Home

(SMOKE) Modeling System

1. CAMx CB IV or CB4 CB05 CEMPD CMAS CMAQ CTM CVS FIPS GIS GMT I O API IDA IE MCIP MM5 NCAR NEI NOAA ORL PAVE PinG PM PM PPB PPM PSU SAPRC SCC SMOKE SO UNC UTC WRF ACRONYMS Comprehensive Air Quality Model with eXtensions Carbon Bond IV chemical mechanism Carbon Bond 05 chemical mechanism Center for Environmental Modeling for Policy Development UNC IE Community Modeling and Analysis System Community Multiscale Air Quality model Chemical Transport Model Concurrent Versions System Federal Information Processing Standards Geographic Information System Greenwich Mean Time Input Output Applications Programming Interface Inventory Data Analyzer Institute for the Environment UNC Meteorology Chemistry Interface Processor Fifth Generation Mesoscale Model National Center for Atmospheric Research National Emissions Inventory National Oceanic and Atmospheric Administration Oxides of nitrogen Ozone One Record per Line Package for Analysis and Visualization of Environmental data Plume in Grid Particulate Matter Particulate Matter less than 2 5 um in diameter Parts Per Billion Parts Per Million or Piecewise Parabolic Method advection scheme Pennsylvania State University State Air Pollution Research Center chemical mechanism Source Classification Code Sparse Matrix Operator Kernel Emissions processor Oxides of Sulfur University of North Carolina Universal Time Coordi
2. 3 We will check the log files for notes warnings and errors and also look at the Smkmerge report A Go to the directory with the log files Community Modeling and Analysis System 5 2 2013 5 SMOKE Training Gridded Inventories D gt cd LOGS Confirm that all of the biomass burning source programs completed normally by using the tail command on the log files View the log file for Smkinven gt gedit smkinven bb train lt initials gt log amp Exercise 5 1 What is the name of the inventory file used by Smkinven Hint we imported a gridded netCDF file or a gridded area source file In SMOKE terms this is abbreviated as an AG file Answer 5 1 Exit from the Smkinven log file Use PAVE to view the biomass burning gridded inventory netCDF file gt pave f SINVDIR gridded ag bb gfedv2 UAE36LCC_148X134 2007153 8 ncf 2013 Create a tileplot of the CO inventory data Use the Control gt Configure gt Tile function to bring up the plot configuration window Change the maximum value on the legend from 4789 082 to 100 0 to see the locations of the biomass burning sources in the inventory file After experimenting with PAVE and looking at this inventory for a few minutes exit PAVE and move on to the next step View the log file and input files for Spcmat gt gedit spcmat bb train initials cmaq5 cb05p25 1log amp Exercise 5 2 What are the names the speciation cross referen
3. The abbreviation uae36 in the Assigns file name is the grid name and indicates a 36 km grid centered in Abu Dhabi United Arab Emirates As you will see this grid name is used in naming the SMOKE input and output files B Edit the Assigns file you just created In this documentation we will use an editor called gedit but you can use any Linux text editor you like that is available on your computer Community Modeling and Analysis System 1 4 2013 1 SMOKE Training Overview NOTE The ampersand amp at the end of the command runs the editor in the background so that you can continue the training Remember that you can use the tab key to complete file names gt gedit ASSIGNS train initials cmaq5 cb05p25 uae36 amp In this file change the values of the following environment variables as indicated Change the value of INVOP base year inventory output name to train initials O Change the value of INVEN base year inventory output name with version to train initials When you change INVOP any environment variables that are based on INVOP change as well Exercise 1 1 What is the first environment variable in the file whose value will change because you changed INVOP Answer 1 1 Save the file C To make sure the Assigns file works correctly and to create the input and output directories for your new inventory and scenario source the Assigns file by typing the following
