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CMAQ v4.6 Operational Guidance Document

1. 4 6 1 NCDUMP This program generates an ASCII representation of a netCDF file either with or without an ASCII representation of the variable data in the file NCDUMP was produced by the University Corporation for Atmospheric Research the originators of netCDF and is distributed by Unidata This utility program is useful in determining the dimensions and contents of a MAQSIP file The syntax for invoking ncdump in UNIX is the following ncdump h c n name inputfile where h produces only the header information in the output file i e the declarations of dimensions variables and attributes but no data value c produce the header information in the output file and the data values for coordinate variables n name 4 6 2 M3XTRACT The M3XTRACT program extracts a variable or a selected subset of variables from a CMAQ file for a specified time period and a specified area and writes them to a separate CMAQ file Optionally the variables can be renamed during the process Before running this program or any other of the utilities one is allowed to assign logical names to the physical file names of both files according to IO API conventions using the operation setenv lt Iname gt lt pname gt 42 4 6 3 M3DIFF where Iname equals the logical file name e g INFILE and pname equals the physical file name e g NC_195aa_cc3_g1 The program will prompt the user for the logical names chosen for the
2. The PROD operator is used to compute the total production of a species by summing the IRRs of all reactions in which species 1 appears as a product The optional qualifiers FROM and OR restrict the sum to include only those reac tions in which species2 and or species3 are reactants The speciesi can be any gas phase mechanism species or a family of gas phase species species2 or species3 may also be the keyword HV to restrict the selection to photo lytic reactions NETP species FROM species ANDIOR species3 The NETP operator is very similar to the production oper ator since it is used compute the production of a species Whereas the PROD operator includes every reaction in which species occurs as a product the NETP operator includes only those reactions in which the net production of species is greater than zero Thus if species or any member of the family species appears as both a reactant and a product with equal stoichiometry in a reaction the PROD operator will include it but the NETP operator will not This operator is useful for getting the net production of a family for example LOSS species ANDIOR species gt The LOSS operator is used to compute the total loss of a species by summing the IRRs of all reactions in which species 1 appears as a reactant The optional qualifier AND restricts the sum to include only those reactions in which both species and species are reactants
3. DESC3 commons now contain the file description END IF 39 4 4 Reading Data Files in IO API 4 4 Reading Data Files in lO API There are four routines with varying kinds of selectivity used to read or otherwise retrieve data from files READ3 XTRACT3 INTERP3 and DDTVAR3 All four are logical functions that return TRUE when they succeed FALSE when they fail The descriptions of the routines are listed in Table 4 4 Table 4 4 IOAPI data retrieval routines Routine Description READ3 reads one or all variables and layers from a file for a partic ular date and time XTRACT3 reads a windowed subgrid for one or all variables from a file for a particular INTERP3 interpolates the requested variable from the requested file to the date time DDTVAR3 computes the time derivative of the requested variable at the specified date time Because it optimizes the interpolation problem for the user INTERP3 is probably the most useful of these routines An INTERP3 call to read interpolate the variable HNO3 to 1230 GMT on February 4 1995 is outlined below CHARACTER 16 FNAME VNAME REAL 4 ARRAY NCOLS NROWS NLAYS IF NOT INTERP3 myfile HNO3 1995035 123000 NCOLS NROWS NLAYS ARRAY THEN some kind of error happened deal with it here END IF With READ3 and XTRACTS3 the user can use the magic values ALLVAR3 ALL as defined in PARMS3 EXT or ALLAYS3 1 as also define
4. The GRIDDESC file is a list formatted file delimited by blank spaces unless otherwise specified An example of the two sections of a GRIDDESC file follows mt LAM_40N100W 2 30 0 60 0 100 0 100 0 40 0 mt 99 6 1 1 GRIDDESC Horizontal Domain Definition M_32_99TUTO2 LAM_40N100W 544000 0 992000 0 32000 0 32000 0 38 38 1 The first of the two sections in this example GRIDDESC entry defines a horizontal coordinate named LAM_40N100W The coordinate definition is for a Lambert Conformal Grid keyed by first column of the coordinate description line which corresponds to the numerical code for the different I O API supported grid types 2 Lambert The next two parameters are the Lambert Alpha and Beta latitudes that determine the projection cone The fourth parameter is the central meridian of the projection The last two parameters are the latitude longitude coordinates of the grid center of the Cartesian coordinate system The example grid definition above describes a grid named M_32_99TUT02 The definition of the grid begins with areference to a coordinate name from the coordinate definition section of the file in this example the coordinate named LAM_40N100W is referenced in the grid definition The next two parameters in the grid definition are the East West and North South offsets from the origin in meters respectively The next two parameters are the grid cell size in meters for the X and Y directions follo
5. e Plume chemistry effects ping Control Utility Modules e Model data flow and synchronizing of fractional time steps ctm e Unit conversion gencoor e Initialization init e Process analysis pa Data Estimation Modules e Aerosol deposition velocity estimation aero_depv e Photolytic rate computation phot This modularity makes it easier to modify or introduce a specific scientific process in the CCTM For example the chem module contains several options for different gas phase chemistry solvers that can be used to optimize model performance More discussion will be provided about these modules later in this chapter Without the modular structure such changes could entail coding modifications throughout the CCTM thereby increasing the risk of human error In that case failing to make the correct modification at even a single location in the source code could lead to erroneous results or program execution failure With the modularity featured in CMAQ designing or modifying a model simulation is much more user friendly requiring less or no reprogramming 2 1 3 Quality control 2 1 3 Quality control CMAQ was designed to minimize the potential for model simulation error in several ways For example the generalized coordinate system helps to ensure that mass is conserved when transferring data from a non hydrostatic meteorological model to the CMAQ modeling system Otherwise errors in air density and wind field
6. O301D_CBIV88 1 0 HCHOmol_CBIV88 1 0 HCHOrad_CBIV88 1 0 ALD_CBIV88 1 0 ACROLEIN 1 0 111 5 0964761E 01 4 9923715E 01 4 6422747E 01 4 0129572E 01 3 0394882E 01 1 65902 15E 01 3 2829735E 02 0 0000000E 00 0 0000000E 00 6 1 16 EMISfile Emissions Used by CCTM CMAQ can accept emissions inputs from a variety of emissions models and preprocessors The preferred option is the Sparse Matrix Operator Kernel Emissions SMOKE modeling system which is a collection of programs that efficiently process emissions data for input to air quality models 127 6 1 17 GC2file Two dimensional Grid Cross Product Input GRID_CRO_2D The emissions file sorts the emitted gas phase and aerosol species by grid cell and time The file type is GRDDED3 and the units are in moles s The file data is looped as follows by column by row by layer by variable and by input time step CMAQ does not artificially distinguish between surface and elevated emissions sources elevated sources are provided to CMAQ as vertically resolved emissions At present all emissions estimates are contained within a single input emission file for each day Future versions of CMAQ may allow the online calculation of the vertical plume rise and the addition of process based emissions such as sea salt or windblown dust 6 1 17 GC2file Two dimensional Grid Cross Product Input GRID_CRO_2D Used by CCTM CMAQ requires the following variables to be present i
7. Some other mesoscale meteorology models allow for user defined nest ratios For example if the coarse domain is a 36 km resolution domain its nest will be a 12 km resolution domain This is strictly true for a two way nest but is largely held as a standard for the one way nests in MM5 As discussed in Section 3 5 1 the nest ratio restricts the number of grid points in each dimension of the nest domains to a multiple of 3 plus 1 141 7 6 6 Four Dimensional Data Assimilation Figure 5 3 illustrates a sample simulation domain and its nests Domain A is a 108 km coarse or parent domain Domain B which has a smaller area coverage and a higher or finer resolution is a 36 km nested or child domain Likewise Domain C is a 12 km child domain to Domain B Figure 7 3 Sample domain and its nests 7 6 6 Four Dimensional Data Assimilation The four dimensional data assimilation FDDA scheme included in MM5 is based on Newtonian relaxation or nudging Nudging is a continuous form of FDDA where artificial non physical forcing functions are added to the model s prognostic equations to nudge the solutions toward either a verifying analysis or toward observations The artificial forcing terms are scaled by a nudging coefficient that is selected so that the nudging term will not dominate the prognostic equations In general the nudging terms tend to be an order of magnitude smaller than the dominant terms in the p
8. 5 4 2 1 CHEMMECH input files Table 5 5 CHEMMECH input files File Name Format Description MCFL MECH DEF ASCII CMAQ mechanism definition file photochemical mechanism listing with both mechanistic and kinetic informa tion about all reactions that compose a chemical mechanism SPST ASCH CSV Species table comma delimited file generated from an Excel spreadsheet that lists the atmospheric processes that affect each model species 5 4 2 2 CHEMMECH compilation options The configuration options listed here are set during compilation of the CHEMMECH executable The compiler spe cific options such as the compiler names and flags are set in the make reader script distributed with the program The directory paths of the CHEMMECH source code and working directory are set in the makeit script e FC default pgf90 Fortran compiler path and name e FRLAGS Fortran compilation flags e CC default cc C compiler path and name e C FLAGS C compilation flags e BASE default cwd Working directory for compiling CHEMMECH e SRC default Location of CHEMMECH source code 5 4 2 3 CHEMMECH compilation To compile the CHEMMECH program run the following command in the directory that contains the scripts makeit MP For the compilation to be successful you must have the Portland Group Fortran and Gnu C compilers added to your path To port CHEMMECH to other compilers change the compiler names l
9. Atmos Environ 40 4973 4985 Pleim J E and J S Chang 1992 A non local closure model in the convective boundary layer Atmos Environ 26A 965 981 Pleim J E A Xiu P L Finkelstein and T L Otte 2001 A coupled land surface and dry deposition model and comparison to field measurements of surface heat moisture and ozone fluxes Water Air Soil Pollut Focus 1 243 252 Sandu A J G Verwer J G Blom E J Spee G R Carmichael and F A Potra 1997 Benchmarking stiff ODE solvers for atmospheric chemistry problems II Rosenbrock solvers Atmos Environ 31 3459 3472 Smolarkiewicz P K 1983 A simple positive definite advection scheme with small implicit diffusion Mon Wea Rev 111 479 486 Smyth S C W Jiang D Yin H Roth and E Giroux 2006 Evaluation of CMAQ O and PM 5 performance using Pacific measurement data Atmos Environ 40 2735 2749 Stockwell W R P Middleton J S Chang and X Tang 1990 The second generation regional acid deposition model chemical mechanism for regional air quality modeling J Geophys Res 95 16 343 16 367 U S EPA 2004 National Ambient Air Quality Standards NAAQS Available online at http www epa gov air criteria html U S Standard Atmosphere 1976 National Oceanic and Atmospheric Administration U S Government Printing Office Washington DC NOAA S T76 1562 Unidata 2005 NetCDF Available online at http my unidata ucar
10. M3HOME lib setenv M3MODEL M3HOME models 3 Create the M3LIB directory 4 Download the CMAQ tar files and unpack them in the M3HOME directory using the following commands tar xvzf SCRIPTS tar gz tar xvzf MODELS tar gz tar xvzf M3DATA tar gz tar xvzf M3DATA_REF tar gz 5 The CMAQ scripts assume that the netCDF and IOAPI are already installed on your system You can either copy the precompiled libraries or create symbolic links to the library a files into the appropriate locations in the M3LIB directory For example to copy a precompiled version of the netCDF library use a variation of the following commands mkdir p M3LIB netCDF Linux cp home user netcdf 3 6 1 lib libnetcdf a M3LIB netCDF Linux or to create a symbolic link mkdir p M3LIB netCDF Linux cd M3LIB netCDF Linux In s home user netcdf 3 6 1 lib libnetcdf a libnetcdf a Similarly for the IOAPI either copy a precompiled version of the library to the M3LIB ioapi Linux2_x86pg directory or create a symbolic link to the library a file Compiler flag consistency between the netCDF and IOAPI are critical for building library files compatible with CMAQ For Linux systems with the Portland Group Fortran compilers use the PGI Fortran and Gnu C compilers for building both the IOAPI and netCDF Before compiling the netCDF set the following environment variables CC gcc CPPFLAGS DNDEBUG DpgiFortran CFLAGS O FC pgf90 FFLAGS O w CXX g
11. MC2file Two dimensional Meteorological Cross Product Input MET_CRO_ 2D Used by CCTM CMAQ requires the following variables to be present in the Met Cross 2D meteorology file PRSFC surface pressure pascals JACOBS total Jacobian at surface m USTAR cell averaged horizontal friction velocity m s WSTAR convective velocity scale m s PBL planetary boundary layer height m ZRUF surface roughness length m MOLI inverse Monin Obukhov length 1 m QFX latent heat flux Watts m HFX sensible heat flux Watts m RADYNI inverse aerodynamic resistance m s RBNDYI inverse laminar boundary layer resistance m s RSTOMI inverse bulk stomatal resistance m s TEMPG skin temperature at ground K TEMP10 10 meter temperature K TEMPIPS 1 5 meter temperature K WSPD10 10 meter windspeed m s WDIR1O 10 meter wind direction m s GLW longwave radiation at ground Watts m7 GSW solar radiation absorbed at ground Watts m RGRDN solar radiation reaching the surface Watts m7 RN accumulated non convective precipitation cm RC accumulated convective precipitation cm CFRAC total cloud fraction fraction 129 6 1 21 MC3file Three dimensional Meteorological Cross Product Input MET_CRO_3D WBAR _ KF CLDT_KF CLDB_KF SNOCOV VD_SO2 VD_SULF VD_NO2 VD_NO VD_O3 VD_HNO3 VD_H202 VD_ALD VD_HCHO VD_OP VD_PAA VD_ORA VD_NH3 VD_PAN VD_HONO VD_CO VD_METHANOL VD
12. Similarly the OR qualifier includes all reactions in which either species1 or species2 appears as a reactant where species or species can be any gas phase species in the mechanism a family name that includes only gas phase mechanism species or the keyword HV to restrict the selection of re actions to those that are photolytic NETLIspecies ANDIOR species The NETL operator is very similar to the loss operator since it is used to compute the loss of a species However it includes only those reactions in which there is a net loss of species1 and or species2 Thus if species or any member of the family species appears as both a reactant and a product with equal stoichiometry in reaction the NETL operator will not include it in summing the loss of that species whereas the LOSS operator will include the IRR for that reaction 94 5 11 STENEX Command Description NET species The NET operator is similar to the CYCLE definition since it gives the net of the production and the loss of a species for all reactions in which species appears either as re actant or a product species may be any gas phase mechanism species or any family consisting wholly of gas phase mechanism species 5 10 2 4 PROCAN execution variables The environment variables listed here are invoked during execution of the program and are set in the PROCAN run
13. TIONS required Comment String Description of the reac tions field optional PHOT_NM_1 String Single quote delimited name of photolysis re action 1 required Delimiter Char Comma delimiter sep arating reaction name from multiplier re quired ACLD_1 Real Multiplier for reaction 2 required 10 PHOT_NM_2 String Single quote delimited name of photolysis re action 2 required Delimiter Char Comma delimiter sep arating reaction name from multiplier re quired ACLD_2 Real Multiplier for reaction 2 required PHOT_NM_x String Single quote delimited name of photolysis re action x required Delimiter Char Comma delimiter sep arating reaction name from multiplier re quired ACLD_x Real Multiplier for reaction X required 125 6 1 15 JTABLE Photolysis Rates Lookup Table Line Column Name Type Description x 1 NHTO Int Vertical level cross reference to header data required NLATO Int Latitude cross refer ence to header data required NPHOTO Int Photolysis reaction cross reference to header data required x 2 XJVAL_1 Real or Exp Clear sky photolysis rate at NHTO NLATO NPHOTO and hour angle re quired XJVAL_2 Real or Exp Clear sky photolysis rate at NHTO NLATO NPHOTO and hour angle 2
14. The SMOKE program Smkinven reads in this raw data and outputs an I O API SMOKE intermediate inventory file 8 6 2 Spatial Allocation Grdmat Raw emissions inventory data is typically spatially distributed by county road segment or a single point The SMOKE program Grdmat creates a gridding matrix for area mobile and point sources This gridding matrix is then applied to the intermediate inventory file to transform the source based inventory emissions to gridded emissions 8 6 3 Chemical Speciation Spcmat CMAQ chemical mechanisms such as CB4 use a set of model species to represent atmospheric chemistry see Chapter 5 However the emissions inventory contains a wide variety of pollutants The SMOKE program Spcmat creates a speciation matrix to convert the emission pollutants to the model species for the chemical mechanism used in the CMAQ model 8 6 4 Temporal Allocation Temporal The raw inventory emissions are typically annual or seasonal values CMAQ requires hourly emissions files The SMOKE program Temporal creates a matrix to convert the annual or seasonal values to hourly values This is done through the use of temporal profiles These profiles can be easily changed by the user 148 8 6 5 Emissions Growth and Controls Grwinven and Cntlmat 8 6 5 Emissions Growth and Controls Grwinven and Cntimat Emissions growth processing creates emissions for year s in the future using an available dataset The SM
15. The default location of the BCON output files is the M3DATA bcon directory controlled by the OUTDIR variable in the run script The default naming convention for all BCON output files uses the APPL and GRID_NAME environ ment variables in the file name For boundary conditions created from existing CCTM CONC files the Julian date is also used in the file name through the DATE environment variable All of the file naming variables for BCON outputs are set in the run script 5 3 CCTM 5 3 1 Description The program CCTM is the CMAQ chemistry transport model the Eulerian air quality model component of CMAQ Typically run last in the sequence of the CMAQ programs CCTM uses input data produced by all of the other CMAQ programs and from an emissions model such as SMOKE CCTM produces multiple output files for each simulation The basic CCTM outputs include instantaneous and average hourly concentration files wet and dry deposition files and visibility estimates Other CCTM outputs can include diagnostic aerosol and cloud files hourly plume in grid files and processes analysis files CCTM contains several science configurations for simulating transport chemistry and deposition All of the science configuration options including the chemical mechanism in CCTM are set when compiling the executable The model grid and vertical layer structure for CCTM are set at execution The important distinction between selecting the science configuration and th
16. To compile the IO API set the BIN environment variable to Linux2_x86pg_gcc_mp before running the Unix make command 31 3 2 3 Notes on the CMAQ directory structure BIN Linux2_x86pg_gcc_mp After unpacking all of the CMAQ tar files in the M3HOME directory setting the appropriate environment variables and installing the IOAPI and netCDF libraries in the CMAQ M3LIB directory your system is ready to build the CMAQ executables Before proceeding check that CVS is available on your system by typing the following command If the message cvs Command not found is returned you must install CVS on your system before you can continue with the CMAQ installation 3 2 3 Notes on the CMAQ directory structure The CMAQ installation includes a tutorial dataset for benchmarking the model on your system Unpacking the different tar files of the distribution in the M3HOME directory installs the CMAQ source code scripts and tutorial data files in a directory structure recognized by the default run and build scripts The M3HOME directory is the base location of the CMAQ installation for a specific application Under M3HOME the scripts directory contains the build and run scripts the models directory contains the CVS archive of model source code the data directory contains the input and output data for the model and the lib directory contains the compiled binary library files required to build the CMAQ executables The CMAQ scripts use
17. Wyng 96 Chapter 6 CMAQ FILES Table of Contents 6 1 CMAQ Input Filesi eseni shee sstee ses a E aptes sea hia decane igs T EE a 97 6 2 Basic CMAQ Output Files csin oein ei hese oe a gs Seeds eee eens es Tobe eh Sosve cube setuate devas cugedebenye ce 131 6 3 Diagnostic and advanced CMAQ Output Files 2 0 00 cece ce eee ce cece neceneceeeeeeeeeeseeeeaeeeaeeeaeeae sean eegs 133 The current version of CMAQ utilizes 21 input files for all of the preprocessors and the CCTM combined The input files consist of a domain definition file for all programs two file options for both ICON and BCON one type of input file to MCIP five mandatory and one optional input to JPROC and for the CCTM an emissions initial and boundary conditions files six files which define the meteorological conditions to be simulated and a photolysis rates file For many of these CCTM input file types a separate data set is required for each grid mesh to be modeled CMAQ output files include a basic set of files with aerosol and gas phase species concentrations wet and dry deposition estimates and visibility metrics and an auxiliary set of output files for diagnosing model performance and plume in grid modeling 6 1 CMAQ Input Files This section describes each of the input files required by the different CMAQ programs The section begins with a description of the grid definition file which is used by several CMAQ programs and then goes through a program
18. additional surfaces RAWINS is also used to prepare the analyses for the analysis nudging in the forecast model see Section 4 6 6 RAWINS is described in Manning and Haagenson 1992 7 5 4 Setting the Initial and Boundary Conditions INTER PF The INTERPF program sets the initial and boundary conditions for the meteorology simulation The analysis from RAWINS is interpolated from its native vertical coordinate pressure to the forecast model s vertical coordinate a terrain following sigma coordinate In addition the state variables are converted as necessary e g relative humidity to specific humidity Also INTERPF interpolates the analysis fields for the MM5 staggered grid configuration discussed in Section 3 6 2 and interpolates the lateral boundary conditions to the sigma coordinate and staggered grid 7 6 Meteorology Model MM5 The following subsections provide a brief overview of the science and options that are available in MMS A description of the standard MM5 options is found in Grell et al 1995 The source code for MM5 is documented in Haagenson et al 1994 7 6 1 Brief History MMS is the fifth generation Penn State NCAR mesoscale model It has grown from the model used by Anthes in the early 1970s that was documented in Anthes and Warner 1978 The improvements in MM5 over the previous version MM4 include the option for non hydrostatic physics as well as more sophisticated explicit moisture boundary la
19. km and extinction coefficients deciviews 6 3 Diagnostic and advanced CMAQ Output Files Along with the basic outputs detailed in the previous section CMAQ can be configured to output several auxiliary files for diagnosing model performance and for plume in grid treatment of large point sources 6 3 1 AERODIAM Instantaneous hourly aerosol diameter file 6 3 2 WETDEP2 CCTM cloud diagnostics file 6 3 3 PING Plume in Grid unmerged plume data file 6 3 4 PINGDRYDEP Plume in Grid dry deposition file 6 3 5 PINGAERODIAM Plume in Grid hourly aerosol dia meter file 6 3 6 PA Process analysis output integrated process rate file 6 3 7 IRR Process analysis output integrated reaction rates 133 134 Chapter 7 Developing Meteorological Fields Table of Contents 7 1 Credits and Disclaimers For Use of MM soci 5Sccsscesssvosscapscdisespcuscesaseesasuss sesteed ive sevogassecesssvesensey sans 135 7 22 System REQUIEMENIS 23 S cyedesia es eose e ta Sethe lagceces EERE EEEE E ATEREA ENE KEE ESEE EE EREE 136 7 3 sSoltwate Languages ssir en i a voi Sada E pats E e e Pat dats E E E E E EEEIEE 136 TA Data Requirementt scsscon oeri e en bode Sa E geen S E R EE S S E EEE a pi 136 1 5 Meteorology Model Pre Processihg sess soisissa sersan peso a iio eis PES T TEPES pS ESEI AERE EEE SS ETES 138 7 6 Meteorology Model MM5 0 i oseni ees esie Een EEr EEEE Enere EE EEEE TEETE EESE 139 7 1 Meteorology Mod
20. 1998 is not drawn to scale The vertical grid in MMS is staggered and all of the prognostic meteorological variables except for vertical motion are calculated on half sigma surfaces Each half sigma is located in space approximately half the distance between two full sigma levels Figure 7 1 Example sigma vertical structure in MM5 ix 139 7 6 3 Prognostic Equations The horizontal grid in MM5 has an Arakawa B staggering of the velocity vectors with respect to the scalars Arakawa and Lamb 1977 The momentum variables u and v components of wind and the Coriolis force are on dot points while all other variables e g mass and moisture variables are on cross points The dot points form the regular lattice for the simulation domain while the cross points are offset by 0 5 grid point in both the x and y directions Refer to Figure 5 2 for a sample Arakawa B staggering Note that the interpolation of the variables to the staggered grid is done automatically within the INTERP program The smaller inner box is a representative mesh staggering for a 3 1 coarse grid distance to fine grid distance ratio Figure 7 2 Sample Arakawa B staggering x 7 6 3 Prognostic Equations MMS is based on primitive physical equations of momentum thermodynamics and conservation The state variables are temperature specific humidity grid relative wind components and pressure In the prognostic equations the state variables are
21. 2 2 CMAQ uses the MCIP processor to prepare the meteorological fields for the CCTM The ICON and BCON processors generate the initial and boundary conditions for a CCTM simulation JPROC computes the photolysis rates that will be used when simu lating photochemical reactions in the CCTM The PDM generates plume information for emissions sources that use a subgrid Plume In Grid PinG treatment to characterize their emissions Emissions for CMAQ must be prepared with a modeling system that generates emissions for direct input to the CCTM Brief descriptions of the different CMAQ input processors are presented in this section 2 2 1 MCIP Meteorology Chemistry Interface Processor The flow chart in Figure 2 3 illustrates the role of MCIP and its relationship to the CMAQ chemical transport model In addition to the files shown in this Figure GRIDDESC and GRID_CRO_3D provide necessary grid definition in formation for CMAQ execution 14 2 2 2 ICON and BCON The Initial and Boundary Condi tions Processors Figure 2 3 Meteorology preprocessing for CMAQ with MCIP GRID_DOT_2D Meteorology GRID_CRO_2D 3 CMAQ Chemical Transport Modeling a DOT _ M System MET_CRO_3D pial tal MET_BDY_3D Using output fields from the meteorology model MCIP performs the following functions Extracts meteorological model output for the CCTM horizontal grid domain Important considerations here that CCTM uses a smaller computatio
22. 2 2 Files configuration and environment variables Figure 5 2 BCON input and output files Mechanism Include Files Input T GC_SPC EXT p ype Set Mechanism AE _SPC EXT GC_ICBC EXT Mechanism ModMech etc Conversion Compile Options If Modinpt profile If ModMech user_defined MECH_CONV_FILE If Modinpt m3conc CTM_CONC_1 Shows Input Output S Horizontal grid definition GRIDDESC Vertical layer structure MET_CRO_3D Execution Options Figure 5 2 shows the input and output files for BCON A distinction is made between the inputs that are invoked at compilation versus those invoked at execution of the program When compiling BCON the user specifies a chemical mechanism to determine the gas phase chemistry and aerosol mechanism to calculate chemical boundary conditions for Setting the Mechanism variable in the BCON compile script configures the program to use a specific set of mechanism include files to build an executable Seperate BCON executables are hard wired to a specific mechanism configuration At execution the user provides a data file of chemical conditions that BCON will convert to boundary conditions on a predefined model grid Depending on how the user compiled the model through the specification of the ModInpt variable BCON will input either an ASCII vertical profile file BC_PROFILE or an existing CCTM concentration file CTM_CONC_1 If the input file is not in the same chemical speciation as the simulatio
23. 2 3 JPROC Clear Sky Photolysis Rate Calculator For CMAQ the photolysis rate model JPROC is used to generate clear sky photo dissociation reaction rates JPROC requires temperature profiles from the U S Standard Atmosphere NOAA 1976 a profile of the aerosol extinction coefficients Elterman et al 1969 and can optionally use ozone column totals from the NASA Total Ozone Mapping Spectrometer TOMS satellite to produce the photolysis rates for CCTM Figure 2 5 16 2 2 4 CHEMMECH Chemical Mechanism Compiler Figure 2 5 Clear sky photolysis rate preprocessing for CMAQ Directory of CSQY data CMAQ Chemical Transport Model CCTM Standard Profiles seasonal JPROC uses this information in a radiative transfer model to calculate the actinic flux photons cm min needed for calculating photolysis rates Currently JPROC calculates the actinic flux for clear sky conditions no clouds present and CCTM then attenuates for cloudiness when clouds are present JPROC computes the rate for each photolysis reaction at various latitudes altitudes and zenith angles Within CCTM the subroutine PHOT interpolates the data generated by JPROC to individual grid cells and adjusts for the presence of clouds 2 2 4 CHEMMECH Chemical Mechanism Compiler Gas phase chemical mechanisms are implemented in CMAQ using FORTRAN include files These files are in a machine readable ASCII format and include all of the mechan
24. 2 in 2nd sigma layer required 34 42 LAYER3_IC Exp IC concentration for species 2 in 3rd sigma layer required 45 53 LAYER4_IC Exp IC concentration for species 2 in 4th sigma layer required LAYERX_IC Exp IC concentration for species 2 in Xth sigma layer required Direction String North South East West indicates the hori zontal boundary de scribed by the sub sequent data section required Y 1 SPECIES Y String Pollutant name en closed in double quotes required 12 20 LAYER1_IC Exp IC concentration for species Y in lowest sigma layer required 23 31 LAYER2_IC Exp IC concentration for species Y in 2nd sigma layer required 34 42 LAYER3_IC Exp IC concentration for species Y in 3rd sigma layer required 45 53 LAYER4_IC Exp IC concentration for species Y in 4th sigma layer required LAYERX_IC Exp IC concentration for species Y in Xth sigma layer required A sample of the important sections of a BC_PROFILE file is shown below 107 6 1 4 MECH_CONV_FILE Mechanism Conversion File Optional boundary condition The vertical coordinate of the model to generate these b c is the terrain following sigma coordinate The number of sigma layers and defined sigma levels are listed below 6 55 1 00 0 98 0 93 0 84 0 60 0 30 0 00 1988180 00 North SO2 0 300E 03 0 2
25. 6 2 Files configuration and environment variables 5 6 2 Files configuration and environment variables Figure 5 5 JPROC input and output files Mechanism Include Files GC_SPC EXT Set Mechanism AE_SPC EXT GC_ICBC EXT Extraterrestrial irradiance etc Compile Options Atmospheric vertical profiles PROFILES Molecular cross section and quantum yields JVALUES Total ozone mapping spectrometer Molecular oxygen cross sections Shows Input Output Ozone cross sections F Execution Options Figure 5 shows the input and output files for JPROC Like the rest of the CMAQ programs there is a distinction between the options that are invoked at compilation versus those invoked at execution of the program When compiling JPROC the user specifies a chemical mechanism to determine the gas phase chemistry for which to calculate photo lysis rates Setting the Mechanism variable in the JPROC compile script configures the program to use a specific set of mechanism include files to build an executable JPROC executables are hard wired to a specific mechanism con figuration While JPROC does not require any configuration at execution there are several required and optional input files that the user must provide to the program For the selected photochemical mechanism the user must provide a set of mo lecular absorption cross section and quantum yield data files CSQY that are consistent with the photolysis reactions in
26. ANA E r E NESAS 154 9 3 Vertical LayerSa moe a e R E E e E E le E EE E N RS EERE 155 94 Chemicals Mechanism sosyssresossi deen n geese a a E NE e E EER E eE 156 95 Referentes n ieena a eriat rE N E E S E a R E N dente 158 List of Figures 2 1 CMAQ Modeling Framew rk sicss 0ssaccsdsadante seventies cance ges paved tants E E E R Ea ATGE 12 2 2 Chemical Transport Model CCTM and preprocessors e cece cece cece cece eece cece cece eeae eens eeneeeeeeeeeeeeees 14 2 3 Meteorology preprocessing for CMAQ with MCIP 00 0 cece eecc ence ence ence eeceeeceeeeaeeea seca seen sean sean eegs 15 2 4 Initial and boundary conditions preprocessing for CMAQ 0000 eee ceee cee cence eeea teen cece tenn eeu eeueeeneeeenees 16 2 5 Clear sky photolysis rate preprocessing for CMAQ 0 cece cece cc ence ence ence eeceeeceeeeeeesaeeeaeeeaeeea sean seus esas 17 2 6 Invoking new modified gas phase chemical mechanisms in CMAQ 0 cee ceee cece eee ce cece eeee cena eeneeeneeeenees 17 2 7 Plume in Grid treatment in the CMAQ modeling system 0 0 0 0 cece eee ce eecc ence ence ence eeceeeeeeeeaeeeaeeeaeeaneeaes 18 2 8 Process analysis implementation in the CMAQ modeling system cece cece cece eeceeeceeece teen seca tenn eeaes 19 2 9 CMAQ chemical transport model and associated preprocessors 0 ce eee ceeceeeceeeceeeceeeceeeea seen eens eeueeees 20 5 1 CMAQ core PlOosrams ss 63 2 sede cer E E e dates eae aeeeth
27. Max 7 31641E 02 c 1 1 3 8 1 Min 4 72329E 03 c r D 2 2 1 Mean 4 47600E 02 Sigma 8 93855E 03 Number of times 6 00000E 02 exceeded 18 fraction 0 48913043 Number of times 8 00000E 02 exceeded 0 fraction 0 00000000 Number of times 1 00000E 01 exceeded 0 fraction 0 00000000 Number of times 1 20000E 01 exceeded 0 fraction 0 00000000 File NC_195aa_cc3_g1 lyrlo3 Date and time 1995191 130000 13 00 00 July 10 1995 Variable O3 3 D grid statistics Max 7 29948E 02 c 1 1 3 8 1 Min 1 19016E 02 c r D 2 2 1 Mean 5 12920E 02 Sigma 8 86664E 03 Number of times 6 00000E 02 exceeded 54 fraction 1 46739140 Number of times 8 00000E 02 exceeded 0 fraction 0 00000000 4 6 5 M3TPROC Number of times 1 00000E 01 exceeded 0 fraction 0 00000000 Number of times 1 20000E 01 exceeded 0 fraction 0 00000000 4 6 5 M3TPROC The M3TPROC program computes time aggregation for selected variables from time stepped CMAQ files of types BOUNDARY CUSTOM or GRIDDED For each output time step and for each selected variable the program writes the selected aggregate value of that variable to the output file optionally renaming it in the process For example the program allows the user to construct a file of daily gridded 08 00 16 00 average ozone values derived from a standard MAQSIP output concentration file 4 6 6 M3TSHIFT The M3TSHIFT utility copies a CMAQ data file but allows user specified changes to the time and date stamps o
28. O2ABS Molecular oxygen absorption cross section data Table 6 11 Line Column Name Type Description 1 A Julian Day Int Julian start day of the file DDD preceded by 6 blank spaces re quired B Julian Year Int Start year of the file YYYY preceded by 9 blank spaces required 2 Header String 80 character line de scribing the contents of the file Gf omitted needs line placeholder 3 Header String 80 character line de scribing the contents of the file if omitted needs line placeholder 4 A TOMS Data Int TOMS ozone measure ments as a function of longitude and latitude line starts with a space then space de limited 25 values per line required 6 1 10 O2ABS Molecular oxygen absorption cross section data Used by JPROC O2ABS is the logical name for the ASCII data file containing absorption cross section and quantum yield data for O photolysis The data in these files are listed as a function of wavelength These files follow the same format as the CSQY files described above 6 1 11 OSABS Ozone absorption cross section data Used by JPROC O3ABS is the logical name for the ASCII data file containing absorption cross section and quantum yield data for O3 photolysis The data in this files are listed as a function of wavelength This files follows the same format as the CSQY files described above 6 1 12 Meteorological Data Input Files Used by MCIP MCIP re
29. PBL parameterization schemes are available in MM5 bulk formula Blackadar Burk Thompson MRF Hong Pan Eta Gayno Seaman and Pleim Xiu These parameterizations differ the most in the turbulent closure assumptions that are used The PBL parameterization schemes also differ greatly in CPU usage and median range forecast require ments 7 6 4 4 Surface Layer Processes The surface layer processes in MMS have been parameterized with fluxes of momentum sensible heat and latent heat following Zhang and Anthes 1982 The energy balance equation is used to predict the changes in ground temperature The 13 land use categories are used to seasonally define the physical properties at each grid point e g albedo available moisture emissivity roughness length and thermal inertia In addition a five layer soil temperature model is available but can only be used in conjunction with the Blackadar and MRF PBL schemes 7 6 4 5 Resolvable Scale Microphysics Schemes There are six resolvable scale explicit grid scale microphysics schemes available in MM5 removal of supersaturation the Hsie warm rain scheme the Dudhia simple ice scheme the Reisner mixed phase scheme the Reisner mixed phase scheme with graupel and the NASA Goddard microphysics with hail graupel These microphysics schemes have been designed with varying degrees of complexity for different applications of the model In addition there are new pro gnostic output variables that are ge
30. a function of Level 1 month latitude and vertical level units in molecules cm re quired B Air pressure profiles at Exp E10 3 Air pressure measure Season 1 Latitude 1 ments as a function of Level 2 month latitude and vertical level units in molecules cm re quired 393 A Air pressure profiles at Exp E10 3 Air pressure measure Season 1 Latitude 19 ments as a function of Level 1 season latitude and vertical level units in molecules cm re quired B Air pressure profiles at Exp E10 3 Air pressure measure Season 1 Latitude 19 ments as a function of Level 2 season latitude and vertical level units in molecules cm re quired 1596 A Air pressure profiles at Exp E10 3 Air pressure measure Season 4 Latitude 19 ments as a function of Level 51 season latitude and vertical level units in molecules cm re quired 1597 A Average Dobson Val Real Average Dobson value ues at Latitude 1 as a function of latit Month 1 ude and month re quired 1597 B Average Dobson Val Real Average Dobson value ues at Latitude 2 as a function of latit Month 1 ude and month re quired 1608 A Average Dobson Val Real Average Dobson value ues at Latitude 19 as a function of latit Month 12 ude and month re quired 117 6 1 9 TOMS Total ozone mapping spectrometer data Line Column Name Type Description 1609 A Air Temperature at Real Air temperature
31. an interface that allow a model developer to create complex modeling situations and scenarios or develop entirely new models using a standardized coding framework Model developers can also perform sensitivity analyses on newly developed modules and perform comparisons with existing systems Brief descriptions of the key features in CMAQ are discussed in this chapter More detailed discussions on these features can be found in Byun and Ching 1999 and Byun and Schere 2006 2 1 Features to Achieve the Goals of CMAQ The CMAQ modeling system has a flexible modeling structure Historically air quality model development resulted in separate air quality models that addressed specific issues For instance independent models were developed for ozone modeling and for acid deposition modeling These models had little or no flexibility to be updated with advances in science or to accommodate new regulations With this in mind CMAQ was designed to have more adaptability and flexibility for different applications and for changing or improving methodology The following subsections provide examples of how this is accomplished in CMAQ 2 1 1 Multiple scales and multiple pollutants CMAQ approaches air quality as a whole by including state of the science capabilities for modeling multiple air quality issues including tropospheric ozone fine particles toxins acid deposition and visibility degradation The de velopment of CMAQ includes the scientific expert
32. and can be very helpful Note that neither UCAR NCAR or Penn State is obligated to provide training to users of MM5 For more information on NCAR s MMS tutorial refer to the MM5 home page http www mmm ucar edu mm5 and click on the User Support section The CMAQ user community does not have the resources to fully support users on MM5 related questions NCAR which maintains the official public releases of MM5 offers limited support to the registered users via email Because there is no charge to become a registered user or for user support and there is no help desk per se please be patient when contacting NCAR directly for assistance Note that neither UCAR NCAR or Penn State is obligated to provide any support consulting or assistance to users of MM5 There is also an extensive user community for MM5 that may offer informal help on specific questions via an email distribution list which is described on the MM5 home page 7 10 Using MM5 with CMAQ Output files from MM5 are processed by MCIP to create the I O API files used in the CCTM MCIP can also be used to reduce the number of vertical layers This is sometimes necessary as additional vertical layers greatly increase the required computer resources The coarse MMS grid is considered to be the parent grid for any nested MM5 domain Any MCIP domain uses the MM5 domain that is at the same horizontal resolution as a parent The MCIP output grid has two fewer grid cells
33. by program listing of the CMAQ input file requirements Table 4 1 lists the source file type and temporal and spatial dimensions of each CMAQ input file Sample disk space requirements for desired input data set can be easily calculated from the information in Table 4 1 each data record is four bytes Thus if you know the number of variables ina CMAQ file and the spatial and temporal coverage of the data the file sizes can be calculated 97 6 1 1 GRIDDESC Horizontal Domain Definition Table 6 1 CMAQ Input File Information File Name File Type Time Dependence Spatial Dimensions Source General GRIDDESC ASCII n a n a user MCIP ICON ic_profile ASCII Annual n a user m3conc GRDDED3 Hourly X Y Z CCTM BCON bc_profile ASCII Annual n a user m3conc GRDDED3 Hourly X Y Z CCTM JPROC Extraterrestrial Irradi ASCII Annual n a user ance Default Atmospheric ASCII Annual n a user Profiles O Absorption ASCII Annual n a user O Absorption ASCII Annual n a user TOMS ASCII varies n a user CSQY ASCII Annual n a user MCIP MMOUT Binary Hourly n a MM5 CCTM Initial Conditions GRDDED3 Time invariant X Y Z ICON CCTM Boundary Conditions BNDARY3 Hourly PERIM Z BCON JTABLE ASCII Daily n a JPROC Emissions GRDDED3 Hourly X Y Z SMOKE 2D Grid Cross GRDDED3 Time invariant xX Y MCIP 2D Grid Dot GRDDED3 Time invariant X4 1 Y 1 M
