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CMAQ-4.7.1 Operational Guidance Document

1. 13 INTERFACE 13 SUBROUTINE RDMET DATE MTIME RDEPVHT RJACM RVJACMF RRHOJ DENS1 13 IMPLICIT NONE 13 INTEGER INTENT IN MDATE MTIME 13 REAL INTENT OUT RDEPVHT 13 REAL INTENT OUT 2 RJAC Che 13 REAL INTENT OUT 2 RVJACMF 13 REAL INTENT OU RRHOJ Py y 13 REAL INTENT OUT DENSI 13 END SUBROUTINE RDME 13 SUBROUTINE RDDEPV MDATE MTIME MSTEP CGRID DEPV 13 IMPLICIT NONE 13 INTEGER INTENT IN MDATE MTIME MSTEP 13 REAL POINTER T CGREDIG sygg esses gt 13 REAL INTENT OUT 2 DEPV 13 END SUBROUTINE RDDEPV 13 go S END INTERFACE Cc 14 IF FIRSTIME THEN 14 FIRSTIME FALSE 14 LOGDEV INIT3 LA C Eor emissions from COORD EXT oces naiera ace Gas Bis WSUS eal BG ae oe WA 14 IF GDTYP_GD EQ LATGRD3 THEN 14 DX1 DG2M XCELL_GD inm 14 DX2 DG2M YCELL_GD 14 amp COS PI180 YORIG_GD YCELL_GD FLOAT GL_NROWS 2 inm 14 ELSE 14 DX1 XCELL_GD in m 14 DX2 YCELL_GD in m 14 END IF 14 C create global maps 14 CALL VDIFF_MAP DF2EM DF2DV DD2DV DEPV_MAP
2. 18 EMIS_PA C R L S VDEMIS S L C R 18 END DO 18 END DO 18 END DO 18 END DO 18 CALL PA_UPDATE_EMIS VDIF EMIS_PA JDATE JTIME TSTEP 18 END IF 19 CALL EDYINTB EDDYV DTI JDATE JTIME TSTEP 2 lt Perform other operations to set up for tridiagonal solver gt 20 DO 345 R 1 MY_NROWS 20 DO 344 C 1 MY_NCOLS lt Perform operations gt 21 DO 301 N 1 NSTEPS C R lt Perform operations gt 21 301 CONTINUE end time steps loop lt Update concentration and deposition arrays gt 20 344 CONTINUE end loop on col C 20 345 CONTINUE end loop on row R lt Perform other operations gt C If last call this hour write accumulated depositions 22 WSTEP WSTEP TIME2SEC TSTEP 2 22 IF WSTEP GE TIME2SEC TSTEP 1 THEN 22 DATE JDATE 22 TIME JTIME 22 CALL NEXTIME MDATE MTIME TSTEP 2 22 WSTEP 0 22 DO V 1 N_SPC_DDEP 22 S DD2DV V 22 DO R 1 MY_NROWS 22 DO C 1 MY_NCOLS 22 WRDD C R DDEP S C R 22 END DO 22 END DO 22 IF NOT WRITE3 CIM_DRY_DEP_1 DDEP_SPC V 22 amp MDATE MTIME WRDD THEN 22 XMSG Could not write CTIM_DRY_DEP_1 file 22 CALL M3EXIT PNAME MDATE MTIME XMSG XSTAT1 22 END IF 22 END DO 22 WRITE LOGDEV 5X 3 A AX Jy AEB Z Ml SFOs 6 y gt 22 amp Ti
3. Line Column Name Type Description T A Ozone concentration Exp Ozone measurements as a at Season 1 E10 3 function of season latitude Latitude 1 Level 1 and vertical level units molecules cm required B Ozone concentration Exp Ozone measurements as a at Season 1 E10 3 function of season latitude Latitude 1 Level 2 and vertical level units molecules cm required 127 A Ozone concentration Exp Ozone measurements as a at Season 1 E10 3 function of season latitude Latitude 19 Level 1 and vertical level units molecules cm required B Ozone concentration Exp Ozone measurements as a at Season 1 E10 3 function of season latitude Latitude 19 Level 2 and vertical level units molecules cm required 134 A Temperature profiles Exp Temperature measurements as a at Season 1 E10 3 function of season latitude Latitude 1 Level 1 and vertical level units K required B Temperature profiles Exp Temperature measurements as a at Season 1 E10 3 function of season latitude Latitude 1 Level 2 and vertical level units K required 260 A Temperature profiles Exp Temperature measurements as a at Season 1 E10 3 function of season latitude Latitude 19 Level 1 and vertical level units K required B Temperature profiles Exp Temperature measurements as a at Season 1 E10 3 function of season latitude Latitude 19 Level 2 and ver
4. C P_BET Double Second map projection descriptive parameter dependent on projection type D P_GAM Double Third map projection descriptive parameter dependent on June 2010 6 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document projection type E XCEN Double Longitude for coordinate system center F YCEN Double Latitude for coordinate system center Table 6 3 Grid definition segment of GRIDDESC Line Column Name Type Description 1 A Header String Single quote delimited header describing section contents may be blank i e 2 A GRID NAM GI String Name of the horizontal grid required single quote delimited 3 A COORD NAME String Name of the coordinate description in the previous section required single quote delimited B XORIG Double X coordinate for lower left southwest corner of the grid with respect to XCENT YCENT dependent on projection type C YORIG Double Y coordinate for lower left southwest corner of the grid with respect to XCENT YCENT dependent 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 dependent on projecti
5. June 2010 6 12 http www cmaq model org CMAQv4 7 1 Operational Guidance Document beginning ending centered point required n 2 A Multiplier String Multiplication factor to apply to photolysis rate equation line begins with FAC factor is listed in real or exponential format required n 3 A Wavelength Int or Wavelength corresponding to CSQY Real data units nm required B Absorption Real or Measurement of the cross section of Cross Exp a molecule s spherical receiving Section surface for actinic flux units cm molecule r quired es Quantum Real Ratio of the number of molecules Yield reacting via a specific pathway to the number of molecules absorbing photons in that wavelength interval units molecules photon required n 4 A Wavelength Int Wavelength corresponding to CSQY data units nm required B Absorption Real or Measurement of the cross section of Cross Exp a molecule s spherical receiving Section surface for actinic flux units em molecule required C Quantum Real Ratio of the number of molecules Yield reacting via a specific pathway to the number of molecules absorbing photons in that wavelength interval units molecules photon required 1 n X A sample of the important sections of a CSQY file is shown below ALD_CBIV88 Acetaldehyde Photolysis ALD CH3CHO hv 202
6. TADV Total advection for the PPM scheme ADV3 ADJC ADJC Mass adjustment for the PPM scheme HDIF HDIF Horizontal diffusion VDIF VDIF Vertical diffusion EMIS EMIS Emissions DDEP DDEP Dry deposition CHEM CHEM Chemistry AERO AERO Aerosols CLDS CLDS _ Cloud processes and aqueous chemistry TDIF TDIF Total diffusion HDIF VDIF TRNM TRAN Total transport advection diffusion Table 5 17 Integrated reaction rate output commands Command Description IRRTYPE FULL PARTIAL NONE The IRRTYPE command defines the type of IRR analysis With the type set to FULL IRRs for each individual reaction will be calculated and written to the IRR output file and all other IRR commands will be ignored IRRTYPE set to PARTIAL indicates that the IRR commands following this command are to be processed to produce user defined IRR outputs Type set to NONE causes all IRR commands to be ignored and no IRR output to be generated If the command is omitted type PARTIAL is assumed DEFINE CYCLE 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 reactions in which a species is consumed and then subtracting that sum from the sum of the IRRs for all reactions in which the species is produced The cyclena
7. The multiple spatial scale multiscale capabilities of CMAQ enable applications from local to hemispheric scales By combining this multiscale feature with the temporal flexibility of the model users can perform simulations to evaluate annual and interannual pollutant climatology as well as shorter term transport from localized sources To implement multiscale capabilities in CMAQ several different issues have been addressed such as scalable atmospheric dynamics and generalized coordinates that depend on the desired model resolution 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 cannot be made A set of governing equations for compressible nonhydrostatic atmospheres is available to better resolve atmospheric dynamics at smaller scales these are more appropriate for 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 matrix used by the generalized coordinate system controls the necessary grid and coordinate transformations consult Byun 1999 June 2010 2 2 http www cmaq model org CMA
8. Directory of CSQY data CMAQ Chemistry Transport Model CCTM Standard Profiles seasonal Chemical Mechanism ET Irradiance Data Figure 2 5 Clear sky photolysis rate preprocessing for CMAQ 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 A beta version of an in line photolysis module has been included with v4 7 but it is not yet a part of the official release June 2010 2 8 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 2 2 4 CHEMMECH Chemical mechanism compiler As released CMAQ includes all necessary chemical mechanism information for a series of pre configured atmospheric chemistry parameterizations All the beginning user has to do is choose which mechanism is desired as explained in Section 7 4 Advanced users who wish to generate new chemical mechanism information for use in CMAQ can use the program CHEMMECH to convert a mechanism listing file into the files needed by CMAQ Gas p
9. Nonvolatile sulfate can condense on the coarse mode Variable standard deviation of coarse mode size e HONO enhancements Heterogeneous reaction on aerosol and ground surfaces Emissions from mobile sources e Photolysis options beta versions In line photolysis rate module with aerosol feedback Photolysis rates adjusted using satellite derived cloud information currently table approach only e Aqueous chemistry Added two organic oxidation reactions glyoxal methylglyoxal Updates to Henry s Law constants based on literature review e Base CB05 mechanism with CL2 chemistry e Multipollutant capability Include hazardous air pollutants HAPs and Hg in single modeling platform distribution In Line Options Emissions of sea salt from the surf zone e Heterogeneous reaction probability Rederived parameterization based on Davis et al 2008 Emissions e Speciation changes for HONO and benzene e Biogenic emissions added sesquiterpene emissions e Sea salt emissions e Dry deposition Moved calculation into CCTM e Emissions Integrated the Biogenic Emissions Inventory System BEIS into CCTM Incorporated plume rise into CCTM e Bidirectional NH and Hg surface flux Fertilizer NH emissions will be applied through the flux model under development Updated flux parameterizations amp surf zone emissions Clouds Spatial Allocator can be used to produce the ocean
10. codes that have been deposited into the repository in such a manner that anyone can extract the exact code at a later time This involves some kind of transformation program to maintain master copies of the codes with embedded change tables e The concept of revision control archiving codes results in modifying the tags or unique revision identifiers in the change tables in the master copies in order to recover the exact code at a later date e The concept of released code codes that have reached some state of maturity and have been designated with some kind of released status They can be used with reasonable expectation of reliability The paradigm used employs the following scenario 1 A user modifies or develops code The code may be one subroutine or many possibly constituting whole science modules The code may originate from scratch or be extracted from the repository and modified 2 After testing or reaching a point of being satisfied with his her results he she decides to save it in the repository so that others can have access to it 3 Some archived codes may still be in an experimental or development state while others may be reasonably stable and more completely tested The latter may be designated as released There is no enforceable means to control access based on an experimental or released state The community will have and should have access indiscriminately well aware that using developm
11. It is created by MCIP and used by CCTM ICON BCON and PDM The variables that may exist in MET CRO _ 3D are the same as those that may be in MET _BDY_ 3D 6 1 29 MET_DOT_3D Three dimensional meteorological dot point fields Used by CCTM The MET DOT_3D time dependent file contains 3 D meteorological descriptions at dot points i e at cell corners and at cell faces It is created by MCIP and used by CCTM and PDM The following variables may be in the MET _DOT_3D file June 2010 6 30 http www cmaq model org CMAQv4 7 1 Operational Guidance Document UWIND u component of horizontal wind m s dot points Arakawa B grid VWIND v component of horizontal wind m s dot points Arakawa B grid UHAT JD contravariant U Jacobian density kg m s cell faces Arakawa C grid VHAT JD contravariant V Jacobian density kg m s cell faces Arakawa C grid 6 2 Basic CCTM Output Files The previous section described the output files from JPROC ICON BCON and MCIP that are input to CCTM In this section details on the CCTM output files are provided Except for JPROC which creates ASCH files all CMAQ programs produce output files that adhere to the T O API format Chapter 4 The I O API formatted CMAQ output files are three 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 b
12. It is created by MCIP and used by CCTM and PDM The following variables may be in the MET _BDY_3D file JACOBF total Jacobian at layer face m JACOBM total Jacobian at layer middle m DENSA J Jacobian weighted total air density p J m kg m WHAT JD Jacobian and density weighted vertical contravariant velocity kg m s TA air temperature K QV water vapor mixing ratio kg kg PRES air pressure Pa DENS air density kg m WWIND vertical velocity m s ZH midlayer height above ground m ZF full layer height above ground m QC cloud water mixing ratio kg kg QR rain water mixing ratio kg kg June 2010 6 28 http www cmaq model org CMAOv4 7 1 Operational Guidance Document QI ice mixing ratio kg kg QS snow mixing ratio kg kg QG graupel mixing ratio kg kg 6 1 27 MET_CRO_2D Two dimensional meteorological cross point fields Used by CCTM The MET _CRO_2D time dependent file contains surface and other 2 D meteorological fields at cross points i e at cell centers It is created by MCIP and used by CCTM and PDM The following variables may be in the MET _CRO_2D file PRSFC surface pressure Pa 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 m QFX la
13. Most personal computers PCs running a Linux OS 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 multiprocessor PCs on a high end network or an expandable rack mounted Linux server is recommended In light of the dynamic nature of the computer hardware world the specifications listed in this section are current recommendations not requirements While there are minimum levels of processing power and disk capacity needed for running CMAQ there is no single system on which CMAQ is optimized to run The flexibility of the modeling system enables users to optimize CMAQ for most current hardware configurations CMAQ is distributed and supported for executing on Linux operating systems with the Intel or Portland Group Fortran PGF compilers CMAQ can be ported to most computers running Linux Documented configurations include the SGI Altix Red Hat Enterprise Fedora Mandrake MacOSX and Suse operating systems In addition to the Intel and PGF compilers CMAQ has been built with Sun and gfortran compilers Information about these ports and up to date hardware recommendations are available through the CMAS Center web site http www cmascenter org The hardware recommendations provided below are the minimum level required to run CMAQ The software rec
14. cccccccsscccssscecssececeseeecsseeeesseeeessees 4 7 4 2 Network Common Data Form netCDF ccccccecscceesseceeseecesseeceseeeceeeecseeeesseeeees 4 8 4 3 Message Passing Interface Library MPICH cseicdsteie wcddaceccinteatienddaonnebinisaks 4 8 44 RETCTCNCOS soe raa a a a aA Ma abel lagais Mitesh tua Sada a nda AARE 4 8 CMAQ PROGRAMS AND LIBRARIEG ccccccccceeeeeseeeeeeeeseneseeeeeseeseeeneesenenees 5 1 Sol AIWER VIC Wosis oui n Sy ean te eats cae uote eae el ae ote EE E calcul Ss 5 1 5 2 BCON eoa E E E eed abel Sess ne E E R 5 3 SZL Description sirene aa a a a a a i aed aa 5 3 5 2 2 Files configuration and environment variables c ccccesseeesseeeteceteeeeees 5 4 se aes eB rere ee en ATEA EAE A E E E E AEEA 5 9 SSL Destriptio Nes eriten sgudsieasvastecs baton taadhoed ces mede Rea vasdend Matava head eeat eae Margins 5 9 5 3 2 Files configuration and environment variables cccccsseeeseetteeeteeees 5 10 3 4 CHEMMECH odo aaee E urs lah A E 5 25 5 4 1 Desciptioiisos niese a a a AE A EA TEE 5 25 5 4 2 Files configuration and environment variables c cccccsseeeseeesteeeteeees 5 26 o O D NEEE AE E E A EEE E a aoeas eae 5 30 Side MP ESCHIBHOM riesis iaa e a E E E le R a a 5 30 5 5 2 Files configuration and environment variables cccccsseeeseetseeeteeees 5 30 56 JPROC nin ducts E a eis ag nesta aw etn ad Tc He icee taa OTT mee anes iowa ines 5 36 5 6 1 Description niren a es oc
15. species or species3 may also be the keyword HV to restrict the selection to photolytic reactions NETP species FROM species2 ANDJ OR speciess The NETP operator is very similar to the PROD operator as it also is used to 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 species family 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 AND OR species The LOSS operator is used to compute the total loss of a species by summing the IRRs of all reactions in which species appears as a reactant The optional qualifier AND restricts the sum to include only those reactions in which both Species and species are reactants Similarly the OR qualifier includes all reactions in which either species or species2 appears as a reactant where species or species2 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 reactions to those that are photolytic NETL species AND OR speciesz
16. 3 Output Files File Program Shows Input Output Figure 5 7 MCIP input and output files 5 7 2 1 MCIP input files Table 5 11 MCIP input files File Name Format Description InMetFiles binary MMS or List of MM5 or WRF ARW output files for input to MCIP netCDF WRF ARW InTerFile binary MMS Terrain file with fractional land use categories used for calculating land use dependent vertical diffusivity Not necessary with WRF ARW this information is included in the WRF ARW met file 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 Linux 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 First it is assumed that you have already installed and compiled the I O API and netCDF libraries see Section 3 2 3 or that these are already available from a previous CMAQ compilation June 2010 5 41 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 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 summarized below to compile new versions of MCIP Configure the Makefile for the current operating system compiler combination Comment out
17. 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 in line calculated emissions 6 1 CMAQ Input Files This section describes each of the input files required by the various 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 by program listing of the CMAQ input file requirements Table 6 1 lists the source file type and temporal and spatial dimensions of each CMAQ input file Sample disk space requirements for a desired input data set can easily be calculated from the information in Table 6 1 each data record is four bytes The I O API file sizes can be calculated using the number of variables in a CMAQ file and the spatial and temporal coverage of the data The user should consult the CMAQv4 7 release notes for additional file information Table 6 1 CMAQ Input File Information File Name GRIDDESC horizontal domain definition File Type ASCII Time Dependence n a Spatial Dimensions n a Source user MCIP cross point fields BC_PROFILE boundary conditions vertical profiles ASCII Annual IC_PROFILE initial conditions vertical ASCII Annual n a user profiles CTM_CONC_1 CCTM concentration GRDDED3
18. 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 File descriptions i e I O API file type dimensions start date start time etc can be obtained by using DESC3 which is an I O API Fortran logical function 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 Fortran use of DESC3 is IF NOT DESC3 myfile THEN error message ELSE DESC3 commons now contain the file description END IF 4 1 4 Reading Data Files in I O 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 June 2010 4 5 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Table 4 4 IO API data retrieval routines Routine Description READ3 reads one or all variables and layers from a file for a particular date and time XTRACT3 reads a windowed subgrid for one or all variables
19. Follow the steps outlined in Section 3 3 summarized below to compile new versions of PARIO e Ifyou have not already done so compile M3BLD the CMAQ source code and compilation management program This needs to be done only once the first time CMAQ is installed e Ifneeded configure the PARIO build script to use the available I O API and MPICH libraries e Invoke the build script to create an executable oldit pario 5 8 2 4 PARIO execution options Because PARIO is not a program it does not have an associated run script 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 SM3LIB pario SOS directory 5 9 PROCAN 5 9 1 Description Process analysis is a diagnostic tool that captures model generated data not routinely output by models and provides quantitative information on the contributions of individual physical and chemical processes to model predictions This quantitative information can then be used to form a picture of how the model obtains its predictions In the CMAQ modeling system two types of process analysis data can be captured during a CCTM simulation integrated process rates IPRs and integrated reaction rates IRRs IPRs give the contributions of individual physical processes and the net effect of chemical reactions to the overall model concentrations For example IPR analysis can be used to determine the quantitative contr
20. The NETL operator is very similar to the LOSS operator as it also is used to compute the loss of a species However it includes only those reactions in which there is a net loss of species and or species Thus if species or any member of the species family 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 NET species The NET operator gives the net of the production June 2010 5 53 http www cmaq model org CMAQv4 7 1 Operational Guidance Document and the loss of a species for all reactions in which species appears either as reactant or a product species may be any gas phase mechanism species or any family consisting wholly of gas phase mechanism species 5 9 2 4 PROCAN execution options The environment variables listed here are invoked during execution of the program and are set in the PROCAN run script e EXEC default PACP_S CFG Executable to use for the simulation e PACP_INFILE default M3DATA procan pacp inp PROCAN control file for setting process analysis configuration 5 10 STENEX 5 10 1 Description The stencil exchange STENEX library contains modules for controlling the communication between processors in parallel multiprocessor computing environments A noop version
21. and latitude bands The CMAQ program JPROC Section 2 2 3 generates photolysis rate look up tables for input to CMAQ The photolysis files called JTABLE 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 corresponds to the start date for the simulation that uses the JTABLE data This is followed by four pairs of data that describe the altitude m latitude degrees hour angle from noon and photolytic reaction name for the data contained in the file Each data pair begins with a line describing the number 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 June 2010 6 22 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 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
22. set MPIRUN share linux bin mpich ch_p4 bin mpirun set TASKMAP SBASE machines8 June 2010 9 17 http www cmaq model org CMAQv4 7 1 Operational Guidance Document cat STASKMAP time SMPIRUN v machinefile STASKMAP np SNPROCS SBASE SEXEC date exit 9 5 Testing and Distribution of Development Source Code The CMAS Center collects tests and distributes various operational and development versions of CMAQ through the web site http www cmaq model org An archive of official releases both current and past and development versions of CMAQ is available to the user community The CMAQ MADRID and CMAQ AMSTERDAM developed by AER Inc under funding from the Electric Power Research Institute can be downloaded from this archive As a benefit to the CMAQ community CMAS periodically updates its documentation on testing such development code versions to include additional feedback as it becomes available based on users experiences with these versions Questions or comments about development versions of CMAQ such as CMAQ MADRID should be directed to the developers at AER Questions or comments about downloading the source code and associated documentation and on the software development guidelines may be directed to http www cmascenter org Based on the insights gained from the testing and archiving of a development version of the model such as CMAQ MADRID CMAS recommends the following steps as the minimum level of codi
23. 20hcns54sd eadbendiaytsedeRasaksdentdadmaPaednat aa areeia 8 6 8 37 References nenie e ES eR RE EE Ee RT rE a een 8 7 9 CODE MANAGEMENT AND DEVELOPMENT ccccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeess 9 1 Oat Source Code Ma agementiisresi ionni rein iE sais Seanad seas TEE E A h 9 1 9 1 1 The need for a configuration management tool ssessesesssssseseesesseseesssseees 9 1 MED CV SCR PLA er a ssw sab ae A a E a E meats 9 2 9 VS The CVS TEPOS sipasia i E E ented 9 2 9 2 Guidelines for Developing New CMAQ Source Code eceeeccescceeseeereeetseeeeeneeenaees 9 3 92 L Object oriented concepts ric sess iiatendinnisnteansdlsqeaseldranssedvercnaaiawiaaenanativonens 9 3 9 2 2 Globalname data tablen astinn ara eas E a Sade ea aad te aie es 9 4 92 3 Pin Interface a e a a eaa a E A ET 9 4 O 2A C ding g rdelinesS sinice tar oah AT AE EEE N AT UREA 9 5 9 2 5 Documentation guidelines ssssseesesseesseeseeseesseesreseesstessesrrssressesressressessessees 9 6 9 2 6 SCIENCE process code template s nsesessseeseeseosseeseeseesseesresresseessesrrssresseses 9 7 9 3 Compiling CMAQ with New Source Code ssssesnssseesseeseeseesseessesessseesseserssressesee 9 13 9 4 Guidelines to Writing Shell Scripts for CMAQ sssssssssssessssessesessssessessrssressessessees 9 14 9 5 Testing and Distribution of Development Source Code cece cecceeseeeseeeteeeeeees 9 18 9 6 RISTO CES porta Gy cei aco aaah eye ca aera ean
24. 4 8 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 5 CMAQ PROGRAMS AND LIBRARIES 5 1 Overview The core CMAQ programs that are needed to perform a basic air quality model simulation are MCIP ICON BCON JPROC and CCTM The relationships among these programs are depicted within the green box in Figure 5 1 The blue boxes represent programs that are not part of the CMAQ distribution package but supply data necessary for an air quality simulation emissions and meteorology data The yellow boxes represent the standard 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 and the emissions model to CCTM The green arrows show the data feedbacks from CCTM to create initial and boundary conditions for nested simulations The black arrow illustrates the connection between the meteorological model and MCIP Finally the blue arrow shows that the output from MCIP can be used to drive an emissions model The meteorological model such as MM5 or WRF ARW generates gridded meteorology for input to both CMAQ and the emissions model The emissions model is required to convert annual county level emissions estimates to gridded hourly emissions formatted for CMAQ The S
25. CMAQ is based around a transparent and A Note about the CMAQ Output File Format platform independent code infrastructure that promotes extensibility The CMAQ uses a modified version of the netCDF modularity of CMAQ also leads to file format Although CMAQ output is described multiple science configuration options as being in the netCDF format it is actually a i e how various processes are hybrid format of the I O API and the netCDF represented that model users can choose from when setting up new simulations The trade off for this flexibility is complexity in the model configuration the model user is faced with hundreds of different configuration combinations when designing new simulations To avoid confusing 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 configuration combinations available provide an unprecedented level of flexibility for optimizing model performance for different 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 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 efficient transparent and scientifically credible tool
26. CMAQ with process analysis will not work with the EBI chemical solver discussed in Section 2 3 1 The user is required to use either the Rosenbrock or the SMVGEAR solver 2 4 The CMAQ User Interface The CMAQ user interface that is distributed with the model source code consists of a series of C shell scripts for building and running the various CMAQ programs on Linux operating systems These scripts function primarily to set a series of environment variables that are required by M3BLD described in Section 1 2 4 or by the CMAQ program executables The scripts can be adapted to work with any Linux shell scripting language e g Bash Bourne Tar files for CMAQ can be downloaded from the CMAS Center web site The MODELS tar file contains all of the source code for CMAQ and the SCRIPTS tar file contains all of the C shell scripts for building and executing the individual programs Each of CMAQ s programs has separate build and run scripts The build script is used to check copies of the source code out of a CVS repository and to compile the program the run script is used to set the required environment variables and run the program The user can manipulate the CMAQ scripts using a Linux text editor such as vi http www vim org or nedit http www nedit org There are certain options that need to be set at compilation and some that can be set before running a simulation Details about using the scripts to build and run CMAQ are described
27. CMAQv4 7 1 Operational Guidance Document e END DATE end date of window data YYYYDDD format e cast2ext This utility reads the CASTNET hourly values downloaded from www epa gov castnet and generates an input file for the sitecmp program The various environment variables required by cast2ext are e INFILE hourly CASTNET data file e OUTFILE output file in format to use with sitecmp 10 2 M3tools Main website http www baronams com products ioapi Download http www baronams com products ioapi ioapi 3 0 tar gz Answers to FAQ http www baronams com products ioapi ERRORS html Latest User s Manual http www baronams com products ioapi AA html tools An extensive set of utility programs called m3tools that use the I O API library have been developed and made available for the modeling community These utility routines assist in manipulating dates and times performing coordinate conversions storing and recalling grid definitions sparse matrix arithmetic etc as well as in data manipulation and statistical analyses All m3tools can be run at the command line and the various options can be provided interactively or all of them can be stored in a file and executed as scripts A list of these utility programs and brief descriptions is provided below e airs2m3 Imports air quality monitor data from an AIRS AMP350 format ASCII file and puts them into an I O API observa
28. Called 1 C Revision History 1 C References C lt 2 USE AERO_EMIS inherits GRID_CONF 2 USE SUBST_MODULES stenex USE SUBST_GLOBAL_SUM_MODULE stenex 33 IMPLICIT NONE l INCLUDE SUBST_HGRD_ID horizontal dimensioning parameters INCLUDE SUBST_VGRD_ID vertical dimensioning parameters 4 INCLUDE SUBST_RXCMMN model mechanism name 4 INCLUDE SUBST_GC_SPC gas chemistry species table 4 INCLUDE SUBST_GC_EMIS gas chem emis surrogate names and map table 4 INCLUDE SUBST_GC_DEPV gas chem dep vel surrogate names and map table 4 INCLUDE SUBST_GC_DDEP gas chem dry dep species and map table INCLUDE SUBST_GC_DIFF gas chem diffusion species and map table 4 INCLUDE SUBST_AE_ SPC aerosol species table 1 INCLUDE SUBST_AE_EMIS aerosol emis surrogate names and map table 4 INCLUDE SUBST_AE_DEPV aerosol dep vel surrogate names and map table 4 INCLUDE SUBST_AE_DDEP aerosol dry dep species and map table 4 INCLUDE SUBST_AE_DIFE aerosol diffusion species and map table 4 INCLUDE SUBST_NR_SPC non reactive species tabl 4 INCLUDE SUBST_NR_EMIS non react emis surrogate names and map table 4 INCLUDE SUBST_NR_DEPV non react dep vel surrogate names and map table 4 INCLUDE SUBST_NR_DDEP non react dry dep species and map table 4 INCLUDE SUBST_NR_DIFE non react diffusion species and map table 4 INCLUDE SUBST_TR_SPC tracer species tabl 4 INCLUDE SUBST_TR_EMIS tracer emis surrog
29. DIFF_MAP DDEP_SPC 14 amp DV2DF 14 C set vertical layer definitions from COORD EXT 15 ALLOCATE RDX3F NLAYS STAT ALLOCSTAT 15 ALLOCATE RDX3M NLAYS STAT ALLOCSTAT 15 IF ALLOCSTAT NE 0 THE 15 XMSG Failure allocating RDX3F or RDX3M 15 CALL M3EXIT PNAME JDATE JTIME XMSG XSTAT1 15 END IF 14 lt other calculations that need to be performed only the first time gt END IF if Firstime 16 MDATE JDATE 16 MTIME JTIME 16 MSTEP IME2SEC TSTEP 2 16 DTSEC FLOAT MSTEP 16 CALL NEXTIME MDATE MTIME SEC2TIME MSTEP 2 C read amp interpolate met data June 2010 9 9 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 17 CALL RDMET MDATE MTIME RDEPVHT RJACM RVJACMF RRHOJ DENS1 C read amp interpolate deposition velocities lt perform other operations gt 18 IF LIPR THEN 18 DO S 1 N_SPC_EMIS 1 18 DO L 1 ELAYS 18 DO R 1 MY_NROWS 18 DO C 1 MY_NCOLS 18 EMIS_PA C R L S VDEMIS S L C R 18 END DO 18 END
30. DO 18 END DO 18 END DO 18 CALL PA_UPDATE_EMIS VDIF EMIS_PA JDATE JTIME TSTEP 18 END IF 19 CALL EDYINTB EDDYV DT JDATE JTIME TSTEP 2 lt Perform other operations to set up for tridiagonal solver gt 20 DO 345 R 1 MY_NROWS 20 DO 344 C 1 MY_NCOLS lt Perform operations gt 21 DO 301 N 1 NSTEPS C R lt Perform operations gt 21 301 CONTINUE end time steps loop lt Update concentration and deposition arrays gt 20 344 CONTINUE end loop on col C 20 345 CONTINUE end loop on row R lt Perform other operations gt C If last call this hour write accumulated depositions 22 WSTEP WSTEP TIME2SEC TSTEP 2 22 IF WSTEP GE IME2SEC STEP 1 THEN 22 DATE JDATE 22 TIME JTIME 22 CALL EXTIME MDATE MTIME TSTEP 2 22 WSTEP 0 22 DO V 1 N_SPC_DDEP 22 S DD2DV V 22 DO R 1 MY_NROWS 22 DO C 1 MY_NCOLS 22 WRDD C R DDEP S C R 22 END DO 22 END DO 22 IF NOT WRITE3 CTM_DRY_DEP_1 DDEP_SPC V 22 amp MDATE MTIME WRDD THEN 22 XMSG Could not write CTIM_DRY_DEP_1 file 22 CALL M3EXIT PNAME MDATE MTIME XMSG XSTAT1 22 END IF 22 END DO June 2010 9 10 http www cmaq model org CMAQv4 7 1 Operational Guidance Document
31. Group or Intel Fortran compiler 3 2 2 Notes on the CMAQ directory structure The CMAQ installation includes a dataset for benchmarking the modeling system Unpacking the various tar files of the distribution in the M3HOME directory installs the CMAQ source code scripts and benchmark 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 ib directory contains the compiled binary library files June 2010 3 5 http www cmaq model org CMAQv4 7 1 Operational Guidance Document required to build the CMAQ executables The CMAQ scripts use the following environment variables to alias the locations of these directories M3LIB M3HOME 1lib M3DATA M3HOME data M3MODEL M3HOME models The CMAQ scripts require users to select only the location of the M3HOME directory the other CMAQ directories are relative to M3HOME While this directory structure is convenient for the benchmark case and most CMAQ applications other configurations are possible Detailed instructions for installing and compiling CMAQ are contained in the next section 3 2 3 Configuring your system for compiling CMAQ Before instal
32. MDN SEARCH e M3 FILE n I O API input files that contain modeled species data maximum of 12 files e SITE FILE site file containing site ID longitude latitude tab delimited e IN TABLE observed data comma delimited with header e OUT_TABLE output data table with columns of observed and modeled values c rd_airs This utility reads the raw AQS data and writes hourly values in one day per record format The various environment variables required by rd_airs are e INFILE AIRS data file downloaded from web site http www epa gov ttn airs airsaqs detaildata downloadaqsdata htm SITEFILE list of AIRS site codes with latitude and longitude values OUTFILE output data file hourly values in 24 record format STATES list of states to process default is all states YEARS list of years to process default is all years PARAMETER code of species to process default is 44201 OZONE CHECKUNITS switch to check for valid units d airs2ext This utility reads the output from the rd_airs program and writes hourly or daily values in the siteemp CASTNET input format CSV The various environment variables required by airs2ext are INFILE data file generated with the rd_airs program OUTFILE output data file used with sitecmp hourly or daily values SPECIES name of species for header line STEP time step of output DAY or HOUR START_DATE starting date to window data YYYYDDD format June 2010 10 2 http www cmaq model org
33. 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 Venkatram A 1988 Dispersion in the stable boundary layer Chapter 5 in Lectures on Air Pollution Modeling A Venkatram and J Wyngaard Eds American Meteorology Society Boston MA Weil J C 1988 Dispersion in the convective boundary layer Chapter 4 in Lectures on Air Pollution Modeling A Venkatram and J Wyngaard Eds American Meteorology Society Boston MA Wesely M L 1989 Parameterization of surface resistances to gaseous dry deposition in regional scale numerical models Atmos Environ 23 1293 1304 June 2010 5 56 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 6 CMAQ FILES The input files for CMA Qv4 7 consist of a domain definition file for all programs two sets of file options for both ICON and BCON two types of input files WRF MMS and terrain for MCIP five mandatory and one optional input file for JPROC and for CCTM emissions initial conditions and boundary conditions files six files that define the meteorological conditions to be simulated and a photolysis rates file For most CCTM input a separate data set is required for each horizontal domain that is modeled When CMAQv4 7 is configured for in line emissions and deposition there are additional emissions input files that are required
34. 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 doi 10 1115 1 2128636 Carlton A G B J Turpin K Altieri S Seitzinger R Mathur S Roselle R J Weber 2008 CMAQ model performance enhanced when in cloud SOA is included comparisons of OC predictions with measurements Environ Sci Technol 42 23 8799 8802 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 Colella P and P L Woodward 1984 The piecewise parabolic method PPM for gas dynamical simulations J Comput Phys 54 174 201 Edney E O T E Kleindienst M Lewandowski and J H Offenberg 2007 Updated SOA chemical mechanism for the Community Multi Scale Air Quality model EPA 600 X 07 025 U S EPA Research Triangle Park NC Elterman L R Wexler and D T Chang 1969 Features of tropos
35. The initial and boundary conditions processors 2 6 2 2 3 JPROC Clear sky photolysis rate calculator ccccceecceeeeeeeeeteeeteeeseeees 2 8 2 2 44 CHEMMECH Chemical mechanism compilet ccccccceesseeeteeeeteeeeeeeees 2 9 2 2 5 PROCAN Process analysis preprocessor ccsccesceeseeesceceeceeeceseeesseeesseeees 2 9 2 3 CMAQ Chemistry Transport Model Science Modules cccecccesceeeteceeeeeeeeeeeeees 2 10 2 3 1 Gas phase Chemistr yoSONVerS sci ieed t couadintesoad Laatste nndtetesacageiseacdatakadne 2 10 2 3 2 SPHOUY SIS sschctaote ste seetauateatnagiscueaauee Geer a sth Sarvaues Gotan etn ui ee elton uate 2 11 2 3 3 Advection and GITTUST OMS sc sis yc slus sass Siege Sees odca tesa vs san sav enssans ts eave ohataantoees 2 12 2 3 4 Particulate matter aerosols sc seecdactbaconncspacveiest ino as vivtedsbacdiesh mde Rigeavbeat tate 2 14 2 3 5 Clouds and aqueous phase Chemistry cccccesccesceeeseeesseceeeeeeeeeteeeeeeeeseees 2 15 2 3 0 PEOCESS ANAL VIS wit ose aun na ccc ial uccaueealon aieicennsdagseomsvane meckenuectnaudsesousareauaneutioets 2 15 ZA The CMAQ Us r Interfaces nobis e austria sci shat aesssto a a S 2 16 XS References ennnen n a a a a ae ae OR mL eSa 2 16 3 CMAQ SYSTEM REQUIREMENTS AND INSTALLATION cccceeeeeeeeeeeeeeees 3 1 3 1 System Recommendations sec casecsy sass aaciy esses hr nneuaee ea ae eee behets 3 1 INI Hardware sssccss casecaig Seiteawksesc
36. a parallel architecture or algorithm is termed scalable if its performance behaves linearly in terms of the number of processors employed For example doubling the number of processors does not cause new communications bottlenecks to appear but doubles the performance achieved Scale flexibility The modeling system s ability to accurately simulate physical and chemical processes that describe atmospheric pollutants at different spatial and temporal scales A modeling system with scalable algorithms for physical and chemical processes and with a generic grid system has this quality Science module A component that is part of a modeling program such as a meteorological model an emissions model or CMAQ and that computes data for a discrete category of environmental phenomena e g dry deposition photochemistry vertical advection Screening models These models have simplified science processes designed for quick assess ment studies These models are employed when users are willing to sacrifice some accuracy for faster turnaround time A typical screening study involves making a large number of runs in order to identify episodes or situations that warrant more detailed modeling Source Classification Code SCC The SCC system is used for classifying emissions sources at the level of individual processes e g automobiles boilers solvent sources within an emissions data inventory Source With respect to air pollution a point area
37. acceptable for all applications of the model it is not the only configura June 2010 8 6 http www cmaq model org CMAQv4 7 1 Operational Guidance Document tion that can be used with CMAQ The ICON and BCON science options depend on the nature of the input data the chemical mechanism chosen and whether one way nests are being used JPROC science options are limited by the choice of chemical mechanism MCIP output is affected by the source of input meteorological model output i e WRF ARW or MM5 the option to recalculate some of the meteorology variables and the method used to compute dry deposition velocities for various species CCTM science configuration is the most complex of all the CMAQ programs because it contains a number of combinations of different transport algorithms chemistry options and special features such as process analysis To see a choice of all the different options available for configuring CCTM refer to Section 5 3 2 2 Not all of the combinations of the various CCTM configuration options have been tested It is possible that some combinations of different science modules will not build a working executable Generally here are few rules to follow when configuring CCTM e For configurations that use the Yamartino model driver the Yamartino options must be used for the initialization module the advection routines and the concentration adjustment scheme e For configurations that do not use the Yamartino mode
38. are then combined to obtain a cumulative hourly concentration PA tracks the mass throughput of these individual processes and provides quantitative information about how each process affected the predicted hourly species concentrations PA is an optional configuration in CMAQ that is implemented by compiling CCTM with Fortran INCLUDE files that define PA configuration options A PA instrumented version of CCTM outputs additional June 2010 2 9 http www cmaq model org CMAQv4 7 1 Operational Guidance Document files that contain hourly concentrations by physical and or chemical process for selected model species PROCAN is the PA preprocessor in the CMAQ modeling system As shown in Figure 2 7 PROCAN takes as input a configuration file Pacp inp that is used to define the model species and processes to be tracked using PA and outputs three INCLUDE files PA_CMN EXT PA_CTL EXT and PA_DAT EXT that are used when compiling CCTM PA_DAT EXT Figure 2 7 Process analysis implementation in the CMAQ modeling system CMAQ Chemistry Transport Model CCTM Chemical Mechanism 2 3 CMAQ Chemistry Transport Model Science Modules Figure 2 8 illustrates the CMAQ modeling system used to simulate the chemistry and transport of pollutants This figure also shows how CMAQ relates to other parts of an air quality modeling system the meteorological model emissions model and analysis package To perform a model simulation CMAQ n
39. caaads 5 27 Table 5 6 CHEMMECE Gut pet Ties vaisncss0315ekancedudeseen wen nwdads eur waded dannii 5 29 Table 5 7 ICON input TCS eta totes a a an a ae ite Fa ooo alate eyes 5 31 Table 5 8 ICON output files soi e584 Je Seace wreak Caducasvee aces ccaecceoucdce ist aieanveeses oa cieeae eon ees 5 36 Table 5 9 JPROG imputtiles 2 j 2vs2e aicanseeattasansdenphsadsaadeesdicsbannedeaayatent ieee ates teptatae bia 5 37 Tabte 5 10 JPROCo tp t Tiles iensen n a i a aa iiaa 5 39 Table 5 11 MCIP inp t files oescsscniceeisersirisesesriisssissesressicreessisresserssssecssins ereis senses seinas 5 41 Table 5 12 MCIP outp t Tes cnet renere nrnna a a a a a a is teats 5 45 Table 5 13 PROCAN inp t filesi encient iee aeaa i Saa EES aA 5 48 Table 5 14 Process analysis global commands ccsccsseceseceeeeeeseeeseeceaeceeenseeeeseecsaeeneeeaes 5 50 Table 5 15 Integrated process rate output commands c ce eecceeceeseeeeeeeceeeseceeeeeeeeeseeesaeeees 5 50 Table 5 16 Integrated process rates process codes cecceceseceseceeeeeeseeescecaeceeeeeeeeeseeenseeneenaes 5 50 Table 5 17 Integrated reaction rate output commands eee eeeceeeeeeeeeeeceeceeeeeeeeenseeenseenes 5 51 Table 11 1 CMAS contact information and important links 00 0 0 eect cee eeeeeeeeeeeeseeeneeeees 11 3 June 2010 xi http www cmaq model org CMAOv4 7 1 Operational Guidance Document AE AIRS AQ ASCII BC BCON BEIS3 CB IV CB05 CCTM CEMPD CMAS CMA
40. chemistry this is for the multipollutant model see CMAQvV4 7 release notes ModAdepv default aero_depv2 CMAQ aerosol deposition velocity module o aero_depv_noop deactivate aerosol deposition o aero_depv2 use second generation CMAQ aerosol deposition velocity routine ModCloud default cloud_acm_ae5 CMAQ cloud module for modeling the impacts of clouds on deposition mixing photolysis and aqueous chemistry o cloud_noop deactivate clouds in modeling o cloud_acm_ae5 use ACM cloud processor that uses the ACM methodology to compute convective mixing o cloud_acm_ae5 tx use ACM cloud processor that uses the ACM methodology to compute convective mixing including air toxics o cloud_acm_ae5_ txhg use ACM cloud processor that uses the ACM methodology to compute convective mixing including air toxics and mercury o cloud_acm_ae5_tshgsim use ACM cloud processor that uses the ACM to compute convective mixing including air toxics mercury and chlorine emissions from the sea and surf zone this version is for the multipolutant model with bidirectional exchange of mercury see CMAQV4 7 release notes ModPa default pa Process analysis module o 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 o util only configuration option at the module level Mechanism default cb05_ae5_aq 5 16 http
41. displayed in text that has been saved in Hypertext Markup Language HTML format A hypertext link provides nonsequential access to other entries in a document set In Models 3 the Help facility is done using hypertext Hypertext linking is done to all help entries Input Output Applications Programming Interface I O API A software library that reads and writes files It uses an internal data format that is machine independent and that conforms to the widely used University Corporation for Atmospheric Research Network Common Data Format netCDF The I O API files contain self describing headers with complete information that is necessary to use and interpret the data contained in the file The Models 3 I O API format is slightly more restrictive than the standard netCDF format regarding how the header informa tion must be written The I O API library provides a variety of data structure types and a set of reusable access routines that offer selective direct access to the data in terms that are meaningful to the environmental modeler Supported data types include gridded boundary vertical profile grid nest time series and event driven For additional information on the I O API see Chapter 4 Internal With respect to Models 3 data internal means that the data are available within the software the user does not have to provide them Examples incude look up tables ranges and lists of state county names Inventory Data Analyzer IDA Prog
42. emissions file from the previous day s simulation will be a required input file e CTM_PT3DEMIS default N Calculate plume rise for elevated point sources Set to Y or T to turn on N or F to turn off The CMAQv4 7 release notes file INLINE EMISSIONS DEPV_NOTES txt describes additional settings that are required for calculating elevated point source emissions with CCTM If the option to calculate in line plume rise is activated i e CTM_PT3DEMIS is set to Y or T the following variables must be set e NPTGRPS default 1 The number of input point source emission sector file groups A maximum of 9 sectors is allowed June 2010 5 22 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 STK_GRPS_ Directory path and file name of the stack groups file for sector where 01 02 NPTGRPS Each refers to one of the plume rise point source sectors STK_EMIS_ Directory path and file name of the point emissions file for sector where 01 02 NPTGRPS Each refers to the one of the plume rise point source sectors MERGE_DATES Directory path and file name of a file that lists the Gregorian dates for creating merged emissions files LAPY_STTIME HHMMSS Start time for calculating elevated point source emissions LAPY_NSTEPS HHHHHH Number of time steps for calculating elevated point source emissions CTM_EMLAYS Number of emissions layer