4. gt source ASSIGNS train initials cmaq5 cb05p25 uae36 The Assigns file will print out some information about the system you are working on and then return the Linux prompt D To see all of the environment variables that are now available for running SMOKE type the command env more NOTE The or pipe symbol is above the Enter key on your keyboard In Linux this symbol is used to string commands together Here we are causing the output from the env command to scroll by with the more command Scroll through the list by pressing the space bar on the keyboard The first environment variable that has been set by the Assigns file is INVID You can quit more by typing q 2013 1 5 Community Modeling and Analysis System 1 SMOKE Training Overview E E The Assigns file also created output directories such as INVOPD STATIC SCENARIO OUTPUT and REPSCEN You can confirm this by using the cd command to change to some of these directories For example gt cd SSTATIC gt ls The final step in setting up for a new run is creating the input files The steps in the next section will help you become more familiar with the input directories and files 1 5 Input and output directories and input files Once you have invoked the Assigns file you can directly access many directories using environ ment variables 5 Review the primary input directories and their files
5. of the speciation profile file Hint Look in Chapter 8 of the SMOKE User s Manual to find the logical file name of the speciation profile file then look in the Assigns file for that logical file name J Asa group we will look at the contents of the following files using gedit AGPRO BGPRO MGPRO UAE36 WORLD 1 NOFILL txt UAEI2 WORLD 1 NOFILL txt gridding surrogates 2013 1 7 Community Modeling and Analysis System 1 SMOKE Training Overview AGREF MGREF amgref mideast txt gridding cross references ATPRO MTPRO PTPRO amptpro mideast txt tpro bioburn txt temporal profiles ATREF MTREF PTREF amptref mideast txt GSPRO GSREF GSCNV tref bioburn txt temporal cross references gspro cmaq5 cb05p25 txt gspro_bioburn txt speciation profiles for CMAQ gsref cmaq5 cb05p25 txt gsref bioburn txt speciation cross reference gscnv txt gscnv_cb05 bioburn txt pollutant to pollutant conversion file LAYER_FRACTION layers gfed txt layers areng txt layer allocation fractions 6 There are also files that are used by all source categories that are not cross reference files profiles or surrogates Look at each of the following files with the instructor In the general data directory GRIDDESC COSTCY HOLIDAYS PROCDATES SRGDESC GRIDDESC grid descriptions file costcy txt country state and county file holidays txt list of holiday dates and the day
6. P Confirm that the program completed successfully by looking for the following message on your terminal window after running the script gt gt Normal Completion of program MG2MECH 3 3 Examine the MEGAN output files with PAVE 2 Inthis step you will examine the MEGAN output file in PAVE and create a tileplot of the pollutant ISOP isoprene A Load the MEGAN output file that you created and the reference output file in the SANSWERS step 1 directory into PAVE gt pave f A OUT bgts l f SANSWERS biog step l bgts l B Compare the variables between the two files and ensure that the emissions that you generated are exactly the same as the file in the SANSWERS directory Create a tile plot of the isoprene emissions in the file that you created and animate the plot 2013 3 3 Community Modeling and Analysis System 3 SMOKE Training Biogenic Sources Exercise 3 3 What is the value of the peak hourly isoprene emission on June 1 2007 in the 36 km modeling grid What time does this peak occur and in which grid cell Answer 3 3 3 4 Running the biogenic model with a different temperature variable 3 Inthis step you will process the biogenic emissions using ambient air temperatures A Edit the MEGAN run script and change the temperature variable to use the ambient air temperature TA in the METCRO3D file Change the name of MEGAN output file EROUT so that you don t overwrite the output from the previous exer
7. The doc directory location for the release notes for the current version of SMOKE TheLinux2 x86 64pg directory location for the SMOKE programs e The scripts directory location for the installation compilation and run scripts 3 Go to the assigns directory and look at its contents by typing gt cd assigns gt ls Several file names will be displayed in your window e The file starting with ASSIGNS is the Assigns file e The check_settings scr script is used by the Assigns file to ensure that various script settings are initialized The set_case scr script is used by the Assigns file to set the environment variables used in labeling directories and files for the case