34. characteristics of the three dimensional computational grid structure that represent this domain must be specified The domain is also sometimes referred to as the grid or grid domain The domain is divided into individual three dimensional grid cells A horizontal grid specification sets the x and y dimensions of each grid cell for the entire domain All grid cells in a specified domain will have the same horizontal resolution The vertical resolution of each grid cell depends on the vertical layer specification and the selected coordinate system Therefore the physical vertical extent of individual grid cells may vary over space and time This chapter describes how to define new horizontal grids vertical layers and chemical mechanisms in CMAQ These specifications apply to multiple programs in the CMAQ model including ICON BCON JPROC and CCTM When configuring new simulations users must define the location extent and structure of the horizontal and vertical grids and the chemical mechanism for representing pollutant chemical transformations CMAQ contains several default options for these parameters that can be used as templates for setting up new configurations Before deciding to create new definitions for these see if the existing options are sufficient for your model simulation If a predefined choice is not appropriate then follow the steps described in this section to create a new definition Once this information has been established for t
35. configuration similar to the dynamic horizontal grid which is specified at exe cution rather than at compilation The dynamic vertical layers forgo the need to recompile CMAQ each time the user changes the vertical layer configuration between simulations 9 3 1 Using predefined vertical layers Wait until new release to see how they re going to do this 9 3 2 Creating or modifying vertical layers Wait until new release to see how they re going to do this 9 3 3 Tips and recommendations Vertical Layers e CMAQ redefines the vertical coordinates to monotonically increase with height a capability necessary to handle a generalized coordinate system e MCIP may be used to reduce the number of vertical layers by collapsing layers no interpolation capability is provided e Defining the vertical layering structure for CMAQ applications is complicated and model results are sensitive to the number and definition e A six layer vertical grid definition such as the one provided with the tutorial is not recommended for regulatory purposes because this resolution is very coarse e Increasing the number of vertical layers increases the CPU time and the computational complexity e Computational limits arise from the Courant number limitation of vertical advection and diffusion processes When using K theory a very shallow layer definition increases CPU time tremendously under the convective conditions 9 4 Chemical Mechanism The CMAQ
36. configuration in CMAQ set the Mechanism variable in the build scripts to the name of one of the mechanism directories located under M3MODEL include release Table 7 1 lists the available chemical mechanisms in CMAQ version 4 5 and what is included with the each mechanism Set the Mechanism variable in the CMAQ build script to the Mechanism ID in Table 7 1 to select a particular mechanism Table 9 1 Chemical Mechanisms Mechanism ID Gas phase Mechanism 4 generation Aqueous Chem cb4 radm2 saprc99 CMAQ aerosols istry cb4 X cb4_ae4 x x cb4_ae4_aq x x x cb4_aq x x radm2 xX radm2_ae4 x x radm2_ae4_aq x x x radm2_aq x x radm 2_cisl x radm2_cisl_ae4 x x radm2_cis1_ae4_aq x x x radm2_cis1l_aq x x radm 2_cis4 x2 radm2_cis4_ae4 x2 x radm2_cis4_ae4_aq x2 x x radm2_cis4_aq x2 x saprc99 xX saprc99_ae4 x x saprc99_ae4_aq x x x saprc99_aq xX X 1RADM 2 with Carter one product isoprene oxidation mechanism 2RADM 2 with Carter four product isoprene oxidation mechanism If you are unfamiliar with these mechanisms refer to the detailed descriptions found in Byun and Ching 1999 9 4 2 Creating or modifying chemical mechanisms Creating or modifying mechanisms in CMAQ requires the use of the CMAQ chemical mechanism compiler Chemmech to produce the required Fortran include files Chemmech translates an ASCII mechanism listing to the include files required by CMAQ Like all of the CMAQ processor Chemmech is a Fortran pro
37. data are essential to the CMAQ model The Sparse Matrix Operator Kernel Emissions SMOKE modeling system is recommended for the creation of the emissions input into CMAQ The SMOKE model is public domain software and is being widely used in research and operational modeling applications SMOKE is continually being updated and enhanced An overview of the SMOKE modeling system is given below 8 1 Credits and Disclaimers for Use of SMOKE some text here 8 2 Obtaining SMOKE Source Code The SMOKE source code can be downloaded from the CMAS Model Clearinghouse http www cmascen ter org html models html You will need to register before you download The files needed are the default data file the installation script and the source code There are also some precompiled executables for common systems 8 3 System Requirements SMOKE can run on many hardware platforms including SGI Sun Hewlett Packard IBM and personal computers running Linux SMOKE requires a good deal of memory and will require large amounts of disk space this depends on the domain size 8 4 Software Languages SMOKE is written in Fortran 90 All of the code is compiled using the make utility The run scripts are written in C shell to accommodate the wide range of hardware platforms A Fortran 90 compiler is required to compile and run SMOKE 8 5 Data Requirements Several datasets are required to run SMOKE SMOKE requires emissions inventories and ancillary da
38. date time time step length For inputs on emissions CMAQ uses an emissions model to estimate the magnitude location and temporal variability of pollution sources Open source models such as the Sparse Matrix Operator Kernel Emissions SMOKE model CEP 2006 and the Consolidated Community Emissions Processing Tool CONCEPT http www conceptmodel org are available for computing emissions inputs to CMAQ from annual county level emissions inventories CMAQ emissions inputs must be on the same horizontal and vertical spatial scales and cover the same time period used in the air quality model simulation The emissions inputs to CMAQ must also represent volatile organic compound VOC emissions using a chemical parameterization supported by CMAQ currently supported photochemical mechanisms are the Carbon Bond IV CB IV mechanism Gery et al 1989 Dodge 1989 Carter 1996 the 2005 update to the Carbon Bond mechanism CB05 Yarwood et al 2005 and the Statewide Air Pollution Research Center SAPRC 99 mechanism Carter 1990 2000 Additional details about the gas phase chemistry in CMAQ are provided in Chapter 2 below and in Byun and Ching 1999 Those two sources also describe the primary aerosol emissions species that are supported by CMAQ It is possible to add new emissions species to CMAQ that are not supported in the dis tributed version of the software using the chemical mechanism compiler CHEMMECH that is part of the CMAQ utility
39. edu content software netcdf index html Walcek C J and Taylor G R 1986 A Theoretical Method for Computing Vertical Distributions of Acidity and Sulfate Production within Cumulus Clouds J Atmos Sci 43 339 355 Wesely M L 1989 Parameterization of surface resistances to gaseous dry deposition in regional scale numerical models Atmos Environ 23 1293 1304 Yarwood G S Rao M Yocke and G Whitten 2005 Updates to the Carbon Bond chemical mechanism CBO5 Final Report to the U S EPA RT 0400675 Available online at www camx com Zhang K M E M Knipping A S Wexler P V Bhave and G S Tonnesen 2005 Size distribution of sea salt emissions as a function of relative humidity Atmos Environ 39 3373 3379 26 Chapter 3 CMAQ System Requirements and Installation Table of Contents 321 System Recommendations an eser ei eeose EPEE POEP EESE sede sores cgsaedea ssa rnevaseabesssass sovsecdaacdensss 27 3 2 Installing CMAQ Source Code sisisi cece cece cece EEEE ES EEEE ERES ESEE seen eeae eens EE EIEEE E EE EES 30 3 3 Compiling CMAQ for the Tutorial Simulation 2 0 0 0 cee eee cece ca ee ce eeae cena eens eeneeneeeeeeeeeseeeeeeseaees 32 3 4 Running the CMAQ Tutorial Simulation 0 0 eee cece cc ee ce eeceeeeeeeea seca eeeaeeaaeeae eens eeneeeneeteeeeeeea 34 3 5 Benchmarking CMAQ cscs estes otsn cs cesaualsssetaagsend cuss ssoens Ss cgidadssecese ees ESEE EPEA a EO E ESPE ESEESE ESE r
40. executable set the compiler compiler flags and netCDF and I O API library paths in the Makefile distributed with MCIP Use the following commands to compile MCIP cd M3HOME scripts mcip BLD make CCTM has multiple configuration options that can be changed to optimize model performance for different ap plications In addition to selecting the chemical mechanism to model the user can also select from several different science modules The science configuration options for CCTM are discussed in detail in Chapters 2 and 6 The CCTM build script is configured by default to run in multiprocessor mode for the benchmark simulation CMAQ uses the MPICH message passing interface MPI to manage communication between processors in a clustered multiprocessor computing environment Before compiling the CCTM for parallel execution the user must specify the location of the MPICH directory on your system on line 156 of the CCTM build script For single processor systems or first time users of the model configure the build script to create a single processor executable by commenting out the line that activates the variable ParOpt on line 52 of the build script Use the following commands to compile CCTM cd M3HOME scripts cctm bldit cctm pgf Although they are not used for the benchmark simulation PDM and PROCAN can also be compiled using M3BLD 33 3 4 Running the CMAQ Tutorial Simulation 3 4 Running the CMAQ Tutorial Simulation
41. format required n 3 A Wavelength Int or Real Wavelength corres ponding to CSQY data units in nm required B Absorption Cross Sec Real or Exp tion Measurement of the cross section of a mo lecules spherical receiv ing surface for actinic flux units in cm2 mo lecule 1 required C Quantum Yield Real Ratio of the number of molecules reacting via a specific pathway to the number of mo lecules absorbing photons in that wavelength interval units in molecules photon 1 required n 4 A Wavelength Int Wavelength corres ponding to CSQY data units in nm required 112 ET Extraterrestrial irradiance Line Name Type Description Absorption Cross Sec tion Real or Exp Measurement of the cross section of a mo lecules spherical receiv ing surface for actinic flux units in cm2 mo lecule 1 required Quantum Yield Real Ratio of the number of molecules reacting via a specific pathway to the number of mo lecules absorbing photons in that wavelength interval units in molecules photon 1 required n X A sample of the important sections of a CSQY file is shown in Table 4 8 Table 6 8 Example CSQY data file 1 ALD_CBIV88 2 Acetaldehyde Photolysis ALD 3 CH3CHO hv 202 CH300 HO2 CO 4 Taken from Gery et al 1988 CSQY from Baulch et al 5 1984 6 format wl abs_cs qy 7 Cent
42. http www bar data in the IO API netCDF format onams com products ioapi netCDF Tools Postprocessing tools for manipulating http my unidata ucar edu content soft data in the netCDF format ware netcdf index html Source code diagnostics PGDBG Portland Group FORTRAN 90 debug http www pgroup com ger PGPROF Portland Group FORTRAN 90 code __ http www pgroup com profiler 3 2 Installing CMAQ Source Code After installing CVS the IOAPI and netCDF libraries and Fortran and C compilers on the hardware system download the CMAQ source code scripts and benchmark data files from the CMAS Center website http www cmascenter org After registering to download CMAQ on the CMAS Center Software Clearinghouse users are redirected to a page that contains links to download UNIX tar files of the CMAQ code scripts and benchmark data along with various documents describing the installation and execution processes The following files and archives comprise the CMAQ distribution e README text file describing the CMAQ installation e CHEM_SOLVER_NOTES text file containing comments on chemical solvers available in CMAQ and their rel ative computational performance and numerical accuracy e CVS_NETCDF text file explaining the CVS configuration management system and the netCDF data system and how to set them up e IOAPI text file explaining how to get the I O API system and set up the libraries e SMOKE text file describing th
43. in each direction than the MM5 domain In addition it is recommended that a number of boundary grid cells be eliminated for the domain used by the CCTM The user may eliminate three or six grid cells on each edge This must be decided when the grids are defined Grids must be defined for MM5 and MCIP to ensure that the CCTM domain is large enough to include the area of interest Defining grids is covered in Chapter 5 You must first identify the desired CCTM domain and resolution and work backwards to establish the MCIPand MM5 domains and resolutions 7 11 References Anthes R A 1977 A cumulus parameterization scheme utilizing a one dimensional cloud model Mon Wea Rev 106 270 286 Anthes R A and T T Warner 1978 Development of hydrodynamic models suitable for air pollution and other mesometeorological studies Mon Wea Rev 106 1045 1078 Arakawa A and V R Lamb 1977 Computational design of the basic dynamical process of the UCLA general circulation model Methods in Computational Physics 17 173 265 Benjamin S G and N L Seaman 1985 A simple scheme for objective analysis in curved flow Mon Wea Rev 113 1184 1198 Blackadar A K 1979 High resolution models of the planetary boundary layer Advances in Environmental Science and Engineering 1 No 1 Pfafflin and Ziegler Eds Gordon and Briech Sci Publ New York 50 85 Dudhia J 1993 A nonhydrostatic version of the Penn State NCAR mesoscale mo
44. input to BCON Also optionally looks for the variable MECH_CONV_FILE to point to a user defined mechanism conversion file e m3conc used for nested simulations sets the output file name to include a start date in the name uses the variable CTM_CONC_1 to point to a CCTM CONC file for input to BCON Also looks for optional Plume in Grid inputs if the BCON_PING variable is set to YES DATE Sets the Julian date to use for tagging the BCON output file for nested runs BCON_PING Flag controlling the creation of boundary conditions for a plume in grid simulation e YES Use plume in grid input files e NO Do not use plume in grid input files SDATE Julian start date for extracting boundary conditions from a CCTM CONC file for a nested simulation If SDATE is not set it will be set automatically from the CTM_CONC_1 file STIME Start time for extracting boundary conditions from a CCTM CONC file for a nested simulation If STIME is not set it will be set automatically from the CTM_CONC_1 file RUNLEN Number of hours of boundary conditions to extract from a CCTM CONC file for a nested simulation If RUNLEN is not set it will be set automatically from the CTM_CONC_ file 54 5 3 CCTM 5 2 2 5 BCON output files Table 5 2 BCON output files File Name Format Description BNDY_CONC_1 BNDARY3 Name and location of the gridded boundary conditions data output on the model grid defined by GRID_NAME
45. levels contained in the file required NUM_POLL Int Number of pollutants contained in the file required SIGMA_LVL Real Vertical coordinate values of sigma p levels number of val ues n matches NUM_SIGMA_LVL required STDATE String Julian start date of the file YY YYDDD op tional STTIME String Start time of the file HH optional Direction String North South East West indicates the boundary described by the subsequent data section required SPECIES 1 String Pollutant name en closed in double quotes required 12 20 LAYER1_IC Exp IC concentration for species in lowest sigma layer required 23 31 LAYER2_IC Exp IC concentration for species in 2nd sigma layer required 34 42 LAYER3_IC IC concentration for species 1 in 3rd sigma layer required 45 53 LAYER4_IC IC concentration for species in 4th sigma layer required LAYERX_IC Exp IC concentration for species in Xth sigma layer required 106 6 1 3 BC_PROFILE Boundary conditions vertical profiles Line Column Name Type Description 1 10 SPECIES2 String Pollutant name en closed in double quotes required 12 20 LAYER1_IC Exp IC concentration for species 2 in lowest sigma layer required 23 31 LAYER2_IC Exp IC concentration for species
46. mass weighted with a modified surface pressure MM5 can be run as either a hydrostatic or non hydro static model In the hydrostatic model the state variables are explicitly forecast In the non hydrostatic model Dudhia 1993 pressure temperature and density are defined in terms of a reference state and perturbations from the reference state The vertical sigma coordinate is defined as a function of pressure 7 6 3 1 Time Differencing The hydrostatic and non hydrostatic versions of MM5 use different time differencing schemes to filter the fast waves from the prognostic solutions in the model In the non hydrostatic model a semi implicit scheme based on Klemp and Wilhelmson 1978 is used to filter the acoustic waves from the model solution In the hydrostatic model a split explicit scheme based on Madala 1981 is used to filter gravity waves from the model solution The time differencing in MM5 is extensively discussed in Grell et al 1995 7 6 3 2 Lateral Boundary Conditions There are five options for lateral boundary conditions in MM5 fixed relaxation time dependent time dependent and inflow outflow dependent and sponge The lateral boundaries in MM5 consist of the outer five grid points on the ho rizontal perimeter of the simulation domain The outer four grid points are used for boundary conditions for cross point variables The lateral boundary conditions for the coarse domain are derived from the meteorological backgro
47. measurements at Season 1 Latitude as a function of season 1 Level 2 latitude and vertical level units in mo lecules cm required 127 A Ozone concentration Exp E10 3 Ozone measurements at Season 1 Latitude as a function of season 19 Level 1 latitude and vertical level units in mo lecules cm required B Ozone concentration Exp E10 3 Ozone measurements at Season 1 Latitude as a function of season 19 Level 2 latitude and vertical level units in mo lecules cm required 134 A Temperature profiles Exp E10 3 Temperature measure at Season 1 Latitude ments as a function of 1 Level 1 season latitude and vertical level units in K required B Temperature profiles Exp E10 3 Temperature measure at Season 1 Latitude ments as a function of 1 Level 2 season latitude and vertical level units in K required 260 A Temperature profiles Exp E10 3 Temperature measure at Season 1 Latitude ments as a function of 19 Level 1 season latitude and vertical level units in K required B Temperature profiles Exp E10 3 Temperature measure at Season 1 Latitude 19 Level 2 ments as a function of season latitude and vertical level units in K required 116 6 1 8 PROFILES Atmospheric vertical profiles Line Column Name Type Description 267 A Air pressure profiles at Exp E10 3 Air pressure measure Season 1 Latitude 1 ments as
48. modeling system accounts for chemistry in three phases gas phase aerosols solid or liquid and aqueous phase The CMAQ modeling system s existing modules for gas phase chemistry are the Carbon Bond IV CB IV Regional Acid Deposition Model 2 RADM2 and Statewide Air Pollution Research Center 99 SAPRC 99 gas phase mechanisms Several variations of the base gas phase mechanisms with and without aqueous and aerosol chemistry are distributed with CMAQ With the CMAQ s modularity it is also possible to create or modify the chemical mech anism Gas phase chemical mechanisms are defined in CMAQ as a series of Fortran include files Located in subdirectories of the M3MODEL include release directory corresponding to the mechanism name these include files define the species source reaction parameters and atmospheric processes e g diffusion deposition advection of the different mechanism species CMAQ mechanism configuration is more similar to the science module configuration than to the horizontal grid or vertical layer configuration in that the mechanism is defined a compilation and results in executables that are hard wired to a specific gas phase mechanism If you want to change chemical mechanisms between simulations you must recompile a new executable that includes the desired mechanism configuration 156 9 4 1 Using predefined chemical mechanisms 9 4 1 Using predefined chemical mechanisms To select a predefined mechanism
49. represents Beginning Centered or Ending Comment lines are preceded with a The last section of the header is a multiplier FAC that is applied to the photolysis rate calculation The data section of the CSQY file lists the wavelength of the incoming solar radiation nm the absorption cross section cm and the quantum yield as columns with each row corresponding to a specific 110 6 1 6 CSQY Absorption cross section and quantum yields wavelength interval The CSQY file uses a space delimited free form format for the data section of the file A detailed description of the CSQY file format is provided in Table 4 7 111 6 1 6 CSQY Absorption cross section and quantum yields Table 6 7 CSQY format description Line Column Name Type Description 1 A Reaction ID String Text name identifying the data this name is cross referenced in the chemical mechanism description and include files required 2 A Comments String Preceded by com ment lines describe the reaction list the stoi chiomtery and docu ment the source of the data optional n l A Data Location String Field indicating the location of the data as measured across the wavelength band pos sible answers begin ning ending centered point required n 2 A Multiplier String Multiplication factor to apply to photolysis rate equation line begins with FAC factor lis ted in real or exponen tial
50. scale grid size simulations 36 km and 12 km and it is not invoked for the smaller scale 4 km simulations At fine resolutions the emissions are released directly into the grid cells and subgrid level plume resolution is not needed It is assumed that instantaneous mixing occurs at this fine resolution 2 3 7 Process Analysis CCTM also includes a process analysis pa module Process analysis is a technique for quantifying the contributions of various physical and chemical processes and the changes in the predicted concentrations of a pollutant Process analysis is useful in the quality control of a model because it separates out the influence of individual processes on the pollutant concentration With this information compensating or unresolvable errors in the model or input data can be identified even if they are not reflected in the total change in concentration For example if an error in the emission input data caused negative concentration values it may not be recognized in the predicted concentration because of a large addition in the predicted concentration resulting from chemical processes In addition to its role in the quality control of air quality modeling process analysis is a very strong analysis tool As a tool for model development process analysis can help evaluate the effect of modifications on a model or process module As a tool for regulatory decision making process analysis can help determine if a decision to control a
51. script e EXEC default PACP_ CFG Executable to use for the simulation e PACP_INFILE default M3DATA procan pacp inp PROCAN control file for setting process analysis configuration 5 11 STENEX 5 11 1 Description The Stencil Exchange STENEX library contains modules for controlling the communication between processors in parallel multi processor computing environments A noop version of the library is required for single processor versions of the CCTM and ICON the parallel version is required when compiling for parallel multi processor versions of the CCTM 5 11 2 Files configuration and environment variables 5 11 2 1 STENEX input files STENEX does not require any input files 5 11 2 2 STENEX compilation options Other than configuring the build script for your system i e compiler and library locations STENEX does not require any configuration at compilation 5 11 2 3 STENEX compilation Section 3 3 provides an overview of how to install and compile the CMAQ programs for the tutorial simulation Follow the steps outlined in Section 3 3 to compile STENEX 1 Ifyou have not already done so build the CMAQ source code and compilation management program M3BLD this only needs to be done the first time you install CMAQ 2 Install and compile the I O API and MPICH libraries if these are already available from a previous CMAQ compilation configure the STENEX build script to use the available libraries 3 Invoke
52. sean sean esas 35 4 2 IO API Data Structure and Data File Types 0 cece cece cece c cece cece cene cen ceeeeeeeeeeeeeeesaeseaeeeaeeaa sean eeaes 36 4 3 Opening Creating Data Files in IO APL srera easscesensies gas see ta cs aoe tages ont a ses ven aa i s TTIE 38 4 4 Reading Data Files in TO APL e risiini rero jesse bebe coven cteed geen SE EE VEE EEE E EEEE 40 4 5 Writing Data Files an O API sirai ossei votes ds eacee sus votss Seeds dugess steels us sSaedeavccss Sbasdseegasesbendaseasacsas votes dseass 40 4 6 CMAQ Related I O API Utilities coisinnte eneee iee ere aE n ETE EEEE EEE EEEE EEEE E EnS 41 ATs RELCLENCES iera ea e E A E E aa e e E T e 46 The Models 3 Input Output Applications Programming Interface I O API is an environmental software development library which provides an easy to learn easy to use interface with the data involved in CMAQ applications Coats 2005 The files are self describing Network Common Data Form NetCDF format files in which the file headers have all the dimensioning and descriptive information needed to define the resident data According to Unidata 2005 NetCDF is an interface for array oriented data access and a freely distributed collection of software libraries for several languages that provide implementations of the interface The CMAQ data files all have selective direct access which means the modeling system can be more efficient by only reading the necessary parts of the data files Addition
53. section of the file is fixed format 102 6 1 2 IC_PROFILE Initial conditions vertical profiles Table 6 4 IC_PROFILE format description Line Column Name Type Description 1 3 Text Header String Text description of the contents and source of the initial conditions file optional NUM_SIGMA_LVL Int Number of sigma levels contained in the file required NUM_POLL Int Number of pollutants contained in the file required SIGMA_LVL Real Vertical coordinate values of sigma p levels number of val ues n matches NUM_SIGMA_LVL required STDATE String Julian start date of the file YYYYDDD op tional STTIME String Start time of the file HH optional SPECIES 1 String Pollutant name en closed in double quotes required 12 20 LAYER1_IC Exp IC concentration for species in lowest sigma layer required 23 31 LAYER2_IC Exp IC concentration for species in 2nd sigma layer required 34 42 LAYER3_IC Exp IC concentration for species 1 in 3rd sigma layer required 45 53 LAYER4_IC Exp IC concentration for species in 4th sigma layer required LAYERX_IC Exp IC concentration for species in Xth sigma layer required SPECIES2 String Pollutant name en closed in double quotes required 103 6 1 2 IC_PROFILE Initial
54. shows requested commands as they are executed MakeOpt Uncomment to build a Makefile to compile the executable 5 9 2 3 PDM compilation Section 3 3 provides an overview of how to install and compile the CMAQ programs for the tutorial simulation While the tutorial does not contain an exercise on using the PDM the steps required to compile the PDM are virtually the same as those required to compile the other CMAQ programs such as BCON Follow these steps to compile the PDM 1 If you have not already done so build the CMAQ source code and compilation management program M3BLD this only needs to be done the first time you install CMAQ Install and compile the I O API and MPICH libraries if these are already available from a previous CMAQ compilation configure the PDM build script to use the available libraries Configure the PDM build script for your system by setting the correction name and location of the Fortran compiler Invoke the build script to create an executable bldit pdm pgf 5 9 2 4 PDM execution options EXEC default PDM_ CFG Executable to use for the simulation LOGFILE default BASE APPL log Uncomment to capture CCTM standard output to a log file the LOGFILE variable sets the name and location of the log STDATE format YYYYDDD Beginning date of the PDM simulation STTIME format HHMMSS Beginning time of the PDM simulation NSTEPS format HH Duration of the PDM simulation IOLDFIL de
55. the grid and coordinate descriptions and a set of descriptions for the file variables i e names unit specifications and text descriptions According to the I O API format files and variables are referred to by names layers by number from one to the greatest number of layers in the file and dates and times are stored as integers using the coding formats YY YYDAY commonly called JDATE and HHMMSS commonly called JTMIE as defined in equations 4 1a and 4 1b YYYYDAY 1000 Year Julian Day 4 1a HHMMSS 10000 Hour 100 Minute Seconds 4 1b 35 4 2 IO API Data Structure and Data File Types Rather than forcing the programmer and program user to deal with hard coded file names or hard coded unit numbers the I O API utilizes the concept of logical file names The modelers can define the logical names as properties of a program and then at run time the logical names can be linked to the actual file name using environment variables For programming purposes the only limitations are that file names cannot contain blank spaces and must be at most 16 characters long When a modeler runs a program that uses the I O API environment variables must be used to set the values for the program s logical names This will be discussed further in terms of CMAQ applications in Chapter 5 The remainder of this section will discuss some of the rudimentary details of programming in an environment using TO API data files 4 2
56. the mechanism CMAQ is distributed with a full set of CSQY files for the CB IV and SAPRC 99 mechanism versions supported by the model If new mechanisms are added to CMAQ the user must produce the appropriate CSQY data files for the added mechanism The user also has the option of using the default atmospheric profiles contained in the PROFILES input file or using total ozone mapping spectrometer data TOMS to replace the climatologically derived ozone column data in the PROFILES file 75 5 6 2 Files configuration and environment variables 5 6 2 1 JPROC input files Table 5 9 JPROC input files File Name Format Description ET ASCII Extraterrestrial radiation as a function of wavelength PROFILES ASCII Seasonal vertical profiles of ozone concentrations aerosol attenuation temperature air pressure and Dobson values TOMS ASCII Total ozone column measurements from the Total Ozone Mapping Spec trometer instrument aboard the sun synchronous polar orbiting Nimbus satellite O2ABS ASCII Absorption cross section and quantum yield data for molecular oxygen as a function of wavelength O3ABS ASCII Absorption cross section and quantum yield data for ozone as a function of wavelength CSQY directory path Directory path containing absorption cross section and quantum yield data for gas phase photolysis reactions as a function of wavelength 5 6 2 2 JPROC compilation options The configuration
57. the single processor build script to create serial executables 95 5 12 References bldit se_noop pgf 4 Invoke the multi processor build script to create parallel executables bldit se pgf 5 11 2 4 STENEX execution options As PARIO is not a program it does not require any configuration at execution 5 11 2 5 STENEX output files Successful compilation of STENEX will produce the library files libsef90_noop a for serial compilations and libse_snl a along with several module files in the M3LIB stenex OS directory 5 12 References Arya P 1984 Parametric relations for the atmospheric boundary layer Boundary Layer Meteorology 30 57 73 Hanna S R G A Briggs and R P Hosker 1982 Handbook on atmospheric diffusion U S DOE DOE TIC 11223 DE8 amp 2002045 Nationa Hicks BB 1985 Behavior of turbulence statistics in the convective boundary layer J of Climate and Applied Meteorology 24 607 614 Irwin J S 1979 Scheme for estimating dispersion parameters as a function of release height EPA 600 4 79 062 Research Triangle Park Niewstadt F T M 1984 Some aspects of the turbulent stable boundary layer Boundary Layer Meteorology 30 31 55 Venkatram A 1988 Dispersion in the stable boundary layer Chapter 5 in Lectures on Air Pollution Modeling A Venkatram and J Wyngc Weil J C 1988 Dispersion in the convective boundary layer Chapter 4 in Lectures on Air Pollution Modeling A Venkatram and J
58. training is offered quarterly by CMAS http www cmascenter org html training html User support is also provided by CMAS through the use of the emregional mailing list and the Bugzilla bug reporting system 8 9 References Carolina Environmental Program 2005 SMOKE v2 1 User s Manual http www cep unc edu empd products smoke Vversion 2 1 151 152 Chapter 9 Defining Grids Layers Domains and Chemistry Table of Contents 9 1 Supported CMAQ Coordinate Systems lt riasso nire aree Sa ENIS E Ep TESESSP S SEES sonssensenponseseeesnees 153 9 2 Horizontal Eg a KETE E EEEE AEA E E ASE ESEA A AE bs EEEE 154 9 3 Vertical Layers rei eerie i ena e E AE E a Bate ye TEA E EE E T A ESS 155 94 Chemica Mechanism oriire doesn otc r E lege E O EEE a E A ERE G FeS 156 OLS AIRETETEMCES EE E A T EAA E AE a cles R EE E E A E E E E T 158 The CCTM is a three dimensional Eulerian air quality model With an Eulerian perspective models simulate the chemistry transport and other processes that affect pollutant concentrations within a specific geographical location In this way air parcels are transported into and out of the modeled location In contrast to this Lagrangian models such as the Industrial Source Complex ISC dispersion model follow the path of individual air parcels as they are transported to different geographical locations With an Eulerian model structure the extent of the area of interest or domain and the
59. vertical levels in the model ing domain Thus for example the value for nl must be greater than or equal to one and less than or equal to the number of columns in the domain If any one domain spe cifier is omitted the corresponding end of the modeling domain is used as a default If the command is omitted entirely output is generated for the entire domain DEFINE FAMILY familyname c species c species The DEFINE FAMILY command is used to define a group of species as members of a family The user specified familyname must be unique and can be referenced in subsequent commands The ci are numerical coefficients that default to one if not specified speciesi represents the model species names ENDPA The ENDPA command signifies the end of the command input in the PACP command file Table 5 17 Integrated Process Rate Output Command Command IPR_OUTPUT specieslfamilynamelALL pcode pcode Description The IPR_OUTPUT command defines specific IPR outputs to be generated during a CMAQ CTM simulation A model species name family name or the keyword ALL must follow the IRR_OUTPUT keyword The keyword ALL refers to all model species IPRs are generated for the selected species or family and they are controlled by the specified values of pcodei where pcodei corresponds to one of the process codes listed below If no process codes are specified IPRs will b
60. 00E 03 0 100E 03 0 100E 03 0 200E 04 0 100E 04 West SO2 0 300E 03 0 200E 03 0 100E 03 0 100E 03 0 200E 04 0 100E 04 6 1 4 MECH_CONV_FILE Mechanism Conversion File Used by ICON BCON MECH_CONV_FILE is the logical name of the ASCII input file that contains photochemical mechanism conversion rules This file contains expressions that are used to convert IC s and BC s from one mechanism form to another The default IC and BC profiles distributed with CMAQ contain RADM2 species The ICON and BCON processors have a hardwired routine for converting from RADM2 to CB IV This hardwired routine can be overridden by supplying a MECH_CONV_FILE at run time A detailed description of the MECH_CONV_FILE format is provided in Table 4 6 The file is list formatted 108 6 1 4 MECH_CONV_FILE Mechanism Conversion File Table 6 6 MECH_CONV_FILE format description Line Column Name Type Description 1 1 16 SPP1_OUT String Output mechanism species name re quired 17 wow Char delimits the left hand and right hand side of the conversion equation required 18 SPP1_IN String Input mechanism spe cies name coefficients on right hand side of equation may be either integer real or expo nential format re quired wa Char man conversion rule ter minator allows rules to span multiple lines required SPP2_OUT String Output mechanism species na
61. 10 API Data Structure and Data File Types Each CMAQ data file has an internal file description that contains the file type the file start date and time the file time step the grid and coordinate descriptions and a set of descriptions for the set of variables contained within the file i e names units specifications and text descriptions Some of the items in a file description such as the dates and times for file creation and update and the name of the program which created the file are maintained automatically by the system The remainder of the descriptive information must be provided at the time of file creation All files manipulated by the I O API may have multiple variables and multiple layers Each file has a time step structure that is shared by all of its variables as well There are three kinds of time step structure supported as listed in Table 4 1 Within a file all the variables are data arrays with the same dimensions number of layers and the same data structure type although possibly different basic types e g gridded and boundary variables can not be mixed within the same file but real and integer variables can The data type structures that are supported are listed in Table 4 2 GRDDED3 and BNDARY 3 are the most prevalent file types in a CMAQ simulation Table 4 1 Possible Time Step Structures in 1O API Files File Type Description Time independent The file s time step attribute is set to zero Routines whi
62. 2 and 18 Universal Time Coordinates UTC The three hour files include data observed at 03 09 15 and 21 UTC The more current surface observation files have all observed surface data merged into a single file The upper air data are available for the period from January 1985 to April 1997 for 00 UTC and 12 UTC If you acquire your meteorological observation data from a source other than NCAR e g from special field studies you may need to write software to format the observations into a form that RAWINS expects 7 4 2 3 Meteorological Surface Fields MMS requires analyses data for sea surface temperature and snow to more accurately simulate the meteorological conditions With an account on the NCAR Cray or other arrangements with NCAR see ht tp www mmm ucar edu mm5 fagqMM5 html you may retrieve such data If you acquire sea surface temperature and snow analyses data from a source other than NCAR you may need to write software to convert the data into a form that REGRID discussed in Section 3 5 2 expects or modify REGRID to accept the data NCAR has sea surface temperature data from the U S Navy and NCEP as well as sea surface temperature data gen erated from climatological data The Navy sea surface temperature data is 63 x 63 Northern Hemisphere polar data It is available for cases between November 1961 and December 1993 More current Navy sea surface temperatures 137 7 5 Meteorology Model Pre Processing may be avai
63. 9 gas phase mechanism 4th generation CMAQ aerosol mechanism aqueous cloud chemistry e saprc99_ae3 SAPRC99 gas phase mechanism and 3rd generation CMAQ aerosol mechanism 5 6 2 3 JPROC compilation Section 3 3 provides an overview of how to install and compile the CMAQ programs for the tutorial simulation Follow the steps outlined in Section 3 3 to compile new versions of JPROC 1 Ifyou have not already done so build the CMAQ source code and compilation management program M3BLD this only needs to be done the first time you install CMAQ 2 Install and compile the I O API and netCDF libraries if these are already available from a previous CMAQ compilation configure the JPROC build script to use the available libraries 3 Configure the JPROC build script for your application 4 Invoke the build script to create an executable bldit jproc pgf 5 6 2 4 JPROC execution options The environment variables listed here are invoked during execution of the program and are set in the JPROC run script e EXEC default JPROC_ CFG Executable to use for the simulation 5 6 2 5 JPROC output files Table 5 10 JPROC output files File Name Format Description JVfile SJTABLE_ Date ASCII Daily clear sky photolysis rates file The default location of the JPROC output files is the M3DATA jproc directory controlled by the OUTDIR variable in the run script The default naming convention for all JPROC output files use
64. AQ aerosol mechanism aqueous cloud chemistry sulfate tracking model PAOpt default pa_noop Specifies the process analysis configuration to use for CMAQ The choices for the PAOpt variable are the available directories for process analysis include files under the M3MODEL include release directory 5 3 2 Files configuration and environment variables 5 3 2 3 CCTM compilation Section 3 3 provides an overview of how to install and compile the CMAQ programs for the tutorial simulation Follow the steps outlined in Section 3 3 to compile new versions of CCTM 1 If you have not already done so build the CMAQ source code and compilation management program M3BLD this only needs to be done the first time you install CMAQ Install and compile the I O API netCDF and MPICH libraries if these are already available from a previous CMAQ compilation configure the CCTM build script to use the available libraries If you have not already done so compile the STENEX and PARIO libraries Configure the CCTM build script for your application Invoke the build script to create an executable bldit cctm pgf 5 3 2 4 CCTM execution options The environment variables listed here are invoked during execution of the program and are set in the CCTM run script EXEC default CCTM_ CFG Executable to use for the simulation NPCOL_NPROW default 1 1 Domain decomposition for parallel mode recommended configuration is for the number
65. After successfully compiling the various CMAQ programs use the distributed run scripts to generate the CCTM input files and then to run the CCTM for the CMAQ benchmark case The CCTM must be run last in the simulation sequence there are no other dependencies between the other CMAQ programs except that MCIP must provide necessary inform ation to ICON and BCON so they can be run in any order to create input data for the CCTM If all of the programs compiled and the CMAQ environment variables are set correctly then for all programs other than the CCTM the benchmark simulation will execute without any modifications to the run scripts The CCTM is configured to run in multiprocessor parallel mode and requires setting the number of processors to allocate to the simulation and the loc ation of the MPI initialization command on your system 3 4 1 Notes on running the CCTM in parallel mode Configuring the CCTM run script for parallel processing requires selecting the number of processors to use for the simulation by setting the NPROCS environment variable and choosing the domain decomposition configuration by setting the variable NPCOL_NPROW The number of processors must be equal to the product of the two values selected for NPCOL_NPROW For example if your system has six processors available to run CMAQ set NPROCS to 6 and NPCOL_NPROW equal to 3 2 For single processor computing set NPROCS to 1 and NPCOL_NPROW to 1 1 Most clustered multip
