (continued).
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121 3 2 6.500E-15 1900.0 0.00 300.0

122 3 2 7.000E-13 2160.0 0.00 300.0

123 3 2 1.040E-11 792.0 0.00 300.0

124 4 2 1.000E-28 0.0 -0.80 300.0 8.800E-12 0.0 0.00 

300.0 0.60 1.00

125 3 2 1.200E-14 2630.0 0.00 300.0

126 3 2 3.300E-12 2880.0 0.00 300.0

127 1 2 2.300E-11

128 3 2 1.000E-11 -550.0 0.00 300.0

129 3 2 8.400E-15 1100.0 0.00 300.0

130 3 2 9.600E-13 270.0 0.00 300.0

131 3 2 1.800E-12 -355.0 0.00 300.0

132 1 2 8.100E-12

133 1 1 4.200E+00

134 1 2 4.100E-11

135 1 2 2.200E-11

136 1 2 1.400E-11

137 1 2 5.500E-12

138 1 1 0.000E+00

139 1 2 3.000E-11

140 3 2 5.400E-17 500.0 0.00 300.0

141 3 2 1.700E-11 -116.0 0.00 300.0

142 1 2 1.700E-11

143 1 1 0.000E+00

144 1 2 3.600E-11

145 3 2 2.540E-11 -407.6 0.00 300.0

146 3 2 7.860E-15 1912.0 0.00 300.0

147 3 2 3.030E-12 448.0 0.00 300.0

148 1 2 1.500E-19

149 1 2 3.360E-11

150 1 2 7.100E-18

151 1 2 1.000E-15

152 1 1 0.000E+00

153 1 2 3.600E-11

154 3 2 1.500E-11 -449.0 0.00 300.0

155 3 2 1.200E-15 821.0 0.00 300.0

156 3 2 3.700E-12 -175.0 0.00 300.0

Figure 3-1a (concluded).

CAMx Version |VERSION6.1

Mechanism ID |0

Aerosol Option |NONE

Description |inert test

No of gas species |1

No of aero species |0

No of reactions |0

Prim photo rxns |0

No of sec photo rxn|0

SrfMod #spc, #rxns |0 0

Species Records

 Gas Spec lower bnd H-law T-fact Molwt Reactvty Rscale

 1 TRACER 1.00E-09 1.00e-10 0. 1.00 0.0 1.

Figure 3-1b. Example inert chemistry parameters file (requires chemistry flag to be set false –

see the description of the CAMx control file).
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The section of the file that lists gas species must include the names of radical and state species, 

according to the selected chemical mechanism, along with each species’ lower bound value, 

Henry’s Law solubility parameters, molecular weight, and surface reactivity and resistance 

scaling parameters for use in the dry deposition calculations. The lower bound values set the 

minimum concentration “floor” for any chemical or physical process that reduces 

concentrations to “zero”. The lower bound is also used to set initial and/or boundary 

conditions for species that are omitted from the initial and/or boundary condition files. 

The section of the file that lists aerosol species names must include a lower-bound value, 

particle density, dry extinction efficiency, a hygroscopic flag, and single-scattering albedo. In 

the case of INERT or CF options, the user must also specify the size bin assigned to each species 

at the end of each particulate species record (CMU automatically applies each species to all size 

bins). Since the effect of aerosol water on optical parameters is taken into account through an 

internal relative humidity adjustment, the dry extinction efficiency for particle species PH2O 

must be set to zero.

CAMx supports several equations for specifying gas-phase rate constants, as shown in Table 3-

3a. The type of equation used for each reaction is identified by the second parameter specified 

for each reaction – a number between 1 and 7 (Table 3-3a). The number of additional 

parameters required depends upon the expression type and varies between 2 and 13, as shown 

in Table 3-3b. The CB mechanisms use types 1, 3, 4, and 7, and SAPRC99 uses types 1, 3, 4, 6 

and 7. Expression type 4 (Troe expression) allows for a complete description of dependencies 

on temperature and pressure; background information on Troe expressions may be found in 

the NASA and IUPAC rate constant compilations (NASA, 1997; IUPAC, 1992). 

Rate constants can be specified in molecular units (e.g., cm3 molecule-1 s

-1

) or ppm units (e.g., 

ppm-1 min-1). All the rate constants must be in a single units system; CAMx will determine 

which units system is being used from the magnitude of the rate constants. Diagnostic 

information on the rate constants and units system is output by CAMx at run-time.

3.2 Photolysis Rates File

The rates for the primary photolysis reactions are supplied via the photolysis rates file in units 

of minute-1. This file must be supplied if chemistry is invoked. The photolysis rates file 

comprises a large look-up table of clear-sky photolysis rates specific to the gas-phase chemistry 

mechanism to run. Rates are arranged in a matrix of five dimensions, including variations over 

10 solar zenith angles, 11 altitudes above ground, 5 total ozone column values, 5 ultraviolet 

(UV) surface albedos, and 3 terrain heights. This table is generated using the TUV preprocessor, 

which internally specifies the ranges of solar zenith, albedo, and terrain heights. The ranges of 

altitude are controlled by the user, while the ranges of ozone column are taken from the ozone 

column file (Section 3.3). TUV is run with a typical aerosol profile defined by Elterman (1968).
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Table 3-3a. Rate constant expression types supported in CAMx and order of expression 

parameters for the chemistry parameters file.

Expression 

Type Description Expression

1 Constant 298 k = k

2 UAM (Arrhenius expression) 



 



 



 



 = −

T

k k Ea

1

298

1

exp 298

3 General temperature dependence 



 





− 













 = T

E

T

T k A a

B

R

exp

4 Troe-type temperature and pressure 

dependence

[ ]

[ ]

G F

k M k

k M k 















+ = ∞ 1 / 0

0





 





− 













 = T

E

T

T k A a

B

R

exp 0





 



 ′ − 















′ = ′

′

∞

T

E

T

T k A a

B

R

exp

( ) 1 2 0 log [ ]/ 1

− ∞



































 = +

n

k M k G

5 Equilibrium with a previously defined 

reaction (kref) 



 





− 













 = T

E

T

T k k A a

B

R

ref exp

6 Lindemann - Hinshelwood as used for OH + 

HNO3 3 2

0 3

1 [ ]/

[ ]

k M k

k M k k

+ = +

7 Simple pressure dependence used for OH + 

CO [ ] k = k1 + k2 M

Notes:

T is temperature (K)

TR is reference temperature of 300 K

Ea is an Arrhenius activation energy (K)

k0 is the low pressure limit of the rate constant

k∞ is the high pressure limit of the rate constant

[M] is the concentration of air
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Table 3-3b. List of parameters that must be provided in the CAMx chemistry parameter file 

for each of the seven types of rate constant expressions. Use ppm/minute units for A and 

Kelvin for Ea and TR. The variable O is the order of the reaction (1 to 3). 

Expression

Type

Parameters

1 2 3 4 5 6 7 8 9 10 11 12 13

1 O k298

2 O k298 Ea

3 O A Ea B TR

4 O A Ea B TR A’ Ea’ B’ TR’ F n

5 O kref A Ea B TR

6 O Ao Ea

o Bo TRo A2 Ea2 B2 TR2 A3 Ea3 B3 TR3

7 O A1 Ea

1 B1 TR1 A2 Ea2 B2 TR2

The photolysis rates file is a readable text (ASCII) format and it has the following structure:

where the first record labels the version of TUV used to generate the file, and where variables 

have the following definitions:

ozcl Ozone column value for the current interval (Dobson units)

albcl UV albedo value for the current interval (unitless)

trncl Terrain height value for the current interval (km MSL)

height Altitude (km AGL)

pk Photolysis rates (min-1

) for nsol solar zenith angles 

Figure 3-2 presents an example of a photolysis rates file for the first several panels of data.

3.3 Ozone Column File

This file defines the intervals of total atmospheric ozone column to be used by TUV, as well as 

its spatial and temporal distributions for a specific CAMx domain and episode. This parameter 

is essential for photochemical simulations as it determines the spatial and temporal variation of 

photolysis rates. Therefore, this file must be supplied if chemistry is invoked. Additionally, the 

ozone column file may also provide an optional field defining a land/ocean mask (for mercury 

chemistry).

TUV4.8CAMx6

Loop from 1 to nozn ozone column intervals:

Loop from 1 to nalb UV albedo intervals:

Loop from 1 to ntht terrain height intervals:

ozcl,albcl,trncl (12X,f7.3,8X,f7.3,11X,f7.3)

Loop from 1 to nalt altitudes above ground:

height (*)

Loop from 1 to nphot photolysis reactions:

(pk(n),n=1,nsol) (1X,10F12.0)
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TUV4.8CAMx6

O3 Column = 0.290 Albedo= 0.040 Terrain = 0.000

 0.000 km above surface

 4.562E-01 4.526E-01 4.416E-01 4.224E-01 3.934E-01 3.516E-01 2.921E-01 2.065E-01 1.148E-01 3.074E-02 

 1.670E-03 1.643E-03 1.563E-03 1.427E-03 1.236E-03 9.889E-04 6.936E-04 3.747E-04 1.502E-04 2.570E-05 

 2.211E-03 2.186E-03 2.107E-03 1.973E-03 1.776E-03 1.506E-03 1.152E-03 7.108E-04 3.352E-04 7.560E-05 

 2.078E-03 2.007E-03 1.801E-03 1.485E-03 1.097E-03 6.925E-04 3.382E-04 1.034E-04 2.201E-05 2.056E-06 

 3.131E-04 3.058E-04 2.841E-04 2.491E-04 2.027E-04 1.482E-04 9.100E-05 4.015E-05 1.264E-05 1.517E-06 

 8.728E-05 8.638E-05 8.364E-05 7.891E-05 7.189E-05 6.212E-05 4.892E-05 3.166E-05 1.580E-05 3.934E-06 

 0.150 km above surface

 4.866E-01 4.830E-01 4.717E-01 4.521E-01 4.223E-01 3.794E-01 3.179E-01 2.284E-01 1.308E-01 3.760E-02 

 1.855E-03 1.827E-03 1.742E-03 1.598E-03 1.394E-03 1.130E-03 8.102E-04 4.566E-04 1.956E-04 3.701E-05 

 2.443E-03 2.416E-03 2.334E-03 2.193E-03 1.986E-03 1.701E-03 1.322E-03 8.415E-04 4.159E-04 1.000E-04 

 2.327E-03 2.249E-03 2.024E-03 1.677E-03 1.250E-03 8.008E-04 4.035E-04 1.337E-04 3.383E-05 4.166E-06 

 3.489E-04 3.410E-04 3.177E-04 2.799E-04 2.297E-04 1.704E-04 1.075E-04 5.024E-05 1.755E-05 2.556E-06 

 9.553E-05 9.460E-05 9.176E-05 8.684E-05 7.952E-05 6.928E-05 5.530E-05 3.672E-05 1.910E-05 5.068E-06 

 0.360 km above surface

 5.050E-01 5.013E-01 4.900E-01 4.702E-01 4.402E-01 3.968E-01 3.343E-01 2.426E-01 1.412E-01 4.171E-02 

 1.974E-03 1.945E-03 1.857E-03 1.708E-03 1.497E-03 1.222E-03 8.862E-04 5.096E-04 2.245E-04 4.415E-05 

 2.587E-03 2.560E-03 2.477E-03 2.333E-03 2.120E-03 1.826E-03 1.432E-03 9.258E-04 4.673E-04 1.152E-04 

 2.494E-03 2.411E-03 2.174E-03 1.806E-03 1.353E-03 8.740E-04 4.474E-04 1.536E-04 4.129E-05 5.492E-06 

 3.722E-04 3.640E-04 3.396E-04 3.002E-04 2.475E-04 1.851E-04 1.183E-04 5.679E-05 2.067E-05 3.210E-06 

 1.006E-04 9.970E-05 9.681E-05 9.180E-05 8.433E-05 7.382E-05 5.940E-05 3.999E-05 2.122E-05 5.763E-06 

 0.640 km above surface

 5.230E-01 5.193E-01 5.080E-01 4.882E-01 4.581E-01 4.143E-01 3.510E-01 2.574E-01 1.520E-01 4.577E-02 

 2.092E-03 2.062E-03 1.972E-03 1.819E-03 1.601E-03 1.315E-03 9.632E-04 5.633E-04 2.535E-04 5.126E-05 

 2.731E-03 2.703E-03 2.618E-03 2.471E-03 2.254E-03 1.951E-03 1.544E-03 1.011E-03 5.191E-04 1.304E-04 

 2.664E-03 2.577E-03 2.327E-03 1.939E-03 1.459E-03 9.497E-04 4.928E-04 1.738E-04 4.872E-05 6.809E-06 

 3.958E-04 3.872E-04 3.618E-04 3.207E-04 2.656E-04 2.000E-04 1.294E-04 6.343E-05 2.378E-05 3.860E-06 

 1.057E-04 1.047E-04 1.018E-04 9.672E-05 8.912E-05 7.839E-05 6.354E-05 4.331E-05 2.336E-05 6.448E-06 

 0.980 km above surface

 5.409E-01 5.373E-01 5.260E-01 5.062E-01 4.760E-01 4.321E-01 3.682E-01 2.727E-01 1.635E-01 4.989E-02 

 2.210E-03 2.179E-03 2.087E-03 1.930E-03 1.705E-03 1.409E-03 1.041E-03 6.178E-04 2.827E-04 5.837E-05 

 2.873E-03 2.845E-03 2.758E-03 2.609E-03 2.387E-03 2.077E-03 1.656E-03 1.099E-03 5.718E-04 1.454E-04 

 2.837E-03 2.746E-03 2.483E-03 2.074E-03 1.567E-03 1.028E-03 5.396E-04 1.944E-04 5.611E-05 8.121E-06 

 4.195E-04 4.106E-04 3.842E-04 3.414E-04 2.840E-04 2.152E-04 1.407E-04 7.017E-05 2.689E-05 4.509E-06 

 1.107E-04 1.097E-04 1.068E-04 1.016E-04 9.392E-05 8.299E-05 6.775E-05 4.673E-05 2.556E-05 7.133E-06 

 1.380 km above surface

 5.593E-01 5.556E-01 5.444E-01 5.247E-01 4.947E-01 4.507E-01 3.863E-01 2.892E-01 1.760E-01 5.427E-02 

 2.329E-03 2.298E-03 2.203E-03 2.042E-03 1.811E-03 1.505E-03 1.122E-03 6.743E-04 3.128E-04 6.563E-05 

 3.016E-03 2.988E-03 2.900E-03 2.749E-03 2.524E-03 2.207E-03 1.773E-03 1.190E-03 6.270E-04 1.609E-04 

 3.015E-03 2.920E-03 2.644E-03 2.215E-03 1.681E-03 1.109E-03 5.887E-04 2.158E-04 6.364E-05 9.454E-06 

 4.437E-04 4.345E-04 4.071E-04 3.627E-04 3.029E-04 2.310E-04 1.524E-04 7.716E-05 3.009E-05 5.169E-06 

 1.157E-04 1.148E-04 1.118E-04 1.066E-04 9.883E-05 8.772E-05 7.213E-05 5.031E-05 2.789E-05 7.835E-06 

 1.840 km above surface

 5.782E-01 5.746E-01 5.635E-01 5.440E-01 5.141E-01 4.702E-01 4.056E-01 3.069E-01 1.897E-01 5.904E-02 

 2.451E-03 2.419E-03 2.322E-03 2.157E-03 1.920E-03 1.605E-03 1.206E-03 7.338E-04 3.445E-04 7.312E-05 

 3.162E-03 3.133E-03 3.045E-03 2.892E-03 2.664E-03 2.341E-03 1.894E-03 1.286E-03 6.856E-04 1.769E-04 

 3.200E-03 3.101E-03 2.811E-03 2.361E-03 1.799E-03 1.196E-03 6.407E-04 2.385E-04 7.141E-05 1.082E-05 

 4.685E-04 4.589E-04 4.307E-04 3.846E-04 3.224E-04 2.473E-04 1.647E-04 8.451E-05 3.341E-05 5.848E-06 

 1.209E-04 1.199E-04 1.169E-04 1.117E-04 1.039E-04 9.263E-05 7.671E-05 5.412E-05 3.039E-05 8.570E-06 

 2.350 km above surface

 5.974E-01 5.939E-01 5.829E-01 5.636E-01 5.340E-01 4.904E-01 4.257E-01 3.258E-01 2.046E-01 6.425E-02 

 2.572E-03 2.540E-03 2.441E-03 2.273E-03 2.031E-03 1.706E-03 1.292E-03 7.955E-04 3.775E-04 8.077E-05 

 3.307E-03 3.278E-03 3.190E-03 3.036E-03 2.805E-03 2.477E-03 2.019E-03 1.386E-03 7.476E-04 1.934E-04 

 3.389E-03 3.285E-03 2.983E-03 2.512E-03 1.922E-03 1.285E-03 6.952E-04 2.622E-04 7.936E-05 1.221E-05 

 4.934E-04 4.836E-04 4.544E-04 4.068E-04 3.424E-04 2.641E-04 1.774E-04 9.214E-05 3.685E-05 6.538E-06 

 1.261E-04 1.251E-04 1.221E-04 1.169E-04 1.090E-04 9.763E-05 8.142E-05 5.811E-05 3.305E-05 9.333E-06 

 2.910 km above surface

 6.169E-01 6.134E-01 6.026E-01 5.836E-01 5.543E-01 5.111E-01 4.466E-01 3.458E-01 2.209E-01 7.003E-02 

 2.694E-03 2.661E-03 2.561E-03 2.390E-03 2.143E-03 1.810E-03 1.382E-03 8.602E-04 4.124E-04 8.867E-05 

 3.452E-03 3.423E-03 3.335E-03 3.180E-03 2.948E-03 2.615E-03 2.148E-03 1.492E-03 8.140E-04 2.106E-04 

 3.582E-03 3.474E-03 3.159E-03 2.667E-03 2.049E-03 1.379E-03 7.528E-04 2.874E-04 8.761E-05 1.363E-05 

 5.187E-04 5.086E-04 4.786E-04 4.294E-04 3.628E-04 2.814E-04 1.906E-04 1.002E-04 4.045E-05 7.246E-06 

 1.312E-04 1.303E-04 1.273E-04 1.221E-04 1.142E-04 1.027E-04 8.630E-05 6.231E-05 3.593E-05 1.014E-05 

 3.530 km above surface

 6.368E-01 6.334E-01 6.228E-01 6.041E-01 5.754E-01 5.328E-01 4.687E-01 3.673E-01 2.389E-01 7.670E-02 

 2.818E-03 2.784E-03 2.683E-03 2.510E-03 2.258E-03 1.917E-03 1.476E-03 9.296E-04 4.505E-04 9.704E-05 

 3.599E-03 3.571E-03 3.482E-03 3.328E-03 3.094E-03 2.759E-03 2.283E-03 1.605E-03 8.871E-04 2.291E-04 

 3.783E-03 3.670E-03 3.343E-03 2.830E-03 2.184E-03 1.478E-03 8.148E-04 3.147E-04 9.644E-05 1.512E-05 

 5.446E-04 5.343E-04 5.034E-04 4.528E-04 3.840E-04 2.996E-04 2.046E-04 1.088E-04 4.434E-05 7.989E-06 

 1.365E-04 1.355E-04 1.326E-04 1.274E-04 1.195E-04 1.080E-04 9.142E-05 6.681E-05 3.911E-05 1.103E-05 

 4.210 km above surface

 6.569E-01 6.536E-01 6.433E-01 6.250E-01 5.969E-01 5.550E-01 4.917E-01 3.902E-01 2.588E-01 8.447E-02 

 2.943E-03 2.909E-03 2.807E-03 2.632E-03 2.376E-03 2.029E-03 1.574E-03 1.004E-03 4.925E-04 1.060E-04 

 3.747E-03 3.719E-03 3.631E-03 3.477E-03 3.243E-03 2.906E-03 2.424E-03 1.725E-03 9.679E-04 2.493E-04 

 3.992E-03 3.875E-03 3.534E-03 3.000E-03 2.325E-03 1.585E-03 8.818E-04 3.447E-04 1.060E-04 1.668E-05 

 5.711E-04 5.605E-04 5.289E-04 4.769E-04 4.060E-04 3.186E-04 2.195E-04 1.181E-04 4.859E-05 8.775E-06 

 1.417E-04 1.408E-04 1.379E-04 1.327E-04 1.249E-04 1.135E-04 9.674E-05 7.161E-05 4.262E-05 1.202E-05 

O3 Column = 0.290 Albedo= 0.040 Terrain = 1.000

 0.000 km above surface

 4.655E-01 4.615E-01 4.493E-01 4.279E-01 3.958E-01 3.499E-01 2.855E-01 1.957E-01 1.048E-01 2.871E-02 

 1.688E-03 1.660E-03 1.576E-03 1.435E-03 1.237E-03 9.833E-04 6.824E-04 3.626E-04 1.414E-04 2.142E-05 

 2.240E-03 2.212E-03 2.129E-03 1.987E-03 1.780E-03 1.498E-03 1.132E-03 6.858E-04 3.159E-04 6.495E-05 

 2.098E-03 2.025E-03 1.815E-03 1.492E-03 1.098E-03 6.883E-04 3.334E-04 1.009E-04 2.101E-05 1.716E-06 

 3.162E-04 3.086E-04 2.863E-04 2.503E-04 2.029E-04 1.473E-04 8.961E-05 3.896E-05 1.193E-05 1.254E-06 

 8.857E-05 8.761E-05 8.467E-05 7.961E-05 7.213E-05 6.180E-05 4.802E-05 3.042E-05 1.483E-05 3.488E-06 

 0.150 km above surface

 5.004E-01 4.963E-01 4.839E-01 4.623E-01 4.296E-01 3.828E-01 3.163E-01 2.220E-01 1.237E-01 3.1E-02 

 1.870E-03 1.841E-03 1.752E-03 1.604E-03 1.394E-03 1.123E-03 7.976E-04 4.424E-04 1.847E-04 3.188E-05 

 2.473E-03 2.445E-03 2.359E-03 2.211E-03 1.994E-03 1.697E-03 1.306E-03 8.179E-04 3.956E-04 8.840E-05 

 2.338E-03 2.259E-03 2.030E-03 1.677E-03 1.245E-03 7.929E-04 3.960E-04 1.294E-04 3.180E-05 3.572E-06 

 3.509E-04 3.428E-04 3.189E-04 2.803E-04 2.292E-04 1.690E-04 1.056E-04 4.859E-05 1.651E-05 2.187E-06 

 9.713E-05 9.614E-05 9.312E-05 8.789E-05 8.013E-05 6.934E-05 5.476E-05 3.574E-05 1.823E-05 4.615E-06 

Figure 3-2. Example of the first several panels of lookup data in the photolysis rates input file.
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There are two mandatory and one optional header records in the ozone column file. The first 

record contains an arbitrary file label. The second record defines the intervals for 5 ozone 

column values for the domain and temporal period to be simulated. These intervals must 

exactly match those defined in preparing the photolysis rates file, so the ozone column file is 

also read by the TUV preprocessor to define the photolysis rates lookup table (Section 3.2).

If the optional land/ocean mask is included, then a third header record must be added to 

inform CAMx that this field is to be read. The time-invariant land/ocean mask is used for 

mercury chemistry to define profiles of ambient halogens; it is simply a map of 0 (land and fresh 

water bodies) and 1 (ocean) that must be located directly under its header record. A value 

must be supplied for each cell of the master grid and optionally any nested grids. 

Gridded fields of time-varying ozone column follow the header records and optional land/ocean 

mask data. The gridded fields are maps of the respective “codes” for each interval, as defined 

in the header. For example, 5 ozone column intervals are specified in TUV and in the ozone 

column header record, so the map must consist of a distribution of integers ranging from 1 to 5. 

Ozone column is supplied for the master grid only; CAMx internally assigns master cell values to 

all nested grids cells. Multiple maps of these codes may be provided for arbitrary time intervals 

that span the entire simulation period.

The ozone column file is a readable text (ASCII) format and it has the following structure:

where the variables in the ozone column file have the following definitions:

text Text identifying file and any messages

ozname Text string “OZONE COL”

ozncl Ozone column (Dobson units) for each of nozn ozone values

loname Text string “OCEAN”

igrd Grid index (1 = master grid, 2+=nested grid, 0 = end of data)

nx Number of grid columns for this grid index

ny Number of grid rows for this grid index

jocn Grid igrd, row j land/ocean codes for nx grid columns

idt1 Beginning date (YYJJJ) of time span

tim1 Beginning hour (HHMM) of time span

idt2 Ending date of time span

text (A)

ozname,(ozncl(n),n=1,nozn) (A10,5F10.0)

loname,igrd,nx,ny (A10,3I10) -- Optional

Loop from j = ny grid rows to 1 -- Optional

(jocn(i,j),i=1,nx) (999I1) -- Optional

loname,igrd,nx,ny (A10,3I10) -- Optional

ozname,idt1,tim1,idt2,tim2 (A10,I10,F10.0,I10,F10.0)

Loop from j = ny master grid rows to 1

(jozn(i,j),i=1,nx) (9999I1) 
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tim2 Ending hour of time span

jozn Master grid row j ozone column codes for nx master grid columns

An example of a small ozone column file is given in Figure 3-3.

Sample ozone column file with optional land ocean mask

OZONE COL 0.285 0.315 0.345 0.375 0.405

OCEAN 1 64 10

0000000000000000000011111111100000000000000000000000000000000000

0000000000000000000000000001111111110000000000000000000000000000

0000000000000000000000001111111111111100000000000000000000000000

0000000000000000000000000001111111111110000000000000000000000000

0000000000000000000000011111111111111100000000000000000000000000

0000000000000000000000111111111111111110000000000000000000000000

0000000000000000000000111111111111111111000000000000000000000000

0000000000000000000001111111000000000111111110000000000000000000

0000000000000000000011111111100000000011111111100000000000000000

0000000000000000000000111111111100000000011111111110000000000000

OCEAN 0 0 0

OZONE COL 05213 0.00 05213 2400.00

3333333333333333333333333333333333333333333333333333333333333333

3333333333333333333333333333333333333333333333333333333333333333

2222222222222333333333333333333333333333333333333333333333333333

2222222222222223333333333333333333333333333333333333333333333333

2222222222222223333333333333333333333333333333333333333333333333

2222222222222223333333333333333333333333333333333333333333333333

2222222222222223333333333333333333333333333333333333333333333333

2222222222222223333333333333333333333333333333333333333333333333

2222222222222223333333333333333333333333333333333333333333333333

2222222222222222222222333333333333333333333333333333333333333333

Figure 3-3. Example structure of a single-grid ozone column input file showing panels for the 

optional time-invariant land-ocean mask and time-varying ozone column field.

3.4 Fortran Binary Input/Output Files

3.4.1 What is a Fortran Binary File?

Large CAMx input and output data fields are contained within Fortran “unformatted” (binary) 

files. This means that the data are read and written as represented in memory, without 

translation between binary and ASCII character sets as done for “text” files. Binary files reduce 

file volume and improve program read/write speed, but the user cannot directly view or 

manually edit them. There are two ways to represent binary information in memory: “big 

endian” and “little endian.” The difference between these is essentially the order of bits in a 

word, and which order is used depends on the computer chipset. Historically, big endian has 

been used in many Unix workstations (Sun, SGI, HP, and IBM). The x86 processors on personal 

computer platforms (e.g., Intel and AMD) use little endian, while PowerPC chips are big endian.

CAMx can be compiled and run on machines using their native big or little endian binary

representations, as long as the model and all of its pre- and post-processors are consistently 

compiled and run on the same type of platform. If any component of the modeling system is 

compiled for a different platform using the opposite binary representation, I/O files will not be 
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properly read and will likely lead to a program crash. A typical run-time error message from 

trying to read the wrong binary format is “input record too long,” so if you get this error 

message, check for consistency between your binary files and Fortran compiler options.

Compilers for little endian machines provide compile-time switches that allow binary files to be 

read and written as big endian. The “makefile” compiler script that is distributed with CAMx 

sets compiler flags to consistently use big endian to maximize platform portability. Therefore, 

use of the CAMx Makefile will by default result in the model reading and writing big endian 

binary files. Additional information on this topic is provided in Section 2.

3.4.2 CAMx Binary File Headers

The format of all binary CAMx I/O files follows the convention established by the Urban Airshed 

Model (EPA, 1990). CAMx binary files contain a set of time-invariant header records, followed 

by a set of data records that contain time- and variable-specific fields. All input gridded 

emissions, initial conditions, meteorology1

, and output concentration and deposition files share 

the same basic format. The input boundary condition and point source emissions files are 

similar but include additional records specific to their data structures. The input 3D 

meteorological file may provide wind fields in a staggered or un-staggered grid arrangement. A 

flag to indicate the wind staggering is included in the second header record and is checked only 

when the 3D meteorological file is read.

The four header records within all CAMx binary files have the following structure:

The header variables have the following definitions:

Record 1

name Text string describing file contents (character*4(10) array):

AIRQUALITY Initial conditions

BOUNDARY Boundary conditions

EMISSIONS Gridded emissions

PTSOURCE Point source emissions

AVERAGE Average output concentrations/deposition and

input meteorology/surface variables

INSTANT Instantaneous output concentrations

note Text string containing user note (character*4(60) array)

itzon Integer time zone (0=UTC, 5=EST, etc.)

 1 NOTE: Starting with CAMx v6.00, all binary meteorological files have been converted to the 

UAM convention.

name,note,itzon,nvar,ibdate,btime,iedate,etime

plon,plat,iutm,xorg,yorg,delx,dely,nx,ny,nz,iproj,istag,tlat1,tlat2,rdum

ione,ione,nx,ny

(namvar(l),l=1,nvar)
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nvar Integer number of variables on file

ibdate Integer beginning date span on file (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date span on file (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

Record 2

plon Real projection pole longitude (degrees; west is negative)

plat Real projection pole latitude (degrees; south is negative)

iutm Integer UTM zone (ignored for other projections)

xorg Real grid x-origin at southwest corner of domain (m or degrees longitude)

yorg Real grid y-origin at southwest corner of domain (m or degrees latitude)

delx Real cell size in x-direction (m or degrees longitude)

dely Real cell size in y-direction (m or degrees latitude)

nx Integer number of grid columns (east-west)

ny Integer number of grid rows (north-south)

nz Integer number of vertical layers

iproj Integer projection index:

0 = geodetic (lat/lon)

1 = Universal Transverse Mercator (UTM)

2 = Lambert Conic Conformal (LCP)

3 = Polar Stereographic (PSP)

istag Integer flag to indicate wind staggering (1=staggered, 0=not staggered)

tlat1 Real LCP first true latitude (degrees; south is negative)

tlat2 Real LCP second true latitude (degrees; south is negative)

rdum Real dummy variable

Record 3

ione Integer dummy variable (=1)

ione Integer dummy variable (=1)

nx Integer number of grid columns (east-west)

ny Integer number of grid rows (north-south)

Record 4

namvar Text names for nvar variables (character*4(10,nvar) array)

3.4.3 Input Files

The Fortran binary input files include initial/boundary conditions, gridded and elevated point 

source emissions, and several meteorological files. All times on input files must match the time 

zone specified in the CAMx control file (CAMx.in).

Initial/boundary condition files may include a single time interval covering the entire simulation 

period, or more detailed hour-by-hour (or other interval) variations. The time intervals are 

allowed to be entirely arbitrary to maximize flexibility in defining these inputs. A subset of the 

pollutant species to be simulated may be defined in the initial/boundary condition files; any 

species that are missing will be set to “lower bound” values as defined in the chemistry 

parameters file. 
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Emission inputs are usually developed at one hour intervals, but the file structures allow for any 

other interval as long as a consistent interval is used throughout the file (all one hour, or all 

three hour, but no mixing of these). The time interval on all emission files must match the 

emission update frequency defined in the CAMx control file. A subset of species to be 

simulated may be included in the emission files; zero emission rates will be applied for any 

species that are missing. 

Meteorological fields are separated into two-dimensional and three-dimensional fields. The 

core meteorological file contains the basic parameters needed for most model processes, and 

includes winds and basic thermodynamic properties. Separate vertical diffusivity and cloud files 

allow for easy substitution of alternative inputs without the need to re-generate all of the core 

fields. The time interval on all meteorological files must match the meteorological update 

frequency defined in the CAMx control file. 

3.4.3.1 Input Static 2-D Surface File

The static 2-D surface file contains time-invariant gridded fields of landuse and topographic 

elevation, and optionally leaf area index (LAI). This file must be developed for the master grid, 

and optionally any of the nested fine grids. The fractional distribution of 26 landuse categories, 

consistent with the Zhang dry deposition scheme, is supplied for each grid cell. If the Wesely 

dry deposition option is invoked, CAMx internally maps the 26 categories to the 11 WESELY89 

categories. These are used to define surface UV albedo, surface resistances for dry deposition 

calculations, and to set seasonal default surface roughness lengths and LAI values (if LAI is not 

specified in the file). The landuse categories are described in Tables 3-4 and 3-5. 

Table 3-4. The 11 WESELY89 landuse categories, their default UV surface albedos, and their 

surface roughness values (m) by season. Winter is defined for conditions where there is snow 

present; winter months with no snow are assigned to the Fall category. Roughness for water 

is calculated from the function 6 2.5

0 z 2 10 w− = × , where w is surface wind speed (m/s).

Category

Number Land Cover Category Surface Roughness (meters) UV

Spring Summer Fall Winter Albedo

1 Urban 1.0 1.0 1.0 1.0 0.08

2 Agricultural 0.03 0.2 0.05 0.01 0.05

3 Rangeland 0.05 0.1 0.01 0.001 0.05

4 Deciduous forest 1.0 1.3 0.8 0.5 0.05

5 Coniferous forest, wetland 1.3 1.3 1.3 1.3 0.05

6 Mixed forest* 1.15 1.3 1.05 0.9 0.05

7 Water f(w) f(w) f(w) f(w) 0.04

8 Barren land 0.002 0.002 0.002 0.002 0.08

9 Non-forested wetlands 0.2 0.2 0.2 0.05 0.05

10 Mixed agricultural/range* 0.04 0.15 0.03 0.006 0.05

11 Rocky (with low shrubs) 0.3 0.3 0.3 0.15 0.05

* Roughness for these categories is taken to be the average of their components.
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Table 3-5. The 26 ZHANG03 landuse categories, their UV albedos, and their default annual 

minimum and maximum LAI and surface roughness (m) ranges. Roughness for water is 

calculated from the function 6 2.5

0 z 2 10 w− = × , where w is surface wind speed (m/s).

Category

Number Land Cover Category Roughness (meters) LAI UV

Min Max Min Max Albedo

1 Water f(w) f(w) 0.0 0.0 0.04

2 Ice 0.01 0.01 0.0 0.0 0.5

3 Inland lake f(w) f(w) 0.0 0.0 0.04

4 Evergreen needleleaf trees 0.9 0.9 5.0 5.0 0.05

5 Evergreen broadleaf trees 2.0 2.0 6.0 6.0 0.05

6 Deciduous needleleaf trees 0.4 0.9 0.1 5.0 0.05

7 Deciduous broadleaf trees 0.4 1.0 0.1 5.0 0.05

8 Tropical broadleaf trees 2.5 2.5 6.0 6.0 0.05

9 Drought deciduous trees 0.6 0.6 4.0 4.0 0.05

10 Evergreen broadleaf shrubs 0.2 0.2 3.0 3.0 0.05

11 Deciduous shrubs 0.05 0.2 0.5 3.0 0.05

12 Thorn shrubs 0.2 0.2 3.0 3.0 0.05

13 Short grass and forbs 0.04 0.04 1.0 1.0 0.05

14 Long grass 0.02 0.1 0.5 2.0 0.05

15 Crops 0.02 0.1 0.1 4.0 0.05

16 Rice 0.02 0.1 0.1 6.0 0.05

17 Sugar 0.02 0.1 0.1 5.0 0.05

18 Maize 0.02 0.1 0.1 4.0 0.05

19 Cotton 0.02 0.2 0.1 5.0 0.05

20 Irrigated crops 0.05 0.05 1.0 1.0 0.05

21 Urban 1.0 1.0 0.1 1.0 0.08

22 Tundra 0.03 0.03 0.1 2.0 0.05

23 Swamp 0.1 0.1 4.0 4.0 0.05

24 Desert 0.04 0.04 0.0 0.0 0.08

25 Mixed wood forest 0.9 0.9 3.0 5.0 0.05

26 Transitional forest 0.9 0.9 3.0 5.0 0.05

The data records for the static 2-D surface file have the following structure:

The variables have the following definitions:

Record 1

ibdate Integer beginning date span on file (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date span on file (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

ibdate,btime,iedate,etime

Loop from l = 1 to nvar variables:

ione,namvar(l),((var(i,j),i=1,nx),j=1,ny)
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Record 2 through nvar+1

ione Integer dummy variable (=1)

namvar Text names for nvar variables (character*4(10,nvar) array):

WATER Water fraction (Zhang 1)

ICE Ice fraction (Zhang 2)

LAKE Lake fraction (Zhang 3)

ENEEDL Evergreen needle leaf forest fraction (Zhang 4)

EBROAD Evergreen broad leaf forest fraction (Zhang 5)

DNEEDL Deciduous needle leaf forest fraction (Zhang 6)

DBROAD Deciduous broad leaf forest fraction (Zhang 7)

TBROAD Tropical broad leaf forest fraction (Zhang 8)

DDECID Drought deciduous tree fraction (Zhang 9)

ESHRUB Evergreen shrub fraction (Zhang 10)

DSHRUB Deciduous shrub fraction (Zhang 11)

TSHRUB Thorn shrub fraction (Zhang 12)

SGRASS Short grass fraction (Zhang 13)

LGRASS Long grass fraction (Zhang 14)

CROPS Cropland fraction (Zhang 15)

RICE Rice crop fraction (Zhang 16)

SUGAR Sugar crop fraction (Zhang 17)

MAIZE Corn crop fraction (Zhang 18)

COTTON Cotton crop fraction (Zhang 19)

ICROPS Irrigated cropland fraction (Zhang 20)

URBAN Urban fraction (Zhang 21)

TUNDRA Tundra fraction (Zhang 22)

SWAMP Swamp fraction (Zhang 23)

DESERT Desert fraction (Zhang 24)

MWOOD Mixed woodland fraction (Zhang 25)

TFOREST Transitional forest fraction (Zhang 26)

TOPO_M Topographic elevation above sea level (m)

LAI Optional Leaf Area Index

var Real variable field values for nx grid columns and ny grid rows

3.4.3.2 Input Time-Variant 2-D Surface File

The time-variant 2-D surface file contains gridded fields of surface temperature and snow 

cover. This file must be developed for the master grid, and optionally any of the nested fine 

grids. The surface temperature is used for dry deposition calculations and to establish surfacelayer atmospheric stability. Snow cover is simply a map of 0 (no snow) and 1 (snow); this 

impacts surface roughness, surface resistances for dry deposition, and photochemistry by 

setting UV albedo to snow values. 

The data records for the time-variant 2-D surface file have the following structure and are 

repeated for each time interval on file:
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The variables have the following definitions:

Record 1

ibdate Integer beginning date of time interval (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date of time interval (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

Record 2 through nvar+1

ione Integer dummy variable (=1)

namvar Text names for nvar variables (character*4(10,nvar) array):

TSURF_K Surface temperature (K)

SNOWCOVER Snow cover (1=present, 0=absent)

var Real variable field values for nx grid columns and ny grid rows

CAMx time-interpolates surface temperature to each model timestep for each grid, and so the 

model requires that data be available on file for an additional update time at the end of the 

simulation. For example, in the case of hourly fields, a 24-hour simulation requires 25 input 

fields on file. The time interval of the data records must match the time zone and input 

frequency of the meteorology as specified in the CAMx.in file.

3.4.3.3 Input Time-Variant 3-D Meteorological File

The time-variant 3-D meteorological file contains gridded fields of state meteorological 

parameters. This file must be developed for the master grid and optionally any fine grid nest 

specified for a given simulation. The layer interface heights define the vertical grid structure for 

each grid. The number of vertical layers and the vertical grid definition must be consistent 

among all grids in a simulation; otherwise CAMx will stop with an error message if this 

condition is not met. The layer interface heights may be specified to vary in space and/or time 

(e.g., to follow the layer structure of meteorological models), or they may be set to a constant 

field. CAMx allows the user to optionally supply wind components at cell center, in which case 

the model will interpolate the components to their respective positions on cell interfaces, or 

the user may supply these components directly on the staggered Arakawa C configuration 

(recommended). In any case, the user must supply a full nx×ny×nz array of wind values for each 

component (even though the CAMx Arakawa C configuration uses only (nx-1)×(ny-1) values in 

the horizontal). The wind staggering flag is set in the second header record. The pressure, 

wind, temperature, and humidity fields are used for transport, plume rise, PiG, dry and wet 

deposition, and chemistry calculations. 

ibdate,btime,iedate,etime

Loop from l = 1 to nvar variables:

ione,namvar(l),((var(i,j),i=1,nx),j=1,ny)
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The data records for the time-variant 3-D meteorological file have the following structure and 

are repeated for each time interval on file:

The variables have the following definitions:

Record 1

ibdate Integer beginning date of time interval (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date of time interval (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

Record 2 through nvar×nz+1

ione Integer dummy variable (=1)

namvar Text names for nvar variables (character*4(10,nvar) array):

ZGRID_M Layer interface heights (m AGL)

PRESS_MB Pressure (mb)

TEMP_K Temperature (K)

HUMID_PPM Humidity as mixing ratio (ppm)

UWIND_MpS U-component (east-west) wind (m/s)

VWIND_MpS V-component (north-south) wind (m/s)

var Real layer k variable field values for nx grid columns and ny grid rows

CAMx time-interpolates these meteorological variables to each model timestep for each grid, 

and so the model requires that data be available on file for an additional update time at the end 

of the simulation. For example, in the case of hourly fields, a 24-hour simulation requires 25 

input fields on file. The time interval of the data records must match the time zone and input 

frequency of the meteorology as specified in the CAMx.in file.

3.4.3.4 Input Time-Variant 3-D Vertical Diffusivity File

The time-variant 3-D vertical diffusivity file contains gridded fields of layer-interface diffusivity 

(i.e., turbulent exchange or diffusion coefficients). This file must be developed for the master 

grid, and optionally any fine grid nests. This file is kept separate from the main meteorological 

data file to facilitate the substitution of alternative vertical mixing rates. Diffusivity is used for 

vertical diffusion and PiG puff growth calculations. 

The data records for the time-variant 3-D meteorological file have the following structure and 

are repeated for each time interval on file:

ibdate,btime,iedate,etime

Loop from l = 1 to nvar variables:

Loop from k = 1 to nz layers:

ione,namvar(l),((var(i,j,k),i=1,nx),j=1,ny)
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The variables have the following definitions:

Record 1

ibdate Integer beginning date of time interval (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date of time interval (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

Record 2 through nvar×nz+1

ione Integer dummy variable (=1)

namvar Text names for nvar variables (character*4(10,nvar) array):

KV_M2pS Vertical diffusivity (m2/s)

var Real layer k variable field values for nx grid columns and ny grid rows

CAMx time-interpolates the diffusivity to each model timestep for each grid, and so the model 

requires that data be available on file for an additional update time at the end of the 

simulation. For example, in the case of hourly fields, a 24-hour simulation requires 25 input 

fields on file. The time interval of the data records must match the time zone and input 

frequency of the meteorology as specified in the CAMx.in file.

3.4.3.5 Input Time-Variant 3-D Cloud/Precipitation File

The time-variant 3-D cloud/precipitation file contains gridded fields of cloud and precipitation 

parameters to be used for photochemistry, aqueous chemistry, and wet/dry deposition 

calculations. Note that precipitation rate is not explicitly provided to the model; instead, it is 

internally calculated from the three precipitation water content forms provided on the 

cloud/rain file. This file also contains layer-specific cloud optical depth to scale down photolysis 

rates for layers within or below clouds to account for UV attenuation, or to scale up the rates 

for layers above clouds to account for UV reflection. This file must be developed for the master 

grid, and optionally any fine grid nests, if chemistry, dry, and/or wet deposition are invoked. 

The data records for the time-variant 3-D cloud/precipitation file have the following structure 

and are repeated for each time interval on file:

ibdate,btime,iedate,etime

Loop from l = 1 to nvar variables:

Loop from k = 1 to nz layers:

ione,namvar(l),((var(i,j,k),i=1,nx),j=1,ny)

ibdate,btime,iedate,etime

Loop from l = 1 to nvar variables:

Loop from k = 1 to nz layers:

ione,namvar(l),((var(i,j,k),i=1,nx),j=1,ny)
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The variables have the following definitions:

Record 1

ibdate Integer beginning date of time interval (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date of time interval (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

Record 2 through nvar×nz+1

ione Integer dummy variable (=1)

namvar Text names for nvar variables (character*4(10,nvar) array):

CLODW_GpM3 Cloud water content (g/m3)

RAINW_GpM3 Rain water content (g/m3)

SNOWW_GpM3 Snow water content (g/m3

)

GRPLW_GpM3 Graupel water content (g/m3)

CLOUDOD Layer-specific cloud optical depth

var Real layer k variable field values for nx grid columns and ny grid rows

The CAMx cloud fields are assumed to be time-averaged, so the model does not require an 

additional update time at the end of the simulation. For example, in the case of hourly fields, a 

24-hour simulation requires only 24 cloud input fields on file. The time interval of the data 

records must match the time zone and input frequency of the meteorology as specified in the 

CAMx.in file.

3.4.3.6 Input 3-D Initial Conditions File

The input 3-D initial conditions file contains gridded concentration fields on the master grid. 

Initial concentration fields may be specified for a sub-set of the total number of modeled 

species. An initial condition file must be developed for the master grid, and contain 

concentration fields for at least one species. For those species not on the initial condition file, 

CAMx sets up uniform fields using the “lower bound” values specified in the chemistry 

parameters file. CAMx then interpolates all master grid initial conditions to each fine grid nest 

at the start of the simulation. 

The data records for the initial conditions file have the following structure and are repeated for 

each time interval on file:

ibdate,btime,iedate,etime

Loop from l = 1 to nspec species:

Loop from k = 1 to nz layers:

ione,namspec(l),((conc(i,j,k),i=1,nx),j=1,ny)
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The variables have the following definitions:

Record 1

ibdate Integer beginning date of time interval (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date of time interval (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

Record 2 through nspec×nz+1

ione Integer dummy variable (=1)

namspec Text names for nspec species (character*4(10,nvar) array):

conc Real layer k concentration field values (ppm for gases, μg/m3 for aerosols)

for nx grid columns and ny grid rows

The time interval of the data records must match the time zone as specified in the CAMx.in file.

3.4.3.7 Input 3-D Lateral Boundary Conditions File

The input 3-D lateral boundary conditions file contains gridded concentration fields on the 

lateral faces of the master grid boundary. Boundary concentration fields may be specified for a 

sub-set of the total number of modeled species. However, if a boundary concentration is 

specified for a given species, it must be supplied for all four boundaries. A boundary 

concentration file must be developed for the master grid, and contain concentration fields for 

at least one species. For those species not on the boundary conditions file, CAMx sets up 

uniform fields using the “lower bound” values specified in the chemistry parameters file. The 

time span of each set of boundary data records may be set arbitrarily; e.g., a set of boundary 

conditions may be specified for a six hour span, followed by a set spanning just an hour.

The boundary conditions file adds an additional set of four header records, resulting in a total 

of eight header records altogether (note that first four records are identical to the header 

records described above):

The additional header variables have the following definitions:

Records 5-8

ione Integer dummy variable (=1)

iedge Integer boundary edge number (1=west, 2=east, 3=south, 4=north)

ncell Integer number of rows or columns on this edge

name,note,ione,nspec,ibdate,btime,iedate,etime

plon,plat,iutm,xorg,yorg,delx,dely,nx,ny,nz,iproj,istag,tlat1,tlat2,rdum

ione,ione,nx,ny

(namspec(l),l=1,nspec)

Loop from 1 to 4 boundaries:

ione,iedge,ncell,(icell(n),idum,idum,idum,n=1,ncell)
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icell Integer index of first cell modeled (edges 1,3), or last cell modeled (edges

2,4): if “0”, this row/column is omitted from the simulation

idum Integer dummy variable

The data records for the boundary conditions file have the following structure, and are 

repeated for each time interval on file:

The variables have the following definitions:

Record 1

ibdate Integer beginning date of time interval (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date of time interval (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

Record 2 through nspec×4+1

ione Integer dummy variable (=1)

namspec Text names for nspec species (character*4(10,nvar) array):

bc Real edge iedge boundary concentrations (ppm for gases, μg/m3 for

aerosols) for ncell grid rows/columns, and nz layers 

The time interval of the data records must match the time zone as specified in the CAMx.in file.

3.4.3.8 Input Elevated Point Source File

The input elevated point source emissions file contains stack parameters and emission rates for 

all elevated point sources, and for all emitted species, to be modeled. If elevated point sources 

are to be modeled, only one point source emissions file must be developed for the entire 

modeling domain. The point source file also flags the individual stacks to be treated by the 

CAMx PiG sub-model by setting the stack diameter as a negative value. The file offers the 

ability to optionally specify the effective plume height or the vertical plume distribution for 

each point source and to bypass the internal plume rise calculation.

The elevated point source file adds two additional set of header records that specify timeinvariant stack parameters, resulting in a total of six header records altogether (note that first 

four records are identical to the header records described above):

ibdate,btime,iedate,etime

Loop from l = 1 to nspec species:

Loop from 1 to 4 boundaries:

ione,namspec(l),iedge,((bc(i,k,iedge,l),k=1,nz),i=1,ncell)
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The additional header variables have the following definitions:

Record 5

ione Integer dummy variable (=1)

nstk Integer number of elevated point source stacks

Record 6

xstk Real stack x-coordinate (m or degrees longitude)

ystk Real stack y-coordinate (m or degrees latitude)

hstk Real stack height (m)

dstk Real stack diameter (m); negative value flags source for PiG

tstk Real stack exit temperature (K)

vstk Real stack exit velocity (m/hr)

The time-variant data records for the elevated point source file have the following structure, 

and are repeated for each time interval on file:

The variables have the following definitions:

Record 1

ibdate Integer beginning date of time interval (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date of time interval (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

Record 2

ione Integer dummy variable (=1)

nstk Integer number of elevated point source stacks

name,note,ione,nspec,ibdate,btime,iedate,etime

plon,plat,iutm,xorg,yorg,delx,dely,nx,ny,nz,iproj,istag,tlat1,tlat2,rdum

ione,ione,nx,ny

(namspec(l),l=1,nspec)

ione,nstk

(xstk(n),ystk(n),hstk(n),dstk(n),tstk(n),vstk(n),n=1,nstk)

ibdate,btime,iedate,etime

ione,nstk

(idum,idum,kcell(n),flow(n),plmht(n),n=1,nstk)

Loop from l = 1 to nspec species:

ione,namspec(l),(ptems(n,l),n=1,nstk)
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Record 3

idum Integer dummy variable

kcell Zero or positive: Ignored

Negative: integer flag for OSAT/PSAT source region override

flow Zero: ignored (plume rise calculation uses time-invariant exit velocity)

Positive: real stack flow rate (m3/hr) for plume rise calculations

Negative: real plume bottom (m) for vertical plume distribution override

plmht Zero or positive: ignored (plume rise calculation is performed)

Negative (flow ≥ 0): real effective plume rise override (m)

Negative (flow < 0): real plume top (m) for vertical plume distribution 

override

Record 4 through nspec+4

ione Integer dummy variable (=1)

namspec Text names for nspec species (character*4(10,nvar) array):

ptems Real point emission rate (mol/time period for gases, g/time period for

aerosols) for nstk point sources

Note that the emission time interval (the denominator for the emissions rate) is normally, but 

not necessarily, 1 hour. The time interval of the emission records must match the time zone 

and input frequency of the emissions as specified in the CAMx.in file.

3.4.3.9 Input Gridded Emissions File

The input gridded emissions file contains gridded fields of low-level (i.e., surface) emission rates 

for all emitted species to be modeled. If gridded emissions are to be modeled, a gridded 

emissions file must be developed for the master grid and optionally any nested fine grids.

The data records of the gridded emissions file have the following structure, and are repeated 

for each time interval on file:

The variables have the following definitions:

Record 1

ibdate Integer beginning date of time interval (YYJJJ)

btime Real beginning decimal hour (e.g., 1:30 PM = 13.5)

iedate Integer ending date of time interval (YYJJJ)

etime Real ending decimal hour (e.g., 1:30 PM = 13.5)

Record 2 through nspec×nz+1

ione Integer dummy variable (=1)

ibdate,btime,iedate,etime

Loop from l = 1 to nspec species:

ione,namspec(l),((emiss(i,j,l),i=1,nx),j=1,ny)
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namspec Text names for nspec species (character*4(10,nvar) array):

emiss Real gridded emission field values (mol/time period for gases, g/time 

period for aerosols) for nx grid columns and ny grid rows

Note that the emission time interval (the denominator for the emissions rate) is normally, but 

not necessarily, 1 hour. The time interval of the emissions record must match the time zone 

and input frequency of the emissions as specified in the CAMx.in file.

3.4.4 Output Files

Master and nested grid instantaneous files contain full three-dimensional fields of all species 

modeled, while the gridded average and deposition files contain only those species specified in 

the run control file. For flexibility, CAMx offers the option to write full three-dimensional 

average concentration fields, or just surface layer two-dimensional fields (see the “3-D average 

file” option in the CAMx control file). It is permissible to change the number of species on the 

average file, or change between 2-D and 3-D average files, from one CAMx simulation period to 

the next (provided the periods are configured as separate CAMx runs). As the instantaneous 

concentration files are used for CAMx restarts, the model only writes instantaneous fields at 

the end of the simulation. PiG output files possess a unique format, and are used primarily for 

model restarts. 

3.4.4.1 Output Concentration Files

The output average files for all grids, and the coarse (master) grid instantaneous file, are all 

written in the CAMx Fortran binary format as described earlier. There are three differences 

between the output concentration files and the input initial concentration files. First, the file 

name given in the file description header record (header record #1) is “AVERAGE” for the 

average output file, “INSTANT” for the instantaneous output file, and “AIRQUALITY” for the 

input initial concentration file. Second, the “note” in the file description header record of the 

output concentration files is the message supplied in the first line of the CAMx run control file, 

whereas the “note” in the air quality file is set as part of the input file preparation. Third, the 

species lists can be different among the files: the output instantaneous file contains all species 

modeled (as specified in the chemistry parameters file), the average output file contains only 

the species specified in the run control file, and the input initial concentration file may contain 

any subset of modeled species as determined when that file is prepared.

Two other differences exist between the average and instantaneous output files. As noted 

above, the average file may contain only surface-level fields or the entire three-dimensional 

fields, as selected by the user. Also, gas concentration fields are output as ppm in average files, 

but as μmol/m3 in instantaneous files (aerosols are in μg/m3 in both files). Because of these 

differences, and because average files usually do not contain all modeled species, CAMx does 

not allow the average output concentration file to be used for simulation restarts. 

3.4.4.2 Output Deposition Files

The output deposition file is identical in format to the two-dimensional surface-level output 

average concentration file. The file name given on the first record of the deposition file is 

“AVERAGE” so that existing post-processing software will recognize the format. However, the 
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output deposition file differs from the output average concentration file in one important way. 

The species list is identical to the list on the average concentration output files, except that four 

parameters are output for each species:

species_DV Real 2-D dry deposition velocity field for species (m/s)

species_DD Real 2-D dry deposited mass field for species (mol/ha for

gases, g/ha for aerosols)

species_WD Real 2-D wet deposited mass field for species (mol/ha for

gases, g/ha for aerosols)

species_LC Real 2-D precipitation liquid concentration for species (mol/l for 

gases, g/l for aerosols)

3.4.4.3 Nested (Fine) Grid Instantaneous Output File

The nested (or “fine”) grid Fortran binary output instantaneous file is unique and contains the 

three-dimensional concentration fields for all nested grids together, as opposed to separate 

files for each grid. All grid definition parameters given in these files are referenced relative to 

the master grid, so specific absolute information about grid cell size or projection coordinates 

for each nested grid must be determined from master grid parameters. If the user utilizes the 

Flexi-nesting capability of CAMx, then the gridded fields output to the nested fine grid files will 

change according to how nests are altered, added, and/or removed during the course of a 

simulation.

The header portion of the nested grid output files contain 3+nnest records with the following 

structure:

The time-variant portion of the nested grid output files have the following structure, where the

following records are repeated for each output time:

message

nnest,nspec

(mspec(l),l=1,nspec)

Loop from 1 to nnest grid nests

ibeg,jbeg,iend,jend,mesh,ione,nx,ny,nz,iparnt,ilevel

time,idate

Loop from 1 to nnest grid nests

Loop from l = 1 to nspec species:

Loop from k = 1 to nz layers:

((conc(i,j,k,l),i=1,nx),j=1,ny)
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The variables on the nested grid output concentration files have the following definitions:

message Text string containing file description (character*60)

nnest Number of fine grid nests on file

nspec Number of species on file

mspec Species names for nspec species

ibeg Grid n x-direction starting index of grid (master grid cell)

jbeg Grid n y-direction starting index of grid (master grid cell)

iend Grid n x-direction ending index of grid (master grid cell)

jend Grid n y-direction ending index of grid (master grid cell)

mesh Grid n meshing factor (number of nested cells per master)

ione Dummy integer = 1

nx Grid n number of grid rows

ny Grid n number of grid columns

nz Grid n number of layers

iparnt Grid n’s parent grid (grid index within which this fine grid is nested; 0 = 

master grid)

ilevel Grid n’s grid level (depth at which this grid is nested; 1=master grid is 

parent)

time Time of output (HHMM); ending hour for average output

idate Date of output (YYJJJ)

conc Grid n, species l, layer k concentrations (ppm for average gases, μg/m3

for average aerosols, μmol/m3 for instantaneous gas species) for nx grid 

columns, and ny grid rows

3.4.4.4 PiG Restart File

When the PiG option is invoked, CAMx outputs all puff parameters each hour for model restart 

capabilities. This file is Fortran binary and is analogous to the instantaneous gridded 

concentration output files in that it represents a “snapshot” of data at the top of each hour. 

The file format is unique and contains information for each puff, including coordinates, grid 

location, size specifications, age, and mass of each of the chemical species carried. While this 

file contains PiG information for the entire simulation, it would be of limited use for certain 

analyses such as plotting puff trajectories. This is because the instantaneous nature of the data,

and the dynamic memory allocation utilized in the PiG submodel, leads to insufficient 

information to identify and track individual puffs hour to hour.

The PiG restart file contains two records with the following structure, and these are repeated 

for each output time:
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The variables on the PiG restart file have the following definitions:

idatpig Date of output (YYJJJ)

timpig Time of output (HHMM)

npig Number of PiG puffs active at this output time

nreactr Number of chemical reactors in each puff

ingrd Grid index for npig puffs

idpig Point source index for npig puffs

xpigf x-coordinate of puff front (km from master grid origin) for npig puffs

xpigb x-coordinate of puff back (km from master grid origin) for npig puffs

ypigf y-coordinate of puff front (km from master grid origin) for npig puffs

ypigb y-coordinate of puff back (km from master grid origin) for npig puffs

zpig Puff height (m AGL) for npig puffs

axisy Puff lateral width (m) for npig puffs

axisz Puff vertical depth (m) for npig puffs

sigy Puff Gaussian lateral dimension (m) for npig puffs

sigx Puff Gaussian longitudinal dimension (m) for npig puffs

sigz Puff Gaussian vertical dimension (m) for npig puffs

pufftop Puff top height (m AGL) for npig puffs

puffbot Puff bottom height (m AGL) for npig puffs

htfms Puff horizontal turbulent flux moment, shear (m2

/s)

htfmb Puff horizontal turbulent flux moment, buoyancy (m2/s)

vtfms Puff vertical turbulent flux moment, shear (m2

/s)

vtfmb Puff vertical turbulent flux moment, buoyancy (m2/s)

agepigf Puff front age since release (s) for npig puffs

agepigb Puff back age since release (s) for npig puffs

fmspig Puff volume parameter (unitless) for npig puffs

ipufmap Puff OSAT region map pointer (unitless) for npig puffs

ipufgrp Puff OSAT group pointer (unitless) for npig puffs

puffrad Puff radical concentrations (ppm) for nrad species, nreactr reactors, and 

npig puffs

puffmass Puff pollutant mass (μmol) for nspec species, nreactr reactors, and npig

puffs

idatpig,timpig,npig,nreactr

(ingrd(n),idpig(n),xpigf(n),xpigb(n),ypigf(n),ypigb(n),zpig(n),

& axisy(n),axisz(n),sigy(n),sigx(n),sigz(n),pufftop(n),puffbot(n),

& htfms(n),htfmb(n),vtfms(n),vtfmb(n),agepigf(n),agepigb(n),fmspig(n),

& ipufmap(n),ipufgrp(n),

& ((puffrad(i,nr,n),i=1,nrad),nr=1,nreactr),

& ((puffmass(i,nr,n),i=1,nspec),nr=1,nreactr),n=1,npig
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3.4.4.5 PiG Sample Grid Files

The optional PiG sampling grid concentrations are time-averaged in the same manner as the 

output average concentrations provided on the computational grids. The same user-defined 

set of output species are written to the sampling grid files, but only two-dimensional surface 

layer concentrations are reported. The sampling grid file format is identical to the CAMx 

average and deposition files, with one file generated per sampling grid, so that they may be 

readily viewed and manipulated with CAMx post-processing software.
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4. CORE MODEL FORMULATION

This section outlines the numerical approach employed in CAMx, and describes the technical 

formulation of the emissions, transport and removal processes. The specific chemical 

mechanisms and their numerical solvers are discussed in detail in Section 5. 

4.1 Numerical Approach

The physical representations and the numerical methods used for each term of the pollutant 

continuity equation (described in Section 1) are summarized in Table 4-1. CAMx includes peeraccepted algorithms and component formulations, and its modular framework eases the

addition and/or substitution of alternative algorithms in the future. 

Table 4-1. Summary of the CAMx models and methods for key physical processes.

Process Physical Models Numerical Methods

Horizontal advection Eulerian continuity equation • Bott (1989)

• PPM (Colella and Woodward,1984)

Horizontal diffusion K-theory 1st order closure Explicit simultaneous 2-D solver

Vertical advection Eulerian continuity equation Implicit backward-Euler (time) hybrid 

centered/upstream (space) solver

Vertical diffusion • K-theory 1st order closure

• Non-local mixing

• Implicit backwards-Euler (time) 

centered (space) solver

• Explicit ACM2 non-local 

convection/diffusion (Pleim, 2007)

Gas-Phase Chemistry

• Carbon Bond 2005 (Yarwood et al., 2005b)

• Carbon Bond 6 (Yarwood et al., 2010, 

2012a,b)

• SAPRC99 (Carter, 2000)

• Inorganic/organic aerosol precursors

• EBI (Hertel et al., 1993)

• IEH (Sun et al., 1994)

• LSODE (Hindmarsh, 1983)

Aerosol Chemistry

• Aqueous inorganic chemistry

• Inorganic thermodynamics/partitioning

• Organic thermodynamics/partitioning

• Static 2-mode or multi-section size models

• RADM-AQ (Chang et al., 1987)

• ISORROPIA (Nenes et al., 1998)

• SOAP (Strader et al., 1999)

• CMU (Pandis et al., 1993)

Dry deposition

• Resistance model for gases (Wesely, 1989) 

and aerosols (Slinn and Slinn, 1980)

• Resistance model for gases (Zhang et al., 

2003) and aerosols (Zhang et al., 2001)

Deposition velocity as surface 

boundary condition in vertical 

diffusion solver

Wet deposition Scavenging model for gases and aerosols 

(Seinfeld and Pandis, 1998)

Exponential decay as a function of 

scavenging coefficient

The continuity equation is numerically marched forward in time over a series of time steps. At 

each step, the continuity equation is integrated by way of an operator-splitting approach that 

calculates the separate contribution of each major process (emission, advection, diffusion, 

chemistry, and removal) to concentration change within each grid cell. The specific equations 

that are solved individually in the operator-splitting process are shown in order below:
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where cl is species concentration (μmol/m3 for gasses, μg/m3 for aerosols), El is the local 

species emission rate (μmol/s for gasses, μg/s for aerosols), ∂t is timestep length (s), u and v are 

the respective east-west (x) and north-south (y) horizontal wind components (m/s), Ayz and Axz

are cell cross-sectional areas (m2) in the y-z and x-z planes, respectively, m is the ratio of the 

transformed distance on the various map projections to true distance (m=1 for curvi-linear 

latitude/longitude coordinates), and Λl is the wet scavenging coefficient (s-1

).

A master driving time step for the model is dynamically determined during the simulation for 

the largest and coarsest (master) grid. Time steps typically range from 5-15 minutes for grid 

cell sizes of 10-50 km, to a minute or less for small cell sizes of 1-2 km. As a result, nested grids 

require multiple driving time steps per master step depending on their grid sizes relative to the 

master grid spacing. Furthermore, multiple transport and chemistry time steps per driving step 

are used as necessary to ensure accurate solutions for these processes on all grids.

The first process in each time step for a given grid is the injection of emissions from all sources. 

CAMx then performs horizontal advection and vertical advection, followed by vertical diffusion, 

horizontal diffusion, chemistry, and finally wet scavenging. 

( )

( )

( ) ( )

Mechanism specific reaction equations

η

Z

2

2

2

2

= − ∂

∂

= −Λ

∂

∂

















 





∂

∂

∂

∂

+ 



 





∂

∂

∂

∂ = ∂

∂





 





∂

∂

∂

∂ = ∂

∂

∂ ∂

∂ − ∂

∂ = ∂∂





 





∂

∂ = − ∂

∂

















∂

∂ = − ∂

∂

∂ ∂ ∂ = ∂

∂

Chemistry

l

l l

Wet Scavenging

l

l

Y

l

X

XY diffusion

l

l

v

 diffusion

l

l

l

Z transport

l

xz l

Y advection xz

l

yz l

X advection yz

l

l

Emission

l

t

c

c

t

c

y

c /ρ m K

x y

c /ρ m K

x

m

t

c

z

c /ρ ρK

t z

c

z t

h

c

z

c

t

c

m

vA c

A y

m

t

c

m

uA c

A x

m

t

c

x y z

E

m

t

c

ρ ρ
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Although advection is performed separately in the x (east-west), y (north-south), and z (vertical) 

directions, the numerical linkage between these components has been developed in a mass 

consistent fashion to preserve the density field at each time step. This maintains the flexibility 

to allow many types of meteorological models, and modeling grid resolutions, projections, and 

layer structures, to characterize transport in CAMx.

Trace gases and particles are removed from the atmosphere via deposition to the ground. Dry 

deposition refers to the direct sedimentation and/or diffusion of material to various terrestrial 

surfaces and uptake into biota. Wet deposition refers to the uptake of material into cloud 

water and precipitation, and its subsequent transfer to the surface. The efficiency with which 

wet and dry deposition processes can remove pollutants from the air depends upon the 

physical and chemical properties of the pollutants, local meteorological conditions, the type of 

surface on which they are being deposited, and on the frequency, duration, and intensity of 

precipitation events. Dry deposition is an important removal mechanism, but it is not explicitly 

treated as a separate process in the time-splitting approach. Instead, deposition velocities for 

each species are used as the lower boundary condition for vertical diffusion. This appropriately 

couples the surface removal of pollutants through each column of cells via the vertical mixing 

process.

4.2 CAMX Grid Configuration

4.2.1 Grid Cell Arrangement

CAMx carries pollutant concentrations at the center of each grid cell volume, representing the 

average concentration over the entire cell. Meteorological fields are supplied to the model to 

quantify the state of the atmosphere in each grid cell for the purposes of calculating transport, 

chemistry, and removal. CAMx internally carries these variables in an arrangement known as 

an “Arakawa C” grid configuration (Figure 4-1). State variables such as temperature, pressure, 

water vapor, and cloud water are located at cell center along with pollutant concentration, and 

represent grid cell average conditions. Wind components and diffusion coefficients are carried 

at cell interfaces to describe the transfer of mass in and out of each cell face. Note in Figure 4-

1, for example, that horizontal wind components u and v are staggered from each other. This 

facilitates the solving of the transport equations in “flux form”. 

Depending upon the source of meteorological data, it is recommended that the user directly 

provide the gridded horizontal wind fields in the staggered Arakawa C configuration. However, 

this is not always feasible, and so CAMx offers the option for the user to supply all 

meteorological variables, including horizontal wind components, at cell center; in this case 

CAMx internally interpolates the winds to cell interfaces. Note that this leads to a slight 

smoothing effect on the horizontal wind fields.

Figure 4-1 also describes the horizontal cell indexing convention used in CAMx. Each cell is 

defined by the index pair (i,j), where i ranges from 1 to nx (the number of cells in the east-west 

direction), and j ranges from 1 to ny (the number of cells in the north-south direction). The

eastern and northern faces of the cell are indexed (i,j), while the western and southern faces 

are indexed (i-1,j) and (i,j-1), respectively.
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Figure 4-1. A horizontal representation of the Arakawa C variable configuration used in 

CAMx.

In the vertical, most variables are carried at each layer midpoint (defined as exactly half way 

between layer interfaces). Again the exceptions are those variables that describe the rate of 

mass transport across the layer interfaces, which include the vertical diffusion coefficient KV

and the vertical transport rate η. These variables are carried in the center of each cell 

horizontally, but are located at the top of the layer (i.e., the interface) vertically.

4.2.2 Grid Nesting

CAMx incorporates two-way grid nesting, which means that pollutant concentration 

information propagates into and out of all grid nests during model integration. Any number of 

grid nests can be specified in a single run, where horizontal grid spacing can vary from one grid 

nest to another (note that vertical grid structures must be consistent among all grids). The 

nested grid capability of CAMx allows cost-effective application to large regions in which 

regional transport occurs, yet at the same time providing fine resolution to address small-scale 

impacts in selected areas.

Each grid nest is defined over a subset of master (coarsest) grid cells. The range of master grid 

row and column indices that define the coverage of each nested grid must be specified in the 

run control file. An integer number of nested grid cells must span one master grid cell; this 

number is referred to as a “meshing factor”. “Buffer” cells are added around the perimeter of 

each nested grid to hold boundary conditions. Buffer cells are added automatically within 

CAMx and should not be specified by the user in the run control file. All nested grid output files 

contain data for the entire array of computational and buffer cells; however, buffer cell 

concentrations are considered invalid and should be ignored. Additionally, all nested grid input 

files must contain data for the entire array of computational and buffer cells. An example of a 

horizontal nesting arrangement is shown in Figure 4-2. Here, two telescoping fine grid nests are 

defined: one with a meshing factor of 2 spanning master grid cells (5,4) to (8,8), and one with a 

meshing factor of 4 spanning master grid cells (6,6) to (6,7).

(i, j)

T, p, q, Kv (i, j)

(i, j)

(i, j-1)

u, Kx (i-1, j) u, Kx

v, Ky

v, Ky
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Figure 4-2. An example of horizontal grid nesting, showing two telescoping nested grids 

within a 10×10 cell master grid. The outer nest contains 10×12 cells (including buffer cells to 

hold internal boundary conditions), and the inner nest contains 6×10 cells (including buffer 

cells).

Restrictions on specifying the size and resolution of all grid nests include the following:

1) The ratio of master grid cell size to nested grid cell size must be an integer (e.g., a 

“meshing factor” of 3 means that 3 nested cells span the distance of 1 master cell, 

resulting in an area of 9 nested cells per master cell);

2) For telescoping grids (a nested grid containing an even finer grid), the cell size of the finest 

grid must be a common denominator for all parent grids above it (e.g., a 36-12-4 km or 

36-12-2 km arrangement is allowed, but a 36-12-9 km is not);

3) The restriction in (2) above does not apply to parallel nested grids of the same generation 

(e.g., 4 km and 5 km grids can be located in different areas of a master grid provided that 

the master cell size is some multiple of 20 km);

4) Nested grids cannot overlap, although they may share a common boundary or edge;

5) Nested grids cannot extend into a boundary, or non-modeled, area of the master grid;

Coarse Grid Boundary Cells

Coarse Grid Boundary Cells

Coarse Grid Boundary Cells

Coarse Grid Boundary Cells

Fine Buffer Cells

Fine Buffer Cells

Fine Buffer Cells

Fine Buffer Cells

Boundary of Fine Grid 1

Boundary of Fine Grid 2

1 2 3 4 5 6 7 8 9 10

10

9

8

7

6

5

4

3

2

1
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6) CAMx is currently configured to allow four “generations” of nests (e.g., four levels of 

telescoping grids); this can be extended in the code if more than four levels of nests are 

required;

7) The total vertical depth of each nested grid must exactly match the depth of the master 

grid, and nested grid vertical layer structures must be consistent with the master grid in 

terms of the number of layers and their thicknesses;

4.2.3 Flexi-Nesting

The following Fortran binary I/O files must be provided for the master grid, and optionally 

provided for each nested grid:

• 2-D surface emissions;

• 2-D time-invariant surface characteristics (landuse and LAI distribution);

• 2-D time-variant surface meteorology (surface temperature, snow cover);

• 3-D time-variant state meteorology (wind, temperature, pressure, moisture, vertical grid);

• 3-D time-variant cloud and precipitation variables;

• 3-D time-variant vertical diffusivities

Any of these input files may be supplied for each nested grid, or none at all. If any of these files 

are not supplied for a particular nested grid, the Flexi-Nest algorithm within CAMx interpolates 

the missing fields from the parent grid. Clearly it is desirable to provide nested grid data 

whenever possible. However, the ability to interpolate data is useful for testing sensitivity to 

grid configurations or for situations when it is not possible to run a meteorological model for all 

grid nests.

The Flexi-Nest option also allows users to redefine the nested grid configuration at any point in 

a simulation. Nested grids can be introduced or removed only at the time of a model restart 

since a new CAMx user control file must be used to redefine the grid configuration. For 

example, the user may wish to “spin-up” the model using a regional-scale master grid and a 

single nest over an area of interest for two days. Starting at 6 AM on the third day, the user 

might introduce one or more nests within the original nested grid for more detailed analysis. 

This would require that the model be restarted at 6 AM of the third day with a new control file 

that defines the position of the two new nests and (optionally) provides any additional input 

fields for these grids. CAMx will internally reconcile the differences in grid structure between 

the nested grid restart files and the new user control file, and then interpolate any data fields 

not supplied to CAMx for the new nests from the parent grid(s). 

4.3 Treatment of Emissions

Pollutant emissions are treated in two basic ways within CAMx: low-level (gridded) emissions 

that are released into the lowest (surface) layer of the model; and elevated stack-specific 

(point) emissions with buoyant plume rise that can be emitted into any model layer. Emission

rates are held constant (not time interpolated) between reading intervals (usually 1 hour) but

are injected at every grid-specific time step during the simulation. Gridded and point emissions 
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are provided to CAMx in separate input files. External emission processing systems are used to 

develop gridded and point, time- and space-resolved, chemically-speciated input files for CAMx. 

These external programs are not discussed in this User’s Guide; see Section 2 for more 

information on emission systems that are used to support CAMx applications.