being run The set_dirs scr script sets input and output directory paths 2013 1 3 Community Modeling and Analysis System 1 SMOKE Training Overview The setmerge_files scr script is used by the Assigns file to ensure that model ready output logical file names are set depending on the run script settings e g if you are running the final merge step in SMOKE to get model ready output files this script will set the output logical file names Thesmk mkdir script is used by the Assigns file for creating input and output directories and setting checking write permissions e The smk_rmfiles scr script is used by the Assigns file for deleting SMOKE intermediate and output files before each script run only when AUTO DELETE setting is
8. at the projection packet used by the Cntlmat program This file is called SPTDAT gcntl 2007 2018 txt Each line in the file lists a FIPS code SCC and growth factor The point sources will be matched to the most specific entry in PROJECTION packet After the programs have finished confirm that they all completed successfully The log files for Cntlmat and Grwinven are in the LOGS directory and the log files for Temporal and Smkmerge are in SSMKDAT run train initials 18 static logs Start PAVE in a new xterm window if it is not already running Compare the base year PGTS3D file with the new SPGTS3D L file The 2007 SPGTS3D L file is in the P OUT directory while the 2018 PGTS3D_L file is in SMKDAT run train initials 18 output cmaq5 cb05p25 directory You can also compare your files to those in SANSWERS point step 4 4 5 Community Modeling and Analysis System 4 SMOKE Training Point Sources Page left intentionally blank Community Modeling and Analysis System 4 6 2013 5 SMOKE Training Gridded Inventories 5 SMOKE Training Processing gridded Inventories 5 1 Introduction During the gridded inventories training you will Copy the biomass burning sources run script examine the script and change options Import a gridded biomass burning inventory into SMOKE and process it for CMAQ e Run the layer allocation program to distribute the emissions vertically Examine the gridded inve
9. name UAE12 C The IOAPI GRIDNAME 1 variable sets the name of the grid definition as defined in the GE DAT GRIDDESC file For these training exercises the 12 km grid information is already entered in the GRIDDESC file with the name UAEI2LCC 78X72 Change the IOAPI GRIDNAME 1 variable to this value When setting up new grids in SMOKE you will need to point the Assigns file to a GRIDDESC file that contains the definition for the new grid and set the IOAPI GRIDNAME 1 variable to the name of the grid listed in the GRIDDESC file D Change the meteorology scenario name METSCEN to UAE MCIPI12 2013 1 9 Community Modeling and Analysis System 1 SMOKE Training Overview E Change the SRGDESC and SRGPRO PATH settings to the directories containing the 12 km spatial surrogates GE DAT UAEI2 SRGDESC txt and GE DAT UAEI2 respectively Save the Assigns file 1 7 Setting up for a new episode 9 Toset up for new dates you must change the following variables in the Assigns file EPI STDATE EPI STTIME EPI RUNLEN EPI NDAY G STDATE G STTIME G RUNLEN ESDATE NDAYS The episode start date in Julian date format Y Y Y YDDD The episode start time HHMMSS The episode run length HHMMSS The number of days in the episode The start date in Julian Y Y Y YDDD for the model ready output files The start time HHMMSS for the model ready output files The length HHMMSS of each model ready output file
10. run A Invoke the area sources script gt smk ar train initials csh B All the reports created by TYPE part1 will go in the SREPSTAT directory Go to this directory and open the inventory reports gt cd SREPSTAT gt gedit a rpt amp Exercise 7 1 Which SCC in the area source inventory has the largest total CO emissions and what is the name of that SCC Answer 7 1 SCC Name 7 4 Run the reporting program for point sources 3 Inthis step you will run the quality assurance option for the point sources script that you have already worked with A Go to the directory that contains the SMOKE run scripts gt cd SCRIPTS run B View your point sources script gt gedit smk pt train initials csh amp C Configure the script to Use the 12 km Assigns file O Do not rerun any point source processing steps Run the emissions reporting program Create all point source reports by setting QA TYPE to all D Invoke the point sources script Community Modeling and Analysis System 722 2013 7 SMOKE Training Quality Assurance E Reports using temporalized emissions will go in the REPSCEN directory while time independent reports will be put in the SREPSTAT directory F Once the reports have been generated go to the LOGS directory Exercise 7 2 How many times did Smkreport run How many times did it complete successfully If it failed what was the ERROR message repo