66. Backward Iterative EBI Hertel et al 1993 and Sparse Matrix Vectorized GEAR SMVGEAR Jacobson and Turco 1994 solvers Version 4 6 includes the provision for mercury and other toxic compounds This version also includes special routines to track sulfate and organic carbon species Different solution algorithms have been investigated for the chemical kinetics in terms of the optimal balance of accuracy generalization and computational efficiency that is required for this component of the atmospheric system CCTM currently contains three options for solving gas phase chemical transformations with the Rosenbrock ROS3 4 Euler Backward Iterative EBI gt and Sparse Matrix Vectorized GEAR SMVGEAR gt solvers 2 3 2 Photolysis Figure 2 9 CMAQ chemical transport model and associated preprocessors Meteorology Modeling MCIP System MAQ Chemical Transport Model CCTM Chemistry Advection Diffusion Analysis Emissions Modeling System Package a Aerosols Convection Clouds Photolysis Rates Initial and Boundary Conditions 2 3 2 Photolysis Photolysis or photo dissociation of trace gases initiates most chemical reactions that take place in the atmosphere Photolysis splits gas phase chemical species with energy from sunlight Photolysis is involved in the formation of smog an air pollution problem that affects human animal and plant health Simulating photochemical reactions accur a
67. CIP 3D Meteorological BNDARY3 Hourly PERIM Z MCIP Boundary 2D Meteorological GRDDED3 Hourly xX Y MCIP Cross 3D Meteorological GRDDED3 Hourly X Y Z MCIP Cross 3D Meteorological Dot GRDDED3 Hourly X4 1 Y 1 Z MCIP 6 1 1 GRIDDESC Horizontal Domain Definition Used by JPROC ICON BCON CCTM The CMAQ grid description file GRIDDESC is used by all programs except JPROC and MCIP to define the hori zontal spatial grid of the modeling domain GRIDDESC is an I O API ASCII file that contains two sections a horizontal 98 6 1 1 GRIDDESC Horizontal Domain Definition coordinate section and grid description section GRIDDESC is the logical name for text files which store horizontal coordinate and grid descriptions and which is read by the DSCGRIDQ and DSCOORDO utility routines This file has two segments Each segment has a 1 line header which by convention provides titles for the columns in the data records a sequence of data records and a terminal record with name field blank i e The first segment is the coordinate system description segment Table 4 2 and consists of text records giving coordinate system name and descriptive parameters P_ALP P_BET P_GAM XCENT and YCENT Note that the standard names for UTM coordinate systems are given in the form UTM_ lt nn gt where nn is the number for the UTM zone Most of the Eastern US would use coordinate system UTM_17 for example The second segment is the grid
68. CMAQ version 4 5 the coefficients of vertical eddy diffusivity are not written to any output file However the physical Kv values are calculated in the model in the subroutine EDYINTB and contravariant diffusivities are computed in the VCONTDIFF subroutine It would be a relatively simple matter to insert code to output the values either as a new individual output file or as an appendage to an existing file In addition to model data output CMAQ can optionally produce log files containing the standard output from the dif ferent CMAQ processors If the log file option is not selected by the user CMAQ will write all of the log information to the screen along with the standard error which can be captured to a text file using basic Unix syntax 6 2 1 CMAQ Output Log All of the CMAQ processors generate standard output and standard error during execution For all of the processors other than the CCTM this diagnostic output information can be captured to a log file at execution using a Unix redirect command For example to capture the standard output and error of a BCON simulation use the following command run bcon csh gt amp run bcon log For the CCTM the LOGFILE environment variable allows users to specify the name of a log file for capturing the standard output from the program If this variable is not set the standard output is written to the terminal and can be captured using the Unix redirect command gt as shown in the example ab
69. CMAQ preprocessors to form the required data for running the CCTM 1 2 3 Summary Descriptions of the Major CMAQ Programs The major CMAQ components and ancillary programs are the following e Model Builder M3BLD The only CMAQ component written in C M3BLD provides an interface to the CVS source code archive for exporting the source code and to the FORTRAN compiler for building binary executables As M3BLD is required to create all of the CMAQ executables except MCIP it is the first program that needs to be compiled after installing the CMAQ source code on your system In addition to creating executables it also provides the option of generating a UNIX Makefile which is particularly useful for porting the CMAQ code to 1 2 3 Summary Descriptions of the Major CMAQ Programs new operating systems testing new code in a development environment or troubleshooting problems with CMAQ compilation or execution Photolysis Rate Preprocessor JPROC JPROC calculates chemical mechanism specific clear sky photolysis rates at fixed altitudes hour angles and latitude bands from tabulated absorption cross section and quantum yield CSQY data While CMAQ is distributed with CSQY data that support the default chemical mechanisms updating or adding new CSQY data is straightforward The only configuration option required for JPROC is the selection of the chemical mechanism to model Output from JPROC is an ASCII lookup table of photolysis rates that th
70. CMAQ v4 6 Operational Guidance Document CMAQ v4 6 Operational Guidance Document Table of Contents 1s IntrOdUChOns 2 scssecaiessustas a E statis seabaloneeaettteu E E E E tttag E dadeedatts seubatea aay A E a 1 1 1 Background and Goals tosc ionere eeno en EE EE E EEE E E E op SETE R 1 1 2 Overview of CMAQ System Components isisisi riti o roepa Er cece cece sE E Sea NTE Epps OPTIE EETRIS T EPRS 3 1 3 Features of CMAQ for Application Users ssessseeessseesrrerererersrrerrsrrerrrresrerrsrrerrsrrerrsresrreresrreert 6 1 4 Features of CMAQ for Air Quality Model Developers ssseisseesieseessrrrsrrerrsrrrrrresrrrrsrrerrsrrerrsresre 6 1 5 New Features in Version 4 6 neso teretes ertoe e o e I EESE EEEE ESES EE EEEE TEE REEE E EEA Ss 7 1 6 About this mantal eesse ereraa ea a aE sensed pees SOE E ETEO sad PEEN SAVE eE sean gies 9 1 7 Referenc s sise t oo shen E aE EA E EEEE kev EE E E EEEE EE EE EEE 9 2 Overview of the Science in the CMAQ Modeling System 0 2 0 0 ee cece cece eee ceeeceeecaeesa essa seen sean eeueeees 11 2 1 Features to Achieve the Goals of CMAQ ccccec ccc ncc ec ee cence cent ee ce been ence eee eens nec ea sees e Gn ea ee ee ee aE EEE 12 2 2 CMAQ Input Processors rehe sees eair obaibasds pies gsees SEEE ROA fyedde adeasreeuisecdeases sebeaagsveseeesss ES 14 2 3 CMAQ Chemical Transport Model Science Modules cece cee ceeeceeeceeeceeeca cece cena eeneeeneeeenees 19 24 The CMAQ User Int
71. DDED3 Time dependent 2 D cross point met eorology file this file is output by MCIP Time dependent 3 D dot point meteor ology file this file is output by MCIP MET_CRO_3D GRDDED3 Time dependent 3 D cross point met eorology file for defining the vertical layer structure of the model grid this file is output by MCIP PDM_PING_O GRDDED3 Previous day PinG output file for re starting the simulation GRIDDESC ASCII 5 9 2 2 PDM compilation options Horizontal grid description file for de fining the model grid this file is output by MCIP or can be created by the user The configuration options listed here are set during compilation of the PDM executable None of these options will affect the results of the PDM simulation they only control the behavior of the program M3BLD in creating the PDM executable e Opt default verbose Defines the action to be taken by the program M3BLD when extracting source code from CVS and compiling an executable e compile_all force compile even if all the object files are current e clean_up remove all source files upon successful compilation e no_compile do everything except compile no_link do everything except link one_step compile and link in one step 85 5 9 2 Files configuration and environment variables e parse_only checks configuration file syntax e show_only shows requested commands but does not execute them e verbose
72. EMMECH input and output files CHEMMECH Include_generator pl GC_CONC EXT GC_ICBC EXT GC_DDEP EXT GC_SCAV EXT Shows Input Output Pa GC_DEPV EXT GC_WDEP EXT Output Files Figure 3 shows the input and output files and configuration options for CHEMMECH The full set of mechanism include files required by the CMAQ programs are generated in two steps In the first step the program CHEMMECH is run with the mechanism definition file MECH DEF provided as input The resulting RKDM EXT and RXCM EXT include files are then input to the Python script include_generator py along with the Species_Table csv file to create the full set of include files needed to compile CMAQ with a new chemical mechanism configuration The Species_Table csv file defines the atmospheric processes that each species undergoes in the model and is generated by the Excel spreadsheet Species_Table xls that is distributed with CHEMMECH 66 5 4 2 Files configuration and environment variables To implement a new mechanism in CMAQ edit a MECH DEF file that is associated with a base mechanism and provide this new MECH DEF files as input to CHEMMECH Edit the default run script MP saprc99 csh to point to the new MECH DFEF file This script will call both the CHEMMECH executable and the include_generator py script to create the full set of mechanism include files required by the CMAQ programs There are no horizontal grid vertical layer or temporal settings for CHEMMECH
73. I and netCDF libraries if these are already available from a previous CMAQ compilation configure the BCON build script to use the available libraries Configure the BCON build script for your application Invoke the build script to create an executable bldit bcon pgf 5 2 2 4 BCON execution options The environment variables listed here are invoked during execution of the program and are set in the BCON run script EXEC default BCON_ CFG Executable to use for the simulation NPCOL_NPROW default 1 1 Domain decomposition for parallel mode BCON is normally run in a single processor environment so this setting should alw GRIDDESC default GRIDDESC1 Grid description file for setting the horizontal grid definition GRID_NAME Name of the grid definition contained in the GRIDDESC file that specifies the horizontal grid for the current application of the 53 5 2 2 Files configuration and environment variables LAYER_FILE Name and location of a MET_CRO_3D file for specifying the vertical layer structure for the current application of the model OUTDIR default M3DATA bcon Output data directory BC Sets the input file type The setting of this variable determines how the input and output environment variables are set by the run script e profile sets the output file name to include the tag profile in the name uses the variable BC_PROFILE to point to an ASCII vertical profile file for
74. ILE Boundary conditions vertical profiles 1988180 00 SO2 0 300E 03 0 200E 03 0 100E 03 0 100E 03 0 200E 04 0 100E 04 6 1 3 BC_PROFILE Boundary conditions vertical profiles Used by BCON Like ICON BCON can generate boundary conditions from two different input file types The first file type is an ASCII vertical profile file that list species concentrations at different model layers that are fixed in space in time BCON is configured to generate initial conditions from ASCII vertical profiles by choosing the prof input module when compiling the programs see Section xxx on BCON The ASCII formatted vertical profile files begin with a header that contains a comment section describing the data and a file description section that defines the number of sigma levels in the file the number of pollutants in the file and the vertical coordinate values of the different sigma levels The next entries in these files are the Julian start date and the start time of the data and are not used by BCON The only difference between the ICON and BCON vertical profile files is that the BCON input consists of four data sections corresponding to each horizontal boundary e g north south east west of the model grid The BCON input profiles contain an additional field that precedes each data section in dicating which horizontal boundary the data section describes The format of the data sections in the ICON and BCON input files are exactly the same Ea
75. NC EXT ASCII File listing the gas phase model species to write to the CCTM output CONC file GC_DDEP EXT ASCII File listing the gas phase model species that dry deposit GC_DEPV EXT ASCII File listing the gas phase model species for which to calculate deposition velo cities GC_DIFF EXT ASCII File listing the gas phase model species that are transported by diffusion GC_EMIS EXT ASCII File listing the gas phase model species that are emitted into the model GC_G2AE EXT ASCII File listing the gas phase model species that react to form aerosols GC_ICBC EXT ASCII File listing the gas phase model species that require initial and boundary condi tions GC_SCAV EXT ASCII GC_SPC EXT ASCII File listing the gas phase model species GC_WDEP EXT ASCII File listing the gas phase model species that wet deposit The default location of the CHEMMECH output files is the exts directory controlled by the Opath variable in the run script To compile a version of the CMAQ programs that use the include files created by CHEMMECH these output include files need to be moved to a new directory under the M3MODEL include release directory Point the CMAQ build scripts to this new directory through the Mechanism variable 5 5 ICON 5 5 1 Description The program ICON prepares chemical initial conditions ICs for the CCTM from either ASCII vertical profiles or from an existing CCTM output concentration CONC file ICON creates an output file with a single time s
76. O Determines whether to output static GRID meteorology files MKGRID default T Y coordinate of the lower left corner of the full MCIP X domain including the MCIP lateral boundary based on the input MM5 domain YO refers to the north south direction This setting is only used when doing a subset of the input meteorology domain by setting BTRIM 1 NCOLS Number of columns in the output MCIP domain excluding MCIP lateral boundaries NROWS Number of rows in the output MCIP domain excluding MCIP lateral boundaries LPRT_COL default 0 Column cell coordinate for diagnostic outputs on the MCIP modeling domain LPRT_ROW default 0 Row cell coordinate for diagnostic outputs on the MCIP modeling domain 81 5 8 PARIO 5 7 2 5 MCIP output files Table 5 12 MCIP output files File Name Format Description GRIDDESC ASCII Grid description file with coordinate and grid definition information GRID_BDY_2D BNDARY3 Time independent 2 D boundary met eorology file GRID_CRO_2D GRDDED3 Time independent 2 D cross point meteorology file GRID_CRO_3D GRDDED3 Time independent 3 D cross point meteorology file GRID_DOT_2D GRDDED3 Time independent 2 D dot point met eorology file MET_BDY_3D BNDARY3 Time dependent 3 D boundary meteor ology file MET_CRO_2D GRDDED3 Time dependent 2 D cross point met eorology file MET_CRO_3D GRDDED3 Time dependent 3 D cross point met eorology file MET_DOT_3D GRDDED3 Tim
77. O EEE eeu y as EEEE EE ae eae Sees 48 5 2 BCON input and output fles sssr riesaa Seedaceass PAA ETRE EE E OE IE EESE EOS EERTE EIEEE she 50 5 3 CHEMMECH input and output files 2 00 c cence eee e cee eee eee eeeeeceeeeaeeeaeeea seen sean eeu eeueeeneeeenees 66 5 4 ICON input and output files issis san tasa nated e ao aysebet say hantbad hes Dede ye ee costae SeevedE eepag saa e 70 35 JPROC input and output S sssrin ees eda peseets i oc cb steeces erii re E E ieie peta e 75 5 6 MCIP input and Output files ssri erreser snaran eea E ooe dev eP op EEE SETE spas EES Ee io r Snes ss dean dass 78 5 7 PDM anput and output files eiren cnni iee e arer EEES E EA EE ET OEE rE SEES 84 5 8 PROCAN input and output files ssie tries enera sos eE seeder a E E E T S 89 6 1 Illustration of CMAQ boundary condition file eeneeeesneeeeseeeesereereresrrersrrerrsrrsrrrrrsrrrerrrerrsrrerrereseeee 120 6 2 Graphical example of a CMAQ gridded boundary conditions file cece cece cece ee ee ne eeneeeneeeneees 121 6 3 Graphical example of a CMAQ gridded initial conditions file 0 0 00 eee cece cnee cece ee eeeeeeneeeneeennees 122 7 1 Example sigma vertical structure in MM3 0 0 0 0 cece cee cece eee ce ee ceeeca ceca cena ceae eens E E Tp E Eei 139 7 2 Sample Arakawa B staggering onines etnei err Terei seca seca cena ecae eens EES EEEE OE ES EEOSE EERS esas 140 7 3 Sample domain and Its Nests ssecci sc ssssess ss dese ayseseew ss ch oni iieiea
78. OKE program Cntlmat will create a growth matrix that contains the growth factors for each source and pollutant in the inventory Next the SMOKE program Grwinven combines this growth matrix with the inventory to create a grown emissions inventory Cntlmat can also be used to apply controls to the emissions inventory These controls can be designed to change the emissions values based on regulations Grwinven is also used to combine this control matrix with the inventory to create a controlled emissions inventory 8 6 6 Mobile Modeling MOBILE6 There are three SMOKE programs to handle mobile emissions processing Mbsetup Premobl and Emisfac The Mbsetup program groups the reference counties handles the set up of the user defined spatial and temporal averaging approach for the meteorology data assigns the speed profiles to the sources and creates the speed summary file The Premobl program spatially and temporally aggregates the temperature humidity and pressure data from the meteorology files for input into Emisfac The Emisfac program runs the MOBILE6 model to create emission factor files for all mobile sources 8 6 7 Biogenic Modeling BEIS3 Biogenic processing in SMOKE is very different from the processing of the anthropogenic sources SMOKE currently uses the BEIS version 3 model to process biogenic emissions First the Normbeis3 program reads in the gridded land use data Next the Tmpbeis3 program creates the hourly emissions These fi
79. PETES ree eebodss Gaedsangs sevieasPsrosaessssedasay 142 8 1 Schematic of SMOKE approach to emissions Processing 0 ce eee cess ce eeceeece neces ceeeeeeeeaeeeaeeeueeaneeaes 150 Vi List of Tables 3 1 Software required for running CMAQ csser a dogaedantas eouavansendsep ses S E a T EES 29 3 2 Optional support software for CMAQ sssesssessesseessssrssrerrsresrrrresrerresreersrrsrreresrrrrssreersrreerseesreeessreeet 30 4 1 Possible Time Step Structures in IO API Files 20 0 0 rosei aereos oe teui esien pE rE T Esse ESPERIE TEISSE 36 4 2 Possible Data Type Structures in IO API Files 20 0 0 cece cece cece cece cece nsec eeeeeeeeeeceeesaeeeaeseaeeea sean eeaes 37 4 3 Possible values for OPEN 3 FSTATUS crre aar n eee ence cece a e E ee eens eee AG a aT 39 4 4 JOAPI data retrieval routines essor esros sos toe eedes anya E E S E EEEE EE EEKE EEEE 40 4 5 CMAQ data manipulation utilities s ss ss rreir ssepe rio sees cde osessovssgpeeds seus sboean daseosnodsssoreosbesdepensasnieagess 42 5 1 BCON input fles eeri e tea E Ee ES ids E EE E EE EE E EEE EA ES 51 3 2 BEON output TS css scccadsiccts waupentiats desaeass sabes Seats dates sas PA agente as eeen tants Sta yss Modadseeeete esate 55 5 3 CCTM input tiles ecien sete EEEE one es oes eee Ses Ses ees ses aes Si ae cee OSes 37 SA4 CCIM output fles 555 osc cost se ii rer a assas EEES naegs sagen od APESS E POAST SEEE EPOS PEE ETS PIRES REINER 65 9 5 CHEMMECH i
80. Q programs for the tutorial simulation Follow the steps outlined in Section 3 3 to compile PARIO 1 If you have not already done so build the CMAQ source code and compilation management program M3BLD this only needs to be done the first time you install CMAQ 2 Install and compile the I O API and MPICH libraries if these are already available from a previous CMAQ compilation configure the PARIO build script to use the available libraries 3 Invoke the build script to create an executable bldit pario pgf 5 8 2 4 PARIO execution options As PARIO is not a program it does not require any configuration at execution 5 8 2 5 PARIO output files Successful compilation of PARIO will produce the library file libpario a along with several module files in the M3LIB pario OS directory 5 9 PDM 5 9 1 Description The Plume Dynamics Model PDM is the plume in grid PinG preprocessor for PinG instrumented versions of the CCTM Using input emissions files that identify the elevated point sources within the modeling domain to treat with PinG the PDM simulates plume rise plume transport and plume dispersion for each of the selected point sources The PDM also specifies when a particular plume cross section is to be transferred to the parent grid All PDM configuration happens during execution of the program A series of environment variables for specifying different configurations of the PDM are located in the run script By defaul
81. S and columns NCOLS should be an even integer e The smallest grid domain must contain at least two radiosonde observations e Use no more than four grids in a nested grid family simulation e Set Delta X equal to Delta Y to maintain accuracy of finite difference schemes e External boundary thickness should be set to 0 e Horizontal grid spacing for the MM5 nested grids generally have a 3 1 ratio although a 4 1 ratio has been employed CCTM Grids e A CTM grid uses the same horizontal resolution as its MM5 parent grid e Minimum grid dimensions of 30 rows and 30 columns are recommended e External boundary thickness should be set to 1 e ACCTM grid should be smaller than its parent MM5 grid by at least four grid cells and preferably by six 9 3 Vertical Layers Two types of vertical coordinates are available in CMAQ version 4 4 For hydrostatic conditions the time dependent hydrostatic sigma pressure vertical coordinate system can be used in the MM5 meteorological model This coordinate system can also be used for non hydrostatic conditions such cases as nested grid simulations where the nested grids are too small to make the same hydrostatic assumptions used in the coarser grids of the model The other vertical co ordinate system is the time independent reference non hydrostatic sigma pressure vertical coordinate system which is used for non hydrostatic simulations in the MM5 meteorological model Resolving the surface b
82. S latitude band The 20th data block begins the spring air temperature profiles at the latitude band ranging from 90 N to 80 N and is followed by 18 more data blocks of spring air temperature profiles The following 19 data blocks follow an identical format for air density and round out the spring profiles These 19 3 data blocks are then repeated for summer profiles autumn profiles and finally winter profiles The second data section in the PROFILES file contains monthly average Dobson Units The data are organized in twelve rows January through December and 19 columns 90 N to 80 N through 80 S to 90 S The last data section in the PROFILES file contains vertical profiles from the 1976 U S Standard Atmosphere of temperature K air density molecules cm3 ozone concentrations molecules cm3 and aerosol attenuation coefficients km The data are organized in 51 rows corresponding to altitude 0 50km with four columns per row for each of the four variables mentioned above A detailed description of the file format is provided in Table 4 10 115 6 1 8 PROFILES Atmospheric vertical profiles Table 6 10 PROFILE file format description Line Column Name Type Description 1 A Ozone concentration Exp E10 3 Ozone measurements at Season 1 Latitude as a function of season 1 Level 1 latitude and vertical level units in mo lecules cm required B Ozone concentration Exp E10 3 Ozone
83. SMOKE is designed to take advantage of these facts by formulating emissions modeling in terms of sparse matrix operations which can be performed by optimized sparse matrix libraries Specifically the inventory emissions are ar ranged as a vector of emissions sorted in a particular order with associated vectors that include characteristics about the sources such as the state county and SCCs SMOKE then creates matrices that apply the control gridding and speciation factors to the vector of emissions In many cases these matrices are independent from one another and can therefore be generated in parallel and applied to the inventory in a final merge step which combines the inventory emissions vector now an hourly inventory file with the control speciation and gridding matrices to create model ready emissions Figure 5 1 shows how the matrix approach allows for a more parallel approach to emissions processing in which fewer steps depend on other needed steps Figure 8 1 Schematic of SMOKE approach to emissions processing x 150 8 7 Emissions Model Visualization and Evaluation 8 7 Emissions Model Visualization and Evalu ation The CMAQ ready emissions files output by SMOKE can be visualized in PAVE This allows for evaluation on a spatial and temporal scale The reports output from Smkreport can be loaded into Excel to create plots of the data as well 8 8 Model Training and User Support A two and a half day SMOKE
84. TA QV total Jacobian at layer face m total Jacobian at layer middle m J weighted total air density kg m J and density weighted vertical contra W kg m s air temperature K mixing ratio kg water kg air 130 6 1 22 MD3file Three dimensional Meteorological Dot Product Input MET_DOT_3D PRES air pressure pascals DENS air density kg m WWIND vertical wind velocity m s ZH mid layer height above ground hydrostatic only m ZF full layer height above ground hydrostatic only m Qc cloud water mixing ratio kg kg QR rain water mixing ratio kg kg 6 1 22 MD3file Three dimensional Meteorological Dot Product Input MET _DOT_3D Used by CCTM CMAQ requires the following variables to be present in the Met Dot 3D meteorology file UWIND u component of horizontal wind m s VWIND v component of horizontal wind m s UHAT_JD contra U Jacobian Density kg m s VHAT_JD contra V Jacobian Density kg m s 6 2 Basic CMAQ Output Files As all of the CMAQ programs produce output files that are input to other CMAQ programs differentiating between CMAQ input and output is not entirely clear The previous section dealt with the output files from JPROC ICON BCON and MCIP as inputs to the CCTM In this section we will detail the general structure of all CMAQ binary outputs and provide details on the CCTM output files All CMAQ programs other than JPROC produce output files that adhere t
85. TIE ESTRES EREA SPARE E 97 6 2 Basic CMAQ Output Files csie oeae pit e aoe EEEE EAE EEES EEEE SEET E S 131 6 3 Diagnostic and advanced CMAQ Output Files 200 000 ee ceee cece ee ca cece cena cena cena een eeneeeeneeees 133 7 Developing Meteorological Fields 2 0 0 0 cece ec ee cence cece ne ceneceneceeeeeeeeeeeeeeeaeeea sees eens eeu eeaeeeneeeeeeee es 135 7A Credits and Disclaimers For Use of MMS 2 22 2s scsssosscsssessenssceevecsssesincapesevecdpeedsonssovetessseeabesssenes 135 7 2 System Requirements ieser io enaar EEE E EET E EE EEEE RENEE EEEE E SETTET eves 136 73s SOltWare L nga ges Sire eae E A E a a pats E E T AEE ET E 136 TAs Data Requirements sorsi resons eose eE TEE E OE ETE ETE E IO ETE ati ES ESES 136 7 5 Meteorology Model Pre Proc ssing scsi ss ciis ess ssoeesgssessendsss cots agacesaegs sesesasseevdecsssessseapecduavapeeeeess 138 iii CMAQ v4 6 Operational Guidance Document 7 6 Meteorology Model MM ocsccs sncesspsSsccdapisvenss R oe Ea EE EE E RERNE EEE EOE SES 139 7 7 Meteorology Model Post Processing csceeeceeceecneeeeeeeeeeceeeeeeeeeeeeneeeeeaeeeeeaeeeeeeeeeeaeeeeeaeenes 142 7 8 Meteorology Model Visualization and Evaluation ccc ceeecceece cece ence eeceeeceeeeneseaeceaeeea sean eeaes 142 7 9 Model Training and User Support 0 0 0 0 cece cece cece cece ce eeca ceca cece cena eens eeeeeeneeeaeeeeeseeeseeeeaeseaeeeges 143 TIO Usny MIMS swith CMAQ ane n eea cogs vadeuophs
86. VARS IF NOT WRITE3 myfile HNO3 JDATE JTIME ARRAY THEN some kind of error happened deal with it here END IF IF NOT WRITE3 afile ALL JDATE JTIME ARRAYB THEN some kind of error happened deal with it here END IF 4 6 CMAQ Related I O API Utilities Data files in the CMAQ system can be easily manipulated by using the netCDF and I O API utilities Information re garding the most commonly employed utility routines is listed in Table 4 5 and they are further described in the fol lowing sections 41 4 6 1 NCDUMP Table 4 5 CMAQ data manipulation utilities Utility Description NCDUMP print file as structured ASCII from NCAR M3XTRACT extract a subset of variables from a file for a specified time interval M3DIFF compute statistics for pairs of variables M3STAT compute statistics for variables in a file BCWNDW build a boundary condition file for a sub grid window of a gridded file M3EDHDR edit header attributes file descriptive parameters M3TPROC compute time period aggregates and write them to an output file M3TSHIFT copy time shift data from a file M3WNDW window data from a gridded file to a sub grid M3FAKE build a file according to user specifications filled with dummy data VERTOT compute vertical column totals of variables in a file UTMTOOL coordinate conversions and grid related computations for Lat Lon Lambert and UTM
87. _N205 VD_NO3 VD_GEN_ALD average liquid water content of clouds g m cloud top m cloud bottom m snow cover 1 yes 0 no deposition velocities for deposited species SO m s deposition velocities for deposited species SULF m s deposition velocities for deposited species NO m s deposition velocities for deposited species NO m s deposition velocities for deposited species O3 m s deposition velocities for deposited species HNO m s deposition velocities for deposited species HO m s deposition velocities for deposited species ALD m s deposition velocities for deposited species HCHO m s deposition velocities for deposited species OP m s deposition velocities for deposited species PAA m s deposition velocities for deposited species ORA m s deposition velocities for deposited species NH m s deposition velocities for deposited species PAN m s deposition velocities for deposited species HONO m s deposition velocities for deposited species CO m s deposition velocities for deposited species METHANOL m s deposition velocities for deposited species N20 m s deposition velocities for deposited species NO m s deposition velocities for deposited species GEN_ALD m s 6 1 21 MC3file Three dimensional Meteorological Cross Product Input MET_CRO_3D Used by CCTM CMAQ requires the following variables to be present in the Met Cross 3D meteorology file JACOBF JACOBM DENSAJ WHAT JD
88. ables in the file name All of the file naming variables for CCTM outputs are set in the run script 65 5 4 CHEMMECH 5 4 CHEMMECH 5 4 1 Description The program CHEMMECH generates mechanism include files for all chemical mechanism dependent CMAQ programs Using an ASCII mechanism definition file as input a combination of the Fortran 77 program CHEMMECH and the Python script include_generator py created by Chao Jung Chien at UC Riverside creates all of the Fortran include files that define the gas phase chemical mechanisms for the CMAQ programs To implement new mechanisms created by CHEMMECH in the CMAQ programs manually move the output include files from CHEMMECH to the M3MODEL include release NewMechanism directory within the CMAQ install ation directories where NewMechanism corresponds to the name of the new mechanism created with CHEMMECH To invoke this new mechanism set the Mechanism variable in the build script for the applicable CMAQ program to the name of the mechanism directory that you created For example if you used CHEMMECH to create include files for a mechanism that you call cb4_2006 create a directory under M3MODEL include release called cb4_2006 move the include files created by CHEMMECH to this directory and compile the CMAQ programs for this new mechanism by setting the Mechanism variable within the build scripts to cb4_2006 5 4 2 Files configuration and environment variables Figure 5 3 CH
89. actor lis ted in real or exponen tial format required n 3 A Wavelength Int or Real Wavelength corres ponding to ET data units in nm required B Extraterrestrial Irradi Real or Exp Estimation of the ance photon flux reaching the exterior of the earths atmosphere units in photons cm second required n 4 A Wavelength Int Wavelength corres ponding to ET data units in nm required B Extraterrestrial Irradi Real or Exp Estimation of the ance photon flux reaching the exterior of the earths atmosphere units in photons cm second required n X A sample of the important sections of an ET file is shown below Extra Terrestrial Irradiance taken from the RADM data derived from the WMO 1985 report Table 7 4 format wl et_irrad Beginning With FAC units are Photons cm 2 s 1 114 6 1 8 PROFILES Atmospheric vertical profiles FAC 1 0 185 185 3 620E 11 186 916 4 730E 11 6 1 8 PROFILES Atmospheric vertical profiles Used by JPROC PROFILES is the logical name for the ASCII data file containing seasonal and vertical profiles for ozone aerosol at tenuation temperature air pressure and Dobson values The ASCII formatted data provided in the atmospheric profiles data file PROFILES are at 19 latitude bands 90 N to 90 S and 51 altitudes 0 to 50 km in three distinct data sections The first data section contains seasonal latitude dependent verti
90. ads either MM5 version 2 or version 3 binary output files MMOUT or WRF binary outputs to generate T O API formatted netCDF files for input to CMAQ and SMOKE For details about the format of the MMOUT files 119 6 1 13 BNDY_CONC_1 Boundary Conditions visit the MM5 homepage at http www mmm ucar edu mmS For information about the format of the WRF output files visit the WRF homepage at http wrf model org 6 1 13 BNDY_CONC_1 Boundary Conditions Used by CCTM CMAQ boundary condition data are of the BNDARY3 file type Produced by the boundary condition processor BCON the CCTM reads these data and correlates them with the interior data by the use of a pointer system This pointer system designates the beginning location of the data in memory which starts a new side of the domain e g South East North and West Figure 4 1 illustrates this input data structure and the relationship of the boundary data to the interior data within CMAQ modules Each species being modeled should be on the boundary conditions file If modeled species are not contained in this file the boundary condition for these species will default to the value 1E 30 The perimeter of the CMAQ domain is NTHIK cells wide where NTHIK 2 NROW 2 NCOL 4 The CMAQ program BCON Section 2 2 2 is used to generate CMAQ boundary condition input files from either existing CMAQ outputs or from ASCII vertical profiles Figure 4 2 is a graphical example of the CMAQ boun
91. ain windowing are allowed with MCIP The boundary trim option uniformly trims grid cells off each of the four horizontal boundaries of the input meteorology grid The non uniform trim option specifies an offset from the lower left corner of the input meteorology domain and the number of cells in the X and Y directions from the revised origin to extract from the input domain More information about how to invoke these options is provided in Section 5 7 2 4 MCIP execution options e MCIP also provides the capability to reconfigure the vertical layer structure in the input meteorology through in terpolation from the input structure to an output structure defined through sigma coordinates in the run script Commonly referred to as layer collapsing this option should be exercised with caution as it can significantly impact the conservation of energy assumption inherent in the meteorology through its affects to the predicted wind fields 5 7 2 Files configuration and environment variables Figure 5 6 MCIP input and output files GRIDDESC MET_BDY_3D GRID_BDY_2D MET_CRO_2D GRID_CRO_2D MET_CRO_3D Execution a og Output Files File C Program Shows Input Output GRID_CRO_3D MET_DOT_3D GRID_DOT_2D 78 5 7 2 Files configuration and environment variables Figure 6 shows the input and output files and configuration options for MCIP All MCIP configurations are accom plished at execution a distinction from the rest of the CMAQ progra
92. air quality forecasters and planners and policy makers While each of these groups has distinct individual requirements of CMAQ they also share a common need for an accurate efficient transparent and economical tool that represents the state of the science to simulate air pollution formation and transport To address these individual and common needs CMAQ has the following goals 1 Community Development Utilize a scientifically sound design that encourages innovations and enhancements by all members of the air quality modeling community 2 Multiscale Modeling Provide adequate technical formulations to address air quality issues on multiple spatial scales from urban to hemispheric 3 One atmosphere Design Provide robust and integrated science for modeling multiple coupled air quality issues in a single simulation 4 Modularity Maintain flexibility to add new or select from existing science modules to optimize model performance for specific applications 5 Transparency Utilize programming practices that promote understanding of the model formulation at the source code level 6 Computational Efficiency Provide scientifically acceptable results without compromising the speed at which the results are generated 7 Open Source Design Enable no cost distribution and application by the modeling community 1 2 Overview of CMAQ System Components 8 State of the Science Provide independent scientific peer review of all scienti
93. ally I O API files are portable across computing platforms This means that the same file can be read for example on a Sun workstation a Red Hat Linux workstation and on a Mac OS X A further benefit of the I O API is that an expansive set of data manipulation utilities and statistical analysis programs are available to help evaluate and post process the binary CMAQ input output data files The I O API system is essentially transparent to those CMAQ users employing a preconfigured application of the model For users planning to modify the code or implement updated modules for research purposes a few key elements of the I O API should be understood and are discussed below This section covers only the barest of necessities in terms of a CMAQ user s interaction with I O API For more detailed information about developing new modules for CMAQ using the I O API code libraries please refer to Chapter 9 4 1 Files Logical Names and Physical Names The I O API stores and retrieves data using files and virtual files which have optionally multiple time steps of multiple layers of multiple variables Files are formatted internally so that they are machine and network independent This behavior is unlike FORTRAN files whose internal formats are platform specific so that the files do not transfer using the File Transfer Protocol FTP or Network File System NFS mount very well Each I O API file has an internal description consisting of the file type
94. ame All of the file naming variables for PDM outputs are set in the run script 5 10 PROCAN 5 10 1 Description must be followed to capture Process Analysis data rather than on what data should be captured and how it might be analyzed 88 5 10 2 Files configuration and environment variables 5 10 2 Files configuration and environment variables Figure 5 8 PROCAN input and output files PA_CMN EXT PA_CTL EXT PA_DAT EXT PROCAN Shows Input Output via The program PROCAN creates a set of include files needed to instrument the CCTM to produce process analysis output This program reads and interprets instructions from a command file and then generates three Fortran include files EXT used by CCTM to produce the Process Analysis outputs that were requested in the commands The process analysis commands themselves are formatted according to a simple set of rules and a free form format Nevertheless each command has a special syntax that must be followed and each command makes use of special keywords and or operators that have specific meaning to PROCAN The commands are of three major types global commands IPR commands and IRR commands The discussion begins first however with a description of some general rules for configuring PROCAN 5 10 2 1 PROCAN input files Table 5 15 PROCAN input files File Name Format Description PACP_INFILE ASCII PROCAN command file specifies configur
95. an simulate the transport and chemistry of ozone particulate matter toxic airborne pollutants and acidic and nutrient pollutant species CMAQ uses state of the science techniques and has many new and important features that are not available in previous modeling systems CMAQ is capable of modeling complex atmospheric processes affecting transformation transport and deposition of air pollutants using a system architecture that is designed for fast and efficient computing CMAQ allows users to easily construct models with different characteristics such as different chemical mechanisms or alternative cloud treatments in order to address a specific air quality issue Figure 2 1 This modeling configuration will allow CMAQ to retain its state of the science status over time with future implementations of new science modules as appropriate At the same time CMAQ can be employed for regulatory applications by using approved standard configurations of the modeling platform that represent the best available modeling technology at a given time CMAQ has been developed to meet the needs of both the research and application communities 2 1 Features to Achieve the Goals of CMAQ Figure 2 1 CMAQ Modeling Framework Interchangeable Modules Driver A an E Adyection D Diffusion oa Chemistry The CMAQ modeling system is also a useful tool for the model developer It is unique in that its components are designed in a modular fashion with
96. and each land use category has a seasonally parameterized set of physical properties that are used to model physics calculations e g albedo available moisture emissivity roughness length thermal inertia The terrain and land use data bases are available in both Cray and IEEE formats from the NCAR anonymous FTP site ftp ftp ucar edu in directory mesouser Data The terrain and land use data are interpolated to the MM5 simulation grid in the TERRAIN program discussed in Section 3 5 1 The data bases are assigned to MM5 simulations based on the resolution of the simulation domain The terrain and land use data bases for an individual domain should be the same resolution wherever possible e g do not assign a 60 minute terrain and a 30 minute land use to the same domain Note that higher resolution terrain and land use data should be used for higher resolution domains even within the same simulation For example a 108 km domain may be assigned the 60 minute terrain and land use while a 36 km nest may be assigned the 30 minute terrain and land use 7 4 2 Case Specific Data Three primary types of case specific data are required for an MM5 simulation meteorological background fields meteorological observations and surface meteorological fields 136 7 4 2 Case Specific Data 7 4 2 1 Meteorological Background Fields The meteorological background fields that are used for an MMS simulation are extracted from a larger scale
97. art I Governing equations in a generalized coordinate system J Atmos Sci 56 3789 3807 Byun D W and J K S Ching 1999 Science Algorithms of the EPA Models 3 Community Multiscale Air Quality CMAQ Modeling System U S Environmental Protection Agency Rep EPA 600 R 99 030 727 pp Available from Office of Research and Development EPA Washington DC 20460 Byun D and K L Schere 2006 Review of the governing equations computational algorithms and other components of the Models 3 Community Multscale Air Quality CMAQ modeling system Appl Mech Rev 59 51 77 Carter W P L 2000 Documentation of the SAPRC 99 chemical mechanism for VOC reactivity assessment Final Report to California Air Resources Board Contract No 92 329 and 95 308 Chang J S R A Brost I S A Isaksen S Madronich P Middleton W R Stockwell and C J Walcek 1987 A Three Dimensional Acid Deposition Model Physical Concepts and Formulation J Geophys Res 92 14 681 14 700 Chang J S P B Middleton W R Stockwell C J Walcek J E Pleim H H Lansford F S Binkowski S Madronich N L Seaman D R Stauffer D Byun J N McHenry P J Samson and H Hass 1990 The regional acid deposition model and engineering model Acidic Deposition State of Science and Technology Report 4 National Acid Precipitation Assessment Program Coats C 2005 The EDSS Models 3 IO API Available online at http www baronam