4.3.1 Gridded Emissions

Two-dimensional gridded low-level emissions are defined by space- and time-varying rates for 

each individual gas and PM species to be modeled. Gridded emissions represent sources that 

emit near the surface and that are not sufficiently buoyant to reach into the upper model 

layers. Such emission categories include:

• Low-level stack (point) emissions that are too small to result in plume rise above the 

model surface layer;

• Other non-point industrial sources (fugitive leaks, tanks, etc.);

• Mobile sources (cars, trucks, non-road vehicles, railroad, marine, aircraft, etc.);

• Residential sources (heating, cooking, consumer products);

• Commercial sources (bakeries, refueling stations, dry cleaners);

• Biogenic sources;

• Natural sources (small fires, wind-blown dust).

The spatial distribution of each individual source within these categories is defined by the 

modeling grid. Information such as population distribution, housing density, roadway 

networks, vegetative cover, etc. is typically used as a surrogate to distribute regional emission 

estimates for each source to the grid system. Processing tools are used to combine emissions 

from all sources into a single input file for each grid (see Sections 2 and 3).

4.3.2 Elevated Point Emissions

Similarly to gridded emissions, elevated point emissions are defined by space- and time-varying 

rates for each individual gas and PM species to be modeled. The only difference is that these 

sources emit from individual stacks with buoyant rise that may take them into upper model 

layers. These types of sources are almost always associated with large industrial processes, 

such as electric generators, smelters, refineries, large factories, etc. but can also represent 

natural elevated sources such as wildfires and lightning NOx. The spatial distribution of these 

points is specifically given by the coordinates of the stacks themselves (grid locations are 

determined within CAMx). Plume rise is determined within CAMx as a function of stack 

parameters (height, diameter, exit velocity and temperature) and ambient meteorological 

conditions, so the point source file provides speciated time-resolved emission rates and stack 

parameters for each individual source. A single point source file provides the definition of all 

stacks and their emissions over the entire modeling domain (see Sections 2 and 3).

Plume rise is calculated using the multi-layer stability-dependent algorithm of Turner et al. 

(1986). This approach calculates the momentum and buoyant plume rise energy from the 

stack, takes the larger of these two values, and determines the dissipation of that energy via 

mixing with ambient air according to the meteorological conditions through the host model 
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layer. If sufficient energy remains to reach into the next model layer, the calculation for 

buoyant rise repeats for the meteorological conditions of that layer, and so on, until a layer is 

found where the plume cannot rise any farther. All emissions from this source are then 

injected into the grid cell directly above the stack at this layer height. This algorithm was 

adopted for CAMx because it provides a more realistic handling of stable layers aloft that can 

trap plume rise, whereas this effect would not be realized based on meteorological conditions 

at stack top alone.

Under neutral/unstable conditions, momentum rise at the stack top is calculated from

while buoyancy rise is the lesser of

and

In these expressions ds is stack diameter (m), vs is stack exit velocity (m/s), hs is stack height 

(m), w is ambient wind speed (m/s), and zb is the distance between the stack top and the base 

of the current model layer. A minimum wind speed of 1 m/s is specified to avoid unrealistically 

large plume rise. Buoyancy flux f is initially calculated from stack parameters, but is set to 

residual flux entering the bottom of any higher layer. The initial buoyancy flux at stack top is 

given by

where g is gravitational acceleration (9.8 m2/s), Ts is stack exit temperature (K), and T is 

ambient temperature (K). The residual flux calculation into the next higher layer depends on 

which neutral/unstable buoyancy rise equation was originally used in the current layer:

or

where zt is the distance between stack top and the top of the current model layer.

Under stable conditions, momentum rise at the stack top is calculated from the lesser of Hmu

and

w

d v H s s

mu

3 =

( ) bu b H = f w + z

3/ 5 30 /

( ) [ ( )] bu s b H = f w h + f w + z

2 / 5 3 3/ 5 3 24 / 200 /















 − =

s

s

s s T

T T f g v d

4

2

0

5/3

30 



 



 − = bu t H z f w

( )

2/3

3 3 5.5 10 1

−

−

















− = × − +

bu t

s

bu t H z

h f w H z
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while buoyancy rise is the lesser of

and

In these expressions, ∂θ/∂z is the potential temperature gradient (a measure of atmospheric 

stability). Here also, buoyancy flux is initially calculated from stack parameters, but is set to 

residual flux if the plume extends into the next higher layer. The residual flux calculation 

depends on which stable buoyancy rise equation was originally used:

or

When final plume rise is reached using stable buoyancy rise, it is adjusted downward to twothirds of the rise through the stable depth. After final plume rise is determined, the rise is 

further adjusted downward by stack tip downwash according to a critical Froude number and 

ambient wind speed. The stack Froude number is given by

For F<3, no downwash adjustment is made to final plume rise. Above that value, the following 

downwash factors (D) are applied depending upon the ambient wind speed at stack top:

1/3 1/ 6 2 2

1/ 2 0.646

−





 





∂

∂















 = T w z

v d H T

s

s s

ms

θ

1/3

3

1

1.8















  + 

 





∂

∂ =

−

bs b z

w z

f T H θ

( ) 3 3 0.56 t b z z

T

w

z

f f − ∂

∂ = − θ

( ) 8/ 3 8 / 3

1/ 3

0 0.24 t b z z

T

f

z

f f − ∂

∂ = − θ

g d (T T )

T v F

s s

s

− =

2

( )

s

s s

s

s

s

D w v

v w v

v

v w D

D v w no plume rise

3

2 1,

3

2 3 ,

0 ,

= <

≤ < − =

= <

3/8

8/3

1

1/3

0

4.1















  + 

 





∂

∂ =

−

bs b z

f z

f T H θ
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CAMx injects point source emissions into all model layers spanned by the plume depth at final 

(adjusted) rise. Plume depth is determined as a function of stack diameter, plume 

temperature, plume velocity, time of plume rise, and ambient wind and temperature 

conditions. A uniform mass distribution through plume depth is assumed. If this depth is 

wholly contained within a single layer, that layer receives all emission mass. If this depth spans 

several layers, then fractions of the emissions are injected into these layers according to the 

fraction of plume depth spanning those layers. We apply the “rule-of-thumb” that plume depth 

equals plume rise (Turner and Schulze, 2007) as a maximum limit for plume depth.

The following equations are used to define the plume depth after reaching final rise. These are 

based on the approach used in the SCIPUFF model (EPRI, 2000) and were developed for use in 

the CAMx plume-in-grid (PiG) submodel. The plume depth Dp at final rise is given by

( )

1/ 2 2 D 3 2 D 2K t p = s +

where Ds is stack diameter, K is plume diffusivity during rise, and t is the time of rise. The time 

of rise is determined by dividing final plume rise by the mean plume rise speed Vp; the latter is 

set to half the stack exit velocity. A lower limit of 1 m/s is applied to the exit velocity, so the 

minimum value of Vp is 0.5 m/s. The plume diffusivity is determined by scaling initial plume 

width (according to stack diameter) by the turbulent flux moment qp

2

:

( ) 2 K = 0.15 2Ds qp

where

































+ = + 2 2

2

2 2 3 0.4

p

p p p

v V

v

q f V

The turbulent flux moment is a function of the mean plume rise speed Vp, the ambient wind 

speed v taken at the level of final rise, and a plume entrainment coefficient fp: 

( ) 













 − = + 2 1 4 2

p

p

p s

T V

T T

f D g

where g is the gravitational constant (9.8 m2/s), T is ambient temperature at the level of final 

rise, and Tp is the mean plume temperature, taken as the mean of the stack exit temperature 

and the ambient temperature at final rise.
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4.4 Three-Dimensional Transport

4.4.1 Fundamentals

The CAMx transport algorithm is both mass conservative and mass consistent. Mass 

conservation refers to the ability to accurately account for all sources and sinks of mass in the 

model, with no spurious loss or gain of mass during model integration. To be mass 

conservative, CAMx internally carries concentrations of each species as a density (μmol/m3 for 

gases, μg/m3 for aerosols), and solves the advection/diffusion equations in flux form. This also 

serves to simplify mass budget accounting, which is used by the various source apportionment 

and process analysis options. Gas concentrations are internally converted to volumetric mixing 

ratio (parts per million, or ppm) for the chemistry step, and when they are written to the 

average output files.

Mass consistency refers to the model’s ability to transport pollutant mass exactly equivalent to 

the input atmospheric momentum field. For example, a model that is perfectly mass consistent 

will preserve a unity pollutant mixing ratio field in a divergent momentum field given constant 

unity boundary and initial conditions and zero sources and sinks. Sources of poor mass 

consistency in air quality models are typically related to the following (in order of importance): 

1) supplying meteorology that is inherently inconsistent, e.g., from an interpolative objective 

analysis or diagnostic model in which wind, temperature, moisture, and pressure fields 

are all independently developed;

2) spatially interpolating or averaging meteorological model fields, especially threedimensional wind vector fields, to an air quality model grid of different resolution and/or 

different mapping projection;

3) relying on a nested grid model to internally interpolate coarse grid meteorological 

parameters to finer grids;

4) employing numerical techniques within the air quality model that are mass inconsistent, 

e.g., holding input wind and density fields constant between meteorological update times, 

assuming non-divergent three-dimensional winds, etc.; and

5) employing different numerical and/or physical methods in the air quality and 

meteorological models.

It is expected that CAMx users will prepare high quality, mass consistent meteorological fields 

using advanced prognostic models so as to minimize inconsistencies in the inputs themselves. 

The practice of developing meteorological input fields using objective analysis or “diagnostic” 

approaches is highly discouraged.

CAMx operates on the map projections and grid systems employed in several widely used 

meteorological models (e.g., WRF, MM5, and RAMS) so that translation of meteorological data 

to CAMx requires as little manipulation as possible.

However, CAMx provides a very important flexibility that allows the air quality grid to differ 

from the meteorological grid in terms of projection and/or resolution when necessary. This, of 

course, leads to a potentially large source of mass consistency error as noted in point (2) above, 
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and if nested grids are specified where higher resolution meteorological fields are unavailable, 

additional error may occur as in point (3). Therefore, adjustments must be made to correct for 

the external inconsistencies coming into the model. Such adjustments could be applied to the 

meteorological fields during the interpolation/averaging procedure, but this approach would 

not account for internal sources of inconsistency within the air quality model itself (points 3-5 

above). To account for all sources of error while maintaining flexibility on input requirements 

and grid configuration, CAMx internally minimizes the sources of mass inconsistency as the 

model integrates forward in time. As discussed below, the model does this in several ways.

First, the transport equations are written and solved in mass “flux” form. Gridded 

meteorological inputs are carried in an “Arakawa C” arrangement (Figure 4-1), which optimizes 

the calculation of mass flux divergences while ensuring mass conservation. These points are 

important for the calculations described further below. Solutions based on the alternative 

“advective” form cannot guarantee mass conservation or consistency.

Second, CAMx can accept input meteorological fields for each individual nested grid, if available 

from a meteorological model. This reduces errors stemming from internal interpolations from 

parent to nested grids. Input gridded fields of layer heights, temperature, pressure, horizontal 

winds, water vapor, and vertical diffusivity are then interpolated in time to the unique time 

steps for each modeling grid. Since the vertical grid structure is defined via external inputs, 

layer interface heights may be specified as any arbitrary function of space and/or time. This 

allows the CAMx vertical grid system to exactly match all or a subset of any meteorological 

model layer structures, whether they are defined in terms of physical height above ground, 

normalized height coordinates (i.e., “sigma-z”), or normalized pressure coordinates (i.e., 

“sigma-p”). Therefore, total vertical transport is the combination of resolved vertical advection 

and mass exchange across undulating layer interfaces.

Third, and most importantly, the grid- and timestep-specific horizontal momentum fields are 

used to determine an instantaneous vertical velocity field that balances the local atmospheric 

continuity equation for the specific grid configuration employed. The presumption of a nondivergent momentum field (∇⋅ ρ V = 0) is usually invalid within air quality models since the 

externally supplied wind and density fields are not balanced in the first place (see points 1-3 

above). In CAMx, such a density-momentum balance obviously does not exist since a linear 

rate of temperature, pressure and horizontal wind change is imposed at each time step 

between meteorological update times. To calculate a vertical velocity profile for a given grid 

column, the divergent atmospheric continuity equation

is locally integrated through the depth of the column

( ) ρV dz

t

ρ ρw z

z

∫ H H 



 



 + ∇ ⋅ ∂

∂ = −

0

ρV

t

ρ = −∇⋅ ∂∂
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where the local time-rate change of atmospheric density ∂ρ/∂t in each grid cell is known from 

the input meteorological fields. In this approach, a vertical velocity profile w(z) is constructed 

that provides a balance between the imposed density tendency and the resolved horizontal 

momentum divergence in each grid cell at each time step.

The total vertical transport rate η at a particular layer interface is defined as the combination of 

resolved vertical velocity and the local time-rate of change of the layer interface height:

The total vertical transport rate is used for subsequent vertical transport calculations for all 

pollutants. A zero vertical velocity is specified at the ground, while a column- and pollutantspecific zero-gradient mixing ratio condition is applied at the top of the model.

The fourth way CAMx ensures mass consistency is to calculate the horizontal flux divergence of 

atmospheric density in a manner that is numerically consistent with the procedure used to 

horizontally transport pollutants. Atmospheric density is advected in and out of each cell using 

the same equation as for pollutants:

and this equation is solved using either the Bott (1989) or PPM (Colella and Woodward, 1984) 

advection solvers, as selected by the user (see Section 4.5 below). Total three-dimensional 

transport thus includes resolved momentum convergence/divergence rates as well as any 

artificial divergences caused by the horizontal and vertical grid specifications (e.g., spatially 

varying vertical grid structure, or systematic distortions associated with the map projections). 

In simple tests in which a uniform pollutant field of unity mixing ratio is transported throughout 

a single regional grid over several days using actual episodic meteorological inputs, this 

approach has been shown to provide nearly exact (to within 10-3

-10-4%) consistency between 

the density and pollutant fields.

4.4.2 Transport Algorithms

Horizontal advection is performed using the area preserving flux-form advection solver of Bott 

(1989) or the Piecewise Parabolic Method (PPM) of Colella and Woodward (1984) as 

implemented by Odman and Ingram (1993). These two finite difference schemes were 

incorporated into CAMx because they provide higher order accuracy with minimal numerical 

diffusion, yet are equivalent in execution speed compared to other simpler advection 

algorithms when operating on equivalent time steps. In CAMx, the Bott scheme is allowed to 

take larger time steps than PPM because Bott remains stable for Courant-Friedrichs-Levy (CFL) 

numbers up to 1 (i.e., the ratio of wind speed to grid spacing per timestep). Time steps are 

determined for Bott using a CFL number of 0.9, while time steps for PPM are restrained by a 

CFL number of 0.5. Therefore, the Bott option results in a faster simulation than the PPM 





 





∂

∂

+ 















∂

∂ ∇ ⋅ = m

vA

A y

m

m

uA

A x

m ρV xz

xz

yz

yz

H H

ρ ρ 2 2

w

t

h − ∂∂

η =
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option, perhaps at the price of some accuracy. We recommend testing both for your specific 

application.

As discussed by Yamartino (2000) the latest advection solvers such as Bott and PPM reduce 

numerical diffusion to the point where modelers need to be concerned about including 

appropriate levels of explicit horizontal diffusion. Currently, there is very little information on 

the appropriate level of horizontal diffusion for Eulerian grid models. We see this issue 

becoming increasingly important as more accurate advection solvers are utilized in grid models. 

This issue is not limited to CAMx.

Explicit horizontal diffusion coefficients are determined within CAMx using a deformation 

approach based on the methods of Smagorinsky (1963):

Separate diffusivity components are generated for fluxes in the x- and y-directions since KX and 

KY are calculated for separate cell faces in the Arakawa C grid arrangement. The value of K0 is 

specified according to the approach in MM5 (Anthes and Warner, 1978):

A maximum value of KX/Y is set to maintain numerical stability for the given grid-specific 

timestep. A minimum value is set to 1 m2/s. Horizontal diffusion is applied using an explicit 

simultaneous two-dimensional flux-divergence calculation.

Vertical transport and K-theory diffusion are both solved using implicit backward-Euler 

integration schemes. Since implicit schemes are absolutely stable, only one solution step is 

necessary per driving time step. Explicit approaches require potentially many sub-steps (on the 

order of 10-100) to maintain a stable solution, which introduces the potential for excessive 

numerical diffusion. Whereas the vertical advection step is implicitly solved in a single step, Ktheory vertical diffusion is implicitly solved over potentially several sub-steps, depending upon 

the magnitude of the vertical diffusivity relative to the vertical layer depths (CAMx uses the 

smaller of the current grid time step or a maximum 5 minute sub-step). This ensures non-local 

diffusive coupling among all layers that exhibit high diffusivity, especially for long driving time 

steps on coarser grids that would otherwise only experience mixing between adjacent layers 

during a single implicit step. Gridded vertical diffusion coefficients must be supplied to the 

model for the master grid via input file; the user may optionally supply vertical diffusion 

coefficients for any or all nested grids.

4.4.3 ACM2 Vertical Diffusion

The representation of sub-grid turbulent diffusion (or “mixing”) in photochemical grid models 

has not significantly advanced for several decades. Simple eddy viscosity (or “K-theory”) firstorder closure approaches have been used in most models. As a “local” closure technique, K1 / 2 2 2

/

4 2 































∂

∂ − ∂

∂

+ 















∂

∂

+

∂

∆ ∆ ∂ = +

y

v

x

u

x

v

y

x y u KX Y Ko

t

x y K

∆

∆ ∆ = × −3

0 3 10
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theory only treats mass transfer cell-by-cell (horizontal) or layer-by-layer (vertical), analogously 

to the diffusion of heat through a solid medium. Whereas K-theory adequately characterizes 

horizontal diffusion and weak vertical mixing during neutral and stable conditions, the 

shortcomings of K-theory are related to its inadequate treatment of deep vertical convective 

boundary layer mixing. In convective situations, buoyant plumes deriving energy in the surface 

layer are quickly and efficiently mixed deep into the atmosphere within eddies that are usually 

much larger than the individual model layers. K-theory therefore mixes the convective 

boundary layer much less efficiently than commonly observed. This has been shown to have 

very important ramifications for chemistry, especially during transition periods between 

stable/neutral and convective conditions. Modelers have commonly adjusted for the lack of 

adequate vertical mixing by arbitrarily increasing the magnitude of the input vertical diffusivity 

fields.

A promising non-local mixing scheme was developed in the early 1990’s called transilient 

theory (Raymond and Stull, 1990). This approach calculates the elements of a transilient 

matrix, where each element specifies the transfer rate from a given layer to any other layer, 

either adjacent or distant. In fact, K-theory is just a special case of transilient theory, in which 

transfer can only occur between adjacent layers above and below, leading to the trivially-solved 

“tri-diagonal” matrix. However, a fully populated transilient matrix is difficult to determine and 

until recently the approach has not been widely used in chemistry models. 

The U.S. Environmental Protection Agency (EPA) has developed an asymmetric convective 

model (ACM2) for the Models-3 Community Scale Air Quality (CMAQ) model (Pleim, 2007). This 

is considered a truncated, or simplified form of the general transilient mixing scheme in that it 

includes: (1) mixing among adjacent layers using K-theory (i.e, symmetrically along the diagonal 

of the transilient matrix); (2) rapid upward non-local mixing from the surface layer to all layers 

through the boundary layer (the convective aspect); and (3) slower compensating downward 

mixing layer-by-layer from the top of the boundary layer to the surface (the asymmetric 

aspect). All other matrix elements outside of these three transport paths are ignored. Figure 4-

3 shows this approach schematically. During non-convective conditions, ACM2 reverts back to 

the local K-theory component. Thus, ACM2 includes the basic features of both local and the 

most important component of non-local exchange. Tests comparing ACM2 against standard Ktheory result in more realistic profiles of ozone precursors, but usually minor impacts on 

surface ozone.

The ACM2 parameterization has been implemented in CAMx as an alternative to the K-theory 

approach. All variables needed to calculate the transfer rates are available from the existing 

input files, or are already calculated within CAMx for other purposes. The CAMx ACM2 option 

does not require that ACM2 be run within the meteorological model used to derive inputs for 

CAMx. However, EPA states that using ACM2 in both meteorological and chemistry models 

does lead to consistent boundary layer characterization. Meteorological interface programs 

(e.g., WRFCAMx, MM5CAMx, and RAMSCAMx) have been updated to include an option to 

generate vertical diffusivities in the same manner as the approach used within the CMAQ ACM2 

algorithm, which performs its diffusivity calculations internally. The CMAQ ACM2 diffusivity 

calculation is a hybrid of two methodologies: (1) boundary layer scaling based on Hostlag and
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Figure 4-3. Schematic representation of the turbulent exchange among layers within a 

vertical grid column during convective adjustment in the ACM2 (taken from Pleim [2007]).

Boville (1993); and (2) local scaling according to Richardson number and vertical shear similar to 

Liu and Carroll (1996). The former is used within the stable boundary layer or if it is larger than 

the latter. The CAMx implementation of ACM2 supports OMP and MPI parallel processing. 

Note that ACM2 increases CAMx runtime considerably. Whereas the original CAMx K-theory 

solver is implicit and does not need to use small time steps, ACM2 and its K-theory counterpart 

both use explicit solvers, which must divide the model time step into many very small sub-steps 

to generate a stable solution. The slow-down can be exacerbated by using the much larger

ACM2 vertical diffusivity values instead of the standard diffusivity options available in the CAMx 

meteorological preprocessors. The larger ACM2 diffusivity values further increase the number 

of integration sub-steps.

NOTE: ACM2 does not work with the Decoupled Direct Method (DDM) or the Integrated 

Process Rate (IPR) component of the Process Analysis (PA) tool.

4.5 Wet Deposition

Wet deposition is the predominant removal process for particles. Particles act as cloud 

condensation nuclei and subsequently the cloud droplets grow and collect into sufficiently large 

sizes to fall as precipitation. Additionally, particles that are entrained into the cloud, and that 

exist below precipitating clouds, can be directly scavenged by precipitation via accretion and 

impaction processes. The rates of nucleation and impaction depend upon cloud type (e.g., 

prolonged stratiform vs. vigorous convective development), precipitation rate, and particle size 

distribution.

Wet deposition can also be an important removal process for relatively soluble gaseous 

pollutants and this occurs through the following series of steps:
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• Mixing of trace gas and condensed water in common air space;

• Absorption of gas molecules by water droplets;

• Possible aqueous-phase reactions of the pollutant within water droplets;

• Precipitation of droplets to the earth’s surface;

• Diffusion of ambient gases into falling precipitation.

It is important to note that each of the above steps may be reversible, so that the overall wet 

deposition rate for gases depends on the net results of the forward and backward processes at 

each step.

The rate at which the first and fourth steps proceed depends on the frequency and nature of 

cloud formation and precipitation events. For example, mid-latitude cyclonic storm events

(e.g., winter storms) will result in different deposition rates than convective precipitation 

events such as summertime thunderstorms. The rates at which the second, third, and fifth 

steps proceed depend on the extent to which the pollutant in question dissolves in water and 

its overall reaction rate once in solution. Cloud water droplets can absorb gases from the air up 

the limit of their solubility in water. For many pollutants this solubility far exceeds the amount 

of pollutant present in the air so that the distribution of the pollutant between the air and 

water droplets is determined by the Henry’s Law constant, which is defined as the ratio of 

pollutant concentrations in the liquid-phase to the gas-phase at equilibrium. High values for 

the Henry’s law constant (greater than about 10,000 M/atm) indicate a strong tendency to 

dissolve in water droplets, whereas low values (less than about 100 M/atm) indicate a tendency 

to remain in the air (Seinfeld and Pandis, 1998). Equilibrium between concentrations of 

pollutants in the air and in water droplets is usually established on time scales of minutes, so 

equilibrium conditions can generally be assumed to exist in the atmosphere.

If a pollutant partitions significantly into water droplets it can be removed by precipitation. 

Averaged globally, highly soluble gases that are removed efficiently by wet deposition (e.g., 

nitric acid) are estimated to have lifetimes due to rainout of about 5 days (Warneck, 1989). 

Clearly, on regional or local scales, lifetimes against wet deposition will depend upon the 

frequency and intensity of rainout events. Gases that are removed less efficiently by wet 

deposition will have longer lifetimes. For example, the corresponding global average lifetime of 

formaldehyde against rainout is estimated to be 14 days (Warneck, 1989).

The basic model implemented in CAMx is a scavenging approach in which the local rate of 

concentration change ∂c/∂t within or below a precipitating cloud depends on a scavenging 

coefficient Λ:

The scavenging coefficient is determined differently for gases and particles, based upon 

relationships described by Seinfeld and Pandis (1998). Two components are calculated for 

gases: (1) direct diffusive uptake of ambient gases into falling precipitation; and (2) accretion of 

cloud droplets that contain dissolved gases. Two components are also determined for particles: 

Λ c

t

c = − ∂

∂
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(1) impaction of ambient particles into falling precipitation with an efficiency that is dependent 

upon particle size; and (2) accretion of cloud droplets that contain particle mass. Each of these 

processes is described below.

The external environmental inputs to the CAMx wet deposition algorithm include the threedimensional gridded distribution of cloud and precipitation water contents, with the 

precipitation contents broken down into liquid, snow, and ice (“graupel”). Scavenging rate 

equations were derived in terms of equivalent liquid precipitation rates, so the input 

precipitation water contents are internally translated into this metric.

The following general assumptions are made in the CAMx scavenging model:

1) Rain drops, snowflakes, and graupel particles are each separately represented by a single 

mean size, mass, and fall speed, which are determined from equivalent liquid 

precipitation rate;

2) There is no mixed-phased precipitation within a given grid cell – the dividing line between 

liquid rainfall and the two frozen forms is 273 K;

3) Snow is only associated with stratiform precipitation, and graupel only with convective 

precipitation;

4) Liquid cloud water is allowed to exist below 273 K – a linear ramp function is applied to 

apportion total cloud water into liquid form between 233-273 K (all cloud water is 

assumed to be in ice crystal form below 233 K);

5) All gasses can directly diffuse into or from liquid rainfall (only strong acids can diffuse into 

frozen precipitation) at a rate according to the precipitation’s state of saturation, 

pollutant diffusivity, and aerodynamic considerations;

6) All gases can dissolve into liquid cloud water, which can be scavenged by all precipitation 

forms – dissolved gasses are in equilibrium with ambient concentrations according to 

Henry’s Law;

7) PM is irreversibly scavenged directly by all precipitation forms via impaction, and by 

uptake into cloud water (liquid and ice) as condensation nuclei that is itself scavenged by 

all precipitation forms;

8) All in-cloud PM mass exists in cloud water (i.e., no “dry” aerosols exist in the interstitial air 

between cloud droplets) – all PM species and sizes are hygroscopic and internally mixed.

4.5.1 Precipitation Parameters

The mean raindrop diameter dd (m) and fall speed vd (m/s) are taken from the empirical 

estimates of Scott (1978). The drop diameter is related to rainfall rate P (mm/hr), and the fall 

speed relationship has been modified to better agree with data provided by Seinfeld and Pandis 

(1998):

4 0.21 dd 9.0 10 P − = ×

d dd v = 3100
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The precipitation water content Lp (g/m3) is related to rainfall rate by

where ρw is liquid water density (g/m3). This equation can be simplified to a dependency on 

just rainfall rate when the above relations for drop velocity and size are substituted. The 

resulting expression for rainfall rate as a function of precipitation water content is

Locatelli and Hobbs (1974) developed power law equations relating average diameters, fall 

speeds, and masses for 15 precipitating ice “habits”. We consolidated these relationships into 

two forms, termed “snow” and “graupel”, by fitting new power law curves to the Locatelli and 

Hobbs data. For snow,

And for graupel,

Note that in these equations for ice, dd is in mm and crystal mass md is in mg. By assuming that 

the number density and mass of snow/graupel crystals are equal to those for rain drops given 

equal precipitation water contents, we can relate the magnitudes of ice size and fall speed to 

equivalent liquid precipitation rate.

4.5.2 Gas Scavenging

Wet scavenging of gases by precipitation occurs within and below precipitating clouds. Below 

the cloud, the total gas concentration in a given grid cell is available for scavenging. Within a 

cloudy cell the total gas concentration must first be partitioned into an aqueous fraction caq

within cloud water and the remaining gaseous fraction cg within the interstitial air. Both 

aqueous and interstitial gasses within a cloudy cell are available for scavenging, but are 

removed at different rates as described below.

4.5.2.1 Scavenging of Gases in Cloud Water

The aqueous concentration in liquid cloud water (or cloud ice in the case of strong acids) is 

determined by Henry’s Law thereby assuming the solution exists in steady-state equilibrium. 

The Henry’s Law constant for a given gas species k0 (M/atm) specifies the ratio of pollutant 

mass in aqueous solution (M or mol/lh2o) to its equilibrium partial pressure (atm) at standard 

pressure and temperature. This constant is adjusted for temperature T and converted to a 

dimensionless molar ratio:

2.6

0.61

0.059

1.1

d d

d d

m d

v d

=

=

1.8

0.20

0.035

0.83

d d

d d

m d

v d

=

=

d

w

p v

P L 6 3.6×10 = ρ

1.27 7 1 10















 × =

w

Lp P

ρ
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where R is the ideal gas constant (8.206×10-2 l atm/mol K), and A is the temperature 

dependence factor. Dissociation of ammonia, nitric acid, and sulfur dioxide as a function of 

cloud and rainwater pH is also considered in the solubility calculation. The effective Henry’s 

Law constant H thus expresses the equilibrium ratio of the aqueous concentration caq (mass per 

volume of water) to the gas concentration cg (mass per volume of air),

which are related to total concentration c by

where Lc is cloud liquid water content (g/m3

).

The fraction of gases present in cloud water can be removed by precipitation via accretion of 

cloud water onto the falling hydrometeor (liquid or ice). As the hydrometeor falls, it sweeps a 

cylindrical volume per unit time equal to

where dc is the size of cloud droplets. This implies that the ambient motion of cloud droplets is 

insignificant compared to the hydrometeor fall speed. Due to aerodynamic perturbations of air 

flow around the falling hydrometeor, a collection efficiency is applied, i.e., the fraction of cloud 

droplets within the collection volume that are scavenged by precipitation. For large 

hydrometeors with sizes greater than 0.5 mm and droplets 10-20 μm, we take this efficiency to 

be 0.9 (Seinfeld and Pandis, 1998). Also, we further assert that (dd + dc)

2 ~ dd

2

. Assuming then 

that a mono-disperse distribution of hydrometeors are falling through a mono-disperse 

distribution of cloud water droplets, the scavenging coefficient for precipitation collecting cloud 

water is

where E is the collection efficiency (0.9) and Nd is the hydrometeor number density. The 

number density can be expressed in terms of equivalent rainfall rate, fall velocity, and drop size:

( ) d c d V d d v

2

4 = +

π

c d dE Nd Λ d v

2

4

π =





 



 



 



 = − T

H k R T A 1

298

1

0 exp

g

aq

c

c

H =

/ 6

2.8 10

3

7

d d

d d v

P N

π

− × =

w

c

g aq

L

c c c

ρ = +
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Substituting the relationship between Nd and rainfall parameters, then

The cloud water scavenging coefficient is scaled by the ratio of aqueous pollutant concentration 

to total grid cell concentration to achieve the aqueous-phase scavenging coefficient:

4.5.2.2 Scavenging of Ambient Gases

Given the relatively short residence times of falling precipitation through a given grid cell, 

aqueous equilibrium between ambient gas and precipitation cannot be assumed and so the 

transfer of ambient gas into liquid rainfall (or ice in the case of strong acids) is explicitly 

calculated. The maximum rate of transfer W of a gas to a falling hydrometeor containing no 

pre-existing pollutant mass is

The mass transfer coefficient Kc can be determined for a falling hydrometeor with speed vd and 

diameter dd by

where Dg and ν are the molecular diffusivity of the gas species and air, respectively.

Following the methodology of Seinfeld and Pandis (1998), the rate of caq increase can be 

represented by a mass balance with the rate of transport to the hydrometeor:

The expression for W is substituted into the equation above, rearranged, and expressed in 

terms of rainfall velocity. We then assume that through a given model layer the ambient gas 

concentration and hydrometeor pH and size is constant. Multiplying by the number density of 

falling hydrometeors Nd described above yields the gas-phase concentration scavenged by all 

drops falling through the layer:

Within cloudy layers, the gas-phase and aqueous-phase scavenging coefficients are added to 

provide the total in-cloud scavenging rate for gases, Λ = Λg+Λa. For below-cloud scavenging, 

Λ = Λg.

c g W = K H c































 



 



 = +

1/ 3 1/ 2

2 0.6

g

d d

d

g

c D

v d

d

D

K ν

ν

d W

dt

dc

d d

aq

d

3 2

6

1

π = π

d

c d

E P Λ 7 4.2 10− = ×

w

aq c

a c c

c L

Λ Λ

ρ =

d d

c g d v

P K Λ 6 1.67 10− = ×
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4.5.2.3 Solubility Limits on Gas Scavenging

There is a chance for rainfall to become super-saturated for sparingly soluble gasses as it falls 

through a grid column. The net scavenging coefficient for gases described above provides for 

the maximum potential uptake rate into clean rain water, so careful consideration must be 

given to appropriately determine the sign and magnitude of ambient grid cell concentration 

change according to the degree of rainfall saturation. The change in gas concentration is 

relaxed toward the difference between the maximum possible gas in solution for the given 

conditions ceq, and the amount of pre-existing gas in solution from layers above c0,

Here ceq is determined from the total liquid water in the cell (rain plus cloud water) and from 

Henry’s law equilibrium according to the total gas concentration in the cell (ambient grid 

concentrations plus total gas in pre-existing solution). If the concentration change is positive, 

mass is added to the rain water (c0 is augmented) and removed from the grid cell; if negative, 

mass is removed from rain water (c0 is decremented) and added to the grid cell.

4.5.3 Aerosol Scavenging

4.5.3.1 Scavenging of Aqueous Aerosols

All aerosols within cloudy layers are assumed to exist within cloud water. Therefore, the 

scavenging coefficient for aqueous aerosols is exactly the same as for the scavenging of cloud 

droplets: Λ = Λc.

4.5.3.2 Scavenging of Dry Particles

Wet scavenging of dry particles only occurs below precipitating clouds. We use the same 

scavenging coefficient as derived for the collection of cloud droplets:

For rain or graupel, the collection efficiency E is a function of particle size dp, and is given by 

Seinfeld and Pandis (1998) as:

where μ and μw are the kinematic viscosity of air (1.8×10-5 kg/m/s) and water (10-3 kg/m/s), 

respectively, φ = dp/dd is the ratio of particle size to hydrometeor size, Re is the Reynolds 

d

c d

E P Λ 7 4.2 10− = ×

( ) ( )

( )

3/ 2

*

*

1/ 2

1/ 2 1/3 1/ 2 1/ 2

2 / 3

4 1 2

1 0.4 0.16 4

















− +

− +





 





+ + +

= + +

S S

S S

R

R S R S

R S

E d

t

t

e

w

e c e c

e c

p

φ

μ

μ φ

c c c [ ( t)] ∆ = ( eq − 0 ) 1 − exp −Λ∆
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number for the hydrometeor, Sc is the Schmidt number for the collected particle, and St is the 

Stokes number of the collected particle. The Reynolds number is given by

while the Schmidt number is

where Dp is the particle Brownian diffusivity:

Here, k is the Boltzman constant (1.38×10-23 J/K) and C is the Cunningham correction factor for 

small particles:

and where λ is the mean free path of air (6.5×10-8 m). The Stokes number is given by

where ρp is the particle density. The S

* parameter is given by

Note that particle size dp and density ρp are affected by aerosol water content, which is 

determined from local humidity and PM deliquescence properties according to the ISORROPIA 

model (see Section 5).

Snow presents a complication for the efficiency calculation, since it is not a single solid mass but 

rather a collection of crystals arranged in a myriad of possible shapes that can lead to significant 

aerodynamic drag. This drag affects particle collection efficiency. To simplify the calculation, 

we use the value for E determined for rain and graupel, but set a lower limit for E of 1×10-3

based on the work of Sauter and Wang (1989).

4.6 Dry Deposition

For many compounds, dry deposition can be as important as wet deposition as a removal 

process. Due to the difficulty of making direct measurements of dry deposition and the need 

for a suitable model parameterization, dry deposition is often treated as a first-order removal 

2ν

d d

e

D v R =

p

c D

S ν =

p

p d

k T C D

3πμ =





 



















 = + + − λ

λ p

p

d

d

C

0.55

1.257 0.4exp

2 1

d

d p p

t d

v d C

S

μ

ρ

9

2

=

( )

( ) e

e

R

R S

+ +

+ + = 1 ln 1

* 1.2 ln 1 /12
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mechanism, where the flux of a pollutant to the surface is the product of a characteristic 

deposition velocity and its concentration in the “surface layer” (i.e., the lowest model layer). 

Deposition velocities are derived from models that account for the reactivity, solubility, and 

diffusivity of gases, the sizes of particles, local meteorological conditions, and seasondependent surface characteristics. The factors affecting deposition are discussed in more detail 

below. 

For a given species, particle size, and grid cell, CAMx determines a deposition velocity for each 

landuse type in that cell and then linearly combines them according to the fractional 

distribution of landuse. The deposition flux is used as the lower boundary condition in the 

vertical diffusion algorithm. Aerosol size spectra and species-dependent properties needed for 

the deposition velocity calculations are externally supplied to CAMx for all pollutant species via 

the chemistry parameters file; gridded landuse is supplied to the master grid and optionally any 

nested fine grids; the season is determined by the simulation date and location on the globe.

Movement of material along a path from the atmosphere, through any plant canopy, and onto 

the various plant and ground surfaces within and below the canopy is typically modeled by 

analogy to an electrical circuit. Resistances in serial and parallel arrangements are used to 

represent the relative ease with which material moves through different portions of the 

deposition pathway. Each branch of the circuit represents a different path by which material 

may be deposited. For example, gaseous pollutants may transfer through the lowest layers of 

the atmosphere partially into a plant canopy, through the stomatal openings on plant leaves 

and into the plant mesophyll tissue. Alternatively, the material may travel all the way through 

the plant canopy and deposit on the ground surface.

CAMx offers two dry deposition options: the original approach based on the work of Wesely

(1989) and Slinn and Slinn (1980); and an updated approach based on the work of Zhang et al. 

(2001; 2003). Both of these options are briefly described below.

4.6.1 The Wesely/Slinn Model

4.6.1.1 Dry Deposition of Gases

Wesely (1989) developed a resistance model that incorporates the major elements described 

above. Deposition velocity vd is calculated from three primary resistances r (s/m) in series:

a b s

d

r r r

V

+ + = 1

The aerodynamic resistance ra represents bulk transport through the lowest model layer by 

turbulent diffusion, and operates equivalently for all gases and small particles. The magnitude 

of this resistance depends on the intensity of turbulent motion, which in turn depends on solar 

insolation, wind speed, surface roughness, and near-surface temperature lapse rate. In CAMx it 

is calculated from





 



 −













 = h

o

a k u z

r φ 1 ln 1

*
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where u* is friction velocity (m/s), k is von Karman’s constant, z is the lowest model layer 

midpoint height (m), z0 is the surface roughness length (m), and φh is a stability correction term. 

The surface layer parameterization of Louis (1979) is used to supply friction velocity and 

stability correction as a function of input surface meteorology and roughness length. 

Roughness length is internally assigned according to season and the input gridded distribution 

of 11 landuse types as described in Section 3. In general, aerodynamic resistance is at a 

minimum on warm, sunny days with strong mixing due to surface heating and mechanical 

turbulence, and at a maximum on cool, calm nights when turbulent mixing is suppressed.

The quasi-laminar sublayer (or boundary) resistance rb represents molecular diffusion through 

the thin layer of air directly in contact with the particular surface to which material is being 

deposited. It is usually assumed to depend only on the molecular diffusivity of each pollutant 

species, and is given by

where Sc is the Schmidt number, or the ratio of air viscosity to species molecular diffusivity.

Over land, surface resistance rs is expressed as several more serial and parallel resistances that 

depend upon the physical and chemical properties of the surface in question:

where the first set of parallel resistances represents the pathway into the stomatal (rst) and 

mesophyll (rm) portions of active plants, the second is the pathway into the upper canopy (ruc), 

the third is the pathway into the lower canopy (rdc and rcl), and the fourth is the pathway to the 

ground surface (rac and rgs). Many of these resistances are season- and landuse-dependent, 

and are built into Wesely’s model; some in turn are adjusted within CAMx for solar insolation 

and surface wetness (vegetation is assumed to be unstressed). A few other resistances have 

been developed by Wesely for SO2 and ozone, and so are scaled for each gaseous species based 

on the following pollutant properties:

• Molecular diffusivity (determined from molecular weight, Mg MH2O / );

• Henry’s law solubility (H);

• Chemical reactivity toward oxidation of biological substances (f).

This allows the resistance approach to be used to estimate deposition velocities for a wide 

range of gaseous pollutants. 

The surface resistances for strong acids (e.g., nitric, sulfuric, and hydrochloric acid, peroxides)

are set to zero given their strong rates of update by biota and other surfaces (Huebert and 

*

2/3 2

k u

S

r c

b =

st m uc dc cl ac gs

s

r r r r r r r

r

+

+

+

+ +

+

= 1 1 1 1

1
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Robert, 1985; Wesely and Hicks, 2000). The species for which surface resistance is set to zero 

are defined in the CAMx chemistry parameters file.

Over water, the surface resistance for all gas species other than ozone is based on some 

improvements adopted by Kumar et al. (1996) in UAM-AERO, following Sehmel (1980):

where Ts is surface temperature (K). For ozone, this equation has been updated to 

parametrically match the tendencies of measured ozone fluxes reported by Helmig et al. (2012) 

from ship-borne measurements: 

*

4 6 3

3

1 10 5 10

1

H T u

r

s

O

s − − × + × =

where Ts is in °C rather than K. The cubic temperature dependence fits the deposition velocity 

response to the range of sea surface temperatures reported in the Helmig et al. data. The 

additional 1×10-4 term sets an upper limit on rs and a lower limit on deposition velocity so that 

the latter does not fall much below 0.01 cm/s. A lower limit of 1500 s/m was placed on rs such 

that ozone deposition over water does not exceed 6.5 cm/s, which is the upper limit in the 

cruise data.

4.6.1.2 Dry Deposition of Aerosols

Surface deposition of particles occurs via diffusion, impaction, and/or gravitational settling. 

Particle size is the dominant variable controlling these processes. The resistance approach of 

Slinn and Slinn (1980), as implemented in UAM-AERO (Kumar et al., 1996), has been adopted in 

CAMx. Particle deposition velocity for a given aerosol size is calculated using the following 

resistance equation:

where vsed is the gravitational settling (or sedimentation) velocity. This velocity is dependent 

on aerosol size and density:

where D is the log-mean particle diameter (m) of a given size section, ρp is particle density 

(g/m3

), g is gravitational acceleration, and ν is the viscosity of air. The factor C is the 

Cunningham correction for small particles, as described earlier for wet scavenging of particles. 

Note that particle size and density are affected by aerosol water content, which is determined 

from local humidity and PM deliquescence properties according to the ISORROPIA model (see 

Section 5).

s *

s

H T u

r

5 3.9 10

1

− ×

=

a b a b sed

d sed

r r r r v

v v

+ + = +

1

ν

ρ

18

2

p

sed

D g C

v =
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Aerodynamic resistance ra is identical to the value used for gaseous dry deposition. Resistance 

to diffusion through the quasi-laminar sub-layer layer depends on aerosol Brownian diffusion 

and inertial impaction. Particles are assumed to remain on a surface once they impact, so 

resuspension effects are ignored. Boundary resistance rb is given by

The stokes number St is calculated from

4.6.1.3 Specification of Season

The Wesely (1989) deposition algorithm specifies the various surface resistances by land cover 

type for five seasons:

• Spring

• Summer

• Fall

• Winter

• Winter with snow cover

CAMx internally defines a season map to determine four of these five seasons by month and 

latitude (Table 4-2). Five latitude bands exist in each hemisphere:

• Tropical < 20°

• Sub-tropical 20° to 35°

• Temperate 35° to 50°

• Cool 50° to 75°

• Polar > 75°

The seasons in the Northern and Southern hemispheres are offset by six months. This offset 

does not cause any discontinuity at the equator because all 12 months are defined as summer 

in the tropical band at the equator. This season map is generalized and may not be ideal for all 

locations. The season map is coded into data statements in the “CAMx/chmdat.f” 

subroutine and could be changed to better suit a specific region.

4.6.1.4 Specifying Snow Cover

The season map shown in Table 4-2 does not specify any snow cover because it is quite variable 

in space and time. Gridded snow cover data are specified in the time-variant 2D surface input 

file (see Section 3). The snow cover input is a binary value where 1 signifies that the grid cell is 

snow covered, while 0 is snow-free. Snow covered grid cells are assigned the Wesely (1989) 

( ) St

c

b

u S

r 2/3 3/

* 10

1 − − + =

g

v u S sed

t ν

2

* =
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surface resistances for the category “winter with snow cover”, regardless of the season. Snow 

cover also impacts photolysis rates (see Section 5).

Generally, snow cover is taken from the meteorological models via the interface programs (e.g., 

WRFCAMx, MM5CAMx, RAMSCAMx). Alternatively, snow cover data can be developed in 

several other ways:

Table 4-2. Relationships between season and month/latitude used in the CAMx Wesely/Slinn 

dry deposition model. Exception: seasons for the area within 50N-75N and 15W-15E are 

internally set to those of latitude band 35-50 to account for regions of Europe in which the 

climate is influenced by the Gulf Stream.

Month Latitude Band

Northern 

Hemisphere

Southern 

Hemisphere

< 20° 20° - 35° 35° - 50° 50° - 75° > 75°

Tropical Sub-tropical Temperate Cool Polar

Jan Jul Summer Winter Winter Winter Winter

Feb Aug Summer Spring Winter Winter Winter

Mar Sep Summer Spring Spring Winter Winter

Apr Oct Summer Spring Spring Spring Winter

May Nov Summer Summer Spring Spring Winter

Jun Dec Summer Summer Summer Summer Spring

Jul Jan Summer Summer Summer Summer Summer

Aug Feb Summer Summer Summer Summer Fall

Sep Mar Summer Summer Fall Fall Winter

Oct Apr Summer Fall Fall Fall Winter

Nov May Summer Fall Fall Winter Winter

Dec Jun Summer Fall Winter Winter Winter

• Spatially interpolated snow cover observations;

• Analyses of snow cover data included in existing metrological data sets, such as the NCEP 

North American Model (NAM);

• Analyses of snow cover based on a mix of observations, models and satellite-based 

information (e.g., SNODAS).

ENVIRON does not provide any pre-processors to develop snow cover data from external 

datasets, other than the meteorological interface programs.

4.6.2 The Zhang Model

At the time it was developed, the Wesely model was the most comprehensive algorithm 

applicable for regional-scale air quality modeling, but it no longer represents the current state 

of the science. Furthermore, it was defined for a limited number of land cover types that were 

characterized according to typical eastern U.S. vegetation types, density, and seasonal 

conditions. The deposition velocities calculated with the Wesely/Slinn model may not be 

sufficiently accurate outside the eastern U.S. or for atypical conditions (e.g., seasonal 

transitions, drought stress). It was desirable to implement a dry deposition algorithm in CAMx 
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that incorporates updates in theory as well as recent measurements. One of the most 

important aspects of newer dry deposition schemes is the use of “leaf area index” (LAI) to scale 

pollutant uptake into biota. The LAI is defined as the ratio of the one-sided green leaf area to a 

unit area of the ground. This index characterizes the amount of vegetation present, and can be 

measured by satellites instruments at fairly high spatial resolution.

A recent LAI-based algorithm is used in Environment Canada’s AURAMS air quality model

(Zhang et al. 2003; Zhang et al. 2008). This scheme is a state-of-the-science algorithm that 

possesses an updated representation of non-stomatal deposition pathways and has been 

tested extensively through its use in daily air quality forecasting. It has been shown to 

reproduce observed fluxes of ozone and SO2 with reasonable accuracy.

4.6.2.1 Dry Deposition of Gases

The gas resistance model of Zhang et al. (2003) invokes the same 3-resistance equation for 

deposition velocity as the Wesely (1989) model. The equations for aerodynamic resistance (ra) 

and boundary resistance (rb) are very similar to the Wesely (1989) formulations. However, 

Zhang et al. (2003) replace the surface resistance (rs) equation with a new relationship for the 

overall canopy resistance:

st m cut ac gs

st

c

r r r r r

W r

+

+ +

+

− = 1 1 1

1

where Wst is the fraction of stomatal blocking under wet conditions, rcut is the cuticle 

resistance, and all other resistances have similar meaning to the Wesely model. Stomatal 

resistance (rst) is calculated using a sunlit/shade (so-called “two-big-leaf”) stomatal resistance 

sub-model. Following Wesely (1989), values for rg and rcut are calculated for SO2 and O3 and 

then scaled for other gaseous species. Cuticle resistance is slightly different from that defined 

in traditional big-leaf models in that it also considers the aerodynamic and quasi-laminar 

resistances of individual leaves. This is done by parameterizing rcut as a function of friction 

velocity, similar to the concept of overall cuticle uptake considered in a multi-layer model 

framework.

LAI is used in functions for rac, and rcut, where the LAI for any given day is linearly interpolated 

from monthly default LAI as a function of landuse type. To account for LAI effects on surface 

roughness (z0), a similar daily LAI interpolation is applied to that parameter. Hence, the Zhang 

model does not require the specification of season, as all resistance equations are continuous 

over each month (note that CAMx automatically applies the 6-month offset for applications in 

the southern hemisphere).

For snow on the ground and leaves, both rgs and rcut are adjusted by a snow cover fraction, 

which is assumed to be 0.8 when snow cover is flagged for a grid cell in CAMx. Snow cover is 

defined through the input 2D surface file, as described in Section 3. For surfaces without 

canopies, rgs is defined as the resistance to any surface (e.g. soil, ice, snow and water), rac is set 

to zero, and very large values are used for rst, rm and rcut.
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Over water, the updated temperature-dependent ozone surface resistance equation described 

above for the Wesely scheme is also used for the Zhang scheme.

The Zhang scheme uses 26 landuse categories, whereas the Wesely scheme uses 11. Therefore, 

the CAMx landuse file was expanded to handle up to 26 categories (see Section 3). The Zhang 

model includes a set of embedded annual surface roughness ranges and monthly LAI specific to 

each of the 26 landuse categories. The capabilities of the scheme were extended by adding the 

option to use episode-specific (i.e., satellite-derived) LAI data. Satellite-based LAI data from 

MODIS (MODerate-resolution Imaging Spectroradiometer)2 can be processed into gridded LAI 

fields that are passed to CAMx as an optional record in the time-invariant 2D surface input file 

(see Section 3). The optional gridded LAI fields are used to scale the default landuse-specific LAI 

values. For each grid cell, a landuse-weighted default LAI is determined according to the 

landuse fractions present. An LAI scaling factor is then determined as the ratio of the input LAI 

to the landuse-weighted default LAI. This factor is used to scale the individual default LAI 

values for each landuse type in the grid cell, subject to the annual maximum to minimum range 

among the monthly default values. Figure 4-4 illustrates how the use of satellite LAI data 

introduces additional episode-specific variation into the LAI field.

In developmental tests, the Zhang dry deposition model has tended to generate lower ozone 

deposition rates relative to the Wesely model, which leads to higher ozone predictions overall. 

This effect is seasonally dependent and will vary with the definition of LAI. Ozone is less 

sensitive to the source of LAI (whether Zhang defaults or satellite-enhanced) than to the choice 

of deposition model.

4.6.2.2 Dry Deposition of Aerosols

Many previous particle dry deposition models were evaluated against wind tunnel 

measurements, which may not be representative of field measurements. Ruijgrok et al. (1995) 

showed that estimates from these early models differ greatly, especially in the range of 0.1-1.0 

μm (by 2 to 3 orders of magnitude). Theoretically, particles in this range deposit at rates much 

less than 0.01 cm/s, a value comparable only to laboratory (wind tunnel) studies. According to 

Zhang et al. (2001), much higher values have been obtained in many field studies, including for 

sub-micron sulfate in which deposition velocities of one to two orders of magnitude higher 

have been measured. Gallagher et al. (1997) state that much higher deposition velocity values, 

typically 1 cm/s or more for sub-micron aerosol deposition to a forest, are consistent across the 

aerosol size spectrum. The Zhang et al. (2001) study developed a simple parameterization of 

particle dry deposition as a function of aerosol size and landuse that predicts higher deposition 

velocities for sub-micron aerosols, especially over rough vegetated surfaces.

 2 MODIS provides LAI at 250 meter spatial resolution and 16 day temporal resolution.
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Figure 4-4. Comparison of monthly LAI data embedded in the Zhang dry deposition scheme 

against episode-specific LAI for June 2005.

The deposition of aerosols is based on the model of Slinn (1982), but using simplified empirical 

parameterizations to replace detailed canopy information. The aerosol deposition velocity is 

defined as:

a b

d sed

r r

v v

+ = +

1

where vsed and ra have identical meanings as the Slinn and Slinn (1980) definition described 

earlier for the Wesely/Slinn deposition model. Note that in this case, the virtual serial 

resistance ra⋅rb⋅vsed has been removed, which results in higher values of deposition velocity. 

The quasi-laminar boundary resistance is given by

( ) 0 * 1

1

u E E E R

r

B IM IN

b + + = ε

where the variable E includes the collection efficiencies for Brownian diffusion, impaction, and 

interception, respectively, R1 is a factor representing the fraction of particles that stick to the 

surface, and ε0 is an empirical constant that is set to a value of 3. The Brownian collection 

LAI from Satellite

Zhang Embedded LAI Data

Modified LAI using Satellite Data
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efficiency depends on the Schmidt number, while the impaction efficiency and R1 depend on 

the Stokes number.

The collection efficiency by interception also exists if the particle passes an obstacle at a 

distance shorter than its physical dimensions (e.g., large particles passing near hairy leaves). 

Zhang et al. (2001) adopted a simple equation for this term that is a function of particle 

diameter and a characteristic radius, for which default values are given for different landuse 

and seasonal categories.

Figures 4-5 and 4-6 compare estimated particle deposition velocities from the Zhang model, the 

Slinn and Slinn (1980) model, and the AERMOD model (EPA, 1998). Calculations were made for 

daytime, neutrally stable conditions for a range of wind speeds and landuse categories. Figure 

4-6 shows that the Zhang model increases deposition velocities over forest by roughly an order 

of magnitude for the 0.1-1 μm range, yet reduces deposition velocities above 1 μm. Figure 4-6

clearly shows the Zhang model generates sub-micron deposition velocities that are ten times 

higher than the Slinn and Slinn (1980) model over the five landuse types tested.

Figure 4-5. Comparison of particle dry deposition velocities as a function of size and wind 

speeds (m/s) for three models: black – Zhang et al. (2001); blue – Slinn and Slinn (1980); 

orange – AERMOD (EPA, 1998). Results are shown for a forest landuse category during 

daytime neutral stability. Particle density was set at 1.5 g/cm3

.

Forest

0.01

0.1

1

10

100

0.001 0.01 0.1 1 10 100

Particle diameter (μm)

Vd (cm s-1)

wind = 2

wind = 5

wind = 10

wind = 15

wind = 2

wind = 5

wind = 10

wind = 15

wind = 2

wind = 5

wind = 10

wind = 15
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Figure 4-6 Comparison of particle dry deposition velocities determined by the Zhang et al. 

(2001) and Slinn and Slinn (1980) models, as a function of landuse and wind speed during 

daytime neutrally stable conditions. Particle density was set at 1.5 g/cm3.

4.7 Surface Model for Chemistry and Re-Emission

CAMx includes a simple surface sub-model that treats sorption and penetration of deposited 

pollutant mass into soils and vegetation, chemical degradation and transformation, and 

volatilization back into the air (re-emission). The surface model treats any subset of species 

listed in the core model’s chemical mechanism. Limitations of the current implementation 

include:

• The surface model can only be used with the Wesely (1989) dry deposition option;

• The surface modeling cannot be used with the Plume-in-Grid treatment;

• Wet deposition does not contribute to surface mass, as compounds in aqueous solution 

are assumed to be immediately lost to surface water processes (absorption, runoff, etc.).

4.7.1 Surface Model Algorithms

The surface model incorporates aspects of the approach defined in the model for Pesticide 

Emission Assessment at Regional and Local scales (PEARL v2.1.1-C). Figure 4-7 displays the 

surface model processes schematically and Table 4-3 defines parameters that are referred to in 

Figure 4-7. While core model algorithms are used to deposit compounds to the surface and reemit them to the atmosphere, the surface model tracks the accumulation of mass on terrestrial 

surface media (soil and vegetation) for subsequent physical removal (leaching into soil and 

penetration into plant tissue), chemical transformation (both heterogeneous and photolysis), 

0.0

0.2

0.4

0.6

0.8

0 0.2 0.4 0.6 0.8

Zhang [cm/s]

Slinn 80 [cm/s]

Particle (Dp = 0.35 μm) deposition in day time

water, 0.8m/s

forest, 0.8m/s

crops, 0.8m/s

urban, 0.8m/s

swamp, 0.8m/s

water, 2m/s

forest, 2m/s

crops, 2m/s

urban, 2m/s

swamp, 2m/s

water, 4 m/s

forest, 4m/s

crops, 4m/s

urban, 4m/s

swamp, 4m/s

water, 6m/s

forest, 6m/s

crops, 6m/s

urban, 6m/s

swamp, 6m/s

water, 8m/s

forest, 8m/s

crops, 8m/s

urban, 8m/s

swamp, 8m/s

water, 10m/s

forest, 10m/s

crops, 10m/s

urban, 10m/s

swamp, 10m/s
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and re-emission to the atmosphere. Deposition to water surfaces is assumed to be irreversible 

and thus is not tracked by the surface model.

After deposition to each surface grid cell at each time step, the newly deposited mass 

increment is divided among soil and vegetation according to landuse-dependent split factors, 

and added to total surface mass accumulated during the model run. The fractional coverage of 

11 landuse categories in each grid cell is an existing input to CAMx. For each grid cell, the net 

soil/vegetation split is determined by the combination of landuse-dependent split factors and 

the fractional coverage of each landuse type. The soil/vegetation splits for each of the 11 

landuse categories are assumed to be seasonally constant, and values were estimated based on 

simple conceptual considerations of the amount of annual-averaged vegetation (i.e., leaf area

index) typical of each category (Table 4-4).

The surface model uses partitioning (equilibrium) coefficients to calculate the amount of 

accumulated material sorbed to soil and vegetation. The sorbed fraction is subject to chemical 

reactions and physical removal associated with leaching deep into the soil and penetration into 

plant tissue. Chemistry can simply decay deposited material as a removal process, or it can 

generate products that can be subsequently re-emitted. All surface removal processes are 

assumed to be irreversible and result in a permanent removal of mass. The fraction not sorbed 

to the surface media is subject to a volatilization flux (i.e., re-emission). Separate chemicalspecific soil-air and vegetation-air partitioning coefficients are set in the CAMx chemistry 

parameters file. They represent the equilibrium ratio of chemical on a surface to chemical in air 

at the air-surface interface. For example, a compound with a partitioning coefficient of 10,000 

(unitless) has an equilibrium concentration on the surface that is 10,000 times more than that 

in air.

Chemistry, soil leaching, and plant penetration are dependent on chemical properties of the 

compounds and also on numerous site-specific factors such as soil and vegetation properties,

highly transient meteorological conditions, etc. Often these factors are unknown or fall within 

a range. The rates of these processes are defined as the process rate coefficient (k) times the 

mass on the surface area, or areic mass (A):

Rprocess = kprocess × Asurface

When the actual rate coefficients (or inversely, the half-lives t1⁄2) are unknown for the 

substance, they can be generalized by 5 classes:

1. Very fast: t1⁄2 = 0.04 d k = 17 d-1 = 1.2×10-2 min-1

2. Fast: t1⁄2 = 0.21 d k = 3.3 d-1 = 2.3×10-3 min-1

3. Moderate: t1⁄2 = 1.0 d k = 0.69 d-1 = 4.8×10-4 min-1

4. Slow: t1⁄2 = 5.0 d k = 0.14 d-1 = 9.7×10-5 min-1

5. Very slow: t1⁄2 = 25 d k = 0.03 d-1 = 2.1×10-5 min-1

A 6th class can be added by setting the k-value to zero or a de-minimis value to effectively 

remove the process from consideration. In this manner chemicals can be modeled with an 

estimated half-life that is unique for each process. 
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Figure 4-7. Schematic of the CAMx surface model.

Table 4-3. Description of CAMx surface model variables shown in Figure 1.

Variable Definition Units

Ap Areic mass of compound on vegetation mol ha-1

As Areic mass of compound on the soil mol ha-1

Kveg Vegetation-air partitioning coefficient unitless

Ksoil Soil-air partitioning coefficient unitless

kleach Leaching rate coefficient min-1

kpen Leaf penetration rate coefficient min-1

j Photolysis chemistry rate coefficient min-1

k Heterogeneous chemistry rate coefficient min-1

Rleach Leaching rate mol ha-1 min-1

Rpen Leaf penetration rate mol ha-1 min-1

Rchem Chemistry rate mol ha-1 min-1

Deposition

Soil

As

Vegetation

Ap

Sorption to

Soil

Ksoil

Penetration

Rpen = kpen×Ap

Chemistry

Rchem = (j+k)×As

Chemistry

Rchem = (j+k)×Ap

Sorption to 

Vegetation

Kveg

Re-emission

Irreversible Loss into Surface System

Leaching

Rleach = kleach×As
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Table 4-4. CAMx landuse categories and associated default annual-averaged soil/ vegetation 

split factors and shade factors. 

Category

Number Land Cover Category

Surface Parameters

Soil 

Fraction

Shade 

Fraction

1 Urban 0.7 0.2

2 Agricultural 0.4 0.3

3 Rangeland 0.7 0.2

4 Deciduous forest 0.3 0.4

5 Coniferous forest, wetland 0.2 0.5

6 Mixed forest* 0.3 0.4

7 Water n/a n/a

8 Barren land 0.9 0.0

9 Non-forested wetlands 0.5 0.3

10 Mixed agricultural/range* 0.5 0.3

11 Rocky (with low shrubs) 0.7 0.2

Note that all portioning coefficients and reaction rates other than photolysis are fixed and 

ignore dependence on various environmental conditions (e.g., temperature, pressure, surface 

type, surface moisture, etc.). Photolysis rates are specified by the user to represent peak clearsky values at zero zenith (solar noon) and are internally adjusted for solar angle, cloud 

attenuation, and shade fraction as a function of landuse type (Table 4-4).

The approach for re-emission of volatilized (un-sorbed) mass is consistent with the CAMx dry 

deposition algorithm. Specifically, the surface model is tied to the Wesely (1989) option. Since 

water surfaces are not considered by the surface model, re-emission fluxes from water are 

ignored in this implementation. As described in Section 4.7, dry deposition of material from the 

lowest model layer to the surface is treated as an irreversible (fully sorbed) first-order flux 

through the use of a dry deposition velocity. Re-emission of volatilized (unsorbed) mass is also 

treated as a first-order 1-way flux using an “effective” velocity that is similar in form to vd:

a b

e

r r

v

+ = 1

where the rs term is missing since only the pre-determined un-sorbed fraction of surface mass 

is considered for surface-to-air transfer. The ra and rb terms are calculated by the surface 

model in exactly the same manner as the values used for dry deposition to ensure consistency.
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4.7.2 Running CAMx With the Surface Model

The CAMx surface model parameters that need to be specified for each compound or surface 

reaction to be tracked are as follows:

Kveg Vegetation-air partitioning coefficient unitless

Ksoil Soil-air partitioning coefficient unitless

kleach Leaching rate coefficient min-1

kpen Leaf penetration rate coefficient min-1

j Photolysis chemistry rate coefficient min-1

K Heterogeneous chemistry rate coefficient min-1

These values are set at the end of the CAMx chemistry parameters file; an example of the 

chemistry parameters file format is shown in Figure 4-8. A control record is also needed at the 

top of the chemistry parameters file to define the number of species and reactions to track.

A CAMx namelist control file variable called “SURFACE_MODEL” must be set to “true” in order 

to invoke the surface model. When the surface model is invoked, the surface model section of 

the chemistry parameters file is read and the respective equilibrium and rate variables are set 

accordingly.

Figure 4-8. The portions of the CAMx chemistry parameters file (highlighted) to support the 

surface model. In this example, 3 gases are treated, and NO2 and HNO3 react to form HONO. 

All three are subject to decay by soil leaching and plant penetration.

CAMx Version |VERSION6.1

Mechanism ID |7

Aerosol Option |NONE

Description |CB6: molecular units

No of gas species |76

No of aero species |0

No of reactions |218

Prim photo rxns |23 1 8 9 21 27 28 38 43 47 50 56 88 92 97 98 108 112 114 117 119 128 129 160

No of sec photo rxn|5

ID, prim ID, scale |64 56 1.0

 |90 88 1.0

|197 88 1.0

|199 1 0.05

|203 1 0.028

SrfMod #spc, #rxns |3 2

.

.

.

Surface Model

Species SoilSorb SoilLeach VegSorb VegPen

 1 NO2 1.00E+10 4.80E-04 1.00E+10 4.80E-04

 2 HNO3 1.00E+10 4.80E-04 1.00E+10 4.80E-04

 3 HONO 1.00E+00 4.80E-04 1.00E+00 4.80E-04

Rxn Precursor Product Krate Jrate

 1 NO2 HONO 4.80E-04 4.8E-04

 2 HNO3 HONO 4.80E-04 4.8E-04
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5. CHEMISTRY MECHANISMS

The photochemical mechanisms currently supported in CAMx are listed in Table 5-1 and include

the 2005 version of Carbon Bond (CB05; Yarwood et al., 2005b), version 6 of Carbon Bond (CB6; 

Yarwood et al., 2010; Yarwood et al., 2012a,b), and the 1999 version of the Statewide Air 

Pollution Research Center (SAPRC99) mechanism (Carter, 2000). All are balanced for nitrogen 

conservation so that predicted NOy can be calculated as the sum of nitrogen containing species. 

All can be linked to optional modal and size-segregated primary and secondary particulate 

matter (PM) treatments. The secondary PM chemistry includes organic and inorganic 

formation/partitioning from condensable gases derived from gas-phase chemistry, and aqueous 

inorganic chemistry. The modal PM treatment also supports several optional mercury species. 

Additionally, there is an interface that allows a simpler user-defined chemical mechanism to be 

employed in the model (Mechanism 10). A listing of the explicit species, reactions, and VOC 

species properties in all photochemical mechanisms listed in Table 5-1 are provided in 

Appendices A through E.

Table 5-1. Gas-phase chemical mechanisms currently implemented in CAMx.

Mechanism ID Description

5 The fixed parameter version of the SAPRC99 gas-phase mechanism (Carter, 2000). 217 

reactions and up to 114 species (76 state gases, up to 22 state particulates, and 16 radicals). 

6 CB05 (Yarwood et al., 2005b). 156 reactions and up to 89 species (54 state gases, up to 22 

state particulates, and 13 radicals).

7 CB6 (Yarwood et al., 2010). 218 reactions and up to 114 species (69 state gases, up to 22 

state particulates, and 23 radicals).

1 Mechanism 7 with updates to include reactions involving oceanic iodine compounds 

(Yarwood et al., 2012b).

2 CB6 “Revision 2” (CB6r2; Yarwood et al., 2012a; Ruiz and Yarwood, 2013).

10

A user-defined simple chemistry mechanism can be developed for any gas and/or 

particulate species, which is defined by a “Mechanism 10” parameters file and solved within 

a user-supplied subroutine called “chem10.f.”

The selection of which mechanism to employ in a given CAMx application is determined by the 

“chemistry parameter” input file. This file defines the mechanism number, the number of gas 

and aerosol species, and the number of reactions for the mechanism, lists the species by name 

with associated physical-chemical properties, lists the reaction rate constants and temperature 

dependencies for each reaction, and defines which reactions are photolytic. Chemistry

parameter input files for the CB05, CB6, and SAPRC99 listed in Table 5-1 are provided with 

CAMx and are not normally modified by users. See Section 3 for additional information on the 

format and usage of these files. Chemistry parameters files are specific to versions of CAMx. 

Always use chemistry parameters files with the right CAMx version number, do not attempt to 

use files for another CAMx version. 
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5.1 Gas-Phase Chemistry

5.1.1 Carbon Bond 2005

The Carbon Bond IV (CB4) mechanism was first developed by Gery et al. (1989), and 

subsequently underwent various updates in the mid 1990’s to include revised PAN chemistry, 

additional radical-radical termination reactions and updated isoprene chemistry (Carter 1996; 

Whitten et al., 1996). Additional updates were then made to expand ozone modeling from 

urban to regional/rural environments and to support secondary aerosol chemistry, mercury and 

toxics (Yarwood et al., 2005a).

Mechanism 6 is the 2005 version of Carbon Bond (CB05) developed for EPA atmospheric 

modeling studies (Yarwood et al., 2005b). Updates in CB05 compared to the earlier CB4 

mechanisms are:

• Updated rate constants based on 2003 – 2005 IUPAC and NASA evaluations.

• An extended inorganic reaction set for urban to remote tropospheric conditions.

• NOx recycling reactions to represent the fate of NOx over multiple days.

• Explicit organic chemistry for methane and ethane.

• Explicit methylperoxy radical, methyl hydroperoxide and formic acid.

• Lumped higher organic peroxides, organic acids and peracids.

• Internal olefin (R-HC=CH-R) species called IOLE.

• Higher aldehyde species ALDX making ALD2 explicitly acetaldehyde.

• Higher peroxyacyl nitrate species from ALDX called PANX.

• Lumped terpene species called TERP.

The CB05 was evaluated against smog chamber data from the Universities of North Carolina 

and California at Riverside. The new higher aldehyde and internal olefin species improve

mechanism performance for these species and produce oxidants more rapidly at low VOC/NOx 

ratios. The new terpene species improves simulation of oxidants and PM from biogenic 

emissions. Several new organic peroxide species improve the simulation of oxidants that are 

involved in PM sulfate formation. The addition of explicit methylperoxy radical improves the 

simulation of hydrogen peroxide under low NOx conditions.

5.1.2 Carbon Bond Version 6

Mechanism 7 is version 6 of Carbon Bond (CB6; Yarwood et al., 2010). Several organic 

compounds that are long-lived and relatively abundant, namely propane, acetone, benzene and

ethyne (acetylene), are added explicitly in CB6 so as to improve oxidant formation from these 

compounds as they are oxidized slowly at the regional scale. Alpha-dicarbonyl compounds 

(glyoxal and analogs), which can from secondary organic aerosol (SOA) via aqueous-phase 

reactions (Carlton et al., 2007), are added in CB6 to improve support for SOA modeling. 

Precursors to alpha-dicarbonyls in CB6 are aromatics, alkenes and ethyne. CB6 includes several 

updates to peroxy radical chemistry that will improve formation of hydrogen peroxide (H2O2) 

and therefore sulfate aerosol formation. The gas-phase reaction of dinitrogen pentoxide 
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(N2O5) with water vapor is slower in CB6, which will reduce nighttime formation of nitric acid 

although heterogeneous reactions on aerosol surfaces may dominate nitric acid formation at 

night (Brown et al, 2006). When CB6 is used in atmospheric models the heterogeneous 

reaction between N2O5 and water vapor should be included. CAMx includes the calculation of 

the heterogeneous N2O5 hydrolysis rate as a function of aerosol size, water content, and pH 

when PM is explicitly simulated; if no PM chemistry is included, CAMx sets the heterogeneous 

rate to the IUPAC (2006) N2O5 hydrolysis rate. The core inorganic chemistry mechanism for 

CB6 is based on evaluated data from the IUPAC tropospheric chemistry panel as of January, 

2010 (Atkinson et al., 2010). IUPAC also is the primary source for photolysis data in CB6 with 

some data from the 2006 NASA/JPL data evaluation (Sander et al., 2006) or other sources for 

photolysis of some organic compounds. There are changes to the organic chemistry for 

alkanes, alkenes, aromatics and oxygenates. The most extensive changes are for aromatics and 

isoprene. Chemistry updates for aromatics were based on the updated toluene mechanism 

(CB05-TU) developed by Whitten et al. (2009) extended to benzene and xylenes. The isoprene 

mechanism was revised based on several recently published studies (Paulot et al., 2010; 

Peeters et al., 2010).

CB6 was evaluated using 339 experiments from several chambers at the University of California 

at Riverside and the Tennessee Valley Authority. The performance of CB6 and CB05 in simulating 

chamber studies was comparable for alkanes, alkenes, alcohols and aldehydes with both CB6 and 

CB05 performing well and exhibiting 20% or less bias for maximum ozone. For species that were 

explicitly added in CB6 (ethyne, benzene and ketones), CB6 performed much better than CB05. For 

aromatics, CB6 improved upon CB05 by reducing under prediction bias in maximum ozone to about 

10% for benzene, toluene and xylene. For isoprene, both CB05 and CB6 show little bias for 

maximum ozone (less than 5%) but CB6 tended to form ozone too slowly. CB6 improved upon 

CB05 for simulating mixtures of VOCs. For mixtures without aromatics, both CB05 and CB6 showed 

minimal bias for maximum ozone. For mixtures including aromatics, both CB05 and CB6 under 

predicted maximum ozone but bias was reduced from about 30% for CB05 to about 20% for CB6.

5.1.3 Carbon Bond Version 6 with Iodine Chemistry

Mechanism 1 is an extension of CB6 chemistry that adds reactions involving ocean-borne iodine 

compounds. Atmospheric reactions of iodine atoms can destroy tropospheric ozone through series 

of chemical reactions. These reactions are referred to as catalytic cycles because the iodine is 

regenerated in the reactions and therefore one iodine atom can potentially destroy many ozone 

molecules. The efficiency of tropospheric ozone destruction by reactive iodine depends upon how 

effectively reactive iodine species are eliminated by other reactions. Emissions from oceans are the 

major source of atmospheric iodine (Carpenter, 2003), including methyl iodide (CH3I), other iodomethanes (CH2I2, CH2ICl, CH2IBr), larger alky iodides, and molecular iodine (I2). Iodine emissions 

result both from biological and photochemical processes in ocean water (Moore and Tokarczyk, 

1993; Moore and Zafirou, 1994). Photochemical processes that cause iodine emissions are linked 

to reactions of dissolved ozone and thereby to enhanced ozone deposition to oceanic waters 

(Ganzeveld et al., 2009; Helmig et al., 2012).

ENVIRON developed a chemical mechanism for iodine and ozone that is suitable for use in regional 

photochemical modeling of ozone (Yarwood et al., 2012b). The chemical reactions included in the 
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mechanism (Appendix C) are based primarily on the recent review by Sommariva et al. (2012), with 

referencesto other recent studies by Ordonez et al. (2012) and Mahajan et al. (2010). The citations 

given for each reaction in Appendix C indicate the data source. Notable differences between the 

mechanisms in Appendix C and Sommariva et al. (2012) are:

• Inclusion of reaction I23 (INO + I) which strongly limits daytime accumulation of INO;

• Inclusion of photolysis reactions I30 to I33 for iodocarbons in addition to CH3I (reaction 

I30).