11. set to Y e The sysflags script is called by the Assigns file to set up compiler and platform specific environment variables Theunset scr script unsets temporary environment variables used by the Assigns file 1 4 Setting up for a new SMOKE run 4 Now you will step through the various tasks needed for setting up for a new SMOKE simulation Not all of these steps are required in all of the training exercises but we will go through them all so that you are familiar with configuring SMOKE for new simulation A Create an Assigns file The first step in using a new inventory episode grid or emissions scenario is creating a new Assigns file You will copy the Assigns file in the assigns directory to a new file that uses your initials in its name NOTE With Linux you can use the tab key to automatically complete file names If you start typing a file name at the prompt and then press the tab key the computer will try to fill in the rest of the file name for you Try this in the next command Type the following at the prompt cp ASSIGNS mideast07 cmaq5 cb05p25 uae36 ASSIGNS train initials cmaq5 cb05p25 uae36 For example if your initials are AB gt cp ASSIGNS mideast07 cmaq5 cb05p25 uae36 ASSIGNS train ab cmaq5 cb05p25 uae36 Typically you will copy a previously created Assigns file to a name that corresponds to the new emissions scenario Here we are using the emissions scenario name train lt initials gt
12. the units needed for CMAQ modeling Configure Smkmerge to output state totals in moles hr OOO000 Do not output county totals C Execute the area sources script from the SCRIPTS run directory After the programs have finished confirm that all of the programs completed successfully using the tail command on the log files in the LOGS directory You can compare your log files and the SREPAGTS L file repagts_l ar 20070601 1 UAE36 train_ lt initials gt rpt in the SREPSCEN directory to the answers in SANSWERS area step 4 2 6 Processing 3 d area sources 5 Emission inventories for sources that are emitted from elevated stacks such power plants and smelters or sources that have a vertical distribution due to the physical nature of the emission process such as biomass burning and airport landing take off cycles require data about emissions heights in order to correctly represent these sources in air quality modeling systems Emissions data are most commonly distributed as area source inventories which do not inherently contain sufficient information to allocate the emissions to vertical model layers Published or a priori information can be used to develop vertical profiles for generating vertically resolved area source emissions for input to air quality modeling systems In this step you will process an area source inventory of energy sector sources which consists primarily of power generation and petroleum refining facilities
13. Analysis System 6 SMOKE Training Gridded Inventories F The important setting in this script for processing gridded inventory data is the environmental variable IMPORT GRDIOAPI YN If this variable is set to Y then SMOKE expects that the input inventory file will be a netCDF file of gridded emissions rather than a text file of country state municipality total inventories Change the Assigns file name to use the uae36 Assigns file that you created in the Overview lab Configure the script to run the following steps by changing the RUN variables Run Smkinven Run Grdmat Run Spemat Run Temporal Run Smkmerge Do not run the 2 d layer allocation program Layalloc DL D D prr Configure Smkmerge Output a gridded file Produce a speciated output file Use moles s for all output Produce temporally allocated output Output neither state nor country totals Save the run script 5 3 Processing gridded inventory data 2 In this step you will import the biomass burning sources inventory create the gridding matrix speciation matrix temporal intermediate files and merge the results to create 2 d CMAQ ready emissions A Invoke the biomass burning sources run script gt smk bb train initials csh While the script is running various messages will be written to the screen This same information is written to the log file for each program 5 4 Examine the log files and output files