98. as it can degrade the quality of the data if used incorrectly Con figuration options for MCIP include the time periods over which to extract data from the meteorological model output files horizontal and vertical grid information and selections for either passing through certain MM5 calculated variables unaltered or recalculating these variables within MCIP CMAQ Chemistry Transport Model CCTM The CCTM integrates the output from all of the preprocessing programs including the emissions and meteorology models to simulate continuous atmospheric chemical conditions The concentrations of relevant species can be captured for output at a user definable frequency typically hourly The CCTM output files some of which are optional are all binary netCDF files of gridded and temporally resolved air pollutant information such as gas and aerosol phase species mixing ratios hourly wet and dry deposition values visibility metrics and integral averaged concentrations The spatial and temporal extent of the CCTM output is dictated by the input meteorology The science configuration is specific to each application of the model and can be adjusted to optimize model performance both computationally and in the numerical reproduction of observed air quality trends Configuration options for the CCTM include the temporal coverage of the simulation the chemical mechanism to model the physics scheme to use for modeling pollutant transport heterogeneous an
99. ation options for the program 5 10 2 2 PROCAN configuration PROCAN configuration is implemented through the command file PACP_INFILE The free form format of the PROCAN command file is similar to that used by the general mechanism processor CHEMECH In general white spaces are ignored and line wrap is allowed i e commands can be continued on a subsequent line after a hard return The free form format also allows embedded comments and makes use of special symbols to indicate the type of input data Special rules for naming species entering labels and specifying numerical values such as stoichiometric coeffi cients and rate constant parameters are also used Each major component of the command file is discussed below e Comments All lines that have an exclamation point in column are treated as comment lines and are ignored by PROCAN Any text enclosed in braces or parentheses is also treated as comment and ignored by PROCAN e Species names PROCAN recognizes two types of species names model species and user defined Process Analysis species Model species refer to species names in the Species Tables Provide link to a table of species names for each mechanism These names must be spelled exactly as they appear in that table The following special rules have been established for user defined species names e The Process Analysis species names must not contain any blanks and can be up to 16 characters l
100. c parameters that describe the mechanism CHEMMECH creates these INCLUDE files from an ASCII mechanism definition file that represents the chemistry as sequential equations of reactants products and reaction rate information This program is needed to modify reactions stoichiometry or kinetics in the existing mechanisms and to add new species that require the addition of new reactions More detailed discussions of the formulation of the above CMAQ programs are available in Chapter 2 below in Byun and Ching 1999 and in Byun and Schere 2006 1 3 Features of CMAQ for Application Users CMAQ is designed to address the complex interactions among multiple air quality issues simultaneously Using a one atmosphere approach to air quality modeling by applying multiscale and multi pollutant modeling techniques CMAQ can provide independent but dynamically consistent predictions of several different pollutants at varying spatial scales The modularity of the CMAQ design provides an unprecedented level of flexibility in air quality model configuration for optimizing model performance for different applications and spatial resolutions In addition to the flexibility of the one atmosphere approach CMAQ provides the following features to users interested in applying the model for research or regulatory applications e Following the Models 3 paradigm close interactions among the development communities for CMAQ and the meteorology and emissions models pr
101. cal profiles of O3 concentrations molecules cm air temperature K and air density molecules cm3 The second data section contains monthly Dobson values at the 19 latitude bands The last data section contains vertical profiles from the 1976 U S Standard Atmosphere of air temper ature K air density molecules cm3 ozone concentrations molecules cm3 and aerosol attenuation coefficients km The first data section of the PROFILES file is divided into 228 19 3 4 data blocks with each block representing one of the three variables O3 air temperature and air density at one of the 19 latitude bands for each of the 4 seasons of the year The individual data blocks contain 51 values per variable representing standard conditions at altitudes ranging from 0 50 km The data are ordered from general to specific by season spring summer autumn winter variable O3 air temperature air density latitude and altitude For example the first block in the PROFILES file contains spring O concentration profiles at the latitude band ranging from 90 N to 80 N from 0 to 50 km above sea level the first value in the block is at O km and the last value is at 50 km The next data block is again spring O concentration profiles but at the latitude band ranging from 80 N to 70 N The next 17 data blocks complete the spring O3 concen tration profiles by continuing through rest the 19 latitude bands with the last block representing the 80 S to 90
102. cales In an effort to decrease ambient levels of criteria pollutants and to better understand the transport of chemicals emission control strategies and air quality models have been approved by the USEPA for use at regional state and local scales within the United States The models have been used to estimate the contribution of different control strategies to improve air quality and ensure cost effective results Historically models were designed and developed for specific air quality issues such as acid deposition or ozone De pending on the release characteristics the pollutants in question and the surrounding meteorological conditions at the time of pollutant release modeling scenarios can range from a localized short term phenomenon to a long term regional event Because some emission sources contribute to the ambient levels of more than one pollutant and can affect an entire regional area on different time scales an integrated modeling approach capable of handling multiple air pollutants and spatiotemporal scales was needed to isolate control strategies that improve overall air quality in a cost effective manner New air quality issues identified by the Clean Air Act Amendments of 1990 such as visibility fine and coarse particles and indirect exposure to toxic pollutants make an integrated modeling approach that can address multiple pollutants even more essential CMAQ is a multi pollutant multi scale air quality modeling system that c
103. ch deal with time independent files ignore the date and time arguments Time stepped The file has a starting date a starting time and a positive time step Read and write requests must be for some posit ive integer multiple of the time step from the starting date and time oom Circular buffer This type of file keeps only two records the even part and the odd part useful for example for restart files where only the last data written in the file are used The file s description has a starting date a starting time and a negative time step set to the negative of the actual time step Read and write requests must be for some positive integer multiple of the time step from the starting date and time and they must reflect a specific time step that is in the file 36 4 2 IO API Data Structure and Data File Types Table 4 2 Possible Data Type Structures in IO API Files File Type Magic Number Data Type Description CUSTOM3 1 Custom User dimensioned array of REAL 4s that these system reads writes reliably DCTNRY3 Dictionary Data type stores and retrieves parts of an FDESC EXT file description GRDDED3 Gridded Dimension as REAL 4 AR RAY NCOLS NROWS NLAYS NVARS BNDARY3 Boundary Dimension as REAL 4 AR RAY SIZE NLAYS NVARS IDDATA3 ID reference Used to store lists of data like pollution monitoring observati
104. ch line corresponds to a different pollutant and begins with the name of the pollutant The subsequent columns on each line list the chemical concentration at each layer contained in the file Gas phase species are provided in ppmV units and aerosol species are provided in ug m3 units in the BCON inputs The layer structure of the BCON vertical profiles does not need to correspond exactly to the layer structure that will be modeled the programs will interpolate the data to the correct vertical format for the simulation Boundary conditions can either be time independent static or time dependent dynamic Boundary conditions gen erated with the ASCII vertical profiles are both static and spatially uniform along each of the four horizontal boundaries For spatially and temporally resolved boundary conditions it is necessary to use the other input file type to BCON an existing CCTM concentration file CTM_CONC_1 A detailed description of the vertical profile file format for boundary conditions is provided in Table 4 5 The header of the profiles file is list formatted while the data section of the file is fixed format 105 6 1 3 BC_PROFILE Boundary conditions vertical profiles Table 6 5 BC_PROFILE format description Line Column Name Type Description 1 3 Text Header String Text description of the contents and source of the initial conditions file optional NUM_SIGMA_LVL Int Number of sigma
105. ch time step A more detailed description of the particulate matter simulation techniques used in CCTM can be found in Binkowski and Shankar 1995 and Byun and Schere 2006 2 3 5 Clouds and Aqueous phase Chemistry Clouds are an important component of air quality modeling and play a key role in aqueous chemical reactions vertical mixing of pollutants and removal of pollutants by wet deposition Clouds also indirectly affect pollutant concentrations by altering the solar radiation which in turn affects photochemical pollutants such as ozone and the flux of biogenic emissions The Cloud module in CMAQ performs several functions related to cloud physics and chemistry Three types of clouds are modeled by CMAQ sub grid convective precipitating clouds sub grid non precipitating clouds and grid resolved clouds The subgrid cloud scheme in the CCTM was derived from the diagnostic cloud model in RADM Version 2 6 Dennis et al 1993 Walcek and Taylor 1986 Chang et al 1987 Chang et al 1990 Grid resolved clouds are diagnosed by MM5 with no additional cloud dynamics considered in CMAQ The aqueous chemistry model in CMAQ evolved from the original RADM model Chang et al 1987 and Walcek and Taylor 1986 The cloud module in the CCTM vertically redistributes pollutants for the sub grid clouds calculates in cloud and precipit ation scavenging performs aqueous chemistry and accumulates wet deposition amounts Version 4 5 1 contains an impor
106. chemistry 72 5 5 2 Files configuration and environment variables e saprc99_ae4_aq SAPRC99 gas phase mechanism 4th generation CMAQ aerosol mechanism aqueous cloud chemistry e saprc99_ae3 SAPRC99 gas phase mechanism and 3rd generation CMAQ aerosol mechanism 5 5 2 3 ICON compilation Section 3 3 provides an overview of how to install and compile the CMAQ programs for the tutorial simulation Follow the steps outlined in Section 3 3 to compile new versions of ICON l If you have not already done so build the CMAQ source code and compilation management program M3BLD this only needs to be done the first time you install CMAQ Install and compile the I O API and netCDF libraries if these are already available from a previous CMAQ compilation configure the ICON build script to use the available libraries If you have not already done so compile the STENEX library Configure the ICON build script for your application Invoke the build script to create an executable bldit icon pgf 5 5 2 4 ICON execution options The environment variables listed here are invoked during execution of the program and are set in the ICON run script EXEC default ICON_ CFG Executable to use for the simulation NPCOL_NPROW default 1 1 Domain decomposition for parallel mode ICON is normally run in a single processor environment so this setting should always be 1 1 GRIDDESC default GRIDDESC1 Grid description fil
107. ciation e radm2_to_cb05 convert the input boundary conditions profiles from RADM72 to CB 05 speciation e radm2_to_saprc99 convert the input boundary conditions profiles from RADM2 to SAPRC99 speciation Mechanism 52 5 2 2 Files configuration and environment variables Specifies the gas phase aerosol and aqueous phase chemical mechanisms to create boundary conditions for The choices for t Mechanism variable are the mechanism directory names under the M3MODEL include release directory Examples include e cb4_ae3_aq CB IV gas phase mechanism 3rd generation CMAQ aerosol mechanism aqueous cloud chemistry e cb4_ae4_aq CB IV gas phase mechanism 4th generation CMAQ aerosol mechanism aqueous cloud chemistry e cb05_ae4_aq CB 05 gas phase mechanism 4th generation CMAQ aerosol mechanism aqueous cloud chemistry e saprc99_ae4_aq SAPRC99 gas phase mechanism 4th generation CMAQ aerosol mechanism aqueous cloud chemistry e saprc99 ae3_aq SAPRC99 gas phase mechanism and 3rd generation CMAQ aerosol mechanism aqueous cloud chemistry 5 2 2 3 BCON compilation Section 3 3 provides an overview of how to install and compile the CMAQ programs for the benchmark simulation Follow the steps outlined in Section 3 3 to compile new versions of BCON l If not already done build the CMAQ source code and compilation management program M3BLD this only needs to be done the first time CMAQ is installed Install and compile the I O AP
108. cifying a linear combination of IRR operators IRR global definitions or IRRs for specified reactions Each individual term in the combination must include either one of the five IRR operators described in Table M 14 e opi acycle name a reaction sum name or a reaction label enclosed in greater than and less than signs The op tional qualifiers quali for cyclename or reaction sum name can be either POSONLY or NEGONLY With these qual ifiers the defined quantity is included as a term only when it is positive or negative respectively If the name is not qualified the quantity is included regardless of sign The numerical coefficients for each term ci are assumed to be one unless they are explicitly included The irrname that is supplied by the user will be assigned as the variable name in the I O API IRR output file 93 5 10 2 Files configuration and environment variables Command Description DESCRIPTION description The description command is provided to allow the user to specify a long description of the output variable that will be included on the I O API IRR output name If a descrip tion is not specified for an IRR_OUTPUT variable the ir rname or short name will be used in the output file If the description command is used it should be located immedi ately following the IRR_OUTPUT command to which it applies PROD species FROM species ANDIOR species3
109. commendations Chemical Mechanisms e The versions of each chemical mechanism that include both aerosols and aqueous chemistry represent the most comprehensive modeling approach e If you are neglecting or removing cloud processes you can use the chemical mechanism that excludes the aqueous chemistry e You must use the same chemical mechanism for the CMAQ chemical transport model CCTM and all of the input processors that are part of the CCTM system e The Euler Backward Iterative EBI chemistry solver is mechanism dependent When you modify a chemical mechanism you will not be able to use the default EBI solver for the new mechanism The Rosenbrock and GEAR solvers are the only mechanism independent choices of chemistry solvers with the CCTM e When adding new species to CMAQ it is important to check that the sources of these new species into the modeling domain are accounted for correctly in the mechanism include files If you are adding these species to the domain through the emissions files the GC_EMIS EXT include file must contain these new species If the new species will also enter the domain as initial and boundary conditions check the GC_ICBC EXT file for the presence of these species 9 5 References 158
110. conditions vertical profiles Line Column Name Type Description 12 20 LAYERI1_IC Exp IC concentration for species 2 in lowest sigma layer required 23 31 LAYER2_IC Exp IC concentration for species 2 in 2nd sigma layer required 34 42 LAYER3_IC Exp IC concentration for species 2 in 3rd sigma layer required 45 53 LAYER4_IC Exp IC concentration for species 2 in 4th sigma layer required LAYERX_IC Exp IC concentration for species 2 in Xth sigma layer required LAYERX_IC Exp IC concentration for species 2 in Xth sigma layer required Y 1 10 SPECIESY String Pollutant name en closed in double quotes required 12 20 LAYERI1_IC Exp IC concentration for species Y in lowest sigma layer required 23 31 LAYER2_IC Exp IC concentration for species Y in 2nd sigma layer required 34 42 LAYER3_IC Exp IC concentration for species Y in 3rd sigma layer required 45 53 LAYER4_IC Exp IC concentration for species Y in 4th sigma layer required LAYERX_IC Exp IC concentration for species Y in Xth sigma layer required A sample of the four sections of an IC_PROFILE file is shown below Optional initial condition The vertical coordinate of the model to generate these b c is the terrain following sigma coordinate The number of sigma layers and defined sigma levels are listed below 6 55 1 00 0 98 0 93 0 84 0 60 0 30 0 00 104 6 1 3 BC_PROF
111. cs cede b chee ois cs Gan aden ida a N coe tee Sate Soo tS nae sn esd agatha ates 49 BC CLM eee eae e e cence ote amp ERS unis sin E sacle sae E tae E ee tei am ae A aie E cei di eine Ieee aes 55 DA CHEM MP C H a hat ecselalennereu lu aeblatochouind E EEEE 66 DOI GON aa eters e e e a a a Natur Gea tenia a E tech tenia e a A Nite a rd 69 DO IPROC eae eso e rees raae S EEE CANES EN e PEE CREATE ENE ih ARR BLN 74 Coe AG Pees tas totaal Arcane Ae E TE E E E a Caco dtsooutg E Gir E cue canes ae naan E E ele nen E thse 78 D8 ARARIO seston sinh chelates tae ots eb bates Woewots Meee oes Soa aba ebala eb nd es Mevtnas oti et debate es ete 82 DO DE Ed BIY thetiss teria sn E E TEE Dea tactee tect E EEE A as Sea ae ontIG Pash OINGea spies cans EE SE A 83 Ss LOM PROGAN maa Sees Sete a a dates Saab a ha iak Gees Ble we SAP RI oon RI Og Tees ha elon eee 88 De SS TENE X cs nips 2s Sanne oes stevia aie ciety a ecb aces eee eee was oh Rots Whats Sed ne nie Seven Mase aie tena E Paine EA 95 JZ RETETENCES EE E hoe Seat SEEE EEE S A EE E E EEEE ES E E 96 5 1 Overview CMAQ consists of aset of core programs that are needed to perform a basic air quality model simulation Figure 5 1 shows these core programs and how they relate to each other Utility programs such as PROCAN and PDM are excluded from this diagram these programs are discussed later in this chapter The lines between the boxes represent one or more files passing between the programs and show the dependenc
112. d Figure 2 4 Initial and boundary conditions preprocessing for CMAQ CMAQ Chemical Transport Model CCTM CCTM 3 D CONC File Both the vertical concentration profile fields and the CCTM concentration fields have specific chemical mechanisms associated with them which are a function of how they were originally generated Figure 2 4 assumes the RADM2 chemical mechanism was used to generate the default vertical profiles and is consistent with the profiles distributed with the CMAQ version 4 4 tutorial dataset Existing CCTM 3 D concentration fields could have been generated using several different chemical mechanisms The chemical mechanism used in the user s CCTM and CMAQ input processors must be consistent with the mechanism used to generate the ICON and BCON concentration fields unless you use the option to convert to either Carbon Bond IV CB IV Gery et al 1989 or Statewide Air Pollution Research Center 1999 SAPRC 99 Carter 2000 from RADM2 ICON and BCON are capable of converting from the RADM2 to either the CB IV or SAPRC 99 chemical mechanisms as discussed in Chapter 5 ICON and BCON can linearly interpolate input concentration profiles from one horizontal or vertical coordinate system to the one needed for the model simulation if the input data are in the standard I O API format If the interpolation is between two different vertical coordinate systems the mid layer height of each vertical layer must also be available 2
113. d aqueous chemistry options plume in grid options and diagnostic options such as process analysis The CCTM has the largest number of configuration options of all the CMAQ programs Plume Dynamics Model PDM The PDM is the plume in grid preprocessor to CMAQ It generates plume dy namics such as dimensions and location from special emissions input files generated by an emissions model for plume in grid simulations see Section 5 9 The information generated by the PDM is supplied to a CCTM ex ecutable instrumented for plume in grid modeling that uses a Lagrangian reactive plume model for sub grid scale 1 3 Features of CMAQ for Application Users representation of plumes from large point sources The output from the PDM is a binary netCDF file of plume parameters for input to the CCTM e Process Analysis Preprocessor PROCAN PROCAN generates FORTRAN INCLUDE files for building a version of the CCTM that can calculate integrated process rates and or integrated reactive rates for diagnosing CMAQ simulations It uses an input configuration file to select the processes analysis options and outputs three INCLUDE files that are used to compile a version of the CCTM instrumented for process analysis e Chemical Mechanism Compiler CHEMMECH This program creates mechanism INCLUDE files for CMAQ from a mechanism definition file Chemical mechanisms are represented in CMAQ through a series of INCLUDE files that contain mechanistic and kineti
114. d for the 2005 release This scheme is globally mass conserving and uses the piecewise parabolic method PPM Colella and Woodward 1984 advection scheme for horizontal advection deriving a vertical velocity component at each grid cell that satisfies the mass continuity equation using the driving meteorology model s air density The mixing ratio correction step used in previous CMAQ versions is not needed with this method Note that the former advection scheme with the same ho rizontal advection but also using PPM for the vertical velocity component is still available along with the mixing ratio correction step The horizontal advection module for CMAQ is the Piecewise Parabolic Method PPM Colella and Woodward 1984 This algorithm is based on the finite volume subgrid definition of the advected scalar In PPM the subgrid distribution is described by a parabola in each grid interval PPM is a monotonic and positive definite scheme Positive definite schemes maintain the sign of input values which means in this case that positive concentrations will remain positive and cannot become negative The vertical advection modules solve for the vertical advection with no mass exchange boundary conditions at the bottom or top of the model CMAQ also uses PPM as its vertical advection module In CCTM the PPM algorithm with a steepening procedure is implemented for vertical advection as the default because of the strong gradients in the tracer specie
115. d in PARMS3 EXT as the variable name and or layer number to read all variables or all layers from the file respectively For time independent files the date and time arguments are ignored 4 5 Writing Data Files in 1O API CMAQ module developers should use the logical function WRITE3 to write data to files For gridded boundary and custom files the code may write either one time step of one variable at a time or one entire time step of data at a time in which case use the magic value ALLVAR3 as the variable name For ID referenced profile and grid nest files the code must write an entire time step at a time LOGICAL FUNCTION WRITE3 FNAME VNAME JDATE JTIME BUFFER where CHARACTER FNAME file name for query CHARACTER VNAME variable name or ALLVAR3 ALL INTEGER JDATE date formatted YY YYDDD 40 4 6 CMAQ Related I O API Utilities INTEGER JTIME time formatted HHMMSS BUFFER array holding output data WRITE3 writes data for the variable with name VNAME for the date and time i e JDATE and JTIME to an I O API formatted data file with logical name FNAME For time independent files JDATE and JTIME are ignored If VNAME is the magic name ALLVAR3 WRITE3 writes all variables If FNAME is a dictionary file WRITE3 treats VNAME as a dictionary index and ignores JDATE and JTIME A typical WRITE3 call to write data for a given date and time might look like this REAL 4 ARRAY NCOLS NROWS NLAYS N
116. d on local wind deformation ModVdiff default acm2 Vertical diffusion module e vdiff_noop deactivate vertical diffusion e eddy calculate vertical diffusion using eddy diffusivity theory e eddy_carb eddy vertical diffusion instrumented for carbonaceous aerosol apportionment 59 5 3 2 Files configuration and environment variables e edd_hg eddy vertical diffusion instrumented for the mercury CMAQ model e eddy_sulf eddy vertical diffusion instrumented for the sulfate tracking model e eddy_tx eddy vertical diffusion instrumented for the air toxics CMAQ model e acm2 calculate vertical diffusion using the Asymmetric Convective Model version 2 e acm2_carb ACM vertical diffusion instrumented for carbonaceous aerosol apportionment e acm2_hg ACM vertical diffusion instrumented for the mercury CMAQ model e acm2_sulf ACM2 vertical diffusion instrumented for the sulfate tracking model e acm2_tx ACM vertical diffusion instrumented for the air toxics CMAQ model ModPhot default phot Photolysis calculation module e phot_noop deactivate photolysis rate calculations e phot calculate photolysis rates ModPing default ping_noop Plume in Grid module e ping_noop deactivate plume in grid model e ping_smvgear_aero3 use the CMAQ plume dynamics model with an internal SMVGEAR chemistry solver for gas phase chemistry with aero3 e ping_smvgear_aero4 use the CMAQ plume dynamics model with an internal SMVGEAR chemistry s
117. d policy analysis to understanding the complex interactions of atmospheric chemistry and physics First generation air quality models simulated air quality using simple chemistry at local scales and Gaussian plume formulation was the basis for prediction Second generation models covered a broader range of scales local urban regional and pollutants addressing each scale with a separate model that often focused on a single pollutant e g ozone Third generation models like CMAQ treat multiple pollutants simultaneously up to continental or larger scales often incorporating feedback between chemical and meteorological components Future efforts toward fourth generation systems will extend linkages and process feedback to include air water land and biota to provide a more holistic approach to simulating transport and fate of chemicals and nutrients throughout an ecosystem 1 1 Background and Goals Air quality models integrate our understandings of the complex processes that affect the concentrations of pollutants in the atmosphere Establishing the relationships among meteorology chemical transformations emissions and removal processes in the context of atmospheric pollutants is the fundamental goal of an air quality model Seinfeld and Pandis 1998 In contrast to statistical air quality models that use historical trends in observed atmospheric conditions to predict air pollution CMAQ uses coupled mathematical representations of actual chem
118. d vertical plume growth and transport of each plume section during the subgrid scale phase of the plume cycle The PDM outputs an active plume file that is input to the CCTM along with the major elevated point source emissions MEPSE file from an emissions processing system to simulate selected point sources with the PinG treatment Figure 2 7 is a schematic that relates PDM to other components in the CMAQ modeling system Figure 2 7 Figure 2 7 Plume in Grid treatment in the CMAQ modeling system Emissions Modeling System Meteorology PDM CMAQ Chemical Transport Modeling Model CCTM compiled for System Output PinG 2 2 6 PROCAN Process Analysis Preprocessor Process Analysis PA is an accounting system that tracks the quantitative effects of the individual chemical and physical processes that combine to produce the predicted hourly species concentrations within a CTM simulation Typically Eulerian grid models such as the CCTM produce output concentration fields that are solutions of systems of partial differential equations for the time rate of change in species concentrations due to a series of individual physical and chemical processes and then combining these results to obtain a cumulative hourly concentration PA tracks the mass throughput of these individual processes and provides quantitative information about how each process impacted the predicted hourly species concentrations PA is an optional conf
119. dary conditions file Figure 6 1 Illustration of CMAQ boundary condition file EXAMPLE One Layer Simple Boundary NTHIK 1 NTHIK 1 Boundary component S B 11 B row 0 JE NCOLS 11 B 2 NCOLS 2 NROWS 4 single indexes the entire boundary a S 1 NCOLS 1 EQUIVALENCE S 1 B 1 E 1 NROWS 1 EQUIVALENCE E 1 B NCOLS 2 N 0 NCOLS EQUIVALENCE N 1 B NCOLS NROWS 4 W 0 NROWS EQUIVALENCE W 1 B 2 NCOLS NROWSs45 120 6 1 14 INIT_CONC_1 Initial Conditions Figure 6 2 Graphical example of a CMAQ gridded boundary conditions file Layer 1 O3 Boundary Conditions file BCON_smoke sapre b1_M_36 NC96mqg profile 0 035 53 ppmV 1 52 January 1 0 0 00 00 Min 0 030 at 2 1 Max 0 035 at 1 1 6 1 14 INIT_CONC_1 Initial Conditions Used by CCTM CMAQ requires the initial concentrations of each species being modeled to be input to the model The initial conditions input file type is GRDDED3 and does not vary with time The file data is looped accordingly by column by row by layer by variable Initial conditions files have the identical structure as concentration files so as to allow the user to initialize the results of day 2 as an example with the predicted concentrations from the last hour of day 1 This allows the CMAQ user flexibility to segment simulations in any way they want The CMAQ program ICON Section 2 2 2 is used to generate CMAQ initial condi
120. deCenter rack mounted nodes with Red Hat Enterprise Linux OS 2 5 GB RAM per node Gigabit Ethernet network 1 5 TB hard drive storage Super DLT 110 GB tapes for system back ups UPS Optimal CMAQ Hardware Solution 2 3 8 dual CPU 2 5 GHz AMD Athlon MP 2000 PC s with Red Hat Fedora Core 1 2 0 GB RAM per PC Gigabit Ethernet network 80 GB system storage 10 TB IDE SCSI RAID 5 array Super DLT 110 GB tapes for system back ups UPS 1 2 Software To run CMAQ the programs listed in Table 3 1 must be installed on the chosen system this list includes the programs distributed with CMAQ Table 3 2 lists additional utility software that is not required for running CMAQ but is useful for model diagnostics and evaluation 28 3 1 2 Software Table 3 1 Software required for running CMAQ Software Description Source CMAQ Programs M3BLD Models 3 program builder for source code management and code compila tion JPROC Photolysis rate processor ICON Initial conditions preprocessor BCON Boundary conditions preprocessor MCIP Meteorology Chemistry Interface Pro cessor for converting MM5 output to CMAQ format Contained in the standard CMAQ dis CCTM CMAQ Chemical Transport Model tribution sata at ene center org PDM Plume Dynamics Model for calculating plume characteristics for Plume in Grid modeling CHEMMECH Chemical mechanism compiler for modifying or adding r
121. del Validation tests and simulation of an Atlantic cyclone and cold front Mon Wea Rev 121 1493 1513 143 7 11 References Dudhia J D Gill Y R Guo D Hansen K Manning and W Wang 1998 PSU NCAR mesoscale modeling system tutorial class notes MM5 modeling system version 2 Available from the National Center for Atmospheric Research P O Box 3000 Boulder CO 80307 Grell G J Dudhia and D R Stauffer 1995 A description of the fifth generation Penn State NCAR mesoscale model MM5 NCAR Tech Note NCAR TN 398 STR 117 pp Available from the National Center for Atmospheric Research P O Box 3000 Boulder CO 80307 Guo Y R and S Chen 1994 Terrain and land use for the fifth generation Penn State NCAR mesoscale modeling system MM5 Program TERRAIN NCAR Tech Note NCAR TN 397 IA 119 pp Available from the National Center for Atmospheric Research P O Box 3000 Boulder CO 80307 Haagenson P J Dudhia D Stauffer and G Grell 1994 The Penn State NCAR mesoscale model MM5 source code documentation NCAR Tech Note NCAR TN 392 STR 200 pp Available from the National Center for Atmospheric Research P O Box 3000 Boulder CO 80307 Kain J S and J M Fritsch 1990 A one dimensional entraining detraining plume model J Atmos Sci 47 2784 2802 Kain J S and J M Fritsch 1993 Convective parameterization for mesoscale models The Kain Fritsch scheme The representatio
122. del time contained in each output time step CTMLAYS Sigma values of the vertical layers in the 3 d MCIP output Comma delimited values for each sigma value must be in descending order starting at 1 and ending with 0 There are a maximum of 100 layers allowed To use the all of the layers from the input meteorology without collapsing or explicitly specifying set CTMLAYS 1 0 MKGRID default T Determines whether to output static GRID meteorology files e BTRIM default 0 The number of boundary points to remove on each of the four horizontal sides of the MCIP domain This setting affects the output MCIP horizontal domain by reducing the input meteorology domain by 2 BTRIM 2 NTHIK 1 where NTHIK is the lateral boundary thickness from the BDY files The extra point reflects the conversion from the grid points dot points to grid cells cross points Setting BTRIM 0 will the maximum of the input meteorology domain To remove the MM5 lateral boundaries set BTRIM 5 For windowing a subset domain of the input meteorology set BTRIM 1 this setting causes BTRIM to be replaced by the information provided by X0 YO NCOLS and NROWS see below XO X coordinate of the lower left corner of the full MCIP X domain including the MCIP lateral boundary based on the input MM5 domain XO refers to the east west direction This setting is only used when doing a subset of the input meteorology domain by setting BTRIM 1 Y
123. description segment Table 4 3 and consists of text records giving grid name related coordinate system name and descriptive parameters XORIG YORIG XCELL YCELL NCOLS NROWS and NTHIK In the usual Models 3 modeling situation there will be both dot point and cross point grids present these grids are topological duals in the sense that the vertices corners of one correspond to the cell centers of the other Each data record in these files consists of two or three list formatted lines i e items are separated by either blanks or commas Name fields are quoted strings and appear on the first of these lines Numeric fields are given in double precision and occur on either the second line or the second and third this allows you to organize the text so that it is easily viewed in a text editor without running off screen The records have the following organization depending upon whether they are in the first or second segments COORD NAME COORDTYPE P_ALP P_BET P_GAM XCENT YCENT or COORD NAME COORDTYPE P_ALP P_BET P_GAM XCENT YCENT and GRID NAME COORD NAME XORIG YORIG XCELL YCELL NCOLS NROWS NTHIK or GRID NAME COORD NAME XORIG YORIG XCELL YCELL NCOLS NROWS NTHIK There are at most 32 coordinate systems and 256 grids listed in one of these files These files are small enough to be archived easily with a study and have a sufficiently simple format that new ones can easily be constructed by hand
124. e CCTM uses to calculate gas phase chemical transformations and pollutant concentrations Initial Conditions Processor ICON ICON generates a gridded binary netCDF file of the chemical conditions in the modeling domain for the first hour of a simulation It can generate these initial conditions from either an ASCII file of vertically resolved concentration profiles or from an existing CCTM output file If the ASCII profiles do not have the same vertical structure as the CCTM configuration ICON will interpolate the data to a vertical structure consistent with the CCTM s Using an existing CCTM output file to generate initial conditions is applicable when extrapolating initial conditions from a coarse to a fine grid simulation as may occur when setting up nested simulations The configuration options for ICON include selecting the chemical mechanism to model defining the horizontal and vertical grids and choosing whether the initial conditions are generated from an ASCII profile or from an existing CCTM output file Boundary Conditions Processor BCON BCON generates a gridded binary netCDF file of the chemical con ditions along the horizontal boundaries of the modeling domain These boundary conditions can be either static or time varying and as with ICON can be generated from either an ASCII file of vertically resolved concentration profiles or from an existing CCTM output file Also as with ICON BCON will interpolate the data in the ASCII profi
125. e data required B Level Field Indicator String LEVELS required C Comment String Description of the level field usually units in m optional 3 A XZJV_1 Real Height of level 1 units in m required B XZJV_2 Real Height of level 2 units in m required x XZJV_x Real Height of level x units in m required 4 A JVLAT Int Number of latitudes covered by the data required B Latitude Field Indicat String LATITUDES re or quired C Comment String Description of the latit udes field usually units in degrees op tional 5 A XLATJV_ 1 Real Latitude 1 units in de grees required B XLATJV_2 Real Latitude 2 units in de grees required x XLATJV_x Real Latitude x units in de grees required 6 A JVTMAX Int Number of hour angles covered by the data required B Hour Angle Field In String HOUR ANGLES re dicator quired C Comment String Description of the hour angles field usually units in hours from noon optional 124 6 1 15 JTABLE Photolysis Rates Lookup Table Line Column Name Type Description XHAJV_1 Real Hour angle 1 units in hours from noon re quired XHAJV_2 Real Hour angle 2 units in hours from noon re quired XHAJV_x Real Hour angle x units in hours from noon re quired JPHOT Int Number of photolytic reactions covered by the data required Reaction Field Indicat or String PHOTOLYTIC REAC
126. e Data Support Section Scientific Computing Division NCAR NCAR is operated by UCAR and is sponsored by the National Science Foundation Published research that uses data from the NCAR archive shall credit the maintainers of the archive and the original source s of the data shall be acknowledged 135 7 2 System Requirements 7 2 System Requirements MMS which superseded its predecessor MM4 was released to the public in the early 1990s MM5 and its supporting software i e pre processing and post processing programs were originally designed to run on a Cray supercomputer Over the past few years the software structure has been modified to enable the model to also run on various workstations Today MM5 can run on many hardware platforms including Cray SGI Sun DEC Hewlett Packard IBM and per sonal computers running Linux In addition MMS has software directives to efficiently use multi processor computers including shared memory distributed memory and massively parallel architectures Although MM5 has been run on workstations not all of the supporting software is available in a workstation version at this time Also there may be significant performance differences when running MM5 on different manufacturers workstations and supercomputers CMAQ Version 4 4 does not include MM5 Users will need to download and install MM5 on their own 7 3 Software Languages MM5 and its supporting software are largely written in Fo
127. e GRIDDESC file Section 4 1 1 CMAQ horizontal grids are selected in the horizontal grid definition section of the CMAQ run scripts by setting the GRIDDESC and GRID_NAME en vironment variables to point to an existing grid definition file and to one of the grids defined in the file respectively Horizontal grids can be selected from either predefined grids contained in the distributed GRIDDESC file or by adding modifying horizontal grids through the GRIDDESC file 9 2 1 Using predefined horizontal grids CMAQ is distributed with a GRIDDESC file that contains definitions for two different coordinate systems and several different grids on these coordinate systems While the tutorial dataset packaged with CMAQ only uses two of these grids M_32_99TUTO2 and M_08_99TUTO02 any of these predefined grids are appropriate for setting up CMAQ simulations For the CCTM which requires gridded meteorology and emissions as input the only viable grid choice is one that coincides with available input datasets For the other meteorology independent processors any of the grid definitions listed in the distributed GRIDDESC file are options To select one of the predefined horizontal grids set the GRID_NAME environment variable in the applicable run script to the name of the grid that you would like to model 9 2 2 Creating or modifying horizontal grids Creating a grid in CMAQ simply involves adding a few lines of text to the GRIDDESC file Using a combinati
128. e SMOKE emissions system and how to set it up not required for the tutorial simulation e PARALLEL NOTES text file containing comments related to running the CMAQ CCTM in Linux MPICH clusters e PROCESS_ANALYSIS_NOTES text file containing comments related to running the CMAQ CCTM with process analysis e PING_PDM_NOTES text file containing comments related to running the CMAQ CCTM with plume in grid treatment e TUTORIAL_PROCEDURE text file describing how to work through the tutorial e RELEASE NOTES text file containing a list of the changes since the last release e MODELS tar gz gzipped tar file 2 3 Mb containing model tools and libraries source code CVS archives e M3DATA tar gz gzipped tar file 106 Mb containing the required datasets not produced by this package e SCRIPTS tar gz gzipped tar file 17 Kb containing C Shell scripts to build and execute the CMAQ models e M3DATA_REF tar gz gzipped tar file 315 Mb containing reference data to compare with datasets produced by the tutorial on a Linux workstation 30 3 2 Installing CMAQ Source Code The default CMAQ installation is configured for a Red Hat Linux system and the Portland Group FORTRAN compiler 1 Set the environment variable M3HOME to alias the directory in which you want to install CMAQ e g 2 Set environment variables for the M3DATA M3LIB and M3MODEL directory paths needed by CMAQ setenv M3DATA M3HOME data setenv M3LIB
129. e dependent 3 D dot point meteor ology file The default location of the MCIP output files is the M3DATA mcip3 GridName directory Since the default file names do not have any information about the model grid that they are simulating the name of the grid is wired in the output directory path The default naming convention for all MCIP output files uses only the APPL environment variable in the file name All of the file naming variables for the MCIP outputs are set in the run script 5 8 PARIO 5 8 1 Description The PARIO library contains modules for controlling the model input and output in parallel multi processor computing environments In addition to a series of CMAQ specific routines it contains special implementations of several of the I O API modules for multi processor computing environments The PARIO library is only necessary when compiling the CCTM for parallel multi processor environments single processor versions of the CCTM and the other CMAQ programs do not use the PARIO library 5 8 2 Files configuration and environment variables 5 8 2 1 PARIO input files PARIO does not require any input files 82 5 9 PDM 5 8 2 2 PARIO compilation options Other than configuring the build script for your system i e compiler and library locations PARIO does not require any configuration at compilation 5 8 2 3 PARIO compilation Section 3 3 provides an overview of how to install and compile the CMA