• Condensation of the reactions forming iodine oxides larger than I2O2 to a single species 

IXOY which is defined as containing two I-atoms. 

• Exclusion of a reaction between IO and CH3O2, which is uncertain (Sommariva et al., 

2012) and does not have a large impact on model results in our tests (Yarwood et al., 

2012b).

5.1.4 Carbon Bond Version 6, Revision 2

Mechanism 2 is CB6 revision 2 (CB6r2). Compared to CB6, CB6r1 (distributed in CAMx v6.0 as 

mechanism 2) has revised chemistry for isoprene and aromatic hydrocarbons and more NOxrecycling from the degradation of organic nitrates (Yarwood et al., 2012a). Compared to CB6r1, 

CB6r2 has a more detailed treatment of the formation and fate of organic nitrates including 

organic nitrate destruction by reactions in aerosols (Ruiz and Yarwood, 2013). 

Organic nitrates (ONs) are formed when VOCs degrade in the presence of NOx and are 

important in the atmosphere because they sequester NOx and can contribute to organic 

aerosol (OA). NO2 is released when ONs degrade by photolysis in the gas-phase, returning NOx 

to the atmosphere where it may contribute to ozone production. CB6r2 differentiates organic 

nitrates between simple alkyl nitrates that remain in the gas-phase and multi-functional ONs 

that can partition into OA (Ruiz and Yarwood, 2013). ONs present in aerosols are then assumed 

to undergo hydrolysis to nitric acid with a lifetime of approximately 6 hours based on 

laboratory experiments and ambient data. These changes tend to reduce regional 

concentrations ozone and ONs, and increase nitric acid. Regional modeling simulations using 

CAMx with CB6r2 show that accounting for ON hydrolysis in aerosols improve performance for 

ozone and in simulating the partitioning of NOy between ONs and nitric acid.

5.1.5 SAPRC 1999

Mechanism 5 is the SAPRC99 chemistry adapted for photochemical grid modeling by selecting a 

specific “fixed parameter” lumping scheme (Carter, 2000). The SAPRC99 mechanism is included 

in CAMx because it has been tested extensively against environmental chamber data, it uses a 

different approach for VOC lumping than the Carbon Bond mechanisms, and has been adopted 

in several regulatory modeling applications in the U.S.

5.1.6 Implicit Gas-Phase Species

All photochemical mechanisms in CAMx employ fixed concentrations for molecular oxygen 

(O2), molecular hydrogen (H2), and methane (CH4). Concentrations for these compounds are 
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set to the following constant mixing ratios (i.e., they are not impacted by the chemical 

solution):

[O2] = 2.095×105 ppm

[H2] = 0.60 ppm

[CH4] = 1.75 ppm

Mechanism 2 (CB6r2) includes a species named ECH4 to represent emitted methane over and 

above the global background of 1.75 ppm.

5.1.7 Photolysis Rates

The rates of atmospheric photolysis reactions depend upon solar irradiance and therefore are 

sensitive to the amount of solar radiation transmitted through the atmosphere as well as 

reflected from the earth’s surface (albedo). Photolysis rates are externally derived assuming 

clear-sky conditions as a function of five parameters: solar zenith angle, altitude above ground, 

total ozone column, surface albedo, and terrain height. The rates are provided to CAMx as a 

large lookup table that spans the range of conditions for each of the five dimensions. The

lookup table is developed using a CAMx pre-processor that incorporates the Tropospheric 

Ultraviolet and Visible (TUV) radiative transfer model (NCAR, 2011). TUV employs a standard 

atmosphere density profile for Rayleigh scattering and other absorbers such as oxygen. Userspecified ozone column values are used to scale a typical vertical ozone profile within TUV. A 

default aerosol profile from Elterman (1968) is combined with typical aerosol optical properties 

within TUV to account for haze.

The CAMx version of TUV is modified to output photolysis rate information in a format directly 

compatible with CAMx for the CB05, CB6, and SAPRC99 chemical mechanisms. See Sections 2

and 3 for more information on developing photolysis inputs.

As CAMx runs, the lookup rates are interpolated to the specific conditions in each grid cell. 

They are then adjusted for any local cloud cover and local aerosol attenuation (if PM is 

simulated). Additionally, solar angle-dependent temperature and pressure adjustments are 

applied to five key photolysis reactions (NO2, O3, acetaldehyde, and two formaldehyde 

reactions).

5.1.7.1 Cloud and Aerosol Adjustments

Photochemistry is strongly influenced by the presence of clouds, which can both attenuate and

enhance the actinic flux of ultraviolet (UV) and visible radiation responsible for photolysis. 

Their specific radiative impacts depend on many factors, including height, depth and fractional 

sky cover; water content; and water phase (i.e., liquid droplets or ice crystals). Aerosols also 

influence photochemistry according to their optical properties and mass loading as a function 

of altitude and depth. CAMx includes a fast in-line version of TUV (Emery et al., 2010) to 

calculate photolysis adjustment profiles through each cloudy, aerosol-laden grid column.

The in-line TUV is run twice for each grid column: first for non-cloudy conditions with the same 

Elterman (1968) aerosol profile used in the full-science TUV pre-processor, and second with 

clouds and simulated aerosols to derive a vertical profile of the cloudy:clear actinic flux ratio (in 
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the case that aerosols are not run in CAMx, the Elterman profile is used consistently). This ratio 

is then applied as a multiplicative factor to the clear-sky value in each grid cell. This approach 

maintains accuracy in the calculation of clear-sky photolysis rates, while allowing clouds and 

aerosols to be directly involved in radiative transfer calculations through each grid column.

TUV includes a calculation of integrated atmospheric density above the CAMx domain, based 

on the U.S. standard atmosphere, so that atmospheric attenuation of the UV stream is properly 

calculated entering the model top. Other aspects of the in-line TUV model were substantially 

streamlined to minimize runtimes. First, radiative calculations are performed for only a single 

representative wavelength (350 nm). Second, since absorption by gases occurs in rather 

narrow UV bands relative to the broad-band influence of clouds, the absorption from oxygen, 

ozone, nitrogen dioxide and sulfur dioxide were removed. Third, the extraterrestrial flux was

not needed as it cancels out in the calculation of the cloudy: clear ratio. Finally, the planeparallel version of the delta-Eddington approach was used in lieu of the more complex and 

expensive pseudo-spherical geometry. Preliminary tests against the full-science TUV showed 

that the streamlined version resulted in less than 1% differences in actinic flux ratio for a range 

of cloudy conditions (Emery et al., 2010).

Optical depth τ expresses the reduction of incident light I0 through a light attenuating medium 

of depth ∆z according to

−τ I = I e0

The in-line TUV adjustment scheme utilizes cloud optical depth fields provided by the CAMx 

cloud/rain file, and aerosol optical depths calculated from the PM mass concentrations 

simulated by CAMx.

The CAMx meteorological interface pre-processors generate cloud water and optical depth 

fields from the variable fields present in the raw meteorological output files. Cloud optical 

depth is calculated in each model grid cell according to the approach of DelGenio et al. (1996) 

and Voulgarkakis et al. (2009), which satisfactorily approximates the effects of random cloud 

overlap according to

( )

3/ 2

2

3

c

w d

F

r

L z

ρ

τ

∆ =

where L is cloud liquid water content (g/m3), ∆z is the cell depth containing cloud water, ρw is 

the density of liquid water (106 g/m3), and Fc is fractional cloud cover. The mean cloud droplet 

radius rd is not dependent on water phase, and is assumed to be a typical tropospheric value of 

1.5×10-5 m for liquid cloud water. TUV assumes constant Mie scattering parameters for clouds: 

a single scattering albedo of 0.99, and an asymmetry factor of 0.85. 

When CAMx is run with PM, vertical haze opacity profiles are calculated from simulated aerosol 

concentration fields. When CAMx is run with only gas-phase chemistry without aerosols, 

photolysis rates are only adjusted for clouds. Aerosol optical parameters are best determined 

from Mie theory, but in the interest of minimizing impacts to model speed and considering the 
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degree of uncertainty in the simulated aerosol concentrations themselves, a simpler method 

was adopted. Aerosols are assumed to exist as an external mixture of their component 

chemical species. Aerosol light extinction (scattering and absorption) is a function of each 

species’ concentration, extinction efficiency, and affinity for hygroscopic growth. Total aerosol 

optical depth is determined by summing extinction over all species and multiplying by layer 

depth. 

Dry extinction efficiencies and single-scattering albedos for each aerosol species, valid at 350 

nm, are externally defined in the CAMx chemistry parameters file. While these can be set by 

the user, the chemistry parameters files that are provided with the CAMx distribution include 

default values according to Takemura et al. (2002), as shown in Table 5-2. 

Table 5-2. Default dry extinction efficiency and single-scattering albedo at 350 nm (Takemura 

et al., 2002) in the distributed CAMx chemistry parameters file.

Species

Dry Extinction Efficiency 

(m2/μg)

Single-Scattering

Albedo

Sulfate 7×10-6 0.99

Nitrate 7×10-6 0.99

Ammonium 7×10-6 0.99

Organics 7×10-6 0.80

Elemental Carbon 18×10-6 0.25

Crustal (Fine+Coarse) 0.4×10-6 0.70

Sea salt (Na+Cl) 1.5×10-6 0.99

Takemura et al. provide extinction efficiencies and single-scattering albedos for sulfate, 

organics, soot, total dust, and sea salt; we have extended the sulfate values to nitrate and 

ammonium. The asymmetry factor is internally set to a default value of 0.61 regardless of the 

composition of the aerosols.

Hygroscopic aerosols are also flagged in the chemistry parameters file. For each flagged 

species, an internal growth factor is applied to the dry extinction efficiencies according to the 

relative humidity conditions in each grid cell. The growth curve is taken from the Phase I report 

of the Federal Land Managers’ Air Quality Related Values Workgroup (FLAG, 2000). By default, 

the relative humidity growth factor is flagged for sulfate, nitrate, ammonium and sea salt; a 

single growth factor is applied for all hygroscopic species (Figure 5-1). Minimum and maximum 

limits on relative humidity are set at 1% and 95%, respectively.
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Figure 5-1. Relative humidity adjustment factor applied to the dry extinction efficiency for 

hygroscopic aerosols (FLAG, 2000).

5.1.7.2 Effects of Surface Albedo and Snow Cover

Photolysis rates depend on the amount of solar radiation reflected from the earth’s surface 

(albedo). The grid-cell specific UV albedo is assigned within CAMx according to the input 

landuse types in the time-invariant 2D surface file (Tables 3-4 and 3-5). This approach results in 

UV albedos that fall in the range 0.04 to 0.08 and are constant in time. Analyses of reflected UV 

radiation recorded in satellite data (Herman and Celarier, 1997) report similar UV albedo values 

in the range 0.02-0.08 for surfaces not covered by snow.

Snow is much more reflective than other types of surfaces and so snow cover enhances the 

rates of photolysis reactions. Since most photolysis reactions depend upon ultra-violet 

radiation it is important to characterize the effect of snow cover on UV albedo. Measurements 

of the UV albedo for Antarctic snow report values of 0.96 to 0.98 over a wide range of snow 

grain sizes and solar zenith angles. However, these high values should be considered an upper 

limit to the reflectivity of snow cover because snow may not cover the entirety of the surface or 

all surface features, and because the snow may be aged or dirty. Satellite climatology shows

surface albedos spanning a wide range of values from 0.2 to nearly 1.0. Potential reasons for 

this wide range of values include coarse resolution (1° latitude by 1.25° longitude) such that 

snow-covered and snow-free surfaces are combined, differences between rough and smooth 

land cover types (e.g., forest vs. open range land), and differences between new/clean and 

aged/dirty snow.

The CAMx photolysis rate input file is generated for five albedo ranges, two of which represent 

the non-snow range (0.04 – 0.08 ) and three that represent the snow range (0.2 – 0.5 – 0.8). 

CAMx determines the landuse-weighted average surface albedo in each grid cell and 

interpolates photolysis rates between the five albedos. For snow-covered grid cells defined in 

the time-variant 2D surface input file, CAMx currently uses the photolysis rates calculated for 

0

5

10

15

20

25

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95

F(RH)

Relative Humidity (%)

Extinction Adjustment, f(RH)
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albedo of 0.5, because this is in the middle of the range reported by Herman and Celarier 

(1997). Use of the full range of snow albedo will be considered in future development.

5.1.8 Gas-Phase Chemistry Solvers

Solving the time evolution of gas-phase chemistry requires numerically integrating a set of 

ordinary differential equations (ODEs) and is among the most computationally expensive 

operations performed in a photochemical grid model. One reason for this is that the ODEs 

describing tropospheric chemistry are “stiff” – meaning that the chemical species involved have 

widely varying production and/or decay times. The computational efficiency of the gas-phase 

chemistry solver strongly influences the overall efficiency of a grid model. CAMx includes three 

chemistry solvers that offer differing trade-offs between accuracy and efficiency.

The most accurate solution methods available for stiff ODEs are “Gear” type implicit solvers 

(Gear, 1971) such as LSODE (Hindmarsh, 1983). Gear solvers are stable when applied to “stiff” 

problems, such as gas-phase chemistry, but are generally too slow for routine use in grid model 

applications. Sun et al. (1994) developed an implicit-explicit hybrid (IEH) method based on 

LSODE that is accurate and much faster than LSODE. Hertel et al. (1993) developed an 

implementation of the Euler Backward Iterative (EBI) method that is very efficient and also 

accurate because it utilizes explicit algebraic formulae to solve several important groups of 

species (HOx, NOx, etc.) Hertel’s EBI solver is the most efficient solver available in CAMx.

5.1.8.1 LSODE

CAMx includes the double precision version of the Livermore Solver for Ordinary Differential 

Equations (LSODE; Hindmarsh, 1983) distributed by the Netlib repository of numerical 

algorithms (http://www.netlib.org/). LSODE is too slow for everyday use but valuable as a 

reference method within CAMx. LSODE is based on Gear’s method with numerical refinements 

to improve efficiency and ease of use (Radhakrishnan and Hindmarsh, 1993). Gear methods 

(Gear, 1971) are implicit and employ backwards-differentiation formulae to step forward in 

time by taking multiple steps. The converged solutions at each step are saved in a history 

matrix and used to predict the next solution. Thus, LSODE must initially take short time steps to 

build the history matrix and may then take progressively longer steps. LSODE is most efficient 

for long integration times (and inefficient for short integration times) and therefore least 

burdensome for coarse grid model applications that have relatively long coupling times 

between gas-phase chemistry and other processes, e.g., advection. 

User-supplied information required by LSODE is essentially the error control parameters and 

the functions defining the system of ODEs, f(y,t), where y is the vector of species concentrations 

and t is time. Supplying a subroutine to evaluate the time derivatives of species concentrations

(f = dy/dt) is mandatory. Supplying a function to evaluate the Jacobian matrix (J = df/dy) is 

optional since, if not supplied, LSODE can derive a numerical Jacobian by finite difference 

between repeated evaluations of f. Supplying an algebraic Jacobian ensures accuracy, although 

a numerical Jacobian may be equally accurate if adequate precision (e.g., double precision) is 

employed. Supplying an algebraic Jacobian is more efficient when J is sparse, but for 

condensed mechanisms such as CB05 J is not sparse and the numerical Jacobian method is 
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faster. CAMx uses the numerical Jacobian method with a relative error tolerance of 10-7 and an 

absolute error tolerance of 10-10.

5.1.8.2 IEH Solver

A stiffly-stable solver, such as LSODE, is only needed to solve the chemical species that have 

time constants comparable to or shorter than the integration time and which interact strongly 

with each other. Slowly changing species may be treated as constant for the duration of an 

LSODE solution and then solved outside LSODE using a simple explicit method. Sun et al. (1993) 

called this approach an implicit-explicit hybrid method and Chock et al. (1994) showed that IEH 

methods offer useful computational efficiency and accuracy. The IEH method is faster than 

LSODE because fewer species are solved using the expensive Gear method, but less accurate 

than LSODE because of inaccuracy in the explicit method. The speed and accuracy of an IEH 

method is influenced by the designation of “fast” species to be solved implicitly and “slow” 

species to be solved explicitly.

The CAMx IEH solver designates species as fast, slow or steady-state (this designation is 

performed when mechanisms are implemented for the IEH solver and can’t be changed by the 

user). Steady-state species are solved by assuming that they are in a quasi-stationary state 

(dy/dt = 0) with respect to other species and, therefore, that y = P/L, where P and L are 

respectively the production and loss rates for species y. Oxygen atoms, O(1

D) and O(3P), are the 

most rapidly changing species in tropospheric chemistry mechanisms. Solving O-atoms with a 

steady-state assumption reduces stiffness and permits the single-precision version of LSODE to 

be used by the IEH solver. To ensure IEH solver accuracy with single precision, the Jacobian 

matrix is supplied algebraically to LSODE (see discussion, above). The relative error tolerance 

for LSODE within IEH is 5 x10-5 and the absolute error tolerance is 10-7. The O-atom 

concentrations are recalculated every time the derivatives (f) or Jacobian (J) are evaluated for 

LSODE. Slow species concentrations are calculated using rates evaluated at the middle of each 

IEH step. The IEH step size is limited to a few minutes for the slow species integration and 

multiple IEH steps are taken sequentially if needed.

5.1.8.3 EBI Solver

The backward Euler method solves concentrations (y) as y(t+h) = y(t) + hf, where f is the time 

derivative of species concentrations (f= dy/dt) evaluated at t+h. The method must be iterated 

to convergence in y(t+h) because species concentrations are interdependent. The basic EBI 

method is not efficient for stiff problems such as tropospheric chemistry because convergence 

is slow and the step size (h) must be short. Hertel et al. (1993) greatly improved the efficiency 

and accuracy of the method by developing analytical solutions to the EBI equation for groups of 

species that are strongly coupled (e.g. HOx and NOx/O3). Time steps of up to 3 minutes are 

taken by the Hertel EBI solver in CAMx.

5.1.9 Chemical Mechanism Compiler

Each of the CAMx chemistry solvers relies upon equations that define the species time 

derivatives (f = dy/dt) and, in some cases, the Jacobian matrix (J = df/dy) for each chemical

mechanism. The preprocessor portion of the CAMx chemical mechanism compiler (CMC) reads 

a listing of the mechanism reactions and generates the Fortran statements for the rate 
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equations and Jacobian matrix. This approach avoids potential errors resulting from coding 

equations by hand. 

For the IEH and EBI chemistry solvers, the CMC preprocessor requires user input that 

determines how each species is solved. The CMC preprocessor could be used to generate many 

different solver implementations for a given mechanism, only some of which will be robust. 

The CMC preprocessor is not distributed with CAMx to avoid potential problems with users 

generating invalid chemistry solvers that produce unreliable results.

5.2 Aerosol Chemistry

The gas-phase chemistry of Mechanisms 5, 6 and 7 may be run alone (no aerosols) by simply 

setting the aerosol option keyword to “NONE” and omitting the entire list of aerosol species in 

the chemistry parameters file (see Section 3). To model aerosols, the user sets the aerosol 

keyword to “INERT”, “CF” or “CMU”. In all three cases, the user defines the number of size 

sections and their size ranges in a separate record in the chemistry parameters file. The aerosol 

keyword “INERT” allows the user to define any number of arbitrarily-named inert particulate 

species to be carried by the model during a photochemical simulation (e.g., modeling the 

dispersion of only wind-blown dust). 

Aerosol chemistry processes can be run together with gas-phase chemistry (Mechanism 5, 6, 

and 7) using two options for treating aerosol size distributions: the CF scheme and CMU 

scheme. The CF scheme divides the size distribution into two static modes (coarse and fine). 

Primary species can be modeled as fine and/or coarse particles, while all secondary (chemicallyformed) species are modeled as fine particles only. The CMU scheme employs a sectional 

approach that dynamically models the size evolution of each primary and secondary aerosol 

constituent across a number of fixed size sections. The CF and CMU options require a minimum 

set of specific aerosol species with associated chemistry. Aerosol water is explicitly treated in 

both CF and CMU options, which affects aerosol size and density. 

5.2.1 Additional Gas-Phase Species

When either the CF or CMU aerosol option is selected, the following gas-phase species are 

added to model gas-aerosol interactions:

1) Ammonia (NH3) as a precursor for inorganic aerosol.

2) Gaseous sulfuric acid (SULF) as a precursor to sulfate aerosol. 

3) Hydrogen chloride (HCL) as a product of acidified sea salt aerosol and aerosol precursor.

4) Condensable organic gases (CG1-CG7) as precursors to secondary organic aerosol (SOA) 

formation.

5) Organic gases that form CG species via oxidation reactions, namely toluene (TOLA), xylene 

(XYLA), monoterpenes (TRP), sesquiterpenes (SQT) and isoprene (ISP).

5.2.1.1 SOA Precursors

Secondary organic aerosol (SOA) species exist in equilibrium with condensable gasses (CG) that 

can be produced by VOC oxidation:
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VOC + oxidant → CG ↔ SOA

CG formation from VOC oxidation reactions (Table 5-3) is handled within the SOA module 

rather than the main gas-phase chemistry, as described below. This approach has the following 

advantages: (1) separates the VOC precursors and lumping schemes for oxidant chemistry and 

SOA formation, e.g., for aromatics, different lumping schemes may be appropriate for oxidant 

and SOA formation; (2) allows the same SOA mechanism to be used with different oxidant 

mechanisms; (3) allows inclusion of SOA precursors without explicitly defining oxidant reactions

– e.g., sesquiterpenes are explicit in the SOA module but their oxidant formation may be

represented by surrogate species.

Table 5-3. SOA precursor reactions included in CAMx.

Precursor Reaction CG Products1 k298

2 (ppm–1 min–1

)

Anthropogenic

 Toluenes TOLA + OH 0.044 CG1 + 0.085 CG2 8.75E+03

 Xylenes XYLA + OH 0.027 CG1 + 0.118 CG2 3.71E+04

Biogenic

 Isoprene ISP + O none 5.32E+04

ISP + OH 0.015 CG3 + 0.12 CG4 1.47E+05

ISP + O3 none 1.90E-02

ISP + NO3 none 9.96E+02

 Terpenes TRP + O 0.065 CG5 + 0.29 CG6 4.12E+04

TRP + OH 0.065 CG5 + 0.29 CG6 7.76E+04

TRP + O3 0.065 CG5 + 0.29 CG6 1.33E-01

TRP + NO3 0.065 CG5 + 0.29 CG6 9.18E+03

 Sesquiterpenes SQT + OH 0.85 CG7 2.91E+05

SQT + O3 0.85 CG7 1.71E+01

SQT + NO3 0.85 CG7 2.81E+04

Notes:

1 Yield values are in ppm/ppm.

2 Rate constants are shown for 298 K and 1 atmosphere in ppm-1 min-1

.

Emissions of SOA precursors must be provided separately from the emissions of oxidant 

precursors, e.g., isoprene emissions must be speciated both as ISOP for oxidant chemistry and

ISP for SOA chemistry. This “double counting” of emissions is correct because the species (e.g., 

ISOP and ISP) serve different purposes. Ideally, emissions processors will develop VOC 

speciation schemes that suit both oxidant and SOA modeling. In the absence of more refined 

information, emissions of SOA precursors may be set equal to emissions of oxidant precursors 

as follows: ISP = ISOP; TRP = TERP; TOLA = TOL or ARO1; XYLA = XYL or ARO2.

Some emitted VOCs are semi-volatile (SVOCs) and can condense directly to SOA, e.g., biogenic 

emissions of oxygenated VOCs. SOA formation from SVOC emissions may be accounted for by 

including the SVOC in the CAMx emissions as one of the CGs listed in Table 5-4. Choose a CG 
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that has appropriate volatility properties, and account for any molecular weight difference 

between the SVOC and surrogate CG (moles CG emitted = moles SVOC x MWSVOC/MWCG).

Table 5-4. Properties of CG/SOA pairs.

Species

Molecular 

Weight

(g mole-1)

Saturation 

Concentration

(μg m-3 at 298 K)

Heat of 

vaporization

(kJ mole-1)

CG1/SOA1 150 7.82 66.8

CG2/SOA2 150 227 66.8

CG3/SOA3 130 0.726 42

CG4/SOA4 130 136 42

CG5/SOA5 180 3.92 75.5

CG6/SOA6 180 55.8 75.5

CG7/SOA7 210 0 –

SOPA 220 – –

SOPB 220 – –

5.2.2 Aerosol Processes

Aerosol processes are modeled using either the CF or CMU algorithm, depending on how the 

aerosol option keyword is set in the chemistry parameters file. The CF and CMU aerosol 

chemistry algorithms both perform the following three processes:

1) Aqueous sulfate and nitrate formation in resolved cloud water using the RADM aqueous 

chemistry algorithm (Chang et al., 1987).

2) Partitioning of condensable organic gases (CG1-CG7) to secondary organic aerosols (SOA1-

SOA7) to form a condensed “organic solution phase” using a semi-volatile, equilibrium 

scheme called SOAP (Strader et al., 1999). 

3) Partitioning of inorganic aerosol constituents (sulfate, nitrate, ammonium, sodium, and 

chloride) between the gas and aerosol phases using the ISORROPIA thermodynamic 

module (Nenes et al., 1998, 1999).

4) Uptake of nitric acid by calcium in soil dust particles is calculated external to ISORROPIA.

The aqueous chemistry does not treat sub-grid scale clouds; clouds are assumed to either 

occupy the entirety of a grid cell volume, or be completely absent from it. Cloudy grid cells are 

determined by cloud liquid water contents above a threshold of 0.05 g/m3 as defined by input 

gridded cloud water fields. Aqueous chemistry is calculated for each cloud grid cell at each 

model time step. The SOAP and ISORRIOPA equilibrium algorithms are called on a unique 

aerosol “coupling” time step that is defined within the chemistry parameters file. By default, 

the aerosol coupling time step is 15 minutes, and this is used for all grids in a simulation

regardless of the grid-specific driving time step.

The CAMx SOA module consists of two parts: gas-phase oxidation chemistry that forms 

condensable gases (CGs), and equilibrium partitioning between gas and aerosol phases for each 

CG/SOA pair. Table 5-3 lists the oxidation reactions and CG products. The CG yields are 
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expressed as ppm of CG formed per ppm of VOC reacted so that CG concentrations follow the 

CAMx convention for gases and are in ppm. The physical properties of CG/SOA pairs are shown 

in Table 5-4. The SOAs formed from the CGs are in units of μg/m3 as are all other aerosol 

species.

Studies are starting to elucidate mechanisms for polymerization reactions in organic aerosol 

phases. Polymerization increases the molecular weight of the condensed aerosol and reduces 

the volatility. Detailed descriptions of polymerization will likely depend upon the chemical 

composition of the organic and inorganic aerosol phases (e.g., aerosol acidity). Based on 

limited available data we assumed that the SOA polymerized to a non-volatile form (i.e., moved 

permanently to the aerosol phase) with a lifetime of about 1 day (Kalberer et al., 2004). 

Polymerization slowly forms organic aerosol polymers called SOPA (anthropogenic) and SOPB 

(biogenic).

Uptake of nitric acid on mineral dust particles is one of the pathways of particle nitrate 

formation. For example, calcium in soil dust particles reacts with nitric acid to form calcium 

nitrate. Based on Saharan dust study (Astitha et al., 2009), we estimate about 6% mass fraction 

of calcium carbonate (CaCO3) in fine dust particles (FCRS), and half of it is assumed to be 

replaced by calcium nitrate. Since the current ISORROPIA implementation in CAMx does not 

consider mineral cations other than sodium, nitrate uptake by calcium in soil dust is calculated 

external to ISORROPIA. CAMx outputs total particulate nitrate, i.e., the sum of particle nitrate 

determined by ISORROPIA and calcium nitrate.

Table 5-5 shows the aerosol species that can be included with the CF scheme. Some species 

must be present for this scheme (“Mandatory Species”) to establish linkages between gas and 

aerosol phase chemistry. Other species are optional (meaning that they can be removed from 

the chemistry parameters input file), except that sodium and chloride must always be present 

or absent together (i.e., one cannot be present without the other). If sodium and chloride are 

not modeled then default background values are used within CAMx.

In the CMU scheme, CRST is used to identify all primary inert material, which replaces the CF 

species of FPRM, FCRS, CPRM, and CCRS in Table 5-5. Individual aerosol species names specify 

both the constituent and the size section using a set naming convention, e.g., PSO4_1 refers to 

particle sulfate in the section 1. The CMU scheme requires that the complete list of all aerosol 

species be present in the chemistry parameters file (i.e., no aerosol species are optional).

5.2.3 Aerosol Sectional Approach

Unlike the CF scheme, where each species is represented by a single particle size, the CMU 

scheme institutes an additional step to distribute the bulk aerosol concentrations from the 

aqueous/aerosol chemistry modules into each size bin. For inorganic aerosol species, 

ISORROPIA yields the bulk aerosol composition at equilibrium. The aerosol size distribution is 

then determined by distributing the change in aerosol mass during the time step into each size 

bin using a weighting factor (Pandis et al., 1993). The fraction fi,k of total flux of species i
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Table 5-5. List of PM species for the CAMx CF aerosol option.

Internal Label Name Mandatory Species

PSO4 Sulfate X

PNO3 Particulate Nitrate X

PNH4 Particulate Ammonium X

PH2O Aerosol Water Content X

SOA1-2 Anthropogenic SOA (see Tables 5-3, 5-4) X

SOA3-7 Biogenic SOA (see Table 5-3, 5-4) X

SOPA Polymerized anthropogenic SOA X

SOPB Polymerized biogenic SOA X

NA Sodium

PCL Particulate Chloride

POA Primary Organic Aerosol

PEC Primary Elemental Carbon

FPRM Fine Other Primary (diameter≤2.5 μm)

FCRS Fine Crustal (diameter≤2.5 μm)

CPRM Coarse Other Primary

CCRS Coarse Crustal

between gas and aerosol phases that condenses onto or evaporates from an aerosol size 

section k is given by,

( ) ( )

∑ ( − ) ( + )

− + =

k

k

eq

k k i i i

k

eq

k k i i i

i k N d D c c

N d D c c f 2 1

2 1 , π β

π β ,

where Nk and dk are the number and mean diameter of particles in the section k, respectively, 

Di, ci, and ci

eq are the diffusivity, bulk gas-phase concentration, and equilibrium concentration 

at the particle surface of species i, respectively, βk=2λ/adk, λ is the mean free path of air, and a

is the accommodation coefficient (Pandis et al., 1993). Assuming that ci

eq is independent of 

particle size, the fraction is reduced to,

( )

( ) k

k

k k k

k k k

i k f N d

N d f = ++ =

∑ 1

1 , β

β .

The above weighting factor then depends on the surface area only.

For organic aerosols, SOAP calculates the bulk equilibrium composition. Using the pseudo-ideal 

solution assumption (Strader et al., 1999), the effect of chemical composition of the particle can 

be incorporated into the weighting factor:

( ) ( )

∑ ( − ) ( + )

− + =

k

k k i i k i k

k k i i k i k

i k N d c x c

N d c x c

f 1

1

*

,

*

,

, β

β .
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where xi,k is the mole fraction of species i in the section k and ci

* is the effective saturation 

concentration of species i. Since the fraction determines the composition of each size section, 

the above equation should be solved iteratively at each time step. Assuming that the chemical 

composition changes slowly during a time step, however, the mole fractions can be 

approximated with those from the previous time step (Koo et al., 2003).

For cloud/fog droplets, RADM is used to calculate sulfate and nitrate formation in the bulk 

aqueous phase. The added mass is then distributed into each size bin by a weighting factor 

which is based on the size-resolved aqueous chemistry model simulation results (Fahey and 

Pandis, 2001).

In addition, mathematical descriptions of nucleation and coagulation have been added to the 

CMU scheme. The nucleation model employs the nucleation rate parameterization proposed 

by Russell et al. (1994). The model assumes a linear sulfuric acid vapor concentration variation 

for the given time step of the aerosol module based on the initially available sulfuric acid and 

assigns all the nucleated mass to the first section of the distribution. The coagulation rate of 

the aerosol particles is modeled according to Seinfeld and Pandis (1998). A high-resolution 

distribution is used for the coagulation calculations by subdividing each section of the original 

distribution into 3 additional sections.

5.3 Mercury Chemistry

Mercury exists in the atmosphere as elemental mercury, Hg(0), and oxidized mercury, Hg(II) 

(Schroeder and Munthe, 1998). Hg(II) can be inorganic (e.g., mercuric chloride, HgCl2) or 

organic (e.g., methyl mercury, MeHg). It can also be present as particulate mercury (e.g., 

mercuric oxide, HgO, or mercury sulfide, HgS). In the global atmosphere, Hg(0) is the dominant 

form. Hg(II) typically constitutes a few percent of total mercury and is predominantly in the gas 

phase. MeHg concentrations in the atmosphere are negligible, about a factor of 10 to 30 lower 

than Hg(II) concentrations, based on analysis of precipitation samples conducted by Frontier 

Geosciences, Inc. (e.g., Seigneur et al., 1998). However, Hg(II) becomes methylated in water 

bodies, where it can bioaccumulate in the food chain. Hg(0) is sparingly soluble and is not 

removed significantly by wet deposition; its dry deposition velocity is also believed to be low. 

As a result, Hg(0) has a long atmospheric lifetime, on the order of several months, that is 

governed by its oxidation to Hg(II). On the other hand, Hg(II) is quite soluble; it is consequently 

removed rapidly by wet and dry deposition processes. Particulate mercury, Hg(p), is mostly 

present in the fine fraction of particulate matter (PM2.5), although some Hg(p) may be present 

in coarse PM (e.g., Landis and Keeler, 2002).

Known transformations among inorganic mercury species include the gas-phase oxidation of 

Hg(0) to Hg(II), the aqueous-phase oxidation of Hg(0) to Hg(II), the aqueous-phase reduction of 

Hg(II) to Hg(0), various aqueous-phase equilibria of Hg(II) species, and the adsorption of Hg(II) 

to PM in both the gas-phase and aqueous-phase. The inorganic mercury chemistry modules 

implemented in CAMx are based on our current knowledge of these transformations. However, 

it should be noted that our knowledge of mercury chemistry continues to evolve as new 

laboratory data become available, and the Hg chemical kinetic mechanisms in CAMx and other 

models that treat the atmospheric fate of mercury will need to be revised accordingly.
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Below, we provide additional details on the gas- and aqueous-phase mercury chemistry 

mechanisms implemented in CAMx, and the implementation approach.

5.3.1 Gas-Phase Chemistry

The gas-phase transformations include the oxidation of Hg(0) to Hg(II) by ozone (O3) (Hall, 

1995), hydrogen peroxide (H2O2) (Tokos et al., 1998) hydroxyl radicals (OH) (Sommar et al., 

2001; Pal and Ariya, 2003; 2004), bromine (Br) (Ariya et al., 2002), and hypobromite (BrO)

(Raofie and Ariya, 2003). The oxidation of Hg(0) by O3, H2O2, and OH are given by the following 

three reactions:

-20 3 -1 -1

3 Hg(0)(g) + O (g) → Hg(II)(g), k = 3×10 cm molec s

-19 3 -1 -1

2 2 2 Hg(0) (g) + H O (g) → Hg(OH) (g), k = 8.5×10 cm molec s

-14 3 -1 -1

2 Hg(0)(g) + OH (g) → Hg(OH) (g), k = 8×10 cm molec s ,

while oxidation by Bromine is based on a sequence of 5 reactions (Seigneur and Lohman, 2008):

3 -1 -1

-1.86 -13

1 cm molec s

298 Hg(0) (g) + Br (g) HgBr (g), = 3.6 10 



 



 → ×

T k P

9 -1

2 s

8537 HgBr (g) Hg(0) (g), = 3.9 10 exp 



 



 − → ×

T

k

3 -1 -1

-0.57 -10

2 3 cm molec s

298 HgBr (g) + Br (g) HgBr (g), = 2.5 10 



 



 → ×

T k

3 -1 -1

-0.57 -10

4 cm molec s

298 HgBr (g) + OH (g) HgBrOH (g), = 2.5 10 



 



 → ×

T k

-15 3 -1 -1

5 Hg(0) (g) + BrO (g) → Hg(II)(g), k =1×10 cm molec s

The reaction rate constants provided above are for temperatures in the range of 20 to 25o

C; no 

temperature dependence information is available. For the bromine reactions, T is the 

temperature in degrees Kelvin, and P is the pressure in atmospheres. The five reactions are 

treated as a single reaction, with an effective Hg(0) first-order rate constant that is a function of 

the individual reaction rates and the concentrations of Br, BrO and OH based on the assumption 

that Br, BrO and OH concentrations don’t change by their reactions with mercury. This 

treatment is similar to that of Holmes et al. (2006), who considered the oxidation of Hg(0) by 

bromine atoms with a set of three reactions. The effective first-order rate constant is calculated 

by the following expression:

[ ]( [ ] [ ])

[ ] [ ] [ ] -1

5

2 3 4

1 3 4 k BrO s

k k Br k OH

k Br k Br k OH keff +

+ +

+ =
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5.3.2 Adsorption of Hg(II) on PM

In the first implementation of mercury in CAMx, Hg(II) adsorption on PM was considered only in 

the aqueous phase (see below), using an adsorption coefficient derived from available 

experimental data (Seigneur et al., 1998; Ryaboshapko et al., 2002). It is essential to also 

consider the adsorption of gaseous Hg species to PM because gas/particle conversion also 

affects Hg deposition (Lindberg et al., 2007). Rutter and Schauer (2007a) reported results of 

laboratory work measuring the adsorption of reactive gaseous mercury (RGM) to atmospheric 

and synthetic particles as a function of temperature. Their experimental results suggest that 

surface area rather than PM mass controls the partitioning process. They reported three 

surface-area adsorption coefficients for urban PM (collected in Milwaukee, WI, and Riverside, 

CA), ammonium sulfate and adipic acid, respectively. They expressed the surface-area 

adsorption coefficient (Ksa) as follows:

K Hg (RGM A PM ) sa p ads sp = ⋅ ⋅ ,

where Ksa is in m3

m-2, Hgp,ads and RGM are in pg m-3, Asp is the specific surface area of ambient 

PM in m2

μg-1 and PM is the ambient urban PM concentration in μg m-3. Here, Hgp,ads refers 

only to the adsorbed RGM, i.e., it does not include non-volatile primary particulate mercury. 

Rutter and Schauer (2007a) also found that the Ksa obtained for urban PM falls between that of 

ammonium sulfate (more RGM adsorption) and adipic acid (less RGM adsorption). Their 

laboratory experiments lead to the following value for Ksa as a function of temperature (in K) 

for adsorption to urban PM:

(4250 / 10) 10 − = T Ksa (1)

Rutter and Schauer’s (2007b) experimental results also show a ten-fold increase in adsorption 

of RGM to sodium chloride compared to ammonium sulfate and organic particulate compounds 

(a larger increase was observed for sodium nitrate). Thus, the adsorption coefficient for RGM 

adsorption to sea-salt is about 10 times that for urban PM:

(4250 / 9) 10 − = T Ksa (2)

Following the approach used in Vijayaraghavan et al. (2008), we treat all non-sea-salt PM as 

urban PM for simplicity and use Equation (1) to simulate RGM adsorption to all non-sea-salt 

PM. The adsorption to sea-salt PM is calculated using Equation (2). Thus, the effective 

adsorption coefficient for each aerosol size section is calculated as:

( ) ( )

( ) ss T ss T Ksa eff = F + − F − − 10 10 1 4250 / 9 4250 / 10 ,

where Fss is the fraction of sea-salt in that size section. In the CAMx implementation, we 

assume that RGM is adsorbed on primary fine and coarse PM.
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5.3.3 Aqueous-Phase Chemistry 

The aqueous-phase chemistry includes the reduction of Hg(II) to Hg(0) via reaction with 

hydroperoxy radicals (HO2) and by the formation of the sulfite complexes (at low HCl 

concentrations), HgSO3 and Hg(SO3)2

2-

, as well as the oxidation of Hg(0) to Hg(II) by dissolved 

O3, OH, and Cl2. Adsorption of Hg(II) species on atmospheric particulate matter (PM) is 

simulated using an adsorption coefficient (K = 34 L g-1

) recommended by Seigneur et al. (1998). 

The relevant reactions are listed below. Note that the gas-liquid equilibria and ionic equilibria 

of the non-mercury species (e.g., SO2, O3) involved in the mercury aqueous-phase chemistry 

are not shown here, since they are identical to those in the other CAMx mechanisms.

5.3.2.1 Gas-liquid Equilibria

-1 Hg(0) (g) ⇔ Hg(0) (aq), K = 0.11M atm (Sanemasa, 1975; Clever et al., 1985)

6 -1

2 2 HgCl (g) ⇔ HgCl (aq), K =1.4×10 M atm (Lindqvist and Rodhe, 1985)

4 -1

2 2 Hg(OH) (g) ⇔ Hg(OH) (aq), K =1.2×10 M atm (Lindqvist and Rodhe, 1985)

The Henry's Law constants listed above are for temperatures in the range of 20 to 25oC. 

Temperature dependence information is available for the Hg(0) Henry's Law constant but the 

validity of this information for temperatures below 0oC is not established.

5.3.2.2 Aqueous-phase Equilibria

2+ - -14 2 HgCl2 (aq) ⇔ Hg + 2Cl , K =10 M (Sillen and Martel, 1964)

2+ - -22 2 Hg(OH)2 (aq) ⇔ Hg + 2OH , K =10 M (Sillen and Martel, 1964)

13 -1

3

2-

3 Hg2+ + SO ⇔ HgSO , K = 2.1×10 M (van Loon et al., 2001)

2- 10 -1

3 2

2- HgSO3 + SO3 ⇔ Hg(SO ) , K =1×10 M (van Loon et al., 2001)

5.3.2.3 Adsorption of Hg(II) on PM in the Aqueous Phase

-1 Hg(II)(aq) ⇔ H(II)(p), K = 34 L g (Seigneur et al., 1998)

5.3.2.4 Aqueous-phase Kinetics

2+ 7 -1 -1

3 Hg(0)(aq) + O (aq) → Hg , k = 4.7 ×10 M s (Munthe, 1992)

2+ 9 -1 -1 Hg(0)(aq) + OH (aq) → Hg , k = 2×10 M s (Lin and Pehkonen, 1997)

-1

3 HgSO (aq) → Hg(0) (aq), k = 0.0106 s (van Loon et al., 2000)

4 -1 -1

2 Hg(II)(aq) + HO (aq) → Hg(0) (aq), k =1.7×10 M s (Pehkonen and Lin, 1998)

2+ 6 -1 -1 Hg(0)(aq) + HOCl(aq) → Hg , k = 2.09×10 M s (Lin and Pehkonen, 1998)

- 2+ 6 -1 -1 Hg(0) (aq) + OCl → Hg , k =1.99×10 M s (Lin and Pehkonen, 1998)
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In the last two reactions listed above, HOCl and OClcome from the dissolution and subsequent 

dissociation of molecular chlorine (Cl2). Note that Hg(II) (aq) refers to all divalent Hg species in 

solution (i.e., Hg2+ + HgCl2(aq) + Hg(OH)2(aq) + HgSO3 + Hg(SO3)2

2-

). The rate constants listed 

for the aqueous-phase kinetics are for temperatures in the range of 20 to 25oC. Temperature 

dependence information is available for the HgSO3 reduction reaction.

As mentioned previously, the gas- and aqueous-phase Hg transformations presented above 

represent the state of the science from a decade ago (Ryaboshapko et al., 2002; Seigneur et al., 

2001a, 2003a) and our knowledge of mercury chemistry continues to evolve. For example, 

Gardfeldt and Johnson (2003) challenged the aqueous-phase reduction of Hg(II) to Hg(0) by 

dissolved HO2, suggesting that this pathway is unimportant. There also seems to be some 

circumstantial evidence of reduction of Hg(II) to Hg(0) in power plant plumes from various 

experimental studies that is not accounted for in current treatments of Hg chemistry (e.g., 

Edgerton et al., 2001; Seigneur et al., 2001b). Additional details are provided in a scoping study 

for mercury deposition conducted for the Midwest Regional Planning Organization by Seigneur 

et al. (2003b).

5.3.4 Implementation Approach

The approach used to implement the mercury transformation pathways, discussed above, into 

CAMx is based on the assumption that the mercury species concentrations are much smaller 

than those of the species with which they react. Thus, the concentrations of the non-mercury 

species can be assumed to be constant during the mercury chemistry calculations and analytical 

solutions are available for both the gas-phase and aqueous-phase conversions.

The mercury chemistry discussed in the previous sections requires the concentrations of the 

following non-mercury species: O3, H2O2, OH, SO2, HO2, Cl2, HCl, Br, BrO and atmospheric 

particulate matter (PM). The concentrations of most of these species are available from CAMx. 

However, Cl2, Br, and BrO are not explicitly simulated because the emissions data required to 

model these species are generally inadequate or unavailable. Thus, we specify typical vertical 

profiles of Cl2, Br, and BrO concentrations. The Cl2 concentrations are prescribed to be nonzero over oceans and zero elsewhere. Also, daytime Cl2 concentrations are lower than 

nighttime values to account for the fact that Cl2 is photolyzed during the day. The zenith angle 

is used for the determination of night/day. A 2-D array of integer values (1 if ocean, 0 if not) is 

used to determine if the grid column is predominantly over ocean. This array is initialized at the 

beginning of the simulation from an input file and is specific for the modeling domain and grid. 

For Br and BrO, vertical profiles over land and ocean are prescribed, with higher values over 

ocean than over land. During the night, the concentrations of these species are assumed to be 

zero, since the photolysis of Br2 is the primary source for these radicals.

The mercury aqueous-phase chemistry module also requires the specification of cloud liquid 

water content (LWC) and cloudwater pH. Both these variables are available from CAMx – the 

mercury aqueous-phase chemistry module is invoked after the CAMx PM aqueous-phase 

chemistry calculations are performed, so the cloudwater pH has already been calculated. Note 

that the PM aqueous-phase module (based on the RADM aqueous-phase chemistry module 

that is also used in Models-3/CMAQ) does not explicitly simulate the cloud chemistry of OH and 
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HO2 radicals. The concentrations of these radicals can be reduced by their heterogeneous 

chemistry within clouds (e.g., Jacob, 2000; Jaegle et al., 2001). In the CAMx implementation, 

we account for this by reducing the concentrations of OH and HO2 radicals by factors of 2 and 

10, respectively.

5.3.5 Chemistry Parameters for Mercury

The mercury chemistry module requires total PM concentrations, so mercury can only be 

modeled in conjunction with PM chemistry. In CAMx, PM chemistry is modeled using 

Mechanisms 5, 6 and 7. Mercury chemistry is selected by including mercury species among the 

list of modeled species for these three mechanisms. The CAMx mercury species names are:

HG0 – elemental gaseous mercury, or Hg(0)

HG2 – reactive gaseous mercury, or Hg(II)

HGP – primary particulate mercury, or Hg(P)

HGIIP – reactive gaseous mercury, or Hg(II) adsorbed onto fine PM

HGIIPC – reactive gaseous mercury, or Hg(II) adsorbed onto coarse PM

CAMx requires that all five or none of these species be included in a simulation. Therefore, 

mercury chemistry is not required for PM modeling, but if mercury chemistry is selected then 

all five mercury species must be modeled. All of the rate constants and equilibrium constants 

for the mercury chemistry module are hard-coded and so no mercury reaction rate data are 

included in the chemistry parameters input file (see Section 3). This is similar to the RADM 

aqueous chemistry and ISORROPIA inorganic aerosol equilibrium modules. 

Several physical properties of the mercury species must be specified on the chemistry 

parameters file (see Figure 3-3a). The physical properties specified for the gas species (Henry’s 

Law, molecular weight, surface reactivity) influence the deposition characteristics. The Henry 

constant for HG2 is assumed to be similar to that of HNO3 because these two gases have similar 

solubility. The HG2 species represents HgCl2 and Hg(OH)2; the Henry constant for the former is 

1.4×106 M atm-1 and for the latter it is 1.2×104 M atm-1. The surface resistance factor is set to 

zero for strong acids, such as HNO3, that have a strong tendency to stick to surfaces – this 

forces the surface resistance calculated in the dry deposition algorithms to zero. The reactivity 

parameter for HG2 is set to 0, as for HNO3. 

The dry deposition of HG0 is set to zero by choosing a very low Henry constant (similar to CO). 

This is based on the assumption that natural emissions and dry deposition of HG0 balance each 

other over the modeling domain. This assumption is justified by the fact that the atmospheric 

lifetime of HG0 (about 1 year) greatly exceeds its residence time (days to weeks) within a 

regional modeling domain. If natural emissions of HG0 are not included in the mercury 

emissions inventory, the dry and wet deposition of HG0 should be zero by setting a Henry 

constant of smaller than 1×10-8 M atm-1

. However, if natural emissions of Hg(0) are used in the 

CAMx simulation, the Henry constant should be set to 0.111 with a temperature factor of -4970 

K (Clever et al., 1985).
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5.4 Simple Chemistry Via Mechanism 10

CAMx offers three different chemical mechanisms for ozone and particulate matter modeling. 

However, the minimum level of chemistry is the CB05 mechanism for ozone (Table 5-1), which 

requires significant effort to prepare all of the input data, particularly with regard to emissions. 

There are many cases when air pollution problems could be investigated with a much simpler 

chemistry scheme. An example of this would include modeling SO2 from a few specific sources 

over a relatively small region, and treating conversion to sulfate by assuming a representative 

decay rate. An approach was necessary to provide a simple and flexible scheme that can be 

used for modeling chemical reactions other than the ozone or secondary PM reactions treated 

by the full-science mechanisms. 

The new simple chemistry scheme is selected by specifying a mechanism ID of 10 in the 

chemistry parameters input file. The specific chemical reactions to be modeled must be set in 

the subroutine CAMx/chem10.f in the source code directory. The user must modify this 

subroutine to implement whatever reactions are desired. Follow the guidelines for 

implementing reactions that are included in the subroutine. This approach requires some 

knowledge from the user, but also provides complete flexibility in implementing reactions. 

The simple chemistry has been tested using a modeling database for primary PM species in 

Cairo, Egypt (personal communication from Mr. Usama Faramawy, Egyptian Environmental 

Affairs Agency). Results of the tests are shown in Figures 5-2 and 5-3. A simple chemical 

reaction was implemented where the species PMT decayed to PM2 with a first-order rate 

constant of 10% per hour. These species were selected because PMT has high emissions and 

PM2 has low emissions. This modeling is not intended to represent any actual chemical 

reactions for PM species in Cairo, but rather is just a hypothetical testing scenario. The 

expected result is that the chemical reaction will lower the concentration of PMT and raise the 

concentration of PM2. Figure 5-2 shows the expected result, that the PMT concentration is 

lowered by the reaction. The reduction in PMT becomes proportionately greater at longer 

downwind distances because there has been more time for reaction to take place. Figure 5-3

shows the complementary increase in PM2 due to chemical production.
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No Chemical Decay Chemical Decay

Figure 5-2. Impact of chemical decay on the concentration of the donor species PMT.

No Chemical Production Chemical Production

Figure 5-3. Impact of chemical production on the concentration of the recipient species PM2.
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6. PLUME-IN-GRID SUBMODEL

Photochemistry is a highly non-linear problem because chemical reaction rates among most 

compounds depend upon their ambient concentrations. In Eulerian air quality models, ambient 

concentrations depend on how well the modeling grid resolves emissions, transport, and 

chemical history. Thus, grid resolution plays a vital role in the ability of the model to properly 

characterize photochemical conditions. Increasing resolution should in theory lead to a better 

model as the time/space discretization tends toward a continuum. However, practical and 

theoretical considerations suggest that the lower limit on horizontal grid spacing is about 1000 

meters for Eulerian air quality models such as CAMx. Nevertheless, even higher resolution is 

often necessary to adequately simulate chemistry within concentrated point source plumes.

Some current photochemical models contain plume-in-grid treatments that track individual 

plume segments (or puffs) in a Lagrangian sense, accounting for plume-scale dispersion and 

chemical evolution until such time as puff mass can be adequately represented within the 

larger grid model framework. Then the puff mass is added to the grid system as a virtual 

source, and that mass is subsequently carried by the grid model processes. It is important to 

understand that the inclusion of a Lagrangian puff model within an Eulerian grid model is a 

forced construct. The formulations of the two modeling approaches are fundamentally 

different and there is no theoretically “correct” methodology.

Historically there have been two schools of thought regarding the appropriate times at which to 

transfer puff mass into the host model grid system. The first primarily considers the physical 

size of puffs relative to grid cells; once puff mass is dispersed to scales that are adequately 

resolved by a grid, that mass should be transferred. The two principle problems associated 

with this approach are deciding what the appropriate size criteria are to be, and how to 

distribute puff mass into the grid system. The second considers chemical evolution of the puffs 

(e.g., Gillani and Pleim, 1996) to find a balance between aging plume constituents adequately 

and sequestering plume mass from grid processes for too long. The main problem with this 

approach is identifying chemically mature plume mixtures within ever-evolving puffs relative to 

ever-evolving grid chemistry. Puffs may reach a stage of chemical maturity after very long 

simulation periods (say 24 hours), however it is unrealistic to assume that puffs should maintain

physical coherence with no influence on grid chemistry over such time scales.

The CAMx Plume-in-Grid (PiG) sub-model addresses both chemical and size considerations. 

Two PiG options are available that vary in their chemical complexity. Both approaches share 

common design features for puff initialization, puff structure, transport, and growth. They 

deviate in how they treat chemistry and when they transfer mass from puffs to grid cells. This 

section details the structure and functionality of both options.

The first PiG approach is aimed at treating the early chemical evolution of large NOx plumes 

when mostly inorganic gas-phase reactions are operative. The method is called the Greatly 

Reduced Execution and Simplified Dynamics (GREASD) PiG. The streamlining employed in this 

version was based upon our experiences in developing, utilizing, and studying the responses of 

more detailed PiG algorithms for large NOx plumes. The GREASD PiG model works with the 

Ozone and Particulate Source Apportionment Technology (OSAT/PSAT). This is possible 
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because of the simplified approach used in GREASD PiG and because compatibility with the 

source apportionment Probing Tools was an explicit design objective.

The second approach treats the full suite of gas-phase photochemistry for all types of point 

sources and so by necessity incorporates much more chemical complexity than the first. This 

CAMx plume treatment is called the Incremental Reactions for Organics and NOx (IRON) PiG. 

Gas-phase chemistry is simulated within each plume segment using an “incremental chemistry” 

approach, whereby puffs carry the incremental contributions of the puff relative to the grid 

concentrations. Incremental puff concentrations can be positive or negative, depending upon 

the species and stage of plume evolution. A similar chemistry approach is used in the SCICHEM 

Lagrangian model (EPRI, 2000). IRON PiG supports the Reactive Tracer (RTRAC) Probing Tool, 

but it does not work with the source apportionment Probing Tools and it does not treat PM.

6.1 CAMx PiG Formulation

6.1.1 Basic Puff Structure and Diffusive Growth

Both GREASD and IRON PiG sub-models share a common physical structure and growth 

algorithm. A stream of plume segments (puffs) is released from a designated point source. 

Each puff possesses a longitudinal length and directional orientation defined by the separation 

of a leading and a trailing point. Initial separation of these points is determined by the wind 

vector at final plume rise. Each point is then subsequently and independently transported 

through the gridded wind fields, which directly accounts for puff stretching and changes to 

centerline orientation due to deforming shears. The "position" of each puff is defined at the 

center point of each puff between the endpoints, and is used to identify the grid cell in which 

the puff resides for the calculation of diffusive growth and chemistry. 

Like other puff models, the shape of each puff is characterized by a spread tensor, which is 

defined from a set of Gaussian standard deviations (σ) along the three spatial axes (σx, σy, σz). 

Diffusive growth is described by the evolution of these values. The total cross-sectional width 

extends ±1.5σy from puff centerline. Similarly, the total cross-sectional depth extends ±1.5σz

from puff centerline (with limits placed on depth by the ground and by capping stable layers 

aloft). The total longitudinal length is the distance between the puff endpoints with an 

additional ±1.5σx added in each direction. Horizontal area and total volume are calculated 

using the formulae for an ellipse. Figure 6-1 presents a schematic representation of each puff 

in horizontal cross-section.

We have developed an explicit solution approach for puff growth that shares SCICHEM theory 

and concepts (EPRI, 2000), but includes some simplifications. SCICHEM solves predictive spatial 

moment equations with second-order closure that relate the evolution of the puff spread 

tensor (σij=σi×σj) to resolved mean shears and turbulent velocity statistics. The Reynoldsaveraged second-moment transport equation is given as

Q

x u c

Q

x u c

x

u

x

u

dt

d i j j i

k

i

jk

k

j

ik

ij ′ ′ ′ +

′ ′ ′ +

∂

∂

+

∂

∂ = σ σσ
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Figure 6-1. Schematic representation of CAMx PiG puff shape in the horizontal plane. 

Directional orientation of the puff is arbitrary, and evolves according to wind direction, 

shears and diffusive growth along its trajectory.

where u is the mean wind vector component, the primed values represent turbulent 

fluctuations from the mean, and the angle brackets denote integrals over space. The Reynolds 

averaging process always introduces higher-order fluctuation correlations, and this is given by 

the turbulent flux moments x′u′c′ , where u′c′ represents the turbulent flux of 

concentration. It is these last two diffusion terms that SCICHEM solves in its second-order 

closure scheme. 

For sub-puff scale turbulence, SCICHEM employs the restriction that the only active off-diagonal 

component of x′u′c′ is the symmetric horizontal term (i=x, j=y), but it is applied only for the 

large-scale (meso to synoptic) contribution to puff deformation when puff scales reach such 

dimensions. In CAMx, we ignore this off-diagonal flux moment term altogether since puffs are 

ultimately terminated when puff scales approach much smaller grid scales (typically < 50 km). 

SCICHEM also makes the assumption that the horizontal turbulence is isotropic, 

x′u′c′ = y′v′c′ . This results in a single diffusivity equation for both x and y directions, and a 

single diffusivity for the z direction:

Q

y v c

Kx Ky

′ ′ ′ = =

Q

z w c

Kz

′ ′ ′ =

P (lead)

P (trail)

y 1.5

x 1.5
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In our approach for CAMx, we have adopted the SCICHEM second-order tendency equations to 

model the time-evolution of puff turbulent flux moments (represented by diffusivities Kx=Ky

and Kz) and their contribution to the evolution of puff spread (represented by the diagonal 

components of the puff spread tensor, σx

2

, σy

2 and σz2

). Puff spread is defined for puff depth 

(σz), puff width (σy), and puff length (σx). We account for the effects of grid-resolved shears of 

horizontal wind in the evolution of lateral and longitudinal spread. But we assume that the 

evolution of vertical spread is solely the result of turbulent fluxes, which are orders of 

magnitude larger than grid-resolved shears of vertical wind.

The resulting two Reynolds-averaged second-moment transport equations for CAMx PiG are:

where D is total explicit (grid-resolved) horizontal shear of horizontal wind (i.e., “deformation”, 

see Section 4.5). S is the explicit vertical shear of horizontal wind, which is broken down into 

puff-relative lateral and longitudinal components:

The difference between θ and φ represents the relative angle between the puff’s longitudinal 

orientation and the direction of vertical shear; a cross-puff shear results in more lateral spread 

while along-puff shear results in more longitudinal spread. The explicit shear terms containing

D and S may be toggled by the user: (1) shear effects may be applied to puff growth rates at all 

times; (2) shear effects may be applied only during neutral/unstable conditions; or (3) shear 

effects are never applied. 

The SCICHEM tendency equation for the horizontal turbulent flux moment is

where A = 0.75, q2

= v′v′, and Λ is the horizontal turbulent length scale. Separate equations 

are given for two different boundary layer turbulence scales (shear- and buoyancy-produced), 

such that

y y z y x

y D S K

dt

d

2 2 2 2

2

= σ + σ σ +

σ

z

z K

dt

d 2

2

= σ

y v c

q

y v c Qq A

dt

d ′ ′ ′ Λ ′ ′ ′ = −2

( )

1/ 2 2 2

cos 













 = − +

dz

dv

dz

du Sy θ φ

x x z x x

x D S K

dt

d 2 2 2 2

2

= σ + σ σ +

σ

( )

1/ 2 2 2

sin 













 = − +

dz

dv

dz

du Sy θ φ
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Within the surface-based boundary layer, the horizontal velocity variance is given by

where u* is the friction velocity, w* is the convective velocity scale, z is height above the 

surface, and zi is the height of the surface-based boundary layer. The horizontal turbulent 

length scale is given by

In the stable boundary layer, only the shear components of q2 and Λ are applied. Above the 

boundary layer, SCICHEM applies rough approximations for the velocity variance and turbulent 

length scale. In CAMx we have set these values to q2 = 0.1 m2/s2, and Λ = 300 m.

The SCICHEM tendency equation for the vertical turbulent flux moment is

where qv

2

= w′w′ , Λv is the vertical turbulent length scale, and Kz

eq is the equilibrium 

diffusivity. Whereas a specific equation for Kz

eq is formulated for SCICHEM, we have chosen to 

specify the value of this parameter from the gridded fields of vertical diffusivity in CAMx. Again 

SCICHEM gives separate equations for shear- and buoyancy-produced turbulence scales.

Within the surface-based boundary layer, the vertical velocity variance is given by

The vertical turbulent length scale for both shear and buoyancy is equal to Λshear given above 

for horizontal length scale. Above the boundary layer, SCICHEM applies rough approximations 

for the velocity variance and turbulent length scale and we have adopted these for CAMx: qv

2

= 

0.01 m2/s2, and Λv = 10 m.

shear buoyancy

y′v′c′ = y′v′c′ + y′v′c′

( ) shear i q 2.5u 1 z/ z

2

*

2 = −

[ ( )] buoyancy i q 0.13w 1 1.5exp z / z

2

*

2 = +

( ) ( ) 2 2 2 0.65

1

0.3

1 1

z z shear i

= +

Λ

buoyancy i Λ = 0.3 z

(QK z w c ) q

z w c A

dt

d eq

z

v

v − ′ ′ ′ Λ ′ ′ ′ =

( )i shear v q 1.5u 1 z / z

2

*

2 = −

( ) ( ) i i buoyancy v q 1.1w z/ z 1.05 z/ z

2 2 / 3

*

2 = −
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The external variables needed by PiG to complete the dispersion calculations include zi, u* and 

w*. All of these are available from an internal module in CAMx that calculates these boundary 

layer similarity theory parameters. Thus, no additional parameters are needed to be input to 

the model.

6.1.2 Puff Transport

A fresh set of new puffs are released from all PiG point sources within the modeling domain for 

the duration of the smallest time step among the master and all nested grids. The length of 

each puff is determined by the combination of the mean total wind speed at the height of final 

plume rise and time step. Limits are placed on maximum extruded length based on half the 

finest resolution in the given simulation. If winds and time-steps are such that the maximum 

allowed length is violated, then several puffs are automatically emitted from a given stack per 

time step. The user can also set a maximum time interval of release if more puffs (better plume 

resolution) are desired over the default automated release interval. The orientation of the puff 

length is along the total wind vector. Total puff volume is determined by stack volumetric flow 

rate in conjunction with growth due to turbulent entrainment following the SCICHEM approach. 

Initially, σx = σy and σz values are explicitly calculated from this entrainment calculation.

The effects of resolved wind shear on plume deformation (i.e., at plume scales larger than 

individual puff scales) are treated using a “chained puff” approach (Figure 6-2). Points at the 

leading and trailing edges of the puff centerline are individually transported through the 

gridded wind fields, which directly accounts for puff stretching and changes to centerline 

orientation due to deforming shears. Since puffs can extend over multiple layers, layer densityweighted average wind components are determined for each endpoint based on the vertical 

coverage of the puff.

The “chain” aspect means that at least initially (as puffs are emitted from the stack) the trailing 

point of a puff emitted at time t will be the leading point of a puff emitted at time t+dt. 

However, as the puffs are advected downstream, the leading point of one puff will deviate from 

the trailing point the puff behind it due to evolving puff depth and wind fields. Puff volume is 

conserved in convergent/divergent wind fields. Puff endpoints may move closer together or 

further apart, in wind fields that are slowing or accelerating downstream. We compute puff 

end-point separation changes and then adjust puff widths and depths to maintain constant puff 

volume. The change in computed puff endpoint spacing defines puff length tendencies, then 

puff depth tendencies are computed from grid-resolved vertical wind shear (∂w/∂z), and finally 

we determine the puff width tendencies required to conserve puff volume. 

The “position” of each puff is defined by its center point between the endpoints. This position 

defines the grid domain and grid cell in which the puff resides for the calculation of diffusive 

growth and chemistry. This definition holds even if the puff is sufficiently long that the 

endpoints are in different grid cells (or even different nested grids if near a nest boundary). 

With our definition for termination when horizontal area approaches grid cell area, the puff 

length should not extend across more than two grid cells.
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Figure 6-2. Plan-view schematic representation of a chain of PiG puffs emitted from a point 

source into an evolving gridded wind field. The red line connected by dots represents puff 

centerlines, with dots representing leading and trailing points of each puff. The CAMx 

computational grid is denoted by the blue lines.

6.2 GREASD PiG

The GREASD PiG is designed for large NOx point sources, where only inorganic chemistry is 

operative during early plume evolution. The intention of GREASD PiG is to more properly age

emitted NOx within the confined plume volume to mitigate the artificially rapid chemical 

processing of fresh NO to NO2 to ozone that would otherwise occur if immediately released 

into a large grid volume. A condensed inorganic chemical mechanism is employed in GREASD 

PiG that includes 23 reactions involving oxidation of NOx and SOx. Therefore, GREASD PiG 

should not be used for VOC sources. Chemical limitations applied within GREASD PiG cause

puffs to transfer their mass to the grid before oxidant production from VOCs is no longer 

suppressed; this can occur before puffs reach a size threshold determined by the grid spacing. 

The chemical evolution of large NOx point source plumes can be characterized in three stages

(EPRI, 2000), as described below:

• Stage 1: Early plume conditions where NOx concentrations are very high and radical 

concentrations are negligible – simple NO/NO2/O3 photostationary state applies along 

with the NO-NO self reaction;

Stack
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• Stage 2: Mid-range plume conditions where radical concentrations are sufficiently large 

to generate secondary inorganic acids like nitrate and sulfate;

• Stage 3: Long-range plume conditions where sufficient mixing with the ambient air leads 

to the full range of gas-phase reactions involving VOC oxidation and ozone formation.

The objective for GREASD PiG is to transfer mass to the grid at about the time when radical 

production via organic chemistry starts to become important, so GREASD PiG treats plume 

chemistry during Stages 1 and 2. We define the onset of Stage 3 chemistry when the following 

criterion is met:

At this point GREASD puffs transfer all of their mass to the grid before the onset of Stage 3. 

This specific design constraint is also compatible with the requirements of the source 

apportionment Probing Tools.

Kumar and Russell (1996) and Karamchandani et al. (1998) found that PiG models with 

simplified inorganic chemistry produced results that were very similar to full chemistry. The 

chemical mechanism for GREASD PiG includes 23 reactions listed in Table 6-1 that were 

selected as follows:

• Reactions for the NO-NO2-O3 photo-stationary state established in sunlight (1-3)

• Self-reaction of NO important only at very high NO concentrations (4)

• Production of OH by photolysis of O3 and HONO in sunlight (5-9)

• Production of nitric acid in sunlight (10)

• Formation of NO3 and N2O5 at night (11-17)

• Production of nitric acid at night (18)

• Production of sulfuric acid in sunlight (19)

• Removal of OH by CO (20)

• Production of OH by photolysis of formaldehyde (21-22)

• Conversion to OH of any HO2 formed in 20-22 (23)

These reactions dominate gas-phase chemistry in plumes from major NOx emitters during 

stages 1 and 2. Table 6-1 also shows the correspondence between GREASD PiG reactions and 

the complete gas-phase chemical mechanisms implemented in CAMx, namely CB05, CB6 and 

SAPRC99. This mapping is used in CAMx to set the rate constants and photolysis rates for 

GREASD PiG reactions from corresponding reactions in the grid chemical mechanisms. This 

implementation ensures consistency with these chemical mechanisms.

[ ] [ ]

[ ] 1

2

2 >

+

k NO

k CO k SO

OH

OH OH
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Table 6-1. List of 23 reactions for GREASD PiG including correspondence to CAMx reaction 

numbers in the CB05, CB6 and SAPRC99 mechanisms.

Chemical Mechanism for GREASD PIG 

Corresponding Reaction 

Number for Grid Chemistry 

Number Reaction CB05 CB6 S99

1 NO2 = NO + O 1 1 1

2 O + O2 + M = O3 + M 2 2 2

3 O3 + NO = NO2 3 3 7

4 NO + NO + O2 = 2 NO2 22 24 10

5 1 NO + NO2 + H2O = 2 HONO 23 41 N/A

6 O3 = O1D 9 9 18

7 O1D + M = O + M 10 10 20

8 O1D + H2O = 2 OH 11 11 19

9 HONO = NO + OH 25 43 22

10 NO2 + OH = HNO3 28 45 25

11 NO2 + O3 = NO3 7 26 8

12 NO3 = NO2 + O 14 27 16

13 NO3 = NO 15 28 15

14 NO3 + NO = 2 NO2 16 29 9

15 NO3 + NO2 = NO + NO2 17 30 14

16 NO3 + NO2 = N2O5 18 36 11

17 N2O5 = NO3 + NO2 21 37 12

18 2 N2O5 + H2O = 2 HNO3 19 39 13

19 SO2 + OH = SULF + HO2 63 52 44

20 OH + CO = HO2 66 123 29

21 FORM = 2 HO2 + CO 75 97 123

22 FORM = CO 76 98 124

23 HO2 + NO = OH + NO2 30 25 31

1. Rate for GREASD PiG reaction 5 set to zero when used with SAPRC99.

2. Rate for GREASD PiG reaction 18 may be enhanced by reaction on aerosol.

The GREASD PiG performs gas-phase chemistry for only those chemical species emitted directly 

into the plume, and does not include the influence from any background compounds on the 

grid except for ozone, carbon monoxide, and formaldehyde. Assuming zero background for gas 

species is reasonable for the early stages of NOx plumes because puff concentrations are orders 

of magnitude larger than ambient concentrations. On the other hand, background ozone, 

carbon monoxide, and formaldehyde are the primary sources of oxidants in the condensed 

mechanism that drive inorganic processing of plume NOx to other forms of oxidized nitrogen 

(NOz), so these are handled as “incremental” species as described below for IRON PiG. The 

Livermore Solver for Ordinary Differential Equations (LSODE) is used to solve the condensed 

mechanism in double-precision, regardless of the user-chosen solver employed for the grid 

chemistry.
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6.3 Particulate Matter In PiG

Non-linear effects and errors in gas-phase chemistry are transmitted to (and potentially 

amplified by) the PM aqueous chemistry and partitioning algorithms. The implementation of 

PM and PSAT in PiG prompted the need to limit the impact of such issues similarly to the 

constraints imposed by OSAT for gas-phase chemistry. Therefore, PM and PSAT can only be run 

using the GREASD PiG option. As for gas-phase chemistry, only inorganic PM chemistry is 

treated by GREASD PiG.

The GREASD PiG gas-phase chemistry oxidizes NOx and SOx emissions to nitric and sulfuric 

acids, which are PM precursors. To maintain consistency with the grid chemistry, aqueous PM 

chemistry (RADM-AQ) is then performed at every time step if the puff resides in a cloudy grid 

cell. However, inorganic gas/PM partitioning (performed by ISORROPIA) among sulfate, nitrate 

and ammonia is not performed by GREASD PiG, but is delayed until the masses of these 

compounds are dumped to the grid. Additionally, chemistry and partitioning for secondary 

organic aerosols is not performed.

Note that the PiG PM treatment was designed specifically for the static 2-mode PM chemistry 

only (CF), and will not operate for the multi-section PM chemistry (CMU). 

6.4 IRON PiG

The IRON PiG model incorporates a complete treatment of gas-phase chemistry in point source 

pollutant plumes, while secondarily adding additional features central for treating toxic 

pollutants not normally carried by the standard CAMx chemical mechanisms. Therefore the 

IRON PiG can treat a wide variety of point source emissions, including VOC sources.

Several approaches have been developed to treat photochemistry within point source plume 

models. One of the more elegant methodologies is the incremental chemistry idea embodied 

in the SCICHEM model (EPRI, 2000). However, we found that the implementation of 

incremental chemistry in SCICHEM is very complex, especially in its handling of the chemistry of 

overlapping puffs, and is not sufficiently flexible to allow for the adaptation of numerous 

chemistry mechanisms and solvers.

We adopted the incremental idea for IRON PiG whereby each puff carries concentrations 

relative to ambient background. This results in the possibility of both positive and negative puff 

concentrations depending on how the chemistry evolves. The full gas-phase chemistry 

mechanism chosen for a given run (CB05, CB6 or SAPRC99) is solved twice for each puff at each 

time step: first for the vertically-averaged background concentrations from the grid cells 

vertically spanned by the puff; and second for the sum of puff and background concentrations. 

The LSODE solver is used to solve both chemistry steps, regardless of the user-chosen solver 

employed for the grid chemistry. After both steps are completed, the updated background 

concentrations are subtracted from the updated puff+background concentrations, yielding the 

new puff incremental concentrations. These new puff increments are subsequently advected 

and dispersed by the transport portions of the PiG code.
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Note that the updated background concentrations, which may include “virtual dumps” of mass 

from large overlapping puffs (described below), are used for reference only in the puff 

incremental chemistry algorithm; the actual grid concentrations are not affected and are 

separately solved by the grid chemistry routine.

6.5 PiG Features

This section describes specific features of the PiG submodel; certain features are always active 

while others can be optionally invoked for a particular CAMx run. The IRON PiG sub-model 

includes two constructs designed specifically to facilitate the incremental chemistry approach:

• The concept of “virtual dumping” to handle the chemical impacts of large puffs that can 

overlap other puffs within a given grid column;

• The concept of multiple puff “reactor” cells to account for the chemical effects of 

concentration distributions within each puff.

Each of these is described below.

6.5.1 Puff Layer Spanning (IRON and GREASD)

The PiG is designed to chemically process point source plume mass within streams of puffs until 

such time that each puff can be adequately resolved on the horizontal grid. Puffs are allowed 

to vertically span multiple grid model layers before they reach horizontal grid scales. This 

introduces technical implications for defining “background” concentrations and ambient 

conditions for puff chemistry, as well as for transferring plume incremental mass to the grid. 

The solution employed is to:

1) Assume that the vertical distribution of puff concentration is always uniform; 

2) Distribute puff mass transfer (via “leaking” and “dumping”) to the grid according to the 

puff fractional coverage across each model layer and by density-weighting; and

3) Determine mean background concentrations and other ambient conditions (e.g., 

temperature, humidity, etc.) over the puff vertical span via similar fractional layer-density 

weighting.