14. Assigns file gt gedit smk mrgall train initials csh 6 3 Using the Mrggrid program 2 The Mrggrid program lets you merge together previously created model ready files without needing the intermediate files from the various SMOKE programs We will use the Mrggrid program to combine 2 d area 3 d area 3 d gridded and biogenic emissions that you created previously into a single output file A Set the script to run the gridded file merge program Mrggrid B Look at the section of the script labeled Script Settings There are three environment variables that we need to set in this section MRGFILES MRGGRID MOLE and SRCABBR 2013 6 1 Community Modeling and Analysis System 6 SMOKE Training Merging Set the MRGFILES environment variable to L BBGTS3D L AENGGTS3D L BGGTS to merge the area biomass burning area energy and biogenic source model ready files that we created O Set MRGGRID MOLE to Y to match the units of the MRGFILES files moles Set SRCABBR to match the source types we are merging areat biogenic biomass burning arbgbb C Save the merge script D From the SCRIPTS run directory execute the merge script gt smk_mrgall_train_ lt initials gt csh 6 4 Confirm that Mrggrid worked 3 Start PAVE if it is not already running Load the SARGTS L SAENGTS3D L BBGTS3D_L BGGTS L and EGTS L files from their respective output directories Create a formula f
15. De Dent vri abge ute La doge eaa 5 5 ST Problem Solving eee ates eee rate euentu eu bete ete 5 6 6 gt SMOKE Training Mefging nod arcte eie leis AN e ides UU eb QU PASA e 6 1 Gl Introductions 942 5600 o one tug ier tna qui e a det ond aie cM C ped 6 1 6 2 The run script and 5 ret le 6 1 6 3 Using the Mrggrid program ete hips p rosea 6 1 6 4 Confirm that Mrggrid Worked esi desit emiten baee NN Een inue eus an LEN 6 2 6 5 Create a biomass burning emissions sensitivity case ssssssssseeeene 6 2 6 6 Compare the SMOKE output files in PAVE eese 6 3 7 SMOKE Training Quality Assurance ssessssssseseeeeeee eren 7 1 rin ERROR UE DP ES aM ODER PNE DESC 7 1 7 2 The quality assurance script options Reo ee pne cnn 7 1 7 3 Run the reporting program for area sources sssssssssseeeeeeerenerenenee enne 7 2 7 4 Run the reporting program for point Sources rera de CU op Dee dosi 7 2 7 5 Run the quality assurance step for area sources using a custom configuration 7 3 SMOKE version 2 61 Training Answer Sheet esses 8 1 9 SMOKE Training Lecture Slides oe eorr e ore eo eee Ce HER THAI 9 10 SMOKE Training Linux Basics vas tetro se ee IR A IN EXTARE VU Id eu AO Rd Edd 10 1 O 2013 iii Community Modeling and Analysis System SMOKE Training Version 3 1i
16. F Change the Assigns file name in the script to the Assigns file that you created for the UAE12 grid in the Overview lab G Change the appropriate RUN environment variables to Run Smkinven Run Grdmat Run Spemcat Run Temporal Run the layer fractions program Laypoint Run Smkmerge Do not run emissions reporting program Smkreport 4 1 What were the names of the environment variables that were set to Y in this step Answer 4 1 1 4 Exercise 4 2 What environment variable is used to control the output time zone of the emissions What 15 the variable set to Answer 4 2 Variable Exercise 4 3 What environment variable is used to define the ground level temperature variable name for plume rise computation and what is its value Answer 4 3 Variable Community Modeling and Analysis System 4 2 2013 4 SMOKE Training Point Sources H Configure the merge program to O Produce vertically layered output Create temporally allocated and speciated emissions Output gridded emissions in moles s Output state totals from Smkmerge in moles hr I Save the run script 4 3 Running the point sources script 2 Inthis step you will create model ready 3 d point source emission files A Invoke the point sources run script gt smk pt train initials csh B While the script is running various messages from each of the programs will scroll by on the s