130. e e coos vec betes Save cove ncaa dee cabs nese asia EE EEE ES wees 40 4 6 CMAQ Related I O API Uthhittes c5 35ccssscssscossess cooescgsbesteussesoseesseesanuss seseesgsvesteodssveteegsedossasesnons 41 4 7 RELCTENCES i isine e e bib a ei wa EEE stabs EEE A EEEE E EEEE E Bates ies REE AOO ERES 46 5 CMAQ Programs and Libraries srnsisssie ont eiea e EEE E E yas E AEE E a AE EE Ga 47 De 2 OVERVIEWS ise esc PES SS cu seas aes E EEE Go ek eects EN EE VEEE EEE E ESET EEEE e 47 J2 BOON recs sdesey ates ges an a sores Seeds Ss ae vee ots saess sada ss seas sees SERE EO Eoo EEE EE dees Sh EET E na RE ness 49 D3 CCIM niestre oe shes debs ty Selchylotvededs E E ing bebe dy Sebeds ESEE boas E EVO EE EEES ES EEN 55 JA CHEMMECH ariei tert aa a a a aes aa bon a E a a a E iets ees 66 5 9 CON eens o TE A O EEE ENE E EEN Sods Sad Sessa ETE Sea O Sek E e a E 69 PAPAI O CEE EE E TETE ET 74 Dh MOP see e ete eE E E ES EE EE EEEE ESE TE EEE E EEE EE EEE ES 78 5 83 PARIO rociera eaae a E o E a E E E nde AT a a E E E E AETS 82 X9 PDM riitaa a deep rahe dest E OE ee RE EEEE E S E E E de E E EO ESES 83 310 PROCAN spier raie radne oppa T a aE abe RS EEE SEE de used oth ERA TISS PE PEESI NESE EEOSE ES KES 88 5 11 STENEX iaee e vies E ied E E V EE EEE E E E ET ES ESS 95 5 12 ReferenceS siepe n a a E pas E E Ta E T eonoa 96 62 CMAQ FLES o ire E Tis potatoe EE cS eee Seed EEEE E ETE O EO O TE Dee E GA 97 6 1 CMAQ Input File Sa hsrs ernas Eo Ea KE RE NIE ETIR SEEE abes caves RE
131. e for setting the horizontal grid definition GRID_NAME Name of the grid definition contained in the GRIDDESC file that specifies the horizontal grid for the current ap plication of the model LAYER_FILE Name and location of a MET_CRO_3D file for specifying the vertical layer structure for the current application of the model OUTDIR default M3DATA icon Output data directory IC Sets the input file type The setting of this variable determines how the input and output environment variables are set by the run script 73 5 6 JPROC e profile sets the output file name to include the tag profile in the name uses the variable IC_PROFILE to point to an ASCII vertical profile file for input to ICON Also optionally looks for the variable MECH_CONV_FILE to point to a user defined mechanism conversion file e m3conc used for nested simulations sets the output file name to include a start date in the name uses the variable CTM_CONC_1 to point toa CCTM CONC file for input to ICON Also looks for optional Plume in Grid inputs if the ICON_PING variable is set to YES e DATE Sets the Julian date to use for tagging the ICON output file for nested runs e SDATE Julian start date for extracting initial conditions from a CCTM CONC file for a nested simulation If SDATE is not set ICON will use the first hour of the CTM_CONC_1 e STIME Start time for extracting boundary conditions from a CCTM CONC file for a nested
132. e generated for every science process i e the first 12 codes shown in Table 5 3 The output variables that are generated are named either spe cies_pcodei or familyname_pcodei 91 5 10 2 Files configuration and environment variables Table 5 18 IPR process codes Process Code Definition XADV Advection in the E W direction YADV Advection in the N S direction ZADV Vertical advection ADJC Mass adjustment HDIF Horizontal diffusion VDIF Vertical diffusion EMIS Emissions DDEP Dry deposition CHEM Chemistry AERO Aerosols CLDS Cloud processes and aqueous chemistry PING Plume in grid XYADV Sum of XADV and YADV XYZADV Sum of XADV YADV ZADV TOTADV Sum of XADV YADV ZADV and ADJC TOTDIF Sum of HDIF and VDIF TOTTRAN Sum of XADV YADV ZADV ADJC HDIF and VDIF 92 5 10 2 Files configuration and environment variables Table 5 19 Integrated Reaction Rate Output Commands Command Description IRR_TYPE FULLIPARTIALINONE The IRR_TYPE command defines the type of IRR analysis With the type set to FULL IRRs for each individual reac tion will be calculated and written to the IRR output file and all other IRR commands will be ignored IRR_TYPE set to PARTIAL indicates that the IRR commands follow ing this command are to be processed to produce user defined IRR outputs Type set to NONE causes all IRR commands to be ignored a
133. e model grid layer configuration is that CCTM does not need to be recompiled when changing model grids layers but does need to be recompiled when new science options are invoked Optional output files are created when their associated optional processes are invoked in CCTM 5 3 2 Files configuration and environment variables Insert Schematic of CCTM 55 5 3 2 Files configuration and environment variables 5 3 2 1 CCTM input files 56 5 3 2 Files configuration and environment variables Table 5 3 CCTM input files File Name Format Description OCEAN_1 GRDDED3 Name and location of the time inde pendent 2 D file for defining the frac tion of each model grid cell covered by open ocean EMIS_1 GRDDED3 Name and location of the time depend ent 2 D or 3 D emission file speciated for a particular gas phase chemical mechanism and PM model output from an emission model such as SMOKE or CONCEPT MEPSE_1 GRDDED3 Name and location of the major emit ting point sources emissions file re quired only when the CCTM is com piled for PinG simulations output from an emission model such as SMOKE or CONCEPT PDM_PING_1 GRDDED3 Name and location of the active plume file required only when the CCTM is compiled for PinG simulations output from the PDM INIT_ GASCIAERO NONRITRAC _1 GRDDED3 Name and location of the time depend ent single time step 3 D
134. eactions to the CMAQ chemistry PROCAN Process analysis processor for setting up CMAQ to generate integrated reac tion rates or integrated process rates Compilers PGF90 Portland Group or Intel FORTRAN http www pgroup com 90 compiler GCC Gnu C compiler http gcc gnu org Code libraries STENEX CMAQ stencil exchange library for parallel job management Contained in the standard CMAQ dis tribution available at http www cmas PARIO CMAQ parallel input output manage center org ment library netCDF Network Common Data Form library http my unidata ucar edu content soft for controlling CMAQ file formats ware netcdf index html IOAPI Input Output Application Programmers http www bar Interface for controlling internal and onams com products ioapi external communications Source code management CVS Concurrent Versions System for man _http ximbiot com cvs cvshome aging the distributed archive of the CMAQ source code 29 3 2 Installing CMAQ Source Code Table 3 2 Optional support software for CMAQ Software Description Source Evaluation and visualization tools PAVE Package for Analysis and Visualization http www cmascenter org of Environmental Data for graphical analysis of netCDF gridded data IDV Integrated Data Viewer for 3 D graph http www unidata ucar edu soft ical analysys of netCDF gridded data ware idv IO API Tools Postprocessing tools for manipulating
135. eate truncate the code developer may fill in the file description from the INCLUDE file FDESC3 EXT to define the structure for the file and then call OPEN3 If the file doesn t exist in either of these cases OPEN3 will use the information to create a new file according to your specifications and open it for read write access In the unknown case if the file already exists OPEN3 will perform a consistency check between your supplied file description and the description found in the file s own header and will return TRUE and leave the file open only if the two are consistent An example of OPEN3 function is listed below from the CMAQ INITSCEN subroutine This program segment checks for the existence of aCCTM concentration CTM_CONC_1 file which if found will be open read write update If the CCTM CONC file is not found a warning message will be generated IF NOT OPEN3 CTM_CONC_1 FSRDWR3 PNAME THEN MSG Could not open CTM_CONC_1 file for update amp try to open new CALL M3MESG MSG END IF To get a file description i e I O API file type dimensions start date start time etc can be optained bye using DESC3 When DESC3 is called the complete file description is placed in the standard file description data structures in FDESC3 EXT Note that the file must have been opened prior to calling DESC3 A typical call might look like this IF NOT DESC3 myfile THEN error message ELSE
136. ective mixing e cloud_acm_hg ACM cloud model instrumented for modeling mercury e cloud_acm_tx ACM cloud model instrumented for modeling air toxics ModPa default pa Process analysis module e pa only configuration option at the module level to turn process analysis on off in CMAQ use the PAOpt variable see below ModUtil default util CMAQ utility modules e util only configuration option at the module level Mechanism default cbO5_ae4_aq Specifies the gas phase aerosol and aqueous phase chemical mechanisms to use for modeling air quality The choices for the Mechanism variable are the mechanism directory names under the M3MODEL include release directory Examples include e cb4_ae3_aq CB IV gas phase mechanism 3d generation CMAQ aerosol mechanism aqueous cloud chemistry e cb4_ae4_aq CB IV gas phase mechanism 3M generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry e cb05_ae4_aq CB 05 gas phase mechanism 4in generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry e saprc99_ae4_aq SAPRC99 gas phase mechanism ae generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry e saprc99_aq SAPRC99 gas phase mechanism and aqueous cloud chemistry e cb4ae4_ca_aq CB IV gas phase mechanism an generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry carbonaceous aerosol apportionment e saprc99_ae4st_aq SAPRC99 gas phase mechanism qn generation CM
137. ed by several primary parameters number of grid points in each horizontal dimension grid spacing center latitude center longitude map projection Mercator Lambert conformal or polar stereographic and number of nested domains and their horizontal dimensions Some other user specific parameters are also defined based on the primary parameters as required These parameters are processed by software that is executed only when a new domain location is required This software TERRAIN makes use of high resolution global terrain and land use datasets to create static files for the domain The static files currently include values at each grid point for terrain height and land use specification e g deciduous forest desert water Future releases of TERRAIN with Models 3 may include other time independent diurnal and seasonal and location specific information TERRAIN is described by Guo and Chen 1994 With CMAQ you can select a rectangular domain of any horizontal dimensions any grid spacing and most geograph ical locations A nesting capability is also available The number of grid points in the nests is restricted to a multiple of 3 plus 1 if you plan to use a two way nesting option discussed in Section 4 6 5 For example a valid number of grid points for one horizontal dimension can be 100 which is 33 x 3 1 or 85 which is 28 x 3 1 7 5 2 Processing the Meteorological Background Fields REGRID After the
138. ed in the following subsections 2 3 1 Gas Phase Chemistry Solvers Various modules for simulating tropospheric gas phase chemistry within CMAQ have been developed ranging from simple linear and nonlinear systems for engineering model prototypes to comprehensive chemistry representations for detailed chemical pathways related to atmospheric acid and oxidant formation In CMAQ Version 4 6 gas phase chemistry can be simulated with the Carbon Bond IV CB IV the 2005 update to the Carbon Bond mechanism CB05 Yarwood et al 2005 or the Statewide Air Pollution Research Center Version 1999 SAPRC99 photochemical mechanisms Because of CCTM s modularity users can modify the existing photochemical mechanisms or add new mechanisms To compute time varying species concentrations and their rate of formation or depletion called chemical kinetics equations governing chemical reaction kinetics and species conservation need to be solved for the entire species set CCTM uses special numerical techniques called chemistry solvers that compute these concentrations and rates at each time step Different solution algorithms have been investigated for the chemical kinetics in terms of the optimal balance of accuracy generalization and computational efficiency that is required for this component of the atmospheric system CCTM currently contains three options for solving gas phase chemical transformations with the Rosenbrock ROS3 Sandu et al 1997 Euler
139. edssccesudssciaw age sures sdseesdesdeseovas ETIESE pT RISER 98 6 2 Coordinate system description segment 0 cece eee ee cece e cence neeeeeeeeeceeeeeeeeaeeeaeeea seas seas eeu eeeeeeeeees 100 6 3 Coordinate system description SegMeNt icsse ee cece cece cence ence ence ES E E E aa E a E as 101 6 4 IC_PROFILE format description 0 ccccecceeceeceecneeeeceeceeceeceeceeceeeneceeeeceeesereeceeeeeeereseseresapereeenenes 103 6 3 BC PROFILE format description ss sss sas nenau a au sage aua e SPa den PERSEE EAT AR E RE 106 6 6 MECH_CONV_FILE format description eeseesessessesesseseseesessscscscesestessessesesterescerssssesescsetresersesees 157 6 7 CSQY format descriptions sieri aee E shes E EE E tea E E a A E E ETER 112 6 8 Example CSQY data fle o reite ee o E EEEE tes cee EEEN ETEN E E E S Seca REOS 113 6 9 ET file format description 3 ccscsisccosssasaesscuss Eurei anie er PrE S ne ERT E O PES EEEE OAEI NEEE SEPRE ITEE 114 6 10 PROFILE file format description crisser sisser e s T EEE EEVEE EEE EEEREN ESE S 116 Gels sner aeaea a a E E E EE E A E E E a N TEE bas 119 612 JTABLE file format description ssie ierte ee EEE E E EE E E E E EER 124 9 1 Chemical Mechanisins sisse sessir sereo dascascesagsovseahves snes sevotes EESE NEE SEPSAT EKOSE eap EENEI EEAS OS EE SESI SES ie 157 vii Vili Chapter 1 Introduction Table of Contents 1 1 Backsround and Goals ccc ese dest saecaas hates sa teea sea detab
140. either global or regional simulation that geographically covers the MM5 simulation domain and simulation period entirely The background fields are used to generate MM5 s first guess and lateral boundary conditions The first guess is improved with synoptic and mesoscale observations to generate an analysis that is transformed into an initial state for the model The lateral boundary conditions provide forcing to the model throughout the simulation and they can be especially influential in the later stages of the simulation Since CMAQ will be used to simulate very high resolution domains it is important to select a high quality background dataset for the model The MM5 system can ingest and process global analyses data generated by either the European Centre for Medium Range Weather Forecasts ECMWF or the National Centers for Environmental Prediction NCEP With an account on the NCAR Cray or other arrangements with NCAR see ht tp www mmm ucar edu mm5 fagqMM5 html you may retrieve the pre formatted global analyses data for use in MMS ECMWF global analyses data is twice daily at a 2 5 degree resolution from January 1980 to December 1989 A special dataset of the European Centre for Medium Range Tropical Ocean and Global Atmospheric program ECMTOGA global analyses is available for restricted usage in MMS This dataset at a 2 5 degree resolution from January 1985 through December 1997 is available from NCAR for a fee NCEP global troposp
141. el Post Processing nesoni e a a R a O RE 142 7 8 Meteorology Model Visualization and Evaluation seeeneseeseeeresseeresrerrsresrrrrsrrerrsrrerreresereeesreresreet 142 T9 Model Training and User SUpport siise r onn sees a Ene E E PESES AEE SE RA IERE EE PRSES STENE ses 143 7 10 Using MM5 with CMAQ S crises esae EENE EE EEEE EEE EE EES ESETE EE E E EE EEES EEES EE A 143 ANA Referentes snoeren ee a a a a a e E E a E A a ede patented EE EEEa 143 Meteorological data are important in many of the processes simulated in the CMAQ model The meteorology model that has been selected and evaluated as part of Models 3 to supply this data is the MMS All of the software in the Penn State National Center for Atmospheric Research NCAR mesoscale modeling system has been dedicated to the public domain and is presently used for both research and operational purposes by many organizations MM5 was selected to support Models 3 and CMAQ because it is a state of the science meteorological model that is in the public domain of the scientific community Improvements to MM5 within the meteorological community are on going and these enhancements can be evaluated for their applicability to air quality modeling 7 1 Credits and Disclaimers For Use of MM5 MM5 was developed in cooperation with Pennsylvania State University and the University Corporation for Atmospheric Research UCAR Penn State and UCAR make no proprietary claims either statutory or otherwise
142. en the distributed CMAQ tar file is unpacked a CVS directory tree is installed on the user s machine that contains archived copies of the CMAQ code The CMAQ program M3BLD controls the extraction of copies of CMAQ source code from CVS based on the configuration options specified by the user After exporting the CMAQ source code from CVS M3BLD then invokes a FORTRAN compiler to compile the CMAQ source code into FORTRAN object files and link them with the necessary precompiled libraries to create binary CMAQ executables C and FORTRAN compilers must be installed on the user s UNIX system in order to create CMAQ executables Since the model infrastructure was designed to promote modularity CMAQ requires new executables for each suite of science configuration options for all programs except MCIP There are too many combinations of the various chemical mechanisms horizontal and vertical transport schemes cloud routines and chemistry solvers in the CMAQ science configuration to include in a single executable The burden of recompiling CMAQ each time the science con figuration changes is offset by the flexibility to add new science to the model or simply to switch between different configurations This point about modularity is most pertinent to the CCTM although there are configuration options that must be selected when compiling the other CMAQ programs In addition to compile time configuration options with CMAQ there are also execution time configuratio
143. ered 8 With FAC units are cm molecule 9 FAC 1 0E 20 10 280 4 50 0 580 11 281 4 54 0 575 12 282 4 58 0 570 6 1 7 ET Extraterrestrial irradiance Used by JPROC ET is the logical name for the ASCII data file containing extraterrestrial radiation as a function of wavelength The extra terrestrial irradiance file has a format similar to the CSQY file The file begins with a header section comment lines are preceded with a Like the CSQY file the header contains a field describing the location on the wavelength interval that the data represents and a multiplier The data section uses a space delimited free form format and lists the wavelength of the incoming solar radiation nm and the irradiance Photons cm s at each wavelength with each row corresponding to a specific wavelength interval A detailed description of the file format is provided in Table 4 9 113 6 1 7 ET Extraterrestrial irradiance Table 6 9 ET file format description Line Column Name Type Description 1 A Comments String Preceded by com ment lines describe the file contents and document the source of the data optional n 1 A Data Location String Field indicating the location of the data as measured across the wavelength band pos sible answers begin ning ending centered point required n 2 A Multiplier String Multiplication factor to apply to photolysis rate equation line begins with FAC f
144. erface niie ses pantie a E tai leds iebidest bob kee aide int patlegs eda ideas bates attest 23 2 52 References eneore 2h acetates dela Ses Ssastente coves bs obs ah esos eb addes ens E E oe Eea tele 24 3 CMAQ System Requirements and Installation 0 eee cee ce eeceeeeeeecaeeeaeeeaeeaeeeaeeeueeeaeeeeeeeeneeeees 27 3 1 System Recommendations 2 0 0 0 cece cece eene E E EEEE E EEE EEEE sean ES 27 3 2 Installing CMAQ Source Codeseira ae a a sos E RAEE PASE ETES 30 3 3 Compiling CMAQ for the Tutorial Simulation sessseseesseeeseserrsresrrrrerrrrrsrrerrsrrerreresrrreesreresreee 32 3 4 Running the CMAQ Tutorial Simulation 2 0 0 0 eee cee cence eee ceeece ceca occa eeeaeeae eens eeaeeeneeeneeenes 34 3 5 Benchmarking CMAQ 0 csicdscdcin coc etebeccetsag EEE sega cds ERSE TEESEEISE ERES EREET EIEE EEE A EEEE t 34 4 Input Output Applications Programming Interface 2 0 0 0 eee ee cee cee cc eeceeeceeeea seca eesaeeae eeu eeueeeneeeenees 35 4 1 Files Logical Names and Physical Names 0 cccccece cece eee eeceeceeeceeeeeeeeeeeeaeeeaeeeaeeea sean eeneegs 35 4 2 IO API Data Structure and Data File Types 0 0 0 0 cece cece cece e cece cen eceneeeeeceeeeeeeeeeeeaesea seen eeaneeaes 36 4 3 Opening Creating Data Files in IO API 00 oe eee cc nec e cece ce ne ceneeeneceeeeeeeeeeeaesea esau sean eeaes 38 4 4 Reading Data Files in JO A PL S irp eae r ia E ta cesag iss pats E EES 40 4 52 Writing Data Files in TO API erro
145. ero3 takes chemical species concentrations and reactivity rates from the chemistry solvers and primary particulate concentrations from the emissions processor to compute fine and coarse particulate concentrations 21 2 3 5 Clouds and Aqueous phase Chemistry Invoking the AERO3 module will influence the sulfate ammonia and nitric acid concentrations predicted by the gas phase chemistry module The sulfate is partitioned between the vapor sulfuric acid and particle phases The greater part of the sulfate is put into the aerosols with a very small residual amount remaining in the vapor phase Nitric acid and ammonia are equilibrated with the aerosol species The aerosol module in CMAQ version 4 5 is called AERO4 The difference between AERO4 and AERO3 is that AERO4 includes consideration of sea salt aerosols Emissions of sea salt from the open ocean are calculated as a function of wind speed and relative humidity following the parameterizations of Gong 2003 and Zhang et al 27 respectively These emissions are speciated into sodium chloride and sulfate and are distributed by size to the accu mulation and coarse modes by fitting the emission parameterization to a bimodal distribution Note that sea salt emissions are calculated within the CMAQ model and do not require special pre processing in SMOKE Equilibrium between the accumulation mode which now contains sodium and chloride and the gas phase which now contains hydrochloric ac
146. es not execute them e verbose shows requested commands as they are executed MakeOpt Uncomment to build a Makefile to compile the executable ModInpt Defines the format of the boundary conditions input files to be used by BCON e m3conc input a CCTM CONC file used for nested simulations or windows of a parent domain e profile input an ASCII vertical profiles file ModMech Defines if the input boundary conditions data need to be converted from one chemical mechanism to another e mc_noop do not perform any mechanism conversion used when extracting boundary conditions from a CCTM CONC file for a nested simulation or when the input profiles are already formatted for the correct mechanism e user_defined input the file defined by the MECH_CONV_FILE variable used for custom mechanism conver sions e radm2_to_cb4 convert the input boundary conditions profiles from RADM2 to CB IV speciation e radm2_to_saprc99 convert the input boundary conditions profiles from RADM2 to SAPRC99 speciation Mechanism Specifies the gas phase aerosol and aqueous phase chemical mechanisms to create boundary conditions for The choices for the Mechanism variable are the mechanism directory names under the M3MODEL include release directory Examples include e cb4_ae3_aq CB IV gas phase mechanism 3rd generation CMAQ aerosol mechanism aqueous cloud chemistry e cb4_ae4_aq CB IV gas phase mechanism 4th generation CMAQ aerosol mechanism aqueous cloud
147. est battens eattas ee bt EE EA pa vaaN ease AE e TE 1 1 2 Overview of CMAQ System Components cece cece eee ceeece ceca ceca cece cena ceue eeu ceneceeneeeeeeeseeeeaeseaeeeaes 3 1 3 Features of CMAQ for Application Users 2 03 c 05 0ssssecsc apes dieeasssesesinesssougsovoess shsessvagsusstesdSesdeeedsss edness veces 6 1 4 Features of CMAQ for Air Quality Model Developers ce ccc eeceee cece cece cece ee ceneceneeeeeeeeeceneseeeeaeseaeeeues 6 1 5 New Features in Verson 4G r rrera een vsboteg ea antenna gst E EE balsas dateassaber de dea meoae E 7 1 6 About this manual i i raora eE E EE eae oe e IPEE E EE EE eed ee ee eon seek CeO I 9 AF RELCTENCES 5 95 nevis g Seah rA E Es EAEE ESEE PE EAN E EEEE EOS PESEE E PESEN IS EEEE EOS STOE EE RESES InG 9 The U S Environmental Protection Agencys Community Multiscale Air Quality CMAQ model is a three dimensional Eulerian i e gridded atmospheric chemistry and transport modeling system that simulates ozone acid deposition visibility and fine particulate matter throughout the troposphere Designed as a one atmosphere model CMAQ can address the complex couplings among several air quality issues simultaneously across spatial scales ranging from local to hemispheric The CMAQ source code is highly transparent and modular to facilitate extensibility through community development CMAQ is a third generation air quality model that is designed for applications ranging from regulatory an
148. f the CCTM executable When these options are in voked they create a binary executable that is fixed to the specified configuration The change these options it is necessary to recompile CCTM and create a new executable Opt default verbose Defines the action to be taken by the program M3BLD when extracting source code from CVS and compiling an executable e compile_all force compile even if all the object files are current e clean_up remove all source files upon successful compilation e no_compile do everything except compile e no_link do everything except link e one_step compile and link in one step e parse_only checks configuration file syntax e show_only shows requested commands but does not execute them e verbose shows requested commands as they are executed MakeOpt Uncomment to build a Makefile to compile the executable ParOpt Uncomment to build an executable for running on multiple processors Invoking this command requires the avail ability of a parallel Stenex library file a Pario library file and an MPI library include files ModDriver default ctm_yamo The CCTM general coordinate driver module e ctm air density based scheme for mass conserving advection e ctm_yamo Yamartino scheme for mass conserving advection ModInit default init_yamo The CCTM time step initialization module 58 5 3 2 Files configuration and environment variables e init air density based scheme for mas
149. fault 0 Continuation flag set to 0 for the first simulation day and 1 for all other days ICHUST default 1 Methods for calculating the standard deviation of the turbulent component v and the Lagrangian time scale method e 1 Hanna et al 1982 e 2 Hicks 1985 for convection boundary layer Nieustadt 1984 for stable boundary layer Arya 1984 for neutral boundary layer 86 5 9 2 Files configuration and environment variables ICHUSY default 2 Methods for calculating the standard deviation of the turbulent component y e 1 Irwin 1984 e 2 Weil 1988 and Venkatram 1988 ISHEAR default 1 Wind shear effects on plume e 1 calculate wind shear effects e 0 omit wind shear effects IMETHD default 1 Interpolation method need more description e 1 Linear e 0 PBL IDPLUM default 0 Plume thickness calculation methods need more description e 0 Turner Method e 1 Temperature gradient method IPRFLG default F Flag for activating the creation of additional diagnostic files e F omit extra diagnostic files e T print extra diagnostic files IPARTFLG default 0 Vertical partitioning flag need more description FACTC default 1 0 Plume hand over criteria need more description INITC default 1000 Plume initialization width m DDIRC default 1 8 Cross plume wind shear factor need more description DSPDC default 0 7 Wind speed shear factor need more descri
150. fault statistical analysis is a tabular listing by time period of the maximum value minimum value mean value and the standard deviation of the 2 datasets Several other calculations are also available Pointwise difference a b Pointwise difference b a Pointwise ratio a b Pointwise ratio b a Pointwise absolute value of difference la bl Difference normalized by 1st grid a b a Difference normalized by 2nd grid a b b Difference normalized by 2nd grid b a b Absolute value of difference normalized by A la bl a Absolute value of difference normalized by B la bl b Difference normalized by pointwise mean a b 0 5 a b Difference normalized by pointwise mean b a 0 5 a b Difference normalized by joint root mean square a b RMS a amp b Difference normalized by joint root mean square b a RMS a amp b Pointwise sum a b Pointwise maximum max a b 43 4 6 4 M3STAT Pointwise minimum min a b 4 6 4 M3STAT The M3STAT program reports the result of a statistical analysis of user selected variables in a CMAQ file The default analysis identifies the maximum minimum mean and standard deviations of the variable for individual time periods The program can also be used to calculate the number and percentage of grid cells above a particular threshold The following is a sample of m3stat output File NC_195aa_cc3_g1 lyrlo3 Date and time 1995191 120000 12 00 00 July 10 1995 Variable O3 3 D grid statistics
151. fic processes within CMAQ on a recurring basis 1 2 Overview of CMAQ System Components CMAQ is a suite of FORTRAN 90 programs that work in concert to estimate ozone particulate matter PM toxic compounds throughout the troposphere as well as acidic deposition The five main CMAQ programs are e The initial conditions preprocessor ICON e The boundary conditions preprocessor BCON e The clear sky photolysis rate calculator JPROC e The Meteorology Chemistry Interface Processor MCIP e The CMAQ Chemistry Transport Model CCTM Ancillary support programs distributed with CMAQ include e The code builder manager M3BLD e The chemical mechanism compiler CHEMMECH e The process analysis preprocessor PROCAN e The plume dynamics model for plume in grid simulations PDM This section describes the CMAQ system concept followed by summaries describing each of the programs listed above All CMAQ source code except MCIP is distributed in a UNIX tar file as a Concurrent Versions System CVS ht tp ximbiot com cvs cvshome source code management archive CVS is an open source network transparent version control system for managing source code in a software development environment CMAQ uses CVS to control access to the distributed source code by maintaining a protected version of the original source code and using copies of the code when building executables CVS must be installed on the user s UNIX system before installing CMAQ Wh
152. for a Level 1 standard atmospheric profile units in K re quired B Air Pressure at Level Real or Exp Air pressure for a 1 standard atmospheric profile units in mo lecules cm required C Ozone Concentration Real or Exp Ozone concentration at Level 1 for a standard atmo spheric profile units in molecules cm re quired C Aerosol Attenuation at Real or Exp Aerosol attenuation for Level 1 a standard atmospheric profile 1659 A Air Temperature at Real Air temperature for a Level 51 standard atmospheric profile units in K re quired B Air Pressure at Level Real or Exp Air pressure for a 51 standard atmospheric profile units in mo lecules cm required C Ozone Concentration Real or Exp Ozone concentration at Level 51 for a standard atmo spheric profile units in molecules cm re quired D Aerosol Attenuation at Real or Exp Aerosol attenuation for Level 51 a standard atmospheric profile 6 1 9 TOMS Total ozone mapping spectrometer data Used by JPROC TOMS is the logical name for the ASCII data file containing total ozone column measurements taken by the Total Ozone Mapping Spectrometer instrument aboard the sun synchronous polar orbiting Nimbus satellite The data is presented for specific Julian dates as a function of location on the earth latitude and longitude A detailed description of the file format is provided in Table 4 11 below The files are fix formatted 118 6 1 10
153. gative The coordinate system UAM EPS refers to a grid with the kilometer units instead of the UTM standard units which are meters UTMTOOL also provides grid corner calculations assuming either a UTM based or a Lambert based grid as appro priate to get UTM or Lambert corners of a LAT LON based grid work one corner at a time using the coordinate conversion facilities The program will repeatedly prompt you for operation to be performed from the following menu 1 Convert from LAT LON to UTM 45 4 7 References 2 Convert from UTM to LAT LON 3 Convert from UAM EPS to LAT LON 4 Initialize new LAMBERT projection by name 5 Define anew LAMBERT projection by angles 6 Convert from LAMBERT to UTM 7 Convert from UTM to LAMBERT 8 Convert from LAMBERT to LAT LON 9 Convert from LAT LON to LAMBERT 10 Get LAT LON grid corners from UTM specs 11 Get UTM grid corners from LAT LON specs 12 Get LAT LON grid corners from LAMBERT specs 13 Get LAMBERT grid corners from LAT LON specs 14 Quit the program 4 7 References Coats C 2005 The EDSS Models 3 I O API Available online at http www baronams com products ioapi Unidata 2005 NetCDF Available onlie at http www unidata ucar edu software netcdf 46 Chapter 5 CMAQ Programs and Libraries Table of Contents DV OVET VIEW cs sdedns E N Gann Gades pas ou eats sak paTNGaa aad Hebe DANTE aE aL aaa Test Peo E aa ARE t 47 DIEZ BCON es sa
154. gram that must be compiled by the user prior to use Distributed with a Makefile for compilation and run scripts for execution Chemmech reads a mech anism definition mech def file and outputs the mechanism include files 157 9 4 3 Tips and recommendations Chemical Mechanisms To modify an existing mechanism copy the mech def file that is contained in one of the mechanism include file direct ories to a new directory and modify the mechanism accordingly Provide this modified mechanism definition file to Chemmech as input to produce the mechanism include files needed to compile CMAQ Put these mechanism include files in a new directory under the M3MODEL include release directory To invoke this new mechanism set the Mechanism variable in the CMAQ build scripts to the name of the new mechanism directory and compile new ex ecutables To create a new mechanism for CMAQ follow a similar procedure as above for modifying mechanisms Use an existing mech def file as a template to format the new mechanism for inclusion in CMAQ After formatting the mechanism in the form of the mech def file provide this file as an input to Chemmech to create the required include files for CMAQ Move the resulting include files to a new directory under M3MODEL include release To invoke this new mechanism set the Mechanism variable in the CMAQ build scripts to the name of the new mechanism directory and compile new executables 9 4 3 Tips and re
155. he horizontal grids vertical layers and chemical mechanisms go to Chapter 8 to learn how to develop new model executables for running a simulation 9 1 Supported CMAQ Coordinate Systems The choice of coordinate system or map projection for CMAQ is governed by the I O API While the grid resolution horizontal and vertical extent are determined by the meteorology configuration that is input to the model the I O API can be used to perform grid transformations to generate meteorology inputs to CMAQ on a number of different coordinate systems While MM5 supports the Lambert Conformal Polar Stereographic and Mercator coordinate systems and thus directly supports these systems for CMAQ the I O API can expand these choices using its grid to grid transform ation routines The I O API ultimately determines which coordinate systems CMAQ supports The I O API supports the following coordinate systems and can be used to perform grid to grid transformations between them e Lat Lon e Lambert Conformal e Mercator 153 9 2 Horizontal Grids e General Tangent Stereographic e UTM e Polar Stereographic e Equatorial Mercator e Transverse Mercator While MM5 only supports a subset of these coordinate systems the I O API can be used to transform the MM5 met eorology into any of the systems that it supports Therefore the limited number of projections output by MM5 is expanded through the use of the I O API Generally the same meteorology u
156. he third party libraries used by CMAQ such as the IO API netCDF and MPICH is available in Chapter 2 5 2 BCON 5 2 1 Description The program BCON prepares chemical boundary conditions for the CCTM from either ASCII vertical profiles from an existing CCTM output concentration CONC file or from a larger scale e g global CTM The boundary conditions created by BCON can be static in time and space i e time invariant with uniform concentrations in all boundary grid cells dynamic in both time and space or a combination of these two The ASCII vertical profiles are primarily used to create static boundary conditions Dynamic boundary conditions can be extracted from CONC files on either the same horizontal grid spacing i e as a windowed modeling domain or for a finer resolution model grid i e for a nested simulation or they can be interpolated from a larger scale CTM simulation which is analogous to defining lateral boundary conditions for MM5 or WRF ARW There are two distinct modes of operation for BCON and each depends on the nature of the input data When creating BCON executables the user must specify whether the input data will be ASCII vertical profiles or a CONC file by selecting either profile or m3conc respectively for the setting of the ModInpt variable This variable determines the input module to use when creating a BCON executable 49 5 2 2 Files configuration and environment variables 5
157. hemistry aero3 the 3rd generation modal CMAQ aerosol model aero3_carb aero3 instrumented with primary carbonaceous aerosol apportionment aero3_sulf aero3 instrumented with a sulfate tracking model aero3_hg aero3 with mercury chemistry aero4 the 3rd generation modal CMAQ aerosol model with extensions for sea salt emissions and thermody namics aero4_carb aero4 instrumented with primary carbonaceous aerosol apportionment aero4_sulf aero4 instrumented with a sulfate tracking model aero4_hg aero4 with mercury chemistry aero4_tx aero4 with hazard air pollutant aerosol treatment ModAdepv default aero_depv2 CMAQ aerosol deposition velocity module aero_depv_noop deactivate aerosol deposition aero_depv2 oe generation CMAQ aerosol deposition velocity routine aero_depv2_carb aero_depv2 instrumented for carbonaceous aerosol apportionment aero_depv2_hg aero_depv2 instrumented for mercury modeling aero_depv2_sulf aero_depv2 instrumented for the sulfate tracking model ModCloud default acm CMAQ cloud module for modeling the impacts of clouds on deposition mixing photolysis and aqueous chemistry cloud_noop deactivate clouds in modeling 61 5 3 2 Files configuration and environment variables e cloud_radm RADM cloud processor e cloud_radm_sulf RADM cloud processor instrumented for the sulfate tracking model e cloud_acm RADM based cloud processor that uses the asymmetric convective model to compute conv
158. heric analyses data twice daily at a 2 5 degree resolution from July 1976 to April 1997 is also available from NCAR Background analyses data is also available from sources other than NCAR If you acquire such data from a source other than NCAR you may need to write software to format the data into a form that REGRID expects or you may need to modify REGRID to accept the analyses data 7 4 2 2 Meteorological Observations Standard meteorological observations of temperature relative humidity height sea level pressure and wind are required to improve the background fields with synoptic and mesoscale details The analysis model RAWINS discussed in Section 4 5 3 is set up to process surface observations including ship reports and buoys and upper air observations including radiosonde observations and wind profiles Other types of data may be included in the analysis if the appro priate modifications are made to the software With an account on the NCAR Cray or other arrangements with NCAR see ht tp www mmm ucar edu mm5 fagqMM5 html you may retrieve pre formatted surface and upper air observations that were acquired by NCAR from the National Centers for Environmental Prediction NCEP Daily surface observations including both land and water observations are available for the period from January 1978 through today Some of the dates include two sets of files six hour and three hour The six hour files include data observed at 00 06 1
159. ical and physical process to simulate air quality Based upon the underlying concept of preserving mass through a series of contiguous three dimensional grid cells covering a fixed model grid CMAQ belongs to the Eulerian class of mathematical models that calculate a mass balance within each grid cell by solving the transport across each cell boundary and chemical transformations within each cell during a given time period As a framework for simulating the interactions of multiple complex atmo spheric processes CMAQ thus requires two major types of inputs meteorological information and source emissions rates With weather conditions contributing the primary physical driving forces in the atmosphere such as the changes in temperature winds cloud formation and precipitation rates representative gridded meteorology forms the basis of all 3 D air quality model simulations The Fifth Generation Pennsylvania State University National Center for Atmo spheric Research Mesoscale Model MM5 Grell et al 1994 and the Weather Research and Forecasting WRF model Advanced Research WRF WRF ARW Skamrock et al 2005 are two meteorological models that are com patible with CMAQ The meteorology inputs dictate the following CMAQ configuration parameters 1 1 Background and Goals e Horizontal grid coordinate and projection e Horizontal grid resolution e Maximum spatial coverage e Vertical grid extent model top e Temporal extent start end
160. id is calculated within the ISORROPIA thermodynamic module As in previous CMAQ releases mass transfer is not simulated between the coarse mode and the gas phase These sea salt processes can be activated by selecting the AERO4 module and deactivated by using AERO3 For easier comparison of CMAQ output with measurement AERO4 now provides three new variables PM25AT PM25AC and PM25CO that are the fractional amounts of the Aitken accumulation and coarse modes respectively that are composed of particles less than 2 5 m in aerodynamic diameter Jiang et al 2006 Unlike gases the deposition velocity for particles must be calculated from the aerosol size distribution as well as meteorological and land use information The aero_depv2 module calculates the size distribution from the mass and number concentration for each of the three modes and calculates the dry deposition velocity The dry deposition algorithm has been modified to include an impaction term in the coarse and accumulation modes Finally two diagnostic tools for tracking the sulfate budget and sources of elemental and primary organic carbon have been added CCTM s AERO module is also useful for evaluating visibility CCTM integrates Mie scattering a generalized partic ulate light scattering mechanism that follows from the laws of electro magnetism applied to particulate matter over the entire range of particle sizes to obtain a single visibility value for each model grid cell at ea
161. ies among the programs The blue boxes represent programs that are not part of the CMAQ distribution package but supply data necessary for an air quality simulation The yellow boxes represent the basic CMAQ preprocessors MCIP ICON BCON and JPROC The red box represents the CMAQ chemistry transport model CCTM the Eulerian air quality modeling component of CMAQ Data flows between the CMAQ programs are represented in Figure 5 1 by arrows The red arrows illustrate the flow of data from the CMAQ preprocessors to the CCTM The green arrows show the data feedbacks from the CCTM to create initial and boundary conditions for nested simulations The black arrow illustrates the connection between the meteorology model and MCIP Finally the blue arrow shows that the output from MCIP can be used to drive an emissions model such as SMOKE Along with these programs CMAQ also contains several utilities and two code libraries STENEX and PARIO to implement source specific and diagnostic features in CMAQ and for parallel applications of the model 47 5 1 Overview Figure 5 1 CMAQ core programs Third Party Programs E CMAQ Preprocessors CMAQ CTM CCTM Input CCTM Output Met Model Output RR E Emissions Model Input The Emissions Model and Meteorology Model Figure 5 1 are described in detail in Chapters7 and 8 An emissions model is required to convert annual county level emissions estimates to gridded hourly emissions formatted f