43. exit if inconsistent headers are found in the input files DISP default keep Controls the maintenance of existing log files o delete delete output log if it already exists o keep abort simulation if output log exists OUTDIR default SM3DATA cctm CCTM output file directory location CTM_APPL default SAPPL CCTM log file naming extension GRIDDESC default GRIDDESC1 5 19 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 Grid description file for setting the horizontal grid definition GRID_NAME default M_36_2001 Name of the grid definition contained in the GRIDDESC file that specifies the horizontal grid for the current application of the model AVG_CONC_SPCS default O3 NO CO NO2 ASO4I ASO4J NH3 Model 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 CONC_SPCS default if not defined all CONC file species Model species to be written to the CCTM CONC file CONC_BLEV_ELEV default if not defined all layers Vertical model layer range for
44. file Diagnostic Tools e Decoupled Direct Method DDM e Primary carbon source apportionment model e Sulfate tracking model e Convective cloud model Revised to reduce layer configuration differences Changed the integration time step e Resolved cloud model e Correction in precipitation flux calculation June 2010 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 1 7 References Byun D and J K S Ching 1999 Science Algorithms of the EPA Models 3 CommunityMultiscale 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 Multiscale Air Quality CMAQ modeling system Appl Mech Rev 59 51 77 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 IE UNC Institute for the Environment 2008 SMOKE version 2 5 Users Manual Available online at http www smoke model org Davis J M P V
45. for first species coefficients on right hand side of equation may b ither integer real or exponential format required F n 1 n 1 ie Char conversion rule terminator allows rules to span multiple lines required 2 1 16 SPP2_OUT String Output mechanism species name for second species required 17 Char delimits the left hand and right hand side of the conversion equation required 18 SPP2_IN String Input mechanism species name for second species coefficients on right hand side of equation may b ither integer real or exponential format required n 2 n 1 ee Char conversion rule terminator allows rules to span multiple lines required X 1 16 SPPX_OUT String Output mechanism species name for Xth species required 17 mam Char delimits the left hand and right hand side of the conversion equation required 18 SPPX_IN String Input mechanism species name for Xth species coefficients on right hand side of equation may b ither integer real or exponential format required X n X n 1 a Char conversion rule terminator allows rules to span multiple lines required X 1 1 END String END file terminator required A sample of the entries ina 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 June 2010 6 11 http www cmaq model org CMAOv4 7 1 Operational
46. formatted while the data section of the file is fixed format Table 6 4 IC_PROFILE format description Line Column Name Type Description L 3 Text Header String Text description of the contents and source of the initial conditions file June 2010 6 6 http www cmaq model org CMAQv4 7 1 Operational Guidance Document optional 4 A NUM_SIGMA_LVL Int Number of sigma levels contained in the file required B NUM_POLL Int Number of pollutants contained in the file required C SIGMA_LVL Real Vertical coordinate values of sigma p levels number of values n 1 is one more than the NUM_SIGMA_LVL n required 4 n 5 STDATE String Julian start date of the file YYYYDDD optional B STTIME String Start time of the file HH optional 6 1 10 SPECIES1 String Pollutant name enclosed in double quotes required 12 20 AAYER1_IC EXp IC concentration for species 1 in lowest sigma layer required 23 31 AAYER2_IC EXp IC concentration for species 1 in 2nd sigma layer required 34 42 AAYER3_IC EXp IC concentration for species 1 in 3rd sigma layer required 45 53 AAYER4_IC EXP IC concentration for species 1 in 4th
47. grid cell in the process analysis domain which is most likely a subset of the full modeling domain the PA file shows the hourly change in species concentration that is due to the major model processes such as horizontal and vertical advection chemistry and wet deposition The process analysis preprocessor PROCAN Section 2 2 6 is used to select the process analysis domain the model species for which to capture process analysis information and the model processes to track during the process analysis June 2010 6 33 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 6 3 7 IRR Process analysis output integrated reaction rates The 3 D CCTM integrated reaction rate file IRR contains hourly concentrations of selected model output species in terms of the gas phase chemistry pathways that contributed to the predicted concentration at each hour For each grid cell in the process analysis domain which is most likely a subset of the full modeling domain the IRR file shows the hourly change in species concentration that is due to particular gas phase chemistry reactions or reaction groups The process analysis preprocessor PROCAN Section 2 2 6 is used to select the process analysis domain the model species for which to capture process analysis information and the chemistry reactions or groups of reactions to track during the process analysis June 2010 6 34 http www cmaq model org CMAOQv4 7 1 Operational Guida
48. gt CH300 HO2 CO Taken from Gery et al 1988 CSQY from Baulch et al 5 1984 format wl abs_cs qy Centered With FAC units are cm 2 molecule FAC 1 0E 20 280 4 50 0 580 281 4 54 0 575 282 4 58 0 570 6 1 7 ET Extraterrestrial irradiance Used by JPROC June 2010 6 13 http www cmaq model org CMAQv4 7 1 Operational Guidance Document ET is the logical name for the ASCII data file containing extraterrestrial radiation as a function of wavelength The extraterrestrial irradiance file has a format similar to that of the CSQY file Section 6 1 6 The file begins with a header section comment lines are preceded with a 1 Like the CSQY file the header contains a field describing the location on the wavelength interval that the data represent 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 6 8 Table 6 8 ET file format description Line Column Name Type Description 1 A Comments String Preceded by comment lines describe the file contents and document the source of the data optional n fot a l A Data String Field indicating the location of Location the data as
49. horizontal grid definition GRID _NAMF default M_36 2001 Name of the grid definition contained in the GRIDDESC file that specifies the horizontal grid for the current application of the model LAYER_FILE default S m3DATA mcip3 M_36_2001 metcro3d_010722 Name and location of a MET _CRO_ 3D file for specifying the vertical layer structure for the current application of the model OUTDIR default SM3DATA icon Output data directory ECE Sets the input file type The setting of this variable determines how the run script sets the input and output environment variables o 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 o 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 ICON DATE default 2001203 Sets the Julian date to use in naming the ICON output file for nested runs SDATE default S DATE 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 file STIME default 000000 Start time for extracting initial condi
50. in some cases Ensured that the advection timesteps sum up to the synchronization timestep e In line option Asymmetry factor calculation updated using values from Mie theory integrated over log normal particle distribution added special treatment for large particles in asymmetry factor algorithm to avoid numerical instabilities Parallel Processing MPI Instrumented Models e Processor 0 creates the netCDF I O API file e DDM 3D e Sulfur Tracking e Primary Carbon Apportionment header when opening new output files On some parallel platforms message passing latency causes other processors to not have imminent access to the file header resulting in a hung execution or a crash Fixed by deferring access by other processors until later in the computation June 2010 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Table 1 2 CMA Qv4 7 Updates Aerosols Chemistry e Secondary organic aerosol SOA model enhancements Isoprene SOA Sesquiterpene SOA Polymerization Acid catalyzed SOA NO dependent SOA yields Enthalpy of vaporization In cloud SOA formation pathways glyoxal methylglyoxal Changes in gas phase chemistry mechanism emissions speciation and biogenic emissions model to represent SOA precursors Coarse PM Semivolatile inorganic components NO CT and NH can condense and evaporate from the coarse mode via dynamic mass transfer
51. in alphabetical order Information about the third party libraries used by CMAQ such as I O API netCDF and MPICH is available in Chapter 4 When viewing the tables that list each program s input and output files recall that the various file formats shown are described in Table 4 2 5 2 BCON 5 2 1 Description The program BCON prepares lateral chemical boundary conditions BCs for CCTM from either ASCII vertical profiles or from an existing CCTM output concentration CONC file The BCs created by BCON can be static in both 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 the two The ASCII vertical profiles are primarily used to create static BCs Dynamic BCs 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 BCs for MM5 or WRF ARW There are two distinct modes of operation for BCON and the mode used 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
52. installed and compiled the I O API and netCDF libraries see Section 3 2 3 or that these are already available from a previous CMAQ 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 summarized below to compile new versions of ICON e Ifyou have not already done so compile M3BLD the CMAQ source code and compilation management program This needs to be done only once the first time CMAQ is installed e Ifneeded configure the ICON build script to use the available I O API and netCDF libraries e Ifyou have not already done so compile the STENEX library e Configure the ICON build script for your application using the options discussed in Section 5 5 2 2 e Invoke the build script to create an executable Dlr icon 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 e EXEC default ICON_S CFG _Linux2_x86_64_pg Executable to use for the simulation e 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 e GRIDDESC default GRIDDESC1 June 2010 5 34 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 Grid description file for setting the
53. is created by the user used only when ICON is compiled with the ModMech configuration set to user_defined CTM CONC 1 GRDDED3 Name and location of the CMAQ concentration file from which to derive initial conditions this file is output from CCTM used only when the BC environment variable is set to m3conc MET CRO 3D CRS GRDDED3 Name and location of the coarse grid MET _CRO_ 3D file that is required for creating the vertical grid structure if this structure changes between nested simulations 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 defining 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 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 you must recompile ICON and create a new executable e Opt default verbose Defines the action to be taken by the program M3BLD when extrac
54. is set to Y or T the following variables must be set e GSPRO Directory path and file name for input speciation profiles e B3GRD Directory path and file name for grid normalized biogenic emissions input file e BIOSW_YN default Y Use the frost dates switch file to determine whether to use winter or summer biogenic emissions Set to Y or T to turn on N or F to turn off e BIOSEASON Directory path and file name for the frost date switch file e SUMMER_YN default Y 5 21 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Use summer season normalized biogenic emissions This variable is ignored if BIOSW_YN is set to Y Set to Y or T to turn on N or F to turn off e BIOG_SPRO Profile ID for speciating biogenic VOCs This profile ID must be present in the GSPRO file e B3GTS_DIAG default N Generate the calculated biogenic emissions mass units in a diagnostic netCDF output file Set to Y or T to turn on N or F to turn off e B3GTS_S Directory path and file name for the diagnostic output biogenic emissions This variable is ignored if B3GTS_DIAG is turned off e NITIAL_RUN Set to Y or T if this is the first time that biogenic NO soil emissions will be calculated If there is a previously created file set to N or F e SOILINP Directory path and file name of biogenic NO soil emissions file If INITIAL_RUN is set to N or F the soil NO
55. 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 file names This will be discussed further in terms of the CMAQ programs in Chapter 5 The remainder of this section explains some of the rudimentary details of programming in an environment using I O API data files 4 1 2 I O API Data Structure and Data File Types Each CMAQ data file has internal file descriptions that contain 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 1 e names units specifications and text descriptions Some of the elements in a file description such as the dates and times for file creation and update and the name of the program that created the file are maintained automatically by the I O API 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 also has a time step structure that is shared by all of i
56. name or reaction sum name can be either POSONLY or NEGONLY With these qualifiers 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 1 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 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 description is not specified for an IRR_OUTPUT variable the irrname or short name will be used in the output file If the description command is used it should be located immediately following the IRR OUTPUT command to which it applies PROD species FROM species gt ANDJ OR speciess3 The PROD operator is used to compute the total production of a species by summing the IRRs of all reactions in which species appears as a June 2010 5 52 http www cmaq model org CMAOv4 7 1 Operational Guidance Document product The optional qualifiers FROM and AND OR restrict the sum to include only those reactions in which species and or species are reactants The species can be any gas phase mechanism species or a family of gas phase species
57. 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 on the formulations of the above CMAQ programs are available in Chapter 2 below in Byun and Ching 1999 and in Byun and Schere 2006 June 2010 1 8 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 1 3 Features of CMAQ for Application Users The CMAQ modeling system provides a variety of important features to users who are interested in applying the model for investigating scientific research questions or for regulatory applications such as preparation of State Implementation Plans SIPs 1 4 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 multipollutant 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 Close interactions among the development communities for CMAQ and for the meteorology and emissions models provide for a tight integration of the three main components of the air quality modeling system Ser
58. net HFAQ Support website http nco sourceforge net nco html help The netCDF Operators NCO are a suite of programs known as operators Each operator is a stand alone command line program that is executed at the UNIX shell level similar to the commands 1s or mkdir The operators take netCDF files as input then perform a set of June 2010 10 6 http www cmaq model org CMAQv4 7 1 Operational Guidance Document operations e g deriving new data averaging hyperslabbing or metadata manipulation and produce a netCDF file as output The operators are primarily designed to aid manipulation and analysis of gridded scientific data The single command style of NCO allows users to manipulate and analyze files interactively and with simple scripts avoiding the overhead and some of the power of a high level programming environment NCO achieves flexibility by using command line options These options are implemented in all traditional UNIX commands as single letter switches e g 1s 1 NCO supports both short format single letter and long format multiletter options An overview of the various netCDF operators is given below e ncap netCDF Arithmetic Processor ncap and ncap2 arithmetically process netCDF files The processing instructions are contained either in the NCO script file 1 nco or in a sequence of command line arguments e necatted netCDF Attribute Editor ncatted edits a
59. of particles due to gravity and it is useful in determining surface fluxes MCIP can compute dry deposition using the surface exchange aerodynamic method Pleim et al 2001 This method uses surface resistance canopy resistance and stomatal resistance to compute dry deposition velocities The user also has the option to turn off the MCIP dry deposition velocity calculation completely this option is used to process meteorology data for CMAQ simulations that use the in line dry deposition velocity calculations contained in CCTM e 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 MCIP constructs a vertical profile of the adiabatic liquid water mixing ratio as the difference between the saturated mixing ratio at each level and the source level mixing ratio MCIP obtains the cloud coverage fraction by iteratively solving the equations governing th
60. of the library is required for single processor versions of CCTM and ICON the parallel version is required when compiling for parallel multiprocessor versions of CCTM 5 10 2 Files configuration and environment variables 5 10 2 1 STENEX input files STENEX does not require any input files 5 10 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 10 2 3 STENEX compilation First it is assumed that you have already installed and compiled the I O API netCDF and MPICH libraries see Section 3 2 3 or that these are already available from a previous CMAQ compilation June 2010 5 54 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 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 summarized below to compile new versions of STENEX e Ifyou have not already done so compile M3BLD the CMAQ source code and compilation management program This needs to be done only once the first time CMAQ is installed e Ifneeded configure the STENEX build script to use the available I O API and MPICH libraries e Invoke the single processor build script to create serial executables bldit se_noop e Invoke the multiprocessor build script to create parallel executables bldit se Linux
61. or mobile source that produces and or emits air pollutants Speciation In Models 3 speciation refers to using one of the chemical mechanisms available with Models 3 to disaggregate a chemical substance pollutant into simpler compounds Species Typically a chemical substance or group of related substances whose behavior is modeled during environmental simulation modeling Sub grid scale process Physical process that occurs on a scale smaller than the grid resolution of the modeling system such as point source plumes and convective clouds Since the scale is smaller than the grid resolution these processes must be estimated or parameterized Summary report Generally refers to an automatic short report generated after the execution of a process Surface fluxes The exchange of material energy or momentum between the surface of the earth and the atmosphere Time step A time step is a fixed unit of time A model may have one or more internal time steps for various processors In the Models 3 framework a time step is used to indicate the length of DRAFT January 2009 A 8 http www cmaq model org CMAQv4 7 1 Operational Guidance Document time between output of variables from the model or a process within the model Another term might be output time interval Troposphere The troposphere is the lowest portion of Earth s atmosphere It contains approximately 75 of the atmosphere s mass and almost all of its water vapor a
62. organic carbon that were part of CMAQv4 6 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 in CMAQ sub grid convective precipitating clouds sub grid nonprecipitating clouds and grid resolved clouds The meteorological model provides information about grid resolved clouds with no additional cloud dynamics considered in CMAQ For the two types of sub grid clouds the cloud module in CCTM vertically redistributes pollutants calculates in cloud and precipitation scavenging performs aqueous chemistry calculations and accumulates wet deposition amounts An important improvement in the v4 7 convective cloud mixing algorithm corrects a tendency to predict excessive transport from upper layers in the cloud to sub cloud layers In v4 7 a version of ACM is used to model convective clouds 2 3 6 Process analysis As discussed in Section 2 2 5 CCTM also includes a process analysis PA module Process analysis is a technique for separating out and quantifying the contribu
63. parallel fashion with a minimum of time and memory e ncra netCDF Record Averager ncra averages record variables across an arbitrary number of input files The record dimension is by default retained as a degenerate size 1 dimension in the output variables e nercat netCDF Record Concatenator ncrcat concatenates record variables across an arbitrary number of input files The final record dimension is by default the sum of the lengths of the record dimensions in the input files e ncrename netCDF Renamer ncrename renames dimensions variables and attributes in a netCDF file Each object that has a name in the list of old names is renamed using the corresponding name in the list of new names All the new names must be unique e ncwa netCDF Weighted Averager ncwa averages variables in a single file over arbitrary dimensions with options to specify weights masks and normalization 10 7 Python foapiTools Main website http www pcmdi lInl gov software portal Members azubrow ioapiTools index_html http www pemdi IInl gov softwareportal Members azubrow ioapiT ools download source file Download Latest User s Manual http www pcemdi llnl gov software portal Members azubrow ioapiTools index_html Support info http www pcmdi IInl gov software portal Members azubrow 1oap1T ools problems file The ioapiTools package was developed to include I O API data within th
64. path photolysis reactions as a function of wavelength 5 6 2 2 JPROC compilation options The configuration options listed here are set during compilation of the JPROC 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 JPROC and create a new executable June 2010 Opt default verbose Defines the action to be taken by the program M3BLD when extracting source code from CVS and compiling an executable compile _all force compile even if all the object files are current clean_up remove all source files upon successful compilation no_compile do everything except compile no_link do everything except link one_step compile and link in one step parse_only check configuration file syntax show_only show requested commands but do not execute them verbose show requested commands as they are executed Or o0o0o0o00o0o0O MakeOpt Uncomment to build a Makefile to compile the executable Mechanism Specifies the gas phase aerosol and aqueous phase chemical mechanisms for which to create photolysis rates The choices for the Mechanism variable are the mechanism directory names under the M3MODEL include release directory Examples include o cb0Sae5_ aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry o cb05cl_ae5_aq CBO5 gas phase mechani
65. period The temporal extent of a CMAQ simulation is limited by the availability of input meteorology and emission data Similar to the horizontal grid and vertical layer structures the time period to model with CMAQ must be considered when designing the meteorological modeling simulation used to produce CMAQ input data The model output time step and run length of each CMAQ simulation are flexible and can be configured in the run script for the applicable CMAQ program For CCTM it is possible to have output files with a different number of time steps than the corresponding meteorology or emission input data For example it is common to have input meteorology files in 4 or 5 day intervals input emission files in 1 or 2 day intervals and CCTM output files in 1 day intervals The CMAQ scripts allow the user to configure the model to output data with any number of time steps The number of CCTM output time steps does not need to correspond with the input meteorology and emissions output time steps To keep CMAQ output file sizes manageable CMAQ output is generally stored in 1 day 24 hour blocks To configure a new CMAQ simulation the follow steps must be taken to set up the modeling time period e Produce emissions and meteorology data for the time period to be modeled with CMAQ When deciding upon a modeling period it is necessary to have a spin up interval prior to the beginning of the initial time of interest The spin up period is a
66. results and understanding model behavior Because the CMAS supported models use a modular approach with well defined communications between modules developers can upgrade existing processes or add new ones thus ensuring the rapid evolution of the technology to meet the changing needs of the environmental modeling community CMAQ was EPA s first tangible product to evolve out of the community modeling paradigm With a framework for a community model in CMAQ there is a need for centralized coordination of development and application efforts for mutual benefit to scientists model developers practitioners of modeling and regulatory users of modeling results CMAS and its accompany ing center at the CEMPD facilitate the effort to draw the interest of the modeling community toward advancement through cooperation 11 2 Getting Help with CMAQ The CMAS Center website http www cmascenter org includes a help desk with resources that are available to assist with CMAQ related issues The CMAS help desk services are free to the community Many of the services in the help desk benefit from increased usage such as the listserv discussion groups E mail based CMAQ technical consultation is available to registered CMAS participants only The following resources are available through the CMAS Center to address CMAQ related questions Community members should use these resources in the order that follows There is currently a large searchable
67. routines is listed in Table 4 5 Further information about how to use the utilities are available in the I O API documentation Table 4 5 I O API data manipulation utilities Utility Description 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 June 2010 4 7 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Utility Description VERTOT compute vertical column totals of variables in a file UTMTOOL coordinate conversions and grid related computations for lat lon Lambert and UTM 4 2 Network Common Data Form netCDF The Network Common Data Form netCDF is a set of software libraries and machine independent data formats that support the creation access and sharing of array oriented scientific data Unidata 2009 The netCDF library provides an implementation of the netCDF interface for several different programming languages T
68. sequence of days at the beginning of an air quality simulation that are not used in the analysis of the modeling results These days are simulated to minimize the impacts of the initial conditions on the CCTM modeling results Spin up periods vary in length depending on the size of the June 2010 8 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document modeling domain the magnitude of the emissions sources within the modeling domain and the pollutants being studied As a general rule of thumb a period of at least 10 days should be considered for a spin up period e Generate ICs for the first time step of the CCTM simulation if running multiple days in sequence configure the CCTM run script to use the ICs from ICON for the first model day and to initialize the subsequent days with the previous day s CCTM output e Generate either time independent BCs for the grid to be modeled or for a nested simulation generate temporally resolved BCs for the model time period from CCTM outputs for the parent grid e Create photolysis look up tables JTABLE with JPROC for each day to be modeled e Configure the CCTM run script to loop through the days to be modeled using the correct input files for each model day and writing output files with the desired number of time steps 8 2 4 Initial and boundary conditions After preparing the meteorology and emissions input data files and determining the model grid and model time periods the ne
69. the CCTM horizontal grid domain CCTM uses a smaller computational domain that is entirely contained within the computational domain of the meteorological model and the lateral boundaries from the meteorological model are generally not used by CCTM e Processes all required meteorological fields for CCTM and the emissions model The meteorological information such as atmospheric temperature pressure humidity and winds produced by the meteorological model is put into a form required by CMAQ June 2010 2 5 http www cmaq model org CMAQv4 7 1 Operational Guidance Document e Collapses meteorological model fields if coarser vertical resolution data are desired for a given CCTM run This is not a recommended procedure To do this MCIP uses mass weighted averaging on higher vertical resolution meteorological model output e Computes dry deposition velocities for important gaseous species 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 the amount of turbulence or mixing in the atmosphere and the nature and type of the receiving surface information describing this surface is generated by MCIP One measurement used in simulating the dry deposition of pollutants is the dry deposition velocity this is analogous to the settling velocity
70. the Models 3 Pleim dry deposition routine Pleim et al 2001 3 Use the Models 3 dry deposition routine and include chlorine 4 Use the Models 3 dry deposition routine and include chlorine and mercury O O 00 MCIP_START format YYYY MM DD HH MM SS SSSS Beginning date and time UTC of data to output from MCIP The start date and time must be contained within the input data from MM5 or WRF ARW MCIP_END format YYYY MM DD HH MM SS SSSS End date and time UTC of data to output from MCIP The end date and time must be contained within the input data from MM5 or WRF ARW INTVL default 60 Output interval in minutes This setting determines the amount of model time contained in each output time step The output interval for MCIP can be less frequent than the incoming meteorological model output e g process 30 minute data for CCTM from 15 minute WRF ARW output CTMLAYS default 1 0 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 BTRIM default 5 The number of boundary points to remove on each of the four hor
71. the ground by wet or dry deposition both of which are modeled by CMAQ In wet deposition PM is transferred by rainfall Wet deposition is calculated within CMAQ s cloud module In dry deposition the transfer is by turbulent air motion and by direct gravitational sedimentation of larger particles The deposition velocity for particles must be calculated from the aerosol size distribution and from meteorological and land use information CMAQ s dry deposition module calculates the size distribution from the mass and number concentration for each of the three modes and then calculates the dry deposition velocity In v4 7 the dry deposition algorithm has been modified to include an impaction term in the coarse and accumulation modes In CMA QV4 7 several new pathways for secondary organic aerosol SOA formation have been implemented based on the recommendations of Edney et al 2007 and the recent work of Carlton et al 2008 New SOA precursors include isoprene sesquiterpenes benzene glyoxal and methylglyoxal The enthalpies of vaporization of these species have been revised based on recent laboratory data Edney et al 2007 In previous versions of CMAQ all SOA was treated as semivolatile In CMAQv4 7 four types of nonvolatile SOA are simulated There is a new surface interaction module in the multipollutant version of CMAQ that calculates the flux of mercury to and from the surface rather than just depositing mercury In a futur
72. to simulate air pollution formation and transport To address these individual and common needs CMAQ development and maintenance have the following goals 1 Scientific Integrity Ensure that the model remains state of the science through use of regular peer reviews 2 Community Development Utilize a design that encourages innovations and enhancements by all members of the air quality modeling community 3 Multiscale Modeling Provide adequate technical formulations to address air quality issues on multiple spatial scales from urban to hemispheric June 2010 1 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 4 One Atmosphere Design Provide robust and integrated science for modeling multiple coupled air quality issues in a single simulation 5 Modularity Maintain flexibility to add new or select from existing science modules to optimize model performance for specific applications 6 Transparency Utilize programming practices that promote understanding of the model formulation at the source code level 7 Computational Efficiency Provide scientifically acceptable results without compro mising the speed at which the results are generated 8 Open Source Design Enable no cost distribution and application by the modeling community 1 2 Overview of CMAQ System Components CMAQ is a suite of Fortran 90 programs that work in concert to estimate ozone PM toxic compounds and acid depositio
73. use when creating a BCON executable June 2010 5 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 5 2 2 Files configuration and environment variables Figure 5 2 shows the input and output files and configuration options for BCON A distinction is made between the options that are invoked at compilation time versus those invoked at execution of the program When compiling BCON the user specifies a chemical mechanism to configure the gas phase chemistry and aerosol mechanism used to create the chemical BCs 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 Separate BCON executables must be prepared for different mechanism configurations Mechanism Include Files Input Type GC_SPC EXT Set Mechanism AE_SPC EXT GC ICBC EXT Mechanism ModMech etc Conversion Compile Options If ModInpt profile BC_PROFILE BNDY_CONC_1 If ModMech user_defined MECH_CONV_FILE If Modinpt m3conc CTM_CONC_1 Shows Input Output Horizontal grid definition GRIDDESC Vertical layer structure MET_CRO_3D Execution Options Figure 5 2 BCON input and output files At execution the user provides a data file of chemical conditions that BCON converts to BCs on a predefined model grid Through the specification of the ModInpt variable BCON will input either an ASCII vertical profile file BC PROFILE or an existing CCTM co
74. user_defined CTM CONC 1 GRDDED3 CMAQ concentration file from which to derive boundary conditions this file is output from CCTM used only when the BC environment variable is set to m3conc MET CRO 3D CRS GRDDED3 Name and location of the coarse grid MET _CRO_ 3D file that is required for creating the vertical grid structure if this structure changes between nested simulations 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 defining 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 5 2 2 2 BCON compilation 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 To change these options you must recompile BCON and create a new executable June 2010 Opt default verbose Defines the action to be taken by the program M3BLD when extracting source code from CVS and compiling an executable O OOO compile _all force compile even if all the object files are
75. usually contains data for an entire year 365 or 366 days It uses one variable SEASON which is either 0 grid cell should use winter factors for current day or 1 grid cell should use summer factors for current day For additional information about creating the BIOSEASON file see the Metscan documentation in the SMOKE user s manual http www smoke model org version2 5 html ch05s11 html 6 1 22 STK_GRPS_ Stack groups Used by CCTM inline version only The mark is unique and represents the sector identification The stack groups file is an I O API netCDF file containing stack parameters for elevated sources This file can be created using the SMOKE program ELEVPOINT For additional information about creating the stack groups file see the ELEVPOINT documentation in the SMOKE user s manual http www smoke model org version2 5 html ch06s03 html 6 1 23 STK_EMIS_ Point source emissions Used by CCTM inline version only The mark is unique and represents the sector identification The elevated point source emissions file is an I O API GRDDED3 file with emissions for point sources to be treated as elevated sources by CCTM The emissions in this file are distributed through the vertical model layers using a plume rise algorithm contained in CCTM The elevated point source emissions file can be creating using SMOKE For additional information about preparing point source emissions for using the CMAQ in line plume ri
76. will be generated for each science process for that species Similarly if the keyword ALL is used for the species name and no process code is specified 12 IPRs will be generated for every model species This would generate an output file that would be approximately 12 times as large as the corresponding concentration file Also the impact on the CCTM memory requirements would be substantial since adding a single IPR output has roughly the same effect as adding a model species Thus caution should be exercised when formulating the commands to request IPR outputs The IPR outputs are written to an I O API output file in exactly the same format and with the same number of time steps as the concentration output file Since the I O API currently has a limit of 120 output variables in a file multiple files will be output if this limit is exceeded 3 Integrated Reaction Rate Commands These commands Table 5 17 are specific to the configuration of the IRRs The same considerations regarding file size and memory usage detailed in item 2 above should be considered when using these commands Table 5 14 Process analysis global commands Command Description DEFINE FAMILY familyname The DEFINE FAMILY command is used to define a c1 species c2 species2 3 group of species as members of a family The user specified familyname must be unique and can be referenced in subsequent commands The c are numerical coefficients tha
77. www cmascenter org Support http bugz unc edu Several utility tools Fortran based are provided along with the CMAQ code scripts distribution These are included in the MODELS tar gz file and located in the SM3MODEL TOOLS source code directory These tools work directly with the CMAQ outputs and help in processing formatting and preparing datasets from various ambient monitoring networks for subsequent evaluation These networks include the EPA Air Quality System AQS AIRS AQS Interagency Monitoring of Protected Visual Environments IMPROVE Clean Air Status Trends Network CASTNET Speciated Trends Network STN National Atmospheric Deposition Program NADP Mercury Deposition Network MDN and the Southeast Aerosol Research and Characterization Study SEARCH The various CMAQ utility tools are described below June 2010 10 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document a combine This utility combines fields from a set of I O API input files to create an output file The file assigned to the environment variable SPECIES DEF defines the new species variables and how they are constructed b sitecmp This utility site compare generates a CSV comma separated values file that compares CMAQ generated concentrations with an observed dataset The various environment variables required by sitecmp are e TABLE TYPE dataset type AQS IMPROVE CASTNET STN NADP
78. 1 00 0 98 0 93 0 84 0 60 0 30 0 00 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 As with the ICON program 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 various model layers that are fixed in space in time To configure BCON to generate boundary conditions from ASCII vertical profiles the prof input module is chosen when compiling the program see Section 5 2 on BCON These ASCII formatted vertical profile files are BC_PROFILE files and are described in this section BC_PROFILE files must be developed by the user and can be generated from climatologically averaged observational data or as an a priori estimate from previous modeling studies of the region being modeled The second file type that BCON can use to generate initial conditions is a concentration file from a previous CMAQ run These are CTM CONC _1 files and are described later in Section 6 1 5 BC_PROFILE begins with a header that contains a comment section that describes the data and a file description section that defines the number of vertical levels in the file the number of pollutants in the file and the distribution of the vertical levels The next entries in BC_PROFILE are the Julian start date and the start time of the data the
79. 1 2 http www cmaq model org CMAQv4 7 1 Operational Guidance Document SAPRC 99 mechanism Carter 1990 2000 Additional details about the gas phase chemistry in CMAQ are provided in Chapter 2 and in Byun and Ching 1999 Byun and Schere 2006 Those two sources also describe the primary aerosol emissions species that are supported by CMAQ aerosol refers to particulate matter tiny solid or liquid particles suspended in the atmosphere It is possible to add new emissions species to CMAQ that are not supported in the distributed version of the software by using the chemical mechanism compiler CHEMMECH that is one of the CMAQ utility programs see Chapter 5 CMAQ was designed from the start as a community model Community modeling is the concept that air quality model development should be a collective effort by a broad community of developers By adopting a standardized modeling architecture the air quality modeling community can focus its efforts on creating software enhancements and new science modules CMAQ s modular structure facilitates customization and open source development by the community Using the Input Output Applications Programming Interface I O API library http www baronams 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
80. 1 5 IC_PROFILE begins with a header that contains a comment section that describes the data and a file description section that defines the number of vertical levels in the file the number of pollutants in the file and the distribution of the vertical levels The next entries in IC_PROFILE are the Julian start date and the start time of the data they are not used by ICON Each line in IC_PROFILE 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 in ppmV and aerosol species are in ug m The layer structure of the IC_PROFILE vertical profiles does not need to correspond exactly to the layer structure that will be modeled the ICON program will interpolate the data to the correct vertical format for the simulation Initial conditions are provided for only the first hour of a model simulation The initial conditions that are based on an ASCII vertical profile include a gridded file for input to CCTM that has horizontally uniform species concentrations at each model layer For spatially resolved initial conditions in the horizontal direction 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 6 4 The header of the profiles file is list
81. 10 6 23 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 6 A JVTMAX Int Number of hour angles covered by the data required B Hour Angle Field String The words HOUR ANGLES required Indicator C Comment String Description of the hour angles field usually from noon for hours from noon optional 7 A XHAJV_1 Real Hour angle 1 units in hours from noon required B XHAJV_2 Real Hour angle 2 units in hours from noon required x XHAJV_x Real Hour angle x units in hours from noon required 8 A JPHOT Int Number of photolytic reactions covered by the data required B Reaction Field String The words PHOTOLYTIC REACTIONS Indicator required C Comment String Description of the reactions field optional 9 A PHOT_NM_1 String Single quote delimited name of photolysis reaction 1 required B Delimiter Char Comma delimiter separating reaction name from multiplier required C ACLD_1 Real Multiplier for reaction 1 required 10 A PHOT_NM_2 String Single quote delimited name of photolysis reaction 2 required B Delimiter Char Comma delimiter separating reaction name from multiplier required C ACLD_2 Real Multiplier for reaction 2 required x A PHOT_NM_x String Single quote delimited name of photolysis reaction x required B Delimiter Char Comma delimiter separating react
82. 22 Name and location of a MET _CRO_ 3D file for specifying the vertical layer structure for the current application of the model OUTDIR default SM3DATA bcon Output data directory BC Sets the input file type The setting of this variable determines how the run script sets the input and output environment variables o 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 input to BCON Also optionally looks for the variable MECH _CONV_FILE to point to a user defined mechanism conversion file o 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 DATE Sets the Julian date to use in naming the BCON output file for nested runs SDATE default DATE 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 5 8 http www cmaq model org CMAOv4 7 1 Operational Guidance Document e STIME default 000000 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 e RUNLEN default 240000 Number of hours of boundary conditions to extrac
83. 5 10 2 4 STENEX execution options Because STENEX is not a program it does not have an associated run script 5 10 2 5 STENEX output files Successful compilation of STENEX will produce the library files libsef90_noop a for serial compilations and libse_snl a for parallel compilations along with several module files in the SM3LIB stenex S OS directory 5 11 References Arya P 1984 Parametric relations for the atmospheric boundary layer Bound Layer Meteor 30 57 73 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 Hanna S R G A Briggs and R P Hosker 1982 Handbook on atmospheric diffusion U S DOE DOE TIC 11223 DE82002045 National Technical Info Center Springfield VA Hicks B B 1985 Behavior of turbulence statistics in the convective boundary layer J Clim Appl Meteor 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 NC Niewstadt F T M 1984 Some aspects of the turbulent stable boundary layer Bound Layer Meteor 30 31 55 June 2010 5 55 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Pleim J E A Xiu P L Finkelstein and T L
84. Bhave and K M Foley 2008 Parameterization of N2O5 reaction probabilities on the surface of particles containing ammonium sulfate and nitrate Atmos Chem Phys 8 5295 5311 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 Powers 2005 A Description of the Advanced Research WRF Version 2 NCAR Technical Note NCAR TN 468 STR 88 pp U S EPA 2008 National Ambient Air Quality Standards NAAQS Available online at http www epa gov air criteria html Yarwood G S Rao M Yocke and G Whitten 2005 Updates to the Carbon Bond chemical mechanism CBOS Final Report to the U S EPA RT 0400675 Available online at www camx com June 2010 1 14 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 2 Overview of the Science in the CMAQ Modeling System As discussed in Chapter 1 CMAQ is a multipollutant multiscale air quality modeling system that estimates the transport and chemistry of ozone PM toxic airborne pollutants referred to as air toxics visibility and acidic and nutrient pollutant species CMAQ uses state of the science techniques and has ma
85. CMAQ CHEMMECH needs to also be run in SP model 5 4 2 Files configuration and environment variables Figure 5 3 shows the input and output files and configuration options for CHEMMECH The full set of mechanism INCLUDE files required by the CMAQ programs is 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 RXDT 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 CHEMMECH Include_generator py GC_CONC EXT GC_ICBC EXT GC_DDEP EXT GC_SCAV EXT Shows Input Output Program Script F GC_DEPV EXT GC_WDEP EXT Output Files Figure 5 4 CHEMMECH input and output files June 2010 5 26 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 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_genera