Horizontally, the mean background concentration and ambient conditions are taken from the 

single host grid column containing each puff center point, even if the puff is large and/or spans 

a horizontal cell interface. As described earlier, puffs are considered to be elliptical in the 

horizontal, with the minor axis spanning the cross-wind puff width (defined as ±1.5σy), and the 

major axis spanning the along-wind puff length (defined as length ±1.5σy on each end). 

However, given the complications associated with multiple layers spanning and mass-weighting 

of ambient inputs and dumped mass, puffs are rectangular and uniform in the vertical, with 

total puff depth defined as ±1.5σz.

6.5.2 Puff Overlap and the Idea of Virtual Dumping (IRON only)

The chemical effects of puff overlap were considered to be an important attribute of IRON PiG. 

However, we wished to maintain a relatively simple approach, while appropriately accounting 
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for the largest probable effects. We assume that the largest effect is the condition in which 

older expansive puffs span significant fractions of their host grid cell, thereby potentially 

overlapping all other puffs contained within the same cell. Instead of geometrically 

determining fractional overlap puff-by-puff, we instead introduce a process that we refer to as 

“virtual dumping.” 

For a given grid column, the mass from all puffs determined to be “sufficiently” large are 

temporarily dumped to the column, distributed according to each puff’s vertical layer span, and 

added together along with the pre-existing grid concentrations. This process is referred to as a 

“virtual dump” of puff mass to the grid column. The criteria to determine a “sufficiently” large 

puff is the same that initiates puff mass leaking to the grid (as described below). In this 

approach, all large puffs contribute to the background chemistry step for other puffs occupying 

the same grid column. Double-counting is avoided by not including a puff’s contribution to the 

background while its specific background and incremental chemical calculations are performed.

6.5.3 Multiple Puff Reactors (IRON only)

Accounting for full chemistry potentially introduces significant non-linear effects that are highly 

dependent upon the distribution of pollutant mass within each puff. Especially for ozone, 

aircraft flights through power plant plumes have often recorded wide concentration variations 

relative to ambient conditions: within the plume core where NOx remains concentrated, ozone 

is often depressed and follows NO-NO2-ozone equilibrium, whereas on plume fringes where 

NOx is dilute and mixes with ambient VOC, ozone concentrations can exhibit concentration 

maxima. Past models have accounted for cross-plume chemistry variations through the use of 

reactors, with approaches ranging from multiple rectangular slabs to concentric shells. 

The user may select multiple reactors as well to sub-divide the puff. Any number of reactors 

may be chosen (the default is 1). Multiple reactors simply divide the total puff volume evenly, 

and the initial mass assignments for newly emitted puffs are made using the standard error 

function that results in an initial Gaussian-like mass/concentration distribution among the 

reactors. This provides a mechanism for simulating the differing chemical processing that takes 

place in various concentration regimes. As the purpose of the reactors is merely to represent 

the range of photochemical conditions that are likely to occur at various locations within the 

puff as it undergoes differential shearing and mixing, there is no particular physical orientation 

assigned to these reactors with respect to each other or to the puff as a whole. Thus, there is 

no communication (i.e., diffusional mass exchange) between the reactors. The same 

background concentration chemistry applies to all reactors of a given puff. When puff mass is 

leaked or dumped, all reactors shed the same relative fraction of mass.

In summary, chemistry is solved for each puff “reactor” in three steps:

1) The layer-mean background (grid + overlapping puff) concentrations and environmental 

conditions over the volume occupied by the puff are stored and then chemically updated 

via the LSODE gas-phase chemistry mechanism;

2) The pre-updated mean background concentrations are added to the puff increments and 

the total concentrations are chemically updated; and 
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3) The updated results from step 1 are subtracted from the updated results of step 2 to 

provide the updated incremental concentrations.

6.5.4 Puff Dumping (IRON and GREASD)

Mass transfer from puff to grid can happen in two ways: slowly, termed “leaking”, or suddenly, 

termed “dumping.” As described earlier, all mass is transferred to the vertical grid structure in 

a density-weighted fashion according to each puff’s fractional layer coverage. The process of 

leaking ensures that puff mass is transferred to the grid continuously, rather than in discrete 

lumps of pollutants with very different concentrations than those in the grid. Sudden dumping 

can cause unphysical numerical shocks in the grid and can lead to unrealistic gridded 

concentration patterns that appear as “bulls-eyes”. The idea behind puff leakage is to account 

for turbulent shearing of mass from the main plume and its subsequent dispersion to the grid 

scale. This rate of transfer should be directly proportional to the puff size relative to the grid 

scale.

Puff leakage is controlled by comparing the horizontal area of a puff to a specified leakage 

parameter, defined as a fraction of horizontal grid cell area. When a puff is first emitted there 

is no leakage. As the puff grows in volume the concentrations within the reactors are reduced 

accordingly by dilution. When the puff area exceeds the leakage onset parameter, a fraction of 

the mass in each puff reactor is transferred to the grid. This fraction is determined by the 

relative exceedance of the leakage parameter; initial leakage is slow as the exceedance is 

relatively small, but leakage rates grow as the puff continues to grow beyond the leakage 

parameter. 

The reduced mass from leakage is compensated by a reduced effective volume, so that 

concentrations are not artificially diluted by leakage (an essential chemical imperative). Thus, 

two distinct volumes are tracked: the actual volume (defined by the puff spread σ) and the 

effective volume. While these are identical before leakage, they deviate after leakage is 

initiated, and thereafter the relative deformation of the actual puff volume (via diffusion, 

shearing, etc.) is used to scale the deformation of effective puff volume.

Eventually the horizontal span of the puff will exceed the grid cell area, and the remaining mass 

is then dumped all at once to the grid. However, because of the combination of photochemical 

processing and leakage, by the time a puff dumps the potential for producing numerical shocks 

is much reduced. Furthermore, if the puff exceeds a user-defined maximum age, puff mass is 

transferred to the grid at the rate of 10% per timestep.

6.5.5 PiG Rendering (IRON and GREASD)

While the mass confined to the puffs at any given time has not yet affected the grid 

concentrations, it will eventually, so it can be somewhat misleading to sequester this mass from 

visualizations of a model simulation. The puff mass can be optionally incorporated into the 

model average output files for visualization purposes (referred to as “PiG rendering”). 

Rendering employs a “virtual dump” of the puff masses into the average output concentration 

array each time step. As described for chemistry, virtual puff mass is added as an increment 

over the entire grid column according to fractional layer-density weighting over puff depth, 
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thus diluting it’s concentrations relative to that within the puff. The actual puff mass remains 

within each puff over the course of its lifetime, and the actual grid mass in unaffected until 

puffs are killed and their masses truly dumped into the grid. This visualization is available for 

either 2-D surface or 3-D average output files, and can produce some rather startling effects in 

output displays, including very narrow virtual plumes, or streaks, representing mass moving 

through the grid in sub-grid puffs, but not subject to grid-scale eddy diffusion.

6.5.6 High Resolution Puff Sampling (IRON and GREASD)

PiG optionally employs surface-layer puff sampling of CB05, CB6, or SAPRC99 species on a userdefined grid of arbitrary horizontal resolution, similarly to the way nested grids are defined. 

Sampling grids are entirely passive, and intended to provide a display of the plume 

concentrations at scales much smaller than typically used for the finest computational grids 

(i.e., <1 km), primarily around and downwind of a source complex. Sampled PiG concentrations 

are time-averaged like the output concentrations provided on the computational grids, and are 

written to files with similar format so that they may be readily viewed and manipulated with 

CAMx post-processing software. Additional information on configuring and using PiG sampling 

grids is provided in Sections 2 and 4.

Given that the puffs constantly evolve via diffusive growth and reshaping due to deforming 

shears, the sampling procedure includes trigonometric calculations to define which sampling 

points are influenced by each puff. This influence is determined according to the puffs’ twodimensional horizontal Gaussian shape shown in Figure 6-1. To include a sufficiently large 

percentage of mass across each puff for sampling, limits of ±3σx/y in both horizontal dimensions 

are used to define the puffs’ total elliptical area coverage. Puffs are only sampled if they extend 

vertically into the model’s surface layer.

Sampling grids are defined in the CAMx control file (see Section 2), and array dimensions must 

be set sufficiently large in the CAMx Fortran parameters file in ./Includes/camx.prm (see 

Section 2). An example of the type of plume detail that can be visualized using a sampling grid 

is provided in Figure 6-3. In this case, a very fine 200 m sampling grid is set within a 4-km 

computational grid.

6.6 Deposition

The CAMx PiG treats the removal of gas and PM species from each puff via deposition 

processes. Both dry and wet deposition calculations presented unique implementation issues 

for puffs. The most difficult issue for both forms of deposition was how to manage deposition 

exchange between puffs and the ground in the case of negative puff concentration increments.
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Figure 6-3. Example of a single point source PiG plume as depicted by a sampling grid with 

200 m resolution (shown by the extent of the plot; 40 km by 32 km total extent). This 

sampling grid was set within a CAMx computational grid with 4-km resolution. The source 

location is arbitrary and is emitting an inert tracer.

6.6.1 Dry Deposition

Dry deposition needs to consider the following: (1) the point at which puffs begin to deposit to 

the surface; (2) how to handle deposition through potentially deep puffs that may straddle 

several layers of varying stability since the puffs do not themselves resolve these stratifications 

or vertical concentration distributions; (3) managing deposition fluxes of negative 

concentration increments. Our solution to issue (1) was to ignore dry deposition within puffs 

until they diffusively grow to the ground, although in reality deposition occurs on roughness 

elements that extend some distance above the ground (trees, buildings, etc.). We 

implemented a criterion that the bottom of the puff must extend to or below the midpoint of 

the surface layer, or below 10 m (whichever is larger), in order for dry deposition to be active.

Issue (2) can be handled in a variety of ways and complexity. The current implementation 

institutes a simpler solution and we will consider more complicated improvements for future 

developments if evidence suggests that they would be necessary. PiG utilizes pre-computed 

species-dependent deposition velocities derived for the grids. Each puff in a particular grid cell 

is provided the host cell’s deposition velocities for each species, and these are used to 

determine the flux of mass through the fraction of puff depth occupying the model’s surface 

layer.

Issue (3) is unique to the incremental chemistry concept introduced with IRON PiG. The flux of 

material depositing to the ground is given by d F = c ⋅ v , where by the normal definition a 

positive deposition velocity vd leads to a positive deposition flux to the ground. If the puff 
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increment c is negative, then a negative flux is calculated (flux from ground to puff). This is 

appropriate if we consider the following argument. Dry deposition applied to a grid cell 

removes some pollutant mass from the entire volume. If there is a puff existing in that cell with 

a negative concentration increment, then the amount of mass removed from the cell was over 

estimated if we consider the puff’s contribution to total cell mass. The negative deposition flux 

calculated for this puff leads to the addition of mass to the puff increment. Adding mass to a 

negative increment reduces the magnitude of the increment, as expected for a deposition 

process. This mass is taken from the grid cell’s accumulated deposited mass to maintain 

accurate mass accounting within the model.

6.6.2 Wet Deposition

Wet deposition needs to consider the following: (1) how to handle scavenging of pollutants 

through potentially deep puffs that may straddle several layers of varying cloud and rain water 

contents but that do not themselves resolve vertical concentration distributions; (2) managing 

deposition fluxes of negative concentration increments in combination with the potential for 

mass to move in and out of rainwater as it falls (e.g., for slightly soluble gasses); (3) accounting 

for the initial pollutant concentrations in rainwater as they enter the top of each puff. 

It was important to maintain consistency between the treatment of wet deposition and the 

approach for puff chemistry. The chemistry relies on the assumption of vertically well-mixed 

puff reactors that can span multiple layers, and this is why layer-density weighted average 

ambient conditions are passed to the chemistry routines. To maintain this assumption for wet 

deposition, a single scavenging rate is applied through the entire puff depth as effectively a 

single layer of pollutant. This was found to be the simplest implementation approach. This 

single scavenging rate is calculated according to layer-density weighted average ambient cloud 

and rainwater contents.

Wet scavenging is performed throughout the entire depth of the puff to determine the amount 

of flux in or out of rainwater. Total concentrations (puff + background) are used to determine 

species-dependent scavenging rates using the identical algorithm as for grid removal. The rates 

are used to derive removal fractions, and these fractions are then applied directly to the puff 

incremental mass for each species. Removal fractions are considered positive for the standard 

case of mass moving from puff to rain. 

We further assume that the top boundary condition for rainwater entering the top of each puff 

is zero. This means that the removal fraction is always positive (from puff to rain) in the singlelayer puff. In contrast, for gridded concentrations the layer-by-layer buildup of slightly soluble 

species can lead to a reversal of fluxes (from rain to grid) if super saturation is diagnosed in a 

particular layer.

Note that negative puff mass increments in combination with a positive removal fraction lead 

to a reversal of the flux direction (rain to puff), but that is not allowed and in such cases wet 

scavenging is set to zero. We account for impacts on the mass budget appropriately by adding 

to the wet deposition mass array according to the net fluxes into rainwater. 
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6.7 PiG Configuration

Selecting the individual elevated point sources to receive the PiG treatment is accomplished by 

setting their stack diameters negative within the header (time-invariant point list) section of the 

CAMx input point source file. CAMx will run correctly with these negative diameters even if the 

PiG algorithm is not invoked. CAMx preprocessors exist to ease the procedure of ranking 

elevated point sources by emission rate and flagging the sources that the user wishes to treat.

Invoking the CAMx PiG sub-model is controlled by keywords in the CAMx control file 

(CAMx.in), as described in Section 2. The choices are:

PiG_Submodel = 'NONE',

PiG_Submodel = 'GREASD',

PiG_Submodel = 'IRON',

Note that the single choice between GREASD and IRON applies to all flagged point sources. It is 

not possible to make a single CAMx run with IRON PiG applied to a certain group of sources, 

and GREASD PiG applied to another group. Also note that GREASD must be selected to run PiG 

with OSAT, PM and PSAT; IRON must be selected to run PiG with the RTRAC Probing Tool. 

Several additional parameters are used to configure the PiG. It is important to note that all PiG 

configuration parameters exist in the CAMx Fortran parameters file 

(./Includes/camx.prm), as described in Section 2. PiG parameters are grouped together 

and briefly described at the end of that file. By effectively configuring the PiG submodel in the 

code, the default PiG configuration (as recommended by the model developers) is preset within 

the model distribution and alleviates the need for users to select settings on their own.

The default values are shown below:

parameter ( MXPIG = 50000 ) 

parameter ( MXRECTR = 1 )

 parameter ( FLEAK = .25 )

 parameter ( LEAKON = .FALSE. )

 parameter ( LVISPIG = .FALSE. )

 parameter ( OVERLAP = .FALSE. )

 parameter ( DXYMAX = -10000. )

 parameter ( AGEMAX = 18.*3600. )

parameter ( PIGMXDT = 300. )

parameter ( SHRFLG = 1 )

Users should exercise thoughtful consideration when altering these default values. A 

description of each of the remaining parameters is provided below, along with guidance in 

setting values.
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6.7.1 Guidance on the Use of CAMx PiG

6.7.1.1 PiG Keyword

The PiG keyword controls whether the PiG option is to be invoked in a CAMx simulation, and 

whether the emissions are treated with the GREASD or IRON options. This keyword can be 

switched from NONE to GREASD or IRON on a model restart to invoke the PiG treatment at any 

point during a multi-day simulation. To allow for this, it is not mandatory to provide CAMx with 

a pre-existing PiG output file upon a model restart – CAMx will not stop if this file is missing. It 

is recommended that this file be provided on all subsequent restarts since the PiG output file is 

needed to reinitialize the PiG module, otherwise all mass contained in puffs at the end of the 

previous run will be lost. If the PiG keyword is switched to NONE on a model restart, CAMx will 

continue the simulation without PiG, but all mass contained in puffs at the end of the previous 

run will be lost.

• Guidance:

- Invoke GREASD or IRON PiG at any point during a multi-day simulation, or none at all. 

Once PiG is started, provide CAMx with the PiG output file from the previous run for 

all subsequent model restarts so that no point source mass is lost.

- GREASD PiG should be invoked for large NOx point sources only, since it does not 

provide any organic chemistry. GREASD PiG supports PM chemistry (CF but not CMU). 

It can be run in conjunction with the OSAT and PSAT Probing Tools. It does not 

support DDM, PA, or RTRAC.

- IRON PiG can be invoked for any point source to treat gas-phase chemical evolution 

using CB05, CB6 or SAPRC99 mechanisms. IRON PiG does not treat particulate 

chemistry. It can be run in conjunction with the RTRAC Probing Tool. It does not 

support OSAT, PSAT, DDM, or PA.

Both GREASD and IRON options use the LSODE chemistry solver exclusively, so users will notice 

an impact on run time, particularly if many (~thousands) puffs are to be tracked, and IRON PiG 

is invoked (2 solutions of full photochemistry for each puff), and IRON puffs are configured with 

many puff reactor cells (full photochemistry solutions each). Since GREASD chemistry is simpler 

and the lifetime of GREASD puffs are much shorter than their IRON counterparts, GREASD PiG 

will run faster than IRON PiG for the same number of flagged sources. PiG chemistry is 

internally parallelized using OMP to maximize PiG speed performance.

6.7.1.2 Number of PiG Puffs

MXPIG sets the maximum number of PiG puffs to be expected during a simulation. It is used to 

statically allocate memory arrays for the PiG sub-model. A value of 10,000 is usually sufficient 

for most applications in which PiG is used; set this parameter to 1 if PiG is not used to conserve 

memory. If this parameter is exceeded during a simulation, the model will halt. If this happens, 

simply increase MXPIG, recompile the model executable, and restart the simulation.

• Guidance: Use the default value for most simulations, or set to 1 if PiG is not to be used. 

If the model stops because MXPIG is exceeded, increase its value, recompile, and restart 

the model.
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6.7.1.3 Number of PiG Reactors (IRON only)

MXRECTR sets the number of puff reactors; when greater than 1, each puff is separated into 

that number of reactor cells and primary emissions are apportioned among them using a 

Gaussian distribution. Since chemistry is performed for each individual reactor cell (both 

background and puff+background), this parameter can affect the speed of chemical 

computations in the PiG. We have not seen a significant sensitivity to values greater than 1, but 

testing for each application is warranted.

• Guidance: Use the default of 1 for initial simulations, but test the sensitivity to this 

parameter for each unique application.

• Reactors greater than 1 are not allowed for GREASD PiG.

6.7.1.4 Leakage Parameters

FLEAK, LEAKON, and DXYMAX together control puff leakage to the computational grid and 

ultimately puff termination. When LEAKON is true, FLEAK and DXYMAX control when puffs 

begin to leak portions of reactor mass to the grid along their trajectory. When LEAKON is false, 

no leaking is performed and puffs maintain all of their mass until they reach sizes for 

termination, at which point all mass is directly introduced to the grid at that point. DXYMAX 

sets the maximum dimension that puff size will be compared to for leaking and termination:

when it is zero, puff size will be compared to grid area only; when it is positive, puff size will be 

compared to the value of DXYMAX regardless of grid resolution; when it is negative, puff size 

will be compared to DXYMAX or grid resolution, whichever is smaller. FLEAK is the relative

fraction of horizontal puff area to cell area (or DXYMAX) above which leaking will begin and 

continue until sufficient mass is shed and the puff is terminated. In the example above, puffs 

will begin to leak mass when they reach 25% of the host grid cell’s area.

• Guidance: If LEAKON is set to true, maintain FLEAK at the default value of 0.25. Then test 

model sensitivity to different values of FLEAK and/or DXYMAX.

• Guidance: We suggest leaving DXYMAX = -10000, meaning puffs will be terminated when 

they reach the grid scale or 10 km, whichever is smaller. Puffs exceeding this size are 

usually well-aged and go beyond reasonable assumptions of puff coherence (also see 

AGEMAX parameter below).

• Leaking is not allowed when PiG is run with PM.

6.7.1.5 Overlap Flag (IRON only)

OVERLAP controls whether puff overlap is to be treated in the background chemistry step. As 

stated earlier, puffs only overlap if they meet the size criteria for leaking; all puffs smaller than 

this size do not overlap any other puffs in the same grid cell.

• Guidance: We recommend that the OVERLAP flag remain set to the default value of 

“false”.

• Overlap is not allowed for GREASD PiG.
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6.7.1.6 Virtual Puff Rendering

LVISPIG is a flag that turns on puff “rendering” to the computational grid average 

concentrations. When it is false, the chemical effects of puff mass are not seen on the output 

average files until they either begin to leak mass to the grid and/or they are terminated and 

their mass is entirely introduced to the computation grid. However, when the flag is true, all 

puff mass that resides in each grid column is summed, apportioned vertically to each grid cell 

according to puff vertical extent (via density and layer-depth weighting), converted to 

concentrations, and added to the average gridded concentrations for output. This process is 

referred to as rendering since the effects of all puff mass can be readily visualized in the CAMx 

output.

• Guidance: This option has no impact on the actual CAMx chemical solution. However, 

output average concentration files will be affected by puff rendering, and therefore could 

impact graphics of CAMx results and model performance measures.

• Virtual dumps are not allowed when PiG is run with PM.

6.7.1.7 Maximum Puff Age

AGEMAX is the age limit for all PiG puffs (IRON and GREASD). When puffs reach this age limit, 

they are terminated and all of their mass is transferred to the host grid. 

The assumption of a stream of coherent puffs becomes less valid with time as horizontal and 

vertical wind shears increase plume spread. At some point the plume mass is better resolved 

on the grid than within puffs. In CAMx the rate of puff expansion most often determines this 

transfer of mass, and the maximum puff age provides a safety check to ensure that puffs do not 

persist for unrealistic times in stable environments. The maximum puff age should be set long 

enough to allow puffs to persist overnight, but a lifetime of longer than a day is probably not 

realistic.

• Guidance: limit puff age to 12-24 hours – we find that 18 hours works best since it will 

allow puffs emitted in the late afternoon to last through the night and into the following 

morning. The purpose is to restrict growth-limited puffs to terminate overnight simply as 

a result of age constraints. Twelve hours is seen to be too short in this regard; puffs 

usually do not reach 24 hours of age before being terminated by grid constraints.

6.7.1.8 Maximum Puff Release Interval

PIGMXDT sets the maximum frequency of release and by default is set to 300 seconds (5 

minutes). This value should be adequate for most applications. However, if the user wishes to 

improve plume resolution by increasing the number of puffs, the frequency of release can be 

increased by reducing the value of PIGMXDT. This value supersedes the automated puff release 

rate that is determined by wind speed and grid size.

• Guidance: Maintain the default value of 300 s and allow PiG to use the automated PiG 

release frequency. Set to a lower value if better plume resolution is desired; note that 

more puffs will be released and this could slow the model markedly.
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6.7.1.9 Effects of Wind Shear on Puff Growth Rates

SHRFLG sets the approach by which to apply the effects of explicitly resolved (grid scale) wind 

shear on puff growth rates. There are three options available to the user: 

0 = shear is never applied;

1 = shear is applied only within the neutral/unstable boundary layer;

2 = shear is always applied.

• Guidance: The application of wind shear can lead to large growth rates, especially during 

stable conditions at night, and this may over-dilute puff concentrations, lead to early 

transfer of puff mass to the grid, and have markedly reduced impacts on next-day ozone. 

Shear has less relative impact on growth rates during the daytime because turbulent 

growth on its own leads to rapid plume dilution. For these reasons, the default is to 

ignore the effects of shear during the night or when puffs are above the boundary layer. 
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7. OZONE SOURCE APPORTIONMENT TECHNOLOGY

7.1 Introduction

Photochemical grid models are used to develop NOx and/or VOC emission reduction strategies 

to attain ozone air quality objectives. Traditionally, the development of an ozone attainment 

strategy involves iteration through many photochemical grid model scenarios to identify which 

pollutants, source categories and source regions should be controlled. It is impractical to 

analyze every potential control strategy and so there is potential for implementing controls on 

sources that contribute little to the high ozone levels or, conversely, not controlling sources 

that do contribute.

ENVIRON developed an ozone source attribution approach that has become known as the 

“Ozone Source Apportionment Technology”, or OSAT (Yarwood et al., 1996). This method was 

originally implemented in the Urban Airshed Model (UAM) and was then built into CAMx3

. 

OSAT provides a method for estimating the contributions of multiple source areas, categories, 

and pollutant types to ozone formation in a single model run. The capabilities of OSAT are 

summarized below along with an assessment of the strengths and limitations of the approach. 

The main challenges in developing and implementing a methodology to track the relationships 

between separate groups of emission sources and ozone formation are:

• Accounting not only for the presence of ozone precursors from a given source region at a 

given receptor location, but also accurately estimating the cumulative contribution to 

ozone production of those precursors while they were en-route to the receptor.

• Ensuring compatibility with the underlying air quality model formulation so that derived 

source-receptor relationships are consistent with model results for total concentrations.

• Providing sufficient spatial and temporal resolution while managing, within practical 

constraints, the computer resources required to run the software tool. 

OSAT uses multiple tracer species to track the fate of ozone precursor emissions (VOC and NOX) 

and the ozone formation caused by these emissions within a simulation. The tracers operate as 

spectators to the normal CAMx calculations so that the underlying CAMx predicted 

relationships between emission groups (sources) and ozone concentrations at specific locations 

(receptors) are not perturbed. Tracers of this type are conventionally referred to as “passive 

tracers,” however it is important to realize that the tracers in the OSAT track the effects of 

chemical reaction, transport, diffusion, emissions and deposition within CAMx. In recognition 

of this, they are described here as “ozone reaction tracers.” The ozone reaction tracers allow 

ozone formation from multiple “source groupings” to be tracked simultaneously within a single 

simulation. A source grouping can be defined in terms of geographical area and/or emission 

category. Figure 7-1 provides an example of the way that a CAMx domain can be sub-divided 

into multiple source areas – 40 in this example. Also, the emission inventory could be sub- 

 3 Note that the formulation of the Ozone Source Apportionment Technology differs slightly from earlier versions in that it 

accounts for the fact that ozone production and destruction occur simultaneously as it apportions ozone change among 

tracers. Previously, OSAT only considered the net change in ozone in the apportionment algorithm. The approach is 

described later in this section.
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Figure 7-1. Example of the sub-division of a CAMx domain into separate areas for geographic 

source apportionment. 

divided into several source categories – two emission categories over 40 source regions would 

produce 80 separate source groupings. So that all sources of ozone precursors are accounted, 

the CAMx boundary conditions and initial conditions are always tracked as separate source 

groupings. The methodology is designed so that all ozone and precursor concentrations are 

attributed among the selected source groupings at all times. Thus, for all receptor locations 

and times, the ozone (or ozone precursor concentrations) predicted by CAMx is attributed 

among the source groupings selected for OSAT. The methodology also estimates the fractions 

of ozone arriving at the receptor that were formed en-route under VOC- or NOX-limited 

conditions. This information indicates how ozone concentrations at the receptor will respond 

to reductions in VOC and NOX precursor emissions.

An example display of the type of ozone source apportionment information available from 

OSAT is shown in Figure 7-2. The figure shows information for the location of the region wide 

maximum hourly average ozone concentration (the hourly peak) for an example OSAT run (this 

run had 17 geographical source areas and a single emission group). Summary information for 

-95 -90 -85 -80 -75 -70

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scenario and receptor is shown in the center. At top left, a bar chart shows how the total 

amount of ozone was attributed between initial conditions, boundary conditions and emissions, 

Figure 7-2. Example display of ozone source apportionment information provided by OSAT 

for a run with 17 source areas and 1 emission group.

with the emissions contribution being divided between ozone formed under VOC and NOX

limited conditions. At top right, a pie chart shows the relative ozone contributions from initial 

conditions, boundary conditions and emissions, with the emissions contributions broken out by 

numbered geographical source areas. Only the source areas with the largest ozone 

contribution are shown, the remaining source areas are lumped together under “All Others.” 

The display shown in Figure 7-2 is only one of many ways in which OSAT results can be 

displayed to gain insight into ozone source-receptor relationships predicted by CAMx.

An important feature of the ozone reaction tracer approach used in OSAT is that the normal 

CAMx calculations are not perturbed; thus, OSAT estimates the same total ozone and precursor 

Contributions By Type Contributions By Source Area

 Receptor = HourlyPeak

Time = 16 To 17

Date = 8/28/87

Scenario = Evaluation Test 

Total Ozone = 183 ppb

 

 

 

 

 

 

 

 

0

20

40

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Ozone (ppb)

NOx limited

VOC limited

Boundary

Initial

IC

12%

BC

14%

7, 1

19%

6, 1

16%

10, 1

14%

17, 1

7%

16, 1

7%

13, 1

4%

All Others, 

7%
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concentrations as CAMx. Further, since the same inputs are used for meteorology, emissions 

etc., and the same numerical methods are employed throughout the model, the sourcereceptor relationships developed by OSAT inherently have a high degree of consistency with 

those present in CAMx. The level of consistency between the source-receptor relationships 

developed by OSAT and CAMx is limited by three factors:

• The completeness of the conceptual methodology underlying the source apportionments;

• The limitations of the numerical methods employed by CAMx; and 

• The non-linear nature of the ozone formation process.

The completeness of the source apportionment methodology was analyzed by performing a 

series of evaluations of OSAT results against UAM sensitivity tests (Yarwood et al., 1996). These 

tests showed that the OSAT performed well in predicting both the spatial impacts of emissions 

from given source regions and the relative contributions of separate emission regions/groups to 

ozone. OSAT cannot overcome numerical limitations inherent to CAMx (as well as other grid 

models). The UAM evaluation tests referred to above suggested that a potentially serious

numerical limitation was its horizontal advection solver. As discussed below, the non-linear 

numerical limitations of advection algorithms were addressed in the OSAT design. This issue 

was one of the primary reasons for incorporating the Bott (1989) and PPM (Colella and 

Woodward, 1984) advection algorithms into CAMx and redesigning the three-dimensional 

transport scheme to be more mass consistent. Further, the tracer transport routines were 

modified to directly use the advective fluxes diagnosed by the regular model advection solvers 

to minimize inconsistencies between tracers and regular model species.

The biggest limitation of this, or any other, ozone source apportionment approach likely results 

from the third factor mentioned above: namely, the non-linear nature of the chemical 

interactions between emissions from different source groupings. This means that as soon as 

the emission inventory is perturbed, the source receptor relationships begin to change. Thus, 

OSAT can only estimate the contribution to ozone from a specific source grouping under the 

current emissions scenario. It cannot directly quantify the ozone reductions that will result 

from an emission control strategy because the CAMx response may well be non-linear with the 

magnitude of the control applied (e.g. 20 percent or 60 percent control) and the 

presence/absence of other simultaneous controls on other source groupings. 

However, this fundamental truth of photochemical modeling does not limit the usefulness of 

OSAT: arguably it increases its usefulness. At any rate, it suggests the following approach to 

control strategy development with OSAT. For the base CAMx scenario, OSAT could be used to 

identify specific source groupings for which ozone reductions from emissions controls would be 

maximized. Just as important, OSAT will identify source groupings for which emissions controls 

are not effective at reducing ozone concentrations. The most effective and feasible control 

measures identified in this way can be applied to the emission inventory, leading to a revised 

CAMx scenario with different (lower) emissions. If additional controls are needed, OSAT could 

be applied again to identify the most effective control measures under the new conditions. 

Development of the control plan will still proceed by an iterative process, but OSAT can be used 
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to guide the process to develop (and justify) more refined, better-targeted and more costeffective ozone control strategies.

7.2 OSAT Formulation

CAMx has been extended to accommodate extra tracer species needed to perform ozone 

source apportionment. For each user-specified source grouping (geographical area/emissions 

category) ozone reaction tracers track the fate of ozone precursor (NOX and VOC) emissions 

plus the ozone formation attributed to those emissions. The methodology requires that all 

ozone precursors be tracked so that all contributions to ozone can be accounted for, thus ozone 

and precursors originating from the model boundary and initial concentrations are also tracked 

as separate source groupings.

There are four ozone-reaction tracers per source area to account for the contributions of 

emissions of separate source areas to the complex process of the ozone formation activity. It is 

important to recall that the mass of NOX or VOC from a given source area that may be present 

at a given receptor at a selected hour is often not particularly relevant to the amount of ozone 

present there at that time. Rather, it is the contribution to ozone formation activity of source 

areas’ NOX and VOC emissions en-route to a receptor that must be determined. The ozonereaction tracers are designed to integrate these en-route contributions to ozone 

production/destruction activity.

Ozone formation involves both NOX and VOCs, and the NOX and VOCs participating in ozone 

formation in any particular grid cell/time step may have originated from different source 

groupings. The ozone formation process can be controlled more by the availability of VOCs or 

NOX, depending upon the relative abundance of both precursors, and ozone formation is 

described either as VOC limited or NOX limited, respectively. When ozone production at a given 

location and time is NOX limited it makes sense to attribute ozone production to source 

groupings based on their contributions to the local NOX and similarly to allocate based on VOC 

contributions when ozone formation is VOC limited. Consequently, separate tracers are used to 

track ozone formation occurring under NOX and VOC limited conditions. The criterion used to 

determine whether ozone formation is occurring under locally NOX or VOC limited conditions is 

described in detail in a separate section below.

The four types of ozone-reaction tracers that are tracked for each source grouping (i.e., 

geographic area/source category, boundary conditions or initial conditions) are explained 

below. The name of each tracer uniquely identifies the source grouping it represents:

Ni = NOX tracer for source grouping i. Emitted with the same spatial and 

temporal distribution as NOX emissions for source grouping i. Decays with 

local dNOX/dt for each grid cell/time step.

Vi = VOC tracer for source grouping i. Emitted with the same spatial and 

temporal distribution as VOC emissions for source grouping i. Decays with 

local dVOC/dt for each grid cell/time step. Note that VOC tracers are defined 

as single carbon species, so their concentrations are numerically equal in ppb 

and ppbC units.
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O3Vi = Tracer of ozone formation under VOC limited conditions attributed to source 

grouping i. If ozone formation is determined to be VOC-limited for a given 

grid cell/time step, O3Vi is formed in proportion to local dO3/dt in 

proportion weighted by the distribution of VOC precursors (Vi).

O3Ni = Tracer of ozone formation under NOX limited conditions attributed to source 

grouping i. If ozone formation is determined to be NOX-limited for a given 

grid cell/time step, O3Ni is formed in proportion to local dO3/dt in 

proportion weighted by the distribution of NOX precursors (Ni).

7.2.1 Mass Consistency with CAMx

The ozone reaction tracer methodology was designed to be inherently mass consistent with 

CAMx. In other words, the sums of the individual ozone, NOX, and VOC tracers (i) should 

remain consistent with their standard CAMx counterparts as follows:

3 3 3

2

O V O N O

V VOC C

N NO NO

i i

j i j

i

+ =

= ×

= +

∑ ∑

∑ ∑

∑

Note that VOC tracers are weighted by the carbon number of each VOC species (Cj). The 

validity of these relationships was evaluated and it was found that the chemistry, emissions, 

deposition, horizontal diffusion, and vertical diffusion algorithms maintained mass consistency 

on an overall and cell-by-cell basis. However, it was found that the horizontal and vertical 

advection algorithms inherently maintained mass consistency on an overall basis, but not a cellby-cell basis. Accordingly, the advection algorithms for the ozone reaction tracers were 

modified as described below to maintain mass consistency.

7.2.2 Emissions

The tracer families, Ni and Vi, track NOX and VOC emissions from each source grouping to allow 

attribution of ozone formation as it occurs throughout CAMx. The rates of emission of the Ni

and Vi tracers are set equal to the total NOX and VOC emissions in the inventory for a source 

grouping, respectively. For the Vi tracers, the emissions are set equal on a ppmC basis. For the 

initial condition (IC) source grouping, the NIC and VIC tracers are initialized from the CAMx initial 

concentration fields and receive no more mass input after the start of the simulation. For the 

boundary condition (BC) source grouping, the fluxes of NOX and VOC entering CAMx from the 

boundaries are effectively interpreted as emissions of the NBC and VBC tracers at the model 

boundaries. Unlike emission source groupings, boundary and initial conditions also introduce 

ozone directly into CAMx. Since there is no way of determining whether the ozone in the 

boundary and initial conditions was formed under VOC or NOX limited conditions, this ozone is 

divided equally between O3N and O3V tracers. However, subsequent ozone formation within 

CAMx from boundary and initial condition VOCs and NOX is allocated to O3V and O3N tracers 
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on the basis of whether ozone formation occurred under VOC or NOX limited conditions 

(discussed below).

7.2.3 Deposition

The Ni, Vi, O3Ni and O3Vi tracers are deposited at rates determined by the standard CAMx 

deposition calculation on a surface grid cell by grid cell basis. For NOX, the deposition velocity 

for each tracer Ni [Vd( Ni)] is set equal to the concentration weighted average of the deposition 

velocities for NO and NO2:

Similarly, the deposition velocity for each tracer Vi is set equal to the concentration weighted 

average of the deposition velocities for the VOC species (the concentration weighting is 

performed on a ppmC basis). The deposition velocity for the O3N and O3V tracers is set equal 

to the ozone deposition velocity. Gridded fields of deposited OSAT tracer mass can optionally 

be output to a file for viewing or reporting.

7.2.4 Transport and Diffusion

Originally, the Ni, Vi, O3Ni and O3Vi tracers were advected and diffused by the CAMx 

algorithms. As mentioned above, testing of OSAT showed that the CAMx advection routines did 

not accurately preserve the spatial relationships between ozone reaction tracers and their 

corresponding CAMx species (i.e., between the sum of the O3V and O3N species and CAMx O3). 

The distortion in any single model time-step was small, but the distortion built up over time to 

unacceptable levels. This was caused by non-linear dependences on the gradients of the 

advecting material, which can differ substantially between the standard model species and 

each of the OSAT tracers. This resulted in OSAT predictions that differed from the standard 

CAMx concentrations.

Such an outcome was inconsistent with the objectives in developing OSAT, so an alternative 

approach was adopted. As the horizontal and vertical transport operations are carried out for 

all CAMx species, the individual advective fluxes for ozone and each NOx and VOC species are 

reported by the advection solvers. The ozone and individual NOx and VOC fluxes are combined 

(and weighted by carbon number for VOC) and normalized by their respective weighted mean 

concentrations prior to advection. The equations below summarize this process, where f iis the 

flux of the core model species into or out of cell i, C is VOC carbon number, and F i

is bulk 

normalized flux:

( ) ( ) ( ) (1)

2

2 2

NO NO

NO V NO NO V NO V N D D

d i

+

× + × =
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i

i

i O

O

OLE

i

PAR

i

OLE

i

PAR OLE

i

i PAR

VOC

i i

i

NO

i

i NO

NOx

O

f F

PAR C OLE C

f C f C F

NO NO

f f F

3

...

...

2

3

3

2

=

× + × +

× + × + =

+

+ =

These bulk normalized fluxes are used to advect each tracer species directly, rather than 

sending the tracers through the advection algorithms. This approach has significantly improved 

consistency between tracer and regular model concentrations.

The OSAT tracers are sent to the standard CAMx routines for vertical diffusion and horizontal 

diffusion. Since small deviations sometimes occur between the OSAT tracer concentrations and 

the regular CAMx species (due to numerical limitations), the ozone reaction tracer 

concentrations are renormalized after transport to be consistent with the standard CAMx 

concentration fields. The renormalization is applied in the same subroutine as chemical change 

because this is computationally efficient.

7.2.5 Chemical Change

The Ni tracer mass in each grid cell at each time step decays according to the chemical change 

in the CAMx predicted NOX (∆NOX) weighted by the tracer contribution to the total of NOX

tracers from all source groupings:

The Vi tracer mass in each grid cell at each time step decays according to the chemical change 

in the CAMx predicted VOC (∆VOC) weighted by the tracer contribution to the total of VOC 

tracers from all source groupings. However, because the reactivity of VOCs from different 

source groupings can be different, a weighting factor based on the OH-reactivity of each V

tracer (kOHi) is also introduced. The kOHi for each source grouping is calculated at the start of 

each simulation period (typically one day) by averaging the OH rate constants of the speciated 

VOC emissions for each source grouping. The V tracer mass in each grid cell at each time step 

decays at a rate determined by the following equation:

The O3N and O3V tracers for each source grouping accumulate a weighted fraction of the 

ozone production activity (PO3) and ozone destruction activity (DO3) that occurs in each grid 

(2)

∑ = + ∆ × old

i

old

i

x

old

i

new

i

N

N N N NO

(3)

∑ ×

× = + ∆ ×

i

old

i

i

old

old i

i

new

i

V kOH

V kOH V V VOC
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cell at each time step. The process of apportioning PO3 and DO3 across O3N and O3V tracers 

occurs as follows:

1) Determine whether the local (grid cell/time step) ozone production process is NOX or VOC 

limited. As described in detail below, the determination is based on the ratio of the local 

HNO3 and H2O2 production rates. If the H2O2/HNO3 production ratio is greater than 1/3 

during a time step, then ozone formation is NOX limited. If this ratio is less than or equal 

to 1/3, then ozone formation is VOC limited.

2) For allocating ozone production under conditions determined to be:

(a) NOX limited: allocate PO3 across O3N tracers

(b) VOC limited: allocate PO3 across O3v tracers based on maximum 

incremental reactivity (MIR) factors

3) For ozone destruction, allocate across all ozone tracers.

where X = N or V.

This is the algorithm used for OSAT. The GOAT and APCA methods use different algorithms for 

allocating ozone production, as described below. 

The MIRs used in equation (5) are the weighted average MIRs for the emissions in each source 

group. The MIR approach was developed by Carter (1994) to approximate the ozone forming 

potential of VOCs accounting for both kinetic and mechanistic reactivity effects. The MIR 

represents the ozone formation potential of the VOC mixture accounting for the VOC reactions 

with OH as well as the effects of all of the VOC products that produce ozone formation. The 

VOC + OH reaction is the main VOC destruction mechanism so it is appropriate to weight the 

VOC destruction across the VOC reactive tracers by their composite reaction rate with OH 

(kOH). The MIR factors for the CAMx SAPRC99, CB05, and CB6 mechanisms are shown in Tables

A-3, B-3, and C-3, respectively.

7.2.5.1 Accounting for Ozone Destruction Reactions in OSAT

The original OSAT algorithm allocated chemical change to ozone tracers based on the total 

change in ozone (∆O3) across a call to the gas-phase chemistry solver. A positive ∆O3 was 

3 3 (4) 3

∑ = + × old

i

old

old i

i

new

i

N

N O N O N PO

3 3 (5) 3

∑ ×

× = + ×

i

old

i

i

old

old i

i

new

i

V MIR

V MIR O V O V PO

(6) 3 3

3 3 3 3

∑ +∑ = + × old

i

old

i

old

old i

i

new

i O N O V

O X O X O X DO
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equated to ozone production and ozone tracers were incremented according to the OSAT, 

APCA or GOAT rules for apportioning ozone production. A negative ∆O3 was equated to ozone 

destruction and the destruction was distributed equally among all ozone tracers. However, 

ozone production and destruction mechanisms operate simultaneously within the chemical 

mechanism and so the net change in ozone is the balance of production and destruction. For 

example, VOC oxidation can drive photochemical ozone production at the same time that O3 + 

VOC reactions directly consume ozone, and these processes may lead to a net increase or 

decrease in ozone depending mainly upon availability of NOx and sunlight. OSAT has been 

modified to explicitly track several ozone destruction mechanisms as follows:

1) O3 + VOC reactions since these remove ozone;

2) O(3

P) + VOC reactions since these effectively remove ozone;

3) O(1D) + H2O reaction since this effectively removes ozone;

4) HOx + O3 reactions that do not re-form ozone.

Ozone production is then calculated from the difference between ∆O3 and total ozone 

destruction (PO3 = ∆O3 – DO3). The OSAT ozone tracers are adjusted first for ozone 

destruction (applied to all tracers) and second for ozone production (applied using the OSAT, 

APCA or GOAT rules).

The amount of ozone destruction is calculated using integrated reaction rates obtained from 

the Process Analysis (PA) Probing Tool; see Section 10. It is easy to account for processes 1-3 

using PA since the ozone destroyed is simply the integrated rates of the reactions involved. 

Process 4 is less easy to identify but is very important as an ozone destruction mechanism in 

low NOx (rural) environments. Therefore, accounting for process 4 is important to 

understanding long-range ozone transport.

The main reaction pathways between ozone and HOx (OH and HO2) are shown in Figure 7-3.

Figure 7-3. Daytime reactions of ozone with HOx (OH and HO2) showing potential for 

reformation of ozone or ozone destruction via peroxide formation.

OH

HO2

O3

OH HO2

hV

NO Peroxides

NO2

HOx 

Radical 

Pool

HO2, 

RO2
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Ozone reacts directly with both with OH and HO2: 

O3 + OH → O2 + HO2(7) (7)

O3 + HO2 → 2 O2 + OH (8)

Since OH and HO2 radicals inter-convert rapidly during the daytime they can be viewed as a 

radical pool, called HOx. During the daytime, there are two main sinks for HOx:

(1) propagation by reaction with NO, which reforms ozone: 

NO + HO2 → NO2 + OH

NO2 + hν → NO + O(3P)

O(3P) + O2 → O3

Net: HO2 + O2 + hν → O3 + OH

(2) termination by reaction with HO2 or RO2 to form peroxides and other organic 

products, which prevents HOx from propagating to reform ozone:

HO2 + HO2 → H2O2 + O2

HO2 + RO2 → ROOH + O2

RO2 + RO2 → organic products + O2

In the revised OSAT algorithms, the ozone destruction rate due to O3 + HOx reactions is 

estimated as:

This equation is the rate of O3 + HOx reaction (i.e., the rates of [7] plus [8]) multiplied by a 

branching ratio that estimates the fraction of O3 + HOx reactions that result in loss of ozone. 

The reaction of O3 with HO2 is the dominant destruction pathway for ozone under low NOx 

conditions at mid-latitudes (Wang et al., 2003). 

Ozone destruction due to the O3 + NO → NO2 + O2 titration reaction is explicitly excluded from 

the accounting of ozone destruction because it is hard to disentangle its role in ozone 

destruction and production. Under high NOx (ozone titration) conditions and at night this 

reaction becomes clearly an ozone destruction pathway, and in these situations ∆O3 becomes 

negative and ozone destruction due to the O3 + NO reaction is accounted for. Under most 

daytime conditions, this reaction is part of the O3, NO, NO2 photo-stationary state and ozone 

can be reformed again when NO2 photolyzes so this reaction is not clearly an ozone destruction 

pathway.

( ) ( )

( ) ( ) 















+ = ×

+

+

HO NO HO term

HO term

O HOx

2 2

2

3 Rate Rate

Rate

O Destruction Rate 3
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7.2.5.2 Distinguishing VOC-Limited from NOX-Limited Ozone Formation

The classic trajectory model EKMA diagram can be used to distinguish VOC-limited from NOXlimited trajectories and develop a classification based on initial VOC-to-NOX ratio. However, 

this approach classifies VOC- or NOX-limited behavior based on the response of the peak ozone, 

which is the net response from several hours of photochemistry. In reality, many of the 

trajectories start out VOC-limited and become NOX-limited during the course of the day 

essentially because the NOX is depleted more rapidly than the VOC. For OSAT, a more 

fundamental indicator of the instantaneous state of ozone formation with regard to VOC- or 

NOX-limitation is required. 

The sensitivity of ozone formation to VOCs and NOX at any given time is attributable to the fate 

of radicals. The radical pool is often referred to as odd-hydrogen (HOX) and is most usefully 

considered as the sum of OH, HO2 and RO2 radicals. When NOX is plentiful, the main radical 

termination (i.e., HOX removal) pathway is nitric acid formation, i.e.:

OH + NO2 (+M) → HNO3 (+M) (9)

Under these conditions, ozone formation is limited by the rate at which radicals can be formed,

which is generally described as the VOC-limited condition. Thus nitric acid (HNO3) production is 

indicative of plentiful NOX and VOC-limited ozone formation.

When NOX is scarce, radical-radical reactions dominate HOX removal, e.g.:

HO2 + HO2 (+M) → H2O2 + O2 (+M) (10)

HO2 + RO2 → ROOH + O2 (11)

Under these conditions, ozone formation is limited by the availability of NO to react with HO2

and RO2 radicals, which is described as the NOX-limited condition. HO2 and RO2 radicals that 

do not react with NO participate in peroxide formation. Thus, peroxide formation (H2O2 = 

hydrogen peroxide, or ROOH = organic hydroperoxides) is indicative of scarce NOX and NOXlimited ozone formation.

Sillman (1995) has exploited this situation to develop useful indicators of VOC vs. NOX limited 

ozone formation based on the ratio of peroxide production to nitric acid production. Sillman 

proposed that the transition between these conditions occurs when:

(PH2O2 + PROOH) / PHNO3 = 0.5 (12)

The production rates of nitric acid (PHNO3) and hydrogen peroxide (PH2O2) in each CAMx grid cell 

at each time step are readily accessible. The balance between PROOH and PH2O2 depends upon 

the relative production of HO2 and RO2 radicals, and Sillman suggests that it is not highly 

variable within/across simulations. Accordingly, he proposes that equation (12) is equivalent to 

a transition point of:

PH2O2 / PHNO3 = 0.35 (13)
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In other words, when this ratio exceeds 0.35 ozone formation is NOX-limited, and when this 

ratio is less than 0.35 ozone formation is VOC-limited.

7.2.5.3 Evaluation of Sillman’s PH2O2/PHNO3 Indicator

Equation (13) was evaluated as an indicator of VOC vs. NOX-limited ozone formation for several 

trajectory model scenarios using the CB4 mechanism as implemented in the UAM.4

 The ozone 

concentration for a scenario with an initial VOC/NOX ratio of 10 (0.3 ppmC of VOC, 30 ppb of 

NOX) is shown in Figure 7-4. Also plotted, against the right axis, is the ratio PH2O2/PHNO3. 

Sillman’s proposed PH2O2/PHNO3 transition point of 0.35 is shown by the dashed line. Before 

about 12 noon, PH2O2/PHNO3 is less than 0.35 indicating VOC-limited ozone formation, whereas 

from about 12 noon to 7 PM PH2O2/PHNO3 exceeds 0.35 indicating NOX-limited ozone formation. 

After 7 PM, PH2O2/PHNO3 falls below 0.35 again, but this is after the ozone peak when ozone is 

decreasing and the concepts of VOC and NOX-limitation are no longer relevant.

In summary, the PH2O2/PHNO3 indicator suggested a transition from VOC to NOX-limited ozone 

formation at about noon. To investigate whether this prediction is corroborated by responses 

to emission controls, the trajectory model scenario was re-run with 30 percent reductions in 

initial concentrations and emissions of VOC and NOX (Figure 7-5). Figure 7-5 shows that NOX

controls started to be effective at about noon whereas VOC controls had maximum effect 

before noon. This finding is even clearer in Figure 7-6, which shows the difference in ozone 

(control-base) for the reduced VOC and NOX cases. Thus, the response of ozone to reducing 

VOC and NOX was found to be consistent with the prediction of the PH2O2/PHNO3 indicator.

The evaluation described above and shown in Figures 7-4 and 7-6 was repeated for two more 

scenarios with different base VOC/NOX ratios. The results for a base VOC/NOX ratio of 20 (0.3 

ppmC of VOC, 15 ppb of NOX) are shown in Figure 7-7, and for a base VOC/NOX ratio of 5 (0.15 

ppmC of VOC, 15 ppb of NOX) are shown in Figure 7-8. For a base VOC/NOX ratio of 20, Figure 

7-7a shows that the transition from VOC to NOX-limited ozone formation is predicted to occur 

at about 9:30 AM. Figure 7-7b shows that this is confirmed by the response to VOC and NOX

controls. For a base VOC/NOX ratio of 5, Figure 7-8a shows that ozone formation is predicted 

to remain VOC-limited throughout the day. Figure 7-8b confirms this by showing no net benefit 

from NOX control throughout the day.

 4 The scenarios begin at sunrise at 6 a.m. with 10 ppb of O3 plus initial VOCs and NOX. There is no dilution, and 5 percent of the 

initial VOCs and NOX are added in each hour as emissions. 
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Figure 7-4. Box model simulation to evaluate PH202/PHNO3 indicator for VOC vs. NOx limited 

ozone formation (see text). Ozone is plotted against the left axis, PH202/PHNO3 is plotted 

against the right axis. For PH202/PHN03 below 0.35 ozone formation is VOC limited. Thus, the 

transition from VOC to NOx limited ozone formation is predicted to occur about 12 noon. 

Initial VOC/NOx = 10:1.

Figure 7-5. Effect on ozone of controlling VOC and NOx by 30 percent for the base scenario 

shown in Figure 7-4. The vertical dashed line shows the transition from VOC to NOx limited 

ozone formation for the base case derived in Figure 7-4. Initial base case VOC/NOx = 10:1.

0

0.05

0.1

0.15

0.2

0.25

6 9 12 15 18 21 24 3

Time (hours)

0.001

0.01

0.1

1

10

100

1000

10000 Ozone

p(H2O2) / p(HNO3)

NOx

limited

VOC

limited

0

0.05

0.1

0.15

0.2

0.25

6 9 12 15 18 21 24 3

Time (hours)

Base

30% VOC control

30% NOx control

NOx

limited

VOC

limited
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Figure 7-6. Change in ozone (control-base) for the VOC and NOx control scenarios shown in 

Figure 7-5. The vertical dashed line shows the transition from VOC to NOx limited ozone 

formation for the base case derived in Figure 7-4. Initial base case VOC/NOx = 10:1.

Figure 7-7a. As Figure 7-4, but for an Initial VOC/NOx = 20:1.

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

0.18

6 9 12 15 18 21 24 3

Time (hours)

Ozone (ppm)

0.001

0.01

0.1

1

10

100

1000

10000

ratio p(H2O2) / p(HNO3)

Ozone

p(H2O2) / p(HNO3)

NOx

limited

VOC

limited

-0.07

-0.06

-0.05

-0.04

-0.03

-0.02

-0.01

0

0.01

0.02

0.03

69

1215182124

3

Time (hours)

Delta Ozone (Control - Base) 

(ppm)

30% NOx control

30% VOC control

NOx

limited

VOC

limited
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Figure 7-7b. As in Figure 7-6, but for an Initial VOC/NOx = 20:1.

Figure 7-8a. As Figure 7-4, but for an Initial VOC/NOx = 5:1.

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

0.18

6 9 12 15 18 21 24 3

Time (hours)

Ozone (ppm)

0.001

0.01

0.1

1

10

100

1000

10000

ratio p(H2O2) / p(HNO3)

Ozone

p(H2O2) / p(HNO3)

-0.04

-0.035

-0.03

-0.025

-0.02

-0.015

-0.01

-0.005

0

0.005

0.01

69

1215182124

3

Time (hours)

Delta Ozone (Control - Base) 

(ppm)

30% NOx control

30% VOC control

NOx

limited

VOC

limited
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Figure 7-8b. As Figure 7-6, but for an Initial VOC/NOx = 5:1

7.2.6 Alternative Chemical Apportionment Techniques

The formulation of OSAT described above was first methodology implemented into CAMx. 

Several variations on OSAT are now available that use different algorithms to attribute ozone 

contributions. One advantage of the coding framework for OSAT is that it allows for easy 

modification of the source attribution algorithm by modifying a single subroutine. The 

alternative methods currently available in CAMx are described below (other options are 

possible).

Geographic Ozone Assessment Technology (GOAT). GOAT does not attempt to trace 

ozone production back to the source of the precursors, but rather ozone formation is 

tracked based on the geographic location where it occurred. Thus ozone formation in a 

grid cell over “Area A” would be attributed to Area A even if the culpable emissions 

originated upwind in Area B. The disadvantage of GOAT is its simplistic assumption 

regarding the basis for ozone culpability. The advantages of GOAT are: (1) its freedom 

from assumptions about whether ozone formation is NOX or VOC limited; and (2) that 

its results may be more directly comparable to other emerging source attribution 

methodologies (e.g., trajectories, tracers, and possibly the spatial analysis component of 

Process Analysis).

Anthropogenic Precursor Culpability Assessment (APCA). APCA differs from OSAT in 

recognizing that certain emission groups are not controllable (e.g., biogenic emissions) 

and that apportioning ozone production to these groups does not provide information 

that is relevant to control strategies. To address this, in situations where OSAT would 

-0.12

-0.1

-0.08

-0.06

-0.04

-0.02

0

0.02

0.04

0.06

69

1215182124

3

Time (hours)

Delta Ozone (Control - Base) 

(ppm)

30% NOx control

30% VOC control
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attribute ozone production to non-controllable (i.e., biogenic) emissions, APCA reallocates that ozone production to the controllable portion of precursors that 

participated in ozone formation with the non-controllable precursor. In the case where 

biogenic emissions are the uncontrollable source category, APCA would only attribute 

ozone production to biogenic emissions when ozone formation is due to the interaction 

of biogenic VOC with biogenic NOX. When ozone formation is due to biogenic VOC and 

anthropogenic NOX under VOC-limited conditions (a situation in which OSAT would 

attribute ozone production to biogenic VOC), APCA re-directs that attribution to the 

anthropogenic NOX precursors present. The use of APCA instead of OSAT results in 

more ozone formation attributed to anthropogenic NOX sources and less ozone 

formation attributed to biogenic sources. APCA is not really a “source apportionment” 

technique because it expresses biases as to which sources should be implicated (i.e., 

those that are controllable), hence it is referred to as a “culpability assessment.” The

APCA ozone allocation scheme is described in more detail below.

7.2.6.1 The APCA Technique

OSAT identifies which emission source regions, categories, and species (VOC and NOX) that 

contribute to ozone concentrations, and it can be used to approximate which source controls 

would have the greatest effect in reducing ozone concentrations. For regional modeling 

applications of the eastern US, OSAT correctly identifies biogenic VOC emissions as a major 

contributor to ozone formation, and if controlled, would result in large ozone reductions. 

While scientifically and chemically correct, however, this information is irrelevant for 

identifying controllable sources (note that some biogenic NOX emissions are partly from 

fertilizers and thus are not truly “natural”). The presence of a source category that cannot be 

controlled requires special considerations when performing ozone source apportionment 

modeling for the purposes of performing an ozone precursor culpability analysis or aiding in the 

design of anthropogenic emission control strategies.

Biogenic versus anthropogenic ozone source apportionment, as a function of VOC and NOX

precursor interactions, can be divided up into four ozone formation regimes as follows:

Biogenic NOx Anthropogenic NOx

Biogenic VOC 1 2

Anthropogenic VOC 3 4

Regime 1 involves ozone formation due to the interaction between biogenic VOC and biogenic 

NOX and is truly “biogenic ozone”. Regime 4 is truly “anthropogenic ozone” and the OSAT 

attribution scheme will provide control-relevant information by allocating ozone formed in 

Regime 4 to the proper anthropogenic ozone precursors (VOC or NOX). Difficulties arise in the 

mixed anthropogenic/biogenic regimes (Regimes 2 and 3) where precursors from both biogenic 

and anthropogenic sources participate in the ozone formation. Much of the ozone formed in 

rural areas is formed under Regime 2, although Regime 1 may have some influence on ozone 

formation in high biogenic NOX regions (e.g., the Corn Belt). To design effective control 

strategies, an ozone allocation scheme is needed that accounts for the special status of 

biogenic emissions as being uncontrollable.
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In the APCA technique, only the true “biogenic ozone” (Regime 1) is attributed to biogenic 

emissions, while ozone formed in all other regimes is allocated to anthropogenic emissions. 

The standard OSAT approach is used to allocate ozone formed to anthropogenic VOC or NOX

emissions when anthropogenic VOC and NOX emissions interact (Regime 4), and to allocate to 

biogenic VOC or NOX when these two precursors interact (Regime 1). However, when ozone 

forms due to the interaction of biogenic and anthropogenic emissions (Regimes 2 and 3), the 

APCA technique differs from OSAT by allocating ozone formed to anthropogenic emissions; the 

ozone increment is allocated to anthropogenic NOX (if VOC-limited) or anthropogenic VOC (if 

NOX-limited). 

Assuming that N and V are the NOX and reactivity-weighted VOC tracer concentrations in a grid 

cell from different source categories (e.g., biogenic sources and several anthropogenic 

emissions categories) that participated in the formation of an increment of ozone (∆O3), the 

APCA allocation scheme can be expressed mathematically as follows. First, APCA defines the 

fraction of ozone formed due to the interaction of biogenic VOC with biogenic NOX, which will 

be attributed to biogenic emissions (Regime 1):

min , . 













 =

total

bio

total

bio

bio N

N

V

V F

Under VOC-limited conditions, APCA attributes the fraction of ozone formed to biogenic VOC 

emissions:

O3Vbio = Fbio × ∆O3

Second, it then attributes the fraction of ozone increment to anthropogenic VOC source 

groupings due to the interaction of anthropogenic VOC with anthropogenic and biogenic NOX

(Regimes 3 and 4):

O i nanthro

V

V O V

total

anthro

i

anthro

i 3 , 1,..., × ∆ 3 = 













 =

Finally, the remainder of the ozone increment (δO3), which would have been attributed to 

biogenic VOC in OSAT, is attributed to anthropogenic NOX (Regime 2):

= ∆ − − ∑

i

anthro

i δO3 O3 O3Vbio O3V

O i nanthro

N

N O N total

anthro

i

anthro

anthro

i 3 , 1,..., × 3 = 













 = δ

Under NOX-limited conditions, similar formulas are used, switching the N with V and O3N with 

O3V, and considering Regimes 2 and 4 in the second step, and Regime 3 in the final step. Since 

it is expected that biogenic VOC precursors will almost always be greater than biogenic NOX
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precursors (i.e., Fbio = Nbio/Ntotal), then under NOX-limited conditions the APCA ozone allocation 

scheme will produce identical results to OSAT. 

7.3 Running CAMx With OSAT

7.3.1 CAMx Control File

OSAT and its derivatives are invoked similarly to the other Probing Tools within the CAMx 

control file. In the &CAMx_Control namelist module, the variable Probing_Tool must be 

set to “OSAT”, “GOAT”, or “APCA”. An additional namelist module called &SA_Control must 

then be provided in the control file to configure the OSAT portion of the model. The additional 

namelist module is described below. The order of the variables follows the template available 

with the source code. Several examples of the OSAT portion of the CAMx run control file are 

shown in Figures 7-9(a-d).

Description of OSAT Control in the CAMx Run Control File

&SA_Control Label for the Probing Tool namelist module that configures the 

OSAT option; it must begin in column 2

& Flag ending a namelist module; it must be in column 2

SA_Summary_Output Logical flag used to limit the species written to the tracer 

concentration file to a subset of the PSAT treated species. If set 

to true, the output will be restricted to the following species: 

O3N, O3V

SA_File_Root Character root output path/filename

SA_Master_Sfc_Output Logical flag for master grid surface output (TRUE=OSAT 

concentration file will be output for all tracers, FALSE=OSAT 

concentration file will not be output)

SA_Nested_Sfc_Output Logical flag for nested grid surface output (TRUE=OSAT 

concentration file will be output for all tracers, FALSE=OSAT 

concentration file will not be output)

SA_Stratify_Boundary Logical flag to stratify boundary types (TRUE=separate tracer 

types will be used for the N, S, E, W, and Top boundaries, 

FALSE=a single tracer type will be used for all 5 boundaries)

SA_Deposition_Output Logical flag to output deposited tracer mass to a file

(TRUE=output deposited tracer mass, FALSE=do not generate a 

tracer deposition output file)

SA_Number_of_Source_Regions Integer number of source regions for this run. This must be 

the same as the number of source areas defined in the 

SA_Source_Area_Map file.
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SA_Number_of_Source_Groups Integer number of emission groups for this run. Together with 

the Use_Leftover_Group flag, this determines the number 

of paired emission files that must be supplied (additional details 

below).

Use_Leftover_Group Logical flag to define a “leftover” emissions group (TRUE= 

calculate a “leftover” emissions group from the difference 

between the sum of the emission group files and the regular 

CAMx emission files, FALSE=do not calculate a “leftover” 

emissions group)

SA_Receptor_Definitions Character input OSAT receptor definition path/filename. (This is 

an optional file).

SA_Source_Area_Map Character array (by CAMx grid) input OSAT source area 

definition path/filename (required for master grid, optional for 

nested grids)

SA_Master_Restart Character input master grid OSAT restart path/filename 

(ignored if Restart=FALSE)

SA_Nested_Restart Character input nested grid OSAT restart path/filename 

(ignored if Restart=FALSE or Number_of_Grids=1)

SA_Points_Group Character array (by source group) input OSAT elevated point 

source emissions path/filename (optional, ignored if 

Point_Emissions=FALSE)

SA_Emiss_Group_Grid Character array (by source group, by CAMx grid) input OSAT 

gridded emissions path/filename (optional, ignored if 

Gridded_Emissions=FALSE)

7.3.2 Specifying Emission Groups

OSAT can apportion ozone and ozone precursor concentrations among several emission 

categories. To achieve this, the emissions for the separate groups must be supplied as sets of 

separate emissions files for each source group; a low level (gridded) file for each fine grid nest, 

and one elevated point source file. The additional emission files must be in the CAMx emission 

file format, as described in Section 3. If the group being separated has no elevated emissions 

(e.g. biogenics), the point source file name for the group can be left blank. If the emission 

group being separated has no surface emissions (e.g. a utility), the surface file name for the 

group can be left blank for all grids. APCA requires two or more emissions categories, with the 

first category being biogenic emissions.

Imagine a case where the emission inventory is split into three groups. Three sets of emission 

files could be supplied that together have the same total emissions as the regular CAMx 

emissions files. Alternatively, two sets of files could be supplied and the third calculated from 
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the “leftover” emissions (i.e., the regular CAMx emissions minus the two groups specified). 

Both approaches could be useful, depending upon the emissions files available to the user. 

Accordingly, OSAT reads an input flag “Use_Leftover_Group” that can be set true or false. 

If a leftover group is selected, the model verifies that the group is not too small to calculate 

within the numerical precision of the computer (this also traps cases where the flag was set 

true in error). If no leftover group is selected, the model verifies that the total emissions for the 

groups supplied are equal to the regular model emissions, i.e., that a leftover group is not 

needed. In both cases, if appropriate conditions are not met, the model stops with a 

descriptive error message.

The number of emission file sets that need to be supplied for different model configurations is 

summarized in Table 7-1; the table also shows how the emissions groups are numbered, which 

is reflected in the tracer species names (defined below).

Table 7-1. Numbers of emission file sets (i.e., low level files and point source file) needed for 

different model configurations.

Number of 

Emission Groups

Use

Leftover Group

Number of Emission 

File Sets Needed

Numbering of Emission Groups 

and Tracer Species

1 Not Applicable 0 0

n>1 False n 1,2,3,...n

True n-1 1,2,3,...n

When specifying additional point source files to resolve source category groupings, the list of 

point sources on each file must be identical (i.e., same number of sources, same order) to the 

regular model point source file. This formal restriction is necessary to ensure that point sources 

are correctly cross-referenced within CAMx. Thus, a point source file for a specific source group 

may need to contain records for sources that are not in the group: these records should have 

zero emissions.

Geographic resolution is superimposed on emission group resolution using the source area map 

described below. The source area map is defined using grid cells, which may not adequately 

resolve point source locations. To provide finer control of point source assignments to 

geographic areas, the source area can be specified for any source by putting the source area 

index in the (unused) kcell value on the point source file (see file description in section 3). 

This feature is referred to as “point source override.”
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&SA_Control

SA_File_Root = '$TRACOUT/CAMx.OSAT.9507$today',

SA_Master_Sfc_Output = .true.,

SA_Nested_Sfc_Output = .true.,

SA_Summary_Output = .true.,

SA_Stratify_Boundary = .false.,

SA_Deposition_Output = .false.,

SA_Number_of_Source_Regions = 19,

SA_Number_of_Source_Groups = 1,

Use_Leftover_Group = .false.,

SA_Receptor_Definitions = '$TRACIN/receptor.cities ',

SA_Source_Area_Map(1) = '$TRACIN/APCA.source.area.map',

SA_Source_Area_Map(2) = ' ',

SA_Master_Restart = ' ',

SA_Nested_Restart = ' ',

SA_Points_Group(1) = ' ',

SA_Emiss_Group_Grid(1,1) = ' ',

SA_Emiss_Group_Grid(1,2) = ' ',

&

Figure 7-9a. An example of OSAT input records in the CAMx run control file. The options for 

this run are as follows: this is a two-grid run, master and nested grid surface concentrations 

are written to file, a single tracer type is to be used for all boundaries, 19 source regions, and 

one emission group (i.e., zero additional emission files and no leftover group). This is the first 

day of the simulation (i.e., restart is false), so no OSAT restart files are supplied. 
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&SA_Control

SA_File_Root = '$TRACOUT/CAMx.OSAT.9507$today',

SA_Master_Sfc_Output = .true.,

SA_Nested_Sfc_Output = .true.,

SA_Summary_Output = .true.,

SA_Stratify_Boundary = .false.,

SA_Deposition_Output = .false.,

SA_Number_of_Source_Regions = 19,

SA_Number_of_Source_Groups = 1,

Use_Leftover_Group = .false.,

SA_Receptor_Definitions = '$TRACIN/receptor.cities ',

SA_Source_Area_Map(1) = '$TRACIN/APCA.source.area.map',

SA_Source_Area_Map(2) = ' ',

SA_Master_Restart = '$TRACOUT/CAMx.OSAT.9507$yesterday.sa.inst',

SA_Nested_Restart = '$TRACOUT/CAMx.OSAT.9507$yesterday.sa.finst',

SA_Points_Group(1) = ' ',

SA_Emiss_Group_Grid(1,1) = ' ',

SA_Emiss_Group_Grid(1,2) = ' ',

&

Figure 7-9b. As in Figure 7-9(a), but in this case the run is a continuation, and so the restart 

flag is set to TRUE and a “Tracer Restart” files are supplied.
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&SA_Control

SA_File_Root = '$TRACOUT/CAMx.OSAT.9507$today',

SA_Master_Sfc_Output = .true.,

SA_Nested_Sfc_Output = .true.,

SA_Summary_Output = .true.,

SA_Stratify_Boundary = .false.,

SA_Deposition_Output = .false.,

SA_Number_of_Source_Regions = 19,

SA_Number_of_Source_Groups = 3,

Use_Leftover_Group = .true.,

SA_Receptor_Definitions = '$TRACIN/receptor.cities ',

SA_Source_Area_Map(1) = '$TRACIN/APCA.source.area.map',

SA_Source_Area_Map(2) = ' ',

SA_Master_Restart = '$TRACOUT/CAMx.OSAT.9507$yesterday.sa.inst',

SA_Nested_Restart = '$TRACOUT/CAMx.OSAT.9507$yesterday.sa.finst',

SA_Points_Group(1) = ' ',

SA_Points_Group(2) = '$PTSRCE/utilpt.ng.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(1,1) = '$TRACEMS/bio2.cc.$todate-95',

SA_Emiss_Group_Grid(1,2) = '$TRACEMS/bio2.ff.$todate-95.ne',

SA_Emiss_Group_Grid(2,1) = '$TRACEMS/util.cc.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(2,2) = '$TRACEMS/util.ff.$todate-07.ag.07cem1A-run11',

&

Figure 7-9c. As in Figure 7-9(a), but in this case the run is a continuation day of a run with 

three emission groups. The three emission groups are defined by supplying two pairs of extra 

emission files for each grid (AREA group 1, AREA group 2, and POINT group 2), and setting the 

“Use_Leftover_Group” flag to TRUE for the model to calculate the third group internally. The 

POINT group 1 filename is blank because group 1 is a category with no point source emissions 

(e.g., biogenics).
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&SA_Control

SA_Master_Sfc_Output = .true.,

SA_Nested_Sfc_Output = .true.,

SA_Summary_Output = .true.,

SA_Stratify_Boundary = .false.,

SA_Deposition_Output = .false.,

SA_Number_of_Source_Regions = 19,

SA_Number_of_Source_Groups = 3,

Use_Leftover_Group = .false.,

SA_Receptor_Definitions = '$TRACIN/receptor.cities ',

SA_Source_Area_Map(1) = '$TRACIN/APCA.source.area.map',

SA_Source_Area_Map(2) = ' ',

SA_Master_Restart = '$TRACOUT/CAMx.OSAT.9507$yesterday.sa.inst',

SA_Nested_Restart = '$TRACOUT/CAMx.OSAT.9507$yesterday.sa.finst',

SA_Points_Group(1) = ' ',

SA_Points_Group(2) = '$PTSRCE/utilpt.ng.$todate-07.ag.07cem1A-run11',

SA_Points_Group(3) = '$PTSRCE/remain.ng.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(1,1) = '$TRACEMS/bio2.cc.$todate-95',

SA_Emiss_Group_Grid(1,2) = '$TRACEMS/bio2.ff.$todate-95.ne',

SA_Emiss_Group_Grid(2,1) = '$TRACEMS/util.cc.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(2,2) = '$TRACEMS/util.ff.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(3,1) = '$TRACEMS/remain.cc.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(3,2) = '$TRACEMS/remain.ff.$todate-07.ag.07cem1A-run11',

&

Figure 7-9d. As in Figure 7-9(c) (i.e. a continuation day of a run with three emission groups), 

but in this case all three emission groups are defined explicitly by supplying extra emission 

files (AREA group 1, AREA group 2, POINT group 2, AREA group 3, and POINT group 3). 

Therefore, the “Use_Leftover_Group” flag is set to FALSE. The POINT group 1 filename is 

blank because group 1 is a category with no point source emissions (e.g., biogenics).
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7.4 Input File Formats

7.4.1 Source Area Mapping

OSAT can apportion ozone and ozone precursor concentrations among several geographic 

regions within the modeling domain, as shown in Figure 7-1. The “source area mapping” file 

assigns each grid cell to a specific geographic source region. The format of the file is an array of 

integer numbers (i3) corresponding to the CAMx domain. Figure 7-10 shows the source area 

mapping file for the single grid corresponding to Figure 7-1. Since the CAMx domain in Figure 

7-1 has 63 rows and 64 columns of cells, the file shown in Figure 7-10 has 63 lines with 64 

numbers on each line. The first number (top left) always corresponds to the Northwest corner 

of the domain. 

A source area map must be defined for the master grid and optionally any nested grids. The 

source area map for a nest is in the same format as the master grid source area map described 

above, but contains a number of rows and columns corresponding to the nested grid, including 

the boundary (“buffer”) rows and columns. Within a nest for which a nested grid source area 

map is supplied, the source areas as defined by this map will take precedence over the source 

areas defined by the master grid source area map. If a source area map is not provided for a 

specific nest the source area definition will be taken from the source area map of the parent 

grid.

7.4.2 Receptor Definition

Tracer concentrations for selected receptor locations are output to an ASCII file every hour. 

The receptors for each model run are defined in the “Receptor definition” input file. Three 

types of receptors are supported:

POINT a point specified in the coordinate system of the CAMx grid. 

Concentrations at the point are determined by bi-linear 

interpolation of the surrounding four master grid surface cells.

SINGLE CELL a single surface grid cell identified by number.

CELL AVERAGE a group of grid cells identified by number that are averaged 

together to provide multi-cell average tracer concentrations.

WALL OF CELLS a group of grid cells defining a wall (i.e., a flux plane).