162. ified Archive interface refines the com piling of the CMAQ programs and the necessary libraries except for the netCDF library into a single Makeall script The Makeall script is edited with a text editor similar to the original C shell scripts The Makeall script can be configured to either compile all of the CMAQ programs and libraries with one execution or to only compile selected system components There is also a master run script that consolidates the running of all the programs into a single script The Unified Archive is designed to be simpler and faster than editing each individual build and run script as in the original C shell interface The Unified Archive contains all past releases of CMAQ and allows the user to optionally choose which version of CMAQ to compile 2 5 References Binkowski F S and U Shankar 1995 The Regional Particulate Model Part I Model description and preliminary results J Geophys Res 100 26 191 26 209 Binkowski F S and S J Roselle 2003 Models 3 Community Multiscale Air Quality CMAQ model aerosol component 1 Model description J Geophys Res 108 4183 doi 10 1029 2001JD001409 Bott A 1989 A positive definite advection scheme obtained by nonlinear renormalization of the advective fluxes Mon Wea Rev 117 1006 1015 Byun D W 1999 Dynamically consistent formulations in meteorological and air quality 24 2 5 References models for Multiscale atmospheric studies P
163. iguration in CMAQ that is implemented by compiling the CCTM with include files that define PA configuration options A PA instrumented version of the CCTM outputs additional files that contain hourly concentrations by physical and or chemical process for selected model species PROCAN is the PA preprocessor in CMAQ PROCAN inputs a configuration file that is used to define the model species and processes to track using PA and outputs three include files that are used when compiling the CCTM Figure 2 8 is schematic of PA in the CMAQ modeling system 18 2 3 CMAQ Chemical Transport Model Science Modules Figure 2 8 Process analysis implementation in the CMAQ modeling system CMAQ Chemical Transport Model CCTM Pacp inp PA_DAT EXT 2 3 CMAQ Chemical Transport Model Science Modules Figure 2 9 illustrates the CMAQ modeling system used to simulate the chemistry and transport of pollutants Figure 2 9 also illustrates how CMAQ relates to other parts of the Models 3 the meteorological models emissions model and the analysis packages For a model simulation CMAQ needs input information including meteorological and emissions data Using this information the CMAQ Chemistry Transport Model CCTM simulates each of the atmo spheric processes that affect the transport transformation and removal of ozone particulate matter and other pollutants CMAQ uses state of the science techniques to simulate these processes as describ
164. ing the indi vidual scripts for each program There are also previous releases of CMAQ available for download at the CMAS Center website Details about using the scripts to build and run CMAQ are described in Chapter 3 CMAQ System Re quirements and Installation 27 2 4 2 CMAQ GUI The CMAQ GUL is a windows like interface that runs on Linux systems and helps the user download compile and run CMAQ It is designed to be user friendly and uses both a normal and an advanced view to better accommodate different skill levels The GUI is divided into six basic parts and begins by downloading CMAQ and the associated libraries into user defined directories It then helps the user to select the compiler flags and compile the libraries The next step is to compile the various programs that make up CMAQ The GUI will notify the user of any error that occurs while downloading or compiling The different options and environment variables can be set by simply choosing them from drop down menus in the interface After compiling all programs the user can then run CMAQ from the GUI The user also have the option to either run the CMAQ program in batch mode running all the programs sequentially or you can run the programs individually The latter option allows the user to make small changes in an individual program and not have to run the entire simulation over again 2 4 3 Unified Archive The Unified Archive is a consolidated scripting interface for CMAQ The Un
165. initial condi tions file speciated for a particular gas phase chemical mechanism and PM model output from ICON BNDY_ GASCIAEROI NONRITRAC _1 GRDDED3 Name and location of the time depend ent either single time step or multi time step 3 D boundary conditions file speciated for a particular gas phase chemical mechanism and PM model output from BCON GRID_CRO_2D GRDDED3 Name and location of the time inde pendent 2 D cross point meteorology file output by MCIP GRID_DOT_2D GRDDED3 Name and location of the time inde pendent 2 D dot point meteorology file output by MCIP MET_CRO_2D GRDDED3 Name and location of the time depend ent 2 D cross point meteorology file MET_DOT_3D GRDDED3 Name and location of the time depend ent 3 D dot point meteorology file output by MCIP MET_CRO_3D GRDDED3 Name and location of the time depend ent 3 D cross point meteorology file output by MCIP 57 5 3 2 Files configuration and environment variables File Name Format Description MET_BDY_3D BNDARY3 Name and location of the time depend ent 3 D boundary meteorology file output by MCIP XJ_DATA ASCII Name and location of the daily clear sky photolysis rates file speciated for a particular gas phase chemical mech anism output from JPROC 5 3 2 2 CCTM compilation options The configuration options listed here are set during compilation o
166. input file and then extensively for the options to choose The prompts will have default responses which can be accepted by hitting lt RETURN gt The specification of starting date and time target date and time and duration for the run follow CMAQ date and time conventions This program is extremely useful in compressing large data files For instance an output concentration file containing 41 variables for a 16 x 23 x 26 domain occupies 226 Mbytes of disk space The original concentration file can be saved to an archive while the analysis proceeds on a set of smaller files Extracting just the ozone concentrations will result in a5 5 Mbyte file Further extracting only the surface layer ozone values will reduce the file size to 0 2 Mbytes This utility is also useful for changing variable names within a CMAQ input output file 4 6 3 M3DIFF The M3DIFF program performs comparison and other operations on pairs of variables from a user specified pair of GRIDDED I O API files and computes statistics for each specified variable and for the specified difference operation An I O API output file containing all the results of the specified operations can be optionally generated for viewing within scientific visualization tools setenv lt infile A gt lt path name gt setenv lt infile B gt lt path name gt setenv lt reportfile gt lt path name gt m3diff lt infile A gt lt infile B gt lt reportfile gt lt DEFAULT gt The de
167. ion model of the planetary boundary 144 7 11 References layer Sensitivity tests and comparisons with SESAME 79 data J Appl Meteor 21 1594 1609 Zhang D L H R Chang N L Seaman T T Warner and J M Fritsch 1986 A two way interactive nesting procedure with variable terrain resolution Mon Wea Rev 114 1330 1339a 145 146 Chapter 8 Developing Emissions Fields Table of Contents 8 1 Credits and Disclaimers for Use of SMOKE cceccecceccecceeceeeeeceeceeeeeeeseereeeeeeeeneresenereseeresenenes 147 8 2 Obtaining SMOKE Source Code 20 0 0 eee ceeceeececcn even E EEEE EEEE EE S EEEE EEE EEE EESE 147 8 3 System Requirements s consis roeie das ens sE discs sands EEPE EERTSE ESE POETER S ceugsdvetesdsseashageesetesdeardeandes 147 8 4 Software Wan Guages wi eisn oi A E EE EAE EE EE EE EEY EEE R EEEIEE EEEE EE TEE 147 8 5 Data Requirements messer iiim a E pas sages A E E a E E A E E SES 147 8 6 Overview Of SMOKE Version 2l leeden ier e EE ENa EEEE EREE S ENE EEES RA SS EEES 148 8 7 Emissions Model Visualization and Evaluation ccccseceecneceeeneceeeneceeeneceeeneeeeenseeeeneeeeenseaeeneeeeenes 151 8 8 Model Training and User Support 2 2 0 0 cece eee ceec eee ce ee ceeeceeece teen ceca cena eeaeceueceneeeneeeeeeeeeeeeeaeeeaeeeaes 151 8 9 Referentes ic onic tes p a pat tasnd boleh ATa saa baie saa pte meses PANEER APNE TSA IGE EA eae a aa beeen eeies 151 Emissions
168. ions from a CCTM concentration file by selecting the m3conc option for the input file module when compiling the programs The input concentration file must cover a temporal and spatial extent that is consistent with the time period and domain that is being modeled re spectively Both ICON and BCON will require that a Julian start date be specified at execution that identifies the first time step to extract from the input concentration file BCON also requires a run length specification to direct the number of time steps of boundary conditions to extract from the input file For nested runs the nested domain for which initial and boundary conditions are being extracted must be on the same projection and fall within the domain contained in the input concentration file 6 1 6 CSQY Absorption cross section and quantum yields Used by JPROC CSQY is the logical name for the ASCII data file containing absorption cross section and quantum yield data for unique photolysis reactions The data in these files are listed as a function of wavelength and correspond to the standard pho tolysis reactions in each of the chemical mechanisms implemented in CMAQ A flexible format allows users to deviate from these standards and test new data with a trivial amount of effort The ASCII formatted CSQY files begin with a header describing the applicable photolysis reaction comments about the source of the data and the location on the wavelength interval that the data
169. iption section that defines the number of sigma levels in the file the number of pollutants in the file and the vertical coordinate values of the different sigma levels The next entries in these files are the Julian start date and the start time of the data and are not used by ICON Each line in the IC_PROFILE file corresponds to a different pollutant and begins with the name of the pollutant The subsequent columns on each line list the chemical concentration at each layer contained in the file Gas phase species are provided in ppmV units and aerosol species are provided in ug m units in the IC_PROFILE file The layer structure of the ICON vertical profiles does not need to correspond exactly to the layer structure that will be modeled the program will interpolate the data to the correct vertical format for the simulation Initial conditions are inherently temporally static as they correspond to the first hour of a model simulation only Generating initial conditions from an ASCII profile file produces a gridded file for input to the CCTM that has uniform species concentrations across the entire horizontal grid at each model layer For spatially resolved initial conditions it is necessary to use the other input file type to ICON an existing CCTM concentration file CTM_CONC_1 A detailed description of the vertical profile file format for initial conditions is provided in Table 4 4 The header of the profiles file is list formatted while the data
170. ise from each of these areas and combines the capabilities to enable a community modeling practice CMAQ has multi scale capabilities so that separate models are not needed for urban and regional scale air quality modeling The target grid resolutions and domain sizes for CMAQ range spatially and temporally over several orders of magnitude With the temporal flexibility of the model simulations can be performed to evaluate longer term pollutant climatologies as well as short term transport from localized sources By making CMAQ a modeling system that addresses multiple pollutants and different spatial scales CMAQ has a one atmosphere perspective that combines the efforts of the scientific community Developments and improvements to the CMAQ modeling system can continue as the state of the science evolves For example linkages of CMAQ with exposure modeling hydrological modeling climate modeling and multimedia modeling are currently under development To implement multi scale capabilities in CMAQ several different issues such as scalable atmospheric dynamics and generalized coordinates that depend on the desired model resolution are addressed Meteorological models may assume hydrostatic conditions for large regional scales where the atmosphere is assumed to have a balance of vertical pressure and gravitational forces with no net vertical acceleration on larger scales However on smaller scales such as urban scales the hydrostatic assumption ca
171. ism parameters including gas phase species reaction stoichiometry and kinetics information To invoke chemical mechanisms in CMAQ these files are included in the compilation of the different CMAQ programs to generate mechanism specific executables CHEMMECH takes a mechanism definition file often named mech def and generates the mechanism and species include files that define the chemistry parameters for the CMAQ programs The file mech def is a human readable ASCH file that is easy to understand and modify Figure 2 6 demonstrates the relationship between CHEMMECH and the rest of the CMAQ modeling system Figure 2 6 Invoking new modified gas phase chemical mechanisms in CMAQ CMAQ Programs CCTM ICON BCON JPROC 2 2 5 PDM The Plume Dynamics Model for Plume In Grid 2 2 5 PDM The Plume Dynamics Model for Plume In Grid Plume in Grid PinG is a subgrid scale treatment of the plumes from large point emissions sources PinG is a technique to resolve the chemistry and dynamics of the plumes from selected point sources at a finer spatial resolution than the grid being modeled Additional information about the PinG formulation in CMAQ is available in Byun and Ching 1999 and Byun and Schere 2006 The Plume Dynamics Model PDM is the PinG preprocessor in CMAQ that prepares special emissions files with information about sources selected for PinG treatment for input to the CCTM The PDM simulates plume rise horizontal an
172. itions Processors To perform air quality simulations both initial and boundary conditions are required Initial conditions calculated in ICON are needed to provide concentrations at the first time step of individual chemical species for the modeling domain 15 2 2 3 JPROC Clear Sky Photolysis Rate Calculator Boundary conditions calculated in BCON are needed to provide concentrations of individual chemical species at the lateral boundaries of the modeling domain ICON and BCON can generate these concentrations for multiple chemical species ICON and BCON require two inputs Figure 2 4 a concentration file for the chemical species to be simulated and the chemical mechanism The concentration file used in ICON and BCON can come from one of two sources as follows e Time independent set of vertical Regional Acid Deposition Model Version 2 RADM2 Stockwell et al 1990 concentration profiles This approach is usually used when no other information about the initial and boundary concentrations is available e Existing CCTM 3 D concentration fields Usually this is used when performing a nested model simulation and modeling results from a previous CCTM simulation are available from a coarser grid resolution simulation Existing CCTM concentration fields are also used when a CCTM simulation is extended in a separate run step Unlike the profiles mentioned previously these CCTM concentration files are spatially and temporally resolve
173. ity 1 5 New Features in Version 4 6 e A growing community of CMAQ developers provides a forum for discussing development related topics 1 5 New Features in Version 4 6 CMAQ version 4 6 contains several new features and improvements from the previous release of the model An im portant global update that affects ICON BCON and CCTM is the new dynamic layer configuration Similar to the horizontal grid configuration that is defined at execution using a grid description file the vertical layer configuration is now defined using a run time environment variable that points to a 3 d input meteorology file that contains the ap plicable vertical structure It is no longer necessary to recompile these programs when the vertical layer structure changes Additional process specific features are listed below e Aerosols e Updated ISORROPIA to v1 7 includes correction in activity coefficients for temperatures other than 298 K e Revised to use T RH dependent gamma heterogeneous N205 reaction probability from Evans amp Jacob 2005 e Upper limit set for the relative humidity input to ISORROPIA 95 e Updated parameters written to the aerosol diagnostic file e Chemistry e Carbon Bond CB05 mechanism and associated EBI solver e Include the gas phase reactions involving N205 and H2O e Removed obsolete mechanism combinations e g gas aerosols w o aqueous e PBL modeling e New ACM2 combined non local and local closure scheme e Plu
174. l species for calculating integral average concentrations for each output time step Options can be any of the standard output species that are written to the CCTM CONC file The species in this list will be written to the ACONC output file ACONC_BLEV_ELEV default 1 1 Vertical model layer range for integral average concentrations this variable sets the lower and upper layers over which to calculate integral average concentrations OCEANpath default M3DATA emis tut02 Directory path for the input sea salt emissions file EMISpath default M3DATA emis tut02 Directory path for the input emissions file TR_EMpath default commented out Directory path for the input tracer emissions file GCIAEINRITR _ICpath Directory path for the input initial conditions file GCIAEINRITR _BCpath Directory path for the input boundary conditions file METpath Directory path for the input meteorology files JVALpath Directory path for input clear sky photolysis rate files 5 3 2 Files configuration and environment variables 5 3 2 5 CCTM output files Table 5 4 CCTM output files File Name Format Description CTM_CONC_1 GRDDED3 Name and location of hourly 3 D in stantaneous gas and aerosol phase pollutant estimates A_CONC_1 GRDDED3 Name and location of hourly 2 D or 3 D integral average gas and aerosol phase pollutant estimates CTM_DRY_DEP_1 GRDDED3 Name and location of hourly 3 D gas and aerosol
175. lable from NCAR but are not listed in the NCAR catalog The NCEP sea surface temperature data is included as part of the global analysis data and is available at 2 5 degree resolution The climatological sea surface temperature data available from NCAR is at 2 degree resolution When possible it is more advantageous to use the measured and analyzed sea surface temperatures rather than the climatology data The measured and analyzed sea surface temperatures are generally more representative of the actual field during the simulation The use of measured sea surface temperatures can be particularly important e g in an El Nifio year when the actual temperatures deviate strongly from normal e g climatology The snow data base at NCAR includes Northern Hemisphere analyses from NCEP The snow analysis is updated about once a week or following a significant snow event If you are simulating a summer episode you should be able to bypass the need for a snow analysis and MM5 will assume that there is no snow cover in the simulation domain 7 5 Meteorology Model Pre Processing Before the meteorology model can be run several pre processing programs must be run to set up the domain for the simulation and to generate a set of initial and boundary conditions for the meteorology model The pre processing programs are briefly described in this section 7 5 1 Defining the Simulation Domain TERRAIN Domains for the meteorology simulations are defin
176. late within MCIP e J use PBL values from the input meteorology e 2 re calculate PBL values within MCIP using PBL similarity e 3 re calculate PBL values within MCIP using surface layer similarity LRAD default 1 Sets the source of the radiation fields in the MCIP output files The setting of this variable determines whether to use the radiation fields from the input meteorology or to recalculate within MCIP e J use radiation fields from the input meteorology e 2 re calculate radiation fields using the MCIP version 1 algorithm LDDEP default 1 Sets the dry deposition routine The setting of this variable determines which dry deposition routine for calculating deposition velocities e J use the RADM Wesely dry deposition routine e 2 use the Models 3 Pleim dry deposition routine e 1 Use the Models 3 dry deposition routine and include Cl e 2 Use the Models 3 dry deposition routine and include Cl and Hg MCIP_START format YY Y Y MM DD HH MM SS SSSS Beginning date and time UTC of data to output from MCIP The start data and time must be contained within the input data from MM5 or WRF MCIP_END format YY Y Y MM DD HH MM SS SSSS 80 5 7 2 Files configuration and environment variables End date and time UTC of data to output from MCIP The end data and time must be contained within the input data from MM5 or WRF INTVL default 60 Output interval in minutes This setting determines the amount of mo
177. lative dry deposition file The 2 D CMAQ dry deposition file DRYDEP includes instantaneous hourly dry deposition fluxes kg hectare for selected model species CMAQ calculates dry deposition for all of the species listed in the dry deposition include files within the mechanism include directories Dry deposition include files exist for gas phase species GC_DDEP EXT aerosol species AE_DDEP EXT and inert model species NR_DDEP EXT You can remove species from these 132 6 2 5 WETDEP CCTM hourly cumulative wet deposition file DDEP EXT files to adjust the number of species that undergo the dry deposition process and are written to the DRYDEP output file 6 2 5 WETDEP CCTM hourly cumulative wet deposition file The 2 D CMAQ wet deposition file WETDEP includes cumulative hourly wet deposition fluxes kg hectare for se lected model species CMAQ calculates wet deposition for all of the species listed in the wet deposition include files within the mechanism include directories Wet deposition include files exist for gas phase species GC_WDEP EXT aerosol species AE_WDEP EXT and inert model species NR_WDEP EXT You can remove species from these WDEP EXT files to adjust the number of species that undergo the wet deposition process and are written to the WETDEP output file 6 2 6 AEROVIS CCTM hourly instantaneous visibility metrics The 2 D CMAQ visibility file AEROVIS contains hourly Mie and reconstructed visual range
178. les are then merged together in the same way as the anthropogenic sources see Section 5 6 10 8 6 8 Elevated Point Source Selection Elevpoint The SMOKE program Elevpoint is used to select elevated and Plume in Grid PinG sources This is done using cri teria based on emissions values emissions rank stack parameters and an analytical plume rise calculation 8 6 9 Plume Rise Laypoint The SMOKE program Laypoint uses gridded hourly meteorological data and stack parameters to calculate the plume rise for all point sources emissions Laypoint calculates the top and bottom heights of the plume and uses these heights to determine the plumes distributions into the vertical layers it intersects Laypoint outputs an intermediate file con taining the layer fractions for each source 8 6 10 CMAQ Input File Creation SGmkmerge and Mrggrid The SMOKE program Smkmerge is used to combine the speciation gridding and temporal matrices with the inventory In the case of point source processing Smkmerge will also combine the layer fractions The SMOKE program Mrggrid is used to combine Smkmerge outputs from different source categories into a file ready for input into CMAQ 149 8 6 11 SMOKE QA Smkreport 8 6 11 SMOKE QA Smkreport SMOKE contains a very powerful reporting tool called Smkreport Smkreport can generate many types of reports used to perform quality assurance Currently the user can create reports of emissions by sou
179. les to a vertical resolution that is consistent with the CCTM configuration BCON differs from ICON in that it can generate time varying i e dynamic boundary conditions Dynamic boundary conditions are typically ex tracted from CCTM outputs from a coarse grid simulation for nested simulations or from a CTM simulation using a global scale model The file structure of the ASCII input profiles can also support the creation of dynamic boundary conditions but generally these files are used for creating static data The configuration options for BCON include selecting the chemical mechanism to model defining the horizontal and vertical grids and choosing whether the boundary conditions are generated from an ASCII profile or from an existing CCTM output file Meteorology Chemistry Interface Processor MCIP MCIP uses MMS or WRF output files to create netCDF based input meteorology for the emissions model and the CCTM MCIP prepares and diagnoses all meteorological fields that are required for the emissions model and the CCTM In addition MCIP is currently used to calculate the time varying species dependent dry deposition velocities that are used in the CCTM MCIP can be used to uniformly trim cells off the boundary of the domain defined by the meteorological model or to window in on a subset of that domain MCIP can also decrease the vertical resolution of the meteorological data by layer collapsing although this option should be used with caution
180. ll be used Bold type is used for PROCAN keywords and normal type for user supplied inputs Alternative inputs are separated by vertical bars and optional inputs are enclosed in braces The PROCAN commands fall into three general categories e Process Analysis Global Commands These commands include general specifications that are applicable throughout the configuration These specific commands are described in Table 5 1 e Integrated Process Rate Commandhe same number of time steps as the concentration output file Since the I O API currently has a limit of 120 output variables on a file multiple files will be output if this limit is exceeded These commands are described in Table 5 2 e Integrated Reaction Rate Commands The commands are specific to the configuration of the integrated reaction rates The same considerations for file size and memory usage detailed above should be considered when using these commands These commands are described in Table 5 4 90 5 10 2 Files configuration and environment variables Table 5 16 Process Analysis Global Commands Command Description OUTPUT_DOMAIN LOCOL n HICOL n LOROW n3 HIROW n LOLEV n5 HILEV n The OUTPUT_DOMAIN command provides the capability to limit the IPR and IRR output data to a portion of the modeling domain The ni in brackets are numbers that define the bounds of the output domain relative to the number of columns rows and
181. me re quired 17 wow Char delimits the left hand and right hand side of the conversion equation required 18 SPP2_IN String Input mechanism spe cies name coefficients on right hand side of equation may be either integer real or expo nential format re quired n l ww Char man conversion rule ter minator allows rules to span multiple lines required SPPX_OUT String Output mechanism species name re quired 17 wow Char delimits the left hand and right hand side of the conversion equation required 109 6 1 5 CTM_CONC_1 CCTM concentration Files Line Column Name Type Description 18 SPPX_IN String Input mechanism spe cies name coefficients on right hand side of equation may be either integer real or expo nential format re quired X n 1 see Char conversion rule ter minator allows rules to span multiple lines required X 1 1 END String END file terminator required A sample of the entries in a MECH_CONV_FILE file is shown below NO2 NO2 FORM HCHO 1 0 GLY END 6 1 5 CTM_CONC_1 CCTM concentration Files Used by ICON BCON The second file type that can be input to ICON and BCON is a GRDDED3 formatted CCTM output concentration file ICON and BCON are configured to generate initial and boundary condit
182. me in Grid e Capability for AE4 mechanisms e Mercury e Capability for CB05 AE4 mechanism e Hazardous Air Pollutants e Increased number of gas phase HAPs added several toxic metals and diesel components in particulate material adapted for CB05 and SAPRC99 chemical mechanisms and AF4 e Carbon Apportionment e Added capability for CB05 mechanism e Sulfate Tracking e Added capability for CB05 AE4 mechanisms and cloud_acm module 1 5 New Features in Version 4 6 CGRID restart file e Added aCGRID restart file used to initialize next day s simulation permits flexibility in the CONC file can write subset of species and layers for the CONC file Parallel I O library e Various updates new version required for CMAQv4 6 compilation Other e Added a utility program to convert MCIP data into HYSPLIT format Meteorology MCIPv3 2 e Modified I O API header variable settings for WRF ARW WRF EM to reflect additional capability to have center of coarse domain located elsewhere than the center of the projection Note that applications of CMAQ with WRF ARW input will no longer adhere to the grid family paradigm for the Models 3 I O API and a separate GRIDDESC file will be required for each grid e For non PX runs only Corrected error in bookkeeping last wet time in M3Dry dry deposition when Pleim Xiu land surface model is not run Also now use ground temperature rather than 2 m air temperature to calcula
183. ms which contain configuration options at both compilation and execution 5 7 2 1 MCIP input files Table 5 11 MCIP input files File Name Format Description InMetFiles binary List of MM5 or WRF output files for input to MCIP InTerFile binary MMS Terrain file with fractional land use categories used for calculating land use dependent vertical diffusivity 5 7 2 2 MCIP compilation options All model configuration options for MCIP are set during execution System compiler options must be set in the provided Unix Makefile to build the program for different operating system compiler combinations Example compiler paths flags and library locations are provided in the default Makefile 5 7 2 3 MCIP compilation Section 3 3 provides an overview of how to install and compile the CMAQ programs for the tutorial simulation Follow the steps outlined in Section 3 3 to compile new versions of MCIP 1 Configure the Makefile for your operating system compiler combination Comment out the configuration that does not apply to your system Uncomment the configuration that is closest to that of your system and make the necessary changes to point to the compiler path I O API location and netCDF locations on your system 2 Install and compile the I O API and netCDF libraries if these are not already available on your system 3 Invoke the Makefile to create an executable by typing the following command in the directory that c
184. n be visualized after the post processing in MCIP by using either PAVE or Vis5d If you would like to visualize MMS prior to the processing in MCIP several shareware tools are available for this purpose such as Vis5d Vis5d can be freely obtained in its original form from the University of Wisconsin refer to ht tp www ssec wisc edu billh vis5d html for details A processor to reformat MM5 output for Vis5d tovis5d can be freely obtained from NCAR via anonymous FTP at ftp ftp ucar edu in directory mesouser Util vis5d Several other graphics programs e g GEMPAK NCAR Graphics GrADS are available for MM5 visualization either as freeware or for a nominal fee There are limited capabilities using SAS and simple statistics available with visualization tools to evaluate MM5 output There are tools within the MM5 community that are used for model evaluation but none are currently maintained by NCAR 142 7 9 Model Training and User Support 7 9 Model Training and User Support There are no plans for CMAQ users to have specialized training on the use of MM5 NCAR which maintains the official public releases of MM5 offers a periodic tutorial for setting up and running MMS This tutorial has a limited registration to keep class sizes manageable and it often fills several months prior to the course NCAR charges a nominal fee for the tutorial The tutorial notes for each class Dudhia et al 1998 are available on line for no charge
185. n change in each grid cell through the continuity equation which is presented in simplified form below SC St Adv Diff R E Se Adv advection Diff diffusion R chemical transformation of species c E emissions of species c Se loss processes for species c In CMAQ the advection and emissions terms are calculated based on input files generated by the meteorology and emissions models respectively the diffusion chemical transformation and loss process terms are calculated within the CCTM The Eulerian representation of the modeling domain is a series of contiguous grid cells that form a limited area box on a subset of the globe so the domain lateral boundary must define advection into the modeling grid CMAQ currently accounts for advection into the domain only from the horizontal 1 e lateral boundaries assuming there is no exchange through the top boundary of the domain These spatial boundary conditions are estimated in CMAQ using the boundary conditions preprocessor BCON As a temporal boundary condition the first time step of a model simulation is estimated in CMAQ using the initial conditions preprocessor ICON To model solar radiation which provides the energy source for photolysis reactions the program JPROC calculates clear sky photolysis rates at various latitude bands and hours based on sun angles Output from these CMAQ programs is used with output files from the emissions and meteorology models and other
186. n of cumulus in mesoscale models K A Emanuel and D J Raymond Eds Meteorological Monographs Amer Meteor Soc 165 170 Klemp J B and R B Wilhelmson 1978 Simulations of three dimensional convective storm dynamics J Atmos Sci 35 1070 1096 Madala R V 1981 Finite difference techniques for vectorized fluid dynamics calculations Edited by D L Book Springer Verlag New York Manning K and P Haagenson 1992 Data ingest and objective analysis for the PSU NCAR modeling system Programs DATAGRID and RAWINS NCAR Tech Note NCAR TN 396 IA 209 pp Available from the National Center for Atmospheric Research P O Box 3000 Boulder CO 80307 Pleim J E and A Xiu 1995 Development and testing of a surface flux and planetary boundary layer model for application in mesoscale models J Appl Meteor 34 16 32 Stauffer D R and N L Seaman 1990 Use of four dimensional data assimilation in a limited area mesoscale model Part I Experiments with synoptic scale data Mon Wea Rev 118 1250 1277 Stauffer D R N L Seaman and F S Binkowski 1991 Use of four dimensional data assimilation in a limited area mesoscale model Part II Effects of data assimilation within the planetary boundary layer Mon Wea Rev 119 734 754 Stauffer D R and N L Seaman 1994 Multiscale four dimensional data assimilation J Appl Meteor 33 416 434 Zhang D L and R A Anthes 1982 A high resolut
187. n options The horizontal domain configuration and the vertical coordinate are dynamic features in CMAQ that are independent of the executable In other words a user can employ a single executable for a simulation that uses any of the supported 1 2 3 Summary Descriptions of the Major CMAQ Programs map projections or grid definitions without having to recompile the code Distinctions between which CMAQ options must be selected at compilation versus at execution are described in Chapter 5 As the chemistry transport model component of CMAQ the CCTM is the final program to be run in the CMAQ modeling sequence The four other main programs prepare input data for the CCTM Before describing each of the CMAQ programs Section 1 2 4 we present a conceptual formulation of CMAQ and Eulerian air quality modeling to provide a framework for understanding the purposes and relationships of the various programs to each other and to the overall system Eulerian chemistry transport models use coupled ordinary differential equations to solve the changes in concentration of pollutants throughout a three dimensional grid that is fixed relative to a selected map projection The changes in concentration in each grid cell are affected by the following processes e Emissions from sources e Horizontal and vertical advection e Horizontal and vertical diffusion e Chemical transformations e Deposition Mathematically these processes relate to the concentratio
188. n that the user is creating boundary conditions for it is necessary to specify a chemical conversion option by setting the ModMech variable at compilation The default conversion profiles in BCON are set up to convert from RADM2 speciation to either CB IV CB05 or SAPRC99 chemistry It is possible to create a custom conversion file MECH_CONV_FILE and input this file to BCON by setting the ModMech variable to user_defined at compilation The horizontal grid and vertical layer structures for BCON are defined at execution through the input of a grid description GRIDDESC file and a meteorology cross point 3 d MET_CRO_3D file respectively BCON interpolates between the input vertical layer structure and output layer structure if they are different 50 5 2 2 Files configuration and environment variables 5 2 2 1 BCON input files Table 5 1 BCON input files File Name BC_PROFILE Format ASCI Description Vertical chemical profiles from which to derive boundary conditions this file is created by the user only used when BC is set to profile MECH_CONV_FILE ASCII Mapping factors for converting between chemical mechanisms this file is created by the user only used when BCON is compiled with the ModMech configuration set to user_defined CTM_CONC_1 GRDDED3 CMAQ concentration file from which to derive boundary conditions this file is output from the CCTM only used when BC is
189. n the files This tool would prove useful in instances in which one data set was determined to be representative of multiple time periods 4 6 7 M3WNDW The M3WNDW program extracts a windowed set of data from a gridded CMAQ file and outputs this subset to a new gridded file for a specified time period The definition of the sub rectangle is user specified by the entries of LOCOL LOROW HICOL and HIROW One application of this utility would be to create an initial concentration file for a nested grid from the output of a parent grid 4 6 8 BOWNDW The BCWNDW program extracts a windowed set of data from a gridded CMAQ file and outputs this subset to a new BOUNDARY file for a specified time period The definition of the sub rectangle is user specified by the entries of LOCOL LOROW HICOL and HIROW 4 6 9 M3FAKE The complex M3FAKE program prompts the user one item at a time for the contents of aGRIDDED BOUNDARY or CUSTOM file and then builds the file accordingly It is a user friendly means to create dummy data sets In order to describe the horizontal and vertical coordinate systems the user can specify the name of the grid as found in the GRIDDESC file or else may supply all needed parameters entry by entry 4 6 10 UTMTOOL The UTMTOOL program provides coordinate conversion back and forth among LAT LON UTM and LAMBERT coordinate systems Longitudes are specified in signed degrees such that for the United States longitudes are ne
190. n the Grid Cross 2D meteorology file LAT latitude in degrees northern hemisphere is positive LON longitude in degrees western hemisphere is negative MSFX2 squared map scale factor Cross cell interfaces HT terrain elevation m DLUSE dominant land use category 6 1 18 GD2file Two dimensional Grid Dot Product Input GRID_DOT_2D Used by CCTM CMAQ requires the following variables to be present in the Grid Dot 2D meteorology file LAT latitude in degrees northern hemisphere is positive LON longitude in degrees western hemisphere is negative MSFD2 squared map scale factor Dot cell centers 6 1 19 MB3file Three dimensional Meteorological Boundary Input MET_BDY_ 3D Used by CCTM CMAQ requires the following variables to be present in the Met Boundary 2D meteorology file JACOBF total Jacobian at layer face m JACOBM total Jacobian at layer middle m DENSA_J J weighted total air density kg m WHAT _JD J and density weighted vertical contra W kg m s 128 6 1 20 MC2file Two dimensional Meteorological Cross Product Input MET_CRO_2D TA air temperature K QV mixing ratio kg water kg air PRES air pressure pascals DENS air density kg m WWIND vertical wind velocity m s ZH mid layer height above ground hydrostatic only m ZF full layer height above ground hydrostatic only m Qc cloud water mixing ratio kg kg QR rain water mixing ratio kg kg 6 1 20
191. nai 34 This chapter provides recommended hardware configurations and software requirements for installing and running CMAQ The hardware configurations in particular are subject to change with each new release of CMAQ and with the development of new computing technologies The installation instructions in this chapter guide the user through the obtaining the CMAQ source code and unpacking it on your system Brief instructions for running the CMAQ tutorial case and benchmarking the model are also addressed Here the term benchmarking refers to the process of verifying that a model has installed correctly on a new computer Configuring CMAQ for new applications is covered in Chapter 7 3 1 System Recommendations All of the CMAQ programs with the exception of M3BLD are written in FORTRAN and are optimized for use on computers running a version of the UNIX operating system Most personal computers PC s running the Linux oper ating system are sufficiently powerful to handle basic CMAQ applications However to use CMAQ in a production environment where multiple iterations of the model will be executed for different spatial domains and or emissions control strategies either a cluster of multi processor PC s on a high end network or an expandable rack mounted UNIX server is recommended In light of the dynamic nature of the computer hardware world the specifications listed in the section are current recommendations not requirements While the
192. nal domain than meteorological model and the lateral boundaries from the met eorological model are generally not used by the CCTM Processes all required meteorological fields for the CCTM and the emissions model Collapses meteorological model fields if coarser vertical resolution data are desired for the CCTM MCIP uses mass weighted averaging on higher vertical resolution meteorological model output If selected by the user computes surface and planetary boundary layer PBL fields using output from the meteor ological model Computes dry deposition velocities for important gaseous species using the surface and PBL parameters also generated by MCIP Dry deposition is the deposition of pollutants from the air onto the surface of the earth The rate of this removal is determined by various chemical physical and biological factors In addition dry deposition depends on the type of pollutant nature and type of surface and the amount of turbulence or mixing in the atmo sphere A measurement used in simulating the dry deposition of pollutants is the dry deposition velocity The dry deposition velocity is analogous to the settling velocity of particles due to gravity and it is useful in determining surface fluxes MCIP can compute dry deposition using two methods e The RADM dry deposition method Wesely 1989 calculates deposition velocities of 13 chemical species using friction velocities and aerodynamic resistances Inputs required f
193. nate for lower left southwest corner of the grid de pendent on projection type C YORIG Double Y coordinate for lower left southwest corner of the grid de pendent on projection type D XCELL Double X coordinate grid cell size dependent on projection type E YCELL Double Y coordinate grid cell size dependent on projection type F NCOLS Int Number of horizontal grid columns depend ent on projection type G NROWS Int Number of horizontal grid rows dependent on projection type H NTHIK Int Boundary perimeter thickness optional The GRIDDESC file can either be created by hand or generated automatically with MCIP Starting with MCIP version 2 3 the program outputs a GRIDDESC file that is compatible with the other CMAQ programs 6 1 2 C_ PROFILE Initial conditions vertical profiles Used by ICON ICON can generate initial conditions from two different input file types The first file type is an ASCII vertical profile file that list species concentrations at different model layers that are fixed in space in time ICON is configured to generate initial conditions from ASCII vertical profiles by choosing the prof input module when compiling the programs see Section xxx on ICON 101 6 1 2 IC_PROFILE Initial conditions vertical profiles The ASCII formatted vertical profile files begin with a header that contains a comment section describing the data and a file descr