17. REPORTI Include gridding Include temporal allocation Report by state name Report by grid cell Report by hour Report in units of g hr L D DJ D EI DI D DI El Report emissions using float format with 1 decimal place and columns that are 12 spaces wide F Save the report configuration file From the SCRIPTS run directory run the area sources script gt smk ar train initials csh Confirm that Smkreport completed normally by looking at the log file in LOGS Then verify that your custom report was created in the REPSCEN directory and that it matches the description given above Community Modeling and Analysis System 7 4 2013 SMOKE Training Answers SMOKE Version 3 1i Training Answer Sheet 1 ABASE 2 GE_DAT gspro cmaq5 cb05p25 txt 1 3 ESCEN EPI STDATE 2007152 EPI STTIME 000000 EPI RUNLEN 0240000 EPI NDAY 1 1 4 G STDATE 2007152 G STTIME 000000 e RUNLEN 250000 ESDATE 20070601 e NDAYS 1 2 1 1 RUN SMKINVEN 2 RUN GRDMAT 3 RUN SMKMERGE 1 MRG GRDOUT YN 2 MRG REPCNY YN 22 3 REPSTA YN 4 MRG GRDOUT UNIT 5 TOTOUT UNIT 6 MRG TEMPORAL YN 7 MRG SPCMAT YN 1 Missing inventory field for pollutant at line 77 2 Missing SIC code at line line number Default 0000 will be used 2 3 3 No kept pollutant found at line line number The source will be dropped 4 Some base year control efficiency valu
18. SMOKE Training Version 3 1i Sparse Matrix Operator Kernel Emissions SMOKE Modeling System Monthly NO Emissions July 2007 300 00 134 250 00 200 00 150 00 100 00 20 00 0 00 Tons Month July 31 2007 0 00 00 Min 0 00 at 101 1 Max 9858 11 at 99 64 Introduction to SMOKE Version 3 1 International Version TRAINING MANUAL Community Modeling and Analysis System Center UNC Institute for the Environment Chapel Hill NC 2013 Community Modeling and Analysis System SMOKE Training Version 3 1i Disclaimer The statements in this training manual are those of the University of North Carolina at Chapel Hill and not necessarily those of the United State Environmental Protection Agency The material in this training manual has not been subjected to the U S EPA s peer and administrative review nor has it been approved for publication as an EPA document The mention of commercial products their source or their use in connection with material reported herein 15 not to be construed as actual or implied endorsement of such products O 2013 1 Community Modeling and Analysis System SMOKE Training Version 3 1i Contents Introduction the SMOKE Version 3 1 DIsclatnetos ss custo Me RE E EL p DL EE DD eda dut i Contents Introduction the SMOKE Version 2 6 essere ener ii ACRONYNIS a i ide tunt iv COURSE e ia ic emat be aN 8 e ete un b dn V 1 SMOKE
19. The processing sequence is exactly the same as the previous step except for a final post merge Community Modeling and Analysis System 2 6 2013 2 SMOKE Training Area Sources step to allocate the emissions to the vertical model layers using information published in the literature for the energy sector The SMOKE utility Layalloc will be used in this exercise to convert the 2 d energy sector area source emissions to 3 d emissions files A Return to the SSCRIPTS run directory copy the area source run script used in the previous exercise to a new file named smk areng train lt initials gt csh and open this script in a text editor cd SSCRIPTS run gt cp smk ar train initials csh smk areng train initials csh gt gedit smk areng train za csh amp B Configure the script to import the area energy sector inventory grid speciate temporalize and merge Change the SRCABBR environment variable to areng Run the inventory import program Smkinven Run the speciation program Spcmat Run the gridding program Grdmat Run the temporal allocation program Temporal Run the merge program Smkmerge Configure Smkmerge to output temporally allocated and speciated emissions Configure Smkmerge to output gridded emissions in moles s Do not output state totals L DJ D D DJ D D EI DI D Output county totals with units of moles yr Save the run script C Run the energy area sources script from the SSCRIPTS run di
20. The start date Y Y Y YMMDD used in file names The number of days in each model ready output file The SMOKE scripts will loop through the number of days indicated by EPI NDAY incrementing STDATE and creating the model ready output files for each day During each loop the ESDATE variable is also updated and 15 used for naming output files A Look the Assigns file using gedit to see where these variables are in the file Note that the G_TSTEP variable is also in the file but its value will not change SMOKE s output SMOKE can output only hourly data Community Modeling and Analysis System Exercise 1 4 What are the values of the environment variables listed below Answer 1 4 EPI STDATE EPI STTIME EPI RUNLEN EPI NDAY G STDATE G STTIME G RUNLEN ESDATE NDAYS 1 10 2013 1 SMOKE Training Overview You do not need to do anything in this step except review the script settings Confirm that the Julian and Gregorian starting dates are consistent The I O API program juldate will convert a Gregorian date to a Julian date and has the following syntax juldate month day lt 4 digit year For example to determine the Julian date for April 21 2004 gt juldate 4 21 2004 This completes the SMOKE Overview exercise You are now ready to move on to the second exercise which addresses area sources O 2013 1 11 Community Modeling and Analysis System 1 SMOKE Training Over