For the receptor types that are defined by grid cell it is necessary to specify the grid containing 

the receptor. This is done by including the grid number on the receptor definition record. Grid 

numbers are defined using the internal CAMx grid ordering. The grid numbering as defined by 

CAMx is shown in a table in the .diag file. Each receptor can be identified by a 10 character 

name. The formats for specifying each receptor type are given in Table 7-2. An example 

receptor file is shown below:
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31 31 31 31 18 18 18 18 18 18 18 18 18 18 37 37 37 37 17 17 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 17 17 17 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 14 14 14 14 14 14 14 40

31 31 31 31 31 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 22 14 14 14 14 14 14 14 14

31 31 31 31 31 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 40 24 24 24 24 34 34 34 34 22 14 14 14 14 14 14 14 14

31 31 31 31 31 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 40 24 24 24 24 24 34 34 34 34 22 14 14 14 14 14 14 14 14

31 31 31 31 31 18 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 24 24 24 24 24 24 34 34 34 22 22 14 14 14 14 14 14 38 38

31 31 31 31 31 18 18 18 18 18 18 18 18 18 18 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 40 40 40 40 40 24 24 24 24 24 24 34 34 34 22 22 14 14 14 14 14 38 38 38

31 31 31 31 31 10 10 10 10 10 10 10 10 10 10 37 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 24 24 24 24 24 24 24 24 24 24 24 34 34 22 22 22 14 14 38 38 38 38 38 38

31 31 31 31 31 10 10 10 10 10 10 10 10 10 10 10 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 24 24 24 24 24 24 24 24 24 24 24 34 34 22 22 22 14 14 38 38 38 38 38 38

21 21 21 31 31 10 10 10 10 10 10 10 10 10 10 10 37 37 37 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 40 40 24 24 24 24 24 24 24 24 24 24 24 24 34 22 22 22 16 16 38 38 38 38 38 38

21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 10 10 8 8 37 37 37 37 37 17 17 17 17 17 17 17 17 17 40 40 40 40 40 24 24 24 24 24 24 24 24 24 24 24 24 24 16 16 16 16 16 16 16 38 38 38 38 38 38

21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 8 8 17 17 17 17 17 17 17 17 17 40 26 26 26 28 24 24 24 24 24 24 24 24 24 24 24 24 24 16 16 16 16 16 16 16 38 38 38 38 38 38

21 21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 9 9 17 17 17 17 17 17 17 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 24 24 24 3 3 3 29 29 16 16 16 38 38 38 38 38

21 21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 24 24 24 3 3 3 29 29 16 16 16 38 38 38 38 38

21 21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 23 24 24 3 3 24 24 29 16 16 16 38 38 38 38 38

21 21 21 21 21 21 10 10 10 10 10 10 10 10 10 10 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 23 23 24 24 24 24 24 38 38 38 38 38 38 38 38 38

21 21 21 21 21 21 21 20 20 20 20 20 20 20 20 8 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 23 23 24 24 38 38 38 38 38 38 38 38 38 38 38 38

21 21 21 21 21 21 21 20 20 20 20 20 20 20 20 8 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 26 28 28 28 28 28 28 28 28 28 28 28 23 23 23 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 8 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 36 28 28 28 28 28 28 28 28 28 4 28 23 23 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 8 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 26 36 36 36 15 36 36 15 15 15 15 4 23 23 23 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 8 8 8 8 8 8 9 9 9 9 9 26 26 26 26 26 26 26 36 36 36 36 36 36 35 35 15 15 15 4 23 23 23 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 8 8 8 8 8 9 9 9 9 9 12 12 26 26 26 26 36 36 36 36 36 36 35 35 35 15 15 15 15 4 23 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 8 8 8 8 8 9 9 9 9 12 12 12 12 12 12 36 36 36 36 36 36 35 35 35 35 15 15 15 15 4 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 8 8 8 8 9 9 9 9 12 12 12 12 12 12 12 36 36 36 36 36 35 35 35 35 35 35 15 15 15 15 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 8 8 8 8 12 12 12 12 12 12 12 12 12 12 12 36 36 36 36 36 35 35 35 35 35 35 35 35 35 35 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 20 8 8 8 12 12 12 12 12 12 12 12 12 12 12 12 36 36 36 35 35 35 35 35 35 35 35 35 35 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

11 11 11 11 11 11 11 11 11 20 20 20 20 20 20 20 20 20 20 8 8 12 12 12 12 12 12 12 12 12 12 12 12 35 35 35 35 35 35 35 35 35 35 35 35 35 35 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 20 20 20 20 20 20 20 20 20 20 20 12 12 12 12 12 12 12 12 12 12 12 12 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 20 20 20 20 20 20 20 20 20 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 2 20 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 2 32 32 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 2 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 32 32 32 32 32 32 32 32 32 32 32 32 32 25 25 25 30 30 25 25 25 25 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 19 19 19 19 19 1 1 1 1 1 7 7 7 7 30 30 30 30 30 30 25 25 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 2 19 19 19 19 19 1 1 1 1 1 7 7 7 7 7 30 30 30 30 30 30 30 25 25 25 25 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

27 27 27 27 27 27 27 27 27 2 2 2 2 2 2 2 19 19 19 19 19 19 1 1 1 1 1 7 7 7 7 7 7 30 30 30 30 30 30 30 25 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 27 33 33 27 2 2 2 2 2 2 2 19 19 19 19 19 19 1 1 1 1 1 7 7 7 7 7 7 30 30 30 30 30 30 30 30 25 25 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 2 2 2 2 2 2 19 19 19 19 19 1 1 1 1 1 1 7 7 7 7 7 7 7 30 30 30 30 30 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 2 2 2 2 2 2 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 30 30 30 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 30 30 30 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 30 30 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 7 30 30 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 19 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 7 7 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 19 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 7 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 33 13 13 13 13 19 19 19 19 19 19 1 1 1 1 1 1 1 7 7 7 7 7 7 7 7 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 13 19 19 19 1 1 6 6 6 6 6 7 7 7 7 7 7 7 7 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 13 13 19 19 1 1 6 6 6 6 6 6 6 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 13 13 19 19 1 1 6 39 6 6 6 6 6 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 13 13 13 13 13 13 13 13 13 39 39 39 39 39 39 6 6 6 6 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 33 13 39 13 13 13 13 13 13 13 13 39 39 39 39 39 39 39 6 6 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 33 39 39 39 39 39 39 13 13 13 13 13 13 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 13 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

33 33 33 33 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 39 6 6 6 6 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38

Figure 7-10. Example source area mapping file for the domain and source areas shown in Figure 7-1.
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POINT City 1 461.520 3762.040 

SINGLE CELL Cell 1 1 45 18 

CELL AVERAGE Region 10 2 8 

 31 19 

 32 19 

 33 19 

 34 19 

 31 18 

 32 18 

 33 18 

34 18 

WALL OF CELLS Boundary1 2 10 20

 18 18

 1 5

Table 7-2. Format for the receptor definition file.

Receptor Type Line Columns Data

POINT 1 1-15 The word “POINT”

1 21-30 Receptor name

1 31-40 X co-ordinate

1 41-50 Y co-ordinate

SINGLE CELL 1 1-15 The word “SINGLE CELL”

1 21-30 Receptor name 

1 31-40 Grid Number 

1 41-50 X cell number

1 51-60 Y cell number

CELL AVERAGE 1 1-15 The words “CELL AVERAGE”

1 21-30 Receptor name

1 31-40 Grid number

1 41-50 The number of cells to average (M)

2-M 1-10 X cell number

2-M 11-20 Y cell number

WALL OF CELLS 1 1-15 The words “WALL OF CELLS”

1 21-30 Receptor name

1 31-40 Grid number

1 41-50 X-cell begin

1 51-60 X-cell end

2 41-50 Y-cell begin

2 51-60 Y-cell end

3 41-50 Z-cell begin

3 51-60 Z-cell end

7.5 Output File Formats

OSAT writes several output files that are in Fortran binary format, as described in Section 3. 

These include the master and nested grid tracer instantaneous concentration files (.sa.inst

and .sa.finst), the grid-specific surface tracer average concentration file 

(.sa.surf.grdnn), and the grid-specific surface deposited mass file (.sa.depn.grdnn). 
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These files are written in the same format as for the regular model species described in Section 

3. In addition, OSAT writes out tracer concentrations for selected receptor locations to an ASCII 

file (.sa.receptor). The naming conventions for tracer species and the format of the 

receptor concentration file are discussed below.

7.5.1 Tracer Species Names

The names of tracer species uniquely identify the information carried by each species and, 

taken as a group, identify the model configuration in any run. Species names have less than ten 

characters, consistent with the UAM convention. The naming conventions are as follows:

Ozone Reaction Tracers

Emission Sources SSSeeerrr

where:

SSS Species type, i.e., NOX, VOC, O3V or O3N

eee Emissions group:

Single group, always 000

Multiple groups, 001, 002, etc.

rrr Region tracer released from, 001, 002, 003, etc.

Initial/Boundary SSSeeerrr

where:

SSS Species type, i.e., NOX, VOC, O3V or O3N

eee Initial Concentrations: always 000 

Boundary Concentrations not stratified by boundary: always 000

Boundary Concentrations stratified by boundary: WST, EST, STH, NTH, 

TOP indicating boundary of origin

rrr IC for Initial Concentrations, BC for Boundary Concentrations

Examples: NOX000015, VOC002015, O3V000IC, O3NTOPBC

7.5.2 Receptor Concentration File

Hourly average tracer concentrations at user specific receptor locations are output to the 

“receptor concentration” file. The file is in comma delimited ASCII format suitable for 

importing into a spreadsheet. An example output file is shown in Figure 7-11. Two header lines 

at the top of the file identify the model version and the date the run was performed. Next, two 

lines identify the time period covered by the file and the averaging interval (generally one hour, 

determined by the CAMx simulation control file). Next, three lines define the model 

configuration and seven lines specify the numbers of tracer species that result from this 

configuration. The names of each tracer species are given on six lines ordered by tracer species 

type: the order in which species are listed here is the same as the order in which tracer 

concentrations are given later in the file.
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CAMx, SOURCE APPORTIONMENT, VERSION -- 960315 , 

Mon Oct 26 10:37:34 1998 , 

File Duration , 87238, 15.00, 87238, 24.00, 

Average Interval , 1.0000 

Number of source areas , 17 

Number of emission groupings , 1 

Number of tracer species , 144 

Number of NOx species , 19 

Number of VOC species , 19 

Number of O3N species , 19 

Number of O3V species , 19 

Number of INERT TIME species , 34 

Number of DECAY TIME species , 34 

Tracer Names, 

NOX000IC ,NOX000BC ,NOX001001,NOX001002,NOX001003,NOX001004,NOX001005 .. 

VOC000IC ,VOC000BC ,VOC001001,VOC001002,VOC001003,VOC001004,VOC001005 .. 

O3N000IC ,O3N000BC ,O3N001001,O3N001002,O3N001003,O3N001004,O3N001005 .. 

O3V000IC ,O3V000BC ,O3V001001,O3V001002,O3V001003,O3V001004,O3V001005 .. 

I23815001,I23815002,I23815003,I23815004,I23815005,I23815006,I23815007 .. 

D23815001,D23815002,D23815003,D23815004,D23815005,D23815006,D23815007 .. 

Number of receptors , 6 

 No, Name, Type, Xloc, Yloc, 

 1, HourlyPeak, 1, , , 

 2, Rubidoux , 0, 461.5, 3762.0, 

 3, Pasadena , 0, 396.4, 3778.5, 

 4, Lennox , 0, 373.0, 3755.0, 

 5, Peak , 1, 45, 18, 

 6, Region 10 , 8, 31, 19, 

 32, 19

33, 19

34, 19,

31, 18,

32, 18,

33, 18,

34, 18,

Time Varying Tracer Data, 

Data for Period, 87238, 15.00, 87238, 16.00, 

 Receptor, 1, 

1.3265E-02, 1.3544E-09, 1.0000E-16, 1.0974E-15, 1.0000E-16, 1.0000E-16 .. 

1.2237E-01, 3.3869E-08, 1.0000E-16, 1.6165E-14, 1.0000E-16, 1.0000E-16 .. 

8.7304E-02, 1.1926E-08, 1.0000E-16, 1.0000E-16, 1.0000E-16, 1.0000E-16 .. 

9.0300E-02, 1.5269E-08, 1.0188E-16, 2.6997E-15, 1.0213E-16, 1.0162E-16 .. 

1.0036E-16, 4.0640E-15, 1.0036E-16, 1.0036E-16, 1.0036E-16, 1.0029E-16 .. 

1.0000E-16, 3.7563E-15, 1.0000E-16, 1.0000E-16, 1.0000E-16, 1.0000E-16 .. 

1.4500E-02, 1.2663E-01, 1.7770E-01, 

1.4500E-02, 1.2663E-01, 1.7770E-01, 

 Receptor, 2, 

(File continues with data for remaining receptors and hours)

Figure 7-11. Example Receptor Concentration File. Lines ending with “..” are truncated to fit 

the page, and the file would continue with data for additional receptors and hours in the 

same format.
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The tracer species names are followed by the number of receptors and receptor names. Note 

that the first receptor (receptor 1) is always the location of the hourly peak ozone. Since the 

location of the hourly peak varies from hour to hour, the X and Y locations are left blank. 

Receptors 2 and higher are those specified in the “Receptor definition” file. The tracer 

concentrations are reported in blocks with a date and time stamp at the head of each block. 

Within each block, receptors are reported in numerical order. For each receptor, there are six 

lines of data for the tracer species identified at the heading “Tracer Names”. All values are in 

CAMx units of ppm. At the bottom of the data block for each receptor are two lines with three 

numbers: these are the total tracer NOX, VOC, and ozone (first line) and regular CAMx NOX, 

VOC and ozone (second line).

7.6 Postprocessing

The tracer concentrations in the gridded surface concentration files can be displayed using any 

post-processing software normally used for displaying CAMx average file output formats.

The receptor concentration file contains information for all receptors and all hours within the 

model run that created the file. It is left to the user to develop post-processing tools to analyze 

the information contained in this file and prepare displays like Figure 7-2.

7.7 Steps In Developing Inputs And Running OSAT

Below is a simple methodological list of steps to follow in setting up and running OSAT. The 

process is similar among the OSAT, PSAT, and DDM Probing Tools.

1) Define the source groups and regions that you wish to track. Keep in mind that memory 

resources increase dramatically as the number of tracers grows. Probing Tool 

applications with large numbers of tracers, tracer classes, nested grids or grid cells may 

exceed available memory.

2) Build a source region map (Figure 7-10) that defines the spatial allocation of tracer 

emissions. For small domains or small number of regions, this can be done by hand. We 

suggest using GIS software to develop complex source region maps on large grids.

3) Process the emissions inventory into the separate source group files that you want to 

track (e.g., mobile, area, point, biogenic, etc.).

a) Consideration of potential source apportionment or sensitivity applications prior to 

any emissions processing can be very beneficial so that files by group are available 

for later use.

b) Elevated point sources will automatically be assigned to the source region in which 

they reside. However, you may override the region to which each individual point 

source is assigned (see the definition of kcell in Section 3, Elevated Point Source 

File). A point source region does not need to be defined in the source region map, 

e.g., you could have a map with two regions that split the domain in half, with a 

third region assigned arbitrarily to represent elevated point sources only.

4) Edit the CAMx control namelist file (Section 2).
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a) Set the Probing_Tool variable to the technology you wish to use (OSAT, APCA, 

GOAT). This will activate the &SA_Control namelist module.

b) Edit or add the &SA_Control namelist module (described earlier). Provide the 

required information, including:

• output paths

• whether to stratify boundary conditions

• number of source regions

• number of source groups

• whether to use the leftover group option

• receptor definitions

• list of input emission files by group.

c) Note that APCA requires that the biogenic emission files for each grid are listed first. 

Several examples are shown in Figure 7-9.

5) Configure the CAMx source code to define the number of tracers, and build an 

executable. This will ensure that you have sufficient memory for the Probing Tool 

application.

a) Edit the file Includes/camx.prm

b) Change the parameter MXTRSP, following the instructions provided in the file. 

CAMx is distributed with MXTRSP = 1 to minimize memory requirements for 

standard applications of the model. If you run OSAT with an insufficient value, the 

model will stop and tell you the required value of MXTRSP for your application.

c) Execute the CAMx Makefile to build an executable program (Section 2).

6) Run CAMx and review the diagnostic output files to ensure that the model is correctly 

interpreting and running the Probing Tool configuration that you have specified. Ensure 

that CAMx is generating the proper output files that you are expecting. Review the 

table of emissions by source group and region.

7) Review gridded tracer fields using commonly available plotting programs. Utilities such 

as PAVE or Verdi will read Probing Tool files directly. Use of any other software may 

require specialized re-formatting procedures.

8) You may post-process and analyze OSAT receptor files using your own spreadsheet or 

database software.

9) Probing Tool gridded tracer output files are written in the same Fortran binary format as 

the regular CAMx concentration output files. You can post-process gridded output fields 

using any software that reads CAMx files, or you can adapt those programs or build your 

own software to generate specialized analysis and graphical products.
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8. PARTICULATE SOURCE APPORTIONMENT TECHNOLOGY

Airborne particulate matter (PM) is widely recognized as an important pollution issue because it 

causes health problems and environmental degradation. In recent years the emphasis on 

controlling PM has shifted toward fine PM (or PM2.5, with particle diameter less than 2.5 μm) 

because it is more strongly associated with serious health effects than coarse PM. Knowing 

which sources contribute to PM2.5 is essential for developing effective control strategies. 

Many components of PM2.5 are secondary pollutants and so photochemical models are 

important tools for PM air quality planning. The Particulate Source Apportioning Technology 

(PSAT) has been developed for CAMx to provide PM source apportionment among specific 

geographic regions and source categories (Yarwood et al., 2004). PM source apportionment 

information from PSAT is useful for:

1) Understanding model performance and thereby improving model inputs/formulation;

2) Performing culpability assessments to identify sources that contribute significantly to 

PM pollution;

3) Designing the most effective and cost-effective PM control strategies.

Source apportionment for primary PM is relatively simple to obtain from any air pollution 

model because their source-receptor relationships are essentially linear. Gaussian steady-state 

models and Lagrangian puff models have been used extensively to model primary PM pollution 

from specific sources, which is a direct form of source apportionment. The Gaussian and 

Lagrangian approaches work for primary PM because the models can assume that emissions 

from separate sources do not interact. This assumption breaks down for secondary PM 

pollutants (e.g., sulfate, nitrate, ammonium, secondary organic aerosol) and so puff models 

may dramatically simplify the chemistry (to eliminate interactions between sources) so that 

they can be applied to secondary PM. Eulerian photochemical grid models are better suited to 

modeling secondary pollutants because they account for chemical interactions between 

sources. Grid models do not naturally provide source apportionment because the impact of all 

sources has been combined in the total pollutant concentration. PSAT has been developed to 

retain the advantage of using a grid model to describe the chemistry of secondary PM 

formation and also to provide source apportionment.

Consider a chemical species X that has two sources A and B (so X = xA + xB) and which 

undergoes a second order self-reaction with rate constant k. The rate of chemical change is:

( )

A B A B

A B

kx kx kx x

dt

dX

k x x

dt

dX

kX

dt

dX

2 2 2

2

2

= − − −

= − +

= −
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The homogeneous rate terms kxA

2 and kxB2 clearly describe chemical change for pollutants 

from sources A and B (xA and xB), but the inhomogeneous rate term 2kxAxB is not uniquely 

associated with either source A or B. A reactive tracer (or tagged species) source 

apportionment method must deal with this inhomogeneous rate term either by developing 

rules to apportion the inhomogeneous term to sources A and B or by modifying the chemistry 

to eliminate the inhomogeneous term. For a sensitivity method, the homogeneous quadratic 

rate terms generate second-order homogeneous sensitivity coefficients (sAA and sBB) and the 

inhomogeneous rate term generates a second-order inhomogeneous sensitivity coefficient 

(sAB). Consequently, the total concentration of X is incompletely described by the first-order 

sensitivity coefficients (sA and sB) that resemble source apportionments.

The example presented above is a simple case of a non-linear chemical system that illustrates 

why source apportionment and source sensitivity are not the same thing for nonlinear systems. 

The implications are:

1) There is no unique source apportionment for chemical species that depend upon 

nonlinear reactions, such as secondary PM species and ozone. Nonetheless, reasonable 

source apportionment schemes can be developed and are useful tools for achieving the 

objectives listed in the introduction.

2) Sensitivity coefficients are not source apportionments for chemical species that depend 

upon nonlinear reactions, such as secondary PM species and ozone. Sensitivity 

coefficients are most applicable for predicting the model response to an input change 

(e.g., control strategy) and are very useful for this purpose (within the range of linear 

model response), but sensitivity coefficients should be used with care for source 

apportionment or culpability assessment. Likewise, source apportionments should be 

used with care for predicting model response to input changes.

8.1 PSAT Methodology

PSAT is designed to source apportion the following PM species (CF mode only) in CAMx:

• Sulfate (SO4)

• Particulate nitrate (NO3)

• Ammonium (NH4)

• Particulate mercury (Hg(p))

• Secondary organic aerosol (SOA)

• Six categories of primary PM:

- Elemental carbon (EC) 

- Primary organic aerosol (POA)

- Crustal fine (FCRS)

- Other fine (FPRM)

- Crustal coarse (CCRS)

- Other coarse (CPRM)
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The PSAT “reactive tracers” that are added for each source category/region (i) are described 

below. In general, a single tracer can track primary PM species whereas secondary PM species 

require several tracers to track the relationship between gaseous precursors and the resulting 

PM. Particulate nitrate and secondary organics are the most complex species to apportion 

because the emitted precursor gases (NO, VOCs) are several steps removed from the resulting 

PM species (NO3, SOA). The PSAT tracers for each type of PM are listed below. There is a PSAT 

convention that tracer names for particulate species begin with the letter “P.”

Sulfur

SO2i Primary SO2 emissions

PS4i Particulate sulfate ion from primary emissions plus secondarily formed sulfate

Nitrogen

RGNi Reactive gaseous nitrogen including primary NOx (NO + NO2) emissions plus 

nitrate radical (NO3), nitrous acid (HONO) and dinitrogen pentoxide (N2O5).

TPNi Gaseous peroxyl acetyl nitrate (PAN) plus peroxy nitric acid (PNA)

NTRi Organic nitrates (RNO3)

HN3i Gaseous nitric acid (HNO3)

PN3i Particulate nitrate ion from primary emissions plus secondarily formed nitrate

NH3i Gaseous ammonia (NH3)

PN4i Particulate ammonium (NH4)

Secondary Organic

AROi Aromatic (toluene and xylene) secondary organic aerosol precursors

ISPi Isoprene secondary organic aerosol precursors

TRPi Terpene secondary organic aerosol precursors

SQT Sesquiterpene secondary organic aerosol precursors

CG1i Condensable gases from aromatics (low volatility products)

CG2i Condensable gases from aromatics (high volatility products)

CG3i Condensable gases from isoprene (low volatility products)

CG4i Condensable gases from isoprene (high volatility products)

CG5i Condensable gases from terpenes (low volatility products)

CG6i Condensable gases from terpenes (high volatility products)

CG7i Condensable gases from sesqiterpenes

PO1i Particulate organic aerosol associated with CG1

PO2i Particulate organic aerosol associated with CG2

PO3i Particulate organic aerosol associated with CG3

PO4i Particulate organic aerosol associated with CG4

PO5i Particulate organic aerosol associated with CG5

PO6i Particulate organic aerosol associated with CG6

PO7i Particulate organic aerosol associated with CG7

PPAi Anthropogenic organic aerosol polymers (SOPA)

PPBi Biogenic organic aerosol polymers (SOPB)

Mercury

HG0i Elemental Mercury vapor

HG2i Reactive gaseous Mercury vapor
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PHGi Particulate Mercury 

Primary Particulate

PECi Primary Elemental Carbon

POAi Primary Organic Aerosol

PFCi Fine Crustal PM

PFNi Other Fine Particulate

PCCi Coarse Crustal PM

PCSi Other Coarse Particulate

PSAT includes a total of 32 tracers for each source group (i) if source apportionment is applied 

to all types of PM. Since source apportionment may not always be needed for all species, the 

PSAT implementation is flexible and allows source apportionment for any or all of the chemical 

classes in each CAMx simulation (i.e. the SO4, NO3, NH4, SOA, Hg and primary PM classes listed 

above). For example, source apportionment for sulfate/nitrate/ammonium requires just 9 

tracers per source group.

One fundamental assumption in PSAT is that PM should be apportioned to the primary 

precursor for each type of PM. For example, SO4 is apportioned to SOx emissions, NO3 is 

apportioned to NOx emissions, NH4 is apportioned to NH3 emissions, etc. As a source 

apportionment method, PSAT must account for all modeled sources of a PM species. Consider 

two model species A and B that are apportioned by reactive tracers ai and bi, respectively. 

Reactive tracers must be included for all sources of A and B including emissions, initial 

conditions and boundary conditions so that complete source apportionment is obtained, i.e., A 

= Σai and B = Σbi. 

In PSAT, the general approach to modeling change over a model time step ∆t is illustrated for a 

chemical reaction A→B. The general equation for species destruction is:

Here, the relative apportionment of A is preserved as the total amount changes. This equation 

applies to chemical removal of A and also to physical removal of A by processes such as 

deposition or transport out of a specific grid cell. 

The general equation for species production (e.g., chemical production by the chemical reaction 

A→B) is:

Here, production of B inherits the apportionment of the precursor A. The same equation 

applies for “production” of B in a specific grid cell due to emissions or transport. For the case 

where B increases due to emissions, ai is the apportionment of the emissions inventory. For 

the case where B increases due to transport, ai is the apportionment of the upwind grid cell.

( ) ( )

i

i

i i

a

a

a t t a t A

∑

+ ∆ = + ∆

( ) ( )

i

i

i i

a

a b t t b t B

∑

+ ∆ = + ∆
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In some cases, source category specific weighting factors (wi) must be added to the equation 

for species destruction:

An example is chemical decay of the aromatic VOC tracers (ARO), which must be weighted by 

the average OH rate constant of each AROi. ARO tracers for different source groups have 

different average VOC reactivities because the relative amounts of toluenes and xylenes differ 

between source categories.

In some cases, source category specific weighting factors (wi) must be added to the equation 

for species production:

An example is chemical production of condensable gases (CG1 or CG2) from aromatic VOC 

tracers, which must be weighted by aerosol yield weighting factors. The aerosol yield weighting 

factors depend upon the relative amounts of toluenes and xylenes in each source group.

Several aerosol reactions are treated as equilibria, A↔B. If A and B reach equilibrium at each 

time step, it follows that their source apportionments also reach equilibrium:

Examples are the equilibrium between gas phase nitric acid and aerosol nitrate, gas phase 

ammonium and aerosol ammonium, and condensable organic gases (CG) and secondary 

organic aerosols (SOA).

8.2 Running CAMx With PSAT

8.2.1 CAMx Control File

PSAT is invoked similarly to the OSAT Probing Tool within the CAMx control file. In the 

&CAMx_Control namelist module, the variable Probing_Tool must be set to “PSAT”. An 

additional namelist module called &SA_Control must then be provided in the control file to 

configure the PSAT portion of the model – note that this is identically the same module as used 

for OSAT. The PSAT/OSAT namelist module is described in Section 7; the additional variables 

needed for PSAT are described below. The order of the variables follow the template available 

with the source code. An example of the PSAT portion of the CAMx run control file is shown in 

Figure 8-1. All other capabilities and I/O requirements for PSAT mirror those of OSAT.

( ) ()

i i

i i

i i

w a

w a

a t t a t A

∑

+ ∆ = + ∆

( ) ()

i i

i i

i i

w a

w a b t t b t B

∑

+ ∆ = + ∆

( ) [ () ()]

( ) [ () ()] 



 





+

+ ∆ = +





 





+

+ ∆ = +

A B

B b t t a t b t

A B

A

a t t a t b t

i i i

i i i
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Description of PSAT Control in the CAMx Run Control File

&SA_Control Label for the Probing Tool namelist module that configures the 

PSAT and OSAT options; it must begin in column 2

& Flag ending a namelist module; it must be in column 2

SA_Summary_Output Logical flag used to limit the species written to the tracer 

concentration file to a subset of the PSAT treated species. If set 

to true, the output will be restricted to the following species: 

O3N, O3V, PS4, PN3, PN4, PO1, PO2, PO3, PO4, PO5, PEC, POC, 

FCR, FPR, CCR, CPR, HG0, HG2, PHG

PSAT_Treat_SULFATE_Class Logical flag to turn on the sulfate class of tracer species.

PSAT_Treat_NITRATE_Class Logical flag to turn on the nitrate class of tracer species.

PSAT_Treat_SOA_Class Logical flag to turn on the SOA class of tracer species.

PSAT_Treat_PRIMARY_Class Logical flag to turn on the primary PM class of tracer species.

PSAT_Treat_MERCURY_Class Logical flag to turn on the mercury class of tracer species.

PSAT_Treat_OZONE_Class Logical flag to turn on the ozone class of tracer species.
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&SA_Control

SA_File_Root = '$TRACOUT/CAMx.OSAT.9507$today',

SA_Summary_Output = .true.,

SA_Master_Sfc_Output = .true.,

SA_Nested_Sfc_Output = .true.,

SA_Stratify_Boundary = .false.,

SA_Deposition_Output = .false.,

SA_Number_of_Source_Regions = 19,

SA_Number_of_Source_Groups = 3,

Use_Leftover_Group = .false.,

PSAT_Treat_SULFATE_Class = .true.,

PSAT_Treat_NITRATE_Class = .true.,

SA_Receptor_Definitions = '$TRACIN/receptor.cities ',

SA_Source_Area_Map(1) = '$TRACIN/APCA.source.area.map',

SA_Source_Area_Map(2) = ' ',

SA_Master_Restart = '$TRACOUT/CAMx.OSAT.9507$yesterday.sa.inst',

SA_Nested_Restart = '$TRACOUT/CAMx.OSAT.9507$yesterday.sa.finst',

SA_Points_Group(1) = ' ',

SA_Points_Group(2) = '$PTSRCE/utilpt.ng.$todate-07.ag.07cem1A-run11',

SA_Points_Group(3) = '$PTSRCE/remain.ng.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(1,1) = '$TRACEMS/bio2.cc.$todate-95',

SA_Emiss_Group_Grid(1,2) = '$TRACEMS/bio2.ff.$todate-95.ne',

SA_Emiss_Group_Grid(2,1) = '$TRACEMS/util.cc.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(2,2) = '$TRACEMS/util.ff.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(3,1) = '$TRACEMS/remain.cc.$todate-07.ag.07cem1A-run11',

SA_Emiss_Group_Grid(3,2) = '$TRACEMS/remain.ff.$todate-07.ag.07cem1A-run11',

&

Figure 8-1. This figure follows from Figure 7-9(d): it is a continuation day of a 2-grid run with 

three emission groups, and all three emission groups are defined explicitly by supplying extra 

emission files (AREA group 1, AREA group 2, POINT group 2, AREA group 3, and POINT group 

3). Therefore, the “Use_Leftover_Group” flag is set to FALSE. The POINT group 1 filename is 

blank because group 1 is a category with no point source emissions (e.g., biogenics). PSAT 

will trace PM sulfate and nitrate species only.
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8.3 Steps In Developing Inputs And Running PSAT

Below is a simple methodological list of steps to follow in setting up and running PSAT. The 

process is similar among the OSAT, PSAT, and DDM Probing Tools.

1) Define the source groups and regions that you wish to track. Keep in mind that memory 

resources increase dramatically as the number of tracers grows. Probing Tool 

applications with large numbers of tracers, tracer classes, nested grids or grid cells may 

exceed available memory.

2) Build a source region map (Figure 7-10) that defines the spatial allocation of tracer 

emissions. For small domains or small number of regions, this can be done by hand. We 

suggest using GIS software to develop complex source region maps on large grids.

3) Process the emissions inventory into the separate source group files that you want to 

track (e.g., mobile, area, point, biogenic, etc.).

a) Consideration of potential source apportionment or sensitivity applications prior to 

any emissions processing can be very beneficial so that files by group are available 

for later use.

b) Elevated point sources will automatically be assigned to the source region in which 

they reside. However, you may override the region to which each individual point 

source is assigned (see the definition of kcell in Section 3, Elevated Point Source 

File). A point source region does not need to be defined in the source region map, 

e.g., you could have a map with two regions that split the domain in half, with a 

third region assigned arbitrarily to represent elevated point sources only.

4) Edit the CAMx control namelist file (Section 2).

a) Set the Probing_Tool variable to the technology you wish to use (PSAT). This 

will activate the &SA_Control namelist module.

b) Edit or add the &SA_Control namelist module (described earlier). Provide the 

required information, including:

• output paths

• whether to stratify boundary conditions

• number of source regions

• number of source groups

• whether to use the leftover group option

• receptor definitions

• flags to turn on specific PM classes

• list of input emission files by group.

5) Configure the CAMx source code to define the number of tracers, and build an 

executable. This will ensure that you have sufficient memory for the Probing Tool 

application.

a) Edit the file Includes/camx.prm

b) Change the parameter MXTRSP, following the instructions provided in the file. 

CAMx is distributed with MXTRSP = 1 to minimize memory requirements for 

standard applications of the model. If you run PSAT with an insufficient value, the 

model will stop and tell you the required value of MXTRSP for your application.

c) Execute the CAMx Makefile to build an executable program (Section 2).
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6) Run CAMx and review the diagnostic output files to ensure that the model is correctly 

interpreting and running the Probing Tool configuration that you have specified. Ensure 

that CAMx is generating the proper output files that you are expecting. Review the 

table of emissions by source group and region.

7) Review gridded tracer fields using commonly available plotting programs. Utilities such 

as PAVE or Verdi will read Probing Tool files directly. Use of any other software may 

require specialized re-formatting procedures.

8) You may post-process and analyze PSAT receptor files using your own spreadsheet or 

database software.

9) Probing Tool gridded tracer output files are written in the same Fortran binary format as 

the regular CAMx concentration output files. You can post-process gridded output fields 

using any software that reads CAMx files, or you can adapt those programs or build your 

own software to generate specialized analysis and graphical products.
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9. DECOUPLED DIRECT METHOD FOR SENSITIVITY ANALYSIS

Photochemical modelers have traditionally used sensitivity analysis both for model 

performance evaluation and emission control strategy design. The simplest approach to 

sensitivity analysis, often referred to as the “brute-force” approach, involves changing a model 

input parameter, rerunning the model, and then evaluating the change in model output. This 

approach requires an initial base run and a separate sensitivity run for each parameter to be 

investigated. For example, a model performance evaluation may use sensitivity simulations to 

evaluate the impact of changing the initial conditions (ICs), boundary conditions (BCs), biogenic 

emissions, anthropogenic emissions, etc. Sensitivity analysis is also used to aid control strategy 

design. For example, across-the-board VOC and NOx emission reductions are used to determine 

whether VOC and/or NOx reduction strategies are the most effective path to reduce ozone.

The advantages of the “brute force” method for sensitivity analysis are:

• Applicable to any model input parameter;

• Results are conceptually easy to explain and interpret.

The limitations of the “brute force” method are:

• Computationally inefficient;

• Sensitivity depends upon the magnitude of the perturbation if the model response is nonlinear;

• Sensitivity derived from small perturbations may contain significant levels of uncertainty 

(numerical noise).

The last two points bear further explanation. If the model response to an input parameter 

depends upon non-linear components within the model (e.g., chemistry), then the relative 

magnitude or even sign of the output response may change for perturbations of different sizes. 

An example is the response of ozone to NOx reductions in a VOC-limited environment: smaller 

reductions in NOx emissions increase ozone levels whereas larger NOx reductions decrease 

ozone.

This situation can be illustrated mathematically. We define a “sensitivity coefficient” (s) which 

represents the change in concentration (c) with respect to some input parameter (λ), evaluated 

relative to the base state (λ=λ0),

In general, λ can be a vector (denoted as λ), which contains multiple parameters related to 

processes in the model (e.g., rate constants) or inputs to the model (e.g., emissions). The 

response of concentration to a change in λ can be represented by a Taylor series of sensitivity 

coefficients:

o

c

s

∂λ λ

∂ =
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where n is the number of λ vector elements, x is the spatial dimension vector, and t is time. In 

the ozone sensitivity example above, the non-linear response of ozone to large NOx emission 

reductions indicates that high-order sensitivity coefficients (curvatures and inflections) are 

significant relative to the first order sensitivity (linear response). As the magnitude of the input 

perturbation tends to zero, the output response will become dominated by the first-order 

sensitivity. Therefore, very small changes in the input parameter may be required to use the 

“brute force” method to estimate the first-order (local) sensitivity. The practical limitation to 

this approach is that since the change in output must be determined from the difference 

between two simulations, small levels of numerical uncertainty (noise) in two very similar 

outputs will contaminate the sensitivity calculation.

An alternative methodology for evaluating model sensitivity was developed by Dunker (1980 

and 1981) called the decoupled direct method (DDM). The DDM can be used to calculate the 

same type of sensitivity coefficient as is available from the “brute force” method. The 

difference is that with DDM, sensitivity coefficients are calculated explicitly by specialized 

algorithms implemented in the host model. Thus, the DDM offers several advantages over the 

brute force method:

• Improved computational efficiency;

• Improved accuracy since sensitivities need not be contaminated by numerical noise;

• Multiple sensitivities can be calculated simultaneously

The degree to which these advantages are realized depends upon how the method is 

implemented, i.e., the algorithms employed and their coding. Fortunately, the performance of 

the DDM can be evaluated quantitatively by careful comparison of DDM sensitivities against 

“brute-force” sensitivities.

9.1 Implementation

The original implementation of the DDM in CAMx, which considers only first-order sensitivity

for gas-phase species, was performed in a joint project between Dr. Alan Dunker and ENVIRON 

with sponsorship from the Coordinating Research Council (CRC). A rigorous analysis of DDM 

was performed as part of that project, and excellent agreement was demonstrated (Dunker et 

al., 2002a). High-order DDM (HDDM; Hakami et al., 2003; Cohan et al., 2005) has since been 

implemented in CAMx through collaboration with Dr. Daniel Cohan (Rice University) with 

sponsorship from the Texas Commission on Environmental Quality (TCEQ). HDDM enables 

CAMx to calculate second-order sensitivities along with first-order values for gas-phase species 

( ) ( ) ( )

( )( )

...

2

1

, ; , ;

1

0

1

0

2

1

0 0

+

− − ∂ ∂

∂

+

− ∂

∂ = +

∑∑

∑

= =

=

n

i

j j

n

j

i i

i j

n

i

i i

i

o

o

c

c

c x t c x t

λ λ λ λ

λ λ

λ λ

λ

λ λ

λ

λ
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(Koo et al., 2007a,2008). The first-order DDM sensitivity has been extended to PM species (Koo 

et al., 2007b,2009). In the following discussion we use the term DDM generically to mean first 

and/or higher order sensitivity.

The CAMx DDM calculates sensitivity of predicted concentrations to pollutant sources (i.e., 

emissions, ICs and BCs) and to chemical rate constants. In the past, the implementation of 

DDM in other models (Dunker, 1981; Yang et al., 1997) has included sensitivities to other model 

input parameters (e.g., meteorological parameters). The CAMx implementation could be 

extended to other sensitivity parameters in the future.

The CAMx DDM sensitivity to be evaluated may bear a simple relationship to a model input

parameter, such as scaling the ozone boundary concentration by a factor (BCnew = λ × BC0), or 

additively increasing the ozone boundary concentration by a constant amount everywhere 

(BCnew = λ + BC0). To allow complete flexibility, the perturbations are specified by providing 

additional IC, BC, and/or emission input files with the same format as the regular model input 

files.

In mathematical terms, a regular model input file, for example the BC input file, represents 

some set of functions of space and time fi(x,t), where each chemical species i can be defined by 

a unique function. An additional input file provided to the DDM represents another set of 

functions of space, time, and chemical species gi(x,t) that can be different from the regular 

input file. The scalar parameter λi is then defined by

Here, λi×gi(x,t) is the perturbation, and the user desires information on how the model would 

respond if the input fi(x,t) is replaced by the input Fi(x,t). (In the case of sensitivity to rate 

constants, no user-defined input file is provided and the perturbation is always defined as λi×k

where k is a vector of selected rate constants). The DDM calculates the first-order sensitivity 

si

(1)(x,t) and second-order sensitivity si(2)

(x,t) with respect to the scalar parameter λi. The 

Taylor series to second order then gives the estimate:

where cl(x;t;λi) is the estimated model result for species l when Fi(x,t) is used as input, and 

cl(x,t;λi=0) is the base case model result when fi(x,t) is used as input.

For example, to calculate the sensitivity of the predicted ozone concentration to scaling 

boundary ozone by a factor, CAMx would be provided with a DDM BC file that has the same 

ozone values as the regular model BC file. The sensitivity coefficient fields output by CAMx 

could then be used to estimate the resulting ozone concentration if the ozone BCs were 

increased by 20%, as follows:

F (x,t) f (x,t) g (x,t). i = i + λi× i

c (x t ) c (x t ) s (x t) s (x t) l i l i i i i i , 2

1 , ; , ; 0 , (1) 2 (2) λ = λ = + λ × + λ ×

(1) 2 (2) c 0.2 = c 0 + 0.2× s + 0.5× 0.2 × s λ= λ=
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(For simplicity hereafter, the dependence on space, time, and chemical species will be omitted).

To calculate the sensitivity of the predicted ozone concentration to increasing boundary ozone 

by 10 ppb, CAMx would be provided with a DDM BC file that has a constant ozone value of 10 

ppb. The sensitivity coefficient fields could be used to estimate the ozone concentration if the 

ozone BCs were increased by 10 ppb as follows:

where each sensitivity is calculated according to a 10 ppb addition (thus sensitivities are scaled 

by unity). An alternative approach would be to provide CAMx with a DDM BC file that has a 

constant ozone value of 1 ppb. This perturbation would be associated with a new parameter λ′

and a new sensitivity coefficient s′. To estimate the ozone concentration if the ozone BC were 

increased by 10 ppb, one would use

where each sensitivity is calculated according to a 1 ppb addition that must then be scaled by 

10. This would give exactly the same estimate as the preceding approach in which CAMx is 

supplied with a DDM BC file that has an ozone value of 10 ppb everywhere because these

sensitivities are related by s′

(1) = s(1)×0.1 and s′(2)

= s(2)×0.01 (from the first to second approach, 

there has been only a change of the scalar variable from λ to λ′). 

These are examples of relatively simple sensitivities. A more complex example would be to 

calculate the sensitivity to morning (6-9 AM) NOx emissions in specific group of grid cells. In 

this case you would provide CAMx with a DDM emissions file where all values are zero except 

for the NOx emissions in the selected grid cells between 6 AM and 9 AM, which would have the 

same value as the regular emissions file. In this case the sensitivity coefficient for ozone might 

be interpreted as the increase (or decrease) in ozone concentration due to the selected 

emissions (however, caution is warranted because sensitivity coefficients are not directly 

equivalent to a source apportionment). More accurately, the sensitivity coefficient could be 

used to predict the concentration after a scalar change (λ) in the morning NOx emissions using 

the equation: 

Any type of sensitivity perturbation can be described via an input file. However, the CAMx user 

interface also provides easy ways to define some sensitivities that are likely to be used 

frequently. In the first example above, the DDM BC file was described as having the “same 

ozone values as the regular model BC file.” To make such a file you could copy the BC file and 

then remove (or zero out) all species but ozone. To avoid the effort of preparing an input file

that is trivially different from the regular model file, the user interface allows you to select 

specific species from an input file to track - in this case ozone. It is possible to separately track 

the sensitivity to more than one species from the same file (e.g. ozone and NO). It is also 

possible to track the combined sensitivity to a group of species, such as NOx, VOC, HRVOC, or 

(1) 2 (2) c 1.0 = c 0 +1.0× s + 0.5×1.0 × s λ = λ =

(1) 2 (2) c 10 = c 0 + 10.0× s′ + 0.5×10.0 × s′ λ′= λ′=

(1) 2 (2) c = c 0 + × s + 0.5 × s λ λ= λ λ
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ALL. The user interface also provides a simple way to track sensitivities to emissions from 

specific grid cells or groups of cells (sub-regions).

9.1.1 Tracking Sensitivity Coefficients Within CAMx

The conceptual approach in tracking DDM sensitivity coefficients is directly parallel to the way 

in which CAMx calculates three-dimensional concentration fields. The concentration fields are 

calculated by a series of code modules that operate sequentially to represent the impact of 

different physical processes (emissions, advection, diffusion, chemistry, deposition, etc.) on the 

gridded concentrations. Sensitivity coefficients are calculated by a parallel set of modules 

which operate in step with the CAMx modules to calculate gridded sensitivity coefficients. For 

some processes (e.g., chemistry and horizontal advection), the sensitivity coefficient modules 

make use of information saved from the corresponding CAMx modules. The need to employ 

this approach arises in cases where the CAMx algorithm depends non-linearly upon species 

concentrations. In other cases, the sensitivity algorithm turns out to be identical to the CAMx 

algorithm (e.g., horizontal diffusion) and both concentrations and sensitivity coefficients can be 

processed by the single module. Finally, there are cases where the sensitivity algorithm turns 

out to be identical to the CAMx algorithm, but a specialized module has been written for the 

sensitivity coefficients to improve the computational efficiency (e.g., vertical advection).

Priorities in the DDM coding implementation were:

• Ensuring accuracy by using consistent numerical methods for the concentrations and 

sensitivities;

• Ensuring accuracy by calculating the concentrations and sensitivities using the same time 

steps (for original DDM);

• Optimizing the efficiency of the sensitivity coefficient calculations without compromising 

accuracy;

• Providing a flexible User Interface that allows calculation of sensitivities to all sources and 

precursors;

• Ensuring that the DDM algorithms have minimal impact on computer resource 

requirements (memory and CPU time) when the DDM is not being used.

9.1.1.1 Horizontal Advection and Chemistry

Specialized modules were developed to calculate the effects of chemistry and horizontal 

advection upon DDM sensitivity coefficients. These DDM modules are exactly matched to the 

numerical methods employed in the corresponding CAMx modules. CAMx has two separate 

options for the horizontal advection solver (Bott and PPM) and three options for the gas phase 

chemistry solver (the EBI solver, IEH solver, and LSODE [Gear] solver). (H)DDM can be used 

with either of the horizontal advection solvers. The original first-order DDM implementation 

was developed only for the EBI chemistry solver; it cannot be used with other chemistry solver 

options. However, HDDM can be used with any chemistry solver.

The implementation of DDM and HDDM algorithms into the chemistry solvers is performed 

using the chemical mechanism compiler (CMC). Therefore, both DDM and HDDM are available 
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for the CB05, CB6, and SAPRC99 chemical mechanisms, and will be available for additional 

mechanisms implemented in CAMx in the future. 

9.1.1.2 Plume-in-Grid and ACM2

DDM and HDDM algorithms are not currently implemented for the Plume-in-Grid (PiG) 

submodel or the ACM2 vertical diffusion scheme in CAMx.

9.1.1.3 Source Code

The coding of DDM algorithms involved the creation of several new subroutines for CAMx. 

These subroutines are all grouped in a separate directory (called DDM) under the main CAMx 

source code directory. It was necessary to add additional code for DDM in several existing 

CAMx subroutines, and the new code is clearly marked by comments.

9.1.2 Flexi-DDM

Although DDM is computationally much more efficient than the Brute-Force method, it does 

require much more additional CPU time and memory space over and above a standard CAMx 

run, which can be significant especially when many first and second-order sensitivities are 

requested for a nested grid run with multiple source categories and multiple source regions. 

The increased computational cost may not always be worthwhile if only part of the modeling 

domain is of interest. One way to enhance computational efficiency in such cases is to use oneway nesting, where BCs for a nested grid are extracted from the parent grid, and so subsequent 

runs with sensitivities are performed without outer grids. However, differences between the 

two nesting schemes (i.e. 1-way vs. 2-way) sometimes cause discrepancies in the model results. 

An alternative approach is to run the full 2-way nested model while “turning off” sensitivity 

calculations outside nested grids of interest.

CAMx provides a feature called “Flexi-DDM”, which allows the user to turn off sensitivity 

calculations for selected grids (normally grids far outside the area of interest) to improve 

computational efficiency of DDM runs (at the expense of accuracy). This reduces CPU times but 

will not reduce memory requirements. Also, note that turning off sensitivity calculations for 

outer grids is only appropriate for certain types of sensitivity calculations: e.g., sensitivity to 

master grid BCs cannot be calculated with Flexi-DDM.

9.2 Running CAMx With DDM and HDDM

This section describes how to specify the sensitivity coefficients to be calculated and the 

additional input files that must be supplied. The DDM user interface was designed along similar 

lines to the Source Apportionment (OSAT/PSAT) user interface. This makes it easier to learn 

how to use both options and promotes consistency in analyses performed using OSAT/PSAT

and DDM. 

DDM is invoked similarly to the other Probing Tools within the CAMx control file. In the 

&CAMx_Control namelist module, the variable Probing_Tool must be set to either 

“DDM” to utilize the original first-order implementation, or “HDDM” to utilize the high-order 

implementation. An additional namelist module called &DDM_Control must then be 

provided in the control file to configure the DDM portion of the model. The additional namelist 
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module is described below. The order of the variables follow the template available with the 

source code. An example of the DDM portion of the CAMx run control file is shown in 

Figure 9-1.

Description of DDM Control in the CAMx Run Control File

&DDM_Control Label for the Probing Tool namelist module that configures the 

DDM option; it must begin in column 2

& Flag ending a namelist; it must be in column 2

DDM_File_Root Character root output path/filename

DDM_Master_Sfc_Output Logical flag for master grid surface output (TRUE=DDM file will 

be output for all sensitivities, FALSE=DDM file will not be 

output)

DDM_Nested_Sfc_Output Logical flag for nested grid surface output (TRUE=DDM file will 

be output for all sensitivities, FALSE=DDM file will not be 

output)

DDM_Stratify_Boundary Logical flag to stratify boundary types (TRUE=separate 

sensitivity types will be used for the N, S, E, W, and Top 

boundaries, FALSE=a single sensitivity type will be used for all 5 

boundaries)

DDM_Number_of_Source_Regions Integer number of source regions to be tracked. This 

must be the same as the number of source areas defined in the 

DDM_Source_Area_Map file. This value must be greater 

than zero when sensitivity to emissions is requested.

DDM_Number_of_Source_Groups Integer number of emission groups to be tracked. This 

determines the number of emission files that must be supplied 

(additional details below). This value must be greater than zero

when sensitivity to emissions is requested.

Number_of_IC_Species_Groups Integer number of species or species groups in the 

initial conditions to be tracked. This number may be between 

zero and the number of species being simulated plus four 

(allowing for the four species groups VOC, HRVOC, NOX, ALL).

IC_Species_Groups Character array (by IC group) names of the species or species 

groups in the initial conditions to be tracked. Allowed names 

are any species being simulated by the mechanism in use (e.g., 

O3, PAR, NO, etc.) plus the species groups NOX, VOC, HRVOC, 

and ALL. It is permissible to specify both a species and a group 

containing that species, e.g., both NO and NOX. Each name 
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may have up to 10 characters. Note that if you select a species 

that is not present on the IC file provided, the initial sensitivities 

for that species will be set to zero. This variable may be left 

blank if the number of initial condition species groups is zero.

 

Number_of_BC_Species_Groups Integer number of species or species groups in the 

boundary conditions to be tracked. This number may be 

between zero and the number of species being simulated plus 

four (allowing for the four species groups VOC, HRVOC, NOX, 

ALL).

BC_species_Groups Character array (by BC group) names of the species or species 

groups in the boundary conditions to be tracked. See 

description for IC_Species_Group above.

Number_of_EM_Species_Groups Integer number of species or species groups in the 

emissions to be tracked. This number may be between zero 

and the number of species being simulated plus four (allowing 

for the four species groups VOC, HRVOC, NOX, ALL).

Emis_Species_Groups Character array (by emissions group) names of the species or 

species groups in the emissions to be tracked. See description 

for IC_Species_Group above.

Number_of_Rate_Const_Groups Integer number of reaction rate sensitivity groups to be 

tracked. This number may be zero.

Rate_Const_Groups Character string containing each reaction rate sensitivity group 

name and reaction numbers that belong to the group. Group 

name and reaction numbers are separated by colon (:) and each 

reaction number is separated by comma (,).

Number_of_HDDM_Sens_Groups Integer number of second-order sensitivity groups to be tracked

(additional details below). This number may be zero.

HDDM_parameters Character array names of the first-order sensitivity parameters 

to which second-order sensitivity is computed. The naming of 

the first-order parameters is the same as the long name of 

sensitivities with the first 4 characters omitted (see DDM 

sensitivity naming conventions/formats below). For each 

HDDM sensitivity group, two first-order parameters are 

required (the same can be used twice). All the first-order 

parameters must be included in the modeling.

DDM_Receptor_Definitions Character input DDM receptor definition path/filename. (This is 

an optional file).

DDM_Source_Area_Map Character array (by CAMx grid) input DDM source area 

definition path/filename (required for master grid, optional for 
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nested grids). Source regions are defined using a map in the 

same format as an OSAT source area map (Section 7); however, 

DDM does not require that all parts of the modeling domain be 

tracked, therefore it is permissible to define an area numbered 

zero in the source area map (emissions from those areas will 

not be tracked). The non-zero source region numbers must be 

between 1 and the number of regions.

DDM_Calc_Grid Logical array containing Flexi-DDM flag for each grid (.TRUE. = 

calculate sensitivities in the grid; .FALSE. = do not calculate 

sensitivities in the grid).

DDM_Initial_Conditions The name of the sensitivity initial condition file. Leave the file 

name blank for restart days or if sensitivity to initial conditions 

is not being calculated.

DDM_Boundary_Conditions The name of the sensitivity lateral boundary condition file. 

Leave the file name blank if sensitivity to boundary conditions is 

not being calculated.

DDM_Master_Restart Character input master grid DDM restart path/filename 

(ignored if Restart=FALSE)

DDM_Nested_Restart Character input nested grid DDM restart path/filename 

(ignored if Restart=FALSE or Number_of_Grids=1)

DDM_Points_Group Character array (by source group) input DDM elevated point 

source emissions path/filename (optional, ignored if 

Point_Emissions=FALSE)

DDM_Emiss_Group_Grid Character array (by source group, by CAMx grid) input DDM 

gridded emissions path/filename (optional, ignored if 

Gridded_Emissions=FALSE)
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&DDM_Control

DDM_File_Root = '$DDM_OUT/CAMx.08jul95.runA’,

DDM_Master_Sfc_Output = .true.,

DDM_Nested_Sfc_Output = .true.,

DDM_Stratify_Boundary = .false.,

DDM_Number_of_Source_Regions = 4,

DDM_Number_of_Source_Groups = 2,

Number_of_IC_Species_Groups = 1,

IC_Species_Groups(1) = 'ALL',

Number_of_BC_Species_Groups = 1,

BC_species_Groups(1) = 'ALL',

Number_of_EM_Species_Groups = 2,

Emis_Species_Groups(1) = 'NOX',

Emis_Species_Groups(2) = 'VOC',

Number_of_Rate_Const_Groups = 1,

Rate_Const_Groups(1) = 'RXN1: 120,121,122',

Number_of_HDDM_Sens_Groups = 3,

HDDM_parameters(1,1) = 'EM0201NOX_',

HDDM_parameters(1,2) = 'EM0201NOX_',

HDDM_parameters(2,1) = 'EM0201VOC_',

HDDM_parameters(2,2) = 'EM0201VOC_',

HDDM_parameters(3,1) = 'EM0201NOX_',

HDDM_parameters(3,2) = 'EM0201VOC_',

DDM_Receptor_Definitions = '$DDM_IN/receptor.cities',

DDM_Source_Area_Map(1) = '$DDM_IN/source_map.DDM.4areas',

DDM_Source_Area_Map(2) = ' ',

DDM_Calc_Grid(1) = .true.,

DDM_Calc_Grid(2) = .true.,

DDM_Initial_Conditions = ' ',

DDM_Boundary_Conditions = '$DDM_IN/BC.08jul95',

DDM_Master_Restart = '$DDM_OUT/CAMx.07jul95.runA.ddm.inst',

DDM_Nested_Restart = '$DDM_OUT/CAMx.07jul95.runA.ddm.finst',

DDM_Points_Group(1) = ' ',

DDM_Points_Group(2) = '$DDM_PT/ptsr.ng.08jul95',

DDM_Emiss_Group_Grid(1,1) = '$DDM_EMIS/bio.cc.08jul95',

DDM_Emiss_Group_Grid(1,2) = '$DDM_EMIS/bio.ff.08jul95',

DDM_Emiss_Group_Grid(2,1) = '$DDM_EMIS/anthro.cc.08jul95',

DDM_Emiss_Group_Grid(2,2) = '$DDM_EMIS/anthro.ff.08jul95',

&

Figure 9-1. Example input of DDM options and filenames via the CAMx control file. In this case, CAMx 

is run with two grids, and DDM is configured to track emissions from four source regions and two 

source groups (biogenic and anthropogenic). Initial and boundary conditions are tracked as a single 

sensitivity called “ALL”, while emissions are tracked with two sensitivities called “NOX” and “VOC”. 

Sensitivity for a single rate constant group will be calculated involving mechanism reaction numbers 

120, 121, and 122. Three groups of second-order sensitivities to anthropogenic NOx and VOC 

emissions (emissions group 2) from source region 1 will be computed (d2

/dNOx2, d2/dVOC2 and 

d2

/dNOxdVOC). No source region map is provided for the nested grid (the region assignments on the 

nest are defined by the master grid). Initial condition file is not provided (a restart day), and only the 

group 2 point sources are tracked (no biogenic point sources are available).
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9.3 Approaches To Define IC, BC And Emissions Sensitivities

The description above shows how to specify the IC, BC and emissions files for DDM sensitivity 

calculations. The formats for each of these files are identical to the CAMx input files of these 

types. In many cases, users may choose to specify exactly the same file for a CAMx input file 

and a DDM input file. (Be aware that some computer systems do not allow a file to be opened 

twice by the same application. A work around for this problem is to copy or link the file 

“filename” to another file of different name, such as “filename.copy”). 

The user can perform many different sensitivity calculations in a single run according to the 

content of the DDM input files. Take initial conditions (ICs) as an example. If the same IC file is 

specified for both CAMx and DDM, the output sensitivity fields represent the sensitivity of the 

predicted concentrations to the ICs. Therefore, simply scaling the output sensitivity coefficients 

fields provides the incremental concentrations resulting from scaling the ICs.

As another example, if a DDM emissions file is supplied to CAMx that has a constant VOC 

emission rate everywhere, the sensitivity will correspond to a uniform absolute increase in the 

VOC emission rate rather than a percentage increase as described above. Another possibility 

would be a DDM emission file with a different spatial pattern than the CAMx input file. The 

sensitivity coefficient would then correspond to changing both the geographic distribution and 

magnitude of emissions. Still another possibility would be a DDM file that has zero emissions 

for all hours except midnight to 5 AM on the third simulated day. The program would then 

calculate the sensitivity to early morning emissions on the third day. In this case, just the 

concentrations could be simulated for the first two days and the DDM calculation begun on the 

third day, because sensitivities on the first two days are identically zero.

In short, the DDM input file can be arbitrary – different from the CAMx input file in the overall 

magnitude of concentrations or emissions, different in the geographic and temporal 

distribution, and different in the relative proportions of the chemical species. However, the 

user must understand what perturbations are being considered in order to properly interpret 

the resulting output sensitivity coefficient fields. Also, the user should recognize that as the 

size of perturbations increase, the second- and higher-order terms eventually become 

important, usually when the emissions are altered by more than 20-30% (a very crude, variable,

and uncertain approximation).

9.4 DDM Output Files

The output file types for a DDM simulation are described in Table 9-1. These files have the 

same format as corresponding concentration output files, described in Section 2.
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Table 9-1. DDM output file suffix names.

File Name Suffix DDM File Type

.ddm.inst Binary master grid instantaneous sensitivity file at end of simulation (used for restart), 3-

D, all sensitivities, in μmol m-3 for gases and μg m-3 for PM.

.ddm.finst Binary nested grid instantaneous sensitivity file at end of simulation (used for restart), 3-

D, all sensitivities, in μmol m-3 for gases and μg m-3 for PM.

.ddm.grdnn Binary average sensitivity file for grid nn, 2-D, surface layer sensitivities only for affected 

species requested in the CAMx average file, in ppm for gases and μg m-3 for PM.

.ddm.receptor Text hourly average sensitivities at user specific receptor locations. This file is in comma 

delimited ASCII format suitable for importing into a spreadsheet.

9.5 DDM Sensitivity Coefficient Names

Each DDM sensitivity coefficient tracks the influence of a species from a specific source (the 

influencing species) on a predicted concentration (the affected species). The sensitivity 

coefficient names are constructed to show this relationship, as follows:

{Affected Species}{Pollutant Source}{Influencing Species}

This is a lot of information to encode in a name that must conform to the ten character limit 

imposed by the binary I/O file formats. Because of this, two naming systems are used in CAMx:

• Long Names - these names are easy to read, but since they are more than ten characters 

in length they cannot be used in sensitivity coefficient binary output files. If an alternate 

I/O format is implemented in the future it may be possible to use the long names on 

sensitivity output files.

• Short Names - these convey the same information as the long names but require more 

practice to learn. They are used in the sensitivity coefficient binary output files.

At the start of each CAMx run a concordance of Long and Short sensitivity coefficient names is 

written to the diagnostic output file (.diag file). An example concordance is shown in Figure 9-

2, and a detailed explanation of the naming convention follows.
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 Affected Influencing Source Long Short

 Species Species Type Group Region Name Name

-------------------------------------------------------------------------------

NO ALL EM 1 2 NO__EM0102ALL_ 16E0102ALL

NO2 ALL EM 1 2 NO2_EM0102ALL_ 17E0102ALL

O3 ALL EM 1 2 O3__EM0102ALL_ 18E0102ALL

PAN ALL EM 1 2 PAN_EM0102ALL_ 19E0102ALL

PANX ALL EM 1 2 PANXEM0102ALL_ 20E0102ALL

PNA ALL EM 1 2 PNA_EM0102ALL_ 21E0102ALL

FACD ALL EM 1 2 FACDEM0102ALL_ 22E0102ALL

FORM ALL EM 1 2 FORMEM0102ALL_ 23E0102ALL

H2O2 ALL EM 1 2 H2O2EM0102ALL_ 24E0102ALL

HNO3 ALL EM 1 2 HNO3EM0102ALL_ 25E0102ALL

HONO ALL EM 1 2 HONOEM0102ALL_ 26E0102ALL

IOLE ALL EM 1 2 IOLEEM0102ALL_ 27E0102ALL

ISOP ALL EM 1 2 ISOPEM0102ALL_ 28E0102ALL

ISPD ALL EM 1 2 ISPDEM0102ALL_ 29E0102ALL

MEOH ALL EM 1 2 MEOHEM0102ALL_ 30E0102ALL

MEPX ALL EM 1 2 MEPXEM0102ALL_ 31E0102ALL

MGLY ALL EM 1 2 MGLYEM0102ALL_ 32E0102ALL

AACD ALL EM 1 2 AACDEM0102ALL_ 33E0102ALL

ALDX ALL EM 1 2 ALDXEM0102ALL_ 34E0102ALL

CO ALL EM 1 2 CO__EM0102ALL_ 35E0102ALL

ALD2 ALL EM 1 2 ALD2EM0102ALL_ 36E0102ALL

NTR ALL EM 1 2 NTR_EM0102ALL_ 37E0102ALL

Figure 9-2. Example concordance of long and short sensitivity coefficient names from the 

CAMx diagnostic output file. 

9.5.1 Initial Condition Sensitivity Names

Long Name NNNNIC____MMMM

where:

NNNN Affected species name with trailing underscore to pad blanks

IC Indicates the sensitivity coefficient is for initial conditions

____ Four underscores to pad the name to 14 characters

MMMM Influencing species name with trailing underscore to pad blanks

Examples: O3__IC____O3__

HNO3IC____NOX_

ETH_IC____HRVO

Short Name nnnI___mmm

where:

nnn Affected species number

I Indicates the sensitivity coefficient is for initial conditions

___ Three underscores to pad the name to 10 characters

mmm Influencing species number or name of a species group (NOX, 

VOC, HRVOC or ALL).
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Examples: 018I___018 (where O3 is species number 18)

025I___NOX (where HNO3 is species number 25)

042I___HRV (where ETH is species number 42)

9.5.2 Boundary Condition Sensitivity Names

Long Name NNNNBCRRR_MMMM

where:

NNNN Affected species name with trailing underscore to pad blanks

BC Indicates the sensitivity coefficient is for boundary conditions

RRR NTH, STH, EST, WST or TOP if stratified by boundary; ALL if not 

stratified by boundary

_ Underscore to pad the name to 14 characters

MMMM Influencing species name with trailing underscore to pad blanks

Examples: O3__BCTOP_O3__

HNO3BCEST_NOX_

ETH_BCALL_HRVO

Short Name nnnBRRRmmm

where:

nnn Affected species number

B Indicates the sensitivity coefficient is for initial conditions

RRR NTH, STH, EST, WST or TOP if stratified by boundary; ALL if not 

stratified by boundary

mmm Influencing species number or name of a species group (NOX, 

VOC, HRVOC or ALL)

Examples: 018BTOP018 (where O3 is species number 18)

025BESTNOX (where HNO3 is species number 25)

042BALLHRV (where ETH is species number 42)

9.5.3 Emissions Sensitivity Names

Long Name NNNNEMGGRRMMMM

where:

NNNN Affected species name with trailing underscore to pad blanks

EM Indicates the sensitivity coefficient is for emissions

GG Emissions group number

RR Emissions region number
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MMMM Influencing species name with trailing underscore to pad blanks

Examples: O3__EM0101O3__

HNO3EM0201NOX_

ETH_EM0103HRVO

Short Name nnnGGRRmmm

where:

nnn Affected species number

GG Emissions group number

RR Emissions region number

mmm Influencing species number or name of a species group (NOX, 

VOC, HRVOC or ALL)

Examples: 0180101018 (where O3 is species number 18)

0250201NOX (where HNO3 is species number 25)

0420103HRV (where ETH is species number 42)

9.5.4 Reaction Rate Sensitivity Names

Long Name NNNNRATE__MMMM

where:

NNNN Affected species name with trailing underscore to pad blanks

RATE Indicates the sensitivity coefficient is for rate constants

__ Two underscores to pad the name to 14 characters

MMMM Reaction rate sensitivity group name with trailing underscore to 

pad blanks

Examples: NO__RATE__RXN1

O3__RATE__R28_

Short Name nnnRATEmmm

where:

nnn Affected species number

RATE Indicates the sensitivity coefficient is for rate constants

mmm Reaction rate sensitivity group number

Examples: 016RATE001 (where NO is species number 16)

018RATE002 (where O3 is species number 18)
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9.5.5 HDDM Sensitivity Names

Long Name NNNNHDDMLLLMMM

where:

NNNN Affected species name with trailing underscore to pad blanks

HDDM Indicates the sensitivity coefficient is second-order

LLL The index of the first 1st-order sensitivity parameter in the internal 

list of the 1st-order parameters

MMM The index of the second 1st-order sensitivity parameter in the 

internal list of the 1st-order parameters

Examples: NO__HDDM001001

O3__HDDM001002

Short Name nnnHlllmmm

where:

nnn Affected species number

H Indicates the sensitivity coefficient is second-order

lll The index of the first 1st-order sensitivity parameter in the internal 

list of the 1st-order parameters

mmm The index of the second 1st-order sensitivity parameter in the 

internal list of the 1st-order parameters

Examples: 016H001001 (where NO is species number 16)

018H001002 (where O3 is species number 18)

9.6 Steps In Developing Inputs And Running DDM

Below is a simple methodological list of steps to follow in setting up and running DDM. The 

process is similar among the OSAT, PSAT, and DDM Probing Tools.

1) Define the source groups and regions that you wish to track. Keep in mind that memory 

resources increase dramatically as the number of sensitivities grows. Probing Tool 

applications with large numbers of sensitivities, nested grids or grid cells may exceed 

available memory.

2) Build a source region map (Figure 7-10) that defines the spatial allocation of emission 

sensitivities. For small domains or small number of regions, this can be done by hand. We 

suggest using GIS software to develop complex source region maps on large grids.

3) Process the emissions inventory into the separate source group files that you want to 

track (e.g., mobile, area, point, biogenic, etc.).

a) Consideration of potential source apportionment or sensitivity applications prior to 

any emissions processing can be very beneficial so that files by group are available 

for later use.
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b) Elevated point sources will automatically be assigned to the source region in which 

they reside. However, you may override the region to which each individual point 

source is assigned (see the definition of kcell in Section 3, Elevated Point Source 

File). A point source region does not need to be defined in the source region map, 

e.g., you could have a map with two regions that split the domain in half, with a 

third region assigned arbitrarily to represent elevated point sources only.

4) Edit the CAMx control namelist file (Section 2).

a) Set the Probing_Tool variable to the technology you wish to use (DDM, HDDM). 

This will activate the &DDM_Control namelist module.

b) Edit or add the &DDM_Control namelist module (described earlier). Provide the 

required information, including:

• output paths

• whether to stratify boundary conditions

• number of source regions

• number of source groups

• numbers and names of IC, BC, emissions, rate constant, and HDDM groups

• receptor definitions

• IC/BC input files

• list of input emission files by group.

5) Configure the CAMx source code to define the number of tracers, and build an 

executable. This will ensure that you have sufficient memory for the Probing Tool 

application.

a) Edit the file Includes/camx.prm

b) Change the parameters MXTRSP and MXFDDM, following the instructions provided 

in the file. CAMx is distributed with MXTRSP = 1 and MXFDDM = 1 to minimize 

memory requirements for standard applications of the model. If you run DDM with 

an insufficient value, the model will stop and tell you the required value of MXTRSP

and MXFDDM for your application.

c) Execute the CAMx Makefile to build an executable program (Section 2).

6) Run CAMx and review the diagnostic output files to ensure that the model is correctly 

interpreting and running the Probing Tool configuration that you have specified. Ensure 

that CAMx is generating the proper output files that you are expecting. Review the table 

of concordance of long and short sensitivity coefficient names.

7) Review gridded tracer fields using commonly available plotting programs. Utilities such as 

PAVE or Verdi will read Probing Tool files directly. Use of any other software may require

specialized re-formatting procedures.

8) Probing Tool gridded tracer output files are written in the same Fortran binary format as 

the regular CAMx concentration output files. You can post-process gridded output fields 

using any software that reads CAMx files, or you can adapt those programs or build your 

own software to generate specialized analysis and graphical products.
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10. PROCESS ANALYSIS

Process Analysis (PA) allows for in-depth analysis of photochemical model performance by 

revealing the contributions from individual physical and chemical processes operating within 

the model (Jeffries and Tonnesen, 1994). Using PA, one can more fully understand the complex 

interactions between the different processes, explain simulation results within the context of 

the model formulation, and improve the design of control strategies.

A conventional model performance evaluation employs statistical and graphical methods to 

analyze predicted concentrations against observed concentrations. This answers the basic 

question: “How well is the model replicating measurements?” While such comparisons are 

necessary to summarize performance, they are far from sufficient to determine whether the 

model is adequately representing the real situation. This is because compensating errors 

among various model processes can result in predictions that serendipitously agree with limited 

observations but for the wrong reasons. In contrast PA provides information on how the 

specific model predictions were obtained, which can be interpreted to improve model 

performance and/or inform control strategy decisions.

10.1 Process Analysis In CAMx

Three components of PA are implemented in CAMx:

1) Integrated Processes Rate (IPR) analysis. The IPR method provides detailed process rate 

information for each physical process in CAMx (i.e., advection, diffusion, deposition, 

emissions, and chemistry) for selected grid cells and selected species (Wang, Langstaff, 

and Jeffries, 1995). The IPR outputs can be analyzed to determine what processes 

governed the model-predicted concentrations at any time and place. IPR information has 

often been plotted as a time series of process contributions for specific cells or groups of 

cells. IPR outputs have also been used to check the mass balance in the host model, i.e., 

to determine whether model concentrations are fully explained by the diagnosed process 

information or whether unexpected artifacts are occurring. The IPR data are relatively 

easy to interpret and can be analyzed using simple tools such as spreadsheets. Currently, 

only the IPR analysis has been extended to the PM modules in CAMx. IPR does not work 

with the ACM2 vertical diffusion option.

2) Integrated Reaction Rate (IRR) analysis. The IRR method provides detailed reaction rate 

information for all reactions in the chemical mechanism for selected grid cells (Jeffries and 

Tonnesen, 1994). The IRR data can be analyzed to determine how the chemical changes 

occurring in the model are related to the chemical mechanism. For example, by analyzing 

rate information over groups of reactions it is possible to quantify chemically meaningful 

attributes such as radical initiation rates, radical propagation efficiencies, chain lengths, 

etc. Since these analyses tend to be complex, IRR data generally require post-processing 

to be useful. IRR is implemented for the SAPRC99, CB05 and CB6 chemical mechanisms 

(mechanism numbers 5 through 7, respectively: see Chapter 5, Table 5-1).
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3) Chemical Process Analysis (CPA). CPA is related to the IRR method but is designed to be 

more user friendly and accessible. As mentioned above, IRR data are generally only useful 

after the data have been post-processed into chemically meaningful parameters. With 

CPA, a selection of useful parameters is calculated from IRR data within CAMx and then 

output to gridded files (Tonnesen and Dennis, 2000). The gridded CPA files use the same 

format as the gridded concentration outputs and can be visualized and processed using 

standard post-processing tools. CPA is implemented for the SAPRC99, CB05, and CB6

chemical mechanisms (mechanism numbers 5 through 7: see Chapter 5, Table 5-1).

10.1.1 Integrated Process Rate Analysis

The specific processes that are reported by IPR are listed in Table 10-1. This information is 

output for each chemical species selected for inclusion in the average concentration output file, 

and for each grid cell selected for analysis. The process rates are integrated across each model 

output time interval (normally hourly). Taken together, this information provides a complete 

description of how the species concentration changed across the output time interval and the 

magnitude of all of the processes that caused this change. Information is output in the 

concentration units used internally within CAMx (μmole/m3 for gases, μg/m3 for PM species). A 

gas conversion factor (ppm/μmole/m3

) specific to the grid cell/time period is also output to 

allow conversion to mixing ratio (ppm) for comparison of gas species with CAMx average 

concentration outputs. For PM species, the conversion factor is always 1. Grid cell volume is 

also output to allow aggregation across grid cells.

For most of the process rates listed in Table 10-1 the interpretation is straightforward, the rate 

is simply the concentration change caused by the named process across the output time 

interval. The sign convention is such that a positive flux always tends to increase the cell 

concentration. Further explanation is provided for several processes below:

Plume-in-Grid change: The grid cell concentration change caused by Plume-in-Grid puffs 

that transferred mass to the grid cell during the output time interval. 

Point source emissions: Does not include point sources selected for PiG treatment as 

these are reported in Plume-in-Grid Change.

Dilution in the vertical: CAMx allows for layer interface heights to change over time 

which can lead to a “dilution” term for affected grid cells.