194. nd no IRR output to be generated If the command is omitted type PARTIAL is assumed DEFINE RXNSUM cyclename species The DEFINE CYCLE command is used to compute the net of all chemical production and loss of a species Thus this quantity is computed by summing the IRRs for all re actions in which a species is consumed and then subtract ing that sum from the sum of the IRRs for all reactions in which the species is produced The cyclename is a user defined name that must be unique and can be referenced in subsequent IRR_OUTPUT commands DEFINE CYCLE sumname c lt rxlabl gt c lt rxlably gt The RXSUM command is used to compute a linear com bination of the IRRs for individual reactions that can then be referenced in a subsequent IRR_OUTPUT command sumname is user defined and must be unique The linear combination of IRRs is defined according to the expres sions following the equal signs that specify which reac tions s IRRs to sum The rxlabli is the reaction label that is used in the generalized mechanism The ci are optional numerical coefficients that default to one if not specified IRR_OUTPUT irrname c op lcyclname qual sumname qual lt rxlabl gt co opy cycl name qual l sumname qual lt rxlabl gt The IRR_OUTPUT command defines a specific IRR output to be generated during a CMAQ simulation It is construc ted by spe
195. nerated by the more sophisticated schemes These microphysics schemes also differ greatly in CPU usage and memory requirements 7 6 5 Nesting MMS has the capability to simulate nested domains of finer resolutions within the primary simulation domain In MM5 the software is configured to enable up to 9 nests 10 domains within a particular run However due to current hardware resources the state of the science numerical stability and practicality the number of domains in a simulation is gen erally limited to four or fewer Nesting can be accomplished by either one way or two way methods In one way nesting the coarse resolution domain simulation is run independently of the nest That domain then provides the initial and boundary conditions for its nest There are no feedbacks between the coarse domain and its nest in one way nesting Note that the simulated meteorology at the same grid point in the coarse resolution domain is likely to be different if only slightly from the nest in a one way nest simulation Two way interactive nesting Zhang et al 1986 Smolarkiewicz and Grell 1992 allows for feedback to occur between the coarse resolution domain and the nest throughout the simulation The two domains are run simultaneously to enable this feedback When two way nesting is used the portion of the coarse resolution domain that is simulated in the nest must be discarded The nesting ratio between domains in MMS is generally 3 1
196. nged to create working executables Additional information about the configuration options for the different CMAQ programs are provided in Chapter 2 and 6 1 Use the following commands to compile M3BLD cd M3HOME scripts build bldit m3bld 2 Next create the stencil exchange libraries for serial and parallel processing Check that the MPICH include file directory path is correct for the parallel version of the library on line 51 of the file bldit se _pgf Use the following commands to compile the Stenex libraries 32 3 3 Compiling CMAQ for the Tutorial Simulation cd M3HOME scripts stenex bldit se pgf bldit se_noop pgf For parallel CCTM operation create the parallel I O library cd M3HOME scripts pario bldit pario pgf Now create the model executables for JPROC ICON BCON and the CCTM For the benchmark case confirm that JPROC is configured to produce photolysis rates for the mechanism labeled cb05_ae4_aq Use the following command to compile JPROC cd M3HOME scripts jproc bldit jproc pgf ICON and BCON can be configured for different chemical mechanisms and for different kinds of input data The configuration options for ICON and BCON are discussed in detail in Chapters 2 and 6 Use the following commands to compile ICON and BCON cd M3HOME scripts icon bldit icon pgf cd M3HOME scripts bcon bldit bcon pgf MCIP is compiled using a FORTRAN Makefile instead of M3BLD To create the MCIP
197. nnot be made A set of governing equations for compressible non hydrostatic at mospheres is available to better resolve atmospheric dynamics at smaller scales and they are more appropriate for 12 2 1 2 Modular flexibility finer regional scale and urban scale meteorology CMAQ s generalized coordinate system is used so that meteorological fields on different vertical coordinates can easily be accommodated and multiple scales can be simulated with the same CTM The Jacobian used by the generalized coordinate system controls the necessary grid and coordinate transformations cf Byun 1999 2 1 2 Modular flexibility CMAQ s current coding structure is based on a modularity level that distinguishes its main driver science modules data estimation modules and control utility subroutines in the CCTM The distinction remains at a division between the science models including submodels for meteorology emissions chemistry transport models and analysis and visualization subsystems In the CCTM the process modules that affect the pollutant concentration fields are classified as follows Science Modules e Horizontal advection hadv e Vertical advection vadv e Mass conservation adjustments for advection processes adjc e Horizontal diffusion hdiff e Vertical diffusion vdiff e Gas phase chemical reaction solver chem e Aqueous phase reactions and cloud mixing cloud e Aerosol dynamics and size distributions aero
198. nput fles siester is etesen aE EEE EEE EE E E A ES KEE REEE 67 5 0 CHEMMECH output files sssrie im nisn a a a a bee E sages E E ea EE TEE agate 69 5 7 ICON input filesinin ei eee iss Beever S E E e E EEE E i S SOE eT 71 5 8 ICON output fles sri ri renna E apso eo ap E rE TEES I ESEA PESE SEE PEESI stag debotea geeedosnssde ers 74 3 9 JPROE input fles iei eei eane Ee E E EEE EE E vena css bes EAE EEEE E E EEE EEEN EEE EAEE 76 5 10 JPROC output fles vierra erste a E A cua pds E E E a E A TEES 77 S 11 MCIP input flest e cen di baste eee tes es Si en ee eee iis sod See Lah 79 5 12 MEIP output fil s ie eer r ne s ra E S nae E AAT T E OPERET PESARO OISE TEN ISEI ESES kS 82 2 13 PDM Input fess asie nesa ig bells EEEE EEEE EE EEEE EER EE ESEE A as 85 514 PDM output files Sirito n ea E E A E E E T R a A ss alee TE 88 3 15 PROCAN mmput MeS ess vod sacteeee cesses E E E S E E EEEE SEEE EE E ESE SENO E S 89 5 16 Process An lysis Global Commands ss osis sscseccsscesscesseeotscasensieeassdeces sacedseugassctssebeegaves ESTESA EEEE EEEN ONS 91 5 17 Integrated Process Rate Output Command sseessseesresessreresrrerrsrrerrererrrersrrerrsrrerreresrereerreersrerreeeset 91 S21 SAIPR process Codes cstssesiacsie savbavekas a ss a E E E A S e E E IEE aa 92 5 19 Integrated Reaction Rate Output Commands 0 cece cee cece ce ne cence nce eeeeeceeceeesaeeeaeeea seen sean eens eees 93 6 1 CMAQ Input File Information sirs rsin sevens sdseesde
199. o change these options it is necessary to recompile BCON and create a new executable Defines the action to be taken by the program M3BLD when extracting source code from CVS and compiling an executable e compile_all force compile even if all the object files are current e clean_up remove all source files upon successful compilation e no_compile do everything except compile e no_link do everything except link e one_step compile and link in one step e parse_only checks configuration file syntax e show_only shows requested commands but does not execute them e verbose shows requested commands as they are executed MakeOpt Uncomment to build a Makfile to compile the executable ModInpt Defines the format of the boundary conditions input files to be used by BCON e m3conc input a CCTM CONC file used for nested simulations or windows of a parent domain e profile input an ASCII vertical profiles file ModMech Defines if the input boundary conditions data need to be converted from one chemical mechanism to another e mc_noop do not perform any mechanism conversion used when extracting boundary conditions from a CCTM CONC file for a nested simulation or when the input profiles are already formatted for the correct mechanism e user_defined input the file defined by the MECH_CONV_FILE variable used for custom mechanism conver sions e radm2_to_cb4 convert the input boundary conditions profiles from RADM2 to CB IV spe
200. o the IO API format Chapter 8 JPROC produces ASCII output files The IO API formatted CMAQ output files are 3 dimensional gridded time stepped binary files that contain headers with metadata describing the file contents These machine independent and network transparent binary files are transferable between different computer architectures The advantages of using the IO API output format include Coats 2005 e performance visualization and analysis programs looking at selected parts of the data don t need to read unrequested data from the files e modularity data can be read or written in any order or not at all The same input files can serve both simple en gineering models and full chemistry models the former reading just a few of the variables from the files the latter reading most of them The modular model structure used for CMAQ depends upon this feature e robustness data are tagged by name date and time miscounted record numbers don t scramble temperatures with pressures for example The IO API output data are written to files using calls to the WRITE3 logical IO API function The amount of inform ation saved to CMAQ output files is defined almost entirely by the developer of a particular subroutine Should a user 131 6 2 1 CMAQ Output Log decide additional or less output is needed simple code changes could be completed to add or remove the selected data For example in the current release version of
201. ocations and flags in the make reader script 67 5 4 2 Files configuration and environment variables 5 4 2 4 CHEMMECH execution options The environment variables listed here are invoked during execution of the program and are set in the CHEMMECH run script The default run script is called MP saprc99 csh e BASE default cwd Working directory path e Xpath default BASE Executable directory path e Mpath default mech Directory path to the MECH DEF file e Opath default exts Output file directory path e APPL Simulation identifier EXEC default CHEMMECH Executable name e MCEPL default mech def saprc99 Mechanism definition file name e EXSPCS default Opath SPECIES ext Output file name when CHEMMECH is run in SP mode e EXRXDT default Opath RXDT EXT Name of output mechanism data include file e EXRXCM default Opath RXCM EXT Name of output mechanism common include file 68 5 5 ICON 5 4 2 5 CHEMMECH output files Table 5 6 CHEMMECH output files File Name Format Description RXCM EXT ASCII Mechanism common include file lists all of the chemical mechanism vari ables and parameters RXDT EXT ASCII Mechanism data include file chemical mechanism definition formatted as DATA blocks to be read in as CMAQ source code GC_ADV EXT ASCII File listing the gas phase model species that are transported by advection GC_CO
202. of columns to be larger than the number of rows For example if running with 8 processors the recommended setting is 4 2 NPROCS default 1 Number of processors for parallel execution equal to the product of NPCOL x NPROW STDATE Simulation start date YY YYDDD STIME Simulation start time HHMMSS NSTEPS default 240000 Number of simulation time steps HHMMSS TSTEP default 010000 Simulation output time step interval HHMMSS LOGFILE default BASE APPL log Uncomment to capture CCTM standard output to a log file the LOGFILE variable sets the name and location of the log IOAPI_LOG_WRITE default F TIF set to F to turn off excess WRITE3 logging by the I O API FL_ERR_STOP default F TIFIYIN set to F or N 63 5 3 2 Files configuration and environment variables DISP default keep Controls the maintenance of existing log files e delete delete output log if it already exists e keep abort simulation if output log exists OUTDIR default M3DATA cctm CCTM output file directory location CTM_APPL default APPL CCTM log file naming extension GRIDDESC default GRIDDESC1 Grid description file for setting the horizontal grid definition GRID_NAME Name of the grid definition contained in the GRIDDESC file that specifies the horizontal grid for the current ap plication of the model AVG_CONC_SPCS default 03 NO NO2 ASO4I ASO4J NH3 Mode
203. olver for gas phase chemistry with aero4 ModChem default ebi_cb05 Gas phase chemistry solver module e chem_noop deactivate gas phase chemistry e smvgear use the SMVGEAR chemistry solver e ros3 use the Rosenbrock chemistry solver e ebi_cb4 use the Euler Backward Iterative solver optimized for the Carbon Bond IV mechanism e ebi_cb4cl use the Euler Backward Iterative solver optimized for the Carbon Bond IV mechanism with chlorine chemistry e ebi_cb4hg use the Euler Backward Iterative solver optimized for the Carbon Bond IV mechanism with mercury e ebi_cb4txIp use the Euler Backward Iterative solver optimized for the Carbon Bond IV mechanism with air toxics e ebi_cb05 use the Euler Backward Iterative solver optimized for the Carbon Bond 05 mechanism 60 5 3 2 Files configuration and environment variables ebi_cbO5hg use the Euler Backward Iterative solver optimized for the Carbon Bond 05 mechanism with mercury ebi_cbO5cltx use the Euler Backward Iterative solver optimized for the Carbon Bond 05 mechanism with air toxics ebi_saprc99 use the Euler Backward Iterative solver optimized for the SAPRC 99 mechanism ebi_saprc99tx2p use the Euler Backward Iterative solver optimized for the SAPRC 99 mechanism with air toxics ebi_saprc99tx3 use the Euler Backward Iterative solver optimized for the SAPRC 99 mechanism with air toxics ModAero default aero4 CMAQ aerosol module aero_noop deactivate aerosol c
204. on of the file format documentation in Chapter 4 and existing grid definitions as examples you define new grids for CMAQ by adding a coordinate and grid description to the GRIDDESC file Set the GRID_NAME environment variable in the CMAQ run scripts to point to the name of the new grid The most common situation for creating a new CMAQ grid definition is encountered when you receive meteorology and or emissions data that have not yet been modeled with 154 9 2 3 Tips and recommendations Horizontal Grids CMAQ If the meteorology data are raw MM5 outputs by running them through MCIP you will automatically generate a GRIDDESC file that can be input directly to both CMAQ and SMOKE If the meteorology data are already in the CMAQ format and you do not have access to the GRIDDESC file generated by MCIP you can determine the grid definition of the input meteorology and emissions by using the netCDF utility ncdump to view the header of one of the gridded binary input files All of the grid definition information required by CMAQ is contained in the headers of gridded meteorology and emissions netCDF input files If you receive emissions and or meteorology for a CMAQ simulation you can determine the coordinate and grid definitions by viewing the header of any of these files Use a text editor to add the coordinate and grid definitions to a GRIDDESC file 9 2 3 Tips and recommendations Horizontal Grids MM5 Grids e The number of rows NROW
205. ong e The name must begin with an alphabetic character but may contain any alphanumeric character i e A Z a z and 0 9 or the characters and _ after the first position 89 5 10 2 Files configuration and environment variables e The name is case sensitive Thus NO2 and no2 would represent two different species e Aname can have embedded comments but cannot span two lines e Label names For some of the IRR commands reaction labels appearing in the chemical mechanism reaction list input file can be referenced These labels would normally be spelled exactly as they appear in the chemical mech anism reaction list input file except embedded comments and their delimiters should be omitted However any embedded blanks in those label names should be omitted and the label name should contain no more that 16 non blank characters e Numbers Numerical inputs in the command file can be either integer e g 5 floating point e g 5 0 or expo nential e g 5 0E 00 With the exponential format the E may be either upper or lowercase a positive exponent will be assumed if the sign of the exponent is missing e Command Line Terminator Input command lines are terminated by a semicolon 5 10 2 3 PROCAN commands This section describes the individual process analysis commands that are used to construct a PROCAN command file In the description of these commands the following conventions wi
206. ons PROFIL3 Vertical profile Used to store lists of vertical data like rawinsonde obser vations GRNEST3 Nested grid Preliminary and experiment al implementation for storing multiple grids which need not in fact have any particu lar relationship with each other beyond using the same coordinate system SMATRX3 Sparse matrix Sparse matrix data which uses a skyline transpose representation for sparse matrices such as those found in SMOKE KFEVNT3 Cloud event KF Cloud files use the same file description data struc tures from FDESC3 EXT and defining parameters from PARMS3 EXT the usual I O API DESC3 call may be used to retrieve file descriptions from the head ers KF Cloud file on the other hand have their own specialized opening creation lookup indexing input and output operations 37 4 3 Opening Creating Data Files in IO API File Type Magic Number Data Type Description TSRIES3 7 Hydrology Time Series A hydrology time series file behaves much like a degener ate gridded file except that the numbers of rows and columns are usually 1 and that there are additional file attributes found in the in clude file ATDSC3 EXT PTRFLY3 8 Pointer flyer A pointer flyer observation file behaves much like a de generate gridded file with NCOLS3D and NROWS3D set to 1 and certain mandat ory variables and variable naming conventions to be used by analy
207. ontains the Makefile and MCIP source code make 5 7 2 4 MCIP execution options The environment variables listed here are invoked during execution of the program and are set in the MCIP run script e APPL Application name scenario ID for file naming e CoordName Coordinate system name of the MCIP output grid that is written to the GRIDDESC file e GridName Model grid name of the MCIP output grid that is written to the GRIDDESC file e DataPath Input output data directory path InMetDir Path of the input data directory containing the MM5 or WRF output data files 79 5 7 2 Files configuration and environment variables InTerDir Path of the input data directory containing the MM5 TERRAIN file OutDir Path of the MCIP output data directory ProgDir default cwd Working directory containing the MCIP executable WorkDir Temporary working directory for Fortran links and the namelist file InMetFiles List of input meteorology files including the directory path for each file up to 100 files allowed as input to a single MCIP execution IfTer default T Binary flag indicating the availability of an input MM5 TERRAIN file options include T true or F false InTerFile Name and location of input MM5 TERRAIN file LPBL default 1 Sets the source of the PBL values in the MCIP output files The setting of this variable determines whether to use PBL values from the input meteorology file or to recalcu
208. options listed here are set during compilation of the ICON executable When these options are invoked they create a binary executable that is fixed to the specified configuration To change these options it is necessary to recompile ICON and create a new executable e Opt default verbose Defines the action to be taken by the program M3BLD when extracting source code from CVS and compiling an executable e compile_all force compile even if all the object files are current e clean_up remove all source files upon successful compilation e no_compile do everything except compile e no_link do everything except link e one_step compile and link in one step e parse_only checks configuration file syntax e show_only shows requested commands but does not execute them e verbose shows requested commands as they are executed 76 5 6 2 Files configuration and environment variables e MakeOpt Uncomment to build a Makefile to compile the executable e Mechanism Specifies the gas phase aerosol and aqueous phase chemical mechanisms to create initial conditions The choices for the Mechanism variable are the mechanism directory names under the M3MODEL include release directory Examples include e cb4_ae3_aq CB IV gas phase mechanism 3rd generation CMAQ aerosol mechanism aqueous cloud chemistry e cb4_ae4_aq CB IV gas phase mechanism 4th generation CMAQ aerosol mechanism aqueous cloud chemistry e saprc99_ae4_aq SAPRC9
209. or CMAQ The SMOKE and CONCEPT models are two programs available for preparing emissions for CMAQ Meteor ology models such as MM5 and WRF ARW generate gridded meteorology for input to both CMAQ and the emissions models MCIP is the first program in the CMAQ distribution package that a user should run when setting up a new simulation It is used to preprocess the data from a meteorology model for CMAQ the GRIDDESC file output from MCIP is needed to define the modeling grid ICON creates a binary netCDF initial conditions file for input to the CCTM With the option of creating initial conditions from either a text file of vertical concentration profiles or from an existing CCTM output file ICON outputs initial conditions data that are configured for a specific modeling grid and chemical parameterization BCON creates a binary netCDF lateral boundary conditions file for input to the CCTM With the option of creating initial conditions from either a text file of vertical concentration profiles or from an existing CCTM output file BCON outputs boundary conditions data that are configured for a specific modeling grid and chemical parameterization If derived from an existing CCTM or larger scale e g global scale output file BCON produces dynamic boundary conditions that vary in time and space When derived from vertical concentration profiles BCON produces static boundary conditions for input to the CCTM JPROC converts physical information abou
210. or this method include temperature humidity and horizontal wind component profiles e The surface exchange aerodynamic method Pleim et al 2001 uses surface resistance canopy resistance and stomatal resistance to compute dry deposition velocities Computes cloud top cloud base liquid water content and cloud coverage for cumuliform clouds using simple convective schemes The cloud parameters influence CCTM aqueous phase chemistry and cloud mixing as discussed in Section 2 2 5 Walcek and Taylor 1986 Chang et al 1987 First the cloud base is determined as the lifting condensation level computed from the highest saturated equivalent potential temperature below 700 mb Then the cloud top is computed by following a saturated adiabatic lapse rate from cloud base until it reaches a temperature five degrees cooler than the surrounding environment Once the top and bottom of the cloud are determined a vertical profile of the adiabatic liquid water mixing ratio can be constructed as the difference between the saturated mixing ratio at each level and the source level mixing ratio By iteratively solving the equations governing the conservation of total water mass energy conservation for cloud top mixing along with the temperature profile the cloud coverage fraction can be obtained Outputs meteorological geophysical files in the I O API format which is standard within the Models 3 framework 2 2 2 ICON and BCON The Initial and Boundary Cond
211. orithms and other components of the Models 3 Community Multiscale Air Quality CMAQ modeling system Appl Mech Rev 59 51 77 Carter W P L 1996 Condensed atmospheric mechanisms for isoprene Atmos Environ 30 4275 4290 Carter W P L 1990 A detailed mechanism for the gas phase atmospheric reactions of organic compounds Atmos Environ 24A 481 518 Carter W P L 2000 Implementation of the SAPRC 99 chemical mechanism into the Models 3 Framework Report to the U S Environmental Protection Agency 29 January 2000 Available online at http pah cert ucr edu carter reactdat htm CEP 2006 SMOKE version 2 2 Users Manual Available online at http cf unc edu cep empd products smoke Vversion2 2 1 7 References Dodge M C 1989 A comparison of photochemical oxidant mechanisms J Geophys Res 94 5121 5136 Gery M W G Z Whitten J P Killus and M C Dodge 1989 A photochemical kinetics mechanism for urban and regional scale computer modeling J Geophys Res 94 12 925 12 956 Grell G A J Dudhia and D R Stauffer 1994 A Description of the Fifth Generation Penn State NCAR Mesoscale Model MM5 NCAR Technical Note NCAR TN 398 STR 138 pp Seinfeld J and S Pandis 1998 Atmospheric Chemistry and Physics From Air Pollution to Climate Change John Wiley amp Sons New York NY Skamarock W C J B Klemp J Dudhia D O Gill D M Barker W Wang and J G P
212. oundary layer requires high resolution near the surface for meteorological simulations To de termine mass exchange between the boundary layer and free troposphere good resolution near the boundary layer top is preferable In addition different cloud parameterization may perform differently depending on the layering structure Layer definitions should be appropriate for the topographic features of the simulation domain Aerodynamic resistance which influences dry deposition velocities is a function of layer thickness and the boundary layer stability For emissions processing the layer thickness affects the plume rise from major stacks The vertical extent of the emission effects is determined by the thickness of the lowest model layer for the CCTM Although a six layer vertical grid definition is provided with the tutorial simulation examples there is no recommendation that it be used for regulatory applications 155 9 3 1 Using predefined vertical layers In the early versions of CMAQ pre version 4 5 Fortran include files defined the vertical layer configuration The VGRD EXT and COORD EXT files contained a parameter and data statements respectively for defining the number of layers and sigma coordinates of the vertical layer structure to be used for CMAQ CMAQ used these include files during compilation to build executables hard wired with the chosen vertical layers Starting with version 4 5 CMAQ began to use a dynamic vertical layer
213. ove 6 2 2 CONC CCTM hourly instantaneous concentration file The 3 D CMAQ hourly concentration file CONC is the most commonly referenced CMAQ output file Containing gas phase species mixing ratios ppmV and aerosol species concentrations ug m3 CONC files include instantaneous model species concentrations at the end of each model hour The number and types of species contained in the CONC files is dependent on the chemical mechanism and aerosol model configurations selected when compiling the CCTM The species concentration include files CONC EXT within the mechanism include directories list the species that are written to the CONC files for each mechanism configuration The GC_CONC EXT file lists the gas phase species and the AE_CONC EXT file lists the aerosol species written to the CONC file You can remove species from these CONC EXT files to reduce the number of species written to the CONC file 6 2 3 ACONC CCTM hourly average concentration file The 2 D CMAQ integral average concentration file ACONC includes average model species concentrations for each model hour as opposed to instantaneous concentrations at the end of each output time step The species written to the ACONC file are set by the user in the CCTM run script using the variable AVG_CONC_SPCS The model layers across which to derive the integral average concentration are also set in the CCTM run script using the variable ACONC_BLEV_ELEV 6 2 4 DRYDEP CCTM hourly cumu
214. ovide for a tight integration of the three main components of the air quality modeling system e Serial and multiprocessor execution options give the application user various options for optimizing the performance of CMAQ on different computer platforms e Community development expedites the expansion of CMAQ capabilities through the pursuit of multiple research agendas rather than from a single centralized development group e A Comprehensive training program is available through the Community Modeling and Analysis System CMAS Center http www cmascenter org e The growing community of users connected through the CMAS Center is available to share data experiences and provide technical support 1 4 Features of CMAQ for Air Quality Model De velopers Designed under a community modeling modeling paradigm CMAQ is distributed as open source software engineered with a modular code design to facilitate decentralized development Built around a layered I O API and netCDF code framework CMAQ provides an environment for testing new science algorithms chemistry representations and optim ization techniques CMAQ presents the following features to scientists interested in developing new algorithms or adding science to the model e Developed and distributed following open source software conventions CMAQ source code is easily accessible and free to obtain e Designed for modularity the CCTM uses standardized I O routines to facilitate extensibil
215. owers 2005 A Description of the Advanced Research WRF Version 2 NCAR Technical Note NCAR TN 468 STR 88 pp Yarwood G S Rao M Yocke and G Whitten 2005 Updates to the Carbon Bond chemical mechanism CBO5 Final Report to the U S EPA RT 0400675 Available online at www camx com 10 Chapter 2 Overview of the Science in the CMAQ Modeling System Table of Contents 2 1 Features to Achieve the Goals of CMAQ a3 esosa ides Sidesest seca d vcdaved a eacavei oe EEE E EEST EESIN 12 2 2 CMAQ Input ProCeSsors e ihesiis aka iaeegesia secs vies E ia Sockets vege ste SEEE tate Mend SEEE REEE cans ig eens 14 2 3 CMAQ Chemical Transport Model Science Modules cece cece ence ceeceeece seen seca seca eeee eeu eeaeeeneeeeeees 19 24 The CMAQ User Intertace ties dsc en a E anys stden gases toss dastiatigoaeeu sees av E E EE a 23 2 SURCTETENCES sd see hae votes udacasdadite nine fed oles Vea tease voi ale es oa ales Boss nden A amet tes Soe ee decade See ay 24 The National Ambient Air Quality Standards NAAQS were established by the U S Environmental Protection Agency USEPA under the authority of the Clean Air Act U S EPA 2004 These standards are designed to protect human health and the environment from high levels of criteria pollutants such as ozone and particulate matter The complex nature of air pollution scenarios requires control strategies to be effective for a variety of air pollutants regions and s
216. phase dry deposition estim ates CTM_WET_DEP_1 GRDDED3 Name and location of hourly 3 D gas and aerosol phase wet deposition estim ates CTM_VIS_1 GRDDED3 Name and location of hourly 3 D visib ility metrics CTM_DIAM_1 GRDDED3 Name and location of hourly 3 D aero sol diagnostics dp and sigmas for Aitken and Accumulation mode aerosol species set the variable CTM_AERO DIAG to T in the CCTM run script to write this additional file CTM_PING_1 GRDDED3 Name and location of hourly 3 D resid ual plume mass for Plume in Grid sources CTM_PING_DIAM_1 GRDDED3 Name and location of hourly 3 D aero sol diagnostics for Plume in Grid sources CTM_PING_DDEP_1 GRDDED3 Name and location of hourly 3 D gas and aerosol phase dry deposition estim ates for Plume in Grid sources CTM_IPR_ 1 3 GRDDED3 Name and location of hourly 2 D or 3 D integrated process rate files multiple files written when the CCTM is con figured to track a large number of pro cess pollutant combinations CTM_IRR_ 1 3 GRDDED3 Name and location of hourly 2 D or 3 D integrated reaction rate files mul tiple files written when the CCTM is configured to track a large number of reaction pollutant combinations The default location of the CCTM output files is the M3DATA cctm directory controlled by the OUTDIR variable in the run script The default naming convention for all CCTM output files uses the EXEC and APPL environment vari
217. programs see Chapter 5 As acommunity model the modular design of CMAQ facilitates customization and open source development Using the Input Output Applications Programming Interface I O API library http www bar onams com products ioapi AA html to control the internal and external data flows to the model and the network Common Data Form netCDF library http www unidata ucar edu software netcdf to control the input and output file formats CMAQ is based around a transparent and platform independent code infrastructure that promotes extens ibility by a broad community of developers The modularity of CMAQ also leads to multiple science configuration options that model users can choose from when setting up new simulations The trade off for this flexibility is com plexity in the model configuration the model user is faced with hundreds of different configuration combinations when designing new simulations To avoid confusion for new CMAQ users this document provides guidance on a basic configuration to use for getting started with the model For experienced air quality model users the multiple configur ation combinations available provide an unprecedented level of flexibility for optimizing model performance for dif ferent air quality model applications CMAQ is designed to meet the needs of the multiple groups contained within the air quality modeling community research and regulatory modelers algorithm and science module developers
218. ption SPRFA default 15 Vertical plume spread factor need more description SZOFA default 3 545 Width factor for plume sections need more description HSIZE default 1000 87 5 10 PROCAN Starting plume width size m need more description DISP default keep Controls the maintenance of existing log files e delete delete output log if it already exists e keep abort simulation if output log exists OUTDIR default M3DATA pdm PDM output file directory location GRIDDESC default GRIDDESC1 Grid description file for setting the horizontal grid definition GRID_NAME Name of the grid definition contained in the GRIDDESC file that specifies the horizontal grid for the current ap plication of the model LAYER_FILE Name and location of a MET_CRO_3D file for specifying the vertical layer structure for the current application of the model 5 9 2 5 PDM output files Table 5 14 PDM output files File Name Format Description PDM_PING_1 GRDDED3 Name and location of the time depend ent 3 D active plume file NFOUT_1 Optional diagnostic plume rise output NFOUT_2 Optional diagnostic plume parameters NFOUT_3 Standard diagnostic plume parameters The default location of the PDM output files is the M3DATA pdm directory controlled by the OUTDIR variable in the run script The default naming convention for all PDM output files uses the APPL environment variable in the file n
219. put Output F Horizontal grid definition GRIDDESC Vertical layer structure MET_CRO_3D Execution Options Figure 3 shows the input and output files and configuration options for ICON A distinction is made between the options that are invoked at compilation versus those invoked at execution of the program When compiling ICON the user specifies a chemical mechanism to determine the gas phase chemistry and aerosol mechanism for which to calculate chemical ICs Setting the Mechanism variable in the ICON compile script configures the program to use a specific set of mechanism include files to build an executable ICON executables are hard wired to a specific mechanism config uration At execution the user provides a data file of chemical conditions that ICON will convert to ICs on a predefined model grid Depending on how the user compiled the model through the specification of the ModInpt variable ICON will input either an ASCII vertical profile file IC_PROFILE or an existing CCTM concentration file CTM_CONC_1 If the input file is not in the same chemical speciation as the simulation that the user is creating ICs for it is necessary to specify a chemical conversion option by setting the ModMech variable at compilation The default conversion profiles in ICON are set up to convert from RADM2 speciation to either CB IV or SAPRC99 chemistry It is possible to create a custom conversion file MECH_CONV_FILE and input this file to ICON by setting
220. rce source category code region road class layer hour grid cell speciation profile gridding surrogate code temporal profile and elevated status Smkreport allows all of the above to be used in any combination 8 6 12 SMOKE Summary Figure 5 1 is a schematic of the parallel approach to emissions processing employed by SMOKE For each SMOKE processing category i e area biogenic mobile and point sources the following tasks are performed e read emissions inventory data files e optionally grow emissions from the base year to the future or past modeled year except biogenic sources e transform inventory species into chemical mechanism species defined by an AQM e optionally apply emissions controls except for biogenic sources e model the temporal distribution of the emissions including any meteorology effects e model the spatial distribution of the emissions e merge the various source categories of emissions to form input files for the AQM e at every step of the processing perform quality assurance on the input data and the results Each processing category has its particular complexities and deviations from the above list these are described in detail in CEP 2005 For all categories however most of the needed processing steps are factor based they are linear op erations that can be represented as multiplication by matrices Further some of the matrices are sparse matrices i e most of their entries are zeros
221. re quired XJVAL_3 Real or Exp Clear sky photolysis rate at NHTO NLATO NPHOTO and hour angle 3 re quired JVTMAX XJVAL_ JVTMAX Real or Exp Clear sky photolysis rate at NHTO NLATO NPHOTO and hour angle corres ponding to JVUTMAX required x 3 NHTO Int Vertical level cross reference to header data required NLATO Int Latitude cross refer ence to header data required NPHOTO Int Photolysis reaction cross reference to header data required x 4 XJVAL_1 Real or Exp Clear sky photolysis rate at NHTO NLATO NPHOTO and hour angle re quired 126 6 1 16 EMISfile Emissions Line Column Name Type Description B XJVAL_2 Real or Exp Clear sky photolysis rate at NHTO NLATO NPHOTO and hour angle 2 re quired C XJVAL_3 Real or Exp Clear sky photolysis rate at NHTO NLATO NPHOTO and hour angle 3 re quired JVTMAX XJVAL_ JVTMAX Real or Exp Clear sky photolysis rate at NHTO NLATO NPHOTO and hour angle corres ponding to JVTMAX required A sample of the important sections of a JVAL file is shown below 1999181 yyyyddd Julian Date for the file 7 LEVELS m 0 0 1000 0 2000 0 3000 0 4000 0 5000 0 10000 0 6 LATITUDES deg 10 0 20 0 30 0 40 0 50 0 60 0 9 HOUR ANGLES from noon 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 6 PHOTOLYTIC REACTIONS NO2_CBIV88 1 0
222. re are minimum levels of processing power and disk capacity needed for running CMAQ there is no single system that CMAQ is optimized to run on The flexibility of the modeling system enables the users to optimize CMAQ for most current hardware configurations CMAQ is distributed and supported for executing on Red Hat Linux operating systems with the Portland Group Fortran compiler Ports have been made to other brands of Linux such as Mandrake and Suse to other Fortran compilers such as Absoft and Intel and to other hardware systems such as Sun Silicon Graphics and Macintosh Information about these ports and up to date hardware recommendations are able through the CMAS Center website http www cmas center org The hardware recommendations provided below are the minimum level required to run CMAQ these certainly can be expanded to more powerful and larger systems with benefits to the model performance The software recommendations are closer to requirements as all of the necessary source code libraries and utilities needed for running CMAQ are listed 3 1 1 Hardware The minimum hardware requirements to run CMAQ are e PC with a single 1 0 GHz processor with a Red Hat Linux OS e 1GBRAM e 40GB hard drive storage 27 3 1 2 Software Below are two examples of optimal hardware configurations for running CMAQ on multiple processors in a production environment Optimal CMAQ Hardware Solution 1 4 dual CPU 2 8 GHz Xeon IBM Bla
223. rocessor systems require a command to start the MPI run time environment The CCTM run script is configured by default to use the mpirun command Consult your system administrator to find out how to invoke MPI when running multiprocessor applications 3 5 Benchmarking CMAQ CMAQ is distributed with a dataset that can be used to benchmark the CMAQ installation In the CMAQ distribution output data from CMAQ is bundled with the input data including emissions and meteorology that can be used to re produce the reference results After completing the CMAQ benchmark case the CCTM output files can be compared with the reference datasets provided in the distribution If the benchmark case is run on a system similar to that used to create the reference data Red Hat Linux with the Portland Group FORTRAN compiler the results should differ by no more than 0 01 for every model species Changing the optimization of the compiler or compiling on other operating systems with different compilers can lead to larger differences between the benchmark results and the reference datasets The CCTM benchmark targets for operating systems compilers other than the Red Hat Linux Portland Group combination are differences less than 1 for every model species 34 Chapter 4 Input Output Applications Programming Interface Table of Contents 4 1 Files Logical Names and Physical Names 0 ccccseeeseeceeccecececcneceneceeceeeceeeseeeeaeseaeeea seen
224. rognostic equations and represent the inverse of the e folding time of the phenomena that the observations represent There are two types of nudging in MMS analysis nudging and observation nudging obs nudging Analysis nudging gently forces the model solution toward gridded fields Analysis nudging can make use of three dimensional analyses and some surface analyses Obs nudging gently forces the model solution toward individual observations with the in fluence of the observations spread in space and time Obs nudging is better suited for assimilating high frequency asynoptic data that may not otherwise be included in an analysis Nudging in MMS is extensively discussed in Stauffer and Seaman 1990 Stauffer et al 1991 and Stauffer and Seaman 1994 7 7 Meteorology Model Post Processing Since the output variables that are generated by an MMS simulation are not always useful in their raw form those variables must be converted into fields that are required by the chemistry and emission models The conversion of MMS output to useful fields for CMAQ is accomplished in the Meteorology Chemistry Interface Processor MCIP which is discussed in Section 2 3 1 MCIP computes variables that are useful to the subsequent models in CMAQ and it creates an output file written with the I O API libraries in netCDF format which is standard in the CMAQ modeling system 7 8 Meteorology Model Visualization and Evalu ation The MM5 output ca
225. rtran 77 Some of the software has been converted to include features in Fortran 90 A C pre processor is used to compile the software with directives for various hardware platforms All of the MM5 system software is compiled using the make utility The scripts that support the execution of various programs in the software system are written in C shell 7 4 Data Requirements Several datasets are required to run MM5 Those datasets can be classified as static data that are representative of the simulation domain regardless of the episode period and case specific data that are specific to the episode 7 4 1 Static Data Certain static data bases need to be available to define the simulation domain for MM5 There are currently five resol utions of terrain data bases and three resolutions of land use data bases that NCAR distributes to support MM5 simu lations The terrain data bases are 60 minute 1 degree or about 111 km in mid latitudes 30 minute 0 5 degree or about 55 km in mid latitudes 10 minute about 18 5 km in mid latitudes 5 minute about 9 25 km in mid latitudes and 1 minute about 0 925 km in mid latitudes The first four terrain data bases include world wide coverage the 1 minute data base is currently only available for the continental U S The land use data bases are available in 60 minute 30 minute and 10 minute resolutions for world wide coverage The land use data includes 13 categories of land use