21. Training OVErVIe Wes sess teas 1 1 1 1 1 2 Linux commands and information needed for training 1 1 1 3 The SMOKE system directories zone en ceo ense ia CRY dee ev e eR o 1 3 1 4 Setting up fora new SMOKE eere edente rye 1 4 1 5 Input and output directories and input files essere 1 6 1 6 Setting Up dor d Dew PE ders DA epus RN dp SO GRE Dra 1 9 1 7 Setting UD for a new episode ceo distet eI di DR eon ban ER eU RSEN Use 1 10 2 SMOKE Training Ar a So rc s iex nope dep meat ges 2 ee one d 2 1 2 2 Dhe tun script and ba d UU ASH GRANDS 2 2 3 Running area sources inventory import gridding and intermediate merge 2 3 2 44 Examine the log files and output TIl s iua eser eoo rtt doe 2 3 2 5 Running the area sources speciation temporal allocation and merge 2 6 2 6 Processing 3 d area SOULCES re tro cto pterea rdi tle er eec e V e eres 2 6 2 7 Examine the final model ready Tiles cesses esos e eee eae ri esee 2 8 2 8 Problem solving ro oe Eme RU emo ti e E ea e Redes 2 9 3 SMOKE Training Biogenic SOurces cccesccesccsssceescecesecesecseceeeseecaeceeceeeeeeaeecsseceteesaees 3 1 Betis WTEC HO e
22. a single file to input These variables can be changed in the Assigns file Change directories to the area inventory directory and view the area source inventory files arinv_mideast05 orl and aginv mideast05 ida using the more command for discussion about these files with the instructor Community Modeling and Analysis System 1 6 2013 1 SMOKE Training Overview gt cd SARDAT gt more arinv mideast05 orl gt more aginv mideast05 ida F View the point source inventory file ptinv abudhabi04 orl using more for a discussion about this file with the instructor gt cd SPTDAT gt more ptinv abudhabi04 orl G Go to the other directory and examine that directory s contents gt cd SINVDIR other gt ls The SINVDIR other directory contains O The inventory table invtable txt The report configuration files used by Smkreport repconfig Ll The area to point assignments file used by Smkinven artopnt 1999 txt H Open the inventory table that we are using for this training using gedit for a discussion about this file with the instructor gt gedit invtable txt amp I Go to the general data GE DAT directory and look at that directory s contents cd GE DAT gt ls The SGE DAT directory contains files that are shared by all source categories such as cross reference files gridding surrogates and temporal and speciation profiles Exercise 1 2 What is the name including the directory path
23. answers in the SANSWERS area step 2 directory Tip You can use the Linux command diff to compare two text files The syntax of the command is as follows O 2013 diff first file gt second file gt Exit from the text editor Start PAVE so you can use it to look at the gridded inventory file NOTE If you are unfamiliar with PAVE you may need assistance from the instructor s after starting PAVE gt pave f SREPSTAT ag UAE36 train lt initials gt ncf The gridded inventory file ag UAE36 train_ lt initials gt ncf is in the SREPSTAT directory The file can be added to the PAVE session using the command line argument _ lt directory filename gt as shown above or by using the PAVE Add Delect Select Dataset popup window To use the Add Delete Select Datasets_popup window select the Add button in this window to load the gridded inventory file into PAVE Click a variable in the Species List under to select a variable for plotting Highlight the variable that you would like to plot in the Add Delete Select Formula popup window The from the Graphics pull down menu in the main PAVE window select Create Tile Plot Create a second tile plot with the gridded inventory file in the SANSWERS area step 2 directory Compare this with the tile plot of your file to make sure you have processed the area sources correctly Continue to experiment and explore with PAVE You may want to lower the maximum va