Boundary diffusion: In some cases this term will be zero by definition, namely: the 

bottom boundary of surface layer grid cells; the top boundary of top layer grid cells; any 

lateral boundary that coincides with a nest boundary.

Dry deposition: This term is zero by definition for all grid cells above the surface layer.
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Table 10-1. Process information reported by the IPR option.

IPR Parameter Process Information Unitsa

1 Initial concentration μmole/m3 (μg/m3)

2 Gas phase chemistry μmole/m3 (μg/m3)

3 Gridded emissions μmole/m3 (μg/m3)

4 Point source emissions μmole/m3 (μg/m3)

5 Plume-in-Grid change μmole/m3 (μg/m3)

6 West boundary advection μmole/m3 (μg/m3)

7 East boundary advection μmole/m3 (μg/m3)

8 South boundary advection μmole/m3 (μg/m3)

9 North boundary advection μmole/m3 (μg/m3)

10 Bottom boundary advection μmole/m3 (μg/m3)

11 Top boundary advection μmole/m3 (μg/m3)

12 Dilution in the vertical μmole/m3 (μg/m3)

13 West boundary diffusion μmole/m3 (μg/m3)

14 East boundary diffusion μmole/m3 (μg/m3)

15 South boundary diffusion μmole/m3 (μg/m3)

16 North boundary diffusion μmole/m3 (μg/m3)

17 Bottom boundary diffusion μmole/m3 (μg/m3)

18 Top boundary diffusion μmole/m3 (μg/m3)

19 Dry deposition μmole/m3 (μg/m3)

20 Wet deposition μmole/m3 (μg/m3)

21 Inorganic aerosol chemistry μmole/m3 (μg/m3)

22 Organic aerosol chemistry μmole/m3 (μg/m3)

23 Aqueous aerosol chemistry μmole/m3 (μg/m3)

24 Final concentration μmole/m3 (μg/m3)

25 Units conversion ppm/(μmole/m3) (N/A)b

26 Average cell volume m3

a Units in the parentheses are for PM species.

b Unit conversion factor for PM species is always 1.

10.1.2 Integrated Reaction Rate Analysis

IRR provides the integrated rate of each gas-phase chemical reaction in units of ppm hr-1 for 

each grid cell selected for process analysis. Reaction rates are accumulated (integrated) within 

the chemistry solver at the time steps being used to solve the chemical equations, and output 

at the CAMx output time interval (usually 1 hour). 

10.1.3 Chemical Process Analysis

The CPA method calculates a pre-determined set of parameters as listed in Table 10-2. The CPA 

parameters are calculated for all grid cells in either the surface layer or all layers. The selection 

between surface layer or all layer CPA outputs is determined by the “3-D average file” flag 

specified in the CAMx Control File (see Section 2). This is based on the premise that 3-D CPA 

information will be interpreted in conjunction with 3-D concentration fields. 
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Table 10-2. Chemical Process Analysis (CPA) variables calculated in CAMx for the CB6, CB05

and SAPRC99 mechanisms. Concentrations are ppb; production and destruction are ppb/hr; 

photolysis rates are hr-1, ratios are unitless.

CB6 CB05 SAPRC99 Description

Ozone and Oxidant Production and Loss

OxProd OxProd OxProd Production of Ox = Ozone + NOy-NO

OxLoss OxLoss OxLoss Destruction of Ox

PO3_net PO3_net PO3_net Net ozone produced

PO3_VOCsns PO3_VOCsns PO3_VOCsns Net ozone produced under VOC sensitive conditions

PO3_NOxsns PO3_NOxsns PO3_NOxsns Net ozone produced under NOx sensitive conditions

PH2O2_PHN3 PH2O2_PHN3 PH2O2_PHN3 Ratio of H2O2 produced / HNO3 produced. Greater than 

0.35 means NOx sensitive ozone production

O3_dest O3_dest O3_dest Ozone destruction by chemical reactions

Radical Initiation

OH_new OH_new OH_new New OH produced (initiated)

HO2_new HO2_new HO2_new New HO2 produced

HOx_new HOx_new HOx_new New HOx (HOx = OH+HO2) produced

newOH_O1D newOH_O1D newOH_O1D Production of OH from ozone photolysis

newOH_HONO newOH_HONO newOH_HONO Production of OH from HONO photolysis

nOH_O3_OLE nOH_O3_OLE nOH_O3_OLE Production of OH from ozone-alkene reactions 

nwHO2_HCHO nwHO2_HCHO nwHO2_HCHO Production of HO2 from formaldehyde photolysis

RO2_new RO2_new RO2_new New RO2 produced

Radical Propagation

OHw_CO OHw_CO OHw_CO OH reacted with carbon monoxide

OHw_CH4 OHw_CH4 OHw_CH4 OH reacted with methane

OHw_ETHA OHw_ETHA OHw_ALK1

OH reacted with alkanes 

OHw_PRPA OHw_PAR OHw_ALK2

OHw_PAR OHw_ALK3

OHw_ALK4

OHw_ALK5

OHw_BENZ OH reacted with benzene

OHw_TOL OHw_TOL OHw_ARO1 OH reacted with toluene and mono-substituted aromatics

OHw_XYL OHw_XYL OHw_ARO2 OH reacted with xylenes and poly-substituted aromatics

OHw_ETH OHw_ETH OHw_ETHE OH reacted with ethane

OHw_OLE OHw_OLE OHw_OLE1 OH reacted with terminal alkenes (R–HC=CH2, e.g. 

propene)

OHw_IOLE OHw_IOLE OHw_OLE2 OH reacted with internal alkenes (R–HC=CH–R, e.g. 2-

butene)

OHw_ISOP OHw_ISOP OHw_ISOP OH reacted with isoprene

OHw_TERP OHw_TERP OHw_TERP OH reacted with terpenes

OHw_ETHY OH reacted with ethyne 

OHw_all_HC OHw_all_HC OHw_all_HC OH reacted with all organic compounds (including CO)

ISOPwOx ISOPwOx ISOPwOx Isoprene reacted with O3, NO3 and O(3P)

TERPwOx TERPwOx TERPwOx Terpenes reacted with O3, NO3 and O(3P)

OH_rctd OH_rctd OH_rctd Total OH reacted 
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CB6 CB05 SAPRC99 Description

HO2_rctd HO2_rctd HO2_rctd Total HO2 reacted

HOx_rctd HOx_rctd HOx_rctd Total HOx reacted

RO2_rctd RO2_rctd RO2_rctd Total RO2 reacted

OHfromHO2 OHfromHO2 OHfromHO2 OH produced from reactions of HO2

Y_OHperHO2 Y_OHperHO2 Y_OHperHO2 Yield of OH per HO2 reacted (= OHfromHO2 / HO2_rctd)

Radical Termination and HOx Chain Length

OH_term OH_term OH_term OH terminated

HO2_term HO2_term HO2_term HO2 terminated

HOx_term HOx_term HOx_term HOx terminated

RO2_term RO2_term RO2_term RO2 terminated

HOx_CL HOx_CL HOx_CL HOx chain length ( = HOx_rctd / {2 x HOx_new} )

Formaldehyde Production

HCHOp_eth HCHOp_eth HCHOp_ethe Formaldehyde produced from ethene

HCHOp_ole HCHOp_ole HCHOp_ole1 Formaldehyde from terminal alkenes (R–HC=CH2, e.g. 

propene) in the first generation of products

HCHOp_iole HCHOp_iole HCHOp_ole2 Formaldehyde from internal alkenes (R–HC=CH–R, e.g. 2-

butene) in the first generation of products

HCHOp_terp HCHOp_terp HCHOp_terp Formaldehyde from terpenes in the first generation of 

products

HCHOp_isop HCHOp_isop HCHOp_isop Formaldehyde from isoprene in the first generation of 

products

HCHOp_ispd HCHOp_ispd HCHOp_ispd Formaldehyde from isoprene daughter products (isoprod, 

methacrolein and methylvinylketone)

HCHOp_Tot HCHOp_Tot HCHOp_Tot Total formaldehyde produced

NOy Reactions

HNO3_OHNO2 HNO3_OHNO2 HNO3_OHNO2 Nitric acid produced from OH reacting with NO2

HNO3_NO3HC HNO3_NO3HC HNO3_NO3HC Nitric acid produced from NO3 reacting with organics

HNO3_N2O5 HNO3_N2O5 HNO3_N2O5 Nitric acid produced from N2O5 reacting with water

PANprodNet PANprodNet PANSprdNet Net PAN produced (sum of several for SAPRC99) 

PANlossNet PANlossNet PANSlosNet Net PAN destroyed (sum of several for SAPRC99)

RNO3_prod RNO3_prod RNO3prod Organic nitrates (RNO3) produced

NOxrecycl NOxrecycl NOxrecycl Nitrates (HNO3 and RNO3) recycled to NOx

NOw_HO2 NOw_HO2 NOw_HO2 NO reacted with HO2 (forming NO2)

NOw_RO2s NOw_RO2s NOw_RO2s NO reacted with RO2 (forming NO2)

NOw_RCO3s NOw_RCO3s NOw_RCO3s NO reacted with RCO3 (forming NO2)

Photolysis

J_NO2 J_NO2 J_NO2 NO2 photolysis rate

J_O3O1D J_O3O1D J_O3O1D O3 photolysis rate to O(1D) atoms

J_CLDADJ J_CLDADJ J_CLDADJ Cloud/haze adjustment factor

Radical Concentrations

OH OH OH OH radical concentration

HO2 HO2 HO2 HO2 radical concentration
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10.2 Running Process Analysis

PA can be used with most of the physical options available for the “core” CAMx model, e.g., the 

various advection and chemistry mechanisms/solvers. However, PA cannot be used at the 

same time as the other CAMx “Probing Tool” options (e.g., OSAT, PSAT, DDM, or RTRAC) 

because the Probing Tools share internal data structures to minimize the total memory 

resources required by CAMx. IPR cannot be used with the ACM2 diffusion option.

PA is invoked similarly to the other Probing Tools within the CAMx control file. In the 

&CAMx_Control namelist module, the variable Probing_Tool must be set to either “PA” 

(generates all PA output), “IPR”, or “IRR”. Table 10-3 summarizes the types of process analysis 

performed for each keyword and the output files that are produced.

Table 10-3. Process analysis keywords and associated CAMx output files.

Process Analysis Key Word Output

Filename

File

IPR IRR PA Contains

Yes No Yes *.ipr Integrated process rate (IPR) 

information for all selected cells

No Yes Yes *.irr Integrated reaction rate (IRR) 

information for all selected cells

No Yes Yes *.cpa.grdnn Chemical process analysis 

(CPA) parameters for grid nn

An additional namelist module called &PA_Control must then be provided in the control file 

to configure the PA portion of the model. The additional namelist module is described below. 

The order of the variables follow the template available with the source code. An example of 

the PA portion of the CAMx run control file is shown in Figure 10-1.

The rules for defining PA domains are as follows:

1) They must be contained within a single CAMx grid;

2) They may not include cells that contain a nested grid;

3) They may contain as few as 1 grid cells;

4) They may contain up to all of the grid cells in a CAMx grid provided that this does not 

violate the second rule;

5) They may intersect or overlap – the same grid cell may be in several process analysis 

domains.
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Description of PA Control in the CAMx Run Control File

&PA_Control Label for the Probing Tool namelist module that configures the 

PA option; it must begin in column 2

& Flag ending a namelist; it must be in column 2

PA_File_Root Character root output path/filename

Number_of_PA_Domains Integer number of PA analysis domains to be evaluated during 

the simulation.

Within_CAMx_Grid Integer array (by PA domain) pointer into the CAMx grid within 

which the PA domain exists (1=master grid, etc.). Use the CAMx 

internal grid number reported in the *.diag file. Note that this 

may differ from the nest order provided by the user in the 

CAMx control file.

PA_Beg_I_Index Integer array (by PA domain) grid column containing western 

edge of PA domain.

PA_End_I_Index Integer array (by PA domain) grid column containing eastern 

edge of PA domain.

PA_Beg_J_Index Integer array (by PA domain) grid row containing southern edge 

of PA domain.

PA_End_J_Index Integer array (by PA domain) grid row containing northern edge 

of PA domain.

PA_Beg_K_Index Integer array (by PA domain) grid layer containing bottom of PA 

domain.

PA_End_K_Index Integer array (by PA domain) grid layer containing top of PA 

domain.
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Figure 10-1. Example section of a CAMx control file specifying options for Process Analysis.

10.2.1 Setting CAMx Parameters 

PA stores information in data structures that are dimensioned using FORTRAN parameter 

statements. These parameters must be large enough to accommodate the PA configuration 

specified in the CAMx control file. If one of these parameters is exceeded CAMx will stop with 

an error message stating that a parameter must be changed and the model recompiled. It is 

always a good idea to do a complete rebuild (use the Unix command “make clean”) when a 

parameter is changed. The parameters that may need to be changed are in two include files, 

“procan.inc” and “camx.prm”.

procan.inc

MXPADOM – The maximum number of Process Analysis domains.

MXPACEL – The maximum number of Process Analysis cells over all domains

camx.prm

MXTRSP – This parameter defines gridded data structures that are used by several 

probing tools. For PA the data structures store chemical process analysis (CPA) 

variables, so MXTRSP must be set to at least the value of MXCPA (set in procan.inc) 

which is 99.

&PA_Control

PA_File_Root = 'CAMx.OTAG.950707.PA',

Number_of_PA_Domains = 2,

Within_CAMx_Grid(1) = 1,

PA_Beg_I_Index(1) = 8,

PA_End_I_Index(1) = 12,

PA_Beg_J_Index(1) = 9,

PA_End_J_Index(1) = 13,

PA_Beg_K_Index(1) = 1,

PA_End_K_Index(1) = 5,

Within_CAMx_Grid(2) = 2,

PA_Beg_I_Index(2) = 107,

PA_End_I_Index(2) = 110,

PA_Beg_J_Index(2) = 78,

PA_End_J_Index(2) = 82,

PA_Beg_K_Index(2) = 1,

PA_End_K_Index(2) = 7,

&
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10.2.2 Output File Formats

CAMx may output up to four files containing PA information according to the PA option 

selected (see Table 10-3). All of these files are in Fortran binary format to conserve disk space. 

Two files (the *.ipr and *.irr files) contain information for just the grid cells selected for 

PA. The formats for these files are not described here since two Fortran post-processor 

programs are provided to extract data from these files in a comma-delimited ASCII format. The 

files containing CPA information (the *.cpa.grdnn) are gridded files covering the same area 

as the regular model average files (*.avrg.grdnn). The gridded CPA files have the same 

format as a regular model average file as described in Section 3. 

10.3 Postprocessing 

Two post-processors are provided to read the binary *.ipr and *.irr output files and 

extract PA data for further analysis. The CPA output files can be visualized directly.

10.3.1 IPR Output Files

The Fortran program “ext_ipr” extracts IPR data from one or more CAMx *.ipr binary files 

and reformats the data to comma delimited ASCII format (.csv) suitable for subsequent 

analysis (e.g., using spreadsheets). The “ext_ipr” program performs the following tasks:

• Reads and outputs the descriptive header of the *.ipr file;

• Optionally combines data from several consecutive *.ipr files to provide multi-day 

output;

• Selects data for an individual cell within a PA sub-domain or aggregates data over multiple 

cells within a PA sub-domain;

• Outputs the selected IPR data in .csv format in either ppb or molar units for gas species; 

PM species are in either μg/m3 or mass units..

A sample script to run the “ext_ipr” program is provided with its source code, and the script 

includes a description of how to use the program. Also included is a spreadsheet macro that 

can read the .csv format and prepare several plots. This macro is described below. 

10.3.1.1 Aggregating Cells

The “ext_ipr” program can combine IPR information across several cells. This is useful for 

analyzing the contributions of model processes to a geographic area that spans multiple cells 

(e.g., an urban area). For simplicity, the multi-cell area must be defined as a rectangular box. 

The capability of aggregating IPR information across vertical layers is particularly important 

during the day because vertical columns of cells within the mixed layer become strongly 

coupled on time scales shorter than one hour. Thus, if the process contributions for a surface 

grid cell are analyzed during the day vertical diffusion will often completely dominate all other 

processes. In this situation, it is more informative to analyze a column of cells extending from 

the surface to the approximate height of the mixed layer.
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When the “ext_ipr” program aggregates information across grid cells it accounts for 

differences in cell volume. If the output for aggregate cells is requested in ppb units, the output 

from CAMx in molar units is converted to ppb using the volume-weighted average units 

conversion factor for the cells being aggregated.

10.3.1.2 IPR Time Series Analysis

One useful approach to analyzing IPR data is to plot the contributions of several processes as a 

time series. Figures 10-2 through 10-4 present examples of this approach from the CAMx test 

case that is distributed with the model. The figures show process contributions to the PM2.5

sulfate and nitrate concentrations in a multi-cell area around Chicago on June 13 and 14, 2002, 

and are intended solely as an illustration of how PA can be used. The figures were prepared 

using the “ext_ipr” program described above and the spreadsheet macro 

“process_analysis_macro.xls.” The macro reads an output file from “ext_ipr” and 

prepares three charts:

1) Bar chart of the contribution from each process averaged over the duration of the PA 

data. This is useful to see which processes were important (Figure 10-2). 

2) Bar chart showing the time series of contributions from all major processes. To reduce 

the number of processes being displayed, advection and diffusion information for each 

boundary is combined into a single transport term, and any series with zero contribution 

is excluded from the chart. Also, the three PM chemistry processes (organic, inorganic 

and aqueous-phase aerosol chemistry) are aggregated to a single net term 

(Heterogeneous Chemistry). An example of this chart is shown in Figure 10-3.

3) Bar chart showing the time series of contributions from major processes with lateral 

boundary transport and all chemistry processes shown as a single net term. An example 

of this chart is shown in Figure 10-4. For a small region lateral boundary transport often 

leads to large positive and negative terms that approximately cancel (e.g., inflow from the 

east and outflow to the west). This chart provides a comparison of the net effect of 

lateral boundary transport relative to other processes, whereas the second chart resolves 

the transport by boundary. Comparing Figures 10-3 and 10-4, based on the same data, 

shows the difference between these two analysis approaches. 

10.3.2 IRR Output Files

The Fortran program “ext_irr” extracts IRR data from one or more CAMx *.irr binary files 

and reformats the data for subsequent analysis. The “ext_irr” program performs the 

following tasks:

• Reads and outputs the descriptive header of the *.irr file;

• Optionally combines data from several consecutive *.irr files to provide multi-day 

output;

• Selects data for an individual cell or multiple cells within a PA sub-domain; 

• Optionally, outputs the selected IRR data to a .csv format ASCII file; 

• Optionally, outputs the selected IRR data to a UAM average format binary file. 
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Figure 10-2. Time-averaged IPR analysis for PSO4 and PNO3 on June 13 and 14, 2002; all of 

the processes are plotted individually.

Time-Averaged PSO4 Change from the Different Processes in Chicago Area.

Run = postproc_test

Grid cells used from grid number 1: (43, 47) to (52, 56) using layers 1 to 5

-0.2

-0.15

-0.1

-0.05

0

0.05

0.1

0.15

0.2

Gas-phase chemistry

Area emissions

Point source emissions

Plume-in-Grid change

West boundary advection

East boundary advection

South boundary advection

North boundary advection

Bottom boundary advection

Top boundary advection

Dilution in the vertical

West boundary diffusion

East boundary diffusion

South boundary diffusion

North boundary diffusion

Bottom boundary diffusion

Top boundary diffusion

Dry deposition

Wet deposition

Inorganic aerosol chem

Organic aerosol chem

Aqueous chemistry

Change in PSO4 (ug/m3)

Time-Averaged PNO3 Change from the Different Processes in Chicago Area.

Run = postproc_test

Grid cells used from grid number 1: (43, 47) to (52, 56) using layers 1 to 5

-0.25

-0.2

-0.15

-0.1

-0.05

0

0.05

0.1

0.15

0.2

0.25

Gas-phase chemistry

Area emissions

Point source emissions

Plume-in-Grid change

West boundary advection

East boundary advection

South boundary advection

North boundary advection

Bottom boundary advection

Top boundary advection

Dilution in the vertical

West boundary diffusion

East boundary diffusion

South boundary diffusion

North boundary diffusion

Bottom boundary diffusion

Top boundary diffusion

Dry deposition

Wet deposition

Inorganic aerosol chem

Organic aerosol chem

Aqueous chemistry

Change in PNO3 (ug/m3)
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Figure 10-3. IPR time series analysis for PSO4 and PNO3; Lateral boundary/Chemistry terms 

are not aggregated.

Hourly PSO4 Change from Different Processes in Chicago Area.

Run = postproc_test

Grid cells used from grid number 1: (43, 47) to (52, 56) using layers 1 to 5

-1.5

-1

-0.5

0

0.5

1

 Jun 13, 2002 Jun 14, 2002 Change in PSO4 (ug/m3)

Top Boundary Deposition Emissions

Gas-Phase Chemistry Heterogeneous Chemistry West Boundary

East Boundary South Boundary North Boundary

Hourly PNO3 Change from Different Processes in Chicago Area.

Run = postproc_test

Grid cells used from grid number 1: (43, 47) to (52, 56) using layers 1 to 5

-2.5

-2

-1.5

-1

-0.5

0

0.5

1

1.5

2

 Jun 13, 2002 Jun 14, 2002 Change in PNO3 (ug/m3)

Top Boundary Deposition Emissions

Gas-Phase Chemistry Heterogeneous Chemistry West Boundary

East Boundary South Boundary North Boundary
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Figure 10-4. IPR time series analysis for PSO4 and PNO3; Lateral boundary/Chemistry terms 

are aggregated to a single net term, in contrast to Figure 10-3.

Hourly PSO4 Change from Different Processes in Chicago Area.

Run = postproc_test

Grid cells used from grid number 1: (43, 47) to (52, 56) using layers 1 to 5

-1

-0.8

-0.6

-0.4

-0.2

0

0.2

0.4

0.6

0.8

 Jun 13, 2002 Jun 14, 2002 Change in PSO4 (ug/m3)

Top Boundary Deposition Emissions Chemistry Lateral Boundaries

Hourly PNO3 Change from Different Processes in Chicago Area.

Run = postproc_test

Grid cells used from grid number 1: (43, 47) to (52, 56) using layers 1 to 5

-2.5

-2

-1.5

-1

-0.5

0

0.5

1

1.5

 Jun 13, 2002 Jun 14, 2002 Change in PNO3 (ug/m3)

Top Boundary Deposition Emissions Chemistry Lateral Boundaries
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The ASCII IRR data are suitable for subsequent analysis (e.g., using spreadsheets) but at this 

time there is no “pre-packaged” analysis available comparable to the macro for analyzing IPR 

data. The binary IRR output from “ext_irr” can be displayed using any post-processing software 

that can display CAMx average concentration outputs.

10.3.3 CPA Output Files

CPA results are output from CAMx as gridded files in the same format as the average 

concentration files, and therefore can be visualized using any post-processing software that can 

display CAMx concentration outputs. These files may optionally include just the surface layer 

or all layers according to how the “3-D output” flag is set in the CAMx control file. Surface layer 

species concentrations reflect the balance between several model processes including surface 

emissions/deposition, vertical mixing, and chemical reactions in surface (and possibly aloft) grid 

cells. In contrast, the CPA output data are grid cell specific and reflect chemical change in 

single grid cells. The fact that vertical mixing tends to average species concentrations over 

multiple layers whereas CPA variables are layer specific may complicate and bias the 

interpretation of CPA results. A solution is to place both the concentrations and CPA variables 

on a comparable basis by averaging them over all layers within the planetary boundary layer.

A post-processor (VERTAVG) was developed to average CPA variables and concentrations over 

multiple layers contained within the depth of the planetary boundary layer (PBL). The PBL 

depth varies in space and time according to the strength and vertical extent of turbulent 

mixing. Vertical turbulent mixing is specified for CAMx by the input diffusivity (Kv) fields. The 

VERTAVG processor reads CAMx Kv, height, temperature, and pressure input files, and then 

calculates the PBL depth for each grid column at each hour. VERTAVG also reads a CAMx 3-D 

output file of CPA variables (or species concentrations) and calculates air-mass weighted PBL 

values for each grid column at each hour. The output from VERTAVG is a 2-D file in average file 

format where the single layer represents the PBL average values rather than surface layer 

values.

VERTAVG appends two extra variables to the file being processed to aid with interpretation and 

to make clear that the data have been vertically averaged. The added variables are:

• PBL_Z is the diagnosed height of the PBL for each grid column.

• PBL_I is the layer index of the top layer within the diagnosed PBL for each grid column.

CAMx must be run using the option to create 3-D species concentration (and therefore CPA) 

output files in order to use VERTAVG.
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11. REACTIVE TRACERS

The CAMx reactive tracer algorithm provides a flexible approach for simulating the emission, 

dispersion, chemistry, and deposition of multiple trace gas and particulate tracers on the 

computational grid(s) and within the IRON PiG treatment. Originally developed to model air 

toxics, it was extended and generalized to be able to track a variety of user-defined organic and 

inorganic species. 

Reactive tracers are carried separately from the core model photochemical/PM chemistry 

mechanisms, and thus can be used to address a variety of issues, separately or in combination:

• Reactive and inert gaseous and particle air toxic compounds;

• Chemical decay of individual VOC compounds into multiple generations of daughter 

products;

• Source tagging of primary emitted inert and reactive compounds from specific source 

types/classes, or from individual stacks, facilities and/or complexes.

The reactive tracer algorithm is implemented as a CAMx “Probing Tool” and thus shares model 

data structures with other Probing Tools such as the Ozone/Particulate Source Apportionment 

Technology (OSAT/PSAT) and the Decoupled Direct Method (DDM/HDDM). This streamlines 

the CAMx code, improves efficiency, and maximizes consistency with the core model since it 

allows reactive tracer calculations for emissions, transport, and deposition to use the existing 

CAMx algorithms. However, this means that reactive tracers cannot be used simultaneously 

with other Probing Tools.

The reactive tracer implementation employs two approaches to define tracer chemistry. The 

original approach, referred to as RTRAC, allows tracers to decay and form multiple generations 

of daughter products through photolysis and user-specified thermal reactions with ozone and 

radicals (OH, NO3) that are extracted from the core gas-phase chemistry (CB05, CB6, or 

SAPRC99). The newer approach, referred to as the RTRAC Chemical Mechanism Compiler 

(RTCMC), allows the user to externally define a full chemistry mechanism with no limits on 

complexity (within available computer resources). RTCMC can also access any gas-phase 

concentrations from the core gas-phase mechanism as well. Neither option allows chemistry 

for particulate tracers.

11.1 Description of RTRAC

Reactive tracers are defined for each CAMx run by providing an RTRAC chemistry parameters 

file similar to that used for the core model. The examples in Figure 11-1 and 11-2 illustrate an 

RTRAC air toxics application using the older CB4 and SAPRC99 chemical mechanisms, 

respectively (ENVIRON, 2002; Morris et al., 2003). The number and names of the tracers are 

arbitrary; i.e. information on the tracer species’ chemical identities, structure, reaction 

pathways, and kinetics are kept separate from the core model. Consistent with the chemistry 

parameters files used for CB4 and SAPRC99, the physical characteristics for each reactive tracer 

must be specified for deposition calculations, and their reaction pathways and rates must be 

defined. 
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Figure 11-1. Example RTRAC chemistry input file for modeling the MATES toxic species using 

CB4 as the host chemical mechanism (CB4 is no longer available in CAMx).

CAMx Version |VERSION6.1

Description |MATES Toxics for CRC project A-42

No of gas tracers |6

No of aero tracers |8

No photolysis rxns |4

No thermal rxns |12

Gas Tracers

No. Name P/S SNAM lower bnd H-law T-fact Molwt Reactvty Rscale

 1 PACET PRIM 1.00E-12 6.30e+03 -6492. 44.00 0.0 1.0

 2 HCHO PRIM 1.00E-12 6.30e+03 -6492. 30.00 0.0 1.0

 3 BENZ PRIM 1.00E-12 1.80e-01 0. 78.00 0.0 1.0

 4 BUTA PRIM 1.00E-12 1.00e-02 0. 54.00 0.0 1.0

 5 SACET SEC ALD2 1.00E-12 6.30e+03 -6492. 44.00 0.0 1.0

 6 SFORM SEC FORM 1.00E-12 6.30e+03 -6492. 30.00 0.0 1.0

Aero Tracers

No. Name lower bnd Density Low cut Upper cut

 7 DSLF 1.00E-09 1.5 0.10 2.50

 8 ECF 1.00E-09 1.5 0.10 2.50

 9 CRF 1.00E-09 1.5 0.10 2.50

10 CR6F 1.00E-09 1.5 0.10 2.50

11 DSLC 1.00E-09 1.5 2.50 10.00

12 ECC 1.00E-09 1.5 2.50 10.00

13 CRC 1.00E-09 1.5 2.50 10.00

14 CR6C 1.00E-09 1.5 2.50 10.00

Photolysis reactions

Toxic Rxn # Factor

PACET 45 1.0

SACET 45 1.0

HCHO 39 1.6

SFORM 39 1.6

Thermal reactions and rates

Toxic React A(ppm-1min-1) Ea(K) B Tref

PACET OH 8.2015E+03 -3.1099E+02 0.0 300.0

PACET NO3 2.0689E+03 1.8599E+03 0.0 300.0

HCHO OH 1.6699E+03 -6.4815E+02 2.0 300.0

HCHO NO3 4.1377E+03 2.5161E+03 0.0 300.0

BENZ OH 3.6944E+03 1.9978E+02 0.0 300.0

BUTA OH 2.1871E+04 -4.4787E+02 0.0 300.0

BUTA O3 4.8766E+01 2.5000E+03 0.0 300.0

BUTA NO3 2.1871E+04 1.4890E+03 0.0 300.0

SACET OH 8.2015E+03 -3.1099E+02 0.0 300.0

SACET NO3 2.0689E+03 1.8599E+03 0.0 300.0

SFORM OH 1.6699E+03 -6.4815E+02 2.0 300.0

SFORM NO3 4.1377E+03 2.5161E+03 0.0 300.0
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Figure 11-2. Example RTRAC chemistry input file for modeling toxic species with SAPRC99 as 

the host chemical mechanism.

CAMx Version |VERSION6.1

Description |Toxics for CRC project A-42 with SAPRC99 host mechanism

No of gas tracers |14

No of aero tracers |0

No photolysis rxns |8

No thermal rxns |28

Gas Tracers

No. Name P/S SNAM lower bnd H-law T-fact Molwt Reactvty Rscale

 1 mPACET PRIM 1.00E-12 6.30e+03 -6492. 44.00 0.0 1.0

 2 mPFORM PRIM 1.00E-12 6.30e+03 -6492. 30.00 0.0 1.0 

 3 mBENZ PRIM 1.00E-12 1.80e-01 0. 78.00 0.0 1.0

 4 mBUTA PRIM 1.00E-12 1.00e-02 0. 54.00 0.0 1.0

 5 SACET SEC CCHO 1.00E-12 6.30e+03 -6492. 44.00 0.0 1.0

 6 SFORM SEC HCHO 1.00E-12 6.30e+03 -6492. 30.00 0.0 1.0

 7 oPACET PRIM 1.00E-12 6.30e+03 -6492. 44.00 0.0 1.0

 8 oPFORM PRIM 1.00E-12 6.30e+03 -6492. 30.00 0.0 1.0

 9 oBENZ PRIM 1.00E-12 1.80e-01 0. 78.00 0.0 1.0

10 oBUTA PRIM 1.00E-12 1.00e-02 0. 54.00 0.0 1.0

11 pPACET PRIM 1.00E-12 6.30e+03 -6492. 44.00 0.0 1.0

12 pPFORM PRIM 1.00E-12 6.30e+03 -6492. 30.00 0.0 1.0

13 pBENZ PRIM 1.00E-12 1.80e-01 0. 78.00 0.0 1.0

14 pBUTA PRIM 1.00E-12 1.00e-02 0. 54.00 0.0 1.0 

Photolysis reactions

Toxic Rxn # Factor

mPACET 131 1.0

oPACET 131 1.0

pPACET 131 1.0

SACET 131 1.0

mPFORM 123 1.6

oPFORM 123 1.6

pPFORM 123 1.6

SFORM 123 1.6

Thermal reactions and rates

Toxic React A(ppm-1min-1) Ea(K) B Tref

mPACET OH 8.2015E+03 -3.1099E+02 0.0 300.0

mPACET NO3 2.0689E+03 1.8599E+03 0.0 300.0

oPACET OH 8.2015E+03 -3.1099E+02 0.0 300.0

oPACET NO3 2.0689E+03 1.8599E+03 0.0 300.0

pPACET OH 8.2015E+03 -3.1099E+02 0.0 300.0

pPACET NO3 2.0689E+03 1.8599E+03 0.0 300.0

mPFORM OH 1.6699E+03 -6.4815E+02 2.0 300.0

mPFORM NO3 4.1377E+03 2.5161E+03 0.0 300.0

oPFORM OH 1.6699E+03 -6.4815E+02 2.0 300.0

oPFORM NO3 4.1377E+03 2.5161E+03 0.0 300.0

pPFORM OH 1.6699E+03 -6.4815E+02 2.0 300.0

pPFORM NO3 4.1377E+03 2.5161E+03 0.0 300.0

mBENZ OH 3.6944E+03 1.9978E+02 0.0 300.0

oBENZ OH 3.6944E+03 1.9978E+02 0.0 300.0

pBENZ OH 3.6944E+03 1.9978E+02 0.0 300.0

mBUTA OH 2.1871E+04 -4.4787E+02 0.0 300.0

mBUTA O3 4.8766E+01 2.5000E+03 0.0 300.0

mBUTA NO3 2.1871E+04 1.4890E+03 0.0 300.0

oBUTA OH 2.1871E+04 -4.4787E+02 0.0 300.0

oBUTA O3 4.8766E+01 2.5000E+03 0.0 300.0

oBUTA NO3 2.1871E+04 1.4890E+03 0.0 300.0

pBUTA OH 2.1871E+04 -4.4787E+02 0.0 300.0

pBUTA O3 4.8766E+01 2.5000E+03 0.0 300.0

pBUTA NO3 2.1871E+04 1.4890E+03 0.0 300.0

SACET OH 8.2015E+03 -3.1099E+02 0.0 300.0

SACET NO3 2.0689E+03 1.8599E+03 0.0 300.0

SFORM OH 1.6699E+03 -6.4815E+02 2.0 300.0

SFORM NO3 4.1377E+03 2.5161E+03 0.0 300.0
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The structure of the RTRAC tracer definition provides complete flexibility in the selection of the 

compounds and tracers to be included in each analysis. The user is able to easily alter or 

expand the compounds as needed.

For gas species, the required deposition parameters are the Henry’s Law constant and 

molecular weight Mg, the latter of which defines a diffusivity parameter according to

Mg MH2O / . The deposition calculation for gases that react in plant tissue also needs a 

reactivity parameter that describes whether a species reacts when dissolved inside leaf tissues 

(Wesely, 1989). This parameter is intended for modeling the deposition of reactive species, 

such as ozone, and should be set to zero for air toxics. The deposition calculation for gasses 

also uses an “Rscale” factor to adjust the surface resistance. This is used to set the surface 

resistance to zero for strong acids (e.g., HNO3) and should be set to 1.0 for modeling air toxics.

The deposition calculation for particles requires the particle density and size associated with 

each species. The particle size is calculated as the geometric mean of the lower and upper cut 

points (see Figure 11-1). If possible, the particle size and density should be based on the 

measured size of particles associated with each RTRAC species (e.g., for a compound associated 

with soot particles, use a density and size representing the soot).

The emission rates for the RTRAC species are provided by an extra set of emission files (surface 

and/or point source). Emissions of gases are in moles per time period (normally moles/hour), 

whereas particles are in micro-grams per time period. The emissions file format is the same as 

for a regular CAMx emissions file, as described in Section 3.

11.1.1 RTRAC Gas-Phase Chemistry

The RTRAC chemistry calculations use a special chemistry module. Chemistry may be modeled 

for primary and secondary gas species, meaning that tracers can be formed from the decay of 

primary tracers or from the decay of host model species (e.g., secondary formaldehyde). The 

chemical decay of gaseous tracers can account for thermal reactions with ozone (O3), hydroxyl 

radical (OH) and nitrate radical (NO3), as well as photolysis. The algorithms are coded so that 

all chemical decay pathways are zero by default and only become non-zero if decay rates are 

explicitly specified in the input file (see Figure 11-1). The example RTRAC chemistry input file in 

Figure 11-1 shows how thermal reactions are specified by naming the tracer and oxidant, and 

providing reaction rate parameters. Note that the RTRAC chemical reaction rates depend on 

the rates and parameters provided in the RTRAC input file, and not the rates in the host model 

chemical mechanism; however the host model does provide the oxidizing species 

concentrations (i.e., O3, OH, and NO3).

11.1.1.1 Thermal Reactions

Thermal reactions with oxidants are modeled as second order reactions:

R = k [tracer][oxidant]
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where R is the decay rate and the rate constant k is defined using the generalized temperature 

dependent rate expression:

The Arrhenius factor (A) must be in units (ppm-1

min-1), the activation energy (Ea) must be Kelvin 

and B is dimensionless. This is the same as expression 3 in Table 3-3a. Oxidant concentrations 

for the decay calculation are obtained from the CAMx photochemical simulation for each grid 

cell at each time step. RTRAC can be used with either CB05, CB6, or SAPRC99 chemical 

mechanisms that are available in the current version of CAMx (see Section 5). Choosing 

between the core mechanisms will influence the RTRAC chemical decay rates by changing the 

oxidant concentrations in the host model.

11.1.1.2 Photolysis

Photolysis reactions are specified by naming the tracer undergoing photolysis and providing a 

ratio of the tracer photolysis rate to one of the photolysis reactions in the host photochemical 

mechanism. For example, Figure 11-1 shows that there are both primary and secondary 

acetaldehyde reactive tracers (PACET and SACET) and the photolysis rate for both species is set 

equal to reaction 45. Reaction 45 in the old CB4 mechanism was photolysis of ALD2, which is 

based on acetaldehyde. Figure 11-1 also shows that there are two types of formaldehyde in the 

MATES toxics modeling (PFORM and SFORM). Modeling the photolysis of formaldehyde with 

RTRAC is complicated by the fact that the CB4 mechanism included two photolysis reactions for 

formaldehyde (reactions 38 and 39). The solution shown in Figure 11-1 was to model 

formaldehyde photolysis as 1.6 times the rate of CB4 reaction 39. The CAMx host mechanisms 

are discussed in Section 5 and are defined by the ASCII chemistry parameters files (Section 3) 

and mechanism listings distributed with CAMx and available from the CAMx web page 

(www.camx.com).

11.1.1.3 Secondary Species

RTRAC allows for formation of secondary/daughter products related to the chemical decay of 

one of the primary tracers. Secondary species can also be subject to chemical decay, just like 

primary species, if the user desires. Therefore, the RTRAC chemistry module allows decay 

reactions (thermal and photolysis) to be specified for secondary species using the same method 

as for primary species. In this manner, concentrations of secondary species are determined by 

the balance between chemical production and destruction. RTRAC requires that any secondary 

daughter tracers must be specified after their parent tracer in the chemistry parameters input 

file. 

RTRAC also allows tracers that track the secondary formation of any species that is included in 

the host chemical mechanism. For example, in Figure 11-1 the species SFORM is used to track 

secondary formaldehyde, and so SFORM is defined as a secondary species and identified with 

the host species FORM. This means that the RTRAC chemistry module will identify the chemical 

production of FORM in each grid cell at each time step, and add this chemical production to the 





 



 − 



 



 = T

T E k A a

B

exp 300
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SFORM tracer. Since SFORM is intended to track only secondary formaldehyde, no primary 

emissions should be included for SFORM. 

11.1.1.4 Example for Defining Chemical Rate Data

Reaction rate data for many gases can be found in rate constant compilations such as IUPAC 

(2001), JPL (2001) and Calvert et al. (2000, 2002). For the examples shown in Figures 11-1 and 

11-2, rate constants were obtained from a study by Harley and Cass (1995) that modeled 

detailed VOCs for Los Angeles. Photolysis rates were calculated using the Tropospheric Ultraviolet Visible (TUV) model (NCAR, 2011), which is available as a CAMx pre-processor. TUV 

includes photolysis data (cross-sections and quantum yields) for many species, and data for 

other species are included in IUPAC (2001), JPL (2001) and Calvert et al. (2002).

11.1.1.5 Chemical Decay Rates for Near-Source Modeling

The RTRAC algorithm can output hourly chemical decay rates at user-specified locations for 

input to an external point-source dispersion model (e.g., a Gaussian plume/puff model) for 

subsequent sub-grid scale “fence line” modeling. The objective is to allow the grid model 

(CAMx) to provide local decay rate information to any plume-scale model of the user’s choice.

If subgrid-scale near-source modeling is to be conducted using an external model, then the user 

provides the locations of each of the target emission complexes using the CAMx Probing Tools 

receptor file input format. Figure 11-3 displays an example RTRAC receptor input file for the 

five point source complexes modeled by ENVIRON (2002) and Morris et al. (2003). At each grid 

cell, hourly decay rates for each RTRAC compound and every vertical layer are output and can 

then be interfaced with the user-selected plume model.

Figure 11-3. Example RTRAC receptor input file identifying the grid cells with locations of 

point source complexes where hourly decay rates will be output for subgrid-scale point 

source modeling (see format for OSAT receptor file in Table 7-2).

11.1.2 RTRAC Source-Receptor Relationships and Double Counting

Separate families of reactive tracer compounds can be simulated by providing separate 

emission inputs similarly to OSAT/PSAT (see Section 7). Tracking separate families of RTRAC 

tracers allows for source apportionment and can be used to avoid double counting when an 

external plume model is used to obtain near-source impacts. For example, in the RTRAC air 

toxics example application discussed previously (ENVIRON, 2002; Morris et al., 2003), separate 

air toxic emission inputs were provided to source apportion on-road mobile sources, area plus 

SINGLE CELL Test Cell 1 42 44

SINGLE CELL Test Cell 1 41 36

SINGLE CELL Test Cell 1 39 36 

SINGLE CELL Test Cell 1 50 43

SINGLE CELL Test Cell 1 34 48
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non-road sources, point sources, and secondarily formed species. Furthermore, separate 

families of air toxic tracers were also specified for each point source complex to be modeled by 

the external plume model, so that total concentrations could include the local point source 

impacts (plume model) plus the regional contributions from all other sources (CAMx RTRAC).

11.2 Description of RTCMC

Like RTRAC, the purpose of RTCMC is to add tracer species to a CAMx “core model” simulation 

and have the tracers undergo chemical changes that depend, in part, upon the evolution of 

CAMx core model species. The RTCMC approach differs from the original RTRAC approach by 

allowing arbitrarily complex chemical reaction schemes, but it is exactly like RTRAC in every 

other respect. The current implementation of RTCMC is for gas-phase reactions, i.e., gas-phase 

tracers reacting with each other and/or gas-phase host model species. The core model’s 

photochemical mechanisms remain intact and separate from the reactive tracer chemistry.

11.2.1 RTCMC Gas-Phase Chemistry

The RTCMC allows users to input, in a text-based (ASCII) format, a set of chemical reactions 

(mechanism) for certain target species to be treated by the CAMx Reactive Tracer Probing Tool. 

RTCMC is an extension of the original RTRAC algorithm that reads (and solves) a completely 

independent, user-defined chemical mechanism for reactive tracers that can utilize 

concentrations of any photochemical species from the core model mechanism. Upon startup, 

RTCMC compiles information on the chemical mechanism and configures the reactive tracer 

chemistry solver. During the model simulation, the RTCMC chemistry solver receives ambient 

pollutant information from the core photochemical mechanism and uses this to calculate the 

evolution of RTRAC species.

The format of the RTCMC input file is essentially the same as the “IMC” input file format of the 

SCICHEM Lagrangian puff model (EPRI, 2000). An example IMC format file is shown in Figure 

11-4. There are four sections in an IMC file that are identified by a keyword at the start of each 

section, as follows:

#Control Configuration information identified by keywords

#Species Names of chemical species and associated data

#Table Photolysis rate data for any photolytic reactions

#Equations Chemical reactions and thermal rate constants

The IMC file uses space-delimited free-form ASCII format. Leading white space at the start of 

any line will be ignored. CAMx reads the IMC file as case insensitive.

The hash symbol (#) before each section keyword marks the start of a section and should be 

reserved for this purpose. The four sections should appear in the order shown above. The only 

section that may be unnecessary in some cases (i.e., if there are no photolytic reactions) is the 

#Table section and guidance on handling this case is provided below. 
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Figure 11-4. Example free-format RTCMC IMC chemistry input file.

11.2.1.1 The Control Section

According to the SCICHEM documentation, the #Control section of the IMC file must always 

have at least three lines, as follows:

#CONTROL

 &CONTROL

 &END

The first line is the keyword identifying the control section. The second and third lines are 

additional keywords denoting the start and end of the control section. Note, however, that 

CAMx ignores the &CONTROL and &END lines.

One or more control options may be specified using keywords, inserted one per line, ahead of 

the closing &END line, like this:

#CONTROL

 &CONTROL

 Keyword = ‘option’

 Keyword = ‘option’

 &END

#Control

 rate_species_units = 'ppm'

 rate_time_units = 'min'

 solver = 'dlsode'

 Jacobian = 'numeric'

#Name, Type, Ambient, ATol, Dep, Wet Scav, MW, Spec Map

O3 A 1.0 1.0E-12 0.0 0.0 0.0

OH A 1.0 1.0E-12 0.0 0.0 0.0

ATRAC F 1.0 1.0E-12 0.010 0.0 0.0

BTRAC F 1.0 1.0E-12 0.001 0.0 0.0

CTRAC F 1.0 1.0E-12 0.020 0.0 0.0

DTRAC F 1.0 1.0E-12 0.001 0.0 0.0

ETRAC F 1.0 1.0E-12 0.030 0.0 0.0

FTRAC F 1.0 1.0E-12 -0.001 0.0 0.0 NO2

#Table

 0 0. 15. 30. 45. 60. 75.

 80. 86. 87. 88.

 1 4.1590E-04 4.0600E-04 3.7540E-04 3.27E-04 2.6040E-04 9.4990E-05 

2.9930E-05 4.8590E-06 8.3030E-08 1.0000E-09

#Equations

 1 [ATRAC] -> (2.0)[BTRAC] ; 0 0.000E-00

 2 (1.5)[CTRAC] + [OH] -> (0.5)[DTRAC] ; 1 4.2000E+04

 3 [ETRAC] + [O3] -> [FTRAC] ; 1 1.8000E-02
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The keywords used by CAMx and SCICHEM are listed in Table 11-1 and are case insensitive. Not 

all keywords are used by both models, and CAMx will ignore any non-recognized keyword. A 

“=” symbol must separate each keyword and option. The option must be enclosed within 

Table 11-1. Keywords, options and default values for the Control section of the IMC file.

Keyword

Used by 

SCICHEM

Used by 

CAMx Options Allowed by CAMx

Ambient file ● n/a

Species_units ● n/a

Emission_units ● n/a

Rate_species_units ● ● molecules/cm3 (default)

ppm

Rate_time_units ● ●

seconds (default)

minutes

hours

Solver ●

DLSODE (default)

SLSODE

Rosenbrock

Rtol ● ● Real number (default = 1.0E-5)

Atol ● Real number (default = 1.0E-18)

Jacobian ● Numeric (default)

Algebraic

single quotes. In practice, only the first six letters of each keyword and the first three letters of 

each option are considered and you may abbreviate accordingly (i.e., keyword = ‘opt’).

All CAMx recognized keywords have a default option that will be used if the keyword is omitted, 

meaning that the CAMx RTCMC may be run without specifying any keywords provided that that 

all other input data (e.g., rate constants) are consistent with the defaults. The allowed keyword 

options in Table 11-1 are discussed below:

Rate_species_units

The concentration units for thermal rate constant expressions.

Rate_time_units

The time units for photolysis and thermal rate constant expressions.

Solver

The name of the numerical integrator to be used as the chemistry solver. SLSODE and 

DLSODE are, respectively, the single and double precision versions of the Livermore 

Solver for Ordinary Differential Equations (Hindmarsh 1983). The Rosenbrock solver is 

the double precision RODAS solver (Hairer and Wanner, 1991).

Rtol

The relative error tolerance (convergence criterion) employed for all chemical species by 

the chemistry solver. 
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Atol

The absolute error tolerance (convergence criterion) employed for all chemical species 

by the chemistry solver. CAMx does not use species-specific Atol values that may 

appear in the species section, as discussed below.

Jacobian

The chemistry solvers employ a Jacobian matrix of first-order derivatives of each 

chemical species with respect to all species. The Jacobian matrix is constructed 

automatically by the RTCMC. This option controls whether the Jacobian is constructed 

algebraically or numerically. Both options may be used with the double precision 

solvers and numeric may be more efficient. The algebraic option is strongly 

recommended for the single precision SLSODE solver (because single precision may be 

inadequate for constructing a numeric Jacobian by finite difference).

11.2.1.1.1 Concentration Units

CAMx does not use the Species_units or Emission_units keywords and will ignore 

them if they are present. CAMx will output RTCMC species average concentrations in ppm 

units. Emissions of RTCMC species must be provided in moles/hour.

11.2.1.1.2 Setting Error Tolerances

All three RTCMC chemistry solvers use the Rtol and Atol parameters specified in the control 

section to manage errors in predicted concentrations. CAMx does not use the species-specific 

Atol values that may appear in the species section because it is difficult to select reliable 

Atol values for each species. The error (err) in the predicted concentration (con) for species i

should be roughly less than:

err(i) = rtol × con(i) + atol

The combined Rtol and Atol determine accuracy. Setting Atol to zero will result in pure 

relative error control. Relative error control has the advantage of being easily understood (the 

errors should be smaller than X percent) but suffers the disadvantage of excessive 

computational resources that may be expended to manage errors in species concentrations 

that are essentially zero. Note that RTCMC sets a concentration floor of 1.0E-16 ppm. 

The default settings for Rtol and Atol listed in Table 11-1 should be generally applicable 

because they are conservative and effectively result in pure relative error control. We 

recommend against setting Rtol greater than 0.001. Appropriate settings for Atol depend 

upon the magnitude of concentration predictions and the need for accurate predictions in high 

vs. low concentration areas (e.g., plume centerline vs. out of plume).

Do not request infeasible accuracy from single precision SLSODE by setting Rtol and Atol

smaller than about 1.0E-7.
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11.2.1.2 The Species Section

The species section of the IMC file lists chemical species and associated data. All chemical 

species referred to in the equation section must appear in the species section. Extra species 

may appear in the species section, but including numerous extra species may cause a run-time 

error by exceeding the memory available for storing species information (if this happens, delete 

some of the unused species from the species section). 

The first line is the keyword identifying the species section. The following information must be 

provided for each listed species:

Name

Species names may be up to 8 characters and must start with a letter. They are case 

insensitive. Accurate names are important because other CAMx input data (e.g., 

emissions, boundary conditions) will be matched to RTRAC species by name.

Type

There are four permissible species types identified by first letter: Ambient (A), Fast (F), 

Slow (S), and Equilibrium (E). Setting the species type is discussed in more detail below.

Ambient

The ambient value is not used by CAMx, but is used by SCICHEM. Provide a real number 

(e.g., 0.0).

Atol

Species specific error tolerances are not used by CAMx, but are used by SCICHEM. 

Provide a real number (e.g., 0.0).

Dep

The species deposition velocity in m/s. This deposition velocity will be used for all land 

surface types, which is a simplification compared to the CAMx dry deposition scheme. 

Provide a real number (e.g., 0.0).

Wet Scav

The wet scavenging coefficient is not used by CAMx. For SCICHEM, this is a washout 

ratio. CAMx does not use the washout ratio because this approach is incompatible with 

the CAMx wet deposition algorithms. Provide a real number (e.g., 0.0).

MW

The molecular weight is not needed by CAMx. Provide a real number (e.g., 1.0).

Spec Map

The core model species name from which to use internally-calculated dry deposition 

velocity for the RTCMC species. This is triggered by a negative “Dep” value in the same 

record. Provide a 10-character string. In the example below, RTCMC tracer O3A will use 

deposition velocities calculated by CAMx for the core model species O3:

#Name, Type, Ambient, ATol, Dep, Wet Scav, MW, Spec Map

O3A F 1.0 1.000E-08 -3.00E-03 0.0 48.0 O3

11.2.1.2.1 Choosing the Species Type

The Type for each RTCMC species should be set according to: (a) whether the species 

concentration should be obtained from the core model or modeled using the RTCMC; and (b) 

the most accurate and efficient numerical method for performing chemistry within RTCMC. 
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All species to be obtained from the core model (e.g., O3, OH, NO, NO2, H2O, M, O2) must be set 

to type Ambient. This rule will be enforced by CAMx and, for example, the species O3 must 

be set to type A, because it is part of all the core chemical mechanisms. 

Species that are solved by the RTCMC may be type F, S or E. The recommended default type 

is F (fast) in which case chemistry will be performed using the selected chemistry solver (e.g., 

DLSODE). Species that undergo slow chemical change (lifetime of hours or longer) may be set 

to type S (slow) with potential gain in efficiency but some loss in accuracy. Species that 

undergo extremely rapid chemical change (lifetime smaller than a second) may be set to type E

(equilibrium) and solved using a steady-state approximation with some gain in efficiency but 

some loss in accuracy. The Rosenbrock solver does not work well with species types S or E. 

Equilibrium species may be used effectively with the single precision SLSODE solver to avoid the 

need for double precision. You should use types S or E with caution and evaluate both 

computational speed and concentration accuracy by comparing against results with using 

type F. 

11.2.1.3 The Table Section

The table section of the IMC file provides photolysis rates for any photolytic reactions in the 

RTCMC mechanism. It must contain at least two lines:

#Table

0 zenith1, zenith2, zenith3, ...

The first line is the keyword identifying the table section. The second line must begin with 0 

(zero) followed by a list of space-delimited zenith angles (in degrees) starting with zero degrees 

and ascending to the largest angle. If the largest zenith angle specified is less than 90 degrees a 

value of 90 degrees is implicitly added to the list. By default, up to 15 zenith angles are allowed 

(this may be changed as described under adjustable parameters, below). If the final zenith 

angle is not 90 degrees, no more than 14 angles should be listed to allow the 15th angle to be 

implicitly set to 90 degrees. 

If the reaction mechanism has no photolytic reactions, include just the first two lines (keyword 

followed by zenith angles) in the table section. If the reaction mechanism includes photolytic 

reactions, list them one reaction per space-delimited line after the zenith angles:

reaction_ID, rate1, rate2, rate3, ...

The reaction_ID must be the integer identification number of the photolytic reaction 

followed by the photolysis rate at each zenith angle, from zero to the largest angle. Photolysis 

reactions are first order and have rate units of reciprocal time to be provided in the 

Rate_time_units specified in the control section of the IMC file. A photolysis rate of zero 

is implicitly assumed at 90 degrees unless you specify otherwise.

A negative “reaction_ID” in the table section causes the photolysis rate to be set to a core 

model reaction number, which is set in the position of “rate1”. In the example below, 
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RTCMC reaction #1 is photolytic and rates will be set according to the CAMx core photolysis 

reaction number 9:

#Table

 0 0. 10. 20. 30. 40. 50. 60. 70. 78. 86.

-001 9

11.2.1.4 The Equations Section

The equations section of the IMC file lists the chemical reactions and rate constants for the 

RTCMC reaction mechanism and must contain at least two lines:

#Equations

reaction_ID [Reactants] > (Stoichiometry) [Products] ; Rate_Constant

The first line is the keyword identifying the equations section and must be followed by at least 

one reaction line. Reaction lines list reactions and rate constants and are delimited by white 

space and separators. The reaction_ID and the Reactants must be separated by white 

space. The Reactants and Products must be separated by a right arrow symbol (the right 

arrow may be preceded by characters, e.g., => or −>). The Products and the 

Rate_Constant must be separated by a semi-colon.

The reaction_ID must be an integer value that uniquely identifies each reaction. Reactions 

identifiers need not be in order or continuous.

The name of Reactants and Products must be enclosed within square brackets, begin 

with a letter, and not exceed 8 characters in length. All species names used in the equations 

section must also appear in the species section. Zero to three reactants are allowed. Zero to 20 

products are allowed (the maximum is a user adjustable parameter). Reactant and product 

names may be preceded by a stoichiometric coefficient enclosed within round brackets. If the 

stoichiometric coefficient is omitted it is assumed to be unity.

Rate constants are specified using SCICHEM conventions and must be in the units specified by 

the keywords Rate_species_units and Rate_time_units in the control section (the 

defaults are molecules cm-3 and seconds, respectively). SCICHEM supports numerous rate 

constant expression types and CAMx should interpret all of them correctly, although not all 

have been thoroughly tested. Table 11-2 defines a sub-set of the SCICHEM rate constant 

expression types that are recommended for use with CAMx. The format for specifying rate 

expressions is the integer expression type followed by a list of the numerical values required by 

that expression type. It is important that rate expressions are defined in units that are 

consistent with the reaction order, and Table 11-3 defines how the reaction order and rate 

constant unit dimensions may be determined.

The CAMx output “diag” file lists diagnostic information on the mechanism and rate constant 

expressions read by from the IMC file. You should review this diagnostic output to ensure that 

CAMx correctly read and configured the RTCMC chemistry mechanism.
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11.3 Reactive Tracers In IRON PiG

RTRAC/RTCMC calculations for emissions and chemistry have been integrated into the IRON PiG 

algorithms. There are two ways in which RTRAC tracers may enter a PiG plume: as primary 

emissions from specifically flagged sources within the RTRAC point source file, or by formation 

of secondary species from decay of primary plume emissions. There is no entrainment of 

tracers from the grid to the plume as this is likely to result in negative tracer concentrations, 

Table 11-2a. Recommended SCICHEM rate constant expression types for use in CAMx.

Expression Type Description Expression

0 Photolysis k = 0

1 Constant 0 k = k

2 General temperature 

dependence

c (B T ) k AT e − / =

3 Troe-type temperature and 

pressure dependence

G F

k M k

k M k

















+ = ∞ 1 [ ]/

[ ]

0

0

B k = AT 0

D k = CT ∞

F = 0.6

[ ( )] 1 2 0 1 log [ ]/

− ∞











 G = + k M k

8 Equilibrium with a previously 

defined reaction (kref)

(B T ) ref k k Ae / =

13 Lindemann - Hinshelwood 

as used for OH + HNO3

3 2

3

0 1 [ }/

[ ]

k M k

k M k k

+ = +

(B T ) k Ae /

0 =

(D T ) k Ce /

2 =

(F T ) k E e /

3 =

7

Simple pressure 

dependence used for OH + 

CO

k k (1 0.6P) = 0 +
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Table 11-2b. Parameters required by SCICHEM rate constant expression types.

Expression

Type Parameters

1 2 3 4 5 6

0 0

1 ko

2 A B C

3 A B C D

8 kref A B

13 A B C D E F

7 ko

Table 11-3. Determining the reaction order and consequent unit dimensions for rate 

constants.

Number of Reactants Reaction Order

Concentration Unit 

Dimension Time Unit Dimension

0 Zero None Time-1

1 First None Time-1

2 Second Concentration-1 Time-1

3 Third Concentration-2 Time-1

especially if the entrained tracer is a secondary product of a host model species (e.g., secondary 

formaldehyde). Tracers are assumed to have negligible impact on PiG puff chemistry or oxidant 

levels. If the tracer concentration in the plume is high enough to enhance or suppress the 

plume oxidant levels, then the photochemical impacts of the tracer can be accounted for by 

separately adding the tracer emissions into the host model lumped emissions; e.g., for tracing 

high concentrations of propene and butene in a plume, one would track the propene/butene 

concentrations using RTRAC tracers but also add CB-OLE or SAPRC99-OLE1 emissions to the 

plume to account for the oxidant impacts. RTRAC checks to ensure that it is reading its own 

input point source file. RTRAC and host model point source files must have the same number 

of sources in the same order; however, the list of species on each file may be different, and the 

sources flagged to receive the PiG treatment may vary. A pre-processor program was coded to 

help prepare consistent RTRAC and host model point source files.

Tracers released from PiG sources decay according to the oxidant and photolytic environment 

of the plume using user-supplied chemical rate parameters (as described earlier). Oxidant 

concentrations for the decay calculation are obtained from the CAMx PiG incremental 

photochemical simulation for each puff at each time step. RTRAC tracers in each puff reactor

are updated based on the total oxidant concentrations for the reactor, i.e., puff increment plus 

puff ambient/background. RTRAC enforces a rule that no secondary tracer formation from the 

decay of host model species are allowed if IRON PiG is active (e.g., no secondary formaldehyde 

tracer formation is allowed with IRON PiG). Secondary tracer production from primary tracer 

decay is allowed.
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Tracers are transferred from the PiG to the grid using the same approach as for any other host 

model species (see Section 6). Tracer concentrations at any point are the superposition of the 

grid concentration plus any collocated PiG puffs.

11.3.1 Integration of RTRAC Puff Sampling 

RTRAC optionally employs surface-layer IRON puff sampling of tracers on a user-defined 

sampling grid (see Section 6). Sampling grids are entirely passive, and intended to provide a 

display of the reactive tracer plume concentrations at scales much smaller than typically used 

for the finest computational grids (i.e., <1 km). 

Figure 11-5 shows an example plume of hypothetical tracer “TRAC1” emitted from a point 

source in the center of the image as displayed on a 1-km sampling grid. The finest core model 

computational mesh contains 4-km grid spacing and covers a much broader area than shown in 

the figure.

Figure 11-5. Example RTRAC tracer plume emanating from a large point source and displayed 

on a surface sampling grid with 1-km grid spacing. The figure illustrates the entire extent of 

the sampling grid.

11.4 Running CAMx With Reactive Tracers

11.4.1 CAMx Control File

RTRAC is invoked similarly to the other Probing Tools within the CAMx control file. In the 

&CAMx_Control namelist module, the variable Probing_Tool must be set to “RTRAC” or 

“RTCMC”. An additional namelist module called &RT_Control must then be provided in the 

control file to configure the RTRAC portion of the model. The additional namelist module is 
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described below. The order of the variables follows the template available with the source 

code. Figure 11-6 provides an example of the RTRAC control module.

Description of RTRAC Control in the CAMx Run Control File

&RT_Control Label for the Probing Tool namelist module that configures the 

RTRAC option; it must begin in column 2

& Flag ending a namelist; it must be in column 2

RT_File_Root Character root output path/filename

RT_Initial_Conditions Character input master grid RTRAC initial conditions 

path/filename (optional, ignored if Restart=TRUE)

RT_Boundary_Conditions Character input master grid RTRAC boundary conditions 

path/filename (optional)

RT_Master_Restart Character input master grid RTRAC restart path/filename 

(ignored if Restart=FALSE)

RT_Nested_Restart Character input nested grid RTRAC restart path/filename 

(ignored if Restart=FALSE or Number_of_Grids=1)

RT_Chemistry_Parameters Character input RTRAC chemistry parameters path/filename, or 

RTCMC IMC chemistry definition path/filename

RT_Receptor_Definitions Character input RTRAC receptor definition path/filename 

(optional)

RT_Point_Sources Character input RTRAC elevated point source emissions 

path/filename (optional, ignored if

Point_Emissions=FALSE)

RT_Emiss_Grid Character array (by CAMx grid) input RTRAC gridded emissions 

path/filename (optional, ignored if

Gridded_Emissions=FALSE)

RT_PiG_Sample Logical sampling grid flag for RTRAC IRON PiG output; sampling 

grids are defined in the main &CAMx_Control namelist 

(TRUE=sampling grid output will be generated, FALSE=sampling 

grid output will not be generated)
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Figure 11-6. Example input of RTRAC options and filenames within the CAMx control file.

As with the output for the host model and other Probing Tools, a “root” file name is specified 

and suffixes are added depending upon the type of output produced. A separate root name for 

RTRAC (and other Probing Tools) allows the user to direct the output to a completely different 

path. RTRAC writes several output files that are in Fortran binary format, as described in 

Section 3. These include the master and nested grid tracer instantaneous concentration files 

(.rt.inst and .rt.finst), the grid-specific surface tracer average concentration file 

(.rt.surf.grdnn). These files are written in the same format as for the regular model 

species described in Section 3.

The “RT_Chemistry_Parameter” namelist variable specifies the path/filename of either 

the RTRAC chemistry parameters file or the RTCMC IMC chemistry definition file. The choice of 

which type of file format is read is set according the main “Probing_Tool” variable (i.e., 

RTRAC or RTCMC).

RTRAC/IRON PiG sampling grids are invoked in the RTRAC namelist by setting a logical flag. If 

set to TRUE, the user must provide the number of sampling grids and the grid parameters of 

each in the main &CAMx_Control namelist. Sampling grids are set identically to the way 

nested grids are specified for the host model, with one exception: there are no vertical levels to 

define (sampling grids are currently only 2-D surface fields). The same rules that apply for the 

specification of nested grids holds for the specification of all sampling grids (see Sections 3, 4, 

and 6 of the User’s Guide). The “mesh factor” sets the resolution or cell size of the sampling 

&RT_Control

RT_File_Root = 'CAMx6.test.020614',

RT_Initial_Conditions = ' ',

RT_Boundary_Conditions = ' ',

RT_Master_Restart = 'CAMx6.test.020613.rt.inst',

RT_Nested_Restart = 'CAMx6.test.020613.rt.finst',

RT_Chemistry_Parameters = 'CAMx6.chemparam.rtrac_test',

RT_Receptor_Definitions = 'receptor.rtrac.test',

RT_Point_Sources = 'pt.rtrac.test',

RT_Emiss_Grid(1) = 'emiss.rtrac.36km',

RT_Emiss_Grid(2) = 'emiss.rtrac.12km',

RT_Emiss_Grid(3) = 'emiss.rtrac.04km',

RT_PiG_Sample = .true.,

&
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grid relative to the master grid. The CAMx diagnostic output file provides information on the 

location and size of each sampling grid to help ensure proper setup.

11.4.2 User Adjustable Parameters

Once the RTRAC/RTCMC chemistry parameters/definition file is established, the user should be 

sure that a sufficient allocation of memory is provided for this Probing Tool. This is done by 

examining the main Probing Tool parameter and common block file in 

Includes/camx.prm. The parameter MXTRSP should be set to the total number of species 

defined in the chemistry parameters file. If sampling grids are to be used, the user should 

ensure that sufficient memory is available to define the size of sampling grid arrays. This is also 

set in Includes/camx.prm.

User adjustable parameters for RTCMC are set in the CAMx include file

Includes/rtcmcchm.inc. If an error is encountered at model start up because one of 

these RTCMC parameter has been exceeded, consult the list of parameters in Table 11-4 and 

then change the parameter appropriately in the rtcmcchm.inc include file. Rebuild the 

CAMx executable (we recommend performing a “make clean” before making a new CAMx 

executable) after changing any RTCMC parameter.

Table 11-4. RTCMC parameters default settings in the Includes/rtcmcchm.inc include 

file.

Name Description Default

MXRX maximum number of RTCMC reactions 20

MXPHOT maximum number of photolysis reactions 10

MXZEN maximum number of photolysis reaction zenith angles 15

MXRCT Maximum number of reactants in each reaction 3

MXPRD maximum number of products in each reaction 20

MXEQM maximum number of equilibrium species 5

MXSLO maximum number of slow species 25
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Texas Commisision on Environmental Quality, Austin, Texas (September 2012).

Zhang, L., S. Gong, J. Padro, L. Barrie. 2001. A size-segregated particle dry deposition scheme 

for an atmospheric aerosol module. Atmos. Environ., 35, 549-560.

Zhang, L., J. R. Brook, and R. Vet. 2003. A revised parameterization for gaseous dry deposition

in air-quality models. Atmos. Chem. Phys., 3, 2067–2082.
April 2014 CAMx User’s Guide Version 6.1

12. References

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 247 www.camx.com

Zhang, X., S. Kondragunta, C. Schmidt, and F. Kogan. 2008. Near real time monitoring of 

biomass burning particulate emissions (PM2.5) across contiguous United States using 

multiple satellite instruments. Atmospheric Environment, 42, 6959-6972.
April 2014 CAMx User’s Guide Version 6.1

Appendix A: Mechanism 2 – CB6r2

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 248 www.camx.com

Appendix A

CAMx Mechanism 2

CB6r2 Gas-Phase Chemistry

Table A-1. Reactions and rate constants/parameters for the CB6r2 mechanism.

Number Reactants and Products Rate Constant Expression k298

1 NO2 = NO + O Photolysis

2 O + O2 + M = O3 + M k = 5.68E-34 (T/300)^-2.6 5.78E-34

3 O3 + NO = NO2 k = 1.40E-12 exp(-1310/T) 1.73E-14

4 O + NO + M = NO2 + M k = 1.00E-31 (T/300)^-1.6 1.01E-31

5 O + NO2 = NO k = 5.50E-12 exp(188/T) 1.03E-11

6 O + NO2 = NO3 Falloff: F=0.6; n=1

 k

0 = 1.30E-31 (T/300)^-1.5

 k

∞ = 2.30E-11 (T/300)^0.24

2.11E-12

7 O + O3 = k = 8.00E-12 exp(-2060/T) 7.96E-15

8 O3 = O Photolysis

9 O3 = O1D Photolysis

10 O1D + M = O + M k = 2.23E-11 exp(115/T) 3.28E-11

11 O1D + H2O = 2 OH k = 2.14E-10 2.14E-10

12 O3 + OH = HO2 k = 1.70E-12 exp(-940/T) 7.25E-14

13 O3 + HO2 = OH k = 2.03E-16 (T/300)^4.57 exp(693/T) 2.01E-15

14 OH + O = HO2 k = 2.40E-11 exp(110/T) 3.47E-11

15 HO2 + O = OH k = 2.70E-11 exp(224/T) 5.73E-11

16 OH + OH = O k = 6.20E-14 (T/298)^2.6 exp(945/T) 1.48E-12

17 OH + OH = H2O2 Falloff: F=0.5; n=1.13

 k

0 = 6.90E-31 (T/300)^-0.8

 k

∞ = 2.60E-11

5.25E-12

18 OH + HO2 = k = 4.80E-11 exp(250/T) 1.11E-10

19 HO2 + HO2 = H2O2 k = k1 + k2 [M]

 k1 = 2.20E-13 exp(600/T)

 k2 = 1.90E-33 exp(980/T)

2.90E-12

20 HO2 + HO2 + H2O = H2O2 k = k1 + k2 [M]

 k1 = 3.08E-34 exp(2800/T)

 k2 = 2.66E-54 exp(3180/T)

6.53E-30

21 H2O2 = 2 OH Photolysis

22 H2O2 + OH = HO2 k = 2.90E-12 exp(-160/T) 1.70E-12

23 H2O2 + O = OH + HO2 k = 1.40E-12 exp(-2000/T) 1.70E-15

24 NO + NO + O2 = 2 NO2 k = 3.30E-39 exp(530/T) 1.95E-38

25 HO2 + NO = OH + NO2 k = 3.45E-12 exp(270/T) 8.54E-12

26 NO2 + O3 = NO3 k = 1.40E-13 exp(-2470/T) 3.52E-17

27 NO3 = NO2 + O Photolysis

28 NO3 = NO Photolysis

29 NO3 + NO = 2 NO2 k = 1.80E-11 exp(110/T) 2.60E-11

30 NO3 + NO2 = NO + NO2 k = 4.50E-14 exp(-1260/T) 6.56E-16

31 NO3 + O = NO2 k = 1.70E-11 1.70E-11

32 NO3 + OH = HO2 + NO2 k = 2.00E-11 2.00E-11

33 NO3 + HO2 = OH + NO2 k = 4.00E-12 4.00E-12

34 NO3 + O3 = NO2 k = 1.00E-17 1.00E-17
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Number Reactants and Products Rate Constant Expression k298

35 NO3 + NO3 = 2 NO2 k = 8.50E-13 exp(-2450/T) 2.28E-16

36 NO3 + NO2 = N2O5 Falloff: F=0.35; n=1.33

 k

0 = 3.60E-30 (T/300)^-4.1

 k

∞ = 1.90E-12 (T/300)^0.2

1.24E-12

37 N2O5 = NO3 + NO2 Falloff: F=0.35; n=1.33

 k

0 = 1.30E-3 (T/300)^-3.5 exp(-11000/T)

 k

∞ = 9.70E+14 (T/300)^0.1 exp(-11080/T)

4.46E-2

38 N2O5 = NO2 + NO3 Photolysis

39 N2O5 + H2O = 2 HNO3 k = 1.00E-22 1.00E-22

40 NO + OH = HONO Falloff: F=0.81; n=0.87

 k

0 = 7.40E-31 (T/300)^-2.4

 k∞ = 3.30E-11 (T/300)^-0.3

9.77E-12

41 NO + NO2 + H2O = 2 HONO k = 5.00E-40 5.00E-40

42 HONO + HONO = NO + NO2 k = 1.00E-20 1.00E-20

43 HONO = NO + OH Photolysis

44 HONO + OH = NO2 k = 2.50E-12 exp(260/T) 5.98E-12

45 NO2 + OH = HNO3 Falloff: F=0.6; n=1

 k

0 = 1.80E-30 (T/300)^-3

 k∞ = 2.80E-11

1.06E-11

46 HNO3 + OH = NO3 k = k1 + k3 [M] / (1 + k3 [M] / k2)

 k1 = 2.40E-14 exp(460/T)

 k2 = 2.70E-17 exp(2199/T)

 k3 = 6.50E-34 exp(1335/T)

1.54E-13

47 HNO3 = OH + NO2 Photolysis

48 HO2 + NO2 = PNA Falloff: F=0.6; n=1

 k

0 = 1.80E-31 (T/300)^-3.2

 k∞ = 4.70E-12

1.38E-12

49 PNA = HO2 + NO2 Falloff: F=0.6; n=1

 k

0 = 4.10E-5 exp(-10650/T)

 k∞ = 4.80E+15 exp(-11170/T)

8.31E-2

50 PNA = 0.59 HO2 + 0.59 NO2 + 0.41 OH + 0.41 

NO3

Photolysis

51 PNA + OH = NO2 k = 3.20E-13 exp(690/T) 3.24E-12

52 SO2 + OH = SULF + HO2 Falloff: F=0.53; n=1.1

 k

0 = 4.50E-31 (T/300)^-3.9

 k∞ = 1.30E-12 (T/300)^-0.7

8.12E-13

53 C2O3 + NO = NO2 + MEO2 + RO2 k = 7.50E-12 exp(290/T) 1.98E-11

54 C2O3 + NO2 = PAN Falloff: F=0.3; n=1.41

 k

0 = 2.70E-28 (T/300)^-7.1

 k

∞ = 1.20E-11 (T/300)^-0.9

9.40E-12

55 PAN = NO2 + C2O3 Falloff: F=0.3; n=1.41

 k

0 = 4.90E-3 exp(-12100/T)

 k

∞ = 5.40E+16 exp(-13830/T)

2.98E-4

56 PAN = 0.6 NO2 + 0.6 C2O3 + 0.4 NO3 + 0.4 

MEO2 + 0.4 RO2

Photolysis

57 C2O3 + HO2 = 0.41 PACD + 0.15 AACD + 0.15 

O3 + 0.44 MEO2 + 0.44 RO2 + 0.44 OH

k = 5.20E-13 exp(980/T) 1.39E-11

58 C2O3 + RO2 = C2O3 k = 8.90E-13 exp(800/T) 1.30E-11

59 C2O3 + C2O3 = 2 MEO2 + 2 RO2 k = 2.90E-12 exp(500/T) 1.55E-11
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Appendix A: Mechanism 2 – CB6r2

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Number Reactants and Products Rate Constant Expression k298

60 C2O3 + CXO3 = MEO2 + ALD2 + XO2H + 2 RO2 k = 2.90E-12 exp(500/T) 1.55E-11

61 CXO3 + NO = NO2 + ALD2 + XO2H + RO2 k = 6.70E-12 exp(340/T) 2.10E-11

62 CXO3 + NO2 = PANX k = kref K

 kref = k(54)

 K = 1.00E+0

9.40E-12

63 PANX = NO2 + CXO3 k = kref K

 kref = k(55)

 K = 1.00E+0

2.98E-4

64 PANX = 0.6 NO2 + 0.6 CXO3 + 0.4 NO3 + 0.4 

ALD2 + 0.4 XO2H + 0.4 RO2

Photolysis

65 CXO3 + HO2 = 0.41 PACD + 0.15 AACD + 0.15 

O3 + 0.44 ALD2 + 0.44 XO2H + 0.44 RO2 + 

0.44 OH

k = 5.20E-13 exp(980/T) 1.39E-11

66 CXO3 + RO2 = 0.8 ALD2 + 0.8 XO2H + 0.8 RO2 k = 8.90E-13 exp(800/T) 1.30E-11

67 CXO3 + CXO3 = 2 ALD2 + 2 XO2H + 2 RO2 k = 3.20E-12 exp(500/T) 1.71E-11

68 RO2 + NO = NO k = 2.40E-12 exp(360/T) 8.03E-12

69 RO2 + HO2 = HO2 k = 4.80E-13 exp(800/T) 7.03E-12

70 RO2 + RO2 = k = 6.50E-14 exp(500/T) 3.48E-13

71 MEO2 + NO = FORM + HO2 + NO2 k = 2.30E-12 exp(360/T) 7.70E-12

72 MEO2 + HO2 = 0.9 MEPX + 0.1 FORM k = 3.80E-13 exp(780/T) 5.21E-12

73 MEO2 + C2O3 = FORM + 0.9 HO2 + 0.9 MEO2 

+ 0.1 AACD + 0.9 RO2

k = 2.00E-12 exp(500/T) 1.07E-11

74 MEO2 + RO2 = 0.685 FORM + 0.315 MEOH + 

0.37 HO2 + RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13

75 XO2H + NO = NO2 + HO2 k = 2.70E-12 exp(360/T) 9.04E-12

76 XO2H + HO2 = ROOH k = 6.80E-13 exp(800/T) 9.96E-12

77 XO2H + C2O3 = 0.8 HO2 + 0.8 MEO2 + 0.2 

AACD + 0.8 RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11

78 XO2H + RO2 = 0.6 HO2 + RO2 k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13

79 XO2 + NO = NO2 k = kref K

 kref = k(75)

 K = 1.00E+0

9.04E-12

80 XO2 + HO2 = ROOH k = kref K

 kref = k(76)

 K = 1.00E+0

9.96E-12

81 XO2 + C2O3 = 0.8 MEO2 + 0.2 AACD + 0.8 RO2 k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11

82 XO2 + RO2 = RO2 k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13

83 XO2N + NO = NTR k = kref K

 kref = k(75)

 K = 1.00E+0

9.04E-12
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Appendix A: Mechanism 2 – CB6r2

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Number Reactants and Products Rate Constant Expression k298

84 XO2N + HO2 = ROOH k = kref K

 kref = k(76)

 K = 1.00E+0

9.96E-12

85 XO2N + C2O3 = 0.8 HO2 + 0.8 MEO2 + 0.2 

AACD + 0.8 RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11

86 XO2N + RO2 = RO2 k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13

87 MEPX + OH = 0.6 MEO2 + 0.6 RO2 + 0.4 FORM 

+ 0.4 OH

k = 5.30E-12 exp(190/T) 1.00E-11

88 MEPX = MEO2 + RO2 + OH Photolysis

89 ROOH + OH = 0.54 XO2H + 0.06 XO2N + 0.6 

RO2 + 0.4 OH

k = 5.30E-12 exp(190/T) 1.00E-11

90 ROOH = HO2 + OH Photolysis

91 NTR + OH = NO2 + XO2 + RO2 k = 2.00E-12 2.00E-12

92 NTR = HNO3 + XO2H + RO2 Photolysis

93 FACD + OH = HO2 k = 4.50E-13 4.50E-13

94 AACD + OH = MEO2 + RO2 k = 4.00E-14 exp(850/T) 6.93E-13

95 PACD + OH = C2O3 k = 5.30E-12 exp(190/T) 1.00E-11

96 FORM + OH = HO2 + CO k = 5.40E-12 exp(135/T) 8.49E-12

97 FORM = 2 HO2 + CO Photolysis

98 FORM = CO + H2 Photolysis

99 FORM + O = OH + HO2 + CO k = 3.40E-11 exp(-1600/T) 1.58E-13

100 FORM + NO3 = HNO3 + HO2 + CO k = 5.50E-16 5.50E-16

101 FORM + HO2 = HCO3 k = 9.70E-15 exp(625/T) 7.90E-14

102 HCO3 = FORM + HO2 k = 2.40E+12 exp(-7000/T) 1.51E+2

103 HCO3 + NO = FACD + NO2 + HO2 k = 5.60E-12 5.60E-12

104 HCO3 + HO2 = 0.5 MEPX + 0.5 FACD + 0.2 OH 

+ 0.2 HO2

k = 5.60E-15 exp(2300/T) 1.26E-11

105 ALD2 + O = C2O3 + OH k = 1.80E-11 exp(-1100/T) 4.49E-13

106 ALD2 + OH = C2O3 k = 4.70E-12 exp(345/T) 1.50E-11

107 ALD2 + NO3 = C2O3 + HNO3 k = 1.40E-12 exp(-1860/T) 2.73E-15

108 ALD2 = MEO2 + RO2 + CO + HO2 Photolysis

109 ALDX + O = CXO3 + OH k = 1.30E-11 exp(-870/T) 7.02E-13

110 ALDX + OH = CXO3 k = 4.90E-12 exp(405/T) 1.91E-11

111 ALDX + NO3 = CXO3 + HNO3 k = 6.30E-15 6.30E-15

112 ALDX = ALD2 + XO2H + RO2 + CO + HO2 Photolysis

113 GLYD + OH = 0.2 GLY + 0.2 HO2 + 0.8 C2O3 k = 8.00E-12 8.00E-12

114 GLYD = 0.74 FORM + 0.89 CO + 1.4 HO2 + 0.15 

MEOH + 0.19 OH + 0.11 GLY + 0.11 XO2H + 

0.11 RO2

Photolysis

115 GLYD + NO3 = HNO3 + C2O3 k = 1.40E-12 exp(-1860/T) 2.73E-15

116 GLY + OH = 1.8 CO + 0.2 XO2 + 0.2 RO2 + HO2 k = 3.10E-12 exp(340/T) 9.70E-12

117 GLY = 2 HO2 + 2 CO Photolysis

118 GLY + NO3 = HNO3 + 1.5 CO + 0.5 XO2 + 0.5 

RO2 + HO2

k = 1.40E-12 exp(-1860/T) 2.73E-15

119 MGLY = C2O3 + HO2 + CO Photolysis

120 MGLY + NO3 = HNO3 + C2O3 + XO2 + RO2 k = 1.40E-12 exp(-1860/T) 2.73E-15
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Number Reactants and Products Rate Constant Expression k298

121 MGLY + OH = C2O3 + CO k = 1.90E-12 exp(575/T) 1.31E-11

122 H2 + OH = HO2 k = 7.70E-12 exp(-2100/T) 6.70E-15

123 CO + OH = HO2 k = k1 + k2 [M]

 k1 = 1.44E-13

 k2 = 3.43E-33

2.28E-13

124 CH4 + OH = MEO2 + RO2 k = 1.85E-12 exp(-1690/T) 6.37E-15

125 ETHA + OH = 0.991 ALD2 + 0.991 XO2H + 

0.009 XO2N + RO2

k = 6.90E-12 exp(-1000/T) 2.41E-13

126 MEOH + OH = FORM + HO2 k = 2.85E-12 exp(-345/T) 8.95E-13

127 ETOH + OH = 0.95 ALD2 + 0.9 HO2 + 0.1 XO2H 

+ 0.1 RO2 + 0.078 FORM + 0.011 GLYD

k = 3.00E-12 exp(20/T) 3.21E-12

128 KET = 0.5 ALD2 + 0.5 C2O3 + 0.5 XO2H + 0.5 

CXO3 + 0.5 MEO2 + RO2 - 2.5 PAR

Photolysis

129 ACET = 0.38 CO + 1.38 MEO2 + 1.38 RO2 + 

0.62 C2O3

Photolysis

130 ACET + OH = FORM + C2O3 + XO2 + RO2 k = 1.41E-12 exp(-620.6/T) 1.76E-13

131 PRPA + OH = 0.71 ACET + 0.26 ALDX + 0.26 

PAR + 0.97 XO2H + 0.03 XO2N + RO2

k = 7.60E-12 exp(-585/T) 1.07E-12

132 PAR + OH = 0.11 ALDX + 0.76 ROR + 0.13 

XO2N + 0.11 XO2H + 0.76 XO2 + RO2 - 0.11 

PAR

k = 8.10E-13 8.10E-13

133 ROR = 0.2 KET + 0.42 ACET + 0.74 ALD2 + 0.37 

ALDX + 0.04 XO2N + 0.94 XO2H + 0.98 RO2 + 

0.02 ROR - 2.7 PAR

k = 5.70E+12 exp(-5780/T) 2.15E+4

134 ROR + O2 = KET + HO2 k = 1.50E-14 exp(-200/T) 7.67E-15

135 ROR + NO2 = NTR k = 8.60E-12 exp(400/T) 3.29E-11

136 ETHY + OH = 0.7 GLY + 0.7 OH + 0.3 FACD + 

0.3 CO + 0.3 HO2

Falloff: F=0.37; n=1.3

 k

0 = 5.00E-30 (T/300)^-1.5

 k

∞ = 1.00E-12

7.52E-13

137 ETH + O = FORM + HO2 + CO + 0.7 XO2H + 0.7 

RO2 + 0.3 OH

k = 1.04E-11 exp(-792/T) 7.29E-13

138 ETH + OH = XO2H + RO2 + 1.56 FORM + 0.22 

GLYD

Falloff: F=0.48; n=1.15

 k

0 = 8.60E-29 (T/300)^-3.1

 k∞ = 9.00E-12 (T/300)^-0.85

7.84E-12

139 ETH + O3 = FORM + 0.51 CO + 0.16 HO2 + 0.16 

OH + 0.37 FACD

k = 9.10E-15 exp(-2580/T) 1.58E-18

140 ETH + NO3 = 0.5 NO2 + 0.5 NTR + 0.5 XO2H + 

0.5 XO2 + RO2 + 1.125 FORM

k = 3.30E-12 exp(-2880/T) 2.10E-16

141 OLE + O = 0.2 ALD2 + 0.3 ALDX + 0.1 HO2 + 0.2 

XO2H + 0.2 CO + 0.2 FORM + 0.01 XO2N + 

0.21 RO2 + 0.2 PAR + 0.1 OH

k = 1.00E-11 exp(-280/T) 3.91E-12

142 OLE + OH = 0.781 FORM + 0.488 ALD2 + 0.488 

ALDX + 0.976 XO2H + 0.195 XO2 + 0.024 XO2N 

+ 1.195 RO2 - 0.73 PAR

Falloff: F=0.5; n=1.13

 k

0 = 8.00E-27 (T/300)^-3.5

 k∞ = 3.00E-11 (T/300)^-1

2.86E-11

143 OLE + O3 = 0.295 ALD2 + 0.555 FORM + 0.27 

ALDX + 0.15 XO2H + 0.15 RO2 + 0.334 OH + 

0.08 HO2 + 0.378 CO + 0.075 GLY + 0.075 

MGLY + 0.09 FACD + 0.13 AACD + 0.04 H2O2 -

0.79 PAR

k = 5.50E-15 exp(-1880/T) 1.00E-17
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Appendix A: Mechanism 2 – CB6r2

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Number Reactants and Products Rate Constant Expression k298

144 OLE + NO3 = 0.5 NO2 + 0.5 NTR + 0.48 XO2 + 

0.48 XO2H + 0.04 XO2N + RO2 + 0.5 FORM + 

0.25 ALD2 + 0.375 ALDX - 1 PAR

k = 4.60E-13 exp(-1155/T) 9.54E-15

145 IOLE + O = 1.24 ALD2 + 0.66 ALDX + 0.1 XO2H 

+ 0.1 RO2 + 0.1 CO + 0.1 PAR

k = 2.30E-11 2.30E-11

146 IOLE + OH = 1.3 ALD2 + 0.7 ALDX + XO2H + 

RO2

k = 1.05E-11 exp(519/T) 5.99E-11

147 IOLE + O3 = 0.732 ALD2 + 0.442 ALDX + 0.128 

FORM + 0.245 CO + 0.5 OH + 0.3 XO2H + 0.3 

RO2 + 0.24 GLY + 0.06 MGLY + 0.29 PAR + 

0.08 AACD + 0.08 H2O2

k = 4.70E-15 exp(-1013/T) 1.57E-16

148 IOLE + NO3 = 0.5 NO2 + 0.5 NTR + 0.48 XO2 + 

0.48 XO2H + 0.04 XO2N + RO2 + 0.5 ALD2 + 

0.625 ALDX + PAR

k = 3.70E-13 3.70E-13

149 ISOP + OH = ISO2 + RO2 k = 2.70E-11 exp(390/T) 9.99E-11

150 ISOP + O = 0.75 ISPD + 0.5 FORM + 0.25 XO2 + 

0.25 RO2 + 0.25 HO2 + 0.25 CXO3 + 0.25 PAR

k = 3.00E-11 3.00E-11

151 ISO2 + NO = 0.1 INTR + 0.9 NO2 + 0.673 FORM 

+ 0.9 ISPD + 0.818 HO2 + 0.082 XO2H + 0.082 

RO2

k = 2.39E-12 exp(365/T) 8.13E-12

152 ISO2 + HO2 = 0.88 ISPX + 0.12 OH + 0.12 HO2 

+ 0.12 FORM + 0.12 ISPD

k = 7.43E-13 exp(700/T) 7.78E-12

153 ISO2 + C2O3 = 0.598 FORM + 1 ISPD + 0.728 

HO2 + 0.072 XO2H + 0.8 MEO2 + 0.2 AACD + 

0.872 RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11

154 ISO2 + RO2 = 0.598 FORM + 1 ISPD + 0.728 

HO2 + 0.072 XO2H + 0.072 RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13

155 ISO2 = HO2 + HPLD k = 3.30E+9 exp(-8300/T) 2.64E-3

156 ISOP + O3 = 0.6 FORM + 0.65 ISPD + 0.15 ALDX 

+ 0.2 CXO3 + 0.35 PAR + 0.266 OH + 0.2 XO2 + 

0.2 RO2 + 0.066 HO2 + 0.066 CO

k = 1.03E-14 exp(-1995/T) 1.27E-17

157 ISOP + NO3 = 0.35 NO2 + 0.65 NTR + 0.64 

XO2H + 0.33 XO2 + 0.03 XO2N + RO2 + 0.35 

FORM + 0.35 ISPD

k = 3.03E-12 exp(-448/T) 6.74E-13

158 ISPD + OH = 0.056 XO2N + 0.521 XO2 + 0.238 

XO2H + 0.154 MGLY + 0.273 MEO2 + 0.119 

GLY + 0.349 GLYD + 0.23 C2O3 + 0.117 CXO3 + 

0.236 PAR + 0.256 ACET + 0.197 CO + 0.137 

HO2 + 1.088 RO2

k = 5.58E-12 exp(511/T) 3.10E-11

159 ISPD + O3 = 0.04 ALD2 + 0.231 FORM + 0.531 

MGLY + 0.17 GLY + 0.17 ACET + 0.543 CO + 

0.461 OH + 0.15 FACD + 0.398 HO2 + 0.143 

C2O3

k = 3.88E-15 exp(-1770/T) 1.02E-17

160 ISPD + NO3 = 0.717 HNO3 + 0.142 NTR + 

0.142 NO2 + 0.142 XO2 + 0.142 XO2H + 0.113 

GLYD + 0.113 MGLY + 0.717 PAR + 0.717 CXO3 

+ 0.284 RO2

k = 4.10E-12 exp(-1860/T) 7.98E-15
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Number Reactants and Products Rate Constant Expression k298

161 ISPD = 0.76 HO2 + 0.34 XO2H + 0.16 XO2 + 

0.34 MEO2 + 0.208 C2O3 + 0.26 FORM + 0.24 

OLE + 0.24 PAR + 0.17 ACET + 0.128 GLYD + 

0.84 RO2

Photolysis

162 ISPX + OH = 0.904 EPOX + 0.933 OH + 0.067 

ISO2 + 0.067 RO2 + 0.029 IOLE + 0.029 ALDX

k = 2.23E-11 exp(372/T) 7.77E-11

163 HPLD = OH + HO2 + ISPD Photolysis

164 HPLD + NO3 = HNO3 + ISPD k = 6.00E-12 exp(-1860/T) 1.17E-14

165 EPOX + OH = EPX2 + RO2 k = 5.78E-11 exp(-400/T) 1.51E-11

166 EPX2 + HO2 = 0.275 GLYD + 0.275 GLY + 0.275 

MGLY + 1.125 OH + 0.825 HO2 + 0.375 FORM 

+ 0.074 FACD + 0.251 CO + 2.175 PAR

k = 7.43E-13 exp(700/T) 7.78E-12

167 EPX2 + NO = 0.275 GLYD + 0.275 GLY + 0.275 

MGLY + 0.125 OH + 0.825 HO2 + 0.375 FORM 

+ NO2 + 0.251 CO + 2.175 PAR

k = 2.39E-12 exp(365/T) 8.13E-12

168 EPX2 + C2O3 = 0.22 GLYD + 0.22 GLY + 0.22 

MGLY + 0.1 OH + 0.66 HO2 + 0.3 FORM + 0.2 

CO + 1.74 PAR + 0.8 MEO2 + 0.2 AACD + 0.8 

RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11

169 EPX2 + RO2 = 0.275 GLYD + 0.275 GLY + 0.275 

MGLY + 0.125 OH + 0.825 HO2 + 0.375 FORM 

+ 0.251 CO + 2.175 PAR + RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13

170 INTR + OH = 0.63 XO2 + 0.37 XO2H + RO2 + 

0.444 NO2 + 0.185 NO3 + 0.104 INTR + 0.592 

FORM + 0.331 GLYD + 0.185 FACD + 2.7 PAR + 

0.098 OLE + 0.078 ALDX + 0.266 NTR

k = 3.10E-11 3.10E-11

171 TERP + O = 0.15 ALDX + 5.12 PAR k = 3.60E-11 3.60E-11

172 TERP + OH = 0.75 XO2H + 0.5 XO2 + 0.25 

XO2N + 1.5 RO2 + 0.28 FORM + 1.66 PAR + 

0.47 ALDX

k = 1.50E-11 exp(449/T) 6.77E-11

173 TERP + O3 = 0.57 OH + 0.07 XO2H + 0.69 XO2 

+ 0.18 XO2N + 0.94 RO2 + 0.24 FORM + 0.001 

CO + 7 PAR + 0.21 ALDX + 0.39 CXO3

k = 1.20E-15 exp(-821/T) 7.63E-17

174 TERP + NO3 = 0.47 NO2 + 0.28 XO2H + 0.75 

XO2 + 0.25 XO2N + 1.28 RO2 + 0.47 ALDX + 

0.53 NTR

k = 3.70E-12 exp(175/T) 6.66E-12

175 BENZ + OH = 0.53 CRES + 0.352 BZO2 + 0.352 

RO2 + 0.118 OPEN + 0.118 OH + 0.53 HO2

k = 2.30E-12 exp(-190/T) 1.22E-12

176 BZO2 + NO = 0.918 NO2 + 0.082 NTR + 0.918 

GLY + 0.918 OPEN + 0.918 HO2

k = 2.70E-12 exp(360/T) 9.04E-12

177 BZO2 + C2O3 = GLY + OPEN + HO2 + MEO2 + 

RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11

178 BZO2 + HO2 = k = 1.90E-13 exp(1300/T) 1.49E-11

179 BZO2 + RO2 = GLY + OPEN + HO2 + RO2 k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13

180 TOL + OH = 0.18 CRES + 0.65 TO2 + 0.72 RO2 + 

0.1 OPEN + 0.1 OH + 0.07 XO2H + 0.18 HO2

k = 1.80E-12 exp(340/T) 5.63E-12
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Number Reactants and Products Rate Constant Expression k298

181 TO2 + NO = 0.86 NO2 + 0.14 NTR + 0.417 GLY 

+ 0.443 MGLY + 0.66 OPEN + 0.2 XOPN + 0.86 

HO2

k = 2.70E-12 exp(360/T) 9.04E-12

182 TO2 + C2O3 = 0.48 GLY + 0.52 MGLY + 0.77 

OPEN + 0.23 XOPN + HO2 + MEO2 + RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11

183 TO2 + HO2 = k = 1.90E-13 exp(1300/T) 1.49E-11

184 TO2 + RO2 = 0.48 GLY + 0.52 MGLY + 0.77 

OPEN + 0.23 XOPN + HO2 + RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13

185 XYL + OH = 0.155 CRES + 0.544 XLO2 + 0.602 

RO2 + 0.244 XOPN + 0.244 OH + 0.058 XO2H + 

0.155 HO2

k = 1.85E-11 1.85E-11

186 XLO2 + NO = 0.86 NO2 + 0.14 NTR + 0.221 GLY 

+ 0.675 MGLY + 0.3 OPEN + 0.56 XOPN + 0.86 

HO2

k = 2.70E-12 exp(360/T) 9.04E-12

187 XLO2 + HO2 = k = 1.90E-13 exp(1300/T) 1.49E-11

188 XLO2 + C2O3 = 0.26 GLY + 0.77 MGLY + 0.35 

OPEN + 0.65 XOPN + HO2 + MEO2 + RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11

189 XLO2 + RO2 = 0.26 GLY + 0.77 MGLY + 0.35 

OPEN + 0.65 XOPN + HO2 + RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13

190 CRES + OH = 0.025 GLY + 0.025 OPEN + HO2 + 

0.2 CRO + 0.732 CAT1 + 0.02 XO2N + 0.02 RO2

k = 1.70E-12 exp(950/T) 4.12E-11

191 CRES + NO3 = 0.3 CRO + HNO3 + 0.48 XO2 + 

0.12 XO2H + 0.24 GLY + 0.24 MGLY + 0.48 

OPO3 + 0.1 XO2N + 0.7 RO2

k = 1.40E-11 1.40E-11

192 CRO + NO2 = CRON k = 2.10E-12 2.10E-12

193 CRO + HO2 = CRES k = 5.50E-12 5.50E-12

194 CRON + OH = NTR + 0.5 CRO k = 1.53E-12 1.53E-12

195 CRON + NO3 = NTR + 0.5 CRO + HNO3 k = 3.80E-12 3.80E-12

196 CRON = HONO + HO2 + FORM + OPEN Photolysis

197 XOPN = 0.4 GLY + XO2H + 0.7 HO2 + 0.7 CO + 

0.3 C2O3

Photolysis

198 XOPN + OH = MGLY + 0.4 GLY + 2 XO2H + 2 

RO2

k = 9.00E-11 9.00E-11

199 XOPN + O3 = 1.2 MGLY + 0.5 OH + 0.6 C2O3 + 

0.1 ALD2 + 0.5 CO + 0.3 XO2H + 0.3 RO2

k = 1.08E-16 exp(-500/T) 2.02E-17

200 XOPN + NO3 = 0.5 NO2 + 0.5 NTR + 0.45 XO2H 

+ 0.45 XO2 + 0.1 XO2N + RO2 + 0.25 OPEN + 

0.25 MGLY

k = 3.00E-12 3.00E-12

201 OPEN = OPO3 + HO2 + CO Photolysis

202 OPEN + OH = 0.6 OPO3 + 0.4 XO2H + 0.4 RO2 

+ 0.4 GLY

k = 4.40E-11 4.40E-11

203 OPEN + O3 = 1.4 GLY + 0.24 MGLY + 0.5 OH + 

0.12 C2O3 + 0.08 FORM + 0.02 ALD2 + 1.98 

CO + 0.56 HO2

k = 5.40E-17 exp(-500/T) 1.01E-17

204 OPEN + NO3 = OPO3 + HNO3 k = 3.80E-12 3.80E-12

205 CAT1 + OH = 0.14 FORM + 0.2 HO2 + 0.5 CRO k = 5.00E-11 5.00E-11
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Number Reactants and Products Rate Constant Expression k298

206 CAT1 + NO3 = CRO + HNO3 k = 1.70E-10 1.70E-10

207 OPO3 + NO = NO2 + 0.5 GLY + 0.5 CO + 0.8 

HO2 + 0.2 CXO3

k = 1.00E-11 1.00E-11

208 OPO3 + NO2 = OPAN k = kref K

 kref = k(54)

 K = 1.00E+0

9.40E-12

209 OPAN = OPO3 + NO2 k = kref K

 kref = k(55)

 K = 1.00E+0

2.98E-4

210 OPO3 + HO2 = 0.41 PACD + 0.15 AACD + 0.15 

O3 + 0.44 ALDX + 0.44 XO2H + 0.44 RO2 + 

0.44 OH

k = kref K

 kref = k(57)

 K = 1.00E+0

1.39E-11

211 OPO3 + C2O3 = MEO2 + XO2 + ALDX + 2 RO2 k = kref K

 kref = k(59)

 K = 1.00E+0

1.55E-11

212 OPO3 + RO2 = 0.8 XO2H + 0.8 ALDX + 1.8 RO2 

+ 0.2 AACD

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11

213 OPAN + OH = GLY + 2 CO + NO2 k = 3.60E-11 3.60E-11

214 PANX + OH = ALD2 + NO2 k = 3.00E-12 3.00E-12

215 NTR2 = HNO3 k = 2.30E-5 2.30E-5

216 ECH4 + OH = MEO2 + RO2 k = 1.85E-12 exp(-1690/T) 6.37E-15

Table notes:

k298 is the rate constant at 298 K and 1 atmosphere using units molecules cm-3 and s-1

See Table A-2 for species names

See the CAMx chemistry parameters file for the temperature and pressure dependencies (Section 3).

Table A-2. Explicit species in the CB6r2 mechanism.

Species Description

BZO2 Peroxy radical from OH addition to benzene 

C2O3 Acetylperoxy radical

CRO Alkoxy radical from cresol

CXO3 C3 and higher acylperoxy radicals 

EPX2 Peroxy radical from EPOX reaction with OH

HCO3 Adduct from HO2 plus formaldehyde

HO2 Hydroperoxy radical

ISO2 Peroxy radical from OH addition to isoprene 

MEO2 Methylperoxy radical

NO3 Nitrate radical

O Oxygen atom in the O3(P) electronic state

O1D Oxygen atom in the O1(D) electronic state

OH Hydroxyl radical

OPO3 Peroxyacyl radical from OPEN

RO2 Operator to approximate total peroxy radical concentration

ROR Secondary alkoxy radical

TO2 Peroxy radical from OH addition to TOL 

XLO2 Peroxy radical from OH addition to XYL 

XO2 NO to NO2 conversion from alkylperoxy (RO2) radical
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Appendix A: Mechanism 2 – CB6r2

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Species Description

XO2H NO to NO2 conversion (XO2) accompanied by HO2 production

XO2N NO to organic nitrate conversion from alkylperoxy (RO2) radical

AACD Acetic acid

ACET Acetone

ALD2 Acetaldehyde

ALDX Propionaldehyde and higher aldehydes

BENZ Benzene

CAT1 Methyl-catechols

CO Carbon monoxide

CRES Cresols

CRON Nitro-cresols

EPOX Epoxide formed from ISPX reaction with OH

ETH Ethene

ETHA Ethane

ETHY Ethyne

ETOH Ethanol

FACD Formic acid

FORM Formaldehyde

GLY Glyoxal

GLYD Glycolaldehyde

H2O2 Hydrogen peroxide

HNO3 Nitric acid

HONO Nitrous acid

HPLD hydroperoxyaldehyde

INTR Organic nitrates from ISO2 reaction with NO

IOLE Internal olefin carbon bond (R-C=C-R)

ISOP Isoprene

ISPD Isoprene product (lumped methacrolein, methyl vinyl ketone, etc.)

ISPX Hydroperoxides from ISO2 reaction with HO2

KET Ketone carbon bond (C=O)

MEOH Methanol

MEPX Methylhydroperoxide

MGLY Methylglyoxal

N2O5 Dinitrogen pentoxide

NO Nitric oxide

NO2 Nitrogen dioxide

NTR1 Simple organic nitrates

NTR2 Multi-functional organic nitrates

O3 Ozone

OLE Terminal olefin carbon bond (R-C=C)

OPAN Peroxyacyl nitrate (PAN compound) from OPO3

OPEN Aromatic ring opening product (unsaturated dicarbonyl)

PACD Peroxyacetic and higher peroxycarboxylic acids

PAN Peroxyacetyl Nitrate

PANX C3 and higher peroxyacyl nitrate

PAR Paraffin carbon bond (C-C)

PNA Peroxynitric acid

PRPA Propane
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Appendix A: Mechanism 2 – CB6r2

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Species Description

ROOH Higher organic peroxide

SO2 Sulfur dioxide

SULF Sulfuric acid (gaseous)

TERP Monoterpenes

TOL Toluene and other monoalkyl aromatics

XOPN Aromatic ring opening product (unsaturated dicarbonyl)

XYL Xylene and other polyalkyl aromatics

ECH4 Emitted methane

Table A-3. Properties of VOC species in the CB6r2 mechanism: carbon numbers, kOH values 

(ppm-1min-1) and maximum incremental reactivity (MIR) values (mole O3/mole VOC).

Species Carbon Number Average kOH MIR

PAR 1 1.20E+03 0.509

ETHA 2 3.54E+02 0.135

MEOH 1 1.35E+03 0.48

ETOH 2 4.71E+03 1.53

ETH 2 1.20E+04 4.95

OLE 2 4.73E+04 9.66

IOLE 4 9.35E+04 16

ISOP 5 1.47E+05 12.7

TERP 10 1.00E+05 9.91

FORM 1 1.33E+04 4.87

ALD2 2 2.05E+04 5.8

ALDX 2 2.93E+04 8.35

TOL 7 8.75E+03 7.39

XYL 8 3.71E+04 20.5

PRPA 3 1. 58E+03 0.541

ETHY 2 1.80E+03 1.39

BENZ 6 1.11E+03 0.487

ACET 3 2.60E+02 0.564

KET 1 0.0 4.86
April 2014 CAMx User’s Guide Version 6.1

Appendix B: Mechanism 7 – CB6

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Appendix B

CAMx Mechanism 7

CB6 Gas-Phase Chemistry

Table B-1. Reactions and rate constants/parameters for the CB6 mechanism.

Number Reactants and Products Rate Constant Expression k298 Notes

1 NO2 = NO + O Photolysis a

2 O + O2 + M = O3 + M k = 5.68E-34 (T/300)^-2.6 5.78E-34 a

3 O3 + NO = NO2 k = 1.40E-12 exp(-1310/T) 1.73E-14 a

4 O + NO + M = NO2 + M k = 1.00E-31 (T/300)^-1.6 1.01E-31 a

5 O + NO2 = NO k = 5.50E-12 exp(188/T) 1.03E-11 a

6 O + NO2 = NO3 Falloff: F=0.6; n=1

 k

0 = 1.30E-31 (T/300)^-1.5

 k

∞ = 2.30E-11 (T/300)^0.2

2.11E-12 a

7 O + O3 = k = 8.00E-12 exp(-2060/T) 7.96E-15 a

8 O3 = O Photolysis a

9 O3 = O1D Photolysis a

10 O1D + M = O + M k = 2.23E-11 exp(115/T) 3.28E-11 a

11 O1D + H2O = 2 OH k = 2.14E-10 2.14E-10 a

12 O3 + OH = HO2 k = 1.70E-12 exp(-940/T) 7.25E-14 a

13 O3 + HO2 = OH k = 2.03E-16 (T/300)^4.6 exp(693/T) 2.01E-15 a

14 OH + O = HO2 k = 2.40E-11 exp(110/T) 3.47E-11 a

15 HO2 + O = OH k = 2.70E-11 exp(224/T) 5.73E-11 a

16 OH + OH = O k = 6.20E-14 (T/298)^2.6 exp(945/T) 1.48E-12 a

17 OH + OH = H2O2 Falloff: F=0.5; n=1.13

 k

0 = 6.90E-31 (T/300)^-0.8

 k∞ = 2.60E-11

5.25E-12 a

18 OH + HO2 = k = 4.80E-11 exp(250/T) 1.11E-10 a

19 HO2 + HO2 = H2O2 k = k1 + k2 [M]

 k1 = 2.20E-13 exp(600/T)

 k2 = 1.90E-33 exp(980/T)

2.90E-12 a

20 HO2 + HO2 + H2O = H2O2 k = k1 + k2 [M]

 k1 = 3.08E-34 exp(2800/T)

 k2 = 2.66E-54 exp(3180/T)

6.53E-30 a

21 H2O2 = 2 OH Photolysis a

22 H2O2 + OH = HO2 k = 2.90E-12 exp(-160/T) 1.70E-12 a

23 H2O2 + O = OH + HO2 k = 1.40E-12 exp(-2000/T) 1.70E-15 a

24 NO + NO + O2 = 2 NO2 k = 3.30E-39 exp(530/T) 1.95E-38 a

25 HO2 + NO = OH + NO2 k = 3.45E-12 exp(270/T) 8.54E-12 a

26 NO2 + O3 = NO3 k = 1.40E-13 exp(-2470/T) 3.52E-17 a

27 NO3 = NO2 + O Photolysis b

28 NO3 = NO Photolysis b

29 NO3 + NO = 2 NO2 k = 1.80E-11 exp(110/T) 2.60E-11 a

30 NO3 + NO2 = NO + NO2 k = 4.50E-14 exp(-1260/T) 6.56E-16 b

31 NO3 + O = NO2 k = 1.70E-11 1.70E-11 a

32 NO3 + OH = HO2 + NO2 k = 2.00E-11 2.00E-11 a

33 NO3 + HO2 = OH + NO2 k = 4.00E-12 4.00E-12 a 

34 NO3 + O3 = NO2 k = 1.00E-17 1.00E-17 c,k

35 NO3 + NO3 = 2 NO2 k = 8.50E-13 exp(-2450/T) 2.28E-16 b
April 2014 CAMx User’s Guide Version 6.1

Appendix B: Mechanism 7 – CB6

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Number Reactants and Products Rate Constant Expression k298 Notes

36 NO3 + NO2 = N2O5 Falloff: F=0.35; n=1.33

 k

0 = 3.60E-30 (T/300)^-4.1

 k

∞ = 1.90E-12 (T/300)^0.2

1.24E-12 a

37 N2O5 = NO3 + NO2 Falloff: F=0.35; n=1.33

 k

0 = 1.30E-3 (T/300)^-3.5 exp(-11000/T)

 k

∞ = 9.70E+14 (T/300)^0.1 exp(-11080/T)

4.46E-2 a

38 N2O5 = NO2 + NO3 Photolysis a

39 N2O5 + H2O = 2 HNO3 k = 1.00E-22 1.00E-22 a

40 NO + OH = HONO Falloff: F=0.81; n=0.866

 k

0 = 7.40E-31 (T/300)^-2.4

 k

∞ = 3.30E-11 (T/300)^-0.3

9.77E-12 a

41 NO + NO2 + H2O = 2 HONO k = 5.00E-40 5.00E-40 c,l

42 HONO + HONO = NO + NO2 k = 1.00E-20 1.00E-20 c,m

43 HONO = NO + OH Photolysis a

44 HONO + OH = NO2 k = 2.50E-12 exp(260/T) 5.98E-12 a

45 NO2 + OH = HNO3 Falloff: F=0.6; n=1

 k

0 = 1.80E-30 (T/300)^-3

 k∞ = 2.80E-11

1.06E-11 b

46 HNO3 + OH = NO3 k = k1 + k3 [M] / (1 + k3 [M] / k2)

 k1 = 2.40E-14 exp(460/T)

 k2 = 2.70E-17 exp(2199/T)

 k3 = 6.50E-34 exp(1335/T)

1.54E-13 a

47 HNO3 = OH + NO2 Photolysis a

48 HO2 + NO2 = PNA Falloff: F=0.6; n=1

 k

0 = 1.80E-31 (T/300)^-3.2

 k

∞ = 4.70E-12

1.38E-12 a

49 PNA = HO2 + NO2 Falloff: F=0.6; n=1

 k

0 = 4.10E-5 exp(-10650/T)

 k∞ = 4.80E+15 exp(-11170/T)

8.31E-2 a

50 PNA = 0.59 HO2 + 0.59 NO2 + 0.41 OH + 

0.41 NO3

Photolysis a

51 PNA + OH = NO2 k = 3.20E-13 exp(690/T) 3.24E-12 a

52 SO2 + OH = SULF + HO2 Falloff: F=0.53; n=1.1

 k

0 = 4.50E-31 (T/300)^-3.9

 k

∞ = 1.30E-12 (T/300)^-0.7

8.12E-13 a

53 C2O3 + NO = NO2 + MEO2 + RO2 k = 7.50E-12 exp(290/T) 1.98E-11 a

54 C2O3 + NO2 = PAN Falloff: F=0.3; n=1

 k

0 = 2.70E-28 (T/300)^-7.1

 k∞ = 1.20E-11 (T/300)^-0.9

1.05E-11 a

55 PAN = NO2 + C2O3 Falloff: F=0.3; n=1

 k

0 = 4.90E-3 exp(-12100/T)

 k

∞ = 5.40E+16 exp(-13830/T)

3.31E-4 a

56 PAN = 0.6 NO2 + 0.6 C2O3 + 0.4 NO3 + 

0.4 MEO2 + 0.4 RO2

Photolysis a 

57 C2O3 + HO2 = 0.41 PACD + 0.15 AACD + 

0.15 O3 + 0.44 MEO2 + 0.44 RO2 + 0.44 

OH

k = 5.20E-13 exp(980/T) 1.39E-11 a

58 C2O3 + RO2 = C2O3 k = 8.90E-13 exp(800/T) 1.30E-11 a

59 C2O3 + C2O3 = 2 MEO2 + 2 RO2 k = 2.90E-12 exp(500/T) 1.55E-11 a

60 C2O3 + CXO3 = MEO2 + ALD2 + XO2H + 2 

RO2

k = 2.90E-12 exp(500/T) 1.55E-11 a
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Appendix B: Mechanism 7 – CB6

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Number Reactants and Products Rate Constant Expression k298 Notes

61 CXO3 + NO = NO2 + ALD2 + XO2H + RO2 k = 6.70E-12 exp(340/T) 2.10E-11 a

62 CXO3 + NO2 = PANX Falloff: F=0.3; n=1

 k

0 = 3.00E-28 (T/300)^-7.1

 k

∞ = 1.33E-11 (T/300)^-0.9

1.16E-11 a

63 PANX = NO2 + CXO3 Falloff: F=0.3; n=1

 k

0 = 1.70E-3 exp(-11280/T)

 k∞ = 8.30E+16 exp(-13940/T)

3.68E-4 a

64 PANX = 0.6 NO2 0.6 CXO3 + 0.4 NO3 + 

0.4 ALD2 + 0.4 XO2H + 0.4 RO2

Photolysis a

65 CXO3 + HO2 = 0.41 PACD + 0.15 AACD + 

0.15 O3 + 0.44 ALD2 + 0.44 XO2H + 0.44 

RO2 + 0.44 OH

k = 5.20E-13 exp(980/T) 1.39E-11 a

66 CXO3 + RO2 = 0.8 ALD2 + 0.8 XO2H + 0.8 

RO2

k = 8.90E-13 exp(800/T) 1.30E-11 a

67 CXO3 + CXO3 = 2 ALD2 + 2 XO2H + 2 RO2 k = 3.20E-12 exp(500/T) 1.71E-11 a

68 RO2 + NO = NO k = 2.40E-12 exp(360/T) 8.03E-12 a

69 RO2 + HO2 = HO2 k = 4.80E-13 exp(800/T) 7.03E-12 a

70 RO2 + RO2 = k = 6.50E-14 exp(500/T) 3.48E-13 a

71 MEO2 + NO = FORM + HO2 + NO2 k = 2.30E-12 exp(360/T) 7.70E-12 a

72 MEO2 + HO2 = 0.9 MEPX + 0.1 FORM k = 3.80E-13 exp(780/T) 5.21E-12 a

73 MEO2 + C2O3 = FORM + 0.9 HO2 + 0.9 

MEO2 + 0.1 AACD + 0.9 RO2

k = 2.00E-12 exp(500/T) 1.07E-11 a

74 MEO2 + RO2 = 0.685 FORM + 0.315 

MEOH + 0.37 HO2 + RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 a

75 XO2H + NO = NO2 + HO2 k = 2.70E-12 exp(360/T) 9.04E-12 a

76 XO2H + HO2 = ROOH k = 6.80E-13 exp(800/T) 9.96E-12 a

77 XO2H + C2O3 = 0.8 HO2 + 0.8 MEO2 + 

0.2 AACD + 0.8 RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 a

78 XO2H + RO2 = 0.6 HO2 + RO2 k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 a

79 XO2 + NO = NO2 k = kref K

 kref = k(75)

 K = 1.00E+0

9.04E-12 a

80 XO2 + HO2 = ROOH k = kref K

 kref = k(76)

 K = 1.00E+0

9.96E-12 a

81 XO2 + C2O3 = 0.8 MEO2 + 0.2 AACD + 0.8 

RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 a

82 XO2 + RO2 = RO2 k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 a

83 XO2N + NO = NTR k = kref K

 kref = k(75)

 K = 1.00E+0

9.04E-12 a

84 XO2N + HO2 = ROOH k = kref K

 kref = k(76)

 K = 1.00E+0

9.96E-12 a
April 2014 CAMx User’s Guide Version 6.1

Appendix B: Mechanism 7 – CB6

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 262 www.camx.com

Number Reactants and Products Rate Constant Expression k298 Notes

85 XO2N + C2O3 = 0.8 HO2 + 0.8 MEO2 + 

0.2 AACD + 0.8 RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 a

86 XO2N + RO2 = RO2 k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 a

87 MEPX + OH = 0.6 MEO2 + 0.6 RO2 + 0.4 

FORM + 0.4 OH

k = 5.30E-12 exp(190/T) 1.00E-11 a

88 MEPX = MEO2 + RO2 + OH Photolysis a

89 ROOH + OH = 0.54 XO2H + 0.06 XO2N + 

0.6 RO2 + 0.4 OH

k = 3.20E-12 exp(190/T) 6.05E-12 a

90 ROOH = HO2 + OH Photolysis a

91 NTR + OH = HNO3 + XO2H + RO2 k = 8.10E-13 8.10E-13 a,c

92 NTR = NO2 + XO2H + RO2 Photolysis a,c

93 FACD + OH = HO2 k = 4.50E-13 4.50E-13 a

94 AACD + OH = MEO2 + RO2 k = 4.00E-14 exp(850/T) 6.93E-13 a

95 PACD + OH = C2O3 k = 4.00E-14 exp(850/T) 6.93E-13 a

96 FORM + OH = HO2 + CO k = 5.40E-12 exp(135/T) 8.49E-12 a

97 FORM = 2 HO2 + CO Photolysis a

98 FORM = CO + H2 Photolysis a

99 FORM + O = OH + HO2 + CO k = 3.40E-11 exp(-1600/T) 1.58E-13 b

100 FORM + NO3 = HNO3 + HO2 + CO k = 5.50E-16 5.50E-16 a

101 FORM + HO2 = HCO3 k = 9.70E-15 exp(625/T) 7.90E-14 a

102 HCO3 = FORM + HO2 k = 2.40E+12 exp(-7000/T) 1.51E+2 a

103 HCO3 + NO = FACD + NO2 + HO2 k = 5.60E-12 5.60E-12 a

104 HCO3 + HO2 = 0.5 MEPX + 0.5 FACD + 0.2 

OH + 0.2 HO2

k = 5.60E-15 exp(2300/T) 1.26E-11 a

105 ALD2 + O = C2O3 + OH k = 1.80E-11 exp(-1100/T) 4.49E-13 b

106 ALD2 + OH = C2O3 k = 4.70E-12 exp(345/T) 1.50E-11 a

107 ALD2 + NO3 = C2O3 + HNO3 k = 1.40E-12 exp(-1860/T) 2.73E-15 a

108 ALD2 = MEO2 + RO2 + CO + HO2 Photolysis a

109 ALDX + O = CXO3 + OH k = 1.30E-11 exp(-870/T) 7.02E-13 c,n

110 ALDX + OH = CXO3 k = 4.90E-12 exp(405/T) 1.91E-11 a

111 ALDX + NO3 = CXO3 + HNO3 k = 6.30E-15 6.30E-15 a

112 ALDX = ALD2 + XO2H + RO2 + CO + HO2 Photolysis f

113 GLYD + OH = 0.2 GLY + 0.2 HO2 + 0.8 

C2O3

k = 8.00E-12 8.00E-12 a

114 GLYD = 0.74 FORM + 0.89 CO + 1.4 HO2 + 

0.15 MEOH + 0.19 OH + 0.11 GLY + 0.11 

XO2H + 0.11 RO2

Photolysis a,b,f

115 GLYD + NO3 = HNO3 + C2O3 k = 1.40E-12 exp(-1860/T) 2.73E-15 a

116 GLY + OH = 1.7 CO + 0.3 XO2 + 0.3 RO2 + 

HO2

k = 3.10E-12 exp(340/T) 9.70E-12 a

117 GLY = 2 HO2 + 2 CO Photolysis a,q

118 GLY + NO3 = HNO3 + CO + HO2 + XO2 + 

RO2

k = 1.40E-12 exp(-1860/T) 2.73E-15 a

119 MGLY = C2O3 + HO2 + CO Photolysis a

120 MGLY + NO3 = HNO3 + C2O3 + XO2 + 

RO2

k = 1.40E-12 exp(-1860/T) 2.73E-15 a

121 MGLY + OH = C2O3 + CO k = 1.90E-12 exp(575/T) 1.31E-11 a

122 H2 + OH = HO2 k = 7.70E-12 exp(-2100/T) 6.70E-15 a
April 2014 CAMx User’s Guide Version 6.1

Appendix B: Mechanism 7 – CB6

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 263 www.camx.com

Number Reactants and Products Rate Constant Expression k298 Notes

123 CO + OH = HO2 k = k1 + k2 [M]

 k1 = 1.44E-13

 k2 = 3.43E-33

2.28E-13 a

124 CH4 + OH = MEO2 + RO2 k = 1.85E-12 exp(-1690/T) 6.37E-15 a

125 ETHA + OH = 0.991 ALD2 + 0.991 XO2H + 

0.009 XO2N + RO2

k = 6.90E-12 exp(-1000/T) 2.41E-13 a

126 MEOH + OH = FORM + HO2 k = 2.85E-12 exp(-345/T) 8.95E-13 a

127 ETOH + OH = 0.95 ALD2 + 0.9 HO2 + 0.1 

XO2H + 0.1 RO2 + 0.078 FORM + 0.011 

GLYD

k = 3.00E-12 exp(20/T) 3.21E-12 a

128 KET = 0.5 ALD2 + 0.5 C2O3 + 0.5 XO2H + 

0.5 CXO3 + 0.5 MEO2 + RO2 - 2.5 PAR

Photolysis a

129 ACET = 0.38 CO + 1.38 MEO2 + 1.38 RO2 

+ 0.62 C2O3

Photolysis a

130 ACET + OH = FORM + C2O3 + XO2 + RO2 k = 1.41E-12 exp(-620.6/T) 1.76E-13 a

131 PRPA + OH = 0.71 ACET + 0.26 ALDX + 

0.26 PAR + 0.97 XO2H + 0.03 XO2N + RO2

k = 7.60E-12 exp(-585/T) 1.07E-12 a

132 PAR + OH = 0.11 ALDX + 0.76 ROR + 0.13 

XO2N + 0.11 XO2H + 0.76 XO2 + RO2 -

0.11 PAR

k = 8.10E-13 8.10E-13 c

133 ROR = 0.2 KET + 0.42 ACET + 0.74 ALD2 + 

0.37 ALDX + 0.04 XO2N + 0.94 XO2H + 

0.98 RO2 + 0.02 ROR - 2.7 PAR

k = 5.70E+12 exp(-5780/T) 2.15E+4 a,c

134 ROR + O2 = KET + HO2 k = 1.50E-14 exp(-200/T) 7.67E-15 a,c

135 ROR + NO2 = NTR k = 8.60E-12 exp(400/T) 3.29E-11 a,c

136 ETHY + OH = 0.7 GLY + 0.7 OH + 0.3 FACD 

+ 0.3 CO + 0.3 HO2

Falloff: F=0.37; n=1.3

 k

0 = 5.00E-30 (T/300)^-1.5

 k

∞ = 1.00E-12

7.52E-13 a

137 ETH + O = FORM + HO2 + CO + 0.7 XO2H 

+ 0.7 RO2 + 0.3 OH

k = 1.04E-11 exp(-792/T) 7.29E-13 c,o

138 ETH + OH = XO2H + RO2 + 1.56 FORM + 

0.22 GLYD

Falloff: F=0.48; n=1.15

 k

0 = 8.60E-29 (T/300)^-3.1

 k∞ = 9.00E-12 (T/300)^-0.9

7.85E-12 a,g

139 ETH + O3 = FORM + 0.51 CO + 0.16 HO2 + 

0.16 OH + 0.37 FACD

k = 9.10E-15 exp(-2580/T) 1.58E-18 a,g

140 ETH + NO3 = 0.5 NO2 + 0.5 NTR + 0.5 

XO2H + 0.5 XO2 + RO2 + 1.125 FORM

k = 3.30E-12 exp(-2880/T) 2.10E-16 a,g

141 OLE + O = 0.2 ALD2 + 0.3 ALDX + 0.1 HO2 

+ 0.2 XO2H + 0.2 CO + 0.2 FORM + 0.01 

XO2N + 0.21 RO2 + 0.2 PAR + 0.1 OH

k = 1.00E-11 exp(-280/T) 3.91E-12 c,o

142 OLE + OH = 0.781 FORM + 0.488 ALD2 + 

0.488 ALDX + 0.976 XO2H + 0.195 XO2 + 

0.024 XO2N + 1.17 RO2 - 0.73 PAR

Falloff: F=0.5; n=1.13

 k

0 = 8.00E-27 (T/300)^-3.5

 k∞ = 3.00E-11 (T/300)^-1

2.86E-11 a,g

143 OLE + O3 = 0.295 ALD2 + 0.555 FORM + 

0.27 ALDX + 0.15 XO2H + 0.15 RO2 + 

0.334 OH + 0.08 HO2 + 0.378 CO + 0.075 

GLY + 0.075 MGLY + 0.09 FACD + 0.13 

AACD + 0.04 H2O2 - 0.79 PAR

k = 5.50E-15 exp(-1880/T) 1.00E-17 a,g

144 OLE + NO3 = 0.5 NO2 + 0.5 NTR + 0.48 

XO2 + 0.48 XO2H + 0.04 XO2N + RO2 + 

0.5 FORM + 0.25 ALD2 + 0.375 ALDX - 1 

PAR

k = 4.60E-13 exp(-1155/T) 9.54E-15 a,g
April 2014 CAMx User’s Guide Version 6.1

Appendix B: Mechanism 7 – CB6

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 264 www.camx.com

Number Reactants and Products Rate Constant Expression k298 Notes

145 IOLE + O = 1.24 ALD2 + 0.66 ALDX + 0.1 

XO2H + 0.1 RO2 + 0.1 CO + 0.1 PAR

k = 2.30E-11 2.30E-11 c,o

146 IOLE + OH = 1.3 ALD2 + 0.7 ALDX + XO2H 

+ RO2

k = 1.05E-11 exp(519/T) 5.99E-11 a,g

147 IOLE + O3 = 0.732 ALD2 + 0.442 ALDX + 

0.128 FORM + 0.245 CO + 0.5 OH + 0.3 

XO2H + 0.3 RO2 + 0.24 GLY + 0.06 MGLY + 

0.29 PAR + 0.08 AACD + 0.08 H2O2

k = 4.70E-15 exp(-1013/T) 1.57E-16 a,g

148 IOLE + NO3 = 0.5 NO2 + 0.5 NTR + 0.48 

XO2 + 0.48 XO2H + 0.04 XO2N + RO2 + 

0.5 ALD2 + 0.625 ALDX + PAR

k = 3.70E-13 3.70E-13 a,g

149 ISOP + OH = ISO2 + RO2 k = 2.70E-11 exp(390/T) 9.99E-11 a

150 ISO2 + NO = 0.117 INTR + 0.883 NO2 + 

0.803 HO2 + 0.66 FORM + 0.66 ISPD + 

0.08 XO2H + 0.08 RO2 + 0.05 IOLE + 0.042 

GLYD + 0.115 PAR + 0.038 GLY + 0.042 

MGLY + 0.093 OLE + 0.117 ALDX

k = 2.39E-12 exp(365/T) 8.13E-12 r,s

151 ISO2 + HO2 = 0.88 ISPX + 0.12 OH + 0.12 

HO2 + 0.12 FORM + 0.12 ISPD

k = 7.43E-13 exp(700/T) 7.78E-12 r,s

152 ISO2 + C2O3 = 0.709 HO2 + 0.583 FORM 

+ 0.583 ISPD + 0.071 XO2H + 0.044 IOLE + 

0.037 GLYD + 0.102 PAR + 0.034 GLY + 

0.037 MGLY + 0.082 OLE + 0.103 ALDX + 

0.8 MEO2 + 0.2 AACD + 0.871 RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 r,s

153 ISO2 + RO2 = 0.803 HO2 + 0.66 FORM + 

0.66 ISPD + 0.08 XO2H + 0.05 IOLE + 

0.042 GLYD + 0.115 PAR + 0.038 GLY + 

0.042 MGLY + 0.093 OLE + 0.117 ALDX + 

1.08 RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 r,s

154 ISO2 = 0.8 HO2 + 0.04 OH + 0.04 FORM + 

0.8 ISPD

k = 1.00E+0 1.00E+0 j,t

155 ISOP + O3 = 0.6 FORM + 0.65 ISPD + 0.15 

ALDX + 0.2 CXO3 + 0.35 PAR + 0.266 OH + 

0.2 XO2 + 0.2 RO2 + 0.066 HO2 + 0.066 

CO

k = 1.03E-14 exp(-1995/T) 1.27E-17 c

156 ISOP + NO3 = 0.35 NO2 + 0.65 INTR + 

0.64 XO2H + 0.33 XO2 + 0.03 XO2N + RO2 

+ 0.35 FORM + 0.35 ISPD

k = 3.03E-12 exp(-448/T) 6.74E-13 u

157 ISPD + OH = 0.095 XO2N + 0.379 XO2 + 

0.318 XO2H + 0.792 RO2 + 0.843 PAR + 

0.379 C2O3 + 0.209 CXO3 + 0.379 GLYD + 

0.24 MGLY + 0.24 FORM + 0.067 OLE + 

0.079 CO + 0.028 ALDX

k = 6.31E-12 exp(500/T) 3.38E-11 r,s

158 ISPD + O3 = 0.02 ALD2 + 0.15 FORM + 

0.225 CO + 0.85 MGLY + 0.36 PAR + 0.114 

C2O3 + 0.064 XO2H + 0.064 RO2 + 0.268 

OH + 0.09 HO2

k = 4.17E-15 exp(-1900/T) 7.10E-18 c

159 ISPD + NO3 = 0.643 CO + 0.282 FORM + 

0.357 ALDX + 1.282 PAR + 0.85 HO2 + 

0.075 CXO3 + 0.075 XO2H + 0.075 RO2 + 

0.85 NTR + 0.15 HNO3

k = 1.00E-15 1.00E-15 c
April 2014 CAMx User’s Guide Version 6.1

Appendix B: Mechanism 7 – CB6

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 265 www.camx.com

Number Reactants and Products Rate Constant Expression k298 Notes

160 ISPD = 0.333 CO + 0.067 ALD2 + 0.9 

FORM + 0.832 PAR + 0.333 HO2 + 0.7 

XO2H + 0.7 RO2 + 0.967 C2O3

Photolysis c,f

161 ISPX + OH = 0.904 EPOX + 0.933 OH + 

0.067 ISO2 + 0.067 RO2 + 0.029 IOLE + 

0.029 ALDX

k = 2.23E-11 exp(372/T) 7.77E-11 r,s

162 EPOX + OH = EPX2 + RO2 k = 5.78E-11 exp(-400/T) 1.51E-11 r,s

163 EPX2 + HO2 = 0.275 GLYD + 0.275 GLY + 

0.275 MGLY + 1.125 OH + 0.825 HO2 + 

0.375 FORM + 0.074 FACD + 0.251 CO + 

2.175 PAR

k = 7.43E-13 exp(700/T) 7.78E-12 r,s

164 EPX2 + NO = 0.275 GLYD + 0.275 GLY + 

0.275 MGLY + 0.125 OH + 0.825 HO2 + 

0.375 FORM + NO2 + 0.251 CO + 2.175 

PAR

k = 2.39E-12 exp(365/T) 8.13E-12 r,s

165 EPX2 + C2O3 = 0.22 GLYD + 0.22 GLY + 

0.22 MGLY + 0.1 OH + 0.66 HO2 + 0.3 

FORM + 0.2 CO + 1.74 PAR + 0.8 MEO2 + 

0.2 AACD + 0.8 RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 a,r,s

166 EPX2 + RO2 = 0.275 GLYD + 0.275 GLY + 

0.275 MGLY + 0.125 OH + 0.825 HO2 + 

0.375 FORM + 0.251 CO + 2.175 PAR + 

RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 a,r,s

167 INTR + OH = 0.63 XO2 + 0.37 XO2H + RO2 

+ 0.444 NO2 + 0.185 NO3 + 0.104 INTR + 

0.592 FORM + 0.331 GLYD + 0.185 FACD + 

2.7 PAR + 0.098 OLE + 0.078 ALDX + 0.266 

NTR

k = 3.10E-11 3.10E-11 r,s

168 TERP + O = 0.15 ALDX + 5.12 PAR k = 3.60E-11 3.60E-11 c

169 TERP + OH = 0.75 XO2H + 0.5 XO2 + 0.25 

XO2N + 1.5 RO2 + 0.28 FORM + 1.66 PAR 

+ 0.47 ALDX

k = 1.50E-11 exp(449/T) 6.77E-11 c

170 TERP + O3 = 0.57 OH + 0.07 XO2H + 0.69 

XO2 + 0.18 XO2N + 0.94 RO2 + 0.24 

FORM + 0.001 CO + 7 PAR + 0.21 ALDX + 

0.39 CXO3

k = 1.20E-15 exp(-821/T) 7.63E-17 c

171 TERP + NO3 = 0.47 NO2 + 0.28 XO2H + 

0.75 XO2 + 0.25 XO2N + 1.28 RO2 + 0.47 

ALDX + 0.53 NTR

k = 3.70E-12 exp(175/T) 6.66E-12 c

172 BENZ + OH = 0.53 CRES + 0.352 BZO2 + 

0.352 RO2 + 0.118 OPEN + 0.118 OH + 

0.53 HO2

k = 2.30E-12 exp(-190/T) 1.22E-12 a,d,e

173 BZO2 + NO = 0.918 NO2 + 0.082 NTR + 

0.918 GLY + 0.918 OPEN + 0.918 HO2

k = 2.70E-12 exp(360/T) 9.04E-12 d,h

174 BZO2 + C2O3 = GLY + OPEN + HO2 + 

MEO2 + RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 a,d,h

175 BZO2 + HO2 = k = 1.90E-13 exp(1300/T) 1.49E-11 d

176 BZO2 + RO2 = GLY + OPEN + HO2 + RO2 k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 a,d,h
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Appendix B: Mechanism 7 – CB6

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Number Reactants and Products Rate Constant Expression k298 Notes

177 TOL + OH = 0.18 CRES + 0.65 TO2 + 0.72 

RO2 + 0.1 OPEN + 0.1 OH + 0.07 XO2H + 

0.18 HO2

k = 1.80E-12 exp(340/T) 5.63E-12 a,d,e

178 TO2 + NO = 0.86 NO2 + 0.14 NTR + 0.417 

GLY + 0.443 MGLY + 0.66 OPEN + 0.2 

XOPN + 0.86 HO2

k = 2.70E-12 exp(360/T) 9.04E-12 d,h

179 TO2 + C2O3 = 0.48 GLY + 0.52 MGLY + 

0.77 OPEN + 0.23 XOPN + HO2 + MEO2 + 

RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 a,d,h

180 TO2 + HO2 = k = 1.90E-13 exp(1300/T) 1.49E-11 d

181 TO2 + RO2 = 0.48 GLY + 0.52 MGLY + 

0.77 OPEN + 0.23 XOPN + HO2 + RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 a,d,h

182 XYL + OH = 0.155 CRES + 0.544 XLO2 + 

0.602 RO2 + 0.244 XOPN + 0.244 OH + 

0.058 XO2H + 0.155 HO2

k = 1.85E-11 1.85E-11 d,e,p

183 XLO2 + NO = 0.86 NO2 + 0.14 NTR + 

0.221 GLY + 0.675 MGLY + 0.3 OPEN + 

0.56 XOPN + 0.86 HO2

k = 2.70E-12 exp(360/T) 9.04E-12 d,h

184 XLO2 + HO2 = k = 1.90E-13 exp(1300/T) 1.49E-11 d

185 XLO2 + C2O3 = 0.26 GLY + 0.77 MGLY + 

0.35 OPEN + 0.65 XOPN + HO2 + MEO2 + 

RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 a,d,h

186 XLO2 + RO2 = 0.26 GLY + 0.77 MGLY + 

0.35 OPEN + 0.65 XOPN + HO2 + RO2

k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 a,d,h

187 CRES + OH = 0.06 CRO + 0.12 XO2H + 

HO2 + 0.13 OPEN + 0.732 CAT1 + 0.06 CO 

+ 0.06 XO2N + 0.18 RO2 + 0.06 FORM

k = 1.70E-12 exp(950/T) 4.12E-11 d

188 CRES + NO3 = 0.3 CRO + HNO3 + 0.24 

XO2 + 0.36 XO2H + 0.48 ALDX + 0.24 

FORM + 0.24 MGLY + 0.12 OPEN + 0.1 

XO2N + 0.7 RO2 + 0.24 CO

k = 1.40E-11 1.40E-11 d

189 CRO + NO2 = CRON k = 2.10E-12 2.10E-12 d

190 CRO + HO2 = CRES k = 5.50E-12 5.50E-12 d

191 CRON + OH = CRNO k = 1.53E-12 1.53E-12 d

192 CRON + NO3 = CRNO + HNO3 k = 3.80E-12 3.80E-12 d

193 CRNO + NO2 = 2 NTR k = 2.10E-12 2.10E-12 d

194 CRNO + O3 = CRN2 k = 2.86E-13 2.86E-13 d

195 CRN2 + NO = CRNO + NO2 k = 2.54E-12 exp(360/T) 8.50E-12 d

196 CRN2 + HO2 = CRPX k = 2.40E-13 exp(1300/T) 1.88E-11 d

197 CRPX = CRNO + OH Photolysis a,d

198 CRPX + OH = CRN2 k = 1.90E-12 exp(190/T) 3.59E-12 d

199 XOPN = CAO2 + 0.7 HO2 + 0.7 CO + 0.3 

C2O3 + RO2

Photolysis d,p

200 XOPN + OH = CAO2 + MGLY + XO2H + 

RO2

k = 9.00E-11 9.00E-11 d,p

201 XOPN + O3 = 1.2 MGLY + 0.5 OH + 0.6 

C2O3 + 0.1 ALD2 + 0.5 CO + 0.3 XO2H + 

0.3 RO2

k = 1.08E-16 exp(-500/T) 2.02E-17 d,p
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Appendix B: Mechanism 7 – CB6

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 267 www.camx.com

Number Reactants and Products Rate Constant Expression k298 Notes

202 XOPN + NO3 = 0.5 NO2 + 0.5 NTR + 0.45 

XO2H + 0.45 XO2 + 0.1 XO2N + RO2 + 

0.25 OPEN + 0.25 MGLY

k = 3.00E-12 3.00E-12 d,p

203 OPEN = OPO3 + HO2 + CO Photolysis d,p

204 OPEN + OH = 0.6 OPO3 + 0.4 CAO2 + 0.4 

RO2

k = 4.40E-11 4.40E-11 d,p

205 OPEN + O3 = 1.4 GLY + 0.24 MGLY + 0.5 

OH + 0.12 C2O3 + 0.08 FORM + 0.02 ALD2 

+ 1.98 CO + 0.56 HO2

k = 5.40E-17 exp(-500/T) 1.01E-17 d,p

206 OPEN + NO3 = OPO3 + HNO3 k = 3.80E-12 3.80E-12 d,p

207 CAT1 + OH = CAO2 + RO2 k = 7.00E-11 7.00E-11 d

208 CAT1 + NO3 = CRO + HNO3 k = 1.70E-10 1.70E-10 d

209 CAO2 + NO = 0.86 NO2 + 0.14 NTR + 1.2 

HO2 + 0.344 FORM + 0.344 CO

k = 2.54E-12 exp(360/T) 8.50E-12 d

210 CAO2 + HO2 = k = 2.40E-13 exp(1300/T) 1.88E-11 d

211 CAO2 + C2O3 = HO2 + 0.4 GLY + MEO2 + 

RO2

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 d

212 CAO2 + RO2 = HO2 + 0.4 GLY + RO2 k = kref K

 kref = k(70)

 K = 1.00E+0

3.48E-13 d

213 OPO3 + NO = NO2 + XO2H + RO2 + ALDX k = 1.00E-11 1.00E-11 d

214 OPO3 + NO2 = OPAN k = kref K

 kref = k(62)

 K = 1.00E+0

1.16E-11 d

215 OPAN = OPO3 + NO2 Falloff: F=0.3; n=1

 k

0 = 4.60E-4 exp(-11280/T)

 k

∞ = 2.24E+16 exp(-13940/T)

9.92E-5 d

216 OPO3 + HO2 = 0.41 PACD + 0.15 AACD + 

0.15 O3 + 0.44 ALDX + 0.44 XO2H + 0.44 

RO2 + 0.44 OH

k = kref K

 kref = k(57)

 K = 1.00E+0

1.39E-11 d

217 OPO3 + C2O3 = MEO2 + XO2 +ALDX + 2 

RO2

k = kref K

 kref = k(59)

 K = 1.00E+0

1.55E-11 d

218 OPO3 + RO2 = 0.8 XO2H + 0.8 RO2 + 0.8 

ALDX + 0.2 AACD

k = kref K

 kref = k(58)

 K = 1.00E+0

1.30E-11 d

Table notes:

k298 is the rate constant at 298 K and 1 atmosphere using units molecules cm-3 and s-1

See Table B-2 for species names

See the CAMx chemistry parameters file for the temperature and pressure dependencies (Section 3).

a IUPAC: Atkinson et al., (2010) h Arey et al. (2009) o Cvetanovic (1987)

b JPL: Sander et al., (2006) i Hu et al. (2007) p Calvert et al. (2002)

c CB05: Yarwood et al (2005b) j Archibald et al. (2010) q Feierabend et al. (2009)

d CB05-TU: Whitten et al., 2010) k Hjorth et al. (1992) r Paulot et al. (2009a)

e Bloss et al. (2005) l Kaiser and Wu (1977) s Paulot et al. (2009b)

f SAPRC-99: Carter (2000) m Jeffries et al. (2002) t Peeters et al. (2009)

g Calvert et al. (2000) n Herron (1988) u Perring et al. (2009)
April 2014 CAMx User’s Guide Version 6.1

Appendix B: Mechanism 7 – CB6

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Table B-2. Explicit species in the CB6 mechanism.

Species Description

AACD Acetic acid

ACET Acetone

ALD2 Acetaldehyde

ALDX Propionaldehyde and higher aldehydes

BENZ Benzene

BZO2 Peroxy radical from OH addition to benzene 

C2O3 Acetylperoxy radical

CAO2 Peroxy radical from aromatic degradation products 

CAT1 Methyl-catechols

CO Carbon monoxide

CRES Cresols

CRN2 Peroxy radical from nitro-cresol

CRNO Alkoxy radical from nitro-cresols

CRO Alkoxy radical from cresol

CRON Nitro-cresols

CRPX Nitro-cresol hydroperoxides

CXO3 C3 and higher acylperoxy radicals 

EPOX Epoxide formed from ISPX reaction with OH

EPX2 Peroxy radical from EPOX reaction with OH

ETH Ethene

ETHA Ethane

ETHY Ethyne

ETOH Ethanol

FACD Formic acid

FORM Formaldehyde

GLY Glyoxal

GLYD Glycolaldehyde

H2O2 Hydrogen peroxide

HCO3 Adduct from HO2 plus formaldehyde

HNO3 Nitric acid

HO2 Hydroperoxy radical

HONO Nitrous acid

INTR Organic nitrates from ISO2 reaction with NO

IOLE Internal olefin carbon bond (R-C=C-R)

ISO2 Peroxy radical from OH addition to isoprene 

ISOP Isoprene

ISPD Isoprene product (lumped methacrolein, methyl vinyl ketone, etc.)

ISPX Hydroperoxides from ISO2 reaction with HO2

KET Ketone carbon bond (C=O)

M Air

MEO2 Methylperoxy radical

MEOH Methanol

MEPX Methylhydroperoxide

MGLY Methylglyoxal

N2O5 Dinitrogen pentoxide

NO Nitric oxide

NO2 Nitrogen dioxide

NO3 Nitrate radical

NTR Organic nitrates

O Oxygen atom in the O3(P) electronic state
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Appendix B: Mechanism 7 – CB6

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Species Description

O1D Oxygen atom in the O1(D) electronic state

O3 Ozone

OH Hydroxyl radical

OLE Terminal olefin carbon bond (R-C=C)

OPAN Peroxyacyl nitrate (PAN compound) from OPO3

OPEN Aromatic ring opening product (unsaturated dicarbonyl)

OPO3 Peroxyacyl radical from OPEN

PACD Peroxyacetic and higher peroxycarboxylic acids

PAN Peroxyacetyl Nitrate

PANX C3 and higher peroxyacyl nitrate

PAR Paraffin carbon bond (C-C)

PNA Peroxynitric acid

PRPA Propane

RO2 Operator to approximate total peroxy radical concentration

ROOH Higher organic peroxide

ROR Secondary alkoxy radical

SO2 Sulfur dioxide

SULF Sulfuric acid (gaseous)

TERP Monoterpenes

TO2 Peroxy radical from OH addition to TOL 

TOL Toluene and other monoalkyl aromatics

XLO2 Peroxy radical from OH addition to XYL 

XO2 NO to NO2 conversion from alkylperoxy (RO2) radical

XO2H NO to NO2 conversion (XO2) accompanied by HO2 production

XO2N NO to organic nitrate conversion from alkylperoxy (RO2) radical

XOPN Aromatic ring opening product (unsaturated dicarbonyl)

XYL Xylene and other polyalkyl aromatics

Table B-3. Properties of VOC species in the CB6 mechanism: carbon numbers, kOH values 

(ppm-1min-1) and maximum incremental reactivity (MIR) values (mole O3/mole VOC).

Species Carbon Number Average kOH MIR

PAR 1 1.20E+03 0.509

ETHA 2 3.54E+02 0.135

MEOH 1 1.35E+03 0.48

ETOH 2 4.71E+03 1.53

ETH 2 1.20E+04 4.95

OLE 2 4.73E+04 9.66

IOLE 4 9.35E+04 16

ISOP 5 1.47E+05 12.7

TERP 10 1.00E+05 9.91

FORM 1 1.33E+04 4.87

ALD2 2 2.05E+04 5.8

ALDX 2 2.93E+04 8.35

TOL 7 8.75E+03 7.39

XYL 8 3.71E+04 20.5

PRPA 3 1. 58E+03 0.541

ETHY 2 1.80E+03 1.39

BENZ 6 1.11E+03 0.487

ACET 3 2.60E+02 0.564

KET 1 0.0 4.86
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Appendix C: Mechanism 1 – CB6 with Iodine Chemistry

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Appendix C

CAMx Mechanism 1

CB6 with Iodine Chemistry

Table C-1. Listing of the chemical mechanism for iodine and ozone.

Number Reactants and Products Rate Constant Expression k298 Notes

I1 I + O3 = IO k = 2.10E-11 exp(-830/T) 1.30E-12 a

I2 I + HO2 = HI k = 1.50E-11 exp(-1090/T) 3.87E-13 a

I3 I + NO = INO Falloff: F=0.6; n=1

 k

0 = 1.80E-32 (T/300)^-1

 k

∞ = 1.70E-11

3.76E-13 a

I4 I + NO2 = INO2 Falloff: F=0.63; n=1

 k

0 = 3.00E-31 (T/300)^-1

 k

∞ = 6.60E-11

5.24E-12 a

I5 I2 = 2 I Photolysis a

I6 I2 + OH = HOI + I k = 2.10E-10 2.10E-10 a

I7 I2 + NO3 = I + INO3 k = 1.50E-12 1.50E-12 a

I8 HI + OH = I k = 1.60E-11 exp(440/T) 7.00E-11

I9 IO = I + O Photolysis a

I10 IO + NO = I + NO2 k = 7.15E-12 exp(300/T) 1.96E-11 a

I11 IO + NO2 = INO3 Falloff: F=0.4; n=1

 k

0 = 7.70E-31 (T/300)^-5

 k

∞ = 1.60E-11

3.55E-12 a

I12 IO + HO2 = HOI k = 1.40E-11 exp(540/T) 8.57E-11 a

I13 IO + IO = 0.4 I + 0.4 OIO + 0.6 I2O2 k = 5.40E-11 exp(180/T) 9.88E-11 a,b

I14 HOI = I + OH Photolysis a

I15 HOI + OH = IO k = 5.00E-12 5.00E-12 c

I16 OIO = I Photolysis d

I17 OIO + NO = IO + NO2 k = 1.10E-12 exp(542/T) 6.78E-12 a

I18 OIO + OH = HIO3 Falloff: F=0.3; n=1

 k

0 = 1.50E-27 (T/300)^-3.93

 k∞ = 5.50E-10 exp(46/T)

4.72E-10 e

I19 OIO + IO = IXOY k = 1.00E-10 1.00E-10 f

I20 OIO + OIO = IXOY k = 1.50E-10 1.50E-10 f

I21 I2O2 = I + OIO k = 1.00E+1 1.00E+1 g

I22 I2O2 + O3 = IXOY k = 1.00E-12 1.00E-12 h

I23 INO + I = I2 + NO k = 1.66E-10 1.66E-10 i

I24 INO + INO = I2 + 2 NO k = 8.40E-11 exp(-2620/T) 1.28E-14 a

I25 INO2 = I + NO2 Photolysis a

I26 INO2 + INO2 = I2 + 2 NO2 k = 4.70E-13 exp(-1670/T) 1.73E-15 a

I27 INO3 = I + NO3 Photolysis j

I28 INO3 + I = I2 + NO3 k = 9.10E-11 exp(-146/T) 5.58E-11 g

I29 CH3I = I + MEO2 Photolysis a

I30 MI2 = 2 I + FORM Photolysis a

I31 MIB = I + XO2 + FORM Photolysis a

I32 MIC = I + XO2 + FORM Photolysis a

I33 IALK = I + XO2H + ALDX Photolysis a,k

Table notes:

k298 is the rate constant at 298 K and 1 atmosphere using units of molecules cm-3 and s-1

See Table C-2 for species names

See Table C-3 for information on photolysis reactions
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MEO2, FORM and ALDX in reactions I29 – I33 are Carbon Bond species names and should be changed for use with a different 

base mechanism 

References are indicated in the notes column as follows:

a Atkinson et al. (2010) – IUPAC e Plane et al. (2006) i van den Bergh et al. (1976)

b Sommariva et al. (2012) f Gomez-Martin et al. (2007) j Joseph et al. (2005)

c Riffault et al. (2005) g Kaltsoyannis et al. (2008) k Taatjes et al. (2012)

d Sander et al. (2011) – JPL h Saunders et al. (2005) l Cotter et al. (2001)

Table C-2. Model species names and properties in the chemical mechanism for iodine and 

ozone.

Model 

Species 

Name Description

Chemical Formula M. 

Wt.

(g)

Henry Constant

C H O N Cl Br I

H298

(M atm-1) A (K) Notes

I2 molecular iodine 2 253.8 3.10E+00 -4600

I iodine atom 1 126.9 8.00E-02 -2300

IO iodine monoxide 1 1 142.9 8.00E-02 -2300 Same as I

OIO iodine dioxide 2 1 158.9 1.00E+00 -3300 Same as OClO

I2O2 diiodine dioxide 2 2 285.8 1.00E+06 -4000 Large value

IXOY

condensable iodine 

oxides 3 2 301.8 1.00E+06 -4000 Large value

HI hydrogen iodide 1 1 127.9 1.00E+06 -9800

Accounting for 

dissociation

HOI hypoiodous acid 1 1 1 143.9 4.10E+02 -4000

HIO3 iodic acid 1 3 1 175.9 1.00E+06 -4000

INO nitrosyl iodide 1 1 1 156.9 5.00E-02 -4000 Same as ClNO

INO2 nitryl iodide 2 1 1 172.9 3.00E-01 -4000 Same as BrNO2

INO3 iodine nitrate 3 1 1 188.9 1.00E+06 -4000

Same as BrNO3

(large)

CH3I iodomethane 1 3 1 141.9 1.40E-01 -4300

MIC

chloroiodomethan

e 1 2 1 1 176.4 8.90E-01 -4300

MIB

bromoiodomethan

e 1 2 1 1 219.9 8.90E-01 -4300 Same as CH2ICl

MI2 diiodomethane 1 2 2 267.8 2.30E+00 -5000

IALK alkyl iodides 3 7 1 170.0 6.30E-02 -4000

Table notes:

H298 is the Henry Constant at 298 K and T factor is the temperature dependence (K)

Henry constant data from http://www.mpch-mainz.mpg.de/~sander/res/henry.html

Henry constants are for the exact compound unless noted otherwise under comments

Default value for temperature dependence (A) is 4000 K
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Appendix C: Mechanism 1 – CB6 with Iodine Chemistry

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Frequently it is useful to characterize the photolysis rate for one reaction as a ratio to another 

reaction, although the reference reaction should be selected so that the ratio has little dependence 

upon zenith angle. Photolysis rate ratios for iodine compounds are listed below with the reference 

reactions defined in the footnote to Table D-3.

j(I2) = 0.922 x j(NO3_NO2)

j(IO) = 18.5 x j(NO2)

j(OIO) = 0.907 x j(NO3_NO2)

j(HOI) = 10.1 x j(NO2)

j(INO2) = 0.509 x j(NO2)

i(INO3) = 522.2 x j(FORM_M)

j(CH3I) = 1.15 x j(HNO3)

j(MI2) = 198.2 x j(FORM_M)

j(MIB) = 14.2 x j(FORM_R)

j(MIC) = 4.21 x j(FORM_R)

j(IALK) = 2.31 x j(HNO3)

Table C-3. Photolysis rates (s-1

) for iodine-containing species and reference reactions.

Species

Name

Solar Zenith Angle (degrees)

0 10 20 30 40 50 60 70 78 86

I2 1.51E-01 1.50E-01 1.47E-01 1.43E-01 1.36E-01 1.27E-01 1.12E-01 8.88E-02 5.80E-02 1.35E-02

IO 1.72E-01 1.72E-01 1.67E-01 1.60E-01 1.50E-01 1.34E-01 1.12E-01 8.00E-02 4.48E-02 1.10E-02

OIO 1.48E-01 1.47E-01 1.45E-01 1.41E-01 1.34E-01 1.25E-01 1.11E-01 8.78E-02 5.75E-02 1.30E-02

HOI 9.55E-02 9.47E-02 9.22E-02 8.78E-02 8.12E-02 7.17E-02 5.87E-02 4.05E-02 2.20E-02 5.60E-03

INO2 4.83E-03 4.78E-03 4.65E-03 4.43E-03 4.08E-03 3.60E-03 2.93E-03 2.02E-03 1.09E-03 2.80E-04

INO3 2.40E-02 2.38E-02 2.28E-02 2.12E-02 1.88E-02 1.58E-02 1.18E-02 7.18E-03 3.50E-03 9.60E-04

CH3I 7.82E-06 7.65E-06 7.15E-06 6.33E-06 5.25E-06 3.98E-06 2.62E-06 1.33E-06 5.50E-07 1.26E-07

IALK 1.56E-05 1.53E-05 1.43E-05 1.27E-05 1.05E-05 7.97E-06 5.22E-06 2.65E-06 1.10E-06 2.52E-07

MI2 9.33E-03 9.20E-03 8.78E-03 8.07E-03 7.07E-03 5.75E-03 4.15E-03 2.40E-03 1.11E-03 2.87E-04

MIB 5.93E-04 5.83E-04 5.52E-04 5.02E-04 4.30E-04 3.42E-04 2.38E-04 1.32E-04 5.92E-05 1.47E-05

MIC 1.78E-04 1.75E-04 1.65E-04 1.48E-04 1.26E-04 9.90E-05 6.82E-05 3.70E-05 1.63E-05 3.98E-06

NO2 9.58E-03 9.50E-03 9.22E-03 8.73E-03 8.02E-03 7.00E-03 5.60E-03 3.73E-03 1.95E-03 5.27E-04

NO3_NO2 1.63E-01 1.62E-01 1.60E-01 1.55E-01 1.48E-01 1.38E-01 1.22E-01 9.70E-02 6.37E-02 1.46E-02

FORM_R 4.17E-05 4.10E-05 3.88E-05 3.53E-05 3.05E-05 2.42E-05 1.68E-05 9.08E-06 3.95E-06 9.20E-07

FORM_M 4.63E-05 4.58E-05 4.38E-05 4.07E-05 3.60E-05 2.98E-05 2.20E-05 1.31E-05 6.27E-06 1.68E-06

HNO3 6.77E-06 6.62E-06 6.20E-06 5.50E-06 4.57E-06 3.45E-06 2.25E-06 1.12E-06 4.43E-07 9.28E-08

Table notes:

Rates calculated for an ozone column of 300 Dobson units, surface albedo of 0.04, and height above ground of 640 m

NO3_NO2 means NO3 photolysis producing NO2

FORM_R means formaldehyde photolysis producing radical products (HCO + H)

FORM_M means formaldehyde photolysis producing molecular products (CO + H2)
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Appendix C: Mechanism 1 – CB6 with Iodine Chemistry

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References

Atkinson, R.A., D.L. Baulch, R.A. Cox, J.N. Crowley, R.F. Hampson, R.G. Hynes, M.E. Jenkin, J.A. 

Kerr, M.J. Rossi, and J. Troe. 2010. “Evaluated kinetic and photochemical data for 

atmospheric chemistry - IUPAC subcommittee on gas kinetic data evaluation for 

atmospheric chemistry.” 3 January 2010 web version available from http://www.iupackinetic.ch.cam.ac.uk/index.html

Cotter E.S.N., N.J. Booth, and C.E. Canosa-Mas, R.P. Wayne. 2001. Release of iodine in the 

atmospheric oxidation of alkyl iodides and the fates of iodinated alkoxy radicals. 

Atmospheric Environment, 35, 2169–2178.

Gómez-Martín, J.C., P. Spietz, and J.P. Burrows. 2007. Kinetic and mechanistic studies of the 

I2/O3 photochemistry. Journal of Physical Chemistry, 111, 306–320.

Joseph, D.M., S.H. Ashworth and J.M.C. Plane. 2005. The absorption cross-section and 

photochemistry of OIO. Journal of Photochemistry and Photobiology A – Chemistry, 176, 

68–77.

Kaltsoyannis, N., Plane, and J.M.C. 2008. Quantum chemical calculations on a selection of 

iodine-containing species (IO, OIO, INO3, IO2, I2O3, I2O4 and I2O5) of importance in the 

atmosphere. Physical Chemistry Chemical Physics, 10, 1723–1733.

Plane, J.M.C., Joseph, D.M., Allan, B.J., Ashworth, S.H., and Francisco, J.S. 2006. An 

experimental and theoretical study of the reactions OIO + NO and OIO + OH. Journal of 

Physical Chemistry, 110, 93–100.

Riffault, V., Y. Bedjanian, and G. Poulet. 2005. Kinetic and mechanistic study of the reactions of 

OH with IBr and HOI. Journal of Photochemistry and Photobiology A – Chemistry, 176, 

155–161.

Sander, S.P., R.R. Friedl, D. M. Golden, M. J. Kurylo, G. K. Moortgat, P. H. Wine, A. R. 

Ravishankara, C. E. Kolb, M. J. Molina, B. J Finlayson-Pitts, R. E. Huie, and V. L. Orkin. 

2006. “Chemical Kinetics and Photochemical Data for use in Atmospheric Studies, 

Evaluation Number 15. NASA Jet Propulsion Laboratory.” July. Available 

from http://jpldataeval.jpl.nasa.gov/download.html.

Saunders, R.W., and J.M.C. Plane. 2005. Formation pathways and composition of iodine oxide 

ultra-fine particles. Environmental Chemistry, 2, 299–303.

Sommariva R., W.J. Bloss, and R. von Glasow. 2012. Uncertainties in gas-phase atmospheric 

iodine chemistry. Atmospheric Environment, 57, 219–232.

doi:10.1016/j.atmosenv.2012.04.032.

van den Bergh, H. and Troe, J. 1976. Kinetic and thermodynamic properties of INO and INO2

intermediate complexes in iodine recombination. J. Chem. Phys., 64, 736–742.
April 2014 CAMx User’s Guide Version 6.1

Appendix D: Mechanism 6 – CB05

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Appendix D

CAMx Mechanism 6

CB05 Gas-Phase Chemistry

Table D-1. Reactions and rate constants for the CB05 mechanism.

Number Reactants and Products Rate Constant Expression k298

1 NO2 = NO + O Photolysis

2 O + O2 + M = O3 + M k = 6.00E-34 (T/300)^-2.4 6.10E-34

3 O3 + NO = NO2 k = 3.00E-12 exp(-1500/T) 1.95E-14

4 O + NO2 = NO k = 5.60E-12 exp(180/T) 1.02E-11

5 O + NO2 = NO3 Falloff: F=0.6; n=1

 k

0 = 2.50E-31 (T/300)^-1.8 exp(-2/T)

 k

∞ = 2.20E-11 (T/300)^-0.7 exp(-3/T)

3.26E-12

6 O + NO = NO2 Falloff: F=0.6; n=1

 k

0 = 9.00E-32 (T/300)^-1.5

 k∞ = 3.00E-11

1.66E-12

7 NO2 + O3 = NO3 k = 1.20E-13 exp(-2450/T) 3.23E-17

8 O3 = O Photolysis

9 O3 = O1D Photolysis

10 O1D + M = O + M k = 2.10E-11 exp(102/T) 2.96E-11

11 O1D + H2O = 2 OH k = 2.20E-10 2.20E-10

12 O3 + OH = HO2 k = 1.70E-12 exp(-940/T) 7.25E-14

13 O3 + HO2 = OH k = 1.00E-14 exp(-490/T) 1.93E-15

14 NO3 = NO2 + O Photolysis

15 NO3 = NO Photolysis

16 NO3 + NO = 2 NO2 k = 1.50E-11 exp(170/T) 2.65E-11

17 NO3 + NO2 = NO + NO2 k = 4.50E-14 exp(-1260/T) 6.56E-16

18 NO3 + NO2 = N2O5 Falloff: F=0.6; n=1

 k

0 = 2.00E-30 (T/300)^-4.4

 k∞ = 1.40E-12 (T/300)^-0.7

1.18E-12

19 N2O5 + H2O = 2 HNO3 k = 2.50E-22 2.50E-22

20 N2O5 + H2O + H2O = 2 HNO3 k = 1.80E-39 1.80E-39

21 N2O5 = NO3 + NO2 Falloff: F=0.45; n=1

 k

0 = 1.00E-3 (T/300)^-3.5 exp(-11000/T)

 k

∞ = 9.70E+14 (T/300)^0.1 exp(-11080/T)

5.28E-2

22 NO + NO + O2 = 2 NO2 k = 3.30E-39 exp(530/T) 1.95E-38

23 NO + NO2 + H2O = 2 HONO k = 5.00E-40 5.00E-40

24 NO + OH = HONO Falloff: F=0.6; n=1

 k

0 = 7.00E-31 (T/300)^-2.6

 k∞ = 3.60E-11 (T/300)^-0.1

7.41E-12

25 HONO = NO + OH Photolysis

26 OH + HONO = NO2 k = 1.80E-11 exp(-390/T) 4.86E-12

27 HONO + HONO = NO + NO2 k = 1.00E-20 1.00E-20

28 NO2 + OH = HNO3 Falloff: F=0.6; n=1

 k

0 = 2.00E-30 (T/300)^-3

 k∞ = 2.50E-11

1.05E-11

29 OH + HNO3 = NO3 k = k1 + k3 [M] / (1 + k3 [M] / k2)

 k1 = 2.40E-14 exp(460/T)

 k2 = 2.70E-17 exp(2199/T)

 k3 = 6.50E-34 exp(1335/T)

1.54E-13
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Appendix D: Mechanism 6 – CB05

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Number Reactants and Products Rate Constant Expression k298

30 HO2 + NO = OH + NO2 k = 3.50E-12 exp(250/T) 8.10E-12

31 HO2 + NO2 = PNA Falloff: F=0.6; n=1

 k

0 = 3.00E-31 (T/300)^-3.2

 k

∞ = 4.70E-12

1.77E-12

32 PNA = HO2 + NO2 Falloff: F=0.6; n=1

 k

0 = 4.10E-5 exp(-10650/T)

 k∞ = 4.80E+15 exp(-11170/T)

8.31E-2

33 OH + PNA = NO2 k = 1.30E-12 exp(380/T) 4.65E-12

34 HO2 + HO2 = H2O2 k = k1 + k2 [M]

 k1 = 2.30E-13 exp(600/T)

 k2 = 1.70E-33 exp(1000/T)

2.92E-12

35 HO2 + HO2 + H2O = H2O2 k = k1 + k2 [M]

 k1 = 3.22E-34 exp(2800/T)

 k2 = 2.38E-54 exp(3200/T)

6.58E-30

36 H2O2 = 2 OH Photolysis

37 OH + H2O2 = HO2 k = 2.90E-12 exp(-160/T) 1.70E-12

38 O1D + H2 = OH + HO2 k = 1.10E-10 1.10E-10

39 OH + H2 = HO2 k = 5.50E-12 exp(-2000/T) 6.69E-15

40 OH + O = HO2 k = 2.20E-11 exp(120/T) 3.29E-11

41 OH + OH = O k = 4.20E-12 exp(-240/T) 1.88E-12

42 OH + OH = H2O2 Falloff: F=0.6; n=1

 k

0 = 6.90E-31 (T/300)^-1

 k∞ = 2.60E-11

6.29E-12

43 OH + HO2 = k = 4.80E-11 exp(250/T) 1.11E-10

44 HO2 + O = OH k = 3.00E-11 exp(200/T) 5.87E-11

45 H2O2 + O = OH + HO2 k = 1.40E-12 exp(-2000/T) 1.70E-15

46 NO3 + O = NO2 k = 1.00E-11 1.00E-11

47 NO3 + OH = HO2 + NO2 k = 2.20E-11 2.20E-11

48 NO3 + HO2 = HNO3 k = 3.50E-12 3.50E-12

49 NO3 + O3 = NO2 k = 1.00E-17 1.00E-17

50 NO3 + NO3 = 2 NO2 k = 8.50E-13 exp(-2450/T) 2.28E-16

51 PNA = 0.61 HO2 + 0.61 NO2 + 0.39 OH + 0.39 

NO3

Photolysis

52 HNO3 = OH + NO2 Photolysis

53 N2O5 = NO2 + NO3 Photolysis

54 XO2 + NO = NO2 k = 2.60E-12 exp(365/T) 8.85E-12

55 XO2N + NO = NTR k = 2.60E-12 exp(365/T) 8.85E-12

56 XO2 + HO2 = ROOH k = 7.50E-13 exp(700/T) 7.86E-12

57 XO2N + HO2 = ROOH k = 7.50E-13 exp(700/T) 7.86E-12

58 XO2 + XO2 = k = 6.80E-14 6.80E-14

59 XO2N + XO2N = k = 6.80E-14 6.80E-14

60 XO2 + XO2N = k = 6.80E-14 6.80E-14

61 NTR + OH = HNO3 + HO2 + 0.33 FORM + 0.33 

ALD2 + 0.33 ALDX - 0.66 PAR

k = 5.90E-13 exp(-360/T) 1.76E-13

62 NTR = NO2 + HO2 + 0.33 FORM + 0.33 ALD2 + 

0.33 ALDX - 0.66 PAR

Photolysis

63 SO2 + OH = SULF + HO2 Falloff: F=0.6; n=1

 k

0 = 3.00E-31 (T/300)^-3.3

 k∞ = 1.50E-12

8.89E-13

64 ROOH + OH = XO2 + 0.5 ALD2 + 0.5 ALDX k = 3.01E-12 exp(190/T) 5.69E-12

65 ROOH = OH + HO2 + 0.5 ALD2 + 0.5 ALDX Photolysis
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Number Reactants and Products Rate Constant Expression k298

66 OH + CO = HO2 k = k1 + k2 [M]

 k1 = 1.44E-13

 k2 = 3.43E-33

2.28E-13

67 OH + CH4 = MEO2 k = 2.45E-12 exp(-1775/T) 6.34E-15

68 MEO2 + NO = FORM + HO2 + NO2 k = 2.80E-12 exp(300/T) 7.66E-12

69 MEO2 + HO2 = MEPX k = 4.10E-13 exp(750/T) 5.08E-12

70 MEO2 + MEO2 = 1.37 FORM + 0.74 HO2 + 

0.63 MEOH

k = 9.50E-14 exp(390/T) 3.52E-13

71 MEPX + OH = 0.7 MEO2 + 0.3 XO2 + 0.3 HO2 k = 3.80E-12 exp(200/T) 7.43E-12

72 MEPX = FORM + HO2 + OH Photolysis

73 MEOH + OH = FORM + HO2 k = 7.30E-12 exp(-620/T) 9.12E-13

74 FORM + OH = HO2 + CO k = 9.00E-12 9.00E-12

75 FORM = 2 HO2 + CO Photolysis

76 FORM = CO Photolysis

77 FORM + O = OH + HO2 + CO k = 3.40E-11 exp(-1600/T) 1.58E-13

78 FORM + NO3 = HNO3 + HO2 + CO k = 5.80E-16 5.80E-16

79 FORM + HO2 = HCO3 k = 9.70E-15 exp(625/T) 7.90E-14

80 HCO3 = FORM + HO2 k = 2.40E+12 exp(-7000/T) 1.51E+2

81 HCO3 + NO = FACD + NO2 + HO2 k = 5.60E-12 5.60E-12

82 HCO3 + HO2 = MEPX k = 5.60E-15 exp(2300/T) 1.26E-11

83 FACD + OH = HO2 k = 4.00E-13 4.00E-13

84 ALD2 + O = C2O3 + OH k = 1.80E-11 exp(-1100/T) 4.49E-13

85 ALD2 + OH = C2O3 k = 5.60E-12 exp(270/T) 1.39E-11

86 ALD2 + NO3 = C2O3 + HNO3 k = 1.40E-12 exp(-1900/T) 2.38E-15

87 ALD2 = MEO2 + CO + HO2 Photolysis

88 C2O3 + NO = MEO2 + NO2 k = 8.10E-12 exp(270/T) 2.00E-11

89 C2O3 + NO2 = PAN Falloff: F=0.3; n=1

 k

0 = 2.70E-28 (T/300)^-7.1

 k∞ = 1.20E-11 (T/300)^-0.9

1.05E-11

90 PAN = C2O3 + NO2 Falloff: F=0.3; n=1

 k

0 = 4.90E-3 exp(-12100/T)

 k∞ = 5.40E+16 exp(-13830/T)

3.31E-4

91 PAN = C2O3 + NO2 Photolysis

92 C2O3 + HO2 = 0.8 PACD + 0.2 AACD + 0.2 O3 k = 4.30E-13 exp(1040/T) 1.41E-11

93 C2O3 + MEO2 = 0.9 MEO2 + 0.9 HO2 + FORM 

+ 0.1 AACD

k = 2.00E-12 exp(500/T) 1.07E-11

94 C2O3 + XO2 = 0.9 MEO2 + 0.1 AACD k = 4.40E-13 exp(1070/T) 1.60E-11

95 C2O3 + C2O3 = 2 MEO2 k = 2.90E-12 exp(500/T) 1.55E-11

96 PACD + OH = C2O3 k = 4.00E-13 exp(200/T) 7.83E-13

97 PACD = MEO2 + OH Photolysis

98 AACD + OH = MEO2 k = 4.00E-13 exp(200/T) 7.83E-13

99 ALDX + O = CXO3 + OH k = 1.30E-11 exp(-870/T) 7.02E-13

100 ALDX + OH = CXO3 k = 5.10E-12 exp(405/T) 1.99E-11

101 ALDX + NO3 = CXO3 + HNO3 k = 6.50E-15 6.50E-15

102 ALDX = MEO2 + CO + HO2 Photolysis

103 CXO3 + NO = ALD2 + NO2 + HO2 + XO2 k = 6.70E-12 exp(340/T) 2.10E-11

104 CXO3 + NO2 = PANX Falloff: F=0.3; n=1

 k

0 = 2.70E-28 (T/300)^-7.1

 k∞ = 1.20E-11 (T/300)^-0.9

1.05E-11
April 2014 CAMx User’s Guide Version 6.1

Appendix D: Mechanism 6 – CB05

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Number Reactants and Products Rate Constant Expression k298

105 PANX = CXO3 + NO2 Falloff: F=0.3; n=1

 k

0 = 4.90E-3 exp(-12100/T)

 k

∞ = 5.40E+16 exp(-13830/T)

3.31E-4

106 PANX = CXO3 + NO2 Photolysis

107 PANX + OH = ALD2 + NO2 k = 3.00E-13 3.00E-13

108 CXO3 + HO2 = 0.8 PACD + 0.2 AACD + 0.2 O3 k = 4.30E-13 exp(1040/T) 1.41E-11

109 CXO3 + MEO2 = 0.9 ALD2 + 0.9 XO2 + HO2 + 

0.1 AACD + 0.1 FORM

k = 2.00E-12 exp(500/T) 1.07E-11

110 CXO3 + XO2 = 0.9 ALD2 + 0.1 AACD k = 4.40E-13 exp(1070/T) 1.60E-11

111 CXO3 + CXO3 = 2 ALD2 + 2 XO2 + 2 HO2 k = 2.90E-12 exp(500/T) 1.55E-11

112 CXO3 + C2O3 = MEO2 + XO2 + HO2 + ALD2 k = 2.90E-12 exp(500/T) 1.55E-11

113 OH + ETHA = 0.991 ALD2 + 0.991 XO2 + 0.009 

XO2N + HO2

k = 8.70E-12 exp(-1070/T) 2.40E-13

114 OH + ETOH = HO2 + 0.9 ALD2 + 0.05 ALDX + 

0.1 FORM + 0.1 XO2

k = 6.90E-12 exp(-230/T) 3.19E-12

115 PAR + OH = 0.87 XO2 + 0.13 XO2N + 0.11 HO2 

+ 0.06 ALD2 - 0.11 PAR + 0.76 ROR + 0.05 

ALDX

k = 8.10E-13 8.10E-13

116 ROR = 0.96 XO2 + 0.6 ALD2 + 0.94 HO2 - 2.1 

PAR + 0.04 XO2N + 0.02 ROR + 0.5 ALDX

k = 1.00E+15 exp(-8000/T) 2.19E+3

117 ROR = HO2 k = 1.60E+3 1.60E+3

118 ROR + NO2 = NTR k = 1.50E-11 1.50E-11

119 O + OLE = 0.2 ALD2 + 0.3 ALDX + 0.3 HO2 + 0.2 

XO2 + 0.2 CO + 0.2 FORM + 0.01 XO2N + 0.2 

PAR + 0.1 OH

k = 1.00E-11 exp(-280/T) 3.91E-12

120 OH + OLE = 0.8 FORM + 0.33 ALD2 + 0.62 

ALDX + 0.8 XO2 + 0.95 HO2 - 0.7 PAR

k = 3.20E-11 3.20E-11

121 O3 + OLE = 0.18 ALD2 + 0.74 FORM + 0.32 

ALDX + 0.22 XO2 + 0.1 OH + 0.33 CO + 0.44 

HO2 - 1 PAR

k = 6.50E-15 exp(-1900/T) 1.11E-17

122 NO3 + OLE = NO2 + FORM + 0.91 XO2 + 0.09 

XO2N + 0.56 ALDX + 0.35 ALD2 - 1 PAR

k = 7.00E-13 exp(-2160/T) 4.98E-16

123 O + ETH = FORM + 1.7 HO2 + CO + 0.7 XO2 + 

0.3 OH

k = 1.04E-11 exp(-792/T) 7.29E-13

124 OH + ETH = XO2 + 1.56 FORM + 0.22 ALDX + 

HO2

Falloff: F=0.6; n=1

 k

0 = 1.00E-28 (T/300)^-0.8

 k∞ = 8.80E-12

8.15E-12

125 O3 + ETH = FORM + 0.63 CO + 0.13 HO2 + 0.13 

OH + 0.37 FACD

k = 1.20E-14 exp(-2630/T) 1.76E-18

126 NO3 + ETH = NO2 + XO2 + 2 FORM k = 3.30E-12 exp(-2880/T) 2.10E-16

127 IOLE + O = 1.24 ALD2 + 0.66 ALDX + 0.1 HO2 + 

0.1 XO2 + 0.1 CO + 0.1 PAR

k = 2.30E-11 2.30E-11

128 IOLE + OH = 1.3 ALD2 + 0.7 ALDX + HO2 + XO2 k = 1.00E-11 exp(550/T) 6.33E-11

129 IOLE + O3 = 0.65 ALD2 + 0.35 ALDX + 0.25 

FORM + 0.25 CO + 0.5 O + 0.5 OH + 0.5 HO2

k = 8.40E-15 exp(-1100/T) 2.09E-16

130 IOLE + NO3 = 1.18 ALD2 + 0.64 ALDX + HO2 + 

NO2

k = 9.60E-13 exp(-270/T) 3.88E-13

131 TOL + OH = 0.44 HO2 + 0.08 XO2 + 0.36 CRES 

+ 0.56 TO2

k = 1.80E-12 exp(355/T) 5.92E-12

132 TO2 + NO = 0.9 NO2 + 0.9 HO2 + 0.9 OPEN + 

0.1 NTR

k = 8.10E-12 8.10E-12
April 2014 CAMx User’s Guide Version 6.1

Appendix D: Mechanism 6 – CB05

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Number Reactants and Products Rate Constant Expression k298

133 TO2 = CRES + HO2 k = 4.20E+0 4.20E+0

134 OH + CRES = 0.4 CRO + 0.6 XO2 + 0.6 HO2 + 

0.3 OPEN

k = 4.10E-11 4.10E-11

135 CRES + NO3 = CRO + HNO3 k = 2.20E-11 2.20E-11

136 CRO + NO2 = NTR k = 1.40E-11 1.40E-11

137 CRO + HO2 = CRES k = 5.50E-12 5.50E-12

138 OPEN = C2O3 + HO2 + CO Photolysis

139 OPEN + OH = XO2 + 2 CO + 2 HO2 + C2O3 + 

FORM

k = 3.00E-11 3.00E-11

140 OPEN + O3 = 0.03 ALDX + 0.62 C2O3 + 0.7 

FORM + 0.03 XO2 + 0.69 CO + 0.08 OH + 0.76 

HO2 + 0.2 MGLY

k = 5.40E-17 exp(-500/T) 1.01E-17

141 OH + XYL = 0.7 HO2 + 0.5 XO2 + 0.2 CRES + 0.8 

MGLY + 1.1 PAR + 0.3 TO2

k = 1.70E-11 exp(116/T) 2.51E-11

142 OH + MGLY = XO2 + C2O3 k = 1.70E-11 1.70E-11

143 MGLY = C2O3 + HO2 + CO Photolysis

144 O + ISOP = 0.75 ISPD + 0.5 FORM + 0.25 XO2 + 

0.25 HO2 + 0.25 CXO3 + 0.25 PAR

k = 3.60E-11 3.60E-11

145 OH + ISOP = 0.912 ISPD + 0.629 FORM + 0.991 

XO2 + 0.912 HO2 + 0.088 XO2N

k = 2.54E-11 exp(407.6/T) 9.97E-11

146 O3 + ISOP = 0.65 ISPD + 0.6 FORM + 0.2 XO2 + 

0.066 HO2 + 0.266 OH + 0.2 CXO3 + 0.15 ALDX 

+ 0.35 PAR + 0.066 CO

k = 7.86E-15 exp(-1912/T) 1.29E-17

147 NO3 + ISOP = 0.2 ISPD + 0.8 NTR + XO2 + 0.8 

HO2 + 0.2 NO2 + 0.8 ALDX + 2.4 PAR

k = 3.03E-12 exp(-448/T) 6.74E-13

148 NO2 + ISOP = 0.2 ISPD + 0.8 NTR + XO2 + 0.8 

HO2 + 0.2 NO + 0.8 ALDX + 2.4 PAR

k = 1.50E-19 1.50E-19

149 OH + ISPD = 1.565 PAR + 0.167 FORM + 0.713 

XO2 + 0.503 HO2 + 0.334 CO + 0.168 MGLY + 

0.252 ALD2 + 0.21 C2O3 + 0.25 CXO3 + 0.12 

ALDX

k = 3.36E-11 3.36E-11

150 O3 + ISPD = 0.114 C2O3 + 0.15 FORM + 0.85 

MGLY + 0.154 HO2 + 0.268 OH + 0.064 XO2 + 

0.02 ALD2 + 0.36 PAR + 0.225 CO

k = 7.10E-18 7.10E-18

151 NO3 + ISPD = 0.357 ALDX + 0.282 FORM + 

1.282 PAR + 0.925 HO2 + 0.643 CO + 0.85 NTR 

+ 0.075 CXO3 + 0.075 XO2 + 0.15 HNO3

k = 1.00E-15 1.00E-15

152 ISPD = 0.333 CO + 0.067 ALD2 + 0.9 FORM + 

0.832 PAR + 1.033 HO2 + 0.7 XO2 + 0.967 

C2O3

Photolysis

153 TERP + O = 0.15 ALDX + 5.12 PAR k = 3.60E-11 3.60E-11

154 TERP + OH = 0.75 HO2 + 1.25 XO2 + 0.25 

XO2N + 0.28 FORM + 1.66 PAR + 0.47 ALDX

k = 1.50E-11 exp(449/T) 6.77E-11

155 TERP + O3 = 0.57 OH + 0.07 HO2 + 0.76 XO2 + 

0.18 XO2N + 0.24 FORM + 0.001 CO + 7 PAR + 

0.21 ALDX + 0.39 CXO3

k = 1.20E-15 exp(-821/T) 7.63E-17

156 TERP + NO3 = 0.47 NO2 + 0.28 HO2 + 1.03 

XO2 + 0.25 XO2N + 0.47 ALDX + 0.53 NTR

k = 3.70E-12 exp(175/T) 6.66E-12

Table notes:

k298 is the rate constant at 298 K and 1 atmosphere using units molecules cm-3 and s-1

See Table D-2 for species names

See the CAMx chemistry parameters file for the temperature and pressure dependencies (Section 3).
April 2014 CAMx User’s Guide Version 6.1

Appendix D: Mechanism 6 – CB05

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Table D-2. Explicit species in the CB05 mechanism.

Species Name Description

NO Nitric oxide

NO2 Nitrogen dioxide

O3 Ozone

O Oxygen atom in the O3(P) electronic state

O1D Oxygen atom in the O1(D) electronic state

OH Hydroxyl radical

HO2 Hydroperoxy radical

H2O2 Hydrogen peroxide

NO3 Nitrate radical

N2O5 Dinitrogen pentoxide

HONO Nitrous acid

HNO3 Nitric acid

PNA Peroxynitric acid (HNO4)

CO Carbon monoxide

FORM Formaldehyde

ALD2 Acetaldehyde

C2O3 Acetylperoxy radical

HCO3 Adduct from HO2 plus formaldehyde

PAN Peroxyacetyl nitrate 

ALDX Propionaldehyde and higher aldehydes

CXO3 C3 and higher acylperoxy radicals 

PANX C3 and higher peroxyacyl nitrates 

XO2 NO to NO2 conversion from alkylperoxy (RO2) radical

XO2N NO to organic nitrate conversion from alkylperoxy (RO2) radical

NTR Organic nitrate (RNO3)

ETOH Ethanol

MEO2 Methylperoxy radical

MEOH Methanol

MEPX Methylhydroperoxide

FACD Formic acid

ETHA Ethane

ROOH Higher organic peroxide

AACD Acetic and higher carboxylic acids

PACD Peroxyacetic and higher peroxycarboxylic acids

PAR Paraffin carbon bond (C-C)

ROR Secondary alkoxy radical

ETH Ethene

OLE Terminal olefin carbon bond (R-C=C)

IOLE Internal olefin carbon bond (R-C=C-R)

ISOP Isoprene

ISPD Isoprene product (lumped methacrolein, methyl vinyl ketone, etc.)

TERP Terpene

TOL Toluene and other monoalkyl aromatics

XYL Xylene and other polyalkyl aromatics

CRES Cresol and higher molecular weight phenols

TO2 Toluene-hydroxyl radical adduct

OPEN Aromatic ring opening product

CRO Methylphenoxy radical

MGLY Methylglyoxal and other aromatic products

SO2 Sulfur dioxide

SULF Sulfuric acid (gaseous)
April 2014 CAMx User’s Guide Version 6.1

Appendix D: Mechanism 6 – CB05

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Table D-3. Properties of VOC species in the CB05 mechanism: carbon numbers, kOH values 

(ppm-1min-1) and maximum incremental reactivity (MIR) values (mole O3/mole VOC).

Species Carbon Number Average kOH MIR

PAR 1 1.20E+03 0.319

ETHA 2 3.54E+02 0.109

MEOH 1 1.35E+03 0.361

ETOH 2 4.71E+03 1.042

ETH 2 1.20E+04 4.370

OLE 2 4.73E+04 8.235

IOLE 4 9.35E+04 13.109

ISOP 5 1.47E+05 11.555

TERP 10 1.00E+05 8.824

FORM 1 1.33E+04 4.496

ALD2 2 2.05E+04 4.454

ALDX 2 2.93E+04 6.807

TOL 7 8.75E+03 2.941

XYL 8 3.71E+04 14.790
April 2014 CAMx User’s Guide Version 6.1

Appendix E: Mechanism 5 – SAPRC99

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Appendix E

CAMx Mechanism 5

SAPRC99 Gas-Phase Chemistry

Table E-1. Reactions and rate constants for the SAPRC99 mechanism.

Number Reactants and Products Rate Constant Expression k298

1 NO2 = NO + O Photolysis

2 O + O2 + M = O3 + M k = 5.68E-34 (T/300)^-2.8 5.79E-34

3 O + O3 = 2. O2 k = 8.00E-12 exp(-2060.19/T) 7.96E-15

4 O + NO + M = NO2 + M k = 1.00E-31 (T/300)^-1.6 1.01E-31

5 O + NO2 = NO + O2 k = 6.50E-12 exp(119.77/T) 9.72E-12

6 O + NO2 = NO3 Falloff: F=0.8; n=1

 k

0 = 9.00E-32 (T/300)^-2

 k∞ = 2.20E-11

1.82E-12

7 O3 + NO = NO2 + O2 k = 1.80E-12 exp(-1369.77/T) 1.82E-14

8 O3 + NO2 = O2 + NO3 k = 1.40E-13 exp(-2469.81/T) 3.52E-17

9 NO + NO3 = 2. NO2 k = 1.80E-11 exp(110.21/T) 2.61E-11

10 NO + NO + O2 = 2. NO2 k = 3.30E-39 exp(529.89/T) 1.95E-38

11 NO2 + NO3 = N2O5 Falloff: F=0.45; n=1

 k

0 = 2.80E-30 (T/300)^-3.5

 k∞ = 2.00E-12 (T/300)^0.2

1.54E-12

12 N2O5 = NO2 + NO3 Falloff: F=0.45; n=1

 k

0 = 1.00E-3 (T/300)^-3.5 exp(-10999.9/T)

 k∞ = 9.70E+14 (T/300)^0.1 exp(-11079.91/T)

5.28E-2

13 N2O5 + H2O = 2. HNO3 k = 2.60E-22 2.60E-22

14 NO2 + NO3 = NO + NO2 + O2 k = 4.50E-14 exp(-1260.06/T) 6.56E-16

15 NO3 = NO + O2 Photolysis

16 NO3 = NO2 + O Photolysis

17 O3 = O + O2 Photolysis

18 O3 = O1D + O2 Photolysis

19 O1D + H2O = 2. OH k = 2.20E-10 2.20E-10

20 O1D + M = O + M k = 2.09E-11 exp(95.11/T) 2.88E-11

21 OH + NO = HONO Falloff: F=0.6; n=1

 k

0 = 7.00E-31 (T/300)^-2.6

 k

∞ = 3.60E-11 (T/300)^-0.1

7.41E-12

22 HONO = OH + NO Photolysis

23 HONO = HO2 + NO2 Photolysis

24 OH + HONO = NO2 k = 2.70E-12 exp(260.17/T) 6.46E-12

25 OH + NO2 = HNO3 Falloff: F=0.6; n=1

 k

0 = 2.43E-30 (T/300)^-3.1

 k∞ = 1.67E-11 (T/300)^-2.1

8.98E-12

26 OH + NO3 = HO2 + NO2 k = 2.00E-11 2.00E-11

27 OH + HNO3 = NO3 + H2O k = k1 + k3 [M] / (1 + k3 [M] / k2)

 k1 = 7.20E-15 exp(785.02/T)

 k2 = 4.10E-16 exp(1440.22/T)

 k3 = 1.90E-33 exp(725.14/T)

1.47E-13

28 HNO3 = OH + NO2 Photolysis

29 OH + CO = HO2 k = k1 + k2 [M]

 k1 = 1.30E-13

 k2 = 3.19E-33

2.09E-13
April 2014 CAMx User’s Guide Version 6.1

Appendix E: Mechanism 5 – SAPRC99

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Number Reactants and Products Rate Constant Expression k298

30 OH + O3 = HO2 k = 1.90E-12 exp(-999.9/T) 6.63E-14

31 HO2 + NO = OH + NO2 k = 3.40E-12 exp(270.23/T) 8.42E-12

32 HO2 + NO2 = HNO4 Photolysis

33 HNO4 = HO2 + NO2 Photolysis

34 HNO4 = 0.61 HO2 + 0.61 NO2 + 0.39 OH + 

0.39 NO3 

Photolysis

35 HNO4 + OH = NO2 Photolysis

36 HO2 + O3 = OH k = 1.40E-14 exp(-599.84/T) 1.87E-15

37 HO2 + HO2 = HO2H + O2 k = k1 + k2 [M]

 k1 = 2.20E-13 exp(599.84/T)

 k2 = 1.85E-33 exp(979.77/T)

2.87E-12

38 HO2 + HO2 + H2O = HO2H + O2 + H2O k = k1 + k2 [M]

 k1 = 3.08E-34 exp(2799.92/T)

 k2 = 2.59E-54 exp(3179.85/T)

6.45E-30

39 NO3 + HO2 = 0.8 OH + 0.8 NO2 + 0.2 HNO3 k = 4.00E-12 4.00E-12

40 NO3 + NO3 = 2. NO2 + O2 k = 8.50E-13 exp(-2450.18/T) 2.28E-16

41 HO2H = 2. OH Photolysis

42 HO2H + OH = HO2 k = 2.90E-12 exp(-160.02/T) 1.70E-12

43 OH + HO2 = k = 4.80E-11 exp(250.1/T) 1.11E-10

44 OH + SO2 = HO2 + SULF Falloff: F=0.45; n=1

 k

0 = 4.00E-31 (T/300)^-3.3

 k∞ = 2.00E-12

9.77E-13

45 OH + H2 = HO2 k = 7.70E-12 exp(-2099.94/T) 6.70E-15

46 CXO2 + NO = NO2 + HCHO + HO2 k = 2.80E-12 exp(284.82/T) 7.28E-12

47 CXO2 + HO2 = COOH + O2 k = 3.80E-13 exp(779.99/T) 5.21E-12

48 CXO2 + NO3 = HCHO + HO2 + NO2 k = 1.30E-12 1.30E-12

49 CXO2 + CXO2 = MEOH + HCHO + O2 k = 2.45E-14 exp(709.54/T) 2.65E-13

50 CXO2 + CXO2 = 2. HCHO + 2. HO2 k = 5.90E-13 exp(-508.76/T) 1.07E-13

51 RO2R + NO = NO2 + HO2 k = 2.70E-12 exp(359.8/T) 9.03E-12

52 RO2R + HO2 = ROOH k = 1.90E-13 exp(1299.82/T) 1.49E-11

53 RO2R + NO3 = NO2 + O2 + HO2 k = 2.30E-12 2.30E-12

54 RO2R + CXO2 = HO2 + 0.75 HCHO + 0.25 

MEOH 

k = 2.00E-13 2.00E-13

55 RO2R + RO2R = HO2 k = 3.50E-14 3.50E-14

56 R2O2 + NO = NO2 k = 2.70E-12 exp(359.8/T) 9.03E-12

57 R2O2 + HO2 = HO2 k = 1.90E-13 exp(1299.82/T) 1.49E-11

58 R2O2 + NO3 = NO2 k = 2.30E-12 2.30E-12

59 R2O2 + CXO2 = CXO2 k = 2.00E-13 2.00E-13

60 R2O2 + RO2R = RO2R k = 3.50E-14 3.50E-14

61 R2O2 + R2O2 = k = 3.50E-14 3.50E-14

62 RO2N + NO = RNO3 k = 2.70E-12 exp(359.8/T) 9.03E-12

63 RO2N + HO2 = ROOH k = 1.90E-13 exp(1299.82/T) 1.49E-11

64 RO2N + CXO2 = HO2 + 0.25 MEOH + 0.5 MEK 

+ 0.5 PROD + 0.75 HCHO 

k = 2.00E-13 2.00E-13

65 RO2N + NO3 = NO2 + O2 + HO2 + MEK k = 2.30E-12 2.30E-12

66 RO2N + RO2R = HO2 + 0.5 MEK + 0.5 PROD k = 3.50E-14 3.50E-14

67 RO2N + R2O2 = RO2N k = 3.50E-14 3.50E-14

68 RO2N + RO2N = MEK + HO2 + PROD k = 3.50E-14 3.50E-14

69 CCO3 + NO2 = PAN Falloff: F=0.3; n=1

 k

0 = 2.70E-28 (T/300)^-7.1

 k∞ = 1.20E-11 (T/300)^-0.9

1.05E-11
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Appendix E: Mechanism 5 – SAPRC99

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Number Reactants and Products Rate Constant Expression k298

70 PAN = CCO3 + NO2 Falloff: F=0.3; n=1

 k

0 = 4.90E-3 exp(-12099.94/T)

 k

∞ = 4.00E+16 exp(-13600.04/T)

5.20E-4

71 CCO3 + NO = CXO2 + NO2 k = 7.80E-12 exp(299.92/T) 2.13E-11

72 CCO3 + HO2 = 0.75 CO3H + 0.25 CO2H + 0.25 

O3 

k = 4.30E-13 exp(1040.16/T) 1.41E-11

73 CCO3 + NO3 = CXO2 + NO2 k = 4.00E-12 4.00E-12

74 CCO3 + CXO2 = CO2H + HCHO k = 1.80E-12 exp(500.2/T) 9.64E-12

75 CCO3 + RO2R = CO2H k = 7.50E-12 7.50E-12

76 CCO3 + R2O2 = CCO3 k = 7.50E-12 7.50E-12

77 CCO3 + RO2N = CO2H + PROD k = 7.50E-12 7.50E-12

78 CCO3 + CCO3 = 2. CXO2 k = 2.90E-12 exp(500.2/T) 1.55E-11

79 RCO3 + NO2 = PAN2 k = 1.20E-11 (T/300)^-0.9 1.21E-11

80 PAN2 = RCO3 + NO2 k = 2.00E+15 exp(-12799.92/T) 4.43E-4

81 RCO3 + NO = NO2 + CCHO + RO2R k = 1.25E-11 exp(240.04/T) 2.80E-11

82 RCO3 + HO2 = 0.75 RC3H + 0.25 RC2H + 0.25 

O3 

k = 4.30E-13 exp(1040.16/T) 1.41E-11

83 RCO3 + NO3 = NO2 + CCHO + RO2R k = 4.00E-12 4.00E-12

84 RCO3 + CXO2 = RC2H + HCHO k = 1.80E-12 exp(500.2/T) 9.64E-12

85 RCO3 + RO2R = RC2H k = 7.50E-12 7.50E-12

86 RCO3 + R2O2 = RCO3 k = 7.50E-12 7.50E-12

87 RCO3 + RO2N = RC2H + PROD k = 7.50E-12 7.50E-12

88 RCO3 + CCO3 = CXO2 + CCHO + RO2R k = 2.90E-12 exp(500.2/T) 1.55E-11

89 RCO3 + RCO3 = 2. CCHO + 2. RO2R k = 2.90E-12 exp(500.2/T) 1.55E-11

90 BZCO + NO2 = PBZN k = 1.37E-11 1.37E-11

91 PBZN = BZCO + NO2 k = 7.90E+16 exp(-14000.1/T) 3.12E-4

92 BZCO + NO = NO2 + BZO + R2O2 k = 1.25E-11 exp(240.04/T) 2.80E-11

93 BZCO + HO2 = 0.75 RC3H + 0.25 RC2H + 0.25 

O3 

k = 4.30E-13 exp(1040.16/T) 1.41E-11

94 BZCO + NO3 = NO2 + BZO + R2O2 k = 4.00E-12 4.00E-12

95 BZCO + CXO2 = RC2H + HCHO k = 1.80E-12 exp(500.2/T) 9.64E-12

96 BZCO + RO2R = RC2H k = 7.50E-12 7.50E-12

97 BZCO + R2O2 = BZCO k = 7.50E-12 7.50E-12

98 BZCO + RO2N = RC2H + PROD k = 7.50E-12 7.50E-12

99 BZCO + CCO3 = CXO2 + BZO + R2O2 k = 2.90E-12 exp(500.2/T) 1.55E-11

100 BZCO + RCO3 = CCHO + RO2R + BZO + + R2O2 k = 2.90E-12 exp(500.2/T) 1.55E-11

101 BZCO + BZCO = 2. BZO + 2. R2O2 k = 2.90E-12 exp(500.2/T) 1.55E-11

102 MCO3 + NO2 = MPAN k = 1.20E-11 (T/300)^-0.9 1.21E-11

103 MPAN = MCO3 + NO2 k = 1.60E+16 exp(-13486.31/T) 3.55E-4

104 MCO3 + NO = NO2 + HCHO + CCO3 k = 1.25E-11 exp(240.04/T) 2.80E-11

105 MCO3 + HO2 = 0.75 RC3H + 0.25 RC2H + 0.25 

O3 

k = 4.30E-13 exp(1040.16/T) 1.41E-11

106 MCO3 + NO3 = NO2 + HCHO + CCO3 k = 4.00E-12 4.00E-12

107 MCO3 + CXO2 = RC2H + HCHO k = 1.80E-12 exp(500.2/T) 9.64E-12

108 MCO3 + RO2R = RC2H k = 7.50E-12 7.50E-12

109 MCO3 + R2O2 = MCO3 k = 7.50E-12 7.50E-12

110 MCO3 + RO2N = 2 RC2H k = 7.50E-12 7.50E-12

111 MCO3 + CCO3 = CXO2 + HCHO + CCO3 k = 2.90E-12 exp(500.2/T) 1.55E-11

112 MCO3 + RCO3 = HCHO + CCO3 + CCHO + + 

RO2R 

k = 2.90E-12 exp(500.2/T) 1.55E-11

113 MCO3 + BZCO = HCHO + CCO3 + BZO + + R2O2 k = 2.90E-12 exp(500.2/T) 1.55E-11
April 2014 CAMx User’s Guide Version 6.1

Appendix E: Mechanism 5 – SAPRC99

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 284 www.camx.com

Number Reactants and Products Rate Constant Expression k298

114 MCO3 + MCO3 = 2 HCHO + 2 + CCO3 k = 2.90E-12 exp(500.2/T) 1.55E-11

115 TBUO + NO2 = RNO3 k = 2.40E-11 2.40E-11

116 TBUO = ACET + CXO2 k = 7.50E+14 exp(-8152.17/T) 9.87E+2

117 BZO + NO2 = NPHE k = 2.30E-11 exp(149.96/T) 3.80E-11

118 BZO + HO2 = PHEN k = 1.90E-13 exp(1299.82/T) 1.49E-11

119 BZO = PHEN Photolysis

120 BZNO + NO2 = 2 XN k = 2.30E-11 exp(149.96/T) 3.80E-11

121 BZNO + HO2 = NPHE k = 1.90E-13 exp(1299.82/T) 1.49E-11

122 BZNO = NPHE Photolysis

123 HCHO = 2 + HO2 + CO Photolysis

124 HCHO = CO Photolysis

125 HCHO + OH = HO2 + CO k = 8.60E-12 exp(20.13/T) 9.20E-12

126 HCHO + HO2 = HCO3 k = 9.70E-15 exp(625/T) 7.90E-14

127 HCO3 = HO2 + HCHO k = 2.40E+12 exp(-6999.8/T) 1.51E+2

128 HCO3 + NO = HC2H + NO2 + HO2 k = 2.80E-12 exp(284.82/T) 7.28E-12

129 HCHO + NO3 = HNO3 + HO2 + CO k = 2.00E-12 exp(-2430.56/T) 5.74E-16

130 CCHO + OH = CCO3 k = 5.60E-12 exp(309.98/T) 1.58E-11

131 CCHO = CO + HO2 + CXO2 Photolysis

132 CCHO + NO3 = HNO3 + CCO3 k = 1.40E-12 exp(-1859.9/T) 2.73E-15

133 RCHO + OH = 0.034 RO2R + 0.001 RO2N + 

0.965 RCO3 + 0.034 CO + 0.034 CCHO 

k = 2.00E-11 2.00E-11

134 RCHO = CCHO + RO2R + CO + HO2 Photolysis

135 RCHO + NO3 = HNO3 + RCO3 k = 1.40E-12 exp(-1771.34/T) 3.67E-15

136 ACET + OH = HCHO + CCO3 + R2O2 k = 1.10E-12 exp(-519.83/T) 1.92E-13

137 ACET = CCO3 + CXO2 Photolysis

138 MEK + OH = 0.37 RO2R + 0.042 RO2N + 

0.616R2O2 + 0.492 CCO3 + 0.096 RCO3 + 

0.115 HCHO + 0.482 CCHO + 0.37 RCHO 

k = 1.30E-12 (T/300)^2 exp(-25.16/T) 1.18E-12

139 MEK = CCO3 + CCHO + RO2R Photolysis

140 MEOH + OH = HCHO + HO2 k = 3.10E-12 (T/300)^2 exp(-359.8/T) 9.15E-13

141 COOH + OH = 0.35 HCHO + 0.35 OH + 0.65 

CXO2 

k = 2.90E-12 exp(190.22/T) 5.49E-12

142 COOH = HCHO + HO2 + OH Photolysis

143 ROOH + OH = RCHO + 0.34 RO2R + 0.66 OH k = 1.10E-11 1.10E-11

144 ROOH = RCHO + HO2 + OH Photolysis

145 GLY = 2. CO + 2. HO2 Photolysis

146 GLY = HCHO + CO Photolysis

147 GLY + OH = 0.63 HO2 + 1.26 CO + 0.37 RCO3 k = 1.10E-11 1.10E-11

148 GLY + NO3 = HNO3 + 0.63 HO2 + 1.26 CO + 

0.37 RCO3 

k = 2.80E-12 exp(-2376.21/T) 9.64E-16

149 MGLY = HO2 + CO + CCO3 Photolysis

150 MGLY + OH = CO + CCO3 k = 1.50E-11 1.50E-11

151 MGLY + NO3 = HNO3 + CO + CCO3 k = 1.40E-12 exp(-1894.63/T) 2.43E-15

152 BACL = 2. CCO3 Photolysis

153 PHEN + OH = 0.24 BZO + 0.76 RO2R + 0.23 GLY k = 2.63E-11 2.63E-11

154 PHEN + NO3 = HNO3 + BZO k = 3.78E-12 3.78E-12

155 CRES + OH = 0.24 BZO + 0.76 RO2R + 0.23 

MGLY 

k = 4.20E-11 4.20E-11

156 CRES + NO3 = HNO3 + BZO k = 1.37E-11 1.37E-11

157 NPHE + NO3 = HNO3 + BZNO k = 3.78E-12 3.78E-12

158 BALD + OH = BZCO k = 1.29E-11 1.29E-11
April 2014 CAMx User’s Guide Version 6.1

Appendix E: Mechanism 5 – SAPRC99

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 285 www.camx.com

Number Reactants and Products Rate Constant Expression k298

159 BALD = Photolysis

160 BALD + NO3 = HNO3 + BZCO k = 1.40E-12 exp(-1871.98/T) 2.62E-15

161 METH + OH = 0.5 RO2R + 0.416 CO + 0.084 

HCHO + 0.416 MEK + 0.084 MGLY + 0.5 MCO3 

k = 1.86E-11 exp(176.13/T) 3.36E-11

162 METH + O3 = 0.008 HO2 + 0.1 RO2R + 0.208 

OH + 0.1 RCO3 + 0.45 CO + 0.2 HCHO + 0.9 

MGLY + 0.333 HC2H 

k = 1.36E-15 exp(-2113.53/T) 1.13E-18

163 METH + NO3 = 0.5 HNO3 + 0.5 RO2R + 0.5 CO 

+ 0.5 MCO3 + 0.5 XN 

k = 1.50E-12 exp(-1726.05/T) 4.58E-15

164 METH + O = RCHO k = 6.34E-12 6.34E-12

165 METH = 0.34 HO2 + 0.33 RO2R + 0.33 OH + 

0.67 CCO3 + 0.67 CO + 0.67 HCHO + 0.33 

MCO3 

Photolysis

166 MVK + OH = 0.3 RO2R + 0.025 RO2N + 0.675 

R2O2 + 0.675 CCO3 + 0.3 HCHO + 0.675 RCHO 

+ 0.3 MGLY 

k = 4.14E-12 exp(452.9/T) 1.89E-11

167 MVK + O3 = 0.064 HO2 + 0.05 RO2R + 0.164 

OH + 0.05 RCO3 + 0.475 CO + 0.1 HCHO + 0.95 

MGLY + 0.351 HC2H 

k = 7.51E-16 exp(-1519.73/T) 4.58E-18

168 MVK + O = 0.45 RCHO + 0.55 MEK k = 4.32E-12 4.32E-12

169 MVK = 0.3 CXO2 + 0.7 CO + 0.7 PROD + 0.3 

MCO3 

Photolysis

170 ISPD + OH = 0.67 RO2R + 0.041 RO2N + 0.289 

MCO3 + 0.336 CO + 0.055 HCHO + 0.129 

CCHO + 0.013 RCHO + 0.15 MEK + 0.332 PROD 

+ 0.15 GLY + 0.174 MGLY 

k = 6.19E-11 6.19E-11

171 ISPD + O3 = 0.4 HO2 + 0.048 RO2R + 0.048 

RCO3 + 0.285 OH + 0.498 CO + 0.125 HCHO + 

0.047 CCHO + 0.21 MEK + 0.023 GLY + 0.742 + 

MGLY + 0.1 HC2H + 0.372 RC2H 

k = 4.18E-18 4.18E-18

172 ISPD + NO3 = 0.799 RO2R + 0.051 RO2N + 

0.15 MCO3 + 0.572 CO + 0.15 HNO3 + 0.227 

HCHO + 0.218 RCHO + 0.008 MGLY + 0.572 

RNO3 + 0.278 XN 

k = 1.00E-13 1.00E-13

173 ISPD = 1.233 HO2 + 0.467 CCO3 + 0.3 RCO3 + 

1.233 CO + 0.3 HCHO + 0.467 CCHO + 0.233 

MEK 

Photolysis

174 PROD + OH = 0.379 HO2 + 0.473 RO2R + 0.07 

RO2N + 0.029 CCO3 + 0.049 RCO3 + 0.213 

HCHO + 0.084 CCHO + 0.558 RCHO + 0.115 

MEK + 0.329 PROD 

k = 1.50E-11 1.50E-11

175 PROD = 0.96 + RO2R 0.04 + RO2N 0.515 + 

R2O2 0.667 + CCO3 0.333 + RCO3 0.506 + 

HCHO 0.246 + CCHO 0.71 + RCHO 

Photolysis

176 RNO3 + OH = 0.338 NO2 0.113 + HO2 0.376 + 

RO2R 0.173 + RO2N 0.596 + R2O2 0.01 + 

HCHO 0.439 + CCHO 0.213 + RCHO 0.006 + 

ACET 0.177 + MEK 0.048 + PROD 0.31 + RNO3 

0.352 + XN 

k = 7.80E-12 7.80E-12
April 2014 CAMx User’s Guide Version 6.1

Appendix E: Mechanism 5 – SAPRC99

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Number Reactants and Products Rate Constant Expression k298

177 RNO3 = NO2 0.341 + HO2 0.564 + RO2R 0.095 

+ RO2N 0.152 + R2O2 0.134 + HCHO 0.431 + 

CCHO 0.147 + RCHO 0.02 + ACET 0.243 + MEK 

0.435 + PROD 

Photolysis

178 DCB1 + OH = RCHO RO2R + CO k = 5.00E-11 5.00E-11

179 DCB1 + O3 = 1.5 HO2 + 0.5 OH + 1.5 CO + GLY k = 2.00E-18 2.00E-18

180 DCB2 + OH = R2O2 + RCHO CCO3 k = 5.00E-11 5.00E-11

181 DCB2 = RO2R + 0.5 CCO3 + 0.5 HO2 + CO + 

R2O2 + 0.5 GLY + 0.5 MGLY 

Photolysis

182 DCB3 + OH = R2O2 + RCHO + CCO3 k = 5.00E-11 5.00E-11

183 DCB3 = RO2R + 0.5 CCO3 + 0.5 HO2 + CO + 

R2O2 + 0.5 GLY + 0.5 MGLY 

Photolysis

184 CH4 + OH = CXO2 k = 2.15E-12 exp(-1735.1/T) 6.36E-15

185 ETHE + OH = RO2R + 1.61 HCHO + 0.195 CCHO k = 1.96E-12 exp(437.8/T) 8.52E-12

186 ETHE + O3 = 0.12 OH + 0.12 HO2 + 0.5 CO + 

HCHO + 0.37 HC2H 

k = 9.14E-15 exp(-2580.01/T) 1.59E-18

187 ETHE + NO3 = RO2R + RCHO + XN k = 4.39E-13 (T/300)^2 exp(-2282.11/T) 2.05E-16

188 ETHE + O = 0.5 HO2 + 0.2 RO2R + 0.3 CXO2 + 

0.491 CO + 0.191 HCHO + 0.25 CCHO + 0.009 

GLY 

k = 1.04E-11 exp(-792.07/T) 7.29E-13

189 ISOP + OH = 0.907 RO2R + 0.093 RO2N + 

0.079 R2O2 + 0.624 HCHO + 0.23 METH + 0.32 

MVK + 0.357 ISPD 

k = 2.50E-11 exp(407.61/T) 9.82E-11

190 ISOP + O3 = 0.266 OH + 0.066 RO2R + 0.008 

RO2N + 0.126 R2O2 + 0.192 MCO3 + 0.275 CO 

+ 0.592 HCHO + 0.1 PROD + 0.39 METH + 0.16 

MVK + 0.204 HC2H + 0.15 RC2H 

k = 7.86E-15 exp(-1912.24/T) 1.28E-17

191 ISOP + NO3 = 0.187 NO2 + 0.749 RO2R + 

0.064 RO2N + 0.187 R2O2 + 0.936 ISPD + 

0.813 RNO3 

k = 3.03E-12 exp(-447.87/T) 6.74E-13

192 ISOP + O = 0.01 RO2N + 0.24 R2O2 + 0.25 

CXO2 + 0.24 MCO3 + 0.24 HCHO + 0.75 PROD 

k = 3.60E-11 3.60E-11

193 TERP + OH = 0.75 RO2R + 0.25 RO2N + 0.5 

R2O2 + 0.276 HCHO + 0.474 RCHO + 0.276 

PROD 

k = 1.83E-11 exp(449.38/T) 8.27E-11

194 TERP + O3 = 0.567 OH + 0.033 HO2 + 0.031 

RO2R + 0.18 RO2N + 0.729 R2O2 + 0.123 

CCO3 + 0.201 RCO3 + 0.157 CO + 0.235 HCHO 

+ 0.205 RCHO + 0.13 ACET + 0.276 PROD + 

0.001 GLY + 0.031 BACL + 0.103 HC2H + 0.189 

RC2H 

k = 1.08E-15 exp(-821.26/T) 6.86E-17

195 TERP + NO3 = 0.474 NO2 + 0.276 RO2R + 0.25 

RO2N + 0.75 R2O2 + 0.474 RCHO + 0.276 

RNO3 + 0.25 XN 

k = 3.66E-12 exp(174.62/T) 6.58E-12

196 TERP + O = 0.147 RCHO + 0.853 PROD k = 3.27E-11 3.27E-11

197 ALK1 + OH = RO2R + CCHO k = 1.37E-12 (T/300)^2 exp(-498.19/T) 2.54E-13

198 ALK2 + OH = 0.246 OH + 0.121 HO2 + 0.612 

RO2R + 0.021 RO2N + 0.16 CO + 0.039 HCHO + 

0.155 RCHO + 0.417 ACET + 0.248 GLY + 0.121 

HC2H 

k = 9.87E-12 exp(-671.3/T) 1.04E-12
April 2014 CAMx User’s Guide Version 6.1

Appendix E: Mechanism 5 – SAPRC99

COMPREHENSIVE AIR QUALITY MODEL WITH EXTENSION 287 www.camx.com

Number Reactants and Products Rate Constant Expression k298

199 ALK3 + OH = 0.695 RO2R + 0.07 RO2N + 0.559 

R2O2 + 0.236 TBUO + 0.026 HCHO + 0.445 

CCHO + 0.122 RCHO + 0.024 ACET + 0.332 

MEK 

k = 1.02E-11 exp(-433.78/T) 2.38E-12

200 ALK4 + OH = 0.835 RO2R + 0.143 RO2N + 

0.936 R2O2 + 0.011 CXO2 + 0.011 CCO3 + 

0.002 CO + 0.024 HCHO + 0.455 CCHO + 0.244 

RCHO + 0.452 ACET + 0.11 MEK + 0.125 PROD 

k = 5.95E-12 exp(-90.58/T) 4.39E-12

201 ALK5 + OH = 0.653 RO2R + 0.347 RO2N + 

0.948 R2O2 + 0.026 HCHO + 0.099 CCHO + 

0.204 RCHO + 0.072 ACET + 0.089 MEK + 

0.417 PROD 

k = 1.11E-11 exp(-51.83/T) 9.33E-12

202 ARO1 + OH = 0.224 HO2 + 0.765 RO2R + 0.011 

RO2N + 0.055 PROD + 0.118 GLY + 0.119 

MGLY + 0.017 PHEN + 0.207 CRES + 0.059 

BALD + 0.491 DCB1 + 0.108 DCB2 + 0.051 

DCB3 

k = 1.81E-12 exp(354.77/T) 5.95E-12

203 ARO2 + OH = 0.187 HO2 + 0.804 RO2R + 0.009 

RO2N + 0.097 GLY + 0.287 MGLY + 0.087 BACL 

+ 0.187 CRES + 0.05 BALD + 0.561 DCB1 + 

0.099 DCB2 + 0.093 DCB3 

k = 2.64E-11 2.64E-11

204 OLE1 + O3 = 0.91 RO2R + 0.09 RO2N + 0.205 

R2O2 + 0.732 HCHO + 0.294 CCHO + 0.497 

RCHO + 0.005 ACET + 0.119 PROD + OLE1 + O3 

+ 

k = 7.10E-12 exp(451.39/T) 3.23E-11

205 OLE1 + OH = 0.155 OH + 0.056 HO2 + 0.022 

RO2R + 0.001 RO2N + 0.076 CXO2 + 0.345 CO 

+ 0.5 HCHO + 0.154 CCHO + 0.363 RCHO + 

0.001 ACET + 0.215 PROD + 0.185 HC2H + 

0.05 CO2H + 0.119 RC2H

k = 2.62E-15 exp(-1640.5/T) 1.07E-17

206 OLE1 + NO3 = 0.824 RO2R + 0.176 RO2N + 

0.488 R2O2 + 0.009 CCHO + 0.037 RCHO + 

0.024 ACET + 0.511 RNO3 + 0.489 XN 

k = 4.45E-14 exp(-375.91/T) 1.26E-14

207 OLE1 + O = 0.45 RCHO + 0.437 MEK + 0.113 

PROD 

k = 1.07E-11 exp(-234/T) 4.88E-12

208 OLE2 + OH = 0.918RO2R + 0.082 RO2N + 0.001 

R2O2 + 0.244 HCHO + 0.732 CCHO + 0.511 

RCHO + 0.127 ACET + 0.072 MEK + 0.061 BALD 

+ 0.025 METH + 0.025 ISPD 

k = 1.74E-11 exp(384.46/T) 6.32E-11

209 OLE2 + O3 = 0.378OH + 0.003 HO2 + 0.033 

RO2R + 0.002 RO2N + 0.137 R2O2 + 0.197 

CXO2 + 0.137 CCO3 + 0.006 RCO3 + 0.265 CO 

+ 0.269 HCHO + 0.456 CCHO + 0.305 RCHO + 

0.045 ACET + 0.026 MEK + 0.006 PROD + 

0.042 BALD + 0.026 METH + 0.073 HC2H + 

0.129 CO2H + 0.303 RC2H 

k = 5.02E-16 exp(-461.45/T) 1.07E-16

210 OLE2 + NO3 = 0.391 NO2 + 0.442 RO2R + 

0.136 RO2N + 0.711 R2O2 + 0.03 CXO2 + 

0.079 HCHO + 0.507 CCHO + 0.151 RCHO + 

0.102 ACET + 0.001 MEK + 0.015 BALD + 0.048 

MVK + 0.321 RNO3 + 0.288 XN 

k = 7.26E-13 7.26E-13
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Appendix E: Mechanism 5 – SAPRC99

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Number Reactants and Products Rate Constant Expression k298

211 OLE2 + O = 0.013 HO2 + 0.012 RO2R + 0.001 

RO2N + 0.012 CO + 0.069 RCHO + 0.659 MEK 

+ 0.259 PROD + 0.012 METH + ETOH OH + 

2120.05 RO2R + 0.95 HO2 + 0.081 HCHO + 

0.96 CCHO 

k = 2.09E-11 2.09E-11

212 ETOH + OH = 0.05 RO2R + 0.95 HO2 + 0.081 

HCHO + 0.96 CCHO

k = 5.56E-13 exp(533.41/T) 3.33E-12

213 MTBE + OH = 0.743 RO2R + 0.078 RO2N + 

0.381 R2O2 + 0.162 CXO2 + 0.016 TBUO + 

0.234 HCHO + 0.024 ACET + 0.719 MEK + 

0.007 PROD 

k = 5.89E-13 (T/300)^2 exp(483.09/T) 2.94E-12

214 MBUT + OH = 0.935 RO2R + 0.065 RO2N + 

0.311 HCHO + 0.624 CCHO + 0.311 RCHO + 

0.624 ACET 

k = 8.20E-12 exp(608.9/T) 6.33E-11

215 MBUT + O3 = 0.099 OH + 0.099 HO2 + 0.365 

CO + 0.3 HCHO + 0.7 RCHO + 0.015 ACET + 

0.259 HC2H + 0.285 RC2H 

k = 9.30E-18 9.30E-18

216 MBUT + NO3 = 0.935 RO2R + 0.065 RO2N + 

0.935 RCHO + 0.934 ACET + RNO3 

k = 4.60E-14 exp(-402.58/T) 1.19E-14

217 MBUT + O = 0.45 RCHO + 0.55 MEK k = 2.01E-11 2.01E-11

Table notes:

k298 is the rate constant at 298 K and 1 atmosphere using units molecules cm-3 and s-1

See Table E-2 for species names

See the CAMx chemistry parameters file for the temperature and pressure dependencies (Section 3).
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Appendix E: Mechanism 5 – SAPRC99

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Table E-2. Explicit species in the SAPRC99 mechanism.

Species Name Description

NO2 Nitrogen dioxide

NO Nitric oxide

O3 Ozone

O Oxygen atom in the O3(P) electronic state

NO3 Nitrate radical

N2O5 Dinitrogen pentoxide

HNO3 Nitric acid

O1D Oxygen atom in the O1(D) electronic state

OH Hydroxyl radical

HONO Nitrous acid

HO2 Hydroperoxy radical

CO Carbon monoxide

HNO4 Peroxynitric acid

HO2H Hydrogen peroxide

SO2 Sulfur dioxide

SULF Sulfuric acid (gaseous)

CXO2 Methylperoxy radical

HCHO Formaldehyde

COOH Methyl hydroperoxide

MEOH Methanol

RO2R Organic peroxy radical converting NO to NO2 with HO2 production

ROOH Organic hydroperoxide

R2O2 Organic peroxy radical converting NO to NO2

RO2N Organic peroxy radical converting NO to organic nitrate 

RNO3 Organic nitrate

MEK Methylethyl ketone

PROD Organic product

CCO3 Acetylperoxy radical

PAN Peroxyacetyl nitrate

CO3H Peroxyacetic acid

CO2H Acetic acid

RCO3 Higher acylperoxy radical (based on propylperoxy)

PAN2 Higher peroxyacetyl nitrate (based on peroxypropyl nitrate)

CCHO Acetaldehyde

RC3H Higher percarboxylic acid

RC2H Higher carboxylic acid

BZCO Peroxybenxoyl radical

PBZN Peroxybenzoyl nitrate

BZO Phenoxy radical

MCO3 Peroxyacyl radical from methacrolein

MPAN PAN compound from methacrolein

TBUO Tertiary-butoxy radical

ACET Acetone

NPHE Nitrophenol

PHEN Phenol

BZNO Nitrophenol reaction product

XN Other nitrogen containing product

HCO3 Adduct from HO2 plus formaldehyde 

HC2H Formic acid

RCHO Higher aldehyde (based on propionaldehyde)

GLY Glyoxal

MGLY Methylglyoxal

BACL Biacetyl

CRES Cresol

BALD Benzaldehyde
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Appendix E: Mechanism 5 – SAPRC99

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Species Name Description

METH Methacrolein

MVK Methylvinyl ketone

ISPD Isoprene product

DCB1 Aromatic ring opening dicarbonyl product

DCB2 Aromatic ring opening dicarbonyl product

DCB3 Aromatic ring opening dicarbonyl product

ETHE Ethene

ISOP Isoprene

TERP Terpene

ALK1 Lumped alkane 1

ALK2 Lumped alkane 2

ALK3 Lumped alkane 3

ALK4 Lumped alkane 4

ALK5 Lumped alkane 5

ARO1 Lumped aromatic 1

ARO2 Lumped aromatic 2

OLE1 Lumped olefin 1

OLE2 Lumped olefin 2

ETOH Ethanol

MTBE Methyl tertiary butyl ether

MBUT Methylbutenol
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Appendix E: Mechanism 5 – SAPRC99

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Table E-3. Properties of VOC species in the SAPRC99 mechanism: molecular weights, average 

carbon numbers, kOH values (ppm-1min-1) and maximum incremental reactivity (MIR) values 

(mole O3/mole VOC).

Species Molecular Weight Carbon Number Average kOH

1 MIR

ALK1 46.81 1.88 3.75E+02 0.39

ALK2 47.02 2.65 1.53E+03 0.80

ALK3 57.72 2.92 3.51E+03 2.19

ALK4 73.23 4.36 6.49E+03 3.11

ALK5 106.97 6.42 1.38E+04 4.95

ETHE 28.05 2 1.26E+04 5.44

OLE1 61.68 3.99 4.77E+04 9.73

OLE2 79.05 5.67 9.34E+04 10.98

ISOP 68.12 5 1.45E+05 12.62

TERP 136.24 10 1.22E+05 8.54

ARO1 100.47 7.27 8.79E+03 6.72

ARO2 113.93 8.58 3.90E+04 15.36

HCHO 30.03 1 1.36E+04 6.49

CCHO 44.05 2 2.34E+04 5.79

RCHO 67.32 3.66 2.95E+04 9.45

BALD 108.21 7.15

ACET 58.08 3

MEK 72.82 4.03

PROD 106.44 6.48

MEOH 32.04 1 1.35E+03 1.34

GLY 58.04 2

MGLY 72.06 3

BACL 101.31 6.37

PHEN 94.11 6

CRES 115.38 7.52

METH 56.06 3

MVK 112.17 7

ISPD 70.45 4.03

ETOH 46.07 2 4.92E+03 1.62

MTBE 88.15 5 4.34E+03 1.43

MBUT 86.13 5 9.35E+04 9.12

Notes:

1.

. kOH values are given to assist in assigning VOC species to SAPRC99 lumped species.