226. s com products ioapi Colella P and P L Woodward 1984 The piecewise parabolic method PPM for gas dynamical simulations J Comput Phys 54 174 201 Dennis R L J N McHenry W R Barchet F S Binkowski and D W Byun 1993 Correcting RADM s sulfate underprediction Discovery and correction of model errors and testing the corrections through comparisons against field data Atmos Environ 26A 975 997 Elterman L R Wexler and D T Chang 1969 Features of tropospheric and stratospheric dust Appl Optics 8 893 903 Gery M W G Z Whitten J P Killus and M C Dodge 1989 A photochemical kinetics mechanism for urban and regional scale computer modeling J Geophys Res 94 12 925 12 956 Gong S L 2003 A parameterization of sea salt aerosol source function for sub and super micron particles Global Biogeochem Cycles 17 1097 doi 10 1029 2003GB002079 Hertel O R Berkowicz J Christensen and O Hov 1993 Test of two numerical schemes for use in atmospheric transport chemistry models Atmos Environ 27A 2591 2611 Jacobson M and R P Turco 1994 SMVGEAR A sparse matrix vectorized Gear code for atmospheric models Atmos Environ 28 2991 3003 Jiang W S Smyth E Giroux H Roth and D Yin 2006 Differences between CMAQ fine 25 2 5 References mode particle and PM2 5 concentrations and their impact on model performance evaluation in the lower Fraser valley
227. s conserving advection e init_yamo Yamartino scheme for mass conserving advection ModAdje default Yamartino option Mass conservation error adjustment scheme Corrects for mass inconsistencies arising from how the input meteor ology treats density and wind fields This adjustment is only required if the air density based scheme for mass conserving advection is selected e adjcon_noop deactivate the air density based conservation adjustment scheme e denrate adjust the vertical advection error term from the meteorology model by air density from the CCTM e comment out for Yamartino scheme for mass conserving advection ModCpl default gencoor Unit conversion and concentration coupling module The only option is for the CMAQ generalized coordinate gencoor ModHadv default hyamo Horizontal advection module e hadv_noop deactivate horizontal advection e hppm use the unmodified Piecewise Parabolic Method to calculate horizontal advection e hyamo use the global mass conserving scheme to calculate horizontal advection ModVadv default vyamo Vertical advection module e vadv_noop deactivate vertical advection e vppm use the unmodified Piecewise Parabolic Method to calculate vertical advection e vyamo use the global mass conserving scheme to calculate vertical advection ModHdiff default multiscale Horizontal diffusion module e hdiff_noop deactivate horizontal diffusion e multiscale diffusion coefficient base
228. s could induce large errors in the pollutant concentrations predicted by the air quality model Also the modularity of the scientific processes in CMAQ makes modifications and adaptations to the user s model more straightforward The potential for error is minimized because the user is not required to change code or declare variables within the program modules A common error in previous model formulations overlooked necessary program coding changes when making model modifications An other feature of CMAQ that supports quality control is process analysis which is discussed in Section 2 2 6 2 2 CMAQ Input Processors The CCTM uses data from other models and CMAQ subprograms as input for model simulations Figure 2 2 Detailed information about the meteorological model in the context of preparing inputs for CMAQ can be found in Chapter 4 Detailed information about the emissions models for preparing CMAQ input can be found in Chapter 5 Figure 2 2 Chemical Transport Model CCTM and preprocessors Meteorology Emission Modeling System Modeling System me E x Options Selected f 77777 an aie alee upenes Case i l MCIP PDM Grid Domain and Size JPROC a x elas Projection i ma _ 2 ee O i Vertical Structure i ICON A CMAQ Chemical Mechanism f chemical transport model 1 BCON CCTM processor i i aid TES Shet The input data for the CCTM are developed using the five processors shown in Figure
229. s that are observed in photochemical air quality conditions In CCTM turbulent fluxes are expressed in terms of the mixing ratios and an air density weighted Jacobian to handle atmospheric diffusion processes with generalized coordinates This approach is convenient for numerically solving the flux form turbulence mixing because most flux based closure algorithms use parameterizations of turbulent fluxes of conserving quantities such as mass mixing ratios In CMAQ version 4 5 Eddy diffusion is implemented for repres enting vertical diffusion Eddy diffusivity is a local mixing scheme and is estimated using the same planetary boundary layer PBL similarity based algorithm as in the Regional Acid Deposition Model RADM Chang et al 1987 1990 In CCTM the deposition process is simulated as a flux boundary condition that affects the concentration in the lowest layer By treating the deposition process as the loss of mass due to the diffusion flux at the bottom of the model one can relate the bottom boundary condition in the generalized coordinate system to that in the Cartesian coordinate system Version 4 5 has an improved version of the minimum allowable vertical eddy diffusivity The new version interpolates between urban and non urban land cover allowing a larger minimum value for a larger fraction of urban land cover In CMAQ version 4 5 horizontal diffusion is implemented with a single eddy diffusion algorithm that is based on local wind deforma
230. s the Date environment variable in the file name which is aliased to the STDATE environment variable in the run script 77 5 7 MCIP 5 7 MCIP 5 7 1 Description The Meteorology Chemistry Interface Processor MCIP converts meteorology data output from either the PSU NCAR Mesoscale Model MMS or the Weather Research Forecast WRF model to I O API formatted files that are compatible with CMAQ and the Sparse Matrix Operator Kernel Emissions SMOKE model MCIP automatically determines if an input file is MM5 or WRF by trying to open the file as a netCDF file If the file can be read as netCDF MCIP assumes the input is a WRF dataset otherwise MM5 is assumed While most of the variables calculated in the meteorology model are simply passed through by MCIP to the output T O API files radiation fields and dry deposition velocities are calculated by MCIP In addition the user has the option of passing through the planetary boundary layer PBL heights calculated by the meteorology model recommended or recalculating the PBL with MCIP Environment variables in the MCIP run script control these configuration settings MCIP has the capability to extract both temporal and spatial subsets of the input meteorology files e The run script allows the user to specify the beginning and end dates times of the MCIP simulation these dates times can fall anywhere within the range of the input meteorology time period e Two types of horizontal dom
231. sed to drive CMAQ is used to generate emissions for the model The input meteorology emissions and CMAQ must all be configured for the same coordinate system 9 2 Horizontal Grids The extent of the horizontal grid used in CMAQ is limited by the size of the domain of the input meteorology A combination of the CMAQ meteorology processor MCIP and the I O API are used to prepare the input meteorology for the CCTM and contain utilities for windowing subsets of the data performing grid transformations and aggregat ing interpolating between grid cell resolutions Choosing the appropriate horizontal grid scale and extent for your simulation is largely dependent on the issues that you want to address through the modeling practical consideration should also be paid to the relationship between grid size output file size and execution times In early versions of CMAQ pre version 4 3 Fortan include files defined the horizontal configuration The COORD EXT file contained data statements for defining the horizontal coordinate and grid to be used for CMAQ CMAQ used these include files at compilation to create executables that were hard wired to a specific grid configuration Starting with CMAQ version 4 3 CMAQ developers transitioned to a dynamic horizontal grid configuration that could be defined at execution forgoing the need to recompile the program each time a user wanted to simulate a new grid Horizontal grids are now configured in CMAQ through th
232. set to m3conc CTM_PING_1 PING_PDM_1 GRDDED3 GRDDED3 Name and location of the plume in grid concentration file for the coarse do main this file is output from the CCTM only used when BCON_PING is set to Y Name and location of the plume in grid plume dynamics file for the coarse do main this file output from the PDM only used when BCON_PING is set to wy MET_CRO_3D_CRS GRDDED3 Name and location of the course grid MET_CRO_3D file that is required for creating either plume in grid boundary conditions or if the vertical grid struc ture changes between nested simula tions this file is output by MCIP MET_CRO_3D_FIN GRDDED3 Name and location of the fine grid MET_CRO_3D file that is required if the vertical grid structure changes between nested simulations this file is output by MCIP GRIDDESC MET_CRO_3D ASCII GRDDED3 Horizontal grid description file for de fining the model grid this file is output by MCIP or can be created by the user 3 D cross point meteorology file for defining the vertical layer structure of the model grid this file is output by MCIP 51 5 2 2 Files configuration and environment variables 5 2 2 2 BCON configuration options The configuration options listed here are set during compilation of the BCON executable When these options are invoked they create a binary executable that is fixed to the specified configuration T
233. simulation If SDATE is not set ICON will use the first hour of the CTM_CONC_1 5 5 2 5 ICON output files Table 5 8 ICON output files File Name Format Description INIT_CONC_1 GRDDED3 Gridded initial conditions data output on the model grid defined by GRID_NAME The default location of the ICON output files is the M3DATA icon directory controlled by the OUTDIR variable in the run script The default naming convention for all ICON output files uses the APPL and GRID_NAME environment variables in the file name For initial conditions created from existing CCTM CONC files the Julian date is also used in the file name through the DATE environment variable All of the file naming variables for ICON outputs are set in the run script 5 6 JPROC 5 6 1 Description JPROC calculates daily clear sky photolysis rates from look up tables of molecular absorption cross section and quantum yield data and climatologically derived ozone column and optical depth data The output from JPROC are ASCII look up tables of daily clear sky photolysis rates for photochemical reactions in a selected gas phase photochem ical mechanism at different altitudes latitudes and hours from noon The photochemical mechanism that these rates are derived for is selecting during compilation of JPROC The altitudes meters latitudes degrees and hour angles from noon that the rates are derived for are hardwired in the JPROC source code 74 5
234. simulation domain has been established REGRID is run to generate first guess fields for the model simulation by horizontally interpolating a larger scale dataset global or regional coverage to the simulation domain REGRID interpolates the background fields to the simulation domain for times throughout the simulation period these files are used to ultimately generate lateral boundary conditions for the coarse domain simulations nested domains use lateral boundaries from the coarse domain REGRID also processes the sea surface temperature and snow files by interpol ating the analyses data to the simulation domain As a last step REGRID calculates map scale factors and Coriolis parameters at each grid point to be used by MM5 REGRID is described by Manning and Haagenson 1992 7 5 3 Objective Analysis RAWINS The program RAWINS performs an objective analysis by blending the first guess fields generated by REGRID with upper air and surface observations There are four objective analysis techniques available in RAWINS circular shaped Cressman weighting function elliptical shaped weighting function banana shaped weighting function and multi 138 7 5 4 Setting the Initial and Boundary Conditions INTER PF quadric interpolation In addition RAWINS performs some data quality checks against user defined thresholds The objective analysis is performed for a user defined number of pressure surfaces generally mandatory levels plus some
235. sis and visualiz ation software 4 3 Opening Creating Data Files in lO API The I O API function OPEN3 was created to open both new and existing files OPEN3 is a FORTRAN logical function that returns TRUE when it succeeds and FALSE when it fails LOGICAL FUNCTION OPEN3 FNAME FSTATUS PGNAME where CHARACTER FNAME file name for query INTEGER FSTATUS see possible values in Table 4 3 CHARACTER PGNAME name of calling program This function maintains considerable audit trail information in the file header automatically as well as automates various logging activities The arguments to OPEN3 are the name of the file an integer FSTATUS indicating the type of open operation and the caller s name for logging and audit trail purposes OPEN3 can be called many times for the same file FSTATUS values are defined for CMAQ in PARMS3 EXT and are also listed in Table 4 3 38 4 3 Opening Creating Data Files in IO API Table 4 3 Possible values for OPEN 3 FSTATUS FSTATUS Value Description FSREAD3 1 for READ ONLY access to an existing file FSRDWR3 2 for READ WRITE UPDATE access to an existing file FSNEW3 3 for READ WRITE access to create a new file file must not yet exist FSUNKN3 4 for READ WRITE UPDATE access to a file whose existence is unknown FSCREA3 5 for CREATE TRUN CATE READ WRITE access to files 39 66 In the last three cases new unknown and cr
236. specific type of emission would produce the desired results or if another control would be more effective 2 4 The CMAQ User Interface The distributed CMAQ user interface consists of a series of C shell scripts for building and running the different CMAQ programs on Linux operating systems These scripts can be adapted to work with any Unix shell scripting language e g Bash Bourne etc and function primarily to set a series of environment variables required by M3BLD or the CMAQ program executables Manipulating the CMAQ scripts requires the use of a Unix text editor such as vi ht tp www vim org or nedit http www nedit org Alternatives to Unix shell scripts exist in prototype CMAQ graphical users interfaces GUI with the Multimedia Integrated Modeling System MIMS and the CMAQ GUI both available through the CMAS Center http www cmascenter org There are three basic User Interfaces for CMAQ the CMAQ C shell scripts the distributed user interface the CMAQ Graphical User Interface GUD and the CMAQ Unified Archive The C shell scripts and the Unified Archive are both text based UNIX interfaces in which CMAQ is configured and compiled by editing the scripts These scripts can be adapted to work with any Unix shell scripting language e g Bash Bourne etc and function primarily to set a series of environment variables required by M3BLD or the CMAQ program executables Manipulating the CMAQ scripts requires the use of a Unix te
237. t photoreactive molecules into clear sky photolysis rate look up tables for input to the CCTM The CCTM is run last in the sequence of programs All of the other CMAQ programs emissions and meteorology models are used to prepare the inputs to the CCTM By using data that are synchronized for a particular modeling time 48 5 2 BCON period model grid vertical layer configuration and chemical parameterization the CCTM produces hourly estimates of pollutant concentrations wet and dry deposition rates and visibility metrics In addition to the core programs shown in Figure 5 1 CMAQ also includes utilities and libraries for utilizing some of the special features in CMAQ and setting up the CCTM for multi processor computing CMAQ includes the PROCAN utility for preparing process analysis simulations CHEMMECH the CMAQ chemical mechanism compiler and the Plume Dynamics Model PDM for subgrid scale representation of selected point sources also known as plume in grid or PinG The Stencil Exchange library STENEX is a module that the CCTM uses to control the communication between processors in a multiprocessor computing environment Similarly the CCTM uses the PARIO library to synchronize the reading and writing of information across and between multiple processors In the remaining sections of this chapter we provide detailed descriptions of these programs utilities and libraries in alphabetical order Information about t
238. t these variables are commented out To override the default setting of a configuration option uncomment the corresponding variable and change the setting for your application 83 5 9 2 Files configuration and environment variables 5 9 2 Files configuration and environment variables Figure 5 7 PDM input and output files STACK_MEPSE GRID_CRO_2D GRIDDESC GRID_DOT_2D PDM_PING_1 PDM_PING_O MET_CRO_2D Input Files Shows Input Output P Figure 7 shows the input and output files for the PDM The input file PDM_PING_O is only used when continuing a simulation from a previous day Additional output files may also be written in addition to the file shown in Figure 7 These diagnostic outputs are activated by setting the IPRFLG environment variable to T during execution 84 5 9 2 Files configuration and environment variables 5 9 2 1 PDM input files Table 5 13 PDM input files File Name STACK_MEPSE Format GRDDED3 Description GMajor emitting point source emis sions file that identifies the elevated emissions sources to receive PinG treatment in the CCTM output from and emissions program such as SMOKE or CONCEPT GRID_CRO_2D GRDDED3 Time independent 2 D cross point meteorology file this file is output by MCIP GRID_DOT_2D GRDDED3 Time independent 2 D dot point met eorology file this file is output by MCIP MET_CRO_2D MET_DOT_3D GRDDED3 GR
239. ta Both are de scribed below 147 8 5 1 Emissions Inventories 8 5 1 Emissions Inventories The emissions inventories that are input into SMOKE fall into six source categories Stationary area Nonpoint Nonroad mobile On road mobile Point Wildfire and Biogenic sources The inventories should contain data for the pollutant species that are required by CMAQ The emissions inventories used in SMOKE should cover the spatial domain that CMAQ will be covering 8 5 2 Ancillary Data The ancillary data files are all the data files need by SMOKE except for the emissions inventories These files include the inventory table gridding surrogates speciation profiles temporal cross reference files report configuration files grid description file etc 8 6 Overview of SMOKE Version 2 1 The latest version of SMOKE Version 2 1 has many updated features It includes updated versions of BEIS3 and MOBILE6 2 for biogenic and on road mobile emissions modeling respectively Both of these SMOKE features integrate predicted hourly meteorology to estimate hourly emissions fluxes from these emissions sources The latest version also has support for polar stereographic output grids Brief descriptions of the major steps in creating emissions files follow 8 6 1 Importing Inventory Data Smkinven The first step in creating emissions files for input into CMAQ is to import the raw inventory data The raw inventory data is usually in ASCII format
240. tant improvement in the convective cloud mixing algorithm that corrects a tendency to over predict excessive transport from upper layers in the cloud to sub cloud layers 2 3 6 Plume in Grid Modeling PinG When individual sources are added directly into a grid model it is assumed that the emissions are instantaneously mixed into the grid where the source is located In reality stack gases are emitted in conical plumes that disperse and expand gradually as a function of stability wind speed and distance downwind of the stack Thus the assumption that individual sources are instantaneously mixed can cause over dilution of the emissions into large grid cells Also when 22 2 3 7 Process Analysis advection dominates as the transport mechanism for the emissions the source s plume can be mixed too close to the source when it should be mixed into air downwind of the source location Improvements have yielded a more realistic treatment of the subgrid scale physical and chemical processes impacting individual point source plumes CCTM s Plume Dynamics Model PDM treats plume rise vertical horizontal growth due to turbulence and sheer processes and plume position A Lagrangian Reactive Plume Module LRPM accounts for the relevant dynamic and chemical processes of the subgrid plumes and incorporates the plume material into the intercepted grid cells when certain physical size or chemical criteria are met PinG is designed for the larger
241. te ground level relative humidity Allow canopy to dry out gradually between 2 and 3 hours after last wet time e Corrected checking and setting I O API header variables for Mercator and polar stereographic projections e Added restriction that Eta Ferrier microphysics scheme in WRF ARW WRF EM is currently incompatible with CMAQ e Added capability to fill land use lookup table fields in MM5v3 formatted data that have been converted from MM5v2 format e Corrected filling of vertical velocity array for MM5v2 formatted data e Added land water mask to output in GRIDCRO2D e Corrected logic for processing MMS s TERRAIN file to account for expanded grid in coarse domain e Updated condition for GRIDCRO3D output to reflect new WRF ARW WRF EM vertical coordinate descriptor in I O API e Optimized calculations of species specific dry deposition constants e Use land water mask rather than dominant land use array to determine water points e General code clean up removed unused variables moved variables from global to local within subroutines eliminated type mismatches corrected clarified comments e Added ASCII file that includes calling tree for MCIP e Updated frequently asked questions list e Updated version stamp 1 6 About this manual 1 6 About this manual This manual is an operational guidance document for users of the CMAQ modeling system and is designed to support the installation configuration and exec
242. tely is therefore a key issue that strongly influences air quality model performance CCTM uses state of the science techniques to simulate photolytic reactions in the Phot module Photolysis reactions and their rates of reaction are driven by sunlight Similar to kinetic reaction rates for non photochemical reactions the photolysis rate quantifies how much reactant is produced from a photolytic reaction in a given amount of time The rate of photolysis is a function of the amount of solar radiation called actinic flux which varies based on the time of day season latitude and terrestrial features The amount of solar radiation is also affected by the amount of cloudiness and by aerosol absorption and scattering in the atmosphere The photolysis rate also depends on species specific mo lecular properties like the absorption cross section the effective molecular area of a particular species when absorbing solar radiation which results in a shadow region behind the particle and quantum yield the number of molecules that dissociate for each light photon incident on the atmosphere These molecular properties depend on the wavelength of the incident radiation and the temperature and hence on the available photon energy Thus estimating the photolysis rate is further complicated by these temperature and wavelength dependencies As discussed in Section 2 2 3 the CMAQ modeling system includes an advanced photolysis model JPROC to calculate temporally
243. tep that 69 5 5 2 Files configuration and environment variables represents the chemical conditions in each grid cell at the beginning of a CCTM simulation The ICs can be either spatially uniform or variable across the model grid depending on the source of the initial chemical concentration data If deriving ICs from the ASCII vertical profiles ICON can only create spatially uniform ICs within each model layer it can create different initial conditions across model layers ICON can extract spatially varying ICs from CONC files on either the same grid cell resolution as a windowed modeling domain or for a finer resolution model grid as for a nested simulation Two distinct modes of operation exist for ICON depending on the nature of the input data When creating ICON ex ecutables the user must specify whether the input data will be ASCII vertical profiles or a CONC file by selecting either profile or m3conc respectively for the setting of the ModInpt variable This variable determines the input module to use when creating a ICON executable 5 5 2 Files configuration and environment variables Figure 5 4 ICON input and output files Mechanism Include Files GC_SPC EXT Input Type Set Mechanism AE_SPC EXT GC_ICBC EXT pty Mechanism s Conversion Compile Options If ModInpt profile IC_PROFILE INIT_CONC_1 If ModMech user_defined MECH_CONV_FILE If Modinpt m3conc CTM_CONC_1 Shows In
244. the ModMech variable to user_defined at compilation 70 5 5 2 Files configuration and environment variables The horizontal grid and vertical layer structures for ICON are defined at execution through the input of a grid description GRIDDESC file and a meteorology cross point 3 d MET_CRO_3D file respectively ICON interpolates between the input vertical layer structure and output layer structure if they are different 5 5 2 1 ICON input files Table 5 7 ICON input files File Name Format Description IC_PROFILE ASCII Vertical chemical profiles from which to derive initial conditions this file is created by the user MECH_CONV_FILE ASCII Mapping factors for converting between chemical mechanisms this file is created by the user CTM_CONC_1 GRDDED3 Name and location of the CMAQ con centration file from which to derive initial conditions this file is output from the CCTM CTM_PING_1 GRDDED3 Name and location of the plume in grid concentration file for the coarse do main this file is output from the CCTM only used when ICON_PING is set to Y PING_PDM_1 GRDDED3 Name and location of the plume in grid plume dynamics file for the coarse do main this file output from the PDM only used when ICON_PING is set to wy MET_CRO_3D_CRS GRDDED3 Name and location of the course grid MET_CRO_3D file that is required for creating either plume in grid initial conditions or if the vertical grid struc t
245. the following environment variables to alias the locations of these different direct ories M3LIB M3HOME lib M3DATA M3HOME data M3MODEL M3HOME models Using environment variables to specify the CMAQ directories generalizes the CMAQ scripts by only requiring that the user specify the location of the M3HOME directory on their system and then setting the rest of the CMAQ direct ories relative to M3HOME While this directory structure works well for the tutorial case and most CMAQ applications other configurations are possible 3 3 Compiling CMAQ for the Tutorial Simulation For all CMAQ programs other than MCIP the program M3BLD is used to compile the source code into executables The first step in the compilation of CMAQ is to compile M3BLD Then compile the program libraries Stenex and Pario before moving on to the compilation of the rest of the CMAQ programs For all of the CMAQ programs and libraries the directory paths for the Fortran and C compilers in the build scripts will have to be changed to reflect the correct locations on the users system For parallel compilations some of the programs also require directory paths to MPICH include files Program specific compilation instructions are provided below The compilation instructions in this section are for building executables for simulating the tutorial data sets distributed with CMAQ Other than the paths to the compilers the build scripts used in this section will not need to be cha
246. tion and is scaled to the grid cell size The horizontal eddy diffuseness is assumed to be uniform but de pendent on the grid size of the model The diffusivity is larger for a higher resolution run where the numerical diffusion due to the advection process is smaller 2 3 4 Particulate Matter CCTM uses a modal approach to simulate PM2 5 particulate matter of diameter equal to or less than 2 5 microns coarse particulate matter particulate matter of diameter greater than 2 5 microns and equal to or less than 10 microns and PM10 particulate matter of size equal to or less than 10 microns PM2 5 is further divided into the Aitken and accumulation modes Coarse particulate matter is represented currently by fugitive dust and a generic anthropogenic species PM10 is the sum of the PM2 5 and coarse particulate matter Particulate matter in the atmosphere can either be primary or secondary Primary particulate matter is emitted directly into the atmosphere from natural or anthropogenic emissions Secondary particulate matter is formed in the atmosphere either from precursors as a result of chemical reactions or from condensation or deposition onto primary particles that are already present in the atmosphere CCTM can predict fine particulate speciated concentrations of sulfate nitrate ammonium organics and aerosol water and it includes methods for simulating nucleation dry deposition and cloud processes The au generation CMAQ aerosol module a
247. tion input files from either existing CMAQ outputs or from ASCII vertical profiles Figure 4 3 is a graphical example of the CMAQ initial conditions file 121 6 1 15 JTABLE Photolysis Rates Lookup Table Figure 6 3 Graphical example of a CMAQ gridded initial conditions file Layer 1 O3 Initial Conditions file CMAGQ44_necdenr96mp_saprc99_adj IC 1996176 ncf 0 150 51 0 113 0 075 0 038 June 25 1996 0 00 00 Min 0 022 at 5 21 Max 0 131 at 38 32 6 1 15 JTABLE Photolysis Rates Lookup Table Used by CCTM Each of the three default gas phase mechanisms in CMAQ CB IV SAPRC99 and RADM2 contain photolysis reactions that require clear sky reaction rates that are precomputed from kinetics data at various altitudes and latitude bands The CMAQ program JPROC Section 2 2 3 generates photolysis rate lookup tables for input to CMAQ Referred to as JTABLE files in CMAQ terminology these files contain a header section that describes the contents of the file and a data section with clear sky photolysis rates at different times of the day The first line of the header contains the Julian date of the data in the file This date will correspond to the start date for the simulation that inputs the JTABLE data Four pairs of information follow describing the altitude m latitude de grees hour angle from noon and photolytic reaction name for the data contained in the file Each data pair begins with a line describing the n
248. to this version and release of MMS and consider MMS to be in the public domain for use by any person or entity without any fee or charge Penn State and UCAR shall be credited in any publications that result from the use of MM5 The names Penn State and UCAR shall not be used or referenced in any advertising or publicity that endorses or promotes any products or commercial entity associated with or using MMS or any derivative works thereof without the written au thorization of UCAR and Penn State MM5 is provided to the public by Penn State and UCAR on an as is basis and any warranties either express or implied including but not limited to implied warranties of non infringement originality merchantability and fitness for a particular purpose are disclaimed Neither UCAR nor Penn State will be obligated to provide support consulting training or assistance of any kind with regard to the use operation and performance of MMS nor to provide any updates revisions new versions error corrections or bug fixes In no event will UCAR and Penn State be liable for any damages whatsoever whether direct indirect consequential or special which may result from an action in contract negligence or other claim that arises out of or in connection with the access use or performance of MMS including infringement actions Data that are obtained from NCAR e g global analyses and observations are prepared and maintained by th
249. umber of values for each variable and the variable name followed by the values for each variable The altitude variable LEVELS latitude variable LATITUDES and hour angle variable HOUR ANGLES variables have fixed values that are hard coded in the program JPROC routine jproc F The reaction names variable PHOTOLYTIC REACTIONS are mechanism dependent and vary with the choice of gas phase mechanism The data section of the file contains data blocks that are mapped to the header using a three digit code Each block corresponds to an altitude latitude and photolysis reaction and contains nine values of clear sky photolysis rates for the nine hour angles listed in the header The three digit code maps the altitude latitude reaction number to the data block For example the data block that uses the code 3 1 2 corresponds to altitude 3 latitude 1 and reaction 2 as 122 6 1 15 JTABLE Photolysis Rates Lookup Table listed in the file header A detailed description of the JTABLE file format is provided in Table 4 2 The files are list formatted 123 6 1 15 JTABLE Photolysis Rates Lookup Table Table 6 12 JTABLE file format description Line Column Name Type Description 1 A JVDATE String Julian date of the file YYYYDDD required B Comment String Description of the Juli an date field optional 2 A JVHT Int Number of vertical levels covered by th
250. und fields processed in REGRID and INTERP For the nests when the one way nest option is selected the lateral boundary conditions are interpolated from the simulation on the parent domain 7 6 4 Model Physics Several model physics options are available to users of MM5 They are briefly noted below The model physics options are further discussed and compared in Dudhia et al 1998 7 6 4 1 Radiation There are four atmospheric radiation cooling schemes available in MM5 none simple cooling the Dudhia long and short wave radiation scheme and the NCAR CCM2 radiation scheme 7 6 4 2 Convective Parameterization There are currently six convective parameterization schemes available in MM5 Anthes Kuo Fritsch Chappel Arakawa Schubert Kain Fritsch Betts Miller and Grell These convective parameterization schemes have been designed for 140 7 6 5 Nesting use at various simulation scales and they are not interchangeable For example each scheme uses different assumptions for convective coverage on the sub grid scale and for the convective trigger function The convective parameterization schemes also differ greatly in CPU usage and memory requirements The option for no convective parameterization for the domain e g explicitly resolved convection on the grid scale is available in MMS This option is generally used for simulations on domains with horizontal grid spacing smaller than 10 km 7 6 4 3 PBL Processes Six
251. ure changes between nested simula tions this file is output by MCIP MET_CRO_3D_FIN GRDDED3 Name and location of the fine grid MET_CRO_3D file that is required if the vertical grid structure changes between nested simulations this file is output by MCIP GRIDDESC ASCII Horizontal grid description file for de fining the model grid this file is output by MCIP or can be created by the user MET_CRO_3D GRDDED3 3 D cross point meteorology file for defining the vertical layer structure of the model grid this file is output by MCIP 71 5 5 2 Files configuration and environment variables 5 5 2 2 ICON compilation options The configuration options listed here are set during compilation of the ICON executable When these options are invoked they create a binary executable that is fixed to the specified configuration To change these options it is necessary to recompile ICON and create a new executable Opt default verbose Defines the action to be taken by the program M3BLD when extracting source code from CVS and compiling an executable e compile_all force compile even if all the object files are current e clean_up remove all source files upon successful compilation e no_compile do everything except compile e no_link do everything except link e one_step compile and link in one step e parse_only checks configuration file syntax e show_only shows requested commands but do
252. ution of CMAQ on UNIX systems Introductory and overview chapters present the CMAQ concepts terminology installation instructions and guidance on running the tutorial simulation distributed with the model Chapters on developing meteorology and emissions for CMAQ present the basic concepts and the availability of models that generate these critical CMAQ inputs and describe how to configure these systems to produce input for CMAQ e Chapter 2 describes the science used in CMAQ e Chapter 3 describes computer system requirements and installation e Chapter 4 describes the Input Output Applications Programming Interface I O API e Chapter 5 describes the set of CMAQ programs and libraries e Chapter 6 describes the CMAQ input files e Chapter 7 describes how to define the domain grids layers and chemical mechanisms e Chapter 8 describes setting up CMAQ for new simulations e Chapter 9 describes analysis options for CMAQ output e Chapter 10 describes CMAQ code management and development guidelines e Chapter 11 describes how to obtain support for CMAQ 1 7 References Byun D and J K S Ching 1999 Science Algorithms of the EPA Models 3 Community Multiscale Air Quality CMAQ Modeling System United States Environmental Protection Agency Rep EPA 600 R 99 030 727 pp Available from Office of Research and Development EPA Washington DC 20460 Byun D and K L Schere 2006 Review of the governing equations computational alg
253. varying photolysis rates for use in simulating photolysis in CCTM 2 3 0 Diffusion and Advection Pollutant transport includes both advection and sub grid scale diffusion Advection has to do with pollutant transport due to the mean wind fields and diffusion involves sub grid scale turbulent mixing of pollutants If a plume is trans ported primarily by advection then it may travel a long distance without much change in pollutant concentrations On the other hand if a plume is transported primarily by diffusion then the pollutants will mix more quickly and nearer to the source which will result in substantial changes to pollutant concentrations In CCTM the advection process is divided into horizontal and vertical components This distinction is possible because mean atmospheric motion is mostly horizontal Often the vertical motion is related to the interaction of dynamics and thermodynamics The advection process relies on the mass conservation characteristics of the continuity equation Data consistency is maintained for air quality simulations by using dynamically and thermodynamically consistent meteorology data from MCIP When the meteorological data and the numerical advection algorithms are not exactly 20 2 3 4 Particulate Matter mass consistent one needs to solve a modified advection equation Byun 1999 A new mass continuity scheme similar to that used in the air quality forecasting version of CMAQ has been implemente
254. we esate EESE syst suds snp bea teens ewan sop evedeucr es 143 PAT RETELENCES v7 vecavedesnsg cel vc iededehces caus deve tedeiing oc Svea de bal esate eae dene E EE detang ees Mame cadets eaves 143 8 Developing Emissions Fields y s3ccosetedese shanevaurenssngdusedonsyeetdnsg thea den gwel E Asa devua den Seeud Lea ddeteaen ede 147 8 1 Credits and Disclaimers for Use of SMOKE cceeeeeceecceceeecneceec cesses ereeceeeeeeeeeeereseneresenes 147 8 2 Obtaming SMOKE Source CoE pea n a pee veae sep epee shor ERNE EE EE SESE 147 8 3 System Requirement senp i a a Beh E aaa a ee E a E O R bk 147 8 4 SOftwate Lan guages renier n e e E doa E A doer E A A E E AE ISR 147 83 Data Requirements roeier eea EE ne Send cea dada Seed EEO wires o TEE EES 147 8 6 Overview ot SMOKE Versi n 221 p p E T E REEE EREE EERENS REES S EEY 148 8 7 Emissions Model Visualization and Evaluation ccceeceeececceeceeeeeeeeeeeeeeeeeeaeeeeeaeeeeaeeeeeaeenes 151 8 8 Model Training and User Support eissien cece eee cece E A seca ceca eeaneeas EAE SEE a NE E E 151 8 9 RETETENCES aoia E ue E E A EE poetoea ENA RE AEN EE ube ees tale cone ein E NES E 151 9 Defining Grids Layers Domains and Chemistry ssesessssseessseressssesrsrererrrrsesseresesrerereresessssesesrerete 153 9 1 Supported CMAQ Coordinate Systems oeneeeseeseeseerersererererersresrersrsreresserererersereesrerersrerrerere 153 9 2 sHOMZON tal GdS aie a e a A eh naan e A a ae A A
255. wed by the number of cells in the X and Y directions The grid definition concludes with the number of boundary cells Table 6 2 Coordinate system description segment Line Column Name Type Description 1 A Header String Single quote delimited header describing sec tion contents may be blank i e COORD NAME String Name of the coordin ate description re quired single quote delimited COORDTYPE Int County Code re quired P_ALP Double First map projection descriptive parameter dependent on projec tion type P_BET Double Second map projection descriptive parameter dependent on projec tion type P_GAM Double Third map projection descriptive parameter dependent on projec tion type XCENT Double Longitude for coordin ate system origin where X 0 YCENT Double Longitude for coordin ate system origin where Y 0 100 6 1 2 IC_PROFILE Initial conditions vertical profiles Table 6 3 Coordinate system description segment Line Column Name Type Description 1 A Header String Single quote delimited header describing sec tion contents may be blank i e 2 A GRID NAME String Name of the horizontal grid required single quote delimited 3 A COORD NAME String Reference to a coordin ate description re quired single quote delimited B XORIG Double X coordi
256. xt editor such as vi http www vim org or nedit http www nedit org Alternatives to Unix shell scripts exist in prototype CMAQ graphical users interfaces GUI with the Multimedia Integrated Mod eling System MIMS and the CMAQ GUI both available through the CMAS Center http www cmascenter org The CMAQ GUL is a java based program that is designed to download compile configure and run CMAQ all through its interface All three interfaces are available for download at the CMAS center website www cmascenter org The CMAS Center currently fully supports CMAQ on Linux systems using the Portland Group compiler there is limited support for compiling and running CMAQ on other UNIX computing systems 23 2 4 1 C shell Scripts 2 4 1 C shell Scripts The CMAQ C shell scripts are available in separate tar files on the CMAS Center website The MODELS file contains all of the source code for CMAQ and the SCRIPTS file contains all of scripts for building and executing the individual programs Each of CMAQ s programs has a separate build script and a separate run script The build script is used to compile the program and the run script is used to set the required environment variables and run the program You can edit the build script and the run script using a text editor such as the vi editor There are certain options that need to be set at compilation and some that can be set before running a simulation All changes must be done by edit
257. yer processes radiation convective parameterization among other improvements Dudhia 1993 documents the major changes from MM4 to MMS Starting with MMS Version 2 MM5v2 the software has been restructured to run on various hardware platforms in addition to the Cray with emphasis placed on workstation based MMS simulations The latest is MM5 Version 3 MM5v3 and is the recommended version for CMAQ simulations 7 6 2 Horizontal and Vertical Grid The coordinate system for MMS is x y sigma The x and y are a regular lattice of equally spaced points delta x delta y horizontal grid spacing in kilometers forming rows and columns Sigma is a terrain following vertical co ordinate that is a function of the pressure at the point on the grid in hydrostatic runs or the reference state pressure in non hydrostatic runs the surface pressure at the grid point and the pressure at the top of the model Sigma varies from at the surface to 0 at the top of the model The influence of the terrain on the sigma structure diminishes with height so that the sigma surfaces near the top of the model are nearly parallel See Figure 5 1 for a sample sigma structure of 16 vertical layers 17 full sigma levels Dashed lines denote half sigma levels and solid lines denote full sigma levels Vertical velocity is calculated on full sigma levels All other pro gnostic variables a are calculated on half sigma levels The figure based on Dudhia et al

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