24. arately Source specific speciation and temporal cross reference and profile files will also need to be developed and applied to each explicit gridded inventory Close the GSREF file G Navigate to the output data directory and view the processed biomass burning inventory in PAVE gt pave f SA OUT bbgts 1 Use PAVE to explore the biomass burning processed emissions data Note that all of the emissions are allocated to layer 1 only In the next exercise we will distribute these emissions to the vertical model layers 5 5 Generate 3 d emissions data 4 In this step you will run the SMOKE utility Layalloc to distribute the biomass burning emissions to the vertical model layers A Go to the directory containing the SMOKE run scripts gt cd SCRIPTS run B Configure the biomass burning script to run the following steps by changing the RUN variables O Do not run Smkinven Do not run Grdmat Do not run Spcmat O Do not run Temporal Community Modeling and Analysis System 5 4 2013 5 SMOKE Training Gridded Inventories O Do not run Smkmerge O Run Layalloc Save the biomass burning run script C Navigate to the GE DAT directory and open the biomass burning LAYER FRACTION file gt cd GE DAT gt gedit layers gfed txt amp Exercise 5 3 What percentage of the biomass burning emissions will be allocated to the altitude band from 0 50m What is the maximum emission height specified for biomass
25. as ua UR cen CC uaa ok an 3 1 3 2 The run script and scripl OptloDs user rtr eer ir lere tes ere 3 1 3 3 Examine the MEGAN output files with PAVE 3 3 3 4 Running the biogenic model with a different temperature variable 3 4 3 5 Compare the MEGAN results in PAVE 4 eere er 3 5 3 04 Problemi SOWING oos hod Loss ht eiut eR EDS ttem d ied 3 5 4 SMOKE Training Point ette pee qn aet e aden Uer Y e Ye eod 4 1 4 4 Md e Ra 4 1 4 2 The run script and Script 4 4 3 Running the point sources script uso eere e e ace daga din a 4 3 4 4 Examine the log files and output 4 3 4 5 Projecting point source emissions to a future year 4 4 5 SMOKE Training Processing gridded Inventories sse 5 1 Del Inttoduction tere deis tete a Nas 5 1 5 2 The run script and script o ee n CIERRE erp 5 1 5 3 Processing gridded inventory 5 2 5 4 Examine the log files and output Bless ue fei ence ee eater road s 5 2 Community Modeling and Analysis System 11 2013 SMOKE Training Version 3 1i 55 Generate 3 d emissions data esse etae ted ei at de tite oai a dein 5 4 5 6 Compare 2 the
26. burnin by this LAYER FRACTION file Exit from the LAYER FRACTION file after completing the exercise D Navigate back to the SCRIPTS run directory and execute the biomass burning run script gt smk bb train initials csh 5 6 Compare the 2 d and 3 d emissions 5 In this step you will load the 2 d and 3 d biomass burning emissions files into PAVE and compare the results A Load the biomass burning data into PAVE gt pave f A OUT bbgts 1 f A OUT bbgts3d 1 Exercise 5 4 What is the highest model layer into which the biomass burning emissions are allocated What s the maximum hourly NO emissions estimate in this layer 2013 5 5 Community Modeling and Analysis System 6 SMOKE Training Gridded Inventories 5 7 Problem solving 6 Inthis problem solving exercise you will rerun the layer allocation step for the biomass burning sources after changing the vertical profiles for these sources Create a new biomass burning emission file with the following vertical distribution Altitude Band m Emissions 0 25 10 25 75 15 75 500 60 500 1500 15 Instead of following step by step detailed instructions you will need to figure out what files and settings are needed to accomplish this task If you encounter errors along the way you will need to figure out solutions with the help of your instructor You can compare your results to the answers in SANSWERS gridded step 6 Exe
27. ce GSREF and speciation profiles GSPRO used for the biomass burning inventory Navigate to the SMOKE general data directory SGE DAT and view the GSREF file used for the biomass burning inventory gt cd GE DAT 5 3 Community Modeling and Analysis System 6 SMOKE Training Gridded Inventories gt gedit gsref bioburn txt amp This GSREF file contains one entry for each pollutant in the biomass burning inventory and uses the default SCC code 0000000000 to identify the source for each profile Because gridded inventories do not contain source specific identification information such as FIPS codes and SCC s the normal hierarchical cross referencing that SMOKE uses