86. EMENT AND DEVELOPMENT As a public domain model CMAQ is the product of contributions from many developers whose numbers are only expected to increase with the number of users worldwide Some degree of standardization is necessary for management and archiving of these development versions as well as to compile and execute the code once it is ready for use and to submit it to the CMAS Center for archiving and benchmark testing This chapter provides guidance on source code management coding guidelines for new code development the compilation of new source code using the build scripts and guidelines for writing shell scripts usable by CMAQ Much of this information is derived from Chapter 18 Young 1999 in Byun and Ching 1999 with updates where appropriate particularly for new versions of the model code and for the Fortran 90 standard The chapter also includes the procedure that is in place for distributing code versions other than the operational CMAQ that are submitted to the development code archives 9 1 Source Code Management 9 1 1 The need for a configuration management tool Faced with a large and growing community that uses and develops a wide variety of programs modules and codes it is imperative to systematically manage the cross community access to this software Typically successful management of software involves the following e A repository a place where all of the public code resides e The concept of archived code
87. EP includes cumulative hourly wet deposition fluxes kg hectare for selected model species CCTM 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 Species can be removed from the 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 7 AEROVIS CCTM hourly instantaneous visibility metrics The 2 D CCTM visibility file AEROVIS contains hourly Mie and reconstructed visual range coefficients km and normalized extinction coefficients deciviews June 2010 6 32 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 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 6 3 1 AERODIAM Instantaneous hourly aerosol diameter file This diagnostic file contains information on the geometric mean diameters and geometric standard deviations for the lognormal modes 6 3 2 WETDEP2 CCTM cloud diagnostics file The 2 D CCTM wet deposition file WETDEP2 includes cumulative hourly wet deposition fluxes kg hectare for selected model species CCTM calculates wet deposition for all of th
88. FLOOR_ APPL gt horizontal grid defn check GRIDDESC file for GRID_NAME options setenv GRIDDESC GRIDDESC1 setenv GRID_NAME M_36_2001 gt species for standard conc setenv CONC_SPCS 03 NO ANO3I ANO3J NO2 FORM ISOP ANH4J ASO4I ASO4J gt layer range for standard conc setenv CONC_BLEV_ELEV 1 4 gt species for integral average conc setenv AVG_CONC_SPCS 03 NO CO NO2 ASO4I ASO4J NH3 setenv AVG_CONC_SPCS ALL gt layer range for integral average conc setenv ACONC_BLEV_ELEV 1 1 gt input files and directories set OCEANpath SM3DATA emis 2001 set OCEANfile us36_surf 40x44 ncf set EMISpath SM3DATA emis 2001 set EMISfile emis3d 20010722 US36_40X44 ncf 5 set TR_EMpat set TR_EMfile set GC_ICpath SOUTDIR set GC_ICfile CCTM_e3aCGRID dlb set GC_ICpath SM3DATA icon set GC_ICfile ICON_cb05cl_M_36_2001_profile set GC_BCpath SM3DATA bcon set GC_BCfile BCON_cb05cl_M_36_2001_profile set METpath SM3DATA mcip3 M_36_2001 set extn 010722 set GC2file GRIDCRO2D_S extn set GD2file GRIDDOT2D_S extn set MC2file METCRO2D_S extn set MD3file METDOT3D_S extn set MC3file METCRO3D_S extn set MB3file METBDY3D_S extn set TR_DVpath S METpath set TR_DVfile S MC2file gt 7 level photolysis data w file hea
89. Guidance Document An I O API GRDDED3 formatted CCTM output concentration file CTM CONC_1 can be used to create spatially and temporally varying initial and boundary conditions To configure ICON and BCON to generate initial and boundary conditions from a CCTM concentration file the m3conc input module is chosen when compiling the programs see Section 5 5 on ICON and Section 5 2 on BCON The input concentration file must cover a temporal and spatial extent that is consistent with the time period and domain that are being modeled respectively Both ICON and BCON require a Julian start date to 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 indicate 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 photolysis reactions in each of the chemical mechanisms implemented in CMAQ A flexible format allows users to de
90. Hourly X Y Z CCTM files MECH_CONV _ FILE mechanism ASCII n a n a user conversion file MET CRO 3D 3 D meteorological GRDDED3 Hourly X Y Z MCIP user June 2010 6 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document cross point fields CTM_CONC_1 CCTM concentration GRDDED3 Hourly X Y Z CCTM files MECH_CONV _ FILE mechanism ASCII n a n a user conversion file MET CRO 3D 3 D meteorological GRDDED3 Hourly X Y Z MCIP quantum yields ET extraterrestrial irradiance ASCII Annual n a user PROFILES default atmospheric ASCII Annual n a user profiles O2ABS 02 absorption ASCII Annual n a user O3ABS 03 absorption ASCII Annual n a user TOMS total ozone mapping ASCH varies n a user spectrometer data CSQY absorption cross section and ASCII Annual n a User InMetFiles list of MM5 or WRF ARW Binary or typically hourly X Y Z MM5 or output files netCDF but sometimes WRF ARW sub hourly InTerFile MMS terrain file Binary n a X Y MM5 INIT_CONC_1 initial conditions GRDDED3 Time invariant X Y Z ICON CCTM BNDY_CONC_1 boundary conditions BNDARY3 Hourly 2 X4 1 2 Y 1 Z BCON XJ_ DATA photolysis rates look up ASCII Daily n a JPROC table EMIS _1 Emissions GRDDED3 Hourly X Y Z SMOKE OCEAN _1 sea salt mask GRDDED3 Time invariant X Y Spatial Allocator GSPRO speciation profiles ASCII T
91. I O API include files needed to compile MCIP are different from those needed by the other CMAQ components The other CMAQ programs use the include files in the M3LIB ioapi fixed_sre directory For MCIP you must set the T O API include file path in the Makefile to the directory on your system that contains the I O API source code The I O API fixed source directory containing the include files needed by the rest of the CMAQ programs is contained within the base I O API source code directory This base source code directory contains the version of the I O API include files needed to compile MCIP Once you have configured the MCIP Makefile for your system use the following commands to compile MCIP cd SM3HOME scripts mcip sre June 2010 3 9 http www cmaq model org CMAOv4 7 1 Operational Guidance Document make 7 CCTM has multiple configuration options that can be changed to optimize model performance for different applications In addition to selecting the chemical mechanism to model gas phase chemistry 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 create a single processor executable for the benchmark simulation For multiprocessor applications CMAQ uses the MPICH message passing interface MPI to manage communication between processors in a clustered multiprocessor computing envir
92. L are of high quality and highly customizable It runs on many different operating systems including Solaris AIX IRIX Linux MacOSX Dec Alpha and Cygwin X running on Windows It is available for free in binary format NCL can be run in interactive mode where each line is interpreted as it is entered at the user s workstation or it can be run in batch mode as an interpreter of complete scripts The user can also use command line options to set options or variables on the NCL command line The power and utility of the language are evident in three areas e file input and output e data analysis e visualization NCL has many features common to modern programming languages including types variables operators expressions conditional statements loops and functions and procedures The various NCL commands can be executed at the NCL command prompt or all the commands can be stored in a file and invoked as follows ncl commands ncl NCL comes with numerous predefined functions and resources that the user can easily invoke These include functions for data processing visualization and various mathematical and statistical analyses such as empirical orthogonal functions EOFs and singular value decomposition SVD As an example cont ributed ncl isa library of user contributed functions within NCL This library is distributed with NCL and loading the script at the beginning of the user s NCL script therein can access the function
93. LD cd SM3HOME scripts build bldit m3bld June 2010 3 8 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 2 Next create the stencil exchange STENEX libraries for serial and parallel processing Verify on line 37 of the file bldit se Linux that the MPICH INCLUDE file directory path is correct for the parallel version of the library Use the following commands to compile the STENEX libraries cd SM3HOME scripts stenex bldit se_noop Linux bldit se Linux 3 For parallel CCTM operation create the parallel input output PARIO library cd SM3HOME scripts pario bldit pario Linux Now create the model executables for JPROC ICON BCON MCIP and CCTM 4 For the benchmark case confirm that JPROC is configured to produce photolysis rates for the mechanism labeled cb05cl ae5_aq Use the following command to compile JPROC cd SM3HOME scripts jproc bldit jproc 5 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 SM3HOME scripts icon ldit icon d SM3HOME scripts bcon ldit bcon oa O 6 MCIP is compiled using a Fortran Makefile instead of M3BLD To create the MCIP executable set the compiler compiler flags and netCDF and I O API library paths in the Makefile distributed with MCIP The
94. MAQ The meteorology inputs dictate the following CMAQ configuration parameters e Horizontal grid coordinate system e g latitude longitude and map projection e g Lambert Conformal Conic Horizontal grid resolution i e the size of the cells composing the grid Maximum spatial coverage horizontal geographic extent i e the domain of the grid Maximum vertical grid extent model top Temporal extent the starting and ending dates and times and the meteorology update frequency To obtain inputs on emissions CMAQ relies on 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 IE 2008 http www smoke model org 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 These emissions inputs must be on the same horizontal and vertical spatial scales and cover the same time period as are 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 2005 update to the Carbon Bond mechanism CB05 Yarwood et al 2005 and the Statewide Air Pollution Research Center Version 1999 June 2010
95. MAQv4 7 1 Operational Guidance Document CMAQ Programs Third Party Programs E CMAQ Preprocessors CMAQ CTM CCTM Input CCTM Output Met Model Output Jl 1 00 Emissions Model Input Figure 5 1 CMAQ core programs ICON creates a binary netCDF initial conditions file for input to CCTM Users have the option to create initial conditions data either from 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 CCTM Users have the option to create boundary conditions from either a text file of vertical concentration profiles or from an existing CCTM or larger scale e g global scale 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 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 CCTM JPROC converts physical information about photoreactive molecules into clear sky photolysis rate look up tables for input to CCTM CMAQv4 7 includes a feature for calculating photolysis June 2010 5 2 http www cmaq model org CMAOv4 7 1 Operational Guidance Docume
96. MOKE and CONCEPT emissions models are currently available for preparing emissions data for CMAQ With the release of CMA Qv4 7 there are two new in line options for emissions the user can incorporate the processing of biogenic emissions or of point source plume rise or both directly in a CCTM simulation Previous versions of CMAQ required that biogenic emissions and point source plume rise were provided from input files as pre calculated hourly values There are several advantages of incorporating these processes directly in a CCTM simulation 1 the emissions are meteorologically modulated at the synchronization chemistry time step rather than being linearly time interpolated within each simulation hour 2 disk space may be saved because a 3 D emissions file is no longer needed for elevated point sources and 3 CMAQ can more easily be coupled with a meteorological model enabling direct emissions modulation by the underlying freshly computed meteorological variables In line emissions are an option in CMA QvV4 7 1 the traditional approaches of computing biogenic and 3 d point source emissions offline are still available See the CMAQv4 7 release notes for details on in line emissions processing MCIP is the first program in the CMAQ distribution package that a user should run when setting up a new simulation MCIP is used to preprocess the data from a meteorological model for CMAQ and SMOKE June 2010 5 1 http www cmaq model org C
97. MZ3DATA M3LIB and M3MODEL directory paths needed by CMAQ setenv M3DATA SM3HOME data setenv M3LIB SM3HOME 1lib setenv M3MODEL SM3HOME models 3 Create the M3LIB directory mkdir SM3LIB 4 Download the CMAQ tar files and unpack them in the M3HOME directory tar xvzf SCRIPTS CMAQv4 7 1 tar gz tar xvzf MODELS CMAQv4 7 1 tar gz tar xvzf DATA CMAQv4 7 1 tar gz tar xvzf DATA_REF CMAQv4 7 1 tar gz tar xvzf DOCS CMAQv4 7 1 tar gz 5 The CMAQ scripts assume that the netCDF and I O API are already installed and compiled on the hardware system The precompiled libraries can be copied into SM3LIB or symbolic links to each library i e a file can be created in the appropriate locations in SM3LIB The example below is for Portland Group Fortran compiled libraries on a 64 bit operating system To copy a precompiled version of the netCDF library use a variation of the following commands mkdir p SM3LIB netCDF Linux2_x86_64pg cd SM3LIB netCDF Linux2_x86_64pg cp home user netcdf 3 6 1 lib libnetcdf a or to create a symbolic link mkdir p SM3LIB netCDF Linux2_x86_64pg cd SM3LIB netCDF Linux2_x86_64pg In s home user netcdf 3 6 1 lib libnetcdf a libnetcdf a Similarly for the I O API either copy a precompiled version of the library to the SM3LIB ioapi Linux2_x86_64pg directory or create a symbolic link to the library a file You also need to copy or l
98. Medium scale In meteorology mesoscale denotes medium horizontal and vertical spatial scale The horizontal scale extends to several hundred kilometers The vertical scale extends from tens of meters to the depth of the troposphere Metadata Information about data and about the processes that produced them In particular information about the data s structure internal characteristics and history and location within a data storage environment as well as information derived from the data Meteorological model This type of model provides descriptions of atmospheric motions momentum moisture heat fluxes turbulence characteristics clouds and precipitation and atmospheric radiative characteristics Most meteorological models currently in use for air quality modeling were originally developed for the prediction of weather CMAQ models require information from a meteorological model that is designed to address specific issues relevant to air quality modeling such as planetary boundary layer information cloud distribution and mixing characteristics precipitation and surface fluxes Mie scattering A generalized particulate light scattering mechanism that follows from the laws of electromagnetism applied to particulate matter Mixed media Simultaneously involving more than one environmental pollutant medium such as air and water Model developer Those scientists and software developers who construct and study theories to explain physica
99. N will input either an ASCII vertical profile file IC_PROFILE or an existing CCTM concentration file CTM_CONC_ 1 the choice depends on how the user compiled the model If the input file is not in the same chemical speciation as the simulation for which the user is creating ICs 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 CB05 or SAPRC 99 chemistry It is possible to create a custom conversion file MECH_CONV_ FILE and input this file to ICON by setting the ModMech variable to user_defined at compilation 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 used only when the IC environment variable is set to profile June 2010 5 31 http www cmaq model org CMAOv4 7 1 Operational Guidance Document MECH_ CONV FILE ASCII Mapping factors for converting between chemical mechanisms this file
100. NO m s VD_NO deposition velocities for NO m s VD_O3 deposition velocities for O m s VD_HNO3 deposition velocities for HNO m s VD_H202 deposition velocities for H20 m s VD_ALD deposition velocities for ALD m s VD_HCHO deposition velocities for HCHO m s VD_OP deposition velocities for OP m s VD_PAA deposition velocities for PAA m s VD_ORA deposition velocities for ORA m s VD_NH3 deposition velocities for NH m s VD_PAN deposition velocities for PAN m s VD_HONO deposition velocities for HONO m s VD _CO deposition velocities for CO m s VD_METHANOL deposition velocities for methanol m s VD_N205 deposition velocities for N20 m s VD_NO3 deposition velocities for NO m s VD GEN ALD deposition velocities for generic aldehyde m s VD _CL2 deposition velocities for CL2 m s VD_HOCL deposition velocities for HOCL m s VD_HCL deposition velocities for HCL m s VD_FMCL deposition velocities for FMCL m s VD_ICLI deposition velocities for ICL1 m s VD_ICL2 deposition velocities for ICL2 m s VD_HG deposition velocities for HG m s VD_HGIIGAS deposition velocities for HGIIGAS m s 6 1 28 MET _CRO_3D Three dimensional meteorological cross point fields Used by CCTM ICON BCON The MET _CRO_3D time dependent file contains 3 D meteorological descriptions at cross points i e at cell centers
101. Operational Guidance for the Community Multiscale Air Quality CMAQ Modeling System Version 4 7 1 June 2010 Release Prepared in cooperation with the Community Modeling and Analysis System Institute for the Environment University of North Carolina at Chapel Hill Chapel Hill NC 27599 CMAQv4 7 1 Operational Guidance Document Operational Guidance for the Community Multiscale Air Quality CMAQ Modeling System June 2010 ii http www cmaq model org CMAQv4 7 1 Operational Guidance Document Disclaimer The information in this document has been funded wholly or in part by the United States Environmental Protection Agency The draft version of this document has not been subjected to the Agency s peer and administrative review nor has it been approved for publication as an EPA document The draft document has been subjected to review by the Community Modeling and Analysis System Center only this content has not yet been approved by the EPA Mention of trade names or commercial products does not constitute endorsement or recommendation for use June 2010 iii http www cmaq model org CMAQv4 7 1 Operational Guidance Document Foreword The Community Multiscale Air Quality CMAQ modeling system is being developed and maintained under the leadership of the Atmospheric Modeling and Analysis Division of the EPA National Exposure Research Laboratory in Research Triangle Park NC CMAQ represents over two decades of research i
102. Ov4 7 1 Operational Guidance Document 2 1 2 Modular flexibility CMAQ s current coding structure is based on a modularity level that distinguishes from each other the CCTM s main driver science modules data estimation modules and control utility subroutines Also distinguished from each other are the science models including submodels for meteorology emissions chemistry transport modeling and the analysis and visualization subsystems In CCTM the process modules that affect the pollutant concentration fields are classified as listed below Each bullet contains a description of the process followed by module name in parentheses These modules except for gencoor are discussed further later in this chapter Science Modules e Horizontal advection hadv Vertical advection vadv Mass conservation adjustments for advection processes adjc Horizontal diffusion hdiff Vertical diffusion vdiff Gas phase chemical reaction solver chem Aqueous phase reactions and cloud mixing cloud Aerosol dynamics and size distributions aero 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 CCTM For example the che
103. Q CO CPU CSQY CTM CVS EBI EPA FAQ FTP GB GIS GMT GPL GUI HTML HYSPLIT VO API IC ICON IDA IE IPR IRR IRR MB JPROC MCIP MECH MEPSE MM5 June 2010 Abbreviations Aerosol chemistry phase Aerometric Information Retrieval System Aqueous Chemistry Phase American Standard Code for Information Interchange Boundary Condition Boundary Conditions Processor Biogenic Emissions Inventory System Carbon Bond IV Carbon Bond 2005 CMAQ Chemistry Transport Model Center for Environmental Modeling for Policy Development Community Modeling and Analysis System Community Multi Scale Air Quality model Carbon Monoxide Central Processing Unit of a computer Cross Section and Quantum Yield Chemistry Transport Model Concurrent Versions System Euler Backward Iterative chemistry solver Environmental Protection Agency Frequently Asked Question File Transport Protocol Gigabyte Geographic Information System Greenwich Mean Time Gnu General Public License Graphical User Interface HyperText Markup Language Hybrid Single Particle Lagrangian Integrated Trajectory model Input Output Application Programming Interface Initial Concentration Initial Conditions Processor Inventory Data Analyzer Institute for the Environment Integrated Process Rate Integrated Reaction Rate Integrated Reaction Rates Mass Balance Analysis Photolysis Rate Processor Meteorology Chemistry Interface Processor Chemical Mechanism Reader Major E
104. Section 2 2 3 the CMAQ modeling system includes an advanced photolysis model JPROC to calculate temporally varying photolysis rates for use in simulating photolysis in CCTM An in line photolysis module Binkowski et al 2007 was included in CMAQ beginning with version 4 7 The in line photolysis calculations account for the presence of ambient PM and ozone predicted by CMAQ and use these estimates to adjust the actinic flux rather than relying on a look up table of static background PM and ozone values The in line method for calculating photolysis rates also uses newer values of the absorption cross sections and quantum yields than those in the table look up version and these new values are corrected for ambient temperature The extinction coefficients for the ambient aerosols are explicitly calculated using a new efficient parametric algorithm derived from explicit integration of Mie calculations over the lognormal size distributions Refractive indices are calculated based upon the categories of chemical species present i e water soluble insoluble soot like water and sea salt 2 3 3 Advection and diffusion Pollutant transport includes both advection and sub grid scale diffusion Advection has to do with pollutant transport that is due to the mean wind fields while diffusion involves sub grid scale turbulent mixing of pollutants If a pollutant plume is transported primarily by advection then it may travel a long distance without
105. UNCTION 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 INTEGER JTIME time formatted HHMMSS June 2010 4 6 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 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 NVARS 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 1 6 CMAQ Related I O API Utilities Data files in the CMAQ system can be easily manipulated by using the I O API utilities The I O API utilities also known as m3tools are a set of scriptable programs for manipulation and analysis of netCDF I O API formatted files Information regarding the most commonly employed utility
106. Vertical Layers erat Gk estate a iG cada catths soe cle Uae Gd ella r 288 7 3 7 3 1 Vertical layer TESO TOM trea peceaebiesaobans cues atdoctes edacanedoraae teaea eataucte tues ae 7 3 7 3 2 Further information on vertical layers cccssccsssccsessseccesceessensccssecesaces 7 4 7 4 Chemical Mechanist esiou iaaa niai sade aaiae iaaii 7 4 7 4 1 Using predefined chemical mechanisms cccccesceseeeseeeeceeeceseeneeeaeeeneees 7 4 7 4 2 Creating or modifying chemical mechanisms ccccecsceesseeeteeesteeeteeeeees 7 5 7 4 3 Further information on chemical mechanisms cc cccceesseeeteeeeteeeeeeeeees 7 6 8 DEVELOPING NEW CMAQ SIMULATIONS cccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 8 1 8 1 General Introduction to Model Building eee cece cee eeeeeeecneecseeeeeeeeeneeaee 8 1 8 2 Configuring New Simulations cco xce Ay odecasss Sead ss cc cincessstsen ebedeausscasevorsiosucussessncvaseders 8 2 8 2 1 Defining a new horizontal grid c sh03s esheets Gee dade 8 2 8 2 2 Defining a new vertical layer structure ec cecceseceeecetceceeceeeeeeeeenseeenseens 8 3 8 2 3 Setting a new episode time period 5 ssseccssacdeasiabads oessecslcseacdoneabass es sledvacreds 8 3 8 2 4 Initial and boundary Conditions lt i sccc sss aso lnc cnmia a aieGeasuests 8 4 8 2 5 Input output file names and locations 0 c ee eeeceeceeteeesceceeceteeeeeeeeeeeenseees 8 6 8 2 6 Science option configuration 1
107. Viewer IDV and the NCAR Command line Language NCL Several other commercial packages including MATLAB and IDL also support the analysis and visualization of CMAQ inputs and outputs Almost all of the CMAQ input and output files use the I O API file format which is a modified version of the netCDF format If the user has already built the netCDF library http www unidata ucar edu software netcdf index html for compiling CMAQ the ncdump utility should also be available on the user s machine This utility generates an ASCII representation of the netCDF file using the CDF notation developed by NCAR The UNIX syntax for invoking ncdump is the following ncedump h c n name inputfile h produces only the header information in the output file i e the declarations of dimensions variables and attribute but no data values for the variables c produces the header information in the output file and the data values for coordinate variables variables that are also dimensions n name is used to specify a different name for the network Common data form Description Language CDL description than the default This chapter presents a brief overview of each set of tools mentioned above At the beginning of each subsection below is a table listing helpful information for users who wish to use the tools 10 1 CMAQ Utility Tools Latest Version Version 4 7 released on 12 09 2008 Main website __ http
108. YER4_BC EXp BC concentration for species 1 in 4th sigma layer required AAYERX_BC EXp BC concentration for species 1 in Xth sigma layer required 8 1 10 SPECIES2 String Pollutant name enclosed in double quotes required 12 20 AAYER1_BC EXp BC concentration for species 2 in lowest Sigma layer required 23 31 AAYER2_BC EXp BC concentration for species 2 in 2nd sigma layer required June 2010 6 9 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 34 42 AAYER3_BC Exp BC concentration for species 2 in 3rd sigma layer required 45 53 AAYER4_BC Exp BC concentration for species 2 in 4th sigma layer required AAYERX_BC Exp BC concentration for species 2 in Xth sigma layer required Y A Direction String North South East West indicates the horizontal boundary described by the subsequent data section required Z 1 T 10 SPECIESZ String Pollutant name enclosed in double quotes required 12 20 AAYER1_BC Exp BC concentration for species Z in lowest sigma layer required 23 31 AAYER2_BC Exp BC concentration for species Z in 2nd sigma layer required 34 42 AAYER3_BC Exp BC concentration for species Z in 3rd sigma layer required 45 53 AAYER4_BC Exp BC concentration for species Z in 4th sigma layer required AAYERX_BC Exp BC concentration for species Z in Xth sigma laye
109. _COL default 0 Column cell coordinate for diagnostic outputs on the MCIP modeling domain e LPRT_ROW default 0 Row cell coordinate for diagnostic outputs on the MCIP modeling domain 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 meteorology file June 2010 5 45 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 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 meteorology file MET BDY 3D BNDARY3 Time dependent 3 D boundary meteorology file MET CRO 2D GRDDED3 Time dependent 2 D cross point meteorology file MET CRO 3D GRDDED3 Time dependent 3 D cross point meteorology file MET DOT 3D GRDDED3 Time dependent 3 D dot point meteorology file mmheader ASCII Content of MMS header including configuration information not generated for WRF ARW input 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 set in the output directory path The default na
110. _noop deactivate vertical advection o vppm use the unmodified Piecewise Parabolic Method to calculate vertical advection o vyamo use the global mass conserving scheme to calculate vertical advection ModHdiff default multiscale Horizontal diffusion module o hdiff_ noop deactivate horizontal diffusion o multiscale use diffusion coefficient based on local wind deformation ModVdiff default acm2_inline Vertical diffusion module vdiff_noop deactivate vertical diffusion o eddy calculate vertical diffusion using eddy diffusivity theory o eddy txhg use eddy vertical diffusion instrumented for the mercury and air toxics CMAQ model o acm2 calculate vertical diffusion using the Asymmetric Convective Model version 2 ACM2 o acm2_inline use ACM vertical diffusion instrumented for in line calculation of emissions o acm2_inline_txhg use ACM vertical diffusion with in line calculation of emissions and instrumented for the mercury and air toxics CMAQ model this is for the multipollutant model see CMA Qv4 7 release notes o acm2_inline_ txhgsim use ACM vertical diffusion with in line calculation of emissions and instrumented for the mercury and air toxics CMAQ model with bidirectional exchange of mercury this is for the multipollutant model see CMAQv4 7 release notes 5 14 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 ModPhot default phot Photolysis calculation m
111. a i a E ds Gx A eee aaa iia 3 1 June 2010 v http www cmaq model org CMAQv4 7 1 Operational Guidance Document 4 5 I2 SOM WaAne yy tis ech ekcctune Ae te leh te Ce eed Oh eS eh te Sea ae lak at 3 2 3 2 Installing CMAQ Source Code wx occian nanni u a i r a Whee oaos 3 4 32T Distribution contents esigente a a r a a ead es 3 4 3 2 2 Notes on the CMAQ directory structure s sessseeseeseesseesreseessessesressressesse 3 5 3 2 3 Configuring your system for compiling CMAQ s sessesesssessesersesseseesseseesesse 3 6 3 3 Compiling CMAQ for the Benchmark Test Case Simulation 0 ccecceeseeteeeeeee 3 8 3 4 Running the CMAQ Benchmark Simulation cece ecceesseeeteceeeeeeeeeeseecseeenteeeees 3 10 3 5 Benchmarking CMAQ eaii anaia a A E A Societe tc 3 11 REQUIRED LIBRARIES v a a aa a a aaa aiia ariaa 4 1 4 1 Input Output Applications Programming Interface I O APT ss sssssessssssessessesssseseese 4 1 4 1 1 Files Logical Names and Physical Names ccccccesceeeseeesseeeteeeseeeeeeeenees 4 2 4 1 2 I O API Data Structure and Data File Types 0 ceccceccceceseceseceeeeeeeeeeseeees 4 2 41 3 Openiig Creatine Data Files in T OVA P lcs css seece cat aeasicet ace eases 4 4 4 1 4 Reading Data Files in I O API v2 2 sccitetacccantriccrenieds aceesastcuadadsieatvenss 4 5 4 1 5 Writing Data Files in OAPI yy aie ucsc scx csGuesarsanesesetetucvesesdyacdasasesusseuensesstelaes 4 6 4 1 6 CMAQ Related I O API Utilities 0 0
112. a particular gas phase chemical mechanism and PM model output from an emission model such as SMOKE or CONCEPT INIT_ GASC AERO GRDDED3 Name and location of the time dependent single NONR TRAC 1 time step 3 D initial conditions file speciated for a June 2010 5 11 http www cmaq model org CMAOQv4 7 1 Operational Guidance Document particular gas phase chemical mechanism and PM model output from ICON BNDY_ GASC AERO BNDARY3 Name and location of the time dependent either NONR TRAC 1 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 independent 2 D cross point meteorology file output by MCIP GRID _DOT_2D GRDDED3 Name and location of the time independent 2 D dot point meteorology file output by MCIP MET CRO 2D GRDDED3 Name and location of the time dependent 2 D cross point meteorology file output by MCIP MET DOT 3D GRDDED3 Name and location of the time dependent 3 D dot point meteorology file output by MCIP MET CRO 3D GRDDED3 Name and location of the time dependent 3 D cross point meteorology file output by MCIP MET BDY 3D BNDARY3 Name and location of the time dependent 3 D boundary meteorology file output by MCIP XJ DATA ASCII Name and location of the daily clear sky photolysis rates
113. aboard the sun synchronous polar orbiting Nimbus satellite The data are 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 6 11 The files are fixed format Table 6 11 TOMS Data Profile Line Column Name Type Description 1 A Julian Int Julian start day of the file DDD preceded by Day 6 blank spaces required B Year Int Start year of the file YYYY preceded by 9 blank spaces required 2 Header String 80 character line describing the contents of the file if omitted needs line placeholder 3 Header String 80 character line describing the contents of the file if omitted needs line placeholder 4 A TOMS Int TOMS ozone measurements as a function of Data longitude and latitude line starts with a space then space delimited 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 O2 photolysis The data in this file are listed as a function of wavelength This file follows the same format as the CSQY files described in Section 6 1 6 6 1 11 O3ABS Ozone absorption cross section data Used by JPROC June 2010 6 18 http www cmaq model org CMAQv4 7 1 Operational Guidance Document O3ABS is t
114. 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 SM3MODEL include release NewMechanism directory within the CMAQ installation 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 June 2010 5 25 http www cmaq model org CMAQv4 7 1 Operational Guidance Document build script for the applicable CMAQ program to the name of the mechanism directory that you created For example if CHEMMECH was used to create INCLUDE files for a mechanism that is called cb05_ 2006 create a directory SM3MODEL include release c05_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 cb05_ 2006 CHEMMECH can be run in either mechanism processor MP or species processor SP mode The MP mode generates new mechanism include files for CMAQ The SP mode generates a new species table include file for CMAQ If an existing mechanism e g CB05 is modified by the user and no new species are added to the mechanism CHEMMECH only needs to be run in MP mode When new species are added or a new mechanism is being processed for
115. all to process analysis routine to obtain data for the optional integrated process rates function 19 Illustrates call to another science process within the module 20 Main computational loop over the horizontal grid 21 Time step loop over subsynchronization time step intervals 22 Illustrates writing to an I O API file within a module 23 Subroutine end June 2010 9 12 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 9 3 Compiling CMAQ with New Source Code The following steps are recommended for compiling CMAQ when a new module has been developed The procedure creates a Makefile which can then be modified to add the new module in the appropriate class but the same steps can be used to obtain a configuration file that can be similarly modified to add the new module On the computational platform of choice create a working directory for the model download Download the appropriate tar file SCRIPTS tar gz from the CMAS web site www cmascenter org for the chosen platform Users must register before proceeding with the download steps Untar the file using the command gt tar xvfz SCRIPTS tar gz This will expand a directory labeled scripts that contains all the scripts necessary to compile and run CMAQ Either install the CMAQ source code and libraries Chapter 3 or create links to the CMAQ models and libraries as follows gt ln s lt models directory gt models gt In s lt lib
116. ameters and atmospheric processes e g diffusion deposition advection of the various mechanism species The CMAQ mechanism configuration is more similar to the science module configura tion than to the horizontal grid or vertical layer configuration in that the mechanism is defined at compilation resulting in executables that are hard wired to a specific gas phase mechanism To change chemical mechanisms between simulations a new executable that includes the desired mechanism configuration must be compiled 7 4 1 Using predefined chemical mechanisms To select a predefined mechanism configuration in CMAQ set the Mechanism variable in the build scripts to the name of one of the mechanism directories located under June 2010 7 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document SM3MODEL include release Table 7 1 lists the available chemical mechanisms in CMAQvV4 7 and what is included with each mechanism Set the Mechanism variable in the CMAQ build script to the Mechanism ID in Table 7 1 to select a particular mechanism Detailed descriptions of some of these mechanisms can be found in Byun and Ching 1999 Table 7 1 CMAQ chemical mechanisms Mechanism ID cb05 pe ne ee ans eS Additional species gen 5 gen y cb05cl_ae4_aq x x x Cl cb05cl_ae5 aq x x x Cl cb0Scltx_ae5_aq x x Cl air toxics cb0Stxhg_ae5_aq x x x Hg air toxics Hg saprc99 ae4_aq x x saprc99 ae5_aq saprc99
117. and cannot become negative These codes are implemented in a global mass conserving scheme introduced in v4 6 that is similar to the one used in the air quality forecasting version of CMAQ Inspired by discussions with Robert Yamartino of Cambridge Environmental the method uses the PPM scheme for horizontal advection deriving a vertical velocity component at each grid cell that satisfies the continuity equation using the driving meteorological model s air density 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 species that are observed in photochemical air quality conditions Note that the CMAQ v4 5 advection scheme with the same horizontal advection but using PPM for the vertical velocity component is still available in the 2008 release along with the mixing ratio correction step Diffusion In CCTM vertical diffusion is represented by the Asymmetric Convective Method ACM of Pleim and Chang 1992 ACM2 an updated version of ACM is used in v4 7 This method recognizes that under convective conditions when the surface is warming heated air is transported vertically by buoyancy and mixes with ambient air at each level above the surface until t
118. are system users should then download the CMAQ source code scripts and benchmark data files from the CMAS Center web site 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 Linux tar files of the CMAQ code scripts and benchmark data along with various documents describing the installation and execution processes 3 2 1 Distribution contents The following files and archives compose the CMAQ distribution e AEROSOL NOTES description of updates to the CMAQ aerosol routines e BIDIRECTIONAL HG EXCHANGE description of the atmospheric surface exchange mechanism for mercury that is implemented in CMAQ e CHEMISTRY NOTES details about the chemistry updates in the release version of CMAQ e CVS _NETCDF text file explaining the CVS configuration management system and the netCDF data system and how to set them up June 2010 3 4 http www cmaq model org CMAOv4 7 1 Operational Guidance Document e EVALUATION TOOLS text file explaining how to obtain compile and apply CMAQ data analysis utility programs e HAZARDOUS _AIR POLLUTANTS description of the implementation of HAPs modeling in CMAQ e INLINE EMISSIONS DEPV_ NOTES description of how to incorporate the calculation of biogenic emissions and elevated point source plume rise into CMAQ simulations e INLINE RUN SCRIPT example run script for a CCTM simulati
119. ase species and grams per second g s for aerosol species The file data are 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 For CCTM configurations that do not use in line emissions calculations all emissions estimates are contained within a single input emission file for each day In v4 7 CMAQ now has the capability to process point source sea salt and biogenic emissions in line The supplemental input files to use for calculating the in line emissions are described i in the CMAQv4 7 release notes 6 1 18 OCEAN_1 Sea salt mask Used by CCTM The CMAQ aerosol model AEROS can compute sea salt emissions from both open ocean grid cells and surf zone grid cells The addition of the surf zone option simulates the elevated emissions rates of sea salt in coastal regions where wave action occurs The OCEAN_1 file contains data on the fraction of each grid cell that is either open ocean OPEN or in the surf zone SURF When CCTM is compiled with AEROS it will expect the OCEAN _1 file as input 6 1 19 GSPRO Speciation profiles Used by CCTM The speciation profile file GSPRO contains the factors that are used to separate aggregated inventory pollutant emissions totals into emissions of model species in the form required by CMAQ If only biogenic emissio
120. ate names and map table 4 INCLUDE SUBST_TR_DEPV tracer dep vel surrogate names and map table 4 INCLUDE SUBST_TR_DDEP tracer dry dep species and map table 4 INCLUDE SUBST_TR_DIFE tracer diffusion species and map table l INCLUDE SUBST_EMLYRS_ID emissions layers parameter 5 ifdef emis_chem June 2010 9 7 http www cmaq model org CMAQv4 7 1 Operational Guidance Document C5 INCLUDE SUBST_EMPR_CH emissions processing in chem 5 else 5 INCLUDE SUBST_EMPR_VD emissions processing in vdif 5 endif 6 INCLUDE SUBST_PACTL_ID PA control parameters 6 INCLUDE SUBST_CONST constants 6 INCLUDE SUBST_FILES_ID file name parameters 6 INCLUDE SUBST_IOPARMS I O parameters definitions include SUBST_IODECL I O definitions and declarations INCLUDE SUBST_COORD_ID coordinate and domain definitions req IOPARMS 7 CHARACTER 120 XMSG 8 C Arguments REAL CGRID NCOLS NROWS NLAYS concentrations REAL CGRIDt tptetet concentrations 8 REAL POINTER CGRID concentra
121. ault is 720 setenv CTM_MAXSYNC 300 gt aerosol diagnostic file T Y F N default is F N setenv CTM_AERDIAG Y gt sea salt emissions diagnostic file T Y F N default is F N setenv CTM_SSEMDIAG Y gt stop on inconsistent input file Ee fe at ES se iN setenv FL_ERR_STOP F gt remove existing output files set DISP delete set DISP update set DISP keep gt output files and directories set OUTDIR SM3DATA cctm if d SOUTDIR mkdir p SOUTDIR set CONCfile SEXEC CONC SAPPL CTM_CONC_1 set ACONCfile SEXEC ACONC S APPL CTM_ACONC_1 set CGRIDfile SEXEC CGRID S APPL CTM_CGRID_1 set DD1file SEXEC DRYDEP SAPPL CTM_DRY_DEP_1 set WDlfile SEXEC WETDEP1 SAPPL CTM_WET_DEP_1 set WD2file SEXEC WETDEP2 SAPPL CTM_WET_DEP_2 set SSlfile SEXEC SSEMIS1 SAPPL CTM_SSEMTS_1 set AVlfile SEXEC AEROVIS SAPPL CTM_VIS_1 set AD1lfile SEXEC AERODIAM SAPPL CTM_DIAM_1 set PAlfile SEXEC PA_1 SAPPL CTM_IPR_1 set PA2file SEXEC PA_2 SAPPL CTM_IPR_2 set PA3file SEXEC PA_3 SAPPL CTM_IPR_3 set IRR1file SEXEC IRR_1 SAPPL CTM_IRR_1 set IRR2file SEXEC IRR_2 SAPPL CTM_IRR_2 set IRR3file SEXEC IRR_3 SAPPL CTM_IRR_3 set RJlfile SEXEC RJ_1 SAPPL CTM_RJ_1 set RJ2file SEXEC RJ_2 SAPPL CTM_RJ_2 June 2010 9 15 http www cmaq model org CMAQv4 7 1 Operational Guidance Document gt set ancillary log file name extensions setenv CTM_APPL SAPPL gt set floor file neg concs setenv FLOOR_FILE SBASE
122. ava based visualization software tool that allows users to visualize multivariate gridded environmental datasets created by environmental modeling systems such as SMOKE CMAQ and WRF namely gridded concentration and deposition fields that users need to visualize and compare with observational data both spatially and temporally VERDI has been designed keeping most of the functionality of PAVE in mind and hence can help users analyze and visualize model outputs in a very similar vein using both command line driven scripts as well as using a Graphical User Interface GUI Further VERDI is under active development to enhance its features beyond PAVE June 2010 10 5 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 10 5 Atmospheric Model Evaluation Tool AMET Latest Version Version 1 1 released on May 31 2008 Main website http www cmascenter org Download http www cmascenter org Latest User s Manual http www cmascenter org Training Workshop _ http www cmascenter org Answers to FAQ N A Support website http bugz unc edu The Atmospheric Model Evaluation Tool AMET is a suite of software designed to facilitate the analysis and evaluation of meteorological and air quality models AMET matches the model output for particular locations to the corresponding observed values from one or more networks of monitors These pairings of values mode
123. cal resolution of the meteorological data by layer collapsing although this option should be used with caution as it can degrade the quality of the data if used incorrectly Configuration options for MCIP include the time periods over which to extract data from the meteorological model output files horizontal and vertical grid definitions and selections for calculating dry deposition velocities and integrating satellite cloud observations into MCIP output CMAQ Chemistry Transport Model CCTM CCTM integrates the output from the preprocessing programs described above JPROC BCON ICON and MCIP as well as CMAQ ready emissions inputs e g output from SMOKE to simulate continuous atmospheric chemical conditions The modeled concentrations of relevant species can be captured for output at a user definable time frequency typically hourly The CCTM output files 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 coverages of CCTM are dictated by the input meteorology information 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 CCTM include the tempo
124. cessor computing environment The Input Output Applications Programming Interface I O API and the Network Common Data Form netCDF are required for all applications of CMAQ The Message Passing Interface MPICH is only required for multiple processor applications of the CCTM Brief descriptions of these three libraries are provided in this chapter For additional information including how to compile and configure these libraries refer to the documentation associated with each library 4 1 Input Output Applications Programming Interface I O API The Models 3 Input Output Applications Programming Interface I O API is an environmental software development library that provides an interface with the data involved in CMAQ applications Coats 2005 The I O API is the core input output framework of the CMAQ programs providing a set of commonly used subroutines for passing information between source code modules and for reading and writing data files Users should download the latest code for the I O API from http www baronams com products ioapi In addition to providing the input output framework for CMAQ the I O API forms part of the binary file format used by the CMAQ programs The CMAQ input and output files use a hybrid Network Common Data Form netCDF I O API file format The netCDF is described in detail in Section 4 2 The CMAQ data files all use the netCDF convention of self describing selective direct access meaning the modeling sy
125. cross sections profiles animations and value read outs of multidimensional data sets The IDV can display any Earth located data if they are provided in a supported format More recently two features have been added to IDV that make it attractive for use by the air quality modeling community 1 the capability to read I O API netCDF formatted files and 2 a scripting interface to create and manipulate images and movies The scripting is accomplished through an XML file IDV Scripting Language ISL The ISL file can be opened from a running IDV or one can be passed to the IDV as a command line argument runIDV capture isl 10 9 NCAR Command Language NCL Latest Version Version 5 1 1 released on June 16 2009 Main website http www ncl ucar edu Download http www ncl ucar edu Download index shtml Latest User s Manual http www ncl ucar edu Document index shtml Training Workshop _ http www ncl ucar edu Training index shtml June 2010 10 9 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Support info http www ncl ucar edu Support ncl_talk shtml The NCAR Command Language NCL is a free interpreted language designed specifically for scientific data processing and visualization NCL has robust file input and output It can read in netCDF HDF4 HDF4 EOS GRIB binary and ASCII data The output graphics from NC
126. current clean_up remove all source files upon successful compilation no_compile do everything except compile no_link do everything except link 5 5 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 one_step compile and link in one step parse_only check configuration file syntax show_only show requested commands but do not execute them verbose show requested commands as they are executed OO OF O MakeOpt Uncomment to build a Makefile to compile the executable Modinpt default profile Defines the format of the boundary conditions input files to be used by BCON o m 3conc input a CCTM CONC file used for nested simulations or windows of a parent domain o profile input an ASCII vertical profiles file ModMech default module radm2_to_cb05 Defines whether the input boundary conditions data need to be converted from one chemical mechanism to another 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 o user_defined input the file defined by the MECH CONV _FILE variable used for custom mechanism conversions o radm2 to cb05 convert the input boundary conditions profiles from RADM2 to CB05 speciation o radm2_to_saprc99 convert the input boundary conditions profiles from RADM2 to SAPRC 99 speciation Mecha
127. cutable as long as the input files are consistent with the scientific configuration built into the executable For example with the gas phase photochemical mechanism configuration built into a CCTM executable different modeling domains can be simulated with the executable as long as the emissions and IC BC files are consistent with the photochemical mechanism configuration built into the executable June 2010 5 10 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Horizontal grid definition GRIDDESC Open ocean mask OCEANTile Emissions EMISfile Photolysis rates JVALfile Initial conditions GC_ICfile Boundary conditions GC_BCfile Meteorology GRID_DOT_2D MET_CRO_3D Execution Options GRID_CRO_2D MET_CRO_2D MET_DOT_3D MET_BDY_3D nism Fi CTM_CONC_1 GC_SPC EXT eae AE_SPC EXT Sei Mocnaniem GC_ICBC EXT CTM_ACONC_1 etc CTM_DRY_DEP_1 CTM_WET_DEP_2 ia CTM Vist i i IPR_1 Compile Options CTM_IRR CCTM Shows Input Output r Program Figure 5 3 CCTM input and output files 5 3 2 1 CCTM input files Table 5 3 Required CCTM input files File Name Format Description GRIDDESC ASCII Map projection and grid definitions OCEAN 1 GRDDED3 Name and location of the time independent 2 D file for defining the fraction of each model grid cell covered by open ocean EMIS 1 GRDDED3 Name and location of the time dependent 2 D or 3 D emission file speciated for
128. d BCON Both of these processors can perform mechanism conversions from one photochemical mechanism to another The default conversion in ICON and BCON maps RADM2 species to either CB05 or SAPRC 99 speciation Customized mechanism conversions can be coded into ICON and BCON through a Fortran INCLUDE file that maps the species from one photochemical mechanism to another June 2010 2 7 http www cmaq model org CMAQv4 7 1 Operational Guidance Document ICON and BCON can linearly interpolate input concentration profiles from the horizontal or vertical coordinate system used in the profiles 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 2 3 JPROC Clear sky photolysis rate calculator For CMAQ the photolysis rate model JPROC is used to generate clear sky photodissociation reaction rates JPROC requires temperature profiles from the U S Standard Atmosphere document NOAA 1976 a profile of the aerosol extinction coefficients Elterman 1969 data on species cross sections and quantum yields CSQY extraterrestrial radiance ET and standard seasonal profiles of ozone JPROC 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
129. d for other simulations The same steps that are required to build the model for the benchmark case apply to building it for new simulations However not all of the steps need to be June 2010 8 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document repeated for a new model configuration unless new code becomes available or bug fixes are identified In particular it is not necessary to rebuild any of the libraries that CMAQ uses once working versions are built on a user s system A single installation of the CMAQ libraries STENEX and PARIO and the non CMAQ libraries netCDF I O API MPICH can be linked to for multiple configurations and applications of the model Likewise the CMAQ model builder M3BLD can be compiled once and used for all applications of the model Except for MCIP all of the CMAQ programs need to be recompiled when the chemistry mechanism or science configuration of the model change If the science configuration does not change between applications the CMAQ programs can be reused MCIP needs to be compiled only once on a user s system and then reused for all applications of the model unless new source code including libraries becomes available 8 2 Configuring New Simulations The reason for modeling a particular time period evolves from a research question such as determining why a severe air pollution episode happened or studying the dominant sources of visibility degradation in a specific geog
130. database of resolved CMAQ support tickets before submitting a new ticket to the help desk be sure to search the database for keywords to see if the issue has been addressed previously Section 11 3 provides a list of the web pages referenced in Section 11 2 June 2010 11 2 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 11 2 1 Documentation The first place to look for an answer to CMAQ related questions is the on line documentation for the software The CMAS documentation page contains links to available documentation for current and previous releases of the various kinds of software that CMAS supports Peruse these on line manuals as many of them contain FAQs and discussion specific to the various programs 11 2 2 Interactive resources Search the CMAS FAQs and listservs for information about the question that you have These services are organized by topic to facilitate searching Look under the CMAS Model Clearinghouse area to find out about new releases and read through the release notes of past releases for detailed information about the features of the models 11 2 3 Tutorials training General questions regarding model installation or application may be addressed in the online tutorials for the CMAS supported software More specific tutorials will be added over time users can suggest tutorial topics by contacting the CMAS Center The CMAS Center offers quarterly trainings on CMAQ at the Institute for the En
131. der June 2010 9 16 http www cmaq model org CMAQv4 7 1 Operational Guidance Document set set set set set set set set set set set set set set gt input and output files and directories JVALpath JVALfile AE_ICpath NR_ICpath R_ICpath AE_ICfile NR_ICfile TR_ICfile FA H Z o AE N TR_BCfile SM3DATA jJproc JTABLE_S STDATE source in_out q GC_ICpath GC_ICpath GC_ICpath GC_ICfil GC_ICfil S GC_ICfil Le Le GC_BCpath GC_BCpath GC_BCpath GC BCfi l GC_BCfi SGC_BCfil Le Le e if Sstatus exit 1 gt for the run control setenv CTM_STDATE SSTDATE setenv CTM_STTIME SSTTIME setenv CTM_RUNLEN SNSTEPS setenv CTM_TSTEP STSTEP setenv CTM_PROGNAME SEXEC gt look for existing log files boilerplate set test ls CIM_LOG_ S APPL if Stest then if SDISP delete then echo ancillary log files being deleted foreach file Stest echo deleting file rm file end else echo Logs exist run ABORTED exit 1 endif endif gt env ls l S BASE SEXEC size SBASE SEXEC gt Executable call for single PE uncomment to invoke time SBASE SEXEC gt Executable call for multiple PE set location of MPIRUN script
132. developers use any combination of the above for testing code intended for release through the CMAS Center to facilitate benchmarking and portability testing by CMAS staff Any documentation on potential differences in model outputs between different computing platforms would be useful for end users who may not be able to June 2010 9 18 http www cmaq model org CMAQv4 7 1 Operational Guidance Document duplicate the platform on which the model was initially developed and tested To this end code testing and documentation of test results by developers using more than one platform if available are highly desirable 6 The developer should provide all input data for the test case so that interested users may attempt to run the code and reproduce the results on their own platforms 7 Itis recommended that benchmark results from the testing be provided for at least one 5 day simulation Shorter simulations do not provide adequate results from which to discern model trends beyond the spin up period 8 When making incremental changes to model science the developer should provide documentation of the results including a the results for all variables that show a deviation of greater than 1 0e10 ppm for the gas phase species or 1 0e10 ug m for the particulate species from the base model results for the same case b an analysis of what was done to understand these differences and c conclusions of the analysis 9 Note that more tha
133. ding framework Model developers can also perform sensitivity analyses on newly developed modules and perform comparisons with existing systems This chapter describes features of the modeling system that create its adaptability and flexibility Section 2 1 Sections 2 2 and 2 3 then provide brief descriptions of the key air quality modeling science features in various components of the CMAQ system including MCIP ICON BCON JPROC CHEMMECH PROCAN and CCTM More detailed discussions on these features can be found in Byun and Ching 1999 and Byun and Schere 2006 Finally Section 2 4 discusses the CMAQ user interface for building and running CMAQ June 2010 2 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 2 1 Features Implemented to Achieve the Goals of CMAQ As noted previously early air quality model development resulted in separate air quality models that addressed single pollutants or issues such as ozone or acid deposition These models had little or no flexibility to be updated with advances in science or to accommodate new regulations CMAQ was therefore designed to have more adaptability and flexibility for different applications and for changing or improving the modeling methodology Within the context of the model s science the following subsections discuss CMAQ s design in terms of 1 accommodating multiple pollutants and multiple scales 2 providing flexibility through modularity and 3 reduci
134. directory gt lib In the scripts cctm subdirectory modify a file called bldit cctm as follows uncomment the line set MakeOpt by removing the leading character Execute the bldit cctm script This creates a Makefile as well as a configuration file in the subdirectory scripts cctm BLD_e3a where the model code has been copied The Makefile can be modified to compile and link the new module by specifying lt full path name gt o for the object file that needs to be linked in It is essential that a source file with the corresponding name with extension F reside in the same directory as the specified path name for the object file Issue the make command to compile the source code into an executable gt make f Makefile June 2010 9 13 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 9 4 Guidelines to Writing Shell Scripts for CMAQ To run a model executable various UNIX environment variables must be set in the shell that invokes the execute command Generally these variables involve the modeling scenario start date and time the run duration the output time step interval various internal code flags that differ among the models and all the input and output logical symbolic file names There are various ways that external file names can be referenced in the source code and UNIX platforms can link them by using environment variables There are I O API utility functions that all
135. dule corresponds to the directory name in the SM3MODEL include release directory that contains the INCLUDE files for the tracer configuration to implement in CCTM The default setting is to not use tracers in CCTM PABase GlobInc Specifies the base directory location of the process analysis include files to use when compiling the CCTM 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 SM3MODEL include release directory 5 17 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 5 3 2 3 CCTM compilation First it is assumed that you have already installed and compiled the I O API netCDF and MPICH libraries see Section 3 2 3 or that these are already available from a previous CMAQ 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 summarized below to compile new versions of CCTM If you have not already done so compile M3BLD the CMAQ source code and compilation management program This needs to be done only once the first time CMAQ is installed If needed configure the CCTM build script to use the available I O API netCDF and MPICH libraries If you have not already done so compile the STENEX and PARIO libraries Configure t
136. e release this methodology will also be applied to ammonia fluxes to the surface Further discussion is available in the CMAQV4 7 release notes The release notes also contain more information about all of the other scientific improvements to the representation of PM that are included in v4 7 Another type of output available from CMAQ is the reduction in visual range caused by the presence of PM perceived as haze CCTM integrates Mie scattering a generalized particulate light scattering mechanism that follows from the laws of electromagnetism applied to particulate matter over the entire range of particle sizes to obtain a single visibility value for each model June 2010 2 14 http www cmaq model org CMAOv4 7 1 Operational Guidance Document grid cell at each time step More detailed descriptions of the PM calculation techniques used in CCTM can be found in Binkowski and Shankar 1995 Binkowski and Roselle 2003 and Byun and Schere 2006 For easier comparison of CMAQ s output PM values with measurements there are 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 microns in aerodynamic diameter Jiang et al 2006 In the near future two PM diagnostic tools will be available in an update to CMAQv4 7 one for tracking the sulfate budget and one for tracking the sources of elemental and primary
137. e 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 Species can be removed from the WDEP EXT files to adjust the number of species that undergo the wet deposition process These extra species are written to the WETDEP2 output file 6 3 3 SSEMIS Sea salt emissions diagnostic file This optional 2 D CCTM hourly output file contains calculated sea salt emissions The SSEMIS file will be produced by CCTM only if the AEROS aerosol mechanism is being used and if the CTM_SSEMDIAG variable is turned on 6 3 4 B3GTS_S Biogenic emissions diagnostic file This optional 2 D CCTM hourly output file contains calculated biogenic emissions in mass units The B3GTS _S file will be produced only if in line biogenic emissions are being calculated by CCTM and if the B3GTS_ DIAG variable is turned on 6 3 5 RJ In line photolysis output gridded photolysis rates The photolysis diagnostic output files RJ contain the photolysis rates calculated by CCTM when the in line photolysis option is used 6 3 6 PA Process analysis output integrated process rate file The 3 D CCTM integrated process rate file PA contains hourly concentrations of selected model output species in terms of the model process that contributed to the concentration in each grid cell at each hour For each
138. e 2 D CCTM integral average concentration file ACONC contains 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 that are used to calculate the integral average concentration are also set in the CCTM run script using the variable ACONC_BLEV_ELEV where BLEV corresponds to the bottom layer number and ELEV corresponds to the top layer number An example setting for the ACONC_BLEV_ELEV variable is 1 6 which defines layers 1 through 6 as the vertical extent over which to calculate hourly average concentrations 6 2 5 DRYDEP CCTM hourly cumulative dry deposition file The 2 D CCTM dry deposition file DRY DEP includes cumulative hourly dry deposition fluxes kg hectare for selected model species CCTM 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 Species can be removed from the 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 6 WETDEP CCTM hourly cumulative wet deposition file The 2 D CCTM wet deposition file WETD
139. e Climate Data Analyses Tools CDAT framework The ioapiTools module provides functions for extracting and manipulating data individual variables and writing to either an I O API file or a climate and forecast compliant CF netCDF file with I O API metadata The ioapiTools module is a contributed package to CDAT and is built on top of the Climate Data Management System cdms module The key object in ioapiTools iovar is a daughter of the cdms transient variable In other words an iovar object has all the capabilities of a cdms variable plus some extra methods and attributes So one can use the methods and attributes that the user may already be familiar with from cdms variables as well as the new methods and attributes The user needs to install py oapi a low level python interface to the I O API library as well as ioapiTools the high level python module that integrates I O API data into cdms After installing CDAT and the ioapiTools the user should use a python interpreter python idle ipython etc when using the various packages 10 8 Integrated Data Viewer IDV June 2010 10 8 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Main website http www unidata ucar edu software idv Download http www unidata ucar edu software idv docs userguide Starting html Latest User s Manual http www unidata ucar edu software idv docs userguide Training Workshop __ http www unidata uca
140. e also used to generate emissions for CMAQ June 2010 7 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 7 2 Horizontal Grids The extent of the horizontal grid used in CMAQ is limited by the size of the domain of the input meteorology MCIP CCTM and the I O API utilities are all capable of windowing subsets of meteorology data Choosing the appropriate horizontal grid scale and extent for the CCTM simulation is largely dependent on the issues to be addressed through the modeling However practical consideration should also be paid to the relationship between grid size output file size and execution times Prior to CMAQ version 4 3 Fortran 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 the GRIDDESC file Section 6 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 environment variables to point to an existi
141. e conservation of total water mass and energy conservation for cloud top mixing commensurate with the temperature profile e Outputs meteorological and geophysical files in the netCDF format for input to SMOKE and CMAQ 2 2 2 ICON and BCON The initial and boundary conditions processors To perform air quality simulations both initial and boundary conditions are required Initial conditions calculated in ICON are needed to provide concentrations of individual chemical species for the first time step throughout the modeling domain Boundary conditions calculated in BCON are needed to provide concentrations of individual chemical species at the lateral boundaries of the modeling domain In a single run of each processor ICON and BCON can generate these concentrations for all the chemical species required by CMAQ These processors require two inputs Figure 2 4 a concentration file for the chemical species to be simulated and the chemical mechanism June 2010 2 6 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Concentration file The concentration file used in ICON and BCON can come from one of two sources e A time independent set of vertical concentration profiles that are dependent upon the chemical mechanism being used This approach is usually taken when no other information about the initial and boundary concentrations is available The current default profiles available in CMAQ are in RADM2 speciation The
142. e first step in the compilation of CMAQ is to compile M3BLD Then compile the program libraries STENEX and PARIO before moving on to compiling 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 have to be changed to reflect the correct locations on your system The scripts for compiling all of the CMAQ programs with the exception of M3BLD contain compiler flags for both the Portland Group and Intel Fortran compilers In addition to pointing these scripts to the correct location of the compiler on your system you must also uncomment remove at the beginning of the line the compiler flag setting for the Fortran compiler that you will use to create CMAQ executables CMAQ may be run in singale processor serial or in parallel on multiple processors For parallel compilations some of the programs also require directory paths to MPICH INCLUDE files Program specific compilation instructions are provided below These compilation instructions are for building executables for simulating the benchmark data sets distributed with CMAQ Other than the paths to the compilers and libraries and the compilation flags the build scripts used in this section will not need to be changed to create executables Additional information about the configuration options for the various CMAQ programs is provided in Chapters 2 and 5 1 Use the following commands to compile M3B
143. e formats ent software netcdf index html 1 O API Input Output Application Programming http www baronams com prod Interface for controlling internal and external ucts ioapi communications CVS Concurrent Versions System for managing http ximbiot com cvs cvshom the distributed archive of the CMAQ source e code June 2010 3 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Table 3 2 Optional support software for CMAQ Software Description Source VERDI Visualization Environment for Rich Data Interpretation for graphical analysis of http www verdi tool org netCDF gridded data PAVE Package for Analysis and Visualization of Environmental data for graphical analysis of http www cmascenter org netCDF gridded data IDV Integrated Data Viewer for 3 D graphical http www unidata ucar edu so analysis of netCDF gridded data ftware idv I O API Tools Postprocessing tools for manipulating data in http www baronams com prod the I O API netCDF format ucts ioapi netCDF Tools Postprocessing tools for manipulating data in http my unidata ucar edu cont the netCDF format ent software netcdf index html PGDBG Portland Group Fortran 90 debugger http www pgroup com PGPROF Portland Group Fortran 90 code profiler http www pgroup com 3 2 Installing CMAQ Source Code After installing CVS the I O API and netCDF libraries and Fortran and C compilers on the hardw
144. e if CVS has the task of keeping track of the version history of a project with only local developers The server software normally runs on UNIX and Linux Several developers may work on the same project concurrently each one editing files within their own working copy of the project and sending or checking in their modifications to the server To avoid the possibility of people stepping on each other s toes the server will only accept changes made to the most recent version of a file Developers are therefore expected to keep their working copy up to date by incorporating other people s changes on a regular basis This task is mostly handled automatically by the CVS client requiring manual intervention only when a conflict arises between a checked in modification and the yet unchecked local version of a file Thus CVS adds power and features that are attractive for the CMAQ system 9 1 3 The CVS repository The CVS repository structure i e the UNIX directory hierarchy follows the class module organization discussed in Young 1999 The repository is actually divided into many reposi tories one for each generic model This division makes it easier to maintain the class module organization that is important for the model building operation described in Chapter 8 CVS allows for the use of a modules file which enables a user to easily check out or extract a complete CMAQ module For example a user might check out a modu
145. e interest Another CMAQ feature that supports quality control is process analysis which as noted earlier is a technique used to trace the source s of a chemical species within a simulation Process analysis is discussed in Section 2 2 5 2 2 CMAQ Input Processors CCTM uses data from other models and CMAQ input processing programs as input for model simulations Figure 2 2 Emissions Processing System ion l Case Grid Domain and Size Projection Vertical Structure Chemical Mechanism Figure 2 2 CMAQ Chemistry Transport Model CCTM and input processors The input data for CCTM are developed using the four input processors shown in grey in Figure 2 2 All of the CMAQ programs shown in Figure 2 2 bordered by the broken line require five basic configuration options e Case a unique character string that identifies the simulation e Grid Domain and size a definition of the horizontal modeling grid that includes the location relative to a fixed map projection and the size of the domain June 2010 2 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document e Projection defines a horizontal plane on the spherical surface of the earth used to specify the general location of the modeling grid on the globe e Vertical Structure a definition of the layer boundaries for the vertical grid e Chemical Mechanism the name of the photochemical mechanism ae
146. e is shown below LAM 40N100W 2 30 0 60 0 100 0 100 0 40 0 M 32_99TUTO2 LAM 40N100W 544000 0 992000 0 32000 0 32000 0 38 38 1 The horizontal coordinate section first section in this example GRIDDESC file defines a horizontal coordinate named LAM_40N100W The coordinate definition is for a Lambert conformal grid keyed by the first column of the coordinate description line which corresponds to the numeric code for the various I O API supported grid types 2 Lambert The next three parameters P_ALP P_BET and P_GAM have different definitions for different map projections For Lambert conformal P_ALP and P_BET are the true latitudes of the projection cone 30 N and 60 N in the example and P_ GAM 100 W in the example is the central meridian of the projection The last two parameters XCENT and YCENT are the latitude longitude coordinates of the grid center of the Cartesian coordinate system which are 100 W and 40 N in the example If using WRF ARW as the meteorological model the user should be aware of differences from this method The example grid definition section above describes a grid named M_ 32 99TUTO02 The definition of the grid begins with a reference 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 XORIG and YORIG are the eas
147. e used to reduce the number of vertical layers by collapsing layers this is not recommended as dynamical inconsistencies can develop and lead to misleading results This is particularly true when cloud processes are important 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 7 4 Chemical Mechanism The CMAQ modeling system accounts for chemistry in three phases a gas phase aerosols solid or liquid and an aqueous phase The CMAQ modeling system s existing modules for gas phase chemistry are the 2005 update to the Carbon Bond mechanism CB05 and the Statewide Air Pollution Research Center 99 SAPRC 99 gas phase mechanism Several variations of the base gas phase mechanisms with and without chlorine mercury and toxic species chemistry are distributed with CMAQ The modularity of CMAQ makes it possible to create or modify the gas phase chemical mechanism This procedure is described in Sections 5 4 and 7 4 2 Gas phase chemical mechanisms are defined in CMAQ as a series of Fortran INCLUDE files Located in subdirectories of the SM3MODEL include release directory each correspond ing to a mechanism name these INCLUDE files define the species source reaction par
148. ea level pressure and a pressure at the top boundary e g 100 hecto Pascals The sigma coordinate is terrain following Because MM5 and WRF ARW are nonhydrostatic models the vertical coordinate is time varying 7 3 1 Vertical layer resolution Resolving the surface boundary layer requires high resolution near the surface for meteorological simulations To determine mass exchange between the boundary layer and free troposphere June 2010 7 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document good resolution near the boundary layer top is preferable In addition different cloud parameter izations 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 surface based emission effects is determined by the thickness of the lowest model layer for CCTM For consistency CCTM should use the same vertical resolution as the meteorological model used to prepare the input data 7 3 2 Further information on vertical layers e CMAQ redefines the vertical coordinates to monotonically increase with height a capability necessary to handle a generalized coordinate system e Although MCIP may b
149. ecutable The requirement to recompile CMAQ with each science configuration change is offset by the flexibility to add new science to the model or simply to switch between different model configurations This point about modularity is most pertinent to CCTM although there are configuration options that must be selected when compiling the other CMAQ programs as well In addition to compile time configuration options with CMAQ there are also execution time configuration options options that are chosen when the model is run versus when it is compiled The horizontal domain configuration and the vertical coordinate system 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 map projections or grid definitions without having to recompile the source code into a new executable Discussions concerning which CMAQ options must be selected at compilation versus at execution are part of Chapter 5 1 2 3 Chemistry transport model conceptual formulation As the chemistry transport model CTM component of CMAQ CCTM is the final program to be run in the CMAQ modeling sequence There are four other main programs that prepare input data for CCTM i e ICON BCON JPROC and MCIP 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 und
150. ed either with dummy data or with data read in from a set of user supplied files e m3merge Merges selected variables from a set of input files for a specified time period and writes them to a single output file with optional variable renaming in the process e m 3pair Builds an ASCII file of paired values for two variables from two files within a user selected window into the grid according to user specifications e m 3stat Computes statistics for variables in a file e m3tproc Computes time period aggregates e g 08 00 16 00 gridded daily maxima and writes them to an output file Can be used to create running averages e g 8 h O3 data from 1 h O3 daily averages daily maxima etc e m3tshift Copies time shifts data from a file e m3wndw Windows data from a gridded file to a subgrid see bewndw earlier in this list for extracting to the boundary of the subgrid window e m3xtract Extracts a subset of variables from a file for lt time interval gt Can also be used to concatenate data from two or more files with different time periods into one file e m4filter Converts first edition Models 3 files to current version e mtxblend Uses a sparse matrix file to interpolate transform data from an input file to the grid of a base file and to merge it with data from the base file e mtxbuild Builds a sparse matrix transform file from user supplied ASCII coefficient inputs e mtxcalc Builds a grid to grid sparse matrix transform file us
151. eeds input information including meteorological and emissions data Using this information CCTM simulates each of the atmospheric 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 described 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 chemical transformation of atmospheric pollutants In CMAQv4 7 gas phase chemistry can be simulated with the CB05 or SAPRC 99 photochemical mechanisms Because of CCTM s modularity advanced users can modify the existing photochemical mechanisms or even add new ones To compute time varying species concentrations and their rate of formation or depletion differential equations governing chemical reaction kinetics and species conservation need to be solved for June 2010 2 10 http www cmaq model org CMAQv4 7 1 Operational Guidance Document the entire species set CCTM uses special techniques called numerical chemistry solvers to compute these concentrations and rates at each time step Regarding these solvers various solution algorithms for the chemical kinetics have been investigated in
152. eiels ateriapedd metakadeens 6 26 6 1 19 GSPRO Speciation promles cic on 5ve cesta g apeteateraus ecetaaa ee aeeeds 6 26 6 1 20 B3GRD Gridded normalized biogenic emissions cecceeseeesteeeteeees 6 27 6 1 21 BIOSEASON Freeze date Sheers astinan otaran istara ota ense nin 6 27 6 1 22 STK GRPS_ Stack groups 3 008 ea eeo en ak 6 27 6 1 23 STK EMIS Point source emissions cccceesceesteceteceeeeeeeeeeseesseenes 6 27 6 1 24 GRID CRO 2D Two dimensional grid cross point fields 0 eee 6 28 6 1 25 GRID DOT 2D Two dimensional grid dot point fields eee 6 28 6 1 26 MET BDY 3D Three dimensional meteorological boundary input 6 28 6 1 27 MET CRO _ 2D Two dimensional meteorological cross point fields 6 29 6 1 28 MET CRO 3D Three dimensional meteorological cross point fields 6 30 6 1 29 MET DOT_3D Three dimensional meteorological dot point fields 6 30 6 2 Basic CCTM Output Files eenn rae ila dat ie r tk Seb Joie Salta neta I fe Sc casual ag 6 31 6 2 CMAQ output NOG eei Sees cee a a E a Ba oe Steel RE s 6 31 6 2 2 CONC CCTM hourly instantaneous concentration file eee eeeeeeeeee 6 31 62 3 CGRID CCTM restart file isc cccsssdsccceacheiecsnteivesssevsctvessyinwssontecanebseveuesstvaateoiss 6 32 6 2 4 ACONC CCTM hourly average concentration file cee eeceeseeeteeees 6 32 6 2 5 DRYDEP CCTM hourly cumulative dry deposition file eee 6 32 6 2 6 WETDEP CCTM hourly cumulative we
153. eless 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 PA_CMN EXT PA_CTL EXT PA_DAT EXT PROCAN Shows Input Output d A Figure 5 8 PROCAN input and output files 5 9 2 1 PROCAN input files Table 5 13 PROCAN input files File Name Format Description PACP_INFILE ASCII PROCAN command file specifies configuration options for the program 5 9 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 CHEMMECH In general white spaces are ignored and line wrap is allowed 1 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 June 2010 5 48 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Special rules for naming species entering labels and specifying numerical values such as stoichiometric coefficients and rate constant parameters are also used Each major component of the command file
154. em A set of computational models that mathematically represents a simplified version of real world phenomena along with the necessary mechanisms for managing the processing the data produced by it and the analysis and visualization tools necessary for making related decisions For example this could be the creation and behavior of environmental pollutants as a function of weather and chemical interactions Researchers use these scaled down versions of the world to perform experiments that would be too dangerous too costly or simply impossible in the real world DRAFT January 2009 A 2 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Eulerian Fluid motion specification where one concentrates on what happens at a spatial point x so that independent variables are taken as a function of time at that point Evasion Loss of material from the land surface e g the upward flux of mercury from the land surface Exploratory models Test bed models for developing scientific algorithms that are not thoroughly reviewed and evaluated See also operational models and screening models Fortran Formula translator computer programming language Framework A system of mechanisms to manage the scheduling and execution of computational models the data produced by them the analysis and visualization tools necessary for understanding their results for decision making and the interfaces to all these capabil
155. emical models that describe atmospheric processes which are important to trace gas and particulate matter distributions in the atmosphere These systems typically include meteorological models emissions models chemistry transport models and the analysis and visualization tools necessary for supporting decisions related to air quality Aitken mode Aerosol particles with diameters nominally between 0 01 and 0 1 micrometers um Such particles are formed in the atmosphere by nucleation of gas phase precursors or by direct emissions from sources The most common source is combustion e g diesel soot Arakawa B Horizontal grid staggering system described by Arakawa and Lamb 1977 and used by MMS Mass variables and momentum variables are defined on separate horizontal grids of spacing equal to Delta x The two grids are offset by 0 5 x Delta x in the north south and east west directions Arakawa C Horizontal grid staggering system described by Arakawa and Lamb 1977 and used by WRF ARW and CCTM Mass variables and each horizontal component of the momentum are defined using separate horizontal grids of spacing equal to Delta x ArcInfo A high end geographical information system GIS with capabilities for the automation modification management analysis and display of geographical information Automatic quality control QC QC correction that is accomplished automatically without user intervention Bookmark In on line help a book
156. ent state code is risky June 2010 9 1 http www cmaq model org CMAOQv4 7 1 Operational Guidance Document 4 As the user continues to work with the codes he she may make enhancements or discover and fix errors The upgrades are then installed in the repository which automatically assigns unique revision identifiers 5 The repository is located where it is conveniently accessible to all users and is maintained by an administrator who sets and enforces general access rules 9 1 2 CVS explained There are many configuration management tools both free and commercially available We chose The Concurrent Versions System CVS mainly because of its versatility CVS controls the concurrent editing of sources by several users working on releases built from a hierarchical set of directories CVS uses the Revision Control System RCS as the base system Other reasons that CVS was an attractive choice include the following e It works on virtually all UNIX and Linux platforms and on many PCs e It is publicly available and free The CVS wiki states that CVS uses a client server architecture a server stores the current version s of a project and its history and clients connect to the server in order to check out a complete copy of the project work on this copy and then later check in their changes Typically the client and server connect over a LAN or over the Internet but client and server may both run on the same machin
157. er 1 NH emissions e Bug fix to calculate soil NO pulse emissions in BEIS e Remove excessive logging of cases where ambient air temperatures exceed 315 0 K Multi pollutant Model Updates e Bug fix to facilitate in line emissions option e Mercury Advection Dicarboxylic acid reduction mechanism applied to aqueous phase oxidized mercury specie e Added divergence based constraints on advection timestep e Vertical advection now represented with PPM to limit numerical diffusion Cl oxidation pathway based on Donohoue et al 2005 J Phys Chem A 109 34 Lowered CB05 mechanism unit yields for acrolein from 1 3 butadiene tracer reactions to be consistent with laboratory measurements Horizontal Diffusion Photolysis e Error correction T Odman Ga Tech Concentration data may not be correctly initialized if multiple sub cycle timesteps are required Fix to initialize concentrations with values calculated in the previous sub timestep e JPROC phot_table and phot_sat options Expanded lookup tables to facilitate applications across the globe and vertical extent to 20km Updated temperature adjustments for absorption cross sections and quantum yields Revised algorithm that processes TOMS datasets for Model Timestep Determination OMI data format e Error correction T Odman Ga Tech The sum of the advection steps for a given layer might not equal the output timestep duration
158. erstanding the purposes of the various programs and their relationships to each other and to the overall system Eulerian CTMs use coupled ordinary differential equations ODEs to predict changes in pollutant concentrations throughout a three dimensional grid that is fixed in space The following processes affect changes in the predicted concentrations in each grid cell e Emissions from sources e Horizontal and vertical advection e Horizontal and vertical diffusion June 2010 1 5 http www cmaq model org CMAOv4 7 1 Operational Guidance Document e Chemical transformations e Loss processes deposition Mathematically these processes relate to the concentration change in each grid cell over time 0C ct through the continuity equation which is presented in simplified form below OC ot Adv Diff Re Ee Se where 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 CCTM The Eulerian representation of the area to be modeled is a series of contiguous grid cells that form a limited area modeling domain on a subset of the globe A limited area domain requires that boundary conditions be established to account f
159. es 5 ce artets sais eesoacdsaedegadnwiands ena muriredaastatinnantdnss 5 11 Figure 5 4 CHEMMECH input and output files cee cccecsseceseeceeceeeeeeeeeeseecaeceeeseeeensaees 5 26 Figure 5 5 ICON input and output files cece ccccceseceseceeeeeeseecaeceeeneeeesseecsaecnseeneeeeeaeeesaeens 5 31 Figure 5 6 JPROC input and output Miles icsecia y cae io ase sdateaiy dedicate Geena 5 37 Figure 5 7 MCIP input and output files jcsiciscsss ceed catecgs chavieigiededs vivaplatduasdecrsvinteoaemteass 5 41 Figure 5 8 PROCAN input and output files fi cesceisasecpandiacdsaasdriseadvactatauinsationsedalieatedies 5 48 Figure 6 1 Illustration of CMAQ boundary condition file s sessesessseseesessesessssessersesseseesessese 6 20 Figure 6 2 Graphical example of a CMAQ gridded boundary conditions file eee 6 21 Figure 6 3 Graphical example of a CMAQ gridded initial conditions file eee eeeeeeeeee 6 22 Figure 7 1 CMAQ tutorial rid si icccscsclees ocagcats ccgcansdpaasedsventetvatuaatacea sates ea testec ta erecna ge rietedeatelasteaves 7 2 Figure 8 1 36 km four day modeling period IC BC schematic ceceeceseeeseeeeceeeceeenseeaeeeneees 8 5 Figure 8 2 12 km nested two day modeling period IC BC schematic cccccesseeeteeeteeeeees 8 6 June 2010 x http www cmaq model org CMAQv4 7 1 Operational Guidance Document Tables Table 1 1 CMAQVA n1 Update secsve cic toh cette ieee clit esentutl Jadoo actin 1 12 Tabl e 1 2 CMAQv4 7 Upda
160. etween different computer architectures In addition to model data output CMAQ can optionally produce log files that contain the standard output from the various 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 UNIXsyntax 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 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 gt amp bcon_ela log For 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 UNIXredirect command gt as shown in the example above 6 2 2 CONC CCTM hourly instantaneous concentration file The 3 D CCTM hourly concentration file CONC is the most commonly referenced CCTM output file Containing gas phase species mixing ratios ppmV and aerosol species concentra tions ug m CONC files include instantaneous model species concentrations at the end of each model hour The number and types of specie
161. ew species will also enter the domain as initial and boundary conditions check the GC_ICBC EXT file for the presence of these species June 2010 7 6 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 8 DEVELOPING NEW CMAQ SIMULATIONS Second generation air quality modeling systems such as the Regional Oxidant Model were composed of a single air quality model and the associated input data processors Changes in the extent of the modeling domain its horizontal resolution the chemistry mechanism etc required extensive coding changes in the air quality model and several associated input processors Each executable program was then compiled and tested to ensure that errors were not introduced during the code modifications Users had no control over the extent of the model domain and no flexibility to use an alternate chemistry mechanism from an existing model The design of the CMAQ modeling system overcomes the inflexibility of second generation systems through the M3BLD model builder program which builds models and processors according to user specifications For application users of CMAQ M3BLD is used only at the beginning of a simulation to compile executables for a specific science configuration Since the horizontal grid and vertical layer structure are defined dynamically at execution of the model there is no need to recompile the programs when changing these parameters Compilation is required only when either deve
162. figuration options in CCTM such as the chemical mechanism to be used 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 configura tion and the 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 June 2010 5 9 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Optional output files are created when their associated processes are invoked in CCTM For example when CCTM is compiled with process analysis turned on additional output files are created Starting in version 4 7 the CCTM includes options for the in line processing of emissions and photolysis rates In line refers to the handling of processes that had previously been accomplished outside of the CCTM such as emissions processing with SMOKE with algorithms internal to the CCTM The benefits of in line emissions processing include the integration of higher time resolution meteorology in the computation of biogenic emissions and plume rise from point sources and the avoidance of the large data storage burden required for emissions data The benefit of in line photolysis rate calculations is the inclusion of predicted gas and aerosol concentrations in the rate calculations Both in line emissions and photolysis are invoked throu
163. file speciated for a particular gas phase chemical mechanism output from JPROC 5 3 2 2 CCTM compilation options The configuration options listed here are set during compilation of the CCTM executable When these options are invoked they create a binary executable that is fixed to the specified configuration To change these options you must recompile CCTM 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 O O O0OO0O0O0OO0OO e MakeOpt June 2010 compile _all force compile even if all the object files are current clean_up remove all source files upon successful compilation no_compile do everything except compile no_link do everything except link one_step compile and link in one step parse_only check configuration file syntax show_only show requested commands but does not execute them verbose show requested commands as they are executed 5 12 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 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 availability of a parallel STENEX library file a PARIO library file and the MPI library INCLUDE files ModDriver default ctm_yamo The CCTM generalized coordinate driver module o ctm use a
164. files including the directory path for each file without modifying MCIP up to 300 meteorological model output files are 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 recalculate those values within MCIP o 1 use PBL values from the input meteorology o 2 recalculate PBL values within MCIP using PBL similarity o 3 recalculate 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 those fields within MCIP o 1 use radiation fields from the input meteorology o 2 recalculate radiation fields using the MCIP version 1 algorithm 5 43 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 LDDEP default 1 Sets the dry deposition routine The setting of this variable determines which dry deposition routine is used for calculating deposition velocities 1 use the RADM Wesely dry deposition routine Wesely 1989 2 use
165. focused on a single pollutant or issue e g ozone acid deposition It became apparent however that single pollutant models were not sufficient Depending 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 region on various 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 made an integrated modeling approach that could address multiple pollutants even more essential Third generation models were needed that could treat multiple pollutants simultaneously and at scales up to continental or larger The EPA Community Multiscale Air Quality CMAQ modeling system is a third generation air quality model It is available online at http www cmaq model org CMAQ is designed for applications ranging from regulatory and policy analysis to understanding the complex interactions of atmospheric chemistry and physics It is a three dimensio
166. for exporting the source code and to the Fortran 90 compiler for building binary executables Because M3BLD is required to create all of the CMAQ executables except MCIP which has its own makefile procedure 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 to generate a June 2010 1 6 http www cmaq model org CMAOv4 7 1 Operational Guidance Document UNIX makefile These are particularly useful for porting the CMAQ code to new operating systems testing new code in a development environment or troubleshooting problems with CMAQ compilation or execution Photolysis Rate Processor JPROC JPROC calculates chemical mechanism specific clear sky photolysis rates at fixed altitudes solar 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 use in the modeling Output from JPROC is an ASCII look up table of photolysis rates that 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 domai
167. from a file for a particular date and time 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 JNTERP3 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 XTRACT3 you can use the magic values ALLVAR3 ALL as defined in PARMS3 EXT or ALLAYS3 1 as also defined 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 1 5 Writing Data Files in I O 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 F
168. g CMAQv4 7 1 Operational Guidance Document 3 CMAQ SYSTEM REQUIREMENTS AND INSTALLATION 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 obtaining the CMAQ source code and installing it on your system Brief instructions for running the CMAQ benchmarkcase 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 CMAQ is distributed with a reference dataset that can be used to benchmark the CMAQ installation in the distribution output data from CMAQ are bundled with the input data including emissions and meteorology that can be used to reproduce the reference results After benchmarking has been successfully completed the CMAQ system can be configured for other simulations The same steps that are required to build the model for the benchmark case apply to building it for new simulations Configuring CMAQ for new applications is covered in Chapter 7 3 1 System Recommendations All of the CMAQ programs are written in Fortran except for M3BLD written in C and are optimized for use on computers running a version of the Linux operating system OS
169. gh compile time configuration options for the CCTM When the CCTM is instrumented for in line emissions calculations a series of additional input files and environment variables are required at execution The details of these additional inputs are provided below In line photolysis does not require any additional inputs as the CCTM includes all of the photolysis rate data internal to the in line instrumented version of the model 5 3 2 Files configuration and environment variables Figure 5 3 shows the input and output files and configuration options for CCTM A distinction is made between the options that are invoked at compilation time versus those invoked at execution of the program When compiling CCTM the user specifies a chemical mechanism to configure the gas phase chemistry and aerosol mechanism used for the air quality calculations Setting the Mechanism variable in the CCTM compile script configures the program to use a specific set of mechanism INCLUDE files to build an executable All of the science processes simulated by the CCTM must also be selected during the compilation step for the CCTM Separate CCTM executables must be prepared for different mechanism and science configurations During the execution step or when the CCTM is run the user sets the horizontal and vertical grid definitions and the input files used for the simulation Different spatial domains vertical grid structures and input files can be used with a single CCTM exe
170. gram 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 locations and flags in the make reader script 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 SBASE Executable directory path e Mpath default mech Directory path to the MECH DFEF file e Opath default exts Output file directory path e APPL Simulation identifier e EXEC default CHEMMECH Executable name e MCFL default mech def saprc99 June 2010 5 28 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Mechanism definition file name EXSPCS default SOpath SPECIES ext Output file name when CHEMMECH is run in SP mode EXRXI Ds default SOpath RXDT EXT Name of output mechanism data INCLUDE file EXRXCM default SOpath RXCM EXT Name of output mechanism common INCLUDE file 5 4 2 5 CHEMMECH output files Table 5 6 CHEMMECH output files File Name Format Description RXCM EXT ASCII Mechanism c
171. grams are transportable to different machine architectures Those considerations are automatically managed by the Models 3 framework for those who use conforming datasets and conforming programs Nonhydrostatic Used to indicate that the model does not assume that the atmosphere is in hydrostatic equilibrium Air is not assumed to have only horizontal motion relative to the earth Open source software Open source software began as a marketing campaign for free software OSS can be defined as computer software for which the human readable source code is made available under a copyright license or arrangement such as the public domain that meets the open source definition This permits users to use change and improve the software and to redistribute it in modified or unmodified form It is very often developed in a public collabor ative manner Open source software is the most prominent example of open source development and often compared to user generated content DRAFT January 2009 A 6 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Operational models These models offer fully functional modeling of relevant science processes such as atmospheric emissions and chemical transport processes They represent the current state of the art that has undergone significant quality assurance review peer review and evaluation The turnaround time for these models is generally much longer than for screening models but sh
172. hase chemical mechanisms are implemented in CMAQ using Fortran INCLUDE files These files are in a machine readable ASCII format and include all of the mechanism parameters required including gas phase species reaction stoichiometry and kinetics information To invoke chemical mechanisms in CMAQ these files are included in the compilation of the various 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 RXDT EXT RXCM EXT and SPC EXT that define the chemistry parameters for the CMAQ programs The file mech def is an ASCII file that is easy to understand and modify Figure 2 6 shows the relationship between CHEMMECH and other parts of the CMAQ modeling system CMAQ Programs CCTM ICON BCON JPROC Figure 2 6 Invoking new modified gas phase chemical mechanisms in CMAQ 2 2 5 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 output from a CTM simulation The CMAQ CTM and other Eulerian grid models 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 these results
173. hat addresses multiple air quality issues such as regional and urban scale oxidant and acid deposition Module A subset that is part of a larger program such as a meteorological model an emissions model or CMAQ In a modular program all modules of a particular type e g those that compute dry deposition are interchangeable allowing you to replace one module with another to determine for example how each module affects modeling results Examples of modules include science modules and analysis and visualization modules Monotonic A quality of strictly increasing or decreasing within some interval Multilevel nesting Multilevel nesting refers to employing nested grids within nested grids possibly several levels deep National Emissions Inventory A database at EPA containing the information about sources that emit criteria air pollutants and their precursors and hazardous air pollutants Nested grids Nesting refers to fitting a finer resolution grid over part of a coarser resolution grid The finer resolution grid receives information such as boundary conditions from the coarser grid simulation Nonconforming datasets Nonconforming datasets are ones that are not in I O API format They can be used in the Models 3 framework by programs that are specifically designed to read those datasets When nonconforming datasets and programs are used however you must know how to match programs and datasets and which data formats and pro
174. he CCTM build script for your application using the options discussed in Section 5 3 2 2 Invoke the build script to create an executable oldit cctm 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 June 2010 EXEC default CCTM_S APPL _SCFG Executable to use for the simulation NPCOL_NPROW default 1 1 Domain decomposition for parallel mode recommended configuration is for the number 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 5 18 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 Simulation start date in Julian format YYYYDDD 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 SBASE SAPPL 1log Uncomment to capture CCTM standard output to a log file the LOGFILE variable sets the name and location of the log OAPI_LOG_WRITE default F T F set to T to turn on excess WRITE3 logging by the I O API FL ERR_STOP default F T F Y N set to T or Y to configure the program to
175. he data records a sequence of data records and a terminal record with name field blank i e The GRIDDESC file is generated automatically with MCIP alternatively GRIDDESC can be created using a text editor The horizontal coordinate section Table 6 2 consists of text records that provide coordinate system name the map projection and descriptive parameters P_ ALP P_ BET P_GAM XCENT and YCENT The grid description section Table 6 3 consists of text records that indicate the grid name related coordinate system name i e which GRIDDESC horizontal coordinate name that is defined in the previous section that is applied to this grid and descriptive parameters XORIG YORIG XCELL YCELL NCOLS NROWS and NTHIK For a typical CMAQ application both dot point and cross point grids are defined in the GRIDDESC file these grids are topological duals in the sense that the vertices corners of one correspond to the cell centers of the other Table 6 2 Coordinate system description segment of GRIDDESC Line Column Name Type Description 1 A Header String Single quote delimited header describing section contents may be blank das6 7 3 2 A COORD NAME String Name of the coordinate description required single quote delimited 3 A COORDTYPE Int I O API index defining the map projection type required B P_ALP Double First map projection descriptive parameter dependent on projection type
176. he four lateral boundaries of the input meteorology grid The nonuniform 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 MCIP also provides the capability to reconfigure the vertical layer structure in the input meteorology through interpolation 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 effects on the predicted wind fields 5 7 2 Files configuration and environment variables Figure 5 6 shows the input and output files and configuration options for MCIP All MCIP configurations are accomplished at execution rather than at compile time and via Fortran June 2010 5 40 http www cmaq model org CMAQv4 7 1 Operational Guidance Document namelist variables a distinction from the rest of the CMAQ programs The user does not need to directly edit the MCIP namelist file All configuration settings are contained in the MCIP run script which automatically creates a new namelist file each time the script is executed Execution Options
177. he logical name for the ASCII data file containing absorption cross section and quantum yield data for O3 photolysis The data in this file are listed as a function of wavelength This file follows the same format as the CSQY files described in Section 6 1 6 6 1 12 InMetFiles List of MM5 or WRF ARW output files Used by MCIP MCIP can read MMS version 3 binary output files MMOUT and WRF ARW netCDF based files to generate I O API formatted netCDF files for input to CMAQ and emissions modeling For details about the format of the MMOUT files visit the MM5 homepage at http www mmm ucar edu mmS For information about the format of the WRF output files visit the WRF ARW homepage at http www mmm ucar edu wrf users 6 1 13 InTerFile MM5 terrain file Used by MCIP MMS output file containing fractional land use data This file is generated by the MM5 program TERRAIN 6 1 14 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 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 that start a new side of the domain i e south east north or west Figure 6 1 illustrates this input data structure and the relationship of the boundary data to the interior main grid data within CMAQ modules Each species be
178. he netCDF is used in CMAQ to define the format and data structure of the binary input and output files CMAQ input and output files are self describing netCDF format files in which the file headers have all the dimensioning and descriptive information needed to define the resident data Users should download the latest code for the netCDF from http www unidata ucar edu software netcdf Compilation and configuration information for the netCDF is available through the Unidata website 4 3 Message Passing Interface Library MPICH The Message Passing Interface MPI is a standard library specification for message passing or intra software communication on both massively parallel computing hardware and workstation clusters MPICH is a freely available portable implementation of MPI that is available from Argonne National Laboratoryn ANL MPICH is used in CMAQ to control how the CCTM is run on parallel computing systems MPICH can be configured to run the CCTM in parallel on either shared memory systems or on a workstation cluster Users should download the latest code for MPICH from http www mcs anl gov research projects mpi mpich1 Compilation and configuration information for MPICH is available through the ANL website 4 4 References Coats C 2005 The EDSS Models 3 I O API Available online at http www baronams com products ioapi Unidata 2009 NetCDF Available online at http www unidata ucar edu software netcdf June 2010
179. he temperature of the rising air equals the ambient temperature This process results from fast moving air in narrow updrafts and slower moving air in broader downdrafts Thus under convective conditions vertical diffusion is asymmetric In CMAQvV4 7 an in line method for treating biogenic and point source emissions uses ACM to vertically distribute these emissions during a CMAQ calculation Under non convective conditions when the surface is cooling vertical diffusion is represented by an eddy diffusivity approach 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 Chang et al 1987 1990 In CCTM the deposition process is simulated as a flux boundary condition that affects the concentration in the lowest vertical model 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 CMAQv4 7 has an improved version of the minimum allowable vertical eddy diffusivity scheme The new version interpolates between urban and nonurban land cover allowing a larger minimum vertical diffusivity value for grid cells that are primarily urban Horizontal diffusion in v4 7 is implemented with a single eddy diffusion algorithm that is based on local wind deformati
180. hese CMAQ inputs and describe how to configure these systems to produce input for CMAQ In brief the following chapters are included in this manual Chapter 2 provides an overview of the science used in CMAQ Chapter 3 describes computer system requirements and installation Chapter 4 discusses the Input Output Applications Programming Interface I O API Chapter 5 describes the set of CMAQ programs and libraries Chapter 6 describes CMAQ input and output files Chapter 7 discusses how to define modeling grids vertical layers and chemical mechanisms Chapter 8 describes how to set up CMAQ for new simulations Chapter 9 provides CMAQ code management and development guidelines Chapter 10 describes analysis options for CMAQ output Chapter 11 describes how to obtain support for CMAQ June 2010 1 11 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Table 1 1 CMA Qv4 7 1 Updates Aqueous Chemistry Emissions e Mass conservation improvements Imposed 1 second minimum timestep for the remainder of the cloud lifetime after 100 iterations in the solver Force mass balance for the last timestep in the cloud by limiting oxidized amount to the available mass Implemented steady state assumption for OH Only allow sulfur oxidation to control the aqueous chemistry solver timestep Previously the reactions of OH GLY MGLY and Hg also controlled the timestep e Bug fix in EMIS _DEFN F to include point source lay
181. ial and multiprocessor execution options allow the application user to optimize the performance of CMAQ on various computer platforms Community development expedites the expansion of CMAQ s capabilities through the pursuit of multiple research agendas by a variety of research groups Application users thus avoid the limitations inherent in having to rely on a single centralized development group A comprehensive training program is available through the Community Modeling and Analysis System CMAS Center http www cmascenter org The CMAS Center is a support resource for users of CMAQ and other modeling systems it is described in Section 11 1 Members of the large international community of users connected through the CMAS Center can help each other by sharing data and experiences and providing technical support Features of CMAQ for Air Quality Model Developers Designed under a community 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 a valuable flexible platform for testing new science algorithms chemistry representations and optimization techniques CMAQ provides the following features to scientists interested in developing new algorithms or adding science to the model Developed and distributed following open source software conventions CMAQ source code is easi
182. ibution of horizontal transport vertical transport chemistry and emissions to the predicted hourly concentration of ozone in a particular grid cell IRRs give the contributions of individual chemical reactions to the net effects of chemical reaction on species concentrations As an example IRR can be used to calculate the mass throughput for a particular reaction sequence in a photochemical mechanism for a particular grid cell and time period Because the amount of IPR and IRR data that can be June 2010 5 47 http www cmaq model org CMAQv4 7 1 Operational Guidance Document obtained may be large and the analysis of such data can be fairly complex the user is advised to read Chapter 16 in Byun and Ching 1999 before attempting to use this tool The discussion here focuses primarily on the procedures that must be followed to capture process analysis data rather than on what data should be captured and how they might be analyzed 5 9 2 Files configuration and environment variables The program PROCAN creates a set of three output INCLUDE files needed to instrument CCTM to produce process analysis output See Figure 5 7 This program reads and interprets instructions from a command file and then generates three Fortran INCLUDE files 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 Neverth
183. icating units is highly recommended in both subroutines and INCLUDE files to facilitate the correct implementation of any code modifications in the future This information is generally included in comments embedded in line with the declaration of each variable June 2010 9 6 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 9 2 6 Science process code template The following example from CMAQ v4 7 illustrates a science process class driver Fortran 90 subroutine Code developers should follow this template where appropriate to maximize the benefit from the design concepts implemented in CMAQ This template is generic and demonstrates many of the available features Some class drivers and most other subprograms within a module may not have nor require most or any of these features The numbers at the left hand margin refer to footnotes and are not part of the code and the text within lt gt indicates code removed from the example for brevity in this section Example of Science Process Class Driver SUBROUTINE VDIFF CGRID JDATE JTIME TSTEP CL G 1 C Function 1 C Preconditions 1 C Subroutines and Functions
184. if you configured a simulation to run on January 5 2007 Julian date 2007005 an obvious file name for a CMAQ version 4 7 CCTM concentration file would be CCTMv47 CONC Base07 2007005 ncf Additional identifying information such as the chemistry mechanism name versioning identifiers for the input meteorology and emissions and the operating system version i e Linux_x86_64 are also commonly added to CMAQ output file names Before starting a new CMAQ simulation the user needs to confirm the existence of the input files for all of the CMAQ programs and to check the names of the output files and directory locations A common error that occurs with all of the CMAQ programs is an execution failure caused by output files that already exist If a CMAQ program does not run successfully for this reason the incomplete or erroneous output files must be manually deleted or else the DISP variable should be invoked in the CMAQ run scripts Chapter 5 to dispose of the output files before attempting to rerun the program Alternatively if the names of the output files are not correctly configured an error will occur immediately when CMAQ is run Check the last few lines of the standard error from the CMAQ program to determine whether the problem was due to incorrect specifications of input output files 8 2 6 Science option configuration The CMAQ scripts as they are distributed use a default science option configuration While this default configuration is
185. igure 6 2 Graphical example of a CMAQ gridded boundary conditions file 6 1 15 INIT_CONC_1 Initial conditions Used by CCTM The initial concentrations of each species being modeled must be input to CMAQ The initial conditions input file type is GRDDED3 and does not vary with time The file data are looped in this manner by column by row by layer by variable Initial conditions files have the same structure as concentration files so the predicted concentrations from the last hour of day 1 can be used to initialize the following day s simulation This gives CMAQ users the flexibility to segment simulations in any way they choose Figure 6 3 is a graphical example of the CMAQ initial conditions file The file shows spatially varying data that can be used to initialize a following run beginning at the time shown i e June 25 1996 0 00 00 June 2010 6 21 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Layer 1 O3 Initial Conditions file CMAG44_nedenrs mp_saprc99_adj 1C 1996176 ncf 0 150 51 0 113 0 075 0 038 0 000 ppm June 25 1996 0 00 00 Min 0 022 at 5 21 Max 0 131 at 38 32 Figure 6 3 Graphical example of a CMAQ gridded initial conditions file 6 1 16 JTABLE Photolysis rates look up table Used by CCTM Each of the gas phase mechanisms in CMAQ CB05 and SAPRC 99 contains photolysis reactions that require clear sky reaction rates precomputed from kinetics data at various altitudes
186. ime invariant N a User B3GRD grid normalized biogenic GRDDED3 Time invariant Xx Y SMOKE emissions BIOSEASON freeze dates GRDDED3 Time invariant X Y Metscan STK_GRPS_ stack groups GRDDED3 Time invariant X Y SMOKE STK_EMIS_ point source GRDDED3 Hourly X Y SMOKE emissions GRID_CRO_2D 2 D grid cross point GRDDED3 Time invariant X Y MCIP fields GRID_DOT_2D 2 D grid dot point GRDDED3 Time invariant X 1 Y 1 MCIP fields MET BDY_ 3D 3 D meteorological BNDARY3 Hourly PERIM Z MCIP boundary input MET CRO 2D 2 D meteorological GRDDED3 Hourly X Y MCIP cross point fields MET CRO 3D 3 D meteorological GRDDED3 Hourly X Y Z MCIP cross point fields June 2010 6 2 http www cmaq model org CMAOv4 7 1 Operational Guidance Document MET DOT 3D 3 D meteorological GRDDED3 Hourly X 1 Y 1 Z MCIP dot point fields 6 1 1 GRIDDESC Horizontal domain definition Used by ICON BCON CCTM The CMAQ grid description file GRIDDESC is used by all programs except JPROC and MCIP to define the horizontal spatial grid of the modeling domain GRIDDESC is an I O API related ASCII file that contains two sections a horizontal coordinate section and grid description section GRIDDESC is the logical name for text files that store horizontal coordinate and grid descriptions and that are read by the DSCGRID Q and DSCOORD utility routines Each segment has a one line header which by convention provides titles for the columns in t
187. in Chapter 3 with further details in Chapter 5 The CMAS Center see Section 11 1 currently fully supports CMAQ on Linux systems using the Portland Group and Intel Fortran compilers The CMAS Center no longers supports compiling and running CMAQ on other UNIX operating systems In any event good computing practice suggests that the same Fortran compiler be used to compile all components of the CMAQ system including the netCDF and I O API libraries 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 June 2010 2 16 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Binkowski F S S Arunachalam Z Adelman and J Pinto Examining photolysis rates with a prototype on line photolysis module in CMAQ 2007 J Appl Meteor and Clim 46 1252 1256 doi 10 1175 JAM2531 1 Byun D W 1999 Dynamically consistent formulations in meteorological and air quality models for Multiscale atmospheric studies Part 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
188. 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 listed in the file header A detailed description of the JTABLE file format is provided in Table 6 12 The files are list formatted 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 Julian date field optional 2 A JVHT Int Number of vertical levels covered by the data required B Level Field String The word LEVELS required Indicator Comment String Description of the level field usually m for meters optional 3 A XZIV_1 Real Height of level 1 units in m required B XZIV_2 Real Height of level 2 units inm required x XZIV_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 String The word LATITUDES required Indicator Comment String Description of the latitudes field usually deg for degrees optional 5 A XLATJV_1 Real Latitude 1 units in degrees required B XLATJV_2 Real atitude 2 units in degrees required x XLATJV_x Real Latitude x units in degrees required June 20
189. ing a subsampling algorithm e mtxcple Uses a sparse matrix file to interpolate a time sequence of all variables from a source file to a target file under the optional control of an I O API coupling mode synch file e presterp Interpolates from a 3 D sigma coordinate file to a new 3 D pressure coordinate file using coefficients from PRES CRO 3D e selmrg2d Selects multiple 2 D layer variable combinations from multiple gridded input files and writes result to merged 2 D gridded output file e utmtool Performs coordinate conversions and grid related computations for lat lon Lambert and UTM coordinate systems e vertot Computes vertical column totals of variables in a file 10 3 Package for Analyses and Visualization of Environmental Data PAVE Latest Version Version 2 3 released on October 18 2004 Main website http paved sourceforge net Download http paved sourceforge net Downloads Latest User s Manual http paved sourceforge net pave_doc Pave html June 2010 10 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Answers to FAQ http paved sourceforge net pave_doc Pave FAQ html Support website http bugz unc edu PAVE is a flexible and distributed application to visualize multivariate gridded environmental datasets Features include baseline graphics with the option to export data to high end comme
190. ing and writing data Key data structures are defined by globally shared information You define this critical data structure information once and it is automatically made available for use in conforming code throughout the system This globally shared information is permanently stored as objects in an object data base In Models 3 these objects are a stored collection of related information such as grid dimensions and resolution coordinate system definitions chemical mechanism species and reactions Cross point Grid point where all scalars are defined Daemon A process that runs in the background independently and performs a function An example is a printer daemon that controls the job queue for the printer Decision support system An automated system that provides information for decision making Domain The domain for a CMAQ calculation is the horizontal geographic area e g the eastern United States that is of interest CMAQ calculations are performed for physical and chemical processes occurring in the atmosphere above this horizontal geographic area Dot point Grid point where wind components are defined Emission model This type of model calculates the emission rates of trace gas and particulate matter into the atmosphere under ambient meteorological conditions and socioeconomic activities Emissions from both natural and manmade sources are calculated One example of an emissions model is SMOKE Environmental modeling syst
191. ing modeled should be in the BNDY_CONC_1 file If some modeled species are not contained in this file the boundary condition for these species will default to the value 1 x 10 The perimeter of the CMAQ domain is 1 cell wide where the number of boundary cells 2 NROW 2 NCOL 4 Figure 6 2 is a graphical example of the CMAQ boundary conditions file the west and north boundaries have ozone values of 0 035 ppmV while the east and south boundaries have values of 0 030 ppmV June 2010 6 19 http www cmaq model org CMAQv4 7 1 Operational Guidance Document EXAMPLE One Layer Simple Boundary NTHIK 1 NTHIK 1 B 22 1 B 23 Boundary comp nent iN B 33 B 21 row NROWS i 9 oo Arepunog NROWS Mahh Grid GCNCGLS NROWS odum todu A que AA yu row 0 oS pd a o ae s s g e 8 he ba be 8 o NCOLS 11 p E B 2 NCOLS 2 NROWS 4 single indexes the entire boundary E 1 NCOLS 1 EQUIVALENCE S 1 B 1 E 1 NROWS 1 EQUIVALENCE E 1 B NCOLS 2 Ng 0 NC OLS EQUIVALENCE N 1 B NCOLS NROWS 4 WwW 0 NROWS EQUIVALENCE W 1 B 2 NCOLS NROWS 5 Figure 6 1 Illustration of CMAQ boundary condition file June 2010 6 20 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Layer 1 03 Boundary Conditions file BCON_smoke sapre b1_M_36 NC96mqg_profile 0 035 53 ppm 1 52 January 1 0 0 00 00 Min 0 030 at 2 1 Max 0 035 at 1 1 F
192. ink the contents of the I O API fixed source INCLUDE file directory to the SM3LIB ioapi fixed_src directory A list of the alternative library directory names expected by the CMAQ compile and run scripts for 32 bit and 64 bit operating systems using the Intel and Portland Group compilers include June 2010 3 7 http www cmaq model org CMAOQv4 7 1 Operational Guidance Document e Portland Group 32 bit Linux Linux2_x8 6pg e Portland Group 64 bit Linux Linux2_x86_64pg e Intel 32 bit Linux Linux2_x86ifort e Intel 64 bit Linux Linux2_x86_64ifort Other operating systems and compiler combinations are possible but may require manual configuration of the CMAQ scripts to point to the correct directory paths for the netCDF and T O API libraries After unpacking all of the CMAQ tar files under the M3HOME directory setting the CMAQ environment variables and installing the I O API and netCDF libraries in the M3LIB directory the CMAQ executables can then be compiled Before proceeding with the compilation steps check to make sure CVS is available on your system by typing the following command which cvs 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 3 Compiling CMAQ for the Benchmark Test Case Simulation For all CMAQ programs other than MCIP the program M3BLD is used to compile the source code into executables Th
193. ion name from multiplier required C ACLD_x Real Multiplier for reaction x required x A NHTO Int Vertical level cross reference to 1 header data required B NLATO Int Latitude cross reference to header data required Cc NPHOTO Int Photolysis reaction cross reference to header data required x 2 A XJVAL_1 Real or Clear sky photolysis rate at NHTO Exp NLATO NPHOTO and hour angle 1 required June 2010 6 24 http www cmaq model org CMAQv4 7 1 Operational Guidance Document B XJVAL_2 Real or Clear sky photolysis rate at NHTO Exp NLATO NPHOTO and hour angle 2 required C XJVAL_3 Real or Clear sky photolysis rate at NHTO Exp NLATO NPHOTO and hour angle 3 required JVTMAX XJVAL_ JVTMAX Real or Clear sky photolysis rate at NHTO Exp NLATO NPHOTO and hour angle corresponding to JVIMAX required x A NHTO Int Vertical level cross reference to 3 header data required B NLATO Int Latitude cross reference to header data required C NPHOTO Int Photolysis reaction cross reference to header data required x 4 A XJVAL_1 Real or Clear sky photolysis rate at NHTO Exp NLATO NPHOTO and hour angle 1 required B XJVAL_2 Real or Clear sky photolysis rate at NHTO Exp NLATO NPHOTO and hour angle 2 required C XJVAL_3 Real or Clear sky photolysis rate at NHTO Exp NLATO NPHOTO and hou
194. ipt xxx Failure defining horizontal domain For CCTM which uses both a GRIDDESC file and gridded input data emissions meteorology ICs BCs the grid defined in the GRIDDESC file must be consistent across all of the gridded input files or the simulation will fail June 2010 8 2 http www cmaq model org CMAOv4 7 1 Operational Guidance Document To configure a new CMAQ simulation the following steps must be taken to set up the horizontal model grid e Produce emissions and meteorology data on a consistent horizontal model grid to be modeled with CCTM e Create a GRIDDESC file that defines the horizontal model grid e Generate ICs and BCs on the horizontal model grid for nested simulations generate BCs from a parent grid e Configure the CCTM script to use the GRIDDESC file and input data on the desired horizontal model grid 8 2 2 Defining a new vertical layer structure The CMAQ programs that produce 3 D output CCTM ICON BCON use the MET CRO 3D file Section 6 1 21 to define a vertical layer structure The MET _CRO_3D file is output from MCIP and takes the vertical layer structure from the input meteorology The vertical layer structure must be consistent across all of the CMAQ programs used to complete a CCTM simulation New vertical layer structures for CMAQ simulations are configured with MCIP when processing raw meteorological model data See Section 5 7 for details on configuring MCIP 8 2 3 Setting a new episode time
195. ir density based scheme for mass conserving advection o ctm_yamo use Yamartino scheme for mass conserving advection ModInit default init_yamo The CCTM time step initialization module o init use air density based scheme for mass conserving advection o init yamo use Yamartino scheme for mass conserving advection ModAdjc default Yamartino option Mass conservation error adjustment scheme Corrects for mass inconsistencies arising from how the input meteorology treats density and wind fields This adjustment is required only if the air density based scheme for mass conserving advection is selected o adjcon_noop deactivate the air density based conservation adjustment scheme o denrate adjust the vertical advection error term from the meteorological model by air density from CCTM o comment out when using 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 o hadv_noop deactivate horizontal advection 5 13 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 o hppm use the unmodified Piecewise Parabolic Method to calculate horizontal advection o hyamo use the global mass conserving scheme to calculate horizontal advection ModVadv default vyamo Vertical advection module o vadv
196. is discussed below e Comments All lines that have an exclamation point in column 1 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 mechanism species tables These names must be spelled exactly as they appear in that table For user defined species names the following special rules have been established o The process analysis species names must not contain any blanks and can be up to 16 characters long o 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 o The name is case sensitive Thus NO2 and no2 would represent two different species o A name 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 mechanism 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 nonbla
197. ities Generalized coordinate system A scheme for constructing coordinate systems that allows for choices of horizontal map projection type e g latitude longitude Lambert Mercator polar stereographic Universal Transverse Mercator or matrix and projection parameters as well as for choices of various vertical coordinate types e g pressure coordinate height above ground height above sea level sigma p hydrostatic sigma p nonhydrostatic and sigma z The advantage of a generalized coordinate system is that a CMAQ model can adapt to a variety of different possibilities in horizontal and vertical parameters Generic grid system A scheme for constructing grid systems that allows for choices of origin orientation and spatial resolution It allows a model to be expressed in a grid system that is optimal for representing the governing equations For a regular rectangular grid system mapping gridded data to the earth s surface can be achieved by defining the number of rows and columns cell size and location and extent For an irregular grid system grid intersections nodes are described by coordinates from a reference position Geocoded An entity with an identifier associated with geographic boundaries e g state or county code Geographic information system GIS A computer based system for managing analyzing manipulating and displaying geographic information in both numeric and graphical ways Geospatial Refers to the s
198. itions file METpath default SM3DATA mcip3 M_36_2001 Directory path for the input meteorology files U JVALpath U JVALfile defaul defaul M3DATA jproc cfg JTABLE_ STDATE Directory path and file name for input clear sky photolysis rate files 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 instantaneous gas and aerosol phase pollutant estimates CTM_CGRID 1 GRDDED3 Name and location of simulation ending 3 D full CGRID gas and aerosol phase pollutants concentrations for use as a restart file CTM_ACONC 1 GRDDED3 Name and location of hourly 2 D or 3 D integral average gas and aerosol phase pollutant estimates June 2010 5 24 http www cmaq model org CMAQv4 7 1 Operational Guidance Document File Name Format Description CTM_ DRY DEP 1 GRDDED3 Name and location of hourly 3 D gas and aerosol phase dry deposition estimates CTM_WET_DEP_ 1 GRDDED3 Name and location of hourly 3 D gas and aerosol phase wet deposition estimates CTM_SSEMIS 1 GRDDED3 Name and location of hourly 2 D sea salt emissions set the variable CTM_SSEMDIAG to T in CCTM to run script to write this additional file CTM VIS 1 GRDDED3 Name and location of hourly 3 D visibility metrics CTM_DIAM 1 GRDDED3 Name and location of hourly 3 D aeroso
199. ity between the Fortran 77 compiler and Fortran 90 code the following guidance is provided Line length beyond 72 characters is permissible in Fortran 90 with line continuation indicated by an ending amp but not in Fortran 77 therefore insertion of the amp in column 73 of the first line and in column 6 of the next line of the Fortran 90 code will ensure compatibility with both compilers the amp at the beginning of a line is in principle ignored by the Fortran 90 compiler but interpreted as a continuation character by the Fortran 77 compiler if it appears in column 6 The modules must be controlled by a top level class driver routine whose calling arguments must be the computational concentration grid array CGRID the current scenario date Date scenario time Time and the controlling time step vector TimeStep See Section 9 2 3 above The class driver is also responsible for any temporal integration required within the module The time steps for process integration at the module level are usually shorter than those of the CCTM synchronization time step Any reads and writes for the module should be done at the level of the class driver routine Although not absolutely necessary this is strongly suggested because it is usually much easier to control the timing of the data accesses at the highest level of the module where the current scenario date and time are known Use the Fortran decla
200. ively for the setting of the ModInpt variable This variable determines the input module to use when creating an ICON executable 5 5 2 Files configuration and environment variables Figure 5 4 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 Separate ICON executables are required for each mechanism configuration June 2010 5 30 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Mechanism Include Files GC_SPC EXT Input Type Set Mechanism AE_SPC EXT GC_ICBC EXT pie Mechanism 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 Input Output y Horizontal grid definition GRIDDESC Vertical layer structure MET_CRO_3D Execution Options Figure 5 5 ICON input and output files At execution the user provides a data file of chemical conditions that ICON converts to ICs on a predefined model grid Through the specification of the ModInpt variable ICO
201. izontal sides of the MCIP domain Setting BTRIM 0 will specify the maximum extent of the input meteorology domain To remove the MM5 or WRF ARW lateral boundaries set BTRIM 5 recommended 5 44 http www cmaq model org CMAOQv4 7 1 Operational Guidance Document 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 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 e X0 used only if BTRIM 1 The x coordinate of the lower left corner of the full MCIP cross point domain including the MCIP lateral boundary based on the input MM5 or WRF ARW domain X0 refers to the east west direction e Y0 used only if BTRIM 1 The y coordinate of the lower left corner of the full MCIP cross point domain including the MCIP lateral boundary based on the input MM5 or WRF ARW domain YO refers to the north south direction e NCOLS used only if BTRIM 1 Number of columns in the output MCIP domain excluding MCIP lateral boundaries e NROWS used only if BTRIM 1 Number of rows in the output MCIP domain excluding MCIP lateral boundaries e LPRT
202. l and chemical processes and use computer models to study their theories Model users Research production and quality assurance personnel i e applied scientists and engineers who generate valid input for the modeling systems run the modeling systems maintain audit trails analyze input and output for correctness and produce analyses of the modeling results Model A representation of a planned or existing object or condition Modeling structure A design specification that provides the paradigm of operation and the interface specifications for the modules used to construct a particular family of models In a CMAQ model for example the paradigm is that modules act as operators upon a shared concentration field and four types of interfaces call interfaces INCLUDE file interfaces I O interfaces and UNIX environment interfaces must be specified DRAFT January 2009 A 5 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Modeling system A set of computational models and associated data processors that together provide for the simulation of processes of interest Models 3 components The various subsystems within the Models 3 framework Each component is represented by its own icon The available components are Dataset Manager Model Builder Program Manager Science Manager Strategy Manager Study Planner and Tools Manager Models 3 The third generation air quality modeling system It is a flexible system t
203. l and observation are then used to statistically and graphically analyze the model s performance More specifically AMET is currently designed to analyze outputs from MM5 WRF and CMAQ as well as MCIP postprocessed meteorological data surface only The basic structure of AMET consists of two fields and two processes The two fields scientific topics are MET and AQ corresponding to meteorology and air quality data The two processes actions are database population and analysis Database population refers to the underlying structure of AMET after the observations and model data are paired in space and time the pairs are inserted into a MySQL database Analysis refers to the statistical evaluation of these pairings and their subsequent plotting Practically a user may be interested in using only one of the fields either MET or AQ or may be interested in using both fields That decision is based on the scope of the study The three main software components of AMET are MySQL an open source database software system R a free software environment for statistical computing and graphics and perl an open source cross platform programming language 10 6 netCDF Operators NCO Latest version Version 3 9 9 released on July 24 2009 Main website http nco sourceforge net Download http nco sourceforge net Download Latest User s Manual http nco sourceforge net HRTFM Answers to FAQ http nco sourceforge
204. l conditions for start up of the fine grid are also generated using concentrations from the coarse grid Subsequent runs in the period of interest use the last hour of the concentration file generated from the previous day s run See Figure 8 2 for an example of a one way nested simulation This example uses initial and boundary conditions from the coarser 36 km grid simulation to perform the nested finer grid simulation for the same two day period of interest June 2010 8 5 http www cmaq model org CMAQv4 7 1 Operational Guidance Document INIT_CONC_1 12 km CONC 36 km Day3 BNDY_CONC_1 12 km Study Period BNDY_CONC_1 12 km CONC 36 km Day4 CONC 12 km Day4 Figure 8 2 12 km nested two day modeling period IC BC schematic 8 2 5 Input output file names and locations Configuring the CMAQ run scripts for a new simulation involves creating an application identifier to use in the name of the CMAQ outputs and to specify the correct input and output file names and locations on the system where CMAQ will be run Application identifiers are selected to uniquely identify the output files with respect to the simulation For example if you are running a base simulation for the year 2007 a simulation identifier or APPL setting in CMAQ terms could be Base07 For time dependent output files a date identifier is commonly added to the file name to identify the time period covered by the file Following the previous example
205. l diagnostics dp and sigmas for Aitken and accumulation mode aerosol species set the variable CTM_AERODIAG to T in CCTM run script to write this additional file CTM_IPR 1 3 GRDDED3 Name and location of hourly 2 D or 3 D integrated process rate files multiple files written when CCTM is configured to track a large number of process pollutant combinations CTM_IRR 1 3 GRDDED3 Name and location of hourly 2 D or 3 D integrated reaction rate files multiple files written when CCTM is configured to track a large number of reaction pollutant combinations CTM RJ 1 2 GRDDED3 Name and location of hourly photolysis diagnostic output file multiple files written when there are a large number of photolytic reactions in a chemical mechanism The default location of the CCTM output files is the SM3DATA 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 variables in the file name All of the variables for naming the CCTM outputs are set in the run script 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 program CHEMMECH and the Python script include_generator py created by Chao Jung Chien at University of California Riverside creates
206. l driver the Yamartino options cannot be used for the initialization module and the advection routines and the density based concentration adjustment scheme must be used e Ensure that there is consistency in the selection of the chemistry mechanism and the aerosol module for example the aero4aerosol module cannot be used with a chemistry mechanism that is tagged aeS e Ensure that there is consistency in the selection of the chemistry mechanism with the cloud module a chemistry mechanism that contains linkages to aqueous chemistry cannot be used when the noop option for the cloud module is selected e The EBI chemistry solver is mechanism dependent and must be consistent with the chemistry mechanism for example the EBI solver for CB05 cannot be used with a SAPRC 99 based chemistry mechanism The availability of different science options in CMAQ creates the flexibility to select a configuration that optimizes the model performance for different applications Through testing the various science configurations with respect to model accuracy and speed the CMAQ user can find the combination of science options that gives the best performance for a particular modeling study 8 3 References GEOS CHEM 2009 http wiki seas harvard edu geos chem index php Main_ Page MOZART 2009 http www mpimet mpg de en wissenschaft modelle mozart html June 2010 8 7 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 9 CODE MANAG
207. latitude band ranging from 80 N to 70 N The next 17 data blocks complete the spring O concentration profiles by continuing through the rest of the 19 latitude bands with the last block representing the 80 S to 90 S latitude band The 20 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 The 19x3 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 values The data are organized in 12 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 air density ozone concentrations and aerosol attenuation coefficients The data are organized in 51 rows corresponding to altitude 0 to 50 km with four columns per row for each of the four variables A detailed description of the file format is provided in Table 6 10 June 2010 6 15 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Table 6 10 PROFILES file format description
208. le to make code modifications Complete modules are checked out during the CMAQ model building operation 2 The CVS modules file has no intrinsic relationship with the CMAQ classes module design implementation June 2010 9 2 http www cmaq model org CMAQv4 7 1 Operational Guidance Document The following shows a small portion of a symbolic CVS UNIX directory tree that represents the current structure for CCTM gt CCTM gt CVSROOT CVS administrative files gt src gt adjcon gt adjcon_noop gt RCS files gt denrate gt RCS files gt aero gt aero_noop gt RCS files gt aero4 gt RCS files gt aero5 gt RCS files gt aero5_txhg gt RCS files gt aero_depv gt aero_depv_noop gt RCS files gt aero_depv2 gt RCS files gt chem gt chem_noop gt RCS files gt smvgear gt RCS files gt ros3 gt RCS files gt ebi_cbO5cltx_ae5 gt RCS files gt ebi_cb05cltxhg_ae5 gt RCS files gt ebi_saprc99 gt RCS files gt ebi_saprc99 gt RCS files The symbolic tree is shown relative to the subdirectory in the repository named for the CCTM model Similar trees exist for each of the generic models The RCS files are the revision control history files that contain the change tables to reconstruct the actual source code according to a specific revision identifier The tree closely follows the organization of classes and
209. lected during compilation of JPROC The altitudes meters latitudes degrees and hour angles from noon for which the rates are derived are hardwired in the JPROC source code 5 6 2 Files configuration and environment variables Figure 5 5 shows the input and output files for JPROC Some options are invoked at compilation while others are invoked with execution of the program When compiling JPROC the user specifies a chemical mechanism to indicate the gas phase chemistry for which to calculate photolysis 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 configuration June 2010 5 36 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Extraterrestrial irradiance Atmospheric vertical profiles Molecular cross section and quantum yields Total ozone mapping spectrometer Molecular oxygen cross sections Ozone cross sections Execution Options Mechanism Include Files GC_SPC EXT Set Mechanism AE_SPC EXT GC_ICBC EXT etc Compile Options PROFILES JTABLE Shows Input Output ra Figure 5 6 JPROC input and output files While JPROC does not require any technical configuration at execution such as domain specifications there are several required and optional input files that the user must provide to the p
210. les for CMAQ using the I O API code libraries please refer to Chapter 9 and the I O API documentation June 2010 4 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 4 1 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 which means 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 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 are referred to by numbers from 1 to the greatest number of layers in the file and dates and times are stored as integers using the coding formats YYYYDAY commonly called JDATE and HHMMSS commonly called JTIME where YYYYDAY 1000 Year Julian Day HHMMSS 10000 Hour 100 Minute Seconds 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
211. levated Point Source Emission Fifth Generation Penn State NCAR Mesoscale Model xii http www cmaq model org CMAQv4 7 1 Operational Guidance Document ppm ppmV PROCAN QC RADM SAPRC 99 SAS SCC SCCS SMVGEAR SO SPC TOMS TR UAM UNC UTC UTM VOC WRF WRF ARW June 2010 Mechanism Processor National Ambient Air Quality Standards National Aeronautics and Space Administration National Center for Atmospheric Research National Emission Trends network Common Data Form Oxides of Nitrogen National Oceanic and Atmospheric Administration Non Reactive National Weather Service Process Analysis Control Process Package for Analysis and Visualization of Environmental Data Planetary Boundary Layer Personal Computer Particulate matter up to 2 5 microns Particulate matter up to 10 microns Piecewise Parabolic Method Parts per million by weight Parts per million by volume Process Analysis Processor Quality Control Regional Acid Deposition Model State Air Pollution Research Center mechanism version 1999 Statistical Analysis System Source Classification Code Source Code Control System Sparse Matrix Vectorized Gear Sulfur Dioxide Species Total Ozone Mapping Spectrometer Tracer Urban Airshed Model University of North Carolina Universal Time Coordinate Universal Transverse Mercator Volatile Organic Compounds Weather Research and Forecasting model Weather Research and Forecasting m
212. line documentation for the CMAS products e Model related research Learn about the latest developments in modeling research e Data clearinghouse Access air quality modeling data from around the community 11 1 2 CMAS community A primary focus of CMAS is to instill a sense of community among the users of environmental models From the individual to the organizational level the beneficiaries of CMAS include but are not limited to June 2010 11 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document e Government Industry Academia Research Consultants Stakeholder groups By promoting cooperation within and between the various groups in the environmental modeling community CMAS forms the foundation to enable the community to participate in the examina tion of issues and the subsequent development of strategies that meet societal challenges of environmental protection 11 1 3 Why is CMAS needed Historically advancements in air quality model technology could not easily be shared among modelers because of technical incompatibilities By standardizing with open source advanced modeling systems CMAS enables collaborative development and linking of models for meteorology emissions air quality and environmental and health effects CMAS builds on the pioneering work by EPA and other research organizations by developing advanced tools to assist users in building models developing datasets analyzing
213. ling any components of CMAQ users must install CVS netCDF and I O API Compiler flag consistency between the netCDF and I O API is critical for building library files compatible with CMAQ Table 3 3 lists the suggested compilation options for building netCDF and I O API libraries that are compatible with CMAQ Refer to the documentation for these libraries for additional information on installation and compiling Table 3 3 NetCDF and I O API compilation options for CMAQ Library Intel Fortran PGI Fortran type netCDF CC gcc CC gcc CPPFLAGS DNDEBUG DpgiFortran CPPFLAGS DNDEBUG DpgiFortran CFLAGS g O CFLAGS O FC ifort FC pgf90 F77 ifort FFLAGS 0O w FFLAGS g 02 mp recursive CXX gt CXX g I O API IBIN Linux2_x86ifc BIN Linux2_x86pg_pgcc_nomp 32 bit I O API BIN Linux2_x86ifc BIN Linux2_x86_64pg_pgcc_nomp 64 bit To install CMAQ with examples using a C shell environment a Red Hat Linux system and the Portland Group Fortran compiler 1 Set the environment variable M3HOME to alias the directory where CMAQ will be installed For example if you installed the CMAQ source code in the directory home user CMAQ set the M3HOME environment variable using the following command setenv M3HOME home user CMAQ June 2010 3 6 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 2 Set environment variables for the
214. lity 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 nonphotochemical reactions the photolysis rate quantifies how much reactant is produced from a photolytic reaction in a given amount of time The calculation of a photolysis rate must include multiple influences 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 June 2010 2 11 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 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 molecular 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
215. lized June 2010 4 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Magic Me File Type Naer Data Type Description opening creation look up indexing input and output operations TSRIES3 7 Hydrology A hydrology time series file behaves much like a degenerate Time Series gridded file except that the numbers of rows and columns are usually 1 and that there are additional file attributes found in the INCLUDE file ATDSC3 EXT PTRFLY3 8 Pointer A pointer flyer observation file behaves much like a flyer degenerate gridded file with NCOLS3D and NROWS3D set to 1 and certain mandatory variables and variable naming conventions to be used by analysis and visualization software 4 1 3 Opening Creating Data Files in I O API The I O API function OPEN3 is used 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 PANAME name of calling program This function maintains considerable audit trail information in the file header automatically and 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 ca
216. loping CMAQ simulations for the first time or when the chemistry science configuration within the model is changed A model developer would use M3BLD to check out working versions of the CMAQ source code and create a Makefile to facilitate the interchange of science components within a model to modify reaction details within an existing chemistry mechanism or to experiment with source code modifications see Chapter 10 The purpose of this chapter is to demonstrate how to build the executables for the CMAQ programs beyond running the benchmark case Before proceeding with this chapter review Chapter 3 for an overview of the system requirements for CMAQ In general there are three major steps in compiling CMAQ executables Install the CMAQ libraries netCDF and I O API Build M3BLD Configure and build the executables for the various CMAQ programs All compilations of libraries and CMAQ must be done with the same compilers and settings The details of these three major steps with respect to creating new CMAQ simulations are covered in this chapter 8 1 General Introduction to Model Building Before using CMAQ for operational modeling in a new computing environment it is recommended that the model be exercised using the benchmark dataset that is distributed with the model Chapter 3 describes how to configure a minimal hardware system for CMAQ and how to install CMAQ to run the benchmark simulation After benchmarking CMAQ it can be configure
217. ly accessible and free to obtain Designed for modularity CCTM uses standardized input output I O routines to facilitate extensibility June 2010 1 9 http www cmaq model org CMAOv4 7 1 Operational Guidance Document e The diverse and continually growing community of CMAQ developers provides an excellent forum for discussing development related topics of all kinds 1 5 New Features in Version 4 7 1 5 1 Version 4 7 1 CMAQ version 4 7 1 CMAQv4 7 1 is an interim release of CMAQ that addresses bugs and expands the capabilities of CMAQ version 4 7 Table 1 1 summarizes the features in this version of the model 1 5 2 Version 4 7 CMAQ version 4 7 CMAQv4 7 contains many new features and improvements over the previous release of the model Table 1 2 provides a summary of these changes Details are contained in the release notes distributed with CMAQV4 7 Several processes that were previously modeled with other CMAQ components can now be calculated in line meaning that they can be simulated during the execution of the CMAQ calculation An example is the photolysis rates calculation In CMAQV4 7 users have the option of computing clear sky photolysis rates offline using the JPROC program or to calculate them in line in the CCTM For the offline approach which has been the approach used for CMAQ up to this release the outputs from JPROC are provided to the CCTM during execution In the in line approach the CCTM reads in molecular cros
218. m ICON however in that it can generate time varying i e dynamic boundary conditions Dynamic boundary conditions are typically extracted either from CCTM outputs from a coarse grid simulation for nested simulations or from a CCTM 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 only 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 output files from the MM5 or WRF meteorological models to create netCDF formatted input meteorology data that are used by SMOKE the emissions processor that computes emissions inputs to CMAQ and by CMAQ MCIP prepares and diagnoses all meteorological fields that are required for SMOKE and CCTM In addition MCIP is currently used to calculate the time varying species dependent dry deposition velocities that are used in CCTM MCIP can be used to uniformly trim cells off the June 2010 1 7 http www cmaq model org CMAOv4 7 1 Operational Guidance Document horizontal boundary of the domain defined by the meteorological model or to window in on a subset of that domain MCIP can also decrease the verti
219. m module contains several options for different gas phase chemistry solvers that can be used to optimize model performance Without the modular structure changes to just one scientific process could entail having to modify source code throughout CCTM thereby greatly increasing the risk of human error In this situation failing to make the correct modification at even a single location in the source code could lead to erroneous modeling results or program execution failure CMAQ s modularity makes designing or modifying a model simulation much more user friendly requiring either less reprogramming or none at all 2 1 3 Major quality control features The CMAQ system was designed to minimize the potential for model simulation error in several significant ways June 2010 2 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document The formal CMAQ peer review process implemented by the EPA ensures that the model retains scientific credibility Also informal review of the modeling system occurs day to day as the broad international user community applies CMAQ for a wide variety of scientific questions and in locations other than North America The modularity of the scientific processes in CMAQ makes modifications and adaptations to the user s needs more straightforward The potential for error is minimized because the user is not required to change code or declare variables within program modules outside the one of immediat
220. mark marks an entry of a help document so it can be quickly accessed later A list of bookmarks appears in the Bookmarks Menu on the help browser window and also in the bookmark s window Each item on the list is a hypertext link to a marked entry Chemistry transport model CTM A model that simulates various physical and chemical processes that are important for understanding atmospheric trace gas and particles distributions DRAFT January 2009 A 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document The processes include atmospheric transport vertical mixing atmospheric chemistry in the gas phase in the aqueous phase and in aerosols cloud mixing and precipitation scavenging and surface removal processes Generally a chemistry transport model relies on a meteorological model for the description of atmospheric states and motions and depends on an emissions model for the description of anthropogenic and biogenic emissions that are injected into the atmosphere Class A collection of software modules associated with a science process Conforming datasets Conforming datasets are in I O API format Most programs models visualization and analysis routines in the CMAQ system are able to read and write conforming datasets This capability eliminates the need for data conversion even within a distributed computing environment Conforming programs Conforming programs generally use the I O API library routines for read
221. mation on how to configure ICON and BCON for the two input file types Standard operation of CMAQ uses boundary conditions that remain time independent i e the same boundary conditions are used for each day of a multiday case for the outermost coarse grid modeling domain Nested grids use temporally resolved boundary conditions extracted from the results of a parent grid CCTM simulation The initial conditions produced by ICON are time independent for the first spin up day If the initial conditions were generated from vertical profile data then they will also be spatially uniform meaning that for a given layer they will contain the same concentration in every grid cell The remaining days of a simulation should use spatially heterogeneous output from the previous day s CCTM simulation to initialize each day See Figure 8 1 for an example of the initial and boundary conditions used for a CCTM simulation June 2010 8 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document with a two day spin up followed by a two day period of interest In this example each of the days was run separately Spin Up BNDY_CONC_1 36 km study Period Figure 8 1 36 km four day modeling period IC BC schematic When using a nested grid configuration the fine grid resolution grids can use time varying boundary conditions generated by BCON with input from time varying output concentrations from the coarse grid CCTM simulation The initia
222. me is a user defined name that must be unique and can be referenced in subsequent IRR OUTPUT June 2010 5 51 http www cmaq model org CMAOQv4 7 1 Operational Guidance Document commands DEFINE RXNSUM sumname c1 lt rxlabli gt c2 lt rxlablo gt 5 The DEFINE RXNSUM command is used to compute a linear combination 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 expressions following the equal sign that specify which reaction s IRRs to sum The rxlabl is the reaction label that is used in the generalized mechanism The c are optional numerical coefficients that default to 1 if not specified IRR OUTPUT irrname c1 op cyclIname qual sumname qual lt rxlabl gt c2 op gt cyclname qualz sumname qualz lt rxlably gt 5 The IRR_OUTPUT command defines a specific IRR output to be generated during a CMAQ simulation It is constructed by specifying 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 i e opi a cycle name a reaction sum name or a reaction label enclosed in greater than and less than signs The optional qualifiers qualj for cycle
223. measured across the wavelength band possible answers beginning ending centered point required n 2 A Multiplier String Multiplication factor to apply to photolysis rate equation line begins with FAC factor listed in real or exponential format required n 3 A Wavelength Int or Wavelength corresponding to ET Real data units nm required B Extra Real or Estimation of the photon flux terrestrial Exp reaching the exterior of the Irradiance earth s atmosphere units photons cm second required n 4 A Wavelength Int Wavelength corresponding to ET data units nm required B Extra Real or Estimation of the photon flux terrestrial Exp reaching the exterior of the Irradiance earth s atmosphere units photons cm second required n X A sample of the important sections of an ET file is shown below Extraterrestrial 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 FAC 1 0 June 2010 6 14 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 185 185 3 6201 186 916 4 7301 PLL REL ry E ry E 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 attenuation temperature air pressure and Dobson values The ASCI formatted da
224. 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 S M3MODEL include release To invoke this new mechanism set the Mechanism variable in the CMAQ build scripts to the name June 2010 7 5 http www cmaq model org CMAOv4 7 1 Operational Guidance Document of the new mechanism directory and compile new executables See Section 5 4 for additional details about the CHEMMECH program 7 4 3 Further information on chemical mechanisms e The versions of each chemical mechanism that include both aerosols and aqueous chemistry represent the most comprehensive modeling approach e The same chemical mechanism must be used for CCTM and all of the mechanism dependent input processors that are part of the CMAQ system e The Euler Backward Iterative EBI chemistry solver is mechanism dependent If a chemical mechanism is modified then the default EBI solver cannot be used for the new mechanism The Rosenbrock and SMVGEAR solvers are the only mechanism independent choices of chemistry solvers with 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 species are added to the domain through the emissions files the GC_EMIS EXT INCLUDE file must contain these new species If the n
225. mension acts as the glue to bind the input files data together Each variable in each input file becomes one record in the same variable in the output file All input files must contain all extracted variables or else there would be gaps in the output file Each extracted variable must be constant in size and rank across all input files The input files are stored consecutively as a single record in output file Thus the output file size is the sum of the sizes of the extracted variable in the input files e necflint netCDF File Interpolator ncflint creates an output file that is a linear combi nation of the input files This linear combination is a weighted average a normalized weighted average or an interpolation of the input files Coordinate variables are not acted upon in any case they are simply copied from file_ e ncks netCDF Kitchen Sink ncks combines selected features of ncdump ncextr and the nccut and ncpaste specifications into one versatile utility ncks extracts a subset of the June 2010 10 7 http www cmaq model org CMAQv4 7 1 Operational Guidance Document data from input file and prints it as ASCII text to stdout writes it in flat binary format to binary file and writes or pastes it in netCDF format to output file e ncpdq netCDF Permute Dimensions Quickly ncpdq performs one of two distinct functions packing or dimension permutation but not both ncpdq is optimized to perform these actions in a
226. mentation details of the object which are hidden from other objects Encapsulation prevents a program from June 2010 9 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document becoming so interdependent that a small change has massive ripple effects The implementation of an object can be changed without affecting the applications that use it The encapsulation design makes the CMAQ system safer and enables the transaction processing plug and play capability This design also makes it easier for a user to trace data and usage within a module particularly at the class driver level 9 2 4 Coding guidelines To maintain the object oriented concepts implemented in the CMAQ system design we have established a small set of coding guidelines that apply to those who develop CMAQ science modules and affect the low level design of the models We have developed standards to control data dependencies at the class driver level but we have not propagated these coding standards to the submodule level l The models are generally coded in Fortran both Fortran 90 and Fortran 77 conventions are used by various developers It is possible to link in subroutines written in the C language although this has not been done within the current CMAQ implementation While the Fortran 90 compiler will compile Fortran 77 code the reverse is not true Thus the Makefiles are set up to invoke the Fortran 90 compiler To enable code compatibil
227. mestep written to CTM_DRY_DEP_1 22 amp for date and time MDATE MTIME 18 IF LIPR THEN DO V 1 N_SPC_DDEP 18 DO V 1 N_SPC_DEPV 18 DO R 1 MY_NROWS 18 DOC S17 Y_NCOLS 18 DDEP_PA C R V DDEP V C R 18 END DO 18 END DO June 2010 9 11 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 18 END DO 18 CALL PA_UPDATE_DDEP VDIF DDEP_PA JDATE JTIME TSTEP 18 END IF C re set dry deposition array to zero DDEP 0 0 END IF 23 RETURN 23 END Footnotes 1 Header comments Highly recommended for internal documentation 2 USE lt module name gt includes the Fortran source file specified 3 IMPLICIT NONE must be used in Fortran 90 i e implicit declarations are not supported This dramatically reduces errors due to typos and undefined variables 4 Chemical mechanism array dimensioning and looping global variables 5 C preprocessor flags that determine which emissions control dimensioning and looping variables are compiled 6 Other global array dimensioning and looping global variables including those for the I O API The logical variable LIPR is defined in the SUBST PACTL_ID INCLUDE file for use at lines labeled 18 7 Local variable declaration Note syntax differences from Fortran 77 8 Declarations for the argument list standardized 9 Declarations and PARAMETER statements for local Fortran parame
228. ming 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 parallel input output PARIO library contains modules for controlling the model input and output in parallel multiprocessor computing environments In addition to a series of CMAQ specific routines it contains special implementations of several of the I O API modules for multiprocessor computing environments The PARIO library is necessary only when compiling CCTM for parallel multiprocessor environments single processor versions of 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 5 8 2 2 PARIO compilation options Other than configuring the build script for the current system i e compiler and library locations PARIO does not require any configuration at compilation June 2010 5 46 http www cmaq model org CMAOQv4 7 1 Operational Guidance Document 5 8 2 3 PARIO compilation First it is assumed that you have already installed and compiled the I O API netCDF and MPICH libraries see Section 3 2 3 or that these are already available from a previous CMAQ compilation Section 3 3 provides an overview of how to install and compile the CMAQ programs for the tutorial simulation
229. modules for CCTM and contains alternate modules within the classes In particular most classes contain a no operation noop module that allows a user to essentially turn off that particular science process modeling This is useful for example in debugging where rapid turnaround is important and a computationally demanding module that is not needed can be bypassed 9 2 Guidelines for Developing New CMAQ Source Code 9 2 1 Object oriented concepts To make the CMAQ system robust and flexible object oriented concepts were incorporated into the design of the system The incorporation of these ideas helps developers avoid introducing errors when code modifications are needed Additionally the system can easily and efficiently be modified allowing the user to quickly create models for different applications The implementation language for CMAQ is Fortran 90 which imposes limits on how far one can go in terms of object oriented design In particular because Fortran is a static language objects cannot be instantiated dynamically they must be declared explicitly in the source code to be created at compile time However to encourage a user community that will be contributing code for future enhancements every attempt has been made to adhere to the Fortran 90 standard June 2010 9 3 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 9 2 2 Global name data table To implement modularity and data independence we have em
230. 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 Advection 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 consis tency 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 mass consistent one needs to solve a modified advection equation Byun 1999 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 June 2010 2 12 http www cmaq model org CMAQv4 7 1 Operational Guidance Document PPM is a monotonic and positive definite scheme Positive definite schemes maintain the sign of input values which in this case means that positive concentrations will remain positive
231. n atmospheric modeling and has been in active development since the early 1990 s The first release of CMAQ was made available in 1998 without charge for use by air quality scientists policy makers and stakeholder groups to address multiscale multipollutant air quality concerns All subsequent CMAQ releases past current and future will adhere to this same level of code accessibility and scope June 2010 iv http www cmaq model org CMAOv4 7 1 Operational Guidance Document Contents DISCEAIMER E E tree ote oth oth itt ote btn sitet a tno III FOREWORD cicccscecicccccscccnctccccewciccccencieccieuccceccceciecccewccccccewtcevecewececccewtcevecewececccewcdewccewcees IV FIGURES a E E EE E EEE wens sansucwssiteuenssansuenssaieinwswansendt X TABLE Saeaon cat Fear Fae ane ect races ce E hA NNAL NANANA ANALA N Aaina nadaira mi dairi ni dd sarees XI ABBREVIATIONS sso sccssccasccassccssccssccasacescsisccessuesnudasucsasdssucduacasascuacsssocundaserehansiedeiadsieieded XII 1 INTRODUCTION anman ape annn amsami nanma an inanan anina nanan A Manaa anA H abadan Enan P OANE HAR NaN Raiana anii 1 1 1 1 Model Background and Goals s nnosseseesensseessesesssessessrssessessesseesseesessresseessesersseesse 1 2 1 2 Overview of CMAQ System Components i525 efsscs aassderavenedeas i asvenaaedidy aadsiavieeds 1 4 1 2 1 lnistallationOvervie weiss hooves aletautin a a R R eases 1 4 1 2 2 Configuration Options essessesessssesseseessressessrssressesstss
232. n 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 Table 4 3 Possible values for OPEN 3 FSTATUS FSTATUS Value Description FSREAD3 1 for READ ONLY access to an existing file FSRDWR3 for READ WRITE UPDATE access to an existing file FSNEW3 for READ WRITE access to create a new file file must not yet exist 2 3 FSUNKN3 4 for READ WRITE UPDATE access to a file whose existence is unknown FSCREA3 5 for CREATE TRUNCATE READ WRITE access to files In the last three cases new unknown and create 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 OPENS If the file does not exist in either of these cases OPEN3 will use the June 2010 4 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 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 how to use the OPEN3 function is shown below from the CMAQ INITSCEN subroutine This program segment checks for the existence of a CCTM concentration
233. n creating a species produced by reaction rather than transported from somewhere else Process Read a file or a set of data perform the desired functionality quality control reformat ting algebraic operations etc and submit the processed data to the next set of actions Quality control QC The act of reading data inventories files and checking for correctness completeness and consistency QC may involve automatic correction substitution or the filling of missing data All QC processes are followed by QC reports Register data When you register data you are making something that already exists e g a file known to the system Rule effectiveness percent An adjustment to projected estimated emissions data to account for emissions underestimates due to compliance failures and the inability of most inventory techniques to include these failures in an emission estimate The adjustment accounts for known underestimates due to noncompliance with existing rules control equipment downtime or operational problems and process upsets Valid values 0 to 100 DRAFT January 2009 A 7 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Rule penetration percent An adjustment to projected estimated emissions data to account for emissions underestimates due to failure to implement rules throughout the area of intent Valid values 0 to 100 Scalable In the context of parallel computer architectures and algorithms
234. n for the first hour of a simulation It can generate these initial conditions from either an ASCII file of vertically resolved concentration profiles distributed with CMAQ or from an existing CCTM output file If the profiles in an ASCII file do not have the same vertical structure as the CCTM configuration to be used ICON will interpolate the data to a vertical structure consistent with 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 simulations with finer resolution grids that cover part of coarser resolution grids 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 conditions 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 ASCII profiles to a vertical resolution that is consistent with the CCTM configuration BCON differs fro
235. n of the vertical profile file format for boundary conditions is provided in Table 6 5 The header of the profiles file is list formatted while the data section of the file is fixed format Table 6 5 BC_PROFILE format description Line Column Name Type Description 153 Text Header String Text description of the contents and source of the initial conditions file optional 4 A NUM_SIGMA_LVL Int Number of sigma levels contained in the file required B NUM_POLL Int Number of pollutants contained in the file required SIGMA_LVL Real Vertical coordinate values of sigma p levels number of values n 1 is one more than the NUM_SIGMA_LVL n required 4 n 5 STDATE String Julian start date of the file YYYYDDD optional B STTIME String Start time of the file HH optional 6 Direction String North South East West indicates the boundary described by the subsequent data section required 7 T10 SPECIES1 String Pollutant name enclosed in double quotes required 12 20 AAYER1_BC EXp BC concentration for species 1 in lowest sigma layer required 23 3 1 AAYER2_BC EXp BC concentration for species 1 in 2nd Sigma layer required 34 42 AAYER3_BC EXp BC concentration for species 1 in 3rd Sigma layer required 45 53 AA
236. n one simulation may be necessary to adequately demonstrate seasonal or regional biases if any in the results It is also understood that with models still under development the analysis may not resolve all differences from the operational model results It is recommended that these unresolved issues also be documented Model developers are also recommended to check the CMAS website to see if there are any additional guidelines that have been recommended since the first set listed above 9 6 References Fine S S W T Smith D Hwang T L Turner 1998 Improving model development with configuration management IEEE Computational Science and Engineering 5 1 Ja Mr 56 65 J Rumbaugh M Blaha W Premerlani F Eddy and W Lorensen 1991 Object Oriented Modeling and Design Prentice Hall Young J O Integration of Science Code into Models 3 1999 In Science Algorithms of the EPA Models 3 Community Multiscale Air Quality CMAQ Modeling System D W Byun and J K S Ching ed EPA 600 R 99 030 U S EPA Research Triangle Park NC June 2010 9 19 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 10 ANALYSES TOOLS FOR CMAQ Several tools are freely available for visualizing analyzing and evaluating CMAQ inputs and outputs The list includes CMAQ utility tools m3tools PAVE VERDI the Atmospheric Model Evaluation Tool AMET netCDF Operators NCO Python based ioapiTools UNIDATA Integrated Data
237. n the CMAQ modeling system 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 definitions for new grids and mechanisms check to see whether the existing options are sufficient for your model simulation If a predefined choice is not appro priate then follow the steps described in this section to create a new definition Once you have configured a simulation that is suitable for your purposes in terms of the horizontal grid vertical layers and chemical mechanism proceed to Chapter 8 to learn how to develop new model executables for running a CMAQ simulation 7 1 Supported CMAQ Coordinate Systems The choice of horizontal coordinate system or map projection for CMAQ is governed by the input meteorological model fields and stored in the input file headers by MCIP The grid resolution and the maximum horizontal and vertical extent are determined by the meteorological configuration that is input to MCIP MM5 and WRF ARW support the Lambert conformal polar stereographic and Mercator projections which can be directly passed to CMAQ Generally the same meteorological model fields that are used to drive CMAQ ar
238. n throughout the troposphere The five main CMAQ programs are The initial conditions processor ICON The boundary conditions processor BCON The clear sky photolysis rate calculator JPROC The Meteorology Chemistry Interface Processor MCIP 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 Sections 1 2 1 through 1 2 3 describe the CMAQ system concept followed in Section 1 2 4 by summaries describing the programs listed above 1 2 1 Installation overview All CMAQ source code except MCIP is distributed in a Linux tar file as a Concurrent Versions System CVS http ximbiot com cvs wiki source code management archive CVS is an open source network transparent version control system for managing source code in a software development environment The distributors of CMAQ use CVS to control access to the distributed source code CVS maintains a protected version of the original source code and uses copies of the code when building executables Executables are binary files that consist of instructions that have been translated from their original source code e g Fortran into machine code also called machine language or object code so that they are ready to be run executed Executable files are created through the use of a specialized program called a c
239. nal Eulerian i e gridded atmospheric chemistry and transport modeling system that simulates ozone particulate matter PM toxic airborne pollutants visibility and acidic and nutrient pollutant species 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 the model s extensibility through community development by all members of the air quality modeling community 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 June 2010 1 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 1 1 Model 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 of chemical species 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
240. nce Document 7 DEFINING GRIDS LAYERS DOMAINS AND CHEMISTRY CMAQ is a three dimensional Eulerian air quality model In this type of model the extent of the area of interest or domain and the characteristics of the three dimensional computational grid structure that represent this domain must be specified 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 CMAQ domain have the same horizontal resolution The vertical resolution of each grid cell depends on the vertical layer specification the physical vertical extent of individual grid cells can vary in space and time Mathematical algorithms describing atmospheric transport govern the flow of material into and out of individual grid cells Mathematical algorithms describing chemical reactions and aerosol dynamics govern the production and loss of material contained in the grid cells After determining the horizontal and vertical extent of the domain of interest a meteorological model must be run for a horizontal domain slightly larger than the CMAQ domain A larger meteorology domain is necessary for distinguishing the meteorological boundary conditions from the CMAQ boundary conditions This chapter describes how to define new horizontal grids vertical layers and chemical mechan isms in CMAQ These specifications apply to multiple programs i
241. ncentration file CTM_CONC_ 1 the choice depends on how the user compiled the model If the input file is not in the same chemical speciation as the simulation for which the user is creating BCs 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 CB05 or SAPRC 99 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 June 2010 5 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 5 2 2 1 BCON input files Table 5 1 BCON input files File Name Format Description BC_PROFILE ASCII Vertical chemical profiles from which to derive boundary conditions this file is created by the user used only when the BC environment variable is set to profile MECH CONV FILE ASCII Mapping factors for converting between chemical mechanisms this file is created by the user used only when BCON is compiled with the ModMech configuration set to
242. nd aerosols The average depth of the troposphere is about 11 km 7 miles in the middle latitudes It is deeper in the tropical regions up to 20 km 12 miles and shallower near the poles about 7 km 4 miles in summer indistinct in winter Within the troposphere temperature decreases with altitude The lowest part of the troposphere where friction with the Earth s surface influences air flow is the planetary boundary layer PBL This layer is typically a few hundred meters to 2 km 1 2 miles deep depending on the landform and time of day The border between the troposphere and stratosphere is called the tropopause Above this layer is a temperature inversion that is in the stratosphere temperature increases with altitude Visualization An important aspect of scientific computing that provides a method for presenting easily understandable data quickly and compactly in the form of charts and graphs DRAFT January 2009 A 9 http www cmaq model org
243. ne 11 2 LEZ A Docum nt tion a a ennan a a a a a eee a a ai 11 3 11 2 2 Interactive reS0 rCES m in iieri iiiaae ries ntate tinissi see taaie ives 11 3 11 23 Tutorials trainin gsn a Aue oars a aa 11 3 112 4 E mail SUP OTE eienenn eiai an i aaisa as 11 3 WB Contacting CMAS etae a a a T E E E RE E T E A 11 3 GLOSSARY e E E E E E E A 1 June 2010 ix http www cmaq model org CMAQv4 7 1 Operational Guidance Document Figures Figure 2 1 CMAQ Modeling Framework sscs0is3 nissedtnesitaieategdte detiseiaten ai ada auass 2 1 Figure 2 2 CMAQ Chemistry Transport Model CCTM and input processors ceeee 2 4 Figure 2 3 Meteorology preprocessing for CMAQ with MCIP ceseeseseeseeeeeeeeceseeneeeaeeeneees 2 5 Figure 2 4 Initial and boundary conditions preprocessing for CMAQ ccccccesseeeteeeteeeeteeneees 2 7 Figure 2 5 Clear sky photolysis rate preprocessing for CMAQ ou ceceecesseeeeeeeeceseeneeeeeeeeeerens 2 8 Figure 2 6 Invoking new modified gas phase chemical mechanisms in CMAQ eceseeeeees 2 9 Figure 2 7 Process analysis implementation in the CMAQ modeling system cece 2 10 Figure 2 8 CMAQ chemistry transport model and associated preprocessors ccseeees 2 11 Figure 5 1 CMAQ core procrams 4 cai acd ovsaaveeeins Wie ease 5 2 Figure 5 2 BCON input and output TES 0 5 vccccs sates stauseladesses evenes des adaduedursdes ceonvedasssadenedeanorseounets 5 4 Figure 5 3 CCTM input and output fil
244. ng and testing practices to be adopted by developers wishing to contribute code to the public CMAQ archive 1 To make the best use of the CMAQ features in developing new code the developer should review the coding conventions that are provided in the previous sections of this chapter Also see http www epa gov asmdnerl CMAQ CMA QscienceDoc html 2 New code should be built using the current operational CMAQ version as a template whenever possible This will facilitate consistency in coding practices including naming conventions in line documentation and the specification of compile time versus run time parameters 3 Before submitting source code to the CMAS Center the developer should verify that the code is consistent with the operational CMAQ version from which it was built especially in the use of common INCLUDE files such as horizontal and vertical grid definition files and run time parameter settings Mixing code from different operational versions of the CMAQ model within the same development code version can lead to problems in using the generalized CMAQ scripts 4 Comprehensive documentation or other references to peer reviewed literature should be provided for any new science algorithms include in the source code see Section 9 2 5 5 The developer must document the computational platform used for the testing including type and speed of the processor s the compiler version used and CPU usage It is recommended that
245. ng grid definition file and to one of the grids defined in the file respectively Horizontal grids can be selected either from predefined grids contained in the distributed GRIDDESC file or by adding modifying horizontal grids in the GRIDDESC file 7 2 1 Using predefined horizontal grids CMA QvV4 7 is distributed with a GRIDDESC file that contains a definition for a grid covering the northeastern U S named M_36 2001 that uses a coordinate definition named RPO GRID A picture of the grid and the grid definition in the GRIDDESC format is shown in Figure 7 1 RPO_GRID 2 33 00 45 00 97 00 97 00 40 00 M_36_2001 RPO_GRID 936000 00 576000 000 36000 00 36000 00 40 44 1 E Figure 7 1 CMAQ tutorial grid June 2010 7 2 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 7 2 2 Creating or modifying horizontal grids Creating a grid in CMAQ involves simply adding a few lines of text to the GRIDDESC file Using a combination of the file format documentation in Chapter 6 and existing grid definitions as examples new grids can be defined 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 using meteorology and or emissions data that have not yet been modeled with CMAQ MM5 or WRF ARW
246. ng the potential for model simulation error As acommunity model CMAQ is able to leverage the expertise of model developers in many areas of atmospheric science This facilitates improving and enhancing the CMAQ modeling system as the state of the science evolves For example linkages of CMAQ with exposure modeling hydrological modeling climate modeling and multimedia modeling are currently being explored 2 1 1 Multiple pollutants and multiple scales With its one atmosphere design which allows modelers to address the complex interactions among multiple pollutants air quality issues simultaneously CMAQ is a dramatic improvement over the earlier single pollutant models The CMAQ system provides state of the science capabilities for modeling multiple air quality pollutants issues in a single simulation including tropospheric ozone PM air toxics visibility and acidic and nutrient pollutant species The one atmosphere approach is important because the various chemical species interact For example ozone and hydroxyl radicals react with emitted species such as anthropogenic and biogenic organics to generate secondary PM species These PM species can interact with solar radiation to alter photolysis rates The failure of the early simplistic approach of trying to account for the chemistry of sulfur dioxide from power plants without also treating ozone and hydroxyl radicals demonstrated the need for the one atmosphere approach
247. nism default cb05cl_ae5_aq Specifies the gas phase aerosol and aqueous phase chemical mechanisms for which to create boundary conditions The choices for the Mechanism variable are the mechanism directory names under the M3MODEL include release directory Examples include o cb05ae5_ag CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry o cb05cl_ae5_aq CBO5 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry and active chlorine 5 6 http www cmaq model org CMAQv4 7 1 Operational Guidance Document o cb05cltx_ae5_aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry active chlorine and air toxics o cb05cltxhg_ae5 aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry active Chlorine air toxics and mercury this is for the multipollutant model see CMAQvV4 7 release notes o saprc99_ae5 aq SAPRC 99 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry o saprc99tx3_ae5 SAPRC 99 gas phase mechanism with air toxics and fifth generation CMAQ aerosol mechanism 5 2 2 3 BCON compilation First it is assumed that you have already installed and compiled the I O API and netCDF libraries see Section 3 2 3 Section 3 3 provides an overview of how to install and compile
248. nk characters e Numbers Numerical inputs in the command file can be either integer e g 5 floating point e g 5 0 or exponential 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 Terminate input command lines with a semicolon 5 9 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 are 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 1 Process Analysis Global Commands These commands Table 5 14 include general specifications that are applicable throughout the configuration 2 Integrated Process Rate Command This command Tables 5 15 and 5 16 is specific to the configuration of the integrated process rates There is only one command for IPRs and it controls the specific IPRs that are output Note that one command can cause many IPR outputs to be generated For example if one species or family is specified in a June 2010 5 49 http www cmaq model org CMAQv4 7 1 Operational Guidance Document command but no process codes are specified then one IPR
249. ns are being calculated in line in CMAQ the GSPRO file used by CCTM needs to contain split factors only for the biogenic VOC emissions that are input in the B3GRD file If other emissions sources are being calculated by CCTM VOC split factors for these other sources must be included in the GSPRO file The GSPRO file format is listed in the SMOKE user s manual http www smoke model org version2 5 html ch08s05s02 html June 2010 6 26 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 6 1 20 B3GRD Gridded normalized biogenic emissions Used by CCTM An I O API GRDDED3 file of gridded normalized biogenic emissions in grams of carbon or nitrogen per hour depending on the species and leaf area index The B3GRD file contains normalized emissions calculated with both summer and winter emissions factors The B3GRD file is generated with the SMOKE program NORMBEIS3 using gridded land use data For additional information about creating the B3GRD file see the NORMBEIS3 documentation in the SMOKE users manual http www smoke model org version2 5 html ch06s11 html 6 1 21 BIOSEASON Freeze dates Used by CCTM The BIOSEASON switch file is an I O API GRDDED3 file used to indicate which biogenic emissions factor to use on each day in a given year for every grid cell in the modeling domain This file can be created using the Metscan utility program that is distributed with SMOKE The BIOSEASON file is time dependent and
250. nt rates in line in the CCTM The in line photolysis approach allows photolysis rates to be adjusted by simulated gas and aerosol concentrations rather than by climatological values in the offline approach CCTM is run last in the sequence of programs All of the other CMAQ programs and the emissions and meteorological models are used to prepare the inputs to CCTM By using data that are synchronized for a particular modeling time period model grid vertical layer configuration and chemical parameterization CCTM can produce estimates of pollutant concentrations wet and dry deposition rates and visibility metrics at a time granularity set by the user In addition to the core programs shown in Figure 5 1 the CMAQ distribution package also includes utilities and libraries for utilizing some of the special features in CMAQ and for setting up CCTM for multiprocessor computing CMAQ includes the PROCAN utility for preparing process analysis simulations and CHEMMECH for editing existing and preparing new chemical mechanisms for CMAQ The stencil exchange code library STENEX is a module that CCTM uses to control the communication between processors in a multiprocessor computing environment Similarly CCTM uses the parallel I O PARIO code library to synchronize the reading and writing of information among multiple processors In the remaining sections of this chapter we provide detailed descriptions of these programs utilities and libraries
251. ny new and important features that are not available in previous modeling systems It can model complex atmospheric processes affecting transformation transport and deposition of air pollutants using a system architecture that is designed for fast and efficient computing CMAQ has been developed to meet the needs of both the research and application communities The CMAQ system allows users to easily construct model variations with different characteristics such as different chemical mechanisms or alternative cloud treatments in order to address a specific air quality issue illustrated schematically in Figure 2 1 This modeling configuration allows CMAQ to retain its state of the science status over time because it facilitates the implementation of new science modules as appropriate Interchangeable Modules Driver ica my ia Advection amp amp Diffusion J Chemistry Figure 2 1 CMAQ Modeling Framework 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 At the same time the CMAQ modeling system is also a useful tool for the model developer It is unique in that its components are designed in a flexible modular fashion with a user interface model developers can use these design features to create complex modeling situations and scenarios or to develop entirely new models using a standardized co
252. o M N blocks The default value of N is set to 500 For operations in the horizontal x y the cell constraint becomes Xx Y lt N where X number of cells in the x direction and Y number of cells in the y direction For operations in both the horizontal and vertical the constraint becomes Xx YxZ lt N where Z number of cells in the z direction There may be some operations such as for some horizontal advection schemes where this decomposition into blocks becomes more difficult or impossible 9 2 5 Documentation guidelines Appropriate documentation is critical to the ease of use and maintainability of code developed for CMAQ The official released version of CMAQ contains extensive in line documentation and references to pertinent technical information whenever possible Given the increasing number of new developers and code modules the following guidelines are provided for new code developed for CMAQ e The code revision history should be initiated or updated as appropriate for new and modified code indicating the author date and nature of the revision The revision history appears at the top of the subroutine e Complete references to the pertinent technical documents should be provided whenever possible and listed in comment lines immediately following the revision history notes They should be cited in comments preceding or embedded in line with the relevant code segments e In line documentation of the variable definitions ind
253. odel Advanced Research WRF xiii http www cmaq model org CMAQv4 7 1 Operational Guidance Document Page left intentionally blank June 2010 xiv http www cmaq model org CMAQv4 7 1 Operational Guidance Document 1 Introduction Under the authority of the Clean Air Act the U S Environmental Protection Agency EPA has established National Ambient Air Quality Standards NAAQS U S EPA 2008 These standards are designed to protect human health and the environment from high levels of criteria pollutants such as ozone and particulate matter Meeting the NAAQS often requires the use of controls on sources of air pollutants The complex nature of air pollution scenarios requires control strategies to be effective for a variety of air pollutants geographic regions and scales As part of the effort to decrease ambient concentrations of criteria pollutants the EPA has approved air quality simulation models for use at regional state and local scales within the United States The models have been applied to estimate the ability of various control strategies to improve air quality and ensure cost effective results So called 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
254. odule o phot noop deactivate photolysis rate calculations o phot calculate photolysis rates o phot sat o phot inline ModChem default ebi_cb05cl_ae5 Gas phase chemistry solver module o chem_noop deactivate gas phase chemistry o smvgear use the SMVGEAR chemistry solver o ros3 use the Rosenbrock chemistry solver o ebi_cb05cl_ae5 use the Euler Backward Iterative solver optimized for the Carbon Bond 05 mechanism with chlorine and extended aerosols o ebi_cb05cltxhg_ae5 use the Euler Backward Iterative solver optimized for the Carbon Bond 05 mechanism with air toxics mercury and chlorine with extended aerosols this is for the multipollutant model see CMAQV4 7 release notes o ebi_saprc99_ae5 use the Euler Backward Iterative solver optimized for the SAPRC 99 mechanism with extended aerosols o ebi_saprc99tx3 use the Euler Backward Iterative solver optimized for the SAPRC 99 mechanism with air toxics ModAero default aero5 CMAQ aerosol module aero_noop deactivate aerosol chemistry o aero4 use the fourth generation modal CMAQ aerosol model with extensions for sea salt emissions and thermodynamics o aeroS use the fifth generation modal CMAQ aerosol model with extensions for sea salt emissions and thermodynamics and a new formulation for secondary organic aerosol 5 15 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 o aero5_txhg use aero5 with air toxics and mercury
255. ommendations may be considered as 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 for running the CMAQ benchmark case are June 2010 3 1 http www cmaq model org CMAQv4 7 1 Operational Guidance Document e PC with a single 1 0 GHz processor with a Linux operating system OS e 1GBRAM e 10GB hard drive storage Note the benchmark simulation requires 3 GB of free storage capacity Below are two examples of optimal hardware configurations for running CMAQ on multiple processors in a production environment Optimal CMAQ Hardware Solution 1 e 4dual CPU 2 8 GHz Xeon IBM BladeCenter rack mounted nodes with Red Hat Enterprise Linux OS 2 GB RAM per node Gigabit Ethernet network 1 5 TB hard drive storage Super DLT 110 GB tapes for system backups Uninterruptible power supply UPS Optimal CMAQ Hardware Solution 2 8 dual CPU 2 5 GHz AMD Athlon MP 2000 PCs with Ubuntu Linux O S 2 0 GB RAM per PC Gigabit Ethernet network 80 GB system storage 10 TB IDE SCSI RAID 5 array UPS 3 1 2 Software CMAQ requires all of the programs listed in Table 3 1 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 Note that MPICH needs to be installed by the system administrator because thi
256. ommon INCLUDE file lists all of the chemical mechanism variables 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_CONC 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 velocities GC_DIFF EXT ASCII File listing the gas phase model species that are transported by diffusion GC_EMIS EXT ASCII File listing the emitted gas phase model species GC_G2AE EXT ASCII File listing the gas phase model species that react to form aerosols GC_G2AQ EXT ASCII File listing the gas phase model species that have aqueous chemistry pathways GC_ICBC EXT ASCII File listing the gas phase model species that require initial and boundary conditions GC_SCAV EXT ASCII File listing the gas phase species that are scavenged by cloud water GC_SPC EXT ASCII File listing all of the gas phase model species GC_WDEP EXT ASCII File listing the gas phase model species that wet deposit June 2010 http www cmaq model org CMAOv4 7 1 Operational Guidance Document The default location of the CHEMMECH output files is the ext
257. ompiler CVS must be installed on the user s Linux system before installing CMAQ When 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 source code The CMAQ program M3BLD controls the extraction June 2010 1 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document of copies of CMAQ source code from CVS based on the configuration options specified by the user in UNIX C shell scripts After exporting the CMAQ source code from CVS M3BLD then invokes a Fortran 90 compiler to compile the CMAQ source code into binary object files and link them with the necessary precompiled libraries to create binary CMAQ executables C and Fortran 90 compilers must be installed on the user s Linux system in order to create CMAQ executables As noted above MCIP is not distributed in a CVS archive Instead when the CMAQ code is downloaded MCIP appears in its own directory with source code and makefiles for installation 1 2 2 Configuration options Because the model infrastructure was designed to promote modularity the user must create new CMAQ 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 efficiently in a single ex
258. on and is scaled to the grid cell size The horizontal eddy diffusivity is assumed to be uniform but dependent on the grid resolution of the model This diffusivity is larger for a higher resolution run where the numerical diffusion due to the advection process is smaller June 2010 2 13 http www cmaq model org CMAOv4 7 1 Operational Guidance Document 2 3 4 Particulate matter aerosols Within the air quality community atmospheric aerosol particles are referred to as particulate matter PM PM can be either primary or secondary Primary PM is emitted directly into the atmosphere from natural or anthropogenic man made sources Secondary PM is formed in the atmosphere either from precursors that react chemically to form new particles or from vapor phase species that condense or deposit onto primary particles that are already present in the atmosphere Cloud processes also contribute to the formation of PM for example aqueous oxidation of sulfur dioxide in cloud droplets is a significant pathway for production of particulate sulfate CCTM represents PM using three lognormal subdistributions or modes Two interacting modes Aitken and accumulation represent PM gt 5 particulate matter of diameter equal to or less than 2 5 microns A coarse mode represents PM with diameters greater than 2 5 microns and equal to or less than 10 microns Thus PM is modeled as the sum of the PM 5 and coarse mode PM Particulate matter is deposited to
259. on that uses in line emissions processing e IOAPI explanation of how to get the I O API system and set up the libraries e MCIP TO HYSPLIT description of the utility program for converting MCIP data into HYSPLIT format e MULTIPOLLUTANT MODEL description of the multipollutant configuration of CMAQ for simulating mercury air toxics ozone PM and acid deposition e PARALLEL NOTES comments related to running the CMAQ CCTM in Linux MPICH clusters e PROCESS ANALYSIS NOTES description of the CMAQ process analysis option e README description of the CMAQ installation procedures alternative to this installation chapter e RELEASE NOTES list of the changes since the last release e RESTART FILE description of the restart file that was first introduced in CMAQ version 4 6 e SMOKE description of the SMOKE emissions system e MODELS CMAQV4 7 1 tar gz gzipped tar file 7 2 MB containing model tools and libraries source code CVS archives e DATA CMAQV4 7 1 tar gz gzipped tar file 52 MB containing the required datasets necessary to run the benchmark case e SCRIPTS CMAQV4 7 1 tar gz gzipped tar file 16 KB containing C shell scripts to build and execute the CMAQ models e DATA _REF CMAQV4 7 1 tar gz gzipped tar file 217 MB containing reference data to compare with datasets produced by the tutorial on a Linux workstation The CMAQ installation scripts are configured for a Linux system with either the Portland
260. on type n G NROWS Int Number of horizontal grid rows dependent on projection type H NTHIK Int Boundary perimeter thickness number of cells optional 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 lines 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 segment of GRIDDESC COORD NAMI COORDTYPE P_ALP P_B XCENT YCENT GI al T P_GAM June 2010 6 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Qr 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 An example of a GRIDDESC fil
261. onfiguration file can be generated either by the CMAQ system or by the users following a few simple syntactical rules In addition to the global INCLUDE files the configuration file contains module commands that tell M3BLD to extract the codes for that module from the model code repository for compilation 9 2 3 Thin Interface As mentioned in Section 9 2 2 CMAQ is designed to be robust and flexible with respect to the interchange of modules and the elimination of cross module data dependencies Consequently the concept of a thin interface has been employed in the design which applies principally to the class drivers i e the top level call to a science module At a minimum the thin interface implementation implies the following requirements e Eliminate global memory references across modules This implies no common blocks across modules no hidden data paths and no back doors e Each module reads and interpolates its required data independently The I O API helps to ensure this kind of data independence e Standardized argument list CGRID Date Time TimeStep for calling the class driver See the example in Section 9 2 6 These requirements attempt to incorporate the object oriented idea of encapsulation in the CMAQ design Rumbaugh et al 1991 suggest that Encapsulation also information hiding consists of separating the external aspects of an object which are accessible to other objects from the internal imple
262. onment Before compiling CCTM for parallel execution you must specify the location of the MPICH directory on your system in the CCTM build script For single processor systems configure the build script to create a single processor executable by commenting out the line that activates the variable ParOpt of the CCTM build script Use the following commands to compile CCTM cd SM3HOME scripts cctm bldit cctm Although not used for the benchmark simulation the PROCAN processor can also be compiled using M3BLD 3 4 Running the CMAQ Benchmark Simulation After successfully compiling the various CMAQ programs use the distributed run scripts to generate the CCTM input files and then to run CCTM for the CMAQ benchmark case CCTM must be run last in the simulation sequence MCIP must be run first Other than that there are no dependencies among the other CMAQ programs so they can be run in any order to create input data for CCTM If all of the programs were compiled with Intel Fortran on a Linux 64 bit operating system the benchmark simulation will execute without any modifications to the run scripts There will be slight modifications to the run scripts if the CMAQ programs were either compiled on 32 bit operating systems and or they were compiled with other brands of Fortran These modifications will entail changing the name of the program executables to reflect the configuration of your computing system For example by default the ICON run scri
263. or advection of pollutants and other chemical species into the modeling domain from areas outside it CMAQ currently accounts for advection into the domain only from the horizontal i e lateral boundaries assuming there is no exchange through the top boundary of the domain i e vertical exchange These spatial lateral boundary conditions are estimated in CMAQ using the boundary conditions processor BCON Similarly a temporal boundary condition is established with the initial conditions processor ICON which estimates the chemical conditions in the first time step of a CMAQ model simulation To model incoming 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 solar hour angles Output from these three CMAQ programs is used with output files from the emissions and meteorological models and other CMAQ preprocessors to form the required input data for running CCTM 1 2 4 Summary descriptions of the major CMAQ programs The major CMAQ components and ancillary programs are described below The listing is in the order that you as a user will run them The last component listed CHEMMECH is for use by advanced users who wish to define a new or modified chemical mechanism for CMAQ Model Builder M3BLD The only CMAQ component written in the C programming language M3BLD provides an interface to the CVS source code archive
264. ort enough to allow episodic studies Parameterize To create an algorithm that describes the average large scale behavior of a physical phenomenon rather than describing the subgrid scale behavior in terms of the underlying physics and chemistry For example a parameterized cloud algorithm might describe average cloud behavior over 80 km square cells although the individual clouds are much smaller that 80 km across Planetary boundary layer The portion of the atmosphere adjacent to the earth s surface This layer generally ranges from 100 m to 2 km in height and is significantly influenced by surface effects e g heating friction These effects can cause the layer to be well mixed which affects the distribution of pollutants in the air See also troposphere Popup window A popup window is a special window for displaying an on line help entry The window opens when you select a specially designated hypertext link Pop up windows are useful for quickly displaying short concise units of information You cannot jump or step to other entries from a pop up window Prepare Read and process a file or a set of data Process analysis Traces the source s of a chemical species within a simulation One example of process analysis is determining whether a species concentration originated within the cell in which it is found or instead within some other cell s Another example is determining what chemical constituents were involved i
265. outputs can be run through MCIP to generate a GRIDDESC file that can be input directly to both CMAQ and SMOKE If the meteorology data have already been processed by MCIP and the GRIDDESC file is missing the grid definition of the input meteorology and emissions can be determined by using the netCDF utility ncdump to view the header of one of the I O API files and then use that information to manually create a GRIDDESC file 7 2 3 Further information on horizontal grids Meteorological Grids e The lateral boundaries of the meteorological model fields 5 cells on each horizontal side are typically not used in the air quality simulation Therefore the meteorological model domain is often oversized to cover an area that is somewhat larger than is used in CMAQ e Horizontal grid spacing for the meteorology nested grids often has a 3 1 ratio although other ratios have been employed C MAQ Grids e A CMAQ grid uses the same horizontal resolution as its parent meteorology grid e Minimum grid dimensions of 30 rows and 30 columns are recommended e External boundary thickness should be set to 1 e A CMAQ grid should be smaller than its parent meteorology grid by at least four grid cells on a side and preferably by six 7 3 Vertical Layers The vertical structure of CMAQ is inherited from the model used to prepare the meteorological information Both MM5 and WRF ARW use a sigma coordinate that is based upon surface pressure not s
266. ow users to easily access these variables in the code in a generic and portable manner An additional feature that is provided through the I O API is the ability to declare a file volatile by appending a v flag in the shell s declaration for the environment variable By doing this the T O API will cause the netCDF file to update sync its disk copy after every write and thereby update the netCDF header Otherwise netCDF I O API file headers are not updated until the files are closed This feature is useful for example for allowing a user to analyze an open netCDF file using visualization tools while the model is executing It is also useful in case of a system crash A CCTM model can be restarted at the scenario time step after the last successful write using the aborted output file as the input initial data The following is a sample run script that can be downloaded from the CMAS web site The build and run scripts are part of the downloaded tar file from this site bin csh f CCTMv4 7 Run Script Usage run cctm gt amp cctm_e3a log amp The following environment variables must be set for this script to xecute properly setenv M3DATA input output data directory To report problems or request help with this script program http www cmascenter org html help html gt Check that M3DATA is set if e S M3DATA then echo SM3DATA pa
267. patial extent of a geographic boundary Grid cell The smallest subdivision of a grid Grid size Length of shortest side of a rectangular grid cell Grid A network of conceptual locations at which numerical calculations are performed This network extends horizontally to cover the domain of interest and vertically through the troposphere Growth factor An adjustment factor used to estimate the growth in a source s activity level between the inventory base year and a projected year Valid values are 0 00 99 99 DRAFT January 2009 A 3 http www cmaq model org CMAOv4 7 1 Operational Guidance Document Heterogeneous distributed computing environment A heterogeneous computing environment consists of multiple machines of different types e g supercomputers graphics workstations and workstation file servers A distributed computing environment permits the execution of a large computational task to be shared across multiple machines linked together by a network Thus a heterogeneous distributed computing environment consists of many different kinds of machines networked together Hydrostatic Used to indicate to a model that it is to assume that the atmosphere is in hydrostatic equilibrium i e surfaces of constant pressure and constant mass coincide and are horizontal throughout Complete balance exists between the force of gravity and the pressure force Hypertext link A hypertext link is a specially designated word or phrase
268. pheric and stratospheric dust Appl Optics 8 893 903 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 mode particle and PM 5 concentrations and their impact on model performance evaluation in the lower Fraser valley 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 June 2010 2 17 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 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 National Oceanic and Atmospheric Administration 1976 U S Standard Atmosphere U S Government Printing Office Washington DC NOAA S T76 1562 June 2010 2 18 http www cmaq model or
269. ployed design ideas that draw heavily from the object oriented concept of inheritance and code re use The data structures in the codes that deal with the chemical mechanism I O API logical file names general constants and pointers are determined by Fortran declarations in data and parameter statements in the CMAQ system These data structures pertain to a particular application and are meant to apply globally not just to one particular CCTM through all its subroutines but also to all the models that supply data to CCTM for that application These data structures are contained in Fortran INCLUDE files which are essentially header files included in the declaration sections near the top of the Fortran code source files The inclusion of these source files is made automatic by using a generic string that represents the INCLUDE file and that is parsed and expanded to the actual INCLUDE file during a preprocessing stage in the compilation The Fortran global INCLUDE files contain name tables that define 1 The chemical mechanism 2 The I O API interface including logical file names 3 The global modeling constants and 4 Other constants or parameters that apply across the model To effect the implementation of the INCLUDE files into the code a special compiling system M3BLD was developed Fine et al 1998 which reads a configuration file that based on the application completely determines the model executable to be built The ASCII c
270. pt will look for the 64 bit Intel Fortran compiled executable named TCON_ela_Linux2_x86_64ifort If you compiled the program on a 32 bit operating system using the Portland Group compiler change the EXEC variable in the run icon file to ITCON_ CFG _Linux2_x86pg CCTM is configured by default to run in single processor mode For single processor computing set NPROCS to 1 and NPCOL_NPROW to 1 1 Running in multiprocessor mode requires building an executable that includes routines from the MPICH library and setting the number of processors to allocate to the simulation and the location of the MPI initialization command mpirun on your system 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 you have a system with six processors June 2010 3 10 http www cmaq model org CMAQv4 7 1 Operational Guidance Document available to run CMAQ set NPROCS to 6 and NPCOL_NPROW equal to 3 2 Most clustered multiprocessor 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 r
271. r required A sample of the important sections of a BC_PROFILE file is shown 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 200E 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 ICs and BCs from one mechanism form to another The default IC and BC profiles distributed with CMAQ contain RADM2 species The ICON and BCON processors contain routines for converting from RADM2 to CBOS If desired these routines 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 6 6 The file is list formatted June 2010 6 10 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Table 6 6 MECH_CONV_FILE format description Line Column Name Type Description Hi 1 16 SPP1_OUT String Output mechanism species name for first species required 17 Char delimits the left hand and right hand side of the conversion equation required 18 SPP1_IN String Input mechanism species name
272. r angle 3 required JVTMAX XJVAL_ JVTMAX Real or Clear sky photolysis rate at NHTO Exp NLATO NPHOTO and hour angle corresponding to JVTMAX required A sample of the important sections of a JTABLE file is shown below 1999181 yyyyddd Julian Date for the file 7 LEVELS m 6 LATITUDES deg 9 HOUR ANGLES from noon 6 PHOTOLYTIC REACTIONS NO2_CBIV88 My 0 O301D_CBIV88 Mea 10 HCHOmol_CBIV88 1 0 HCHOrad_CBIV88 1 0 June 2010 10 0 20 0 30 0 40 0 50 0 60 0 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 6 25 0 0 1000 0 2000 0 3000 0 4000 0 5000 0 10000 0 http www cmaq model org CMAQv4 7 1 Operational Guidance Document ALD_CBIV88 tp ha ACROLEIN y Leg L l 5 0964761E 01 4 9923715E 01 4 6422747E 01 4 0129572E 01 3 0394882E 01 1 6590215E 01 3 2829735E 02 0 0000000E 00 0 0000000E 00 6 1 17 EMIS_1 Emissions Used by CCTM CMAQ can accept emissions inputs from a variety of emissions models and preprocessors The most commonly used option is the Sparse Matrix Operator Kernel Emissions SMOKE modeling system which is a collection of programs that separately process and merge emissions data for each emissions sector for input to air quality models 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 per second moles s for gas ph
273. r edu software idv docs workshop Answers to FAQ http www unidata ucar edu software idv docs userguide Faq html Support info http www unidata ucar edu software idv docs userguide Support html The Integrated Data Viewer IDV from Unidata is a Java based software framework for analyzing and visualizing geoscience data The IDV release includes a software library and a reference application made from that software It uses the VisAD library http www ssec wisc edu billh visad html and other Java based utility packages The IDV is developed at the Unidata Program Center UPC part of the University Corporation for Atmospheric Research in Boulder CO which is funded by the National Science Foundation The software is freely available under the terms of the GNU Lesser General Public License The IDV reference application is a geoscience display and analysis software system with many of the standard data displays that other Unidata software e g GEMPAK and McIDAS provides It brings together the ability to display and work with satellite imagery gridded data for example numerical weather prediction model output surface observations balloon soundings NWS WSR 88D Level II and Level I RADAR data and NOAA National Profiler Network data all within a unified interface It also provides 3 D views of the earth system and allows users to interactively slice dice and probe the data creating
274. ral coverage of the simulation the chemical mechanism to use in the modeling the physics scheme to use for modeling pollutant transport heterogeneous and aqueous chemistry options and diagnostic options such as process analysis discussed in the next paragraph CCTM has the largest number of configuration options of all the CMAQ programs Process Analysis Preprocessor PROCAN Process analysis is a technique used to trace the source s of a chemical species within a simulation PROCAN generates Fortran INCLUDE files for building a version of CCTM that can calculate integrated process rates and or integrated reaction rates discussed in Section 6 3 these rates can then be used for diagnosing the chemical behavior of CMAQ simulations This preprocessor uses an input configuration file to select the process analysis options desired and outputs three INCLUDE files that are used to compile a version of CCTM that is instrumented for process analysis Chemical Mechanism Compiler CHEMMECH This program creates chemical 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 kinetic parameters that describe a photochemical 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
275. ram used for input and quality control checks of emission inventories Inventory With respect to an emission processing system inventory refers to a file or a database containing emission data for a specific set of pollutants for a specific time period typically for the entirety of a specific year for an area country states counties Irix Operating system for SGI computers Keyword A keyword is a word or phrase up to 40 characters long that can be used to locate an entity in help text or a Models 3 object e g dataset program study or model using a Find screen Layer collapsing A procedure in which the layer structure prepared by a meteorological model is modified by reducing the number of layers This is not recommended DRAFT January 2009 A 4 http www cmaq model org CMAOQv4 7 1 Operational Guidance Document Linux An open source UNIX like operating system It is available and redistributable under the terms of the GNU Public License Makefile A Makefile is a list of UNIX commands that perform activities such as mounting files and compiling source code Massively parallel processing Computer processing employing multiple CPUs to execute multiple computational tasks simultaneously Massively parallel systems employ a large number of CPUs simultaneously on the same task In contrast conventional computer design uses a single CPU to perform computational tasks in a strictly linear sequential order Mesoscale
276. raphic region The selection of episodes in CMAQ however is completely determined by the availability of input meteorology and emissions data The horizontal model grid vertical layer structure and model time periods must be consistent across the meteorology data emissions data and CMAQ Configuring CMAQ for new simulations involves defining the model grid vertical layers time periods initial and boundary conditions input output file locations and science options of the model The following sections cover these topics in the context of setting up a new CMAQ simulation 8 2 1 Defining a new horizontal grid The grid dependent CMAQ programs CCTM ICON BCON use the GRIDDESC grid descrip tion file Section 6 1 1 to define the map projection and horizontal grid for a simulation The GRIDDESC file is either output by MCIP or it can be created manually using a text editor The CMAQ run scripts for the grid dependent CMAQ programs must refer to a GRIDDESC file that contains the definition of the model grid to be simulated The name of the grid for the current application must be specified in the CMAQ run script because a single GRIDDESC file can contain multiple grid definitions Additional information about setting up horizontal grids in CMAQ is contained in Chapter 7 The following error from any of the CMAQ programs can occur if the name and or location of the GRIDDESC file and or the name of the horizontal grid are incorrect in the run scr
277. ration IMPLICIT NONE to maintain some control on typographic errors and undefined variables The use of IMPLICIT NONE forces the developer to declare all internal variables This is standard in Fortran 90 Use the global INCLUDE files for chemical mechanism data and other data where available June 2010 9 5 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 8 Use the I O API for external data references where appropriate For an illustration of these rules see the code template provided in Section 9 2 6 At the submodule level there are no strict I O or coding standards Here it is envisioned that individual researchers programmers use their own coding styles for their algorithms However the following suggestions are offered to facilitate the potential incorporation of a module into the CMAQ system e In general it is expected that MKS units are used for input and output variables as these units have been standardized throughout the CMAQ system Within a submodule subroutine whatever units are most convenient can be used However the developer must be responsible for any unit conversions to MKS for input and output and thus avoid potential errors e For efficiency and performance considerations operations may need to be done on groups of grid cells a block of cells at a time If there are N cells in the block and the entire domain contains M cells then the entire domain can be decomposed int
278. rcial packages the ability to access and manipulate datasets located on remote machines support for multiple simultaneous visualizations an architecture that allows PAVE to be controlled by external processes low computational overhead no software distribution cost PAVE is very widely used by the air quality modeling community and it can produce various types of plots including scatter plots time series plots 2 D tile plots 3 D surface plots bar plots wind vector plots etc The source code for PAVE is also distributed under the terms of the GNU General Public License Version 2 PAVE can be run at the Linux command prompt and the various commands options can be invoked using the graphical user interface GUD or all of them can be stored in a script file and executed by running the script However note that PAVE is not being updated any more and CMAS has ceased support for PAVE and encourages the user community to move towards VERDI discussed next 10 4 Visualization Environment for Rich Data Interpretation VERDI Latest Version Version 1 1 released on May 22 2009 Main website http www verdi tool org Download http www verdi tool org Latest User s Manual http www verdi tool org Answers to FAQ http www verdi tool org Support website http bugz unc edu The Visualization Environment for Rich Data Interpretation VERDI is a flexible and modular J
279. resstestssresseeseesresseesseserst 1 5 1 2 3 Chemistry transport model conceptual formulation s ssssssseseesesseeees seseo 1 5 1 2 4 Summary descriptions of the major CMAQ programs ssssssessesessseesses1 1 6 1 3 Features of CMAQ for Application Users sseseeseesseesseseessressessessreesesresseessesersseesse 1 9 1 4 Features of CMAQ for Air Quality Model Developers ssnsnessssseseseesesseessesessesse 1 9 1 5 New Features in Version 4 7 esesssssesessessesessssseesesseseesessesresteseesessestesesseseesssseesessesee 1 10 LST Verion AT Aeeiiaea a eda aia e a AREER E EEAO TAE 1 10 1 52 PW Eron A en Sth alee tal ed a cas n S 1 10 1 6 About This Manuab gorge S i cue St Mee a a aa don Teed saan leds agar ateN E aae 1 10 UF ReferenCES i in nmana E wes sats ea 0179 eaa pala e aa andy sa ssarencunsaaibaatatns 1 14 2 OVERVIEW OF THE SCIENCE IN THE CMAQ MODELING SYSTEM 2 1 2 1 Features Implemented to Achieve the Goals of CMAQ eececccccsceseeeeeeeteeenteenteenees 2 2 2 1 1 Multiple pollutants and multiple scales 2 0 ec ec cecceeeceeeeeeeeceseeeseeenseeeeees 2 2 2 1 2 Modular flexibility esena anan i a a a eas cade hs 2 3 2 1 3 Major quality control features seeseeseeeseesseeseeseesseesesrosseesesressesseserssresse 2 3 2 2 CMAQ Input PROCES SONS usenet a a E E E 2 4 2 2 1 MCIP Meteorology Chemistry Interface Processor eecceseeeteeneeeeeeeees 2 5 2 2 2 ICON and BCON
280. rogram For the selected photochemical mechanism the user must provide a set of molecular absorption CSQY data files that are consistent with the photolysis reactions in the mechanism CMAQ is distributed with a full set of CSQY files for the CB05 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 TOMS data to replace the climatologically derived ozone column data in the PROFILES file 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 density and Dobson values TOMS ASCII Total ozone column measurements from the Total Ozone Mapping Spectrometer instrument aboard the sun synchronous polar orbiting Nimbus satellite O2ABS ASCII Absorption CSQY data for molecular oxygen as a function of wavelength June 2010 5 37 http www cmaq model org CMAQv4 7 1 Operational Guidance Document O3ABS ASCII Absorption CSQY data for ozone as a function of wavelength CSQY ASCII Directory path containing absorption CSQY data for gas phase directory
281. rom RADM2 to CBO5 speciation o radm2_to_saprc99 convert the input initial conditions profiles from RADM2 to SAPRC 99 speciation Mechanism default cb05cl_ae5_aq Specifies the gas phase aerosol and aqueous phase chemical mechanisms for which to create initial conditions The choices for the Mechanism variable are the mechanism directory names under the M3MODEL include release directory Examples include o cb0Sae5_ aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry o cb05cl_ae5_aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry and active chlorine o cb05cltx_ae5_aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry active chlorine and air toxics o cb05cltxhg_ae5 aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry active Chlorine air toxics and mercury this is for the multipollutant model see CMAQvV4 7 release notes 5 33 http www cmaq model org CMAQv4 7 1 Operational Guidance Document o saprc99_ae5 aq SAPRC 99 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry o saprc99tx3_ae5 SAPRC 99 gas phase mechanism with air toxics and fifth generation CMAQ aerosol mechanism 5 5 2 3 ICON compilation First it is assumed that you have already
282. rosol chemistry mechanism and aqueous chemistry mechanism used for the CMAQ simulation The choices for these options and how they are selected for each of the CMAQ programs are detailed in Chapter 5 CMAQ uses the MCIP processor to prepare the meteorological fields for CCTM The ICON and BCON processors generate the initial and boundary conditions for a CCTM simulation JPROC computes the photolysis rates that are used when simulating photochemical reactions in CCTM Emissions for CMAQ must be prepared with a modeling system that generates emissions for direct input to CCTM currently SMOKE or CONCEPT Brief descriptions of the various CMAQ input processors are presented in this section Also described are two processors CHEMMECH and PROCAN not shown in Figure 2 1 2 2 1 MCIP Meteorology Chemistry Interface Processor MCIP uses output files from a meteorological model such as MMS to create netCDF formatted input meteorology files that are used by the emissions model that computes emissions inputs to CMAQ and by CCTM within CMAQ Figure 2 3 The files created by MCIP are not listed individually here Output Files Meteorology Modeling Needed as CMAQ Chemistry Transport System Input by Model CCTM CMAQ Figure 2 3 Meteorology preprocessing for CMAQ with MCIP Using output fields from the meteorological model MCIP performs the following functions e Extracts meteorological model output that is specific to
283. s load SNCARG_ROOT 1lib ncarg nclscripts csm contributed ncl NCL also has a capability to call external Fortran or C routines This is enabled through an NCL wrapper script called WRAP IT The wrapper file is a C program that describes all of the arguments and passes them back and forth between the function procedure the user wants to call and the NCL script that is calling it Thus when the user invokes WRAP IT on the Fortran code that needs to be called from NCL it creates a special C wrapper file compiles it and the Fortran file and generates a so file that the user can then load into NCL using the external statement June 2010 10 10 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 11 CMAQ SUPPORT Technical and operational user support for CMAQ are available free of charge from the Community Modeling and Analysis System Center http www cmascenter org The CMAS Center offers an e mail help desk and community listservs for posting questions about CMAQ In addition to these community based resources the CMAS Center offers fee based trainings and provides a documentation library for CMAQ that includes operational and technical guidance manuals as well as references to primary literature involving CMAQ The CMAS Center does not offer telephone or on site support Additional CMAQ support can be obtained for a fee through support contracts with modeling contractors experienced in applying and de
284. s contained in the CONC files depend on the chemical mechanism and aerosol model configurations that are selected when CCTM is compiled 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 the AE CONC EXT file lists the aerosol species and the NR_CONC lists the nonreactive inert species written to the CONC file Species can be removed from the CONC EXT files to reduce the number of species that are written to and thus the size of the CONC file June 2010 6 31 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 6 2 3 CGRID CCTM restart file The 3 D CCTM ending concentration file CGRID is the CCTM restart file Containing gas phase species mixing ratios ppmV and aerosol species concentrations ug m the CGRID file includes model species concentrations at the end of each simulation period The number and types of species contained in the output CGRID files depend on the chemical mechanism and aerosol model configurations that are selected when CCTM is compiled This file can be used to initialize CCTM from the simulation period that the model completed For example if the CCTM is configure to produce daily output files a CGRID file will be written out at the end of each simulation day 6 2 4 ACONC CCTM hourly average concentration file Th
285. s 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 CCTM from either ASCII vertical profiles or from an existing CCTM output concentration CONC file ICON creates an output file with a single time step that 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 create only spatially uniform ICs within each model layer it can create different ICs across model layers From CONC files ICON can extract spatially varying ICs either on the same grid cell resolution as a windowed modeling domain or for a finer resolution model grid as for a nested simulation There are two distinct modes of operation for ICON depending on the nature of the input data When creating ICON executables the user must specify whether the input data will be ASCII vertical profiles or a CONC file by selecting either profile or m3conc respect
286. s for calculating elevated point source emissions ASKfile Directory path and location for the output surface media mercury concentrations This variable is used only when CCTM is compiled to calculate the bidirectional surface exchange for mercury OCEANpath default SM3DATA emis 2001 OCEANfile default us36_surf40x44 ncf Directory path and file name for the input sea salt emissions file EM EM ISpath default SM3DATA emis 2001 ISfile default emis3d 10010722 US36_40x44 ncf Directory path and file name for the input emissions file 5 23 http www cmaq model org CMAOv4 7 1 Operational Guidance Document TR_EMpath TR_Emfile defaul defaul t commented out t commented out Directory path and file name for the input tracer emissions file GC AE NR TR _ GC_ICfile ICpath default SM3DATA icon default ICON_ela_S cfg _cb05cl_M_36_2001_profile Directory path and file name for the input initial conditions file SMD_ICpath SMD_ICfile Directory path and file name for the input initial conditions for the bidirectional surface exchange model These variables are used only when CCTM is compiled to calculate the bidirectional surface exchange for mercury GC AE NR TR _BCpath default SM3DATA bcon GC_BCfile default BCON_ela_S cfg _cb05cl_M_36_2001_profile Directory path and file name for the input boundary cond
287. s program is specific to the computing platform June 2010 3 2 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Table 3 1 Software required for running CMAQ Software Description M3BLD Models 3 program builder for source code management and code compilation JPROC Photolysis rate preprocessor ICON Initial conditions preprocessor BCON Boundary conditions preprocessor MCIP Meteorology Chemistry Interface Processor CCTM CMAQ Chemistry Transport Model CHEMMECH Chemical mechanism compiler for modifying or adding reactions to the CMAQ chemistry PROCAN Process analysis preprocessor for setting up CMAQ to generate integrated reaction rates or integrated process rates Source Contained in the standard CMAQ distribution available at http www cmascenter org IFORT Intel Fortran 90 compiler http www intel com PGF90 Portland Group Fortran 90 compiler http www pgroup com GCC Gnu C compiler http gcc gnu org STENEX CMAQ stencil exchange library for parallel job management Contained in the standard CMAQ distribution available at PARIO CMAQ parallel input output management lindane emaccenteror library MPICH Library for the message passing interface http www used for multiprocessor CMAQ simulations unix mcs anl gov mpi mpich1 netCDF Network Common Data Form library for http my unidata ucar edu cont controlling CMAQ fil
288. s section quantum yield CSQY data and computes photolysis rates during execution Also there were several options discontinued in CMAQV4 7 The Plume in Grid option Ping CB IV chemical mechanism replaced by CB05 Aero3 module and AE3 mechanisms replaced by Aero4 Aero5 AE4 and AE5 Regional Acid Deposition Model RADM cloud module Stand alone mercury version of CMAQ this capability is included in the multipollutant version of CMAQ see Table 1 1 For the changes and new features included in the latest version of MCIP please see the release notes for MCIP version 3 4 1 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 execution of CMAQ on Linux systems The users should be familiar with Linux scripting conventions and have some familiarity with the Fortran programming language Users should also have some familiarity with atmospheric structure and the physical and chemical processes occurring in the atmosphere June 2010 1 10 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Introductory and overview chapters present the CMAQ concepts terminology installation instructions and guidance on running the tutorial simulation distributed with the model The chapters on developing meteorology and emissions for CMAQ present the basic concepts and the availability of models that generate t
289. s vertical profiles cee eeeeeeceseeeeeneeeeeees 6 6 6 1 3 BC PROFILE Boundary conditions vertical profiles 0 0 0 0 eeeeeeeseeeeees 6 8 6 1 4 MECH CONV FILE Mechanism conversion file ceseeceeeeceteeeeeeeee 6 10 6 1 5 CTM_CONC _1 CCTM concentration files se ccshscishaaaesscessstcsnthoatdiassanss 6 11 6 1 6 CSQY Absorption cross section and quantum yields cccceeceeteeeteeee 6 12 6 1 7 ET Extraterrestrial Patan Ce oi sx cent assienudannesasce Sucetarasteacinwiecatavanaovaseaesda 6 13 6 1 8 PROFILES Atmospheric vertical profiles cccccccsseceseceeeceseeeeteeeteeeees 6 15 6 1 9 TOMS Total ozone mapping spectrometer data ecceeeeceesteeeteeeteeees 6 18 6 1 10 O2ABS Molecular oxygen absorption cross section data 0 cee 6 18 6 1 11 O3ABS Ozone absorption cross section data cccecceseeseesteceteeeeeeeees 6 18 6 1 12 InMetFiles List of MM5 or WRF ARW output files eeeeeeees 6 19 6 1 13 InTerFile MM5 terrain G16 jen cst toss saleais wesc dckiays Made msnsadeeciy sackeenalass nptentieay 6 19 6 1 14 BNDY CONC_ 1 Boundary conditions eee eecececeteceeeeeeeeeeteeeeseeees 6 19 6 1 15 INIT CONC 1 Initial conditions s 24 4 csccsccssiscesdcbescedescssascnstetecesssansdveeaeas 6 21 6 1 16 JTABLE Photolysis rates look up table eee cesceeeeereeesseeeteeeteenees 6 22 OAL EMIS Pe Emissions nana e ai lem dente ads 6 26 LTS OCEAN 1 Seasalt mask a fais cccstichs taco lspccdin datas enbad
290. se calculation see the ELEVPOINT documentation in the SMOKE user s manual http www smoke model org version2 5 html ch06s03 html June 2010 6 27 http www cmaq model org CMAOQv4 7 1 Operational Guidance Document 6 1 24 GRID _CRO_2D Two dimensional grid cross point fields Used by CCTM The GRID_CRO_2D time independent file contains surface fields at cross points i e at cell centers It is created by MCIP and used by CCTM The following variables are in this file LAT latitude degrees where Northern Hemisphere is positive LON longitude degrees where Western Hemisphere is negative MSFX2 squared map scale factor m m HT terrain elevation m DLUSE dominant land use category LWMASK land water mask 1 land 0 water PURB urban percentage if cell is based on land percent 6 1 25 GRID_DOT_2D Two dimensional grid dot point fields Used by CCTM The GRID_DOT_2D time independent file contains surface fields at dot points 1 e at cell corners It is created by MCIP and used by CCTM The following variables are in the GRID DOT 2D file LAT latitude degrees where Northern Hemisphere is positive LON longitude degrees where Western Hemisphere is negative MSFD2 squared map scale factor m m 6 1 26 MET_BDY_3D Three dimensional meteorological boundary input Used by CCTM The MET BDY_ 3D time dependent file contains 3 D meteorological descriptions at the lateral boundaries on cross points
291. se files are set at the four boundaries north east south west of the computational grid and are thus fixed in space e Existing CCTM 3 D concentration fields Usually this option is selected 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 time in a separate run step Unlike the profiles discussed in the previous bullet these CCTM concentration files are spatially and temporally resolved RADM2 Profile or CCTM 3 D CONC File CMAQ Chemistry Transport Model CCTM Chemical Mechanism Figure 2 4 Initial and boundary conditions preprocessing for CMAQ Chemical mechanism Both the vertical concentration profiles and the CCTM concentration fields have specific chemical mechanisms associated with them which are a function of how the files were originally generated Figure 2 4 assumes that the RADM2 chemical mechanism was used to generate the default vertical profiles this is consistent with the profiles distributed with the CMAQ version 4 7 tutorial dataset Existing CCTM 3 D concentration fields could have been generated using several different chemical mechanisms The chemical mechanism used in CCTM and CMAQ input processors must be consistent with the mechanism used to generate the concentration fields input to ICON an
292. se the available I O API and netCDF libraries e Configure the JPROC build script for your application using the options discussed in Section 5 6 2 2 e Invoke the build script to create an executable bldit jproc 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_S CFG Executable to use for the simulation 5 6 2 5 JPROC output files Table 5 10 JPROC output files File Name Format Description JTABLE Date ASCII Daily clear sky photolysis rates file June 2010 5 39 http www cmaq model org CMAQv4 7 1 Operational Guidance Document The default location of the JPROC output files is the SM3DATA jproc directory controlled by the OUTDIR variable in the run script The default naming convention for all JPROC output files uses the Date environment variable in the file name which is aliased to the STDATE environment variable in the run script 5 7 MCIP 5 7 1 Description The Meteorology Chemistry Interface Processor MCIP processes meteorological model output from either MM5 or WRF ARW model into I O API formatted files that are compatible with CMAQ and SMOKE MCIP automatically determines whether an input file is generated by MMS or WRF ARW 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 ARW datase
293. sigma layer required AAYERX_IC EXP IC concentration for species 1 in Xth sigma layer required oh 1 10 SPECIES2 String Pollutant name enclosed in double quotes required 12 20 AAYER1_IC EXp IC concentration for species 2 in lowest Sigma layer required 23 31 AYER2_IC EXP IC concentration for species 2 in 2nd sigma layer required 34 42 AAYER3_IC EXp IC concentration for species 2 in 3rd Sigma layer required 45 53 AYER4_IC EXP IC concentration for species 2 in 4th sigma layer required AAYERX_IC EXp IC concentration for species 2 in Xth sigma layer required Z 11 0 SPECIESZ String Pollutant name enclosed in double quotes required 12 20 AAYER1_IC EXp IC concentration for species Z in lowest Sigma layer required 23 31 AAYER2_IC EXp IC concentration for species Z in 2nd sigma layer required 34 42 AAYER3_IC EXp IC concentration for species Z in 3rd Sigma layer required 45 53 AAYER4_IC EXp IC concentration for species Z in 4th June 2010 6 7 http www cmaq model org CMAQv4 7 1 Operational Guidance Document sigma layer required LAYERX_IC Exp IC concentration for species Z in Xth Sigma layer required A sample of the four sections of an IC_PROFILE file is shown below Example initial condition The vertical coordinate of the model to generate these i c is the terrain following sigma coordinate The number of sigma layers and defined sigma levels are listed below 6 55
294. sm fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry and active chlorine o cb05cltx_ae5_aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry active chlorine and air toxics o cb05cltxhg_ae5 aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry active Chlorine air toxics and mercury this is for the multipollutant model see CMAQvV4 7 release notes 5 38 http www cmaq model org CMAQv4 7 1 Operational Guidance Document o saprc99_ae5 aq SAPRC 99 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry o saprc99tx3_ae5 SAPRC 99 gas phase mechanism with air toxics and fifth generation CMAQ aerosol mechanism 5 6 2 3 JPROC compilation First it is assumed that you have already installed and compiled the I O API and netCDF libraries see Section 3 2 3 or that these are already available from a previous CMAQ 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 summarized below to compile new versions of JPROC e Ifyou have not already done so compile M3BLD the CMAQ source code and compilation management program This needs to be done only once the first time CMAQ is installed e Ifneeded configure the JPROC build script to u
295. stem can be more efficient by reading only the necessary parts of the data files Additionally netCDF 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 Mac OSX The I O API component of the file format is the way that spatial information is defined in the CMAQ data files The I O API convention of defining horizontal grids is to use a combination of the map projection and an offset from the projection center to the southwest corner of the modeling domain After defining the southwest corner of the domain or the offset from the projection center the I O API grid definition specifies the size of the horizontal grid cells and the number of cells in the X and Y directions In addition to providing A further benefit of the I O API is that an expansive set of data manipulation utilities and statistical analysis programs is available to evaluate and postprocess the binary CMAQ input output data files For CMAQ users performing preconfigured applications of the model the I O API system can be essentially transparent For users who plan to modify the code or implement updated modules for research purposes a few key elements of the I O API should be understood and they 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 modu
296. t west and north south offsets from XCENT and YCENT in meters WRF ARW usages may differ The next two parameters XCELL and YCELL are the horizontal grid spacing in meters for the X and Y directions i e delta x and delta y The next two parameters NCOLS and June 2010 6 5 http www cmaq model org CMAQv4 7 1 Operational Guidance Document NROWS are the numbers of grid cells in the X and Y directions The grid definition concludes with the number of boundary cells NTHIK which is typically set to 1 6 1 2 IC 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 lists species concentrations at various model layers that are fixed in space and time To configure ICON to generate initial conditions from ASCII vertical profiles the prof input module is chosen when compiling the program see Section 5 5 on ICON These ASCII formatted vertical profile files are IC_PROFILE files and are described in this section IC_PROFILE files must be developed by the user and can be generated from climatologically averaged observational data or as an a priori estimate from previous modeling studies of the region being modeled The second file type that ICON can use to generate initial conditions is a concentration file from a previous CMAQ run These are CTM_CONC_1 files and are described later in Section 6
297. t otherwise MM5 is assumed Many of the fields that are simulated by the meteorological model are not modified by MCIP for the emissions model and CCTM and they are written to I O API files Fields that are required for the transformation to CMAQ s generalized coordinate system are calculated within MCIP The dry deposition velocities are also calculated by the current version of MCIP however because CMAQV4 7 can now calculate all deposition velocities MCIPv3 4 will be the last version of MCIP to calculate those velocities In addition the user has the option of either passing through the planetary boundary layer PBL and radiation fields that are calculated by the meteorological model recommended or recalculating those fields with MCIP The MCIP run script contains Fortran namelist variables that control these configuration settings MCIP can extract both temporal and spatial subsets of the input meteorology files 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 meteorological time period but must be consistent with the time granularity of the meteorological files MCIP cannot perform temporal interpolations to artificially increase the temporal resolution of the meteorology fields Two types of horizontal domain windowing are allowed with MCIP The boundary trim option BTRIM uniformly trims grid cells off each of t
298. t default to 1 if not specified species represents the model species names ENDPA The ENDPA command signifies the end of the command input in the PROCAN command file Table 5 15 Integrated process rate output commands Command Description IPR_OUTPUT The IPR OUTPUT command defines specific IPR outputs to be species familyname ALL pcode pcodep 5 generated during a CMAQ CTM simulation A model species name family name or the keyword ALL must follow the IPR_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 pcode where pcode corresponds to one of the process codes listed below If no process codes are specified IPRs will be generated for every science process i e the first 12 codes shown in Table 5 16 The output variables that are generated are named either species_pcode or familyname_pcodej Table 5 16 Integrated process rates process codes Process Definition June 2010 5 50 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Yamo PPM XADV Advection in the E W direction for the PPM scheme YADV Advection in the N S direction for the PPM scheme ZADV ZADV Vertical advection HADV ADV2 Total horizontal advection XADV YADV MADV ADV3 Total advection XADV YADV ZADV
299. t deposition file eee 6 32 6 2 7 AEROVIS CCTM hourly instantaneous visibility metrics cece 6 32 6 3 Diagnostic and Advanced CMAQ Output Files 0 00 ccceceseceeeeeeeeeeteeeseenteeeees 6 33 6 3 1 AERODIAM Instantaneous hourly aerosol diameter file 6 33 6 3 2 WETDEP2 CCTM cloud diagnostics file ce ecccecsseceseceeeeeeeeeeteeenseeees 6 33 6 3 3 SSEMIS Sea salt emissions diagnostic file 0 0 0 eee eececeseceeeeeeeeeeteeeeseeees 6 33 June 2010 vil http www cmaq model org CMAQv4 7 1 Operational Guidance Document 6 3 4 B3GTS_S Biogenic emissions diagnostic file eee eeeeseesteeeteeeeeeeees 6 33 6 3 5 RJ In line photolysis output gridded photolysis rates eceeeeeeeeees 6 33 6 3 6 PA Process analysis output integrated process rate file eee 6 33 6 3 7 IRR Process analysis output integrated reaction rates eceeeeeteees 6 34 7 DEFINING GRIDS LAYERS DOMAINS AND CHEMISTRY cssssseeeeeees 7 1 7 1 Supported CMAQ Coordinate Systems 0 cccceccceesceeceesceceseceseeeeeeeeseecaeeneeeeeeenaees 7 1 T2 Honzontak CHAS isien r amea ecedanta nas annie e a ae rie 7 2 7 2 1 Using predefined horizontal Ord Se sseiess shed srctencs cass sedshoetieand aa sbesanesichetsvictes 7 2 7 2 2 Creating or modifying horizontal grids eee eseesseeeteceseeeeeeeeteeeeaeenteeesees 7 3 7 2 3 Further information on horizontal grids c cc ccccesceceseceeeeeeeeeeeeeseeenteeeeees 7 3 Pad
300. t from a CCTM CONC file for a nested simulation If RUNLEN is not set it will be set automatically from the CTM_CONC 1 file 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 The default location of the BCON output files is the SM3DATA 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 environment 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 CCTM is the Eulerian chemistry and transport component of CMAQ It uses input data produced by the other CMAQ programs and from meteorological and emissions models 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 and processes analysis files CCTM contains several science configurations for simulating transport chemistry and deposition All of the science con
301. ta provided in the PROFILES file are at 19 latitudes 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 vertical profiles of O concentrations molecules cm air temperature K and air density molecules cm 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 temperature K air density molecules cm ozone concentrations molecules cm and aerosol attenuation coefficients km The first data section of the PROFILES file is divided into 228 19x3x4 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 to 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 0 km and the last value is at 50 km The next data block is again spring O concentration profiles but at the
302. tal wi EA ada lt A tS lle tet 5 36 5 6 2 Files configuration and environment variables ccccccsseeeseeseeeteeees 5 36 Dad ILC IP E EE E A capuadeiaeguassacuadas E S 5 40 S t Description santai ah eens E E E A ade eee ER 5 40 5 7 2 Files configuration and environment variables cccccsseeeseetteeeteeees 5 40 5 8 PARIOn tot i a aN teh eR EA A E ol i Bal E E 5 46 5S Descriptio eena aa eg a aa e AE AT aE oem aaa 5 46 5 8 2 Files configuration and environment variables cccccsseeeseesteeeteeees 5 46 529 PROC AN og ae aerate R AR E EE E shai santas Meat cae 5 47 SIL Desci 0151 8 ee ee a a oe etre Pen a See Ae rr Mn tran SRN ere 5 47 5 9 2 Files configuration and environment variables cccccsseeeseeetteeeteeees 5 48 DAN 7S WIN Recreate ll alles Soest eae a tao h Ne aN coe acer nian Yeti ial OAA 5 54 June 2010 vi http www cmaq model org CMAQv4 7 1 Operational Guidance Document SLOT Description senesine e a E ctl a e ie Rete uric Andsnes the ea 5 54 5 10 2 Files configuration and environment variables cccccccesseesseeeteeees 5 54 Dil Referentes rsono eari einan A Mg a Aa eee A oe aks 5 55 Gs CMAQ FILES casa cas taeda cantata cee aes 6 1 Gill gt CMAQ Input Files seee skies asia ceapsh dnd e aaa eaea E A uonsvauieaasadesbiesonsuatasaesbasngs 6 1 6 1 1 GRIDDESC Horizontal domain definition eee eeecceseceteeneeeeeeeeeneeeaes 6 3 6 1 2 IC PROFILE Initial condition
303. tent heat flux W m HFX sensible heat flux W 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 m temperature K TEMP1P5 1 5 m temperature K WSPD10 10 m wind speed m s WDIR10 10 m wind direction m s GLW longwave radiation at ground W m GSW solar radiation absorbed at ground W m RGRND solar radiation reaching the surface W m RN incremental per output time step nonconvective precipitation cm RC incremental per output time step convective precipitation cm CFRAC total cloud fraction fraction WBAR average liquid water content of clouds g m CLDT cloud top layer height m CLDB cloud bottom layer height m SNOCOV snow cover 1 yes 0 no TEMP2 2 m temperature K SOIM1 volumetric soil moisture in top cm m m SOIM2 volumetric soil moisture in top m m m SOIT1 soil temperature in top cm K SOIT2 soil temperature in top m K SLTYP soil texture type category LAI leaf area index area area June 2010 6 29 http www cmaq model org CMAQv4 7 1 Operational Guidance Document The following deposition velocities are calculated by MCIP3 by default and written to the MET _ CRO 2D file VD_SO2 deposition velocities for SO m s VD_SULF deposition velocities for SO m s VD_NO2 deposition velocities for
304. 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 the Rosenbrock ROS3 solver Sandu et al 1997 the Euler Backward Iterative EBT solver Hertel et al 1993 and the Sparse Matrix Vectorized GEAR SMVGEAR solver Jacobson and Turco 1994 CMAQV4 7 includes options for simulating the chemistry of chlorine mercury and other toxic compounds in a multipollutant version of the CB05 See the CMAQv4 7 release notes for addition details on the gas phase chemistry options Meteorology Modeling System CMAQ Chemistry Transport Model CCTM Gas Phase A Packages e g VERDI or AMET Aerosol Aerosol Clouds amp Chemistry Deposition Aqueous Chemistry Emissions Modeling System Photolysis Rates Initial and Boundary Conditions Figure 2 8 CMAQ chemistry transport model and associated preprocessors 2 3 2 Photolysis Photolysis or photodissociation of trace gases initiates most chemical reactions that take place in the atmosphere Photolysis splits gas phase chemical species using 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 accurately is therefore a key issue that strongly influences air qua
305. ters illustrating in line documentation of variables and units Note syntax differences from Fortran 77 10 Declarations for external functions not previously declared 11 Declarations for arrays to hold external file data 12 Declarations and definitions for local and saved variables and dynamic memory allocations 13 Interface is a convenient way to declare calling arguments to a subroutine as input output or both in the calling program through the INTENT variable specification as IN OUT or IN OUT No other declaration of the calling arguments is necessary in the calling program If IN only the values of arguments can be passed explicitly in the subroutine call If OUT the argument must be passed as a variable 14 Code section for subroutine initialization and for any local data that need not be set at every entry into the subroutine Such data would require a SAVE statement in the declarations For example FIRSTIME is initialized to TRUE in the local variables section 15 Illustration of memory allocation for a variable declared as allocatable In this example NLAYS is accessed from the COORD EXT file 16 Illustrates using an I O API function to set file interpolation time 17 Meteorological and other data are read and interpolated through a series of subroutine calls These subroutines in turn use I O API utilities to perform the time interpolation of the desired met variables deposited and emitted species 18 C
306. tes ie accessed cea co aacean e e a A a N a a das 1 13 Table 3 1 Software required for running CMAQ sssssssssessssssessesssssessessessressessresresseesessresseeseese 3 3 Table 3 2 Optional support software for CMAQ sssssssssessssseesseessssresseesresessseessesersseeseessesseesse 3 4 Table 3 3 NetCDF and I O API compilation options for CMAQ s ssssssssesssssessssesrssesseessesessee 3 6 Table 4 1 Possible Time Step Structures in I O API Files 0 0 0 0 cceccccecceesseessecseceseceeeeeeseeesaeens 4 3 Table 4 2 Possible Data Type Structures in I O API Files cc i cecceecceeseeseceteceeeeeeeeeeseeeeaeens 4 3 Table 4 3 Possible values for OPEN 3 FSTATUS c cccssscccssscesssscesssscesssseesssnesssereessaneess 4 4 Table 4 4 IO API data retrieval routines ss icsvccct rel g cal eae iens sheds ass ates aces ceasvee ee 4 6 Table 4 5 I O API data manipulation utilities cece ccesceesceesceceeceeeeeeeeeeseecaeceeeneaeeeseeeaeens 4 7 Table 5 1 BC ONAN RUE TIES tet siesftcctaitiscdsacalnah aati sussctetuast a ura E aac a TSSA 5 5 Tables 2 BC ON output tiles nedenarne aea aa a R ih E ties teal inland ea ok 5 9 Table 5 3 Required CCTM input files ce ccasics ysecud poducarcvsavas cus atocecos boss betaauaacsesuataye ous botateaun vines 5 11 Table 5 4 CE TM output Nlestesscciassersiaetisy i a ie ta dea eee ee 5 24 Table 5 5 CHEMMECH input files ii ccsssiais lt cysksecsted aadactetetecweduend ead ovate corvweges nied ee tiv lass
307. th does not exist exit 1 endif echo echo Input data path M3DATA set to SM3DATA echo set APPL e3a set CFG e3a set CFG SAPPL set EXEC CCTM_SCFG ctm version gt horizontal domain decomposition setenv NPCOL_NPROW 1 1 set NPROCS 1 single processor setting setenv NPCOL_NPROW 4 2 set NPROCS 8 gt for Scyld Beowulf setenv NP SNPROCS setenv BEOWULF_JOB_ MAP 1 1 0 0 1 1 2 2 3 3 4 4 June 2010 9 14 http www cmaq model org CMAQv4 7 1 Operational Guidance Document echo task processor map beomap gt Set the working directory set BASE Scwd cd SBASE date cat SBASE cfg SCFG echo set echo gt timestep run parameters set STDATE 2001203 beginning date set STTIME 000000 beginning GMT time HHMMSS set NSTEPS 240000 time duration HHMMSS for this run set TSTEP 010000 output time step interval HHMMSS gt set log file default unit 6 uncomment to write standard output to a log setenv LOGFILE SBASE SAPPL log gt turn off excess WRITE3 logging setenv IOAPI_LOG_ WRITE F gt max sync time step sec def
308. th tes T esl al oat ae 9 19 10 ANALYSES TOOLS FOR CMAQ 0 c ceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 10 1 10 1 CMAQ Utility Toolse nenacia nna iee ta E AE E venga EAER 10 1 10 2 M3 COGS ecco ech acca ta she aaa a aes aa pica oa ead aw E ta doce AAE a 10 3 June 2010 viii http www cmaq model org CMAQv4 7 1 Operational Guidance Document 10 3 Package for Analyses and Visualization of Environmental Data PAVE 10 4 10 4 Visualization Environment for Rich Data Interpretation VERDI 10 5 10 5 Atmospheric Model Evaluation Tool AMET cc cecccceseceeeeeeeeeeteeceseeeeeeeeeeeeseees 10 6 10 6 metCbR Operators NCO x sesceccsssuccen ysocesevay suas ves a a e steaks eee ees 10 6 10 7 Python oap Toolsin seenen o a a cesnanedacuentedies basrnansausedustabiantieans 10 8 10 8 Integrated Data Viewer IDV ys jccsiss cists toshocstshaviegasbestata esau asdetabee nomen eds 10 8 10 9 NCAR Command Language NCI 5 acdiscsahedsniendvcthes deumedlin want auacseusantine 10 9 11 CMAQ SUPPORT vcsiseinsuctscstsusiecaredncwcbsustawahsuthsued seatswansentenaneustsuniuui revabsuawccansatonss 11 1 PRI Ehe CMAS Center Aene a cececuuanastectaug a ane tease ween 11 1 REL CEMAS functions sieni raii R E ATAS 11 1 DTD CMAS COMMUN Yine a a abe a aa 11 1 11 1 3 Why is CMAS needed oa co estiedaurs ceatote ted ate dagecoaiiesiee tadeonesaremadt ood oagedeanveatiete 11 2 11 2 Getting Help With CMAQ eienenn Ra ne aie are amr a r are
309. the CMAQ programs for the benchmark simulation Follow the steps outlined in Section 3 3 summarized below to compile new versions of BCON e Ifyou have not already done so compile M3BLD the CMAQ source code and compilation management program This needs to be done only once the first time CMAQ is installed e Ifneeded configure the BCON build script to use the available I O API and netCDF libraries e Configure the BCON build script for your application using the options discussed in Section 5 2 2 2 e Invoke the build script to create an executable boldit bcon 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 e EXEC default BCON_S CFG _ Linux2_x86_64pg Executable to use for the simulation e NPCOL NPROW default 1 1 June 2010 5 7 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 Domain decomposition for parallel mode BCON is normally run in a single processor environment so this setting should always be 1 1 GRIDDESC default GRIDDESC1 Grid description file for setting the horizontal grid definition GRID_NAME default M_36_2001 Name of the grid definition contained in the GRIDDESC file that specifies the horizontal grid for the current application of the model LAYER_FILE default SM3DATA mcip3 M_36_2001 METCRO3D_0107
310. the CONC file concentrations this variable sets the lower and upper layers over which to output the CONC file CTM_MAXSYNC default 720 Maximum synchronization time step in seconds CTM_MINSYNC default 60 Minimum synchronization time step in seconds CTM_AERDIAG default Y Generate an instantaneous hourly aerosol diagnostic file with the geometric mean diameters and the geometric standard deviations for the lognormal aerosol modes Set to Y or T to turn on N or F to turn off CTM_SSEMDIAG default Y 5 20 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 Generate the calculated sea salt emissions in a diagnostic netCDF output file Set to Y or T to turn on N or F to turn off CTM_ILDEPV default Y Calculate in line deposition velocities Set to Y or T to turn on N or F to turn off CTM_SFC_HONO default Y Calculate surface HONO interactions This option is ignored if CTM_ILDEPV is turned off Set to Y or T to turn on N or F to turn off CIM_DEPV_FILE default N Generate an hourly diagnostic file for the in line deposition velocity calculations This option is ignored if CTM_ILDEPV is turned off Set to Y or T to turn on N or F to turn off CIM_BIOGEMIS default N Calculate biogenic emissions Set to Y or T to turn on N or F to turn off If the option to calculate in line biogenic emissions is activated i e CTM_BIOGEMIS
311. the configuration that does not apply to the current system Uncomment the configuration that is closest to that of the current system and make the necessary changes to point to the compiler path I O API location and netCDF locations on the current system Invoke the Makefile to create an executable by typing the following command in the directory that contains 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 June 2010 APPL Application name scenario ID for file naming CoordName Coordinate system name of the MCIP output grid that is written to the GRIDDESC file GridName Model grid name of the MCIP output grid that is written to the GRIDDESC file DataPath Input output data directory path InMetDir Path of the input data directory containing the MM5 or WRF ARW output data files InTerDir Path of the input data directory containing the MM5 TERRAIN file not compatible with WRF ARW 5 42 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 OutDir default SM3DATA mcip Path of the MCIP output data directory ProgDir default Scwd Working directory containing the MCIP executable WorkDir Temporary working directory for Fortran links and the namelist file InMetFiles List of input meteorology
312. tical level units K required 267 A Air density profiles Exp Air density at Season 1 E10 3 measurements as a function of Latitude 1 Level 1 month latitude and vertical level units molecules cm required June 2010 6 16 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Air density profiles Exp Air density measurements as a at Season 1 E10 3 function of month latitude Latitude 1 Level 2 and vertical level units molecules cm required 393 Air density profiles Exp Air density measurements as a at Season 1 E10 3 function of season latitude Latitude 19 Level 1 and vertical level units molecules cm required Air density profiles Exp Air density measurements as a at Season 1 E10 3 function of season latitude Latitude 19 Level 2 and vertical level units molecules cm required 1596 Air density profiles Exp Air density measurements as a at Season 4 E10 3 function of season latitude Latitude 19 Level and vertical level units 51 molecules cm required L597 Average Dobson Real Average Dobson value as a Values at Latitude function of latitude and month 1 Month 1 required 1597 Average Dobson Real Average Dobson value as a Values at Latitude function of latitude and month 2 Month 1 required 1608 Average Dobson Real A
313. 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 Table 4 2 Possible Data Type Structures in I O API Files Magic ee File Type Aani Data Type Description CUSTOM3 1 Custom User dimensioned array of REAL 4s that the system reads writes reliably DCTNRY3 0 Dictionary Data type stores and retrieves parts of an FDESC EXT file description GRDDED3 1 Gridded Dimension as REAL 4 ARRAY NCOLS NROWS NLAYS NVARS BNDARY3 2 Boundary Dimension as REAL 4 ARRAY SIZE NLAYS NVARS IDDATA3 3 ID Used to store lists of data such as pollution monitoring reference observations PROFIL3 4 Vertical Used to store lists of vertical data such as rawinsonde profile observations GRNEST3 5 Nested grid Preliminary and experimental implementation for storing multiple grids which need not in fact have any particular relationship with each other beyond using the same coordinate system SMATRX3 6 Sparse Sparse matrix data which uses a skyline transpose matrix representation for sparse matrices such as those found in SMOKE KFEVNT3 3 Cloud event KF Cloud files use the same file description data structures 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 headers KF Cloud files on the other hand have their own specia
314. ting source code from CVS and compiling an executable oOo 0000000 e MakeOpt compile _all force compile even if all the object files are current clean_up remove all source files upon successful compilation no_compile do everything except compile no_link do everything except link one_step compile and link in one step parse_only check configuration file syntax show_only show requested commands but do not execute them verbose show requested commands as they are executed Uncomment to build a Makefile to compile the executable June 2010 5 32 http www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 Modinpt default module profile Defines the format of the initial conditions input files to be used by ICON o m 3conc input a CCTM CONC file used for nested simulations or windows of a parent domain o profile input an ASCII vertical profiles file ModMech default module radm2_to_cb05 Defines whether the input initial conditions data need to be converted from one chemical mechanism to another mc_noop do not perform any mechanism conversion used when extracting initial conditions from a CCTM CONC file for a nested simulation or when the input profiles are already formatted for the correct mechanism o user_defined input the file defined by the MECH CONV _FILE variable used for custom mechanism conversions o radm2_to_cb05 convert the input initial conditions profiles f
315. tional data file e bewndw Extracts data from a gridded file to the boundary of a subgrid window see m3wndw later in this list for extracting to the window itself e datshift Takes calendar date form YYYYMMDD and a number of days D and reports the date D days later e gregdate Computes calendar style date Month DD YYYY day of week Sunday Monday Saturday and whether or not Daylight Saving Time is in effect from Julian date YYYYDDD or from yesterday today or tomorrow e juldate Computes Julian date YYYYDDD day of week Sunday Monday Saturday and whether or not Daylight Saving Time is in effect from calendar style date Month DD YYYY or from yesterday today or tomorrow e m3combo Computes linear combinations of sets of variables from an I O API input file and writes the resulting variables to an I O API output file e m 3cple Copies to the same grid or interpolates to another grid a time sequence of all variables from a source file to a target file under the optional control of an I O API coupling mode synch file June 2010 10 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document e m3diff Computes statistics for pairs of variables and for the results of applying various comparison differencing operations to those variables in a pair of files e m3edhdr Edits header attributes file descriptive parameters e m3fake Builds a file according to user specifications fill
316. tions 8 INTEGER JDATE current model date coded YYYYDDD 8 INTEGER JTIME current model time coded HHMMSS 8 INTEGER TSTEP 2 time step vector HHMMSS STEP 1 local output step STEP 2 sciproc sync step chem 9 C Parameters 9 C explicit THETA 0 implicit THETA 1 9 REAL PARAMETER THETA 0 5 Semi implicit Crank Nicolson 9 amp THBAR 1 0 THETA 9 REAL THRAT THBAR THETA 9 INTEGER PARAMETER _SPC_DDEP N_GC_DDEP 9 amp N_AE_DDEP 9 amp N_NR_DDEP 9 amp N_TR_DDEP 9 lt gt C9 C number of species on the PM emissions input file Set in OPEMIS lt 9 C the value changes with the type of emissions file 9 INTEGER SAVE NAESPCEMIS 9 REAL PARAMETER 2PHA 1 0E 04 1 hectare 1 0e4 m 2 9 REAL PARAMETER CMLMR 1 0E 06 ppmV Molar Mixing Ratio 9 REAL PARAMETER CNVTD M2PHA CMLMR MWAIR combined ddep conversion factor 9 REAL PARAMETER GPKG 1 0E 03 g Kg 9 REAL PARAMETER MGPG 1 0E 06 micro g g 10 C External Functions not previously declared in IODECL3 EXT 10 INTEGER EXTERNAL SECSDIFF SEC2TIME TIME2SEC 10 LOGICAL EXTERNAL ENVYN 11 C File variables 11 lt gt 12 C Local Variables 12 CHARACTER 16 SAVE PNAME VDIFFIM 12 lt gt 12 REAL ALLOCATABLE SAVE VDEMIS total emissions array 12 lt gt June 2010 9 8 http www cmaq model org CMAQv4 7 1 Operational Guidance Document
317. tions 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 file 5 35 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 5 5 2 5 ICON output files Table 5 8 ICON output files File Name Format Description INIT_CONC_1 GRDDED3 Name and location of the gridded initial conditions data output on the model grid defined by GRID_ NAME The default location of the ICON output files is the SM3DATA 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 The program JPROC calculates daily clear sky photolysis rates from look up tables of molecular absorption cross section and quantum yield CSQY data and climatologically derived ozone column and optical depth data The outputs from JPROC are ASCII look up tables of daily clear sky photolysis rates for photochemical reactions in a selected gas phase photochemical mechanism at different altitudes latitudes and hours from noon The photochemical mechanism from which these rates are derived is se
318. tions of various individual physical and chemical processes to the changes in the predicted concentrations of a pollutant This makes PA useful for conducting quality assurance procedures on a model run With the information PA provides 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 emissions input data causes the model to calculate negative concentration values in an intermediate step this occurrence could be masked in the final predicted concentrations if the negative values are more than compensated for by larger positive values resulting from the chemistry calculations In addition to its role in the quality control of air quality modeling runs PA has other important applications June 2010 2 15 http www cmaq model org CMAQv4 7 1 Operational Guidance Document It is a very strong analysis tool for identifying the relative importance of processes chemistry advection diffusion etc that change pollutant concentrations As a tool for model development PA can help evaluate the effect of modifications made to a model or process module As a tool for regulatory decision making PA can help determine whether a decision to control a specific type of emission would produce the desired results and if the answer is no it can help determine another type of control that would be more effective Note that
319. to predict air pollution CMAQ uses coupled mathematical representations of actual chemical and physical processes to simulate air quality The model is based upon the underlying concept of preserving mass through a series of contiguous three dimensional 3 D grid cells covering a fixed model grid i e x y z array that is fixed in space and covers a particular domain i e the geographic area of interest CMAQ therefore 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 atmospheric processes CMAQ thus requires two primary types of inputs meteorological information and emission rates from sources of emissions that affect air quality 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 Atmospheric Research PSU NCAR 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 compatible with C
320. tor 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 5 4 2 1 CHEMMECH input files Table 5 5 CHEMMECH input files File Name Format Description MCFL ASCII CMAQ mechanism definition file photochemical MECH DEF mechanism listing with both mechanistic and kinetic information about all reactions that compose a chemical mechanism SPST ASCII CSV Species table comma delimited file generated from an Species_Table csv 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 specific 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 FFLAGS 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 June 2010 5 27 http www cmaq model org CMAQv4 7 1 Operational Guidance Document e SRC default Location of CHEMMECH source code 5 4 2 3 CHEMMECH compilation To compile the CHEMMECH pro
321. ts variables There are three kinds of time step structure supported Table 4 1 Within a file all the variables are data arrays with the same dimensions number of layers and data structure type although possibly different basic types e g gridded and boundary variables cannot 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 BNDARY3 are the most prevalent file types in a CMAQ simulation Magic number is an indicator associated with the files type June 2010 4 2 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Table 4 1 Possible Time Step Structures in I O API Files File Type Description Time The file s time step attribute is set to zero Routines that use time independent independent files ignore the date and time arguments Time The file has a starting date a starting time and a positive time step Read and stepped write requests must be for some positive integer multiple of the time step from the starting date and time Circular This type of file keeps only two records the even part and the odd part buffer 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
322. ttributes in a netCDF file ncatted can append create delete modify and overwrite attributes all explained below Furthermore ncatted allows each editing operation to be applied to every variable in a file This saves time when changing attribute conventions throughout a file e ncbo netCDF Binary Operator ncbo performs binary operations on variables in file_1 and the corresponding variables those with the same name in fi e_2 and stores the results in file_3 The binary operation operates on the entire files e ncea netCDF Ensemble Averager ncea performs grid point averages of variables across an arbitrary number an ensemble of input files with each file receiving an equal weight in the average Each variable in the output file will be the same size as the same variable in any one of the input files and all input files must be the same size ncea averages entire files and weights each file evenly This is distinct from ncra discussed later in this list which averages only over the record dimension e g time and weights each record in the record dimension evenly ncea always averages coordinate variables regardless of the arithmetic operation type performed on the noncoordinate variables All dimensions including the record dimension are treated identically and preserved in the output file e ncecat netCDF Ensemble Concatenator ncecat concatenates an arbitrary number of input files into a single output file A new record di
323. tx3_ae_aq x x air toxics 7 4 2 Creating or modifying chemical mechanisms Creating or modifying mechanisms in CMAQ requires the use of the CMAQ chemical mecha nism 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 preprocessors CHEMMECH is a Fortran program that must be compiled by the user prior to use Distributed with a Makefile for compilation and run scripts for execution CHEMMECH reads a mechanism definition mech def file and outputs the mechanism INCLUDE files See Section 5 4 for a description of CHEMMECH To modify an existing mechanism copy the mech def file that is contained in one of the existing mechanism INCLUDE file directories 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 executables To create a new mechanism for CMAQ follow a procedure similar to the 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
324. unning multiprocessor applications 3 5 Benchmarking CMAQ After completing the CMAQ benchmark case the CCTM output files can be compared with the reference datasets provided in the CMAQ distribution using PAVE or VERDI A plot of percent difference between the output and the benchmark data is the easiest method 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 or Intel 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 Differences greater than this require a revew of the installation Remember it is necessary that the same compilers be used for all programs June 2010 3 11 http www cmaq model org CMAQv4 7 1 Operational Guidance Document 4 Required Libraries The CMAQ programs require a set of third party libraries that must be installed on the users system before CMAQ can be compiled and run These libraries control the data flow through CMAQ define the binary file formats used by the CMAQ input and output files and control how CMAQ functions in a multiple pro
325. veloping CMAQ source code Contact information for these contractors is available through the links page on the CMAS Center website 11 1 The CMAS Center Under contract to EPA the Center for Environmental Modeling for Policy Development CEMPD at the University of North Carolina at Chapel Hill UNC Institute for the Environment maintains the CMAS Center for supporting community based air quality modeling CMAS is an approach to the development application and analysis of environmental models that leverages the complementary talents and resources of the modeling community in order to set new standards for quality in science and in the reliability of the application of the technology From research to application to outreach the CMAS Center advances the community modeling paradigm through the establishment of a centralized resource to serve the members of the national and international environmental modeling community 11 1 1 CMAS functions Currently the following activities are available through the CMAS Center e On line help desk Get help with the supported CMAS products e Model clearinghouse Download the supported CMAS products e Training courses Attend a training course on emissions modeling air quality modeling or other related topics e Conferences Attend the annual CMAS conference to interact with the community e Development assistance Add new science to the supported CMAS products e Model documentation Access on
326. verage Dobson value as a Values at Latitude function of latitude and month 19 Month 12 required 1609 Air Temperature at Real Air temperature for a standard Level 1 atmospheric profile units K required Air Density at Level Real or Air Density for a standard 1 Exp atmospheric profile units molecules cm required Ozone Concentration Real or Ozone concentration for a at Level 1 Exp standard atmospheric profile units molecules cm required Aerosol Attenuation Real or Aerosol attenuation coefficient at Level 1 Exp for a standard atmospheric profile units km required 1659 Air Temperature at Real Air temperature for a standard evel 51 atmospheric profile units K required Air Pressure at Real or Air pressure for a standard evel 51 Exp atmospheric profile units molecules cm required Ozone Concentration Real or Ozone concentration for a at Level 51 Exp standard atmospheric profile units molecules cm June 2010 6 17 http www cmaq model org CMAOv4 7 1 Operational Guidance Document required D Aerosol Attenuation Real or Aerosol attenuation coefficient at Level 51 Exp for a standard atmospheric profile units km required 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 in Dobson units taken by the Total Ozone Mapping Spectrometer instrument
327. viate from these standards and test new data with minimal effort The ASCII formatted CSQY files begin with a header that describes the applicable photolysis reaction This header includes 1 the reaction name ID 2 comment lines describing the reaction the stoichiometry and the data source note that comment lines are preceded with a 1 3 the location on the wavelength interval that the data represent beginning centered ending or point and 4 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 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 6 7 Table 6 7 CSQY format description Line Column Name Type Description 1 A Reaction ID String Text name identifying the CSQY data this name is cross referenced in the chemical mechanism description and INCLUDE files required 2 A Comments String Preceded by comment lines describe the reaction list the stoichiometry and document the source of the data optional n 1 A Data String Field indicating the location of Location the data as measured across the wavelength band possible answers
328. vironment offices in Chapel Hill North Carolina USA CMAS training staff are also available to travel for on site training anywhere in the world The currently available training is an introductory course to CMAQ that covers configuration compilation and basic operation of the model Visit the CMAS training web page to see an agenda fees and the schedules for upcoming training courses 11 2 4 E mail support E mail support is available to CMAS users who have a support account and provides case specific support for all CMAS supported software which includes CMAQ CMAS e mail support provides direct access to expert CMAQ users for questions about installation or operational issues E mail support also provides direct access to the CMAQ developers for technical questions about model formulation model science and code integration Visit the e mail support page for an explanation of how to use the system and to register 11 3 Contacting CMAS The CMAS Center is available on the web at http www cmascenter org Table 11 1 lists important contacts for the CMAS Center Table 11 1 CMAS contact information and important links Resource Link Main website http www cmascenter org General Questions cmas unc edu June 2010 11 3 http www cmaq model org CMAQv4 7 1 Operational Guidance Document Help Desk http www cmascenter org help_desk cfm Training Information http w
329. ww cmascenter org training cfm Conferences and Workshops http www cmascenter org conference cfm Downloads http www cmascenter org download cfm Release Calendar http www cmascenter org release_calendar cfm FAQs http www cmascenter org help faq cfm CMAQ Home Page http www cmag model org June 2010 11 4 http www cmaq model org CMAQv4 7 1 Operational Guidance Document GLOSSARY Accumulation mode Aerosol particles with diameters nominally between 0 1 and 1 0 micrometers The term is based upon the concept that particles in this size range accumulate in the atmosphere from the growth of much smaller particles See also Aitken mode The growth may be from new mass condensing on the smaller particles or from the coagulation of the smaller particles Adaptive grid A grid structure that varies during model execution according to the value s of some model parameter s For example in a photochemistry model grid resolution may auto matically increase in areas of high spatial gradients of NOx This allows more accurate determ ination of plume to background concentration ratios which greatly influence photochemical ozone production In a meteorological model an adaptive grid may automatically increase the grid resolution in an area of modeling where there is a large atmospheric pressure change across a grid cell Air quality modeling system A computational system environment that combines a set of physical and ch
330. www cmaq model org CMAQv4 7 1 Operational Guidance Document June 2010 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 SM3MODEL include release directory Examples include o cb05ae5_aqg CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry o cb05cl_ae5_aq CBO5 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry and active chlorine o cb05cltx_ae5_aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry active chlorine and air toxics o cb05cltxhg_ae5 aq CB05 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry active chlorine air toxics and mercury this is for the multipollutant model see CMAQvV4 7 release notes o saprc99 ae5 aq SAPRC 99 gas phase mechanism fifth generation CMAQ aerosol mechanism with sea salt aqueous cloud chemistry o saprc99tx3_ae5 SAPRC 99 gas phase mechanism with air toxics and fifth generation CMAQ aerosol mechanism Tracer default traco Specifies tracer species to use from the emissions IC or BC input files Invoking inert tracer species in CMAQ requires defining the tracers using INCLUDE files and compiling CCTM with these files The setting for this mo
331. xt step for setting up a new CMAQ simulation is creating initial and boundary conditions ICs and BCs for CCTM The ICON processor provides initial chemical fields of individual species concentrations for a specific modeling domain BCON provides concentrations of individual chemical species for the grid cells surrounding the modeling domain ICON and BCON both require two inputs concentration values for the chemical species needed in the simulation and a predefined chemical mechanism As described in Chapter 5 there are two types of input concentrations for ICON and BCON either 1 tabulated tropospheric vertical profiles or 2 three dimensional fields from a previous CMAQ or larger scale CTM simulation such as GEOS CHEM 2009 or MOZART 2009 The input file type to use for ICON and BCON depends on whether the simulation is a restart of a previous run and or whether the simulation is a nest of a larger parent grid The same chemical mechanism must be selected for ICON BCON and CCTM Both ICON and BCON assume that the input species concentrations are for the selected mechanism however a module can be included in each processor to convert from the RADM2 to the CB05 or SAPRC 99 mechanisms This option would be necessary for example when the CB05 mechanism is to be used in the model but the tabulated tropospheric vertical profiles that are used as inputs to ICON and BCON were constructed using RADM2 mechanism species Refer to Chapter 5 for infor
332. y are not used by BCON The BCON input consists of four data sections that correspond to the lateral boundaries i e north south east and west of the model grid The BCON input profiles contain a field that precedes each data section to indicate which horizontal boundary the data section describes The format of the data sections in BC_PROFILE files is the same as in IC_PROFILE files Each 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 in ppmV and aerosol species are in ug m The layer structure of the BC_PROFILE vertical profiles does not need to correspond exactly to the layer structure that will be modeled the BCON program 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 generated with BC_PROFILE s ASCII vertical profiles are both static and spatially uniform along each of the four horizontal boundaries at each model layer For spatially June 2010 6 8 http www cmaq model org CMAQv4 7 1 Operational Guidance Document resolved in the horizontal direction 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 descriptio

CMAQ-4.7.1 Operational Guidance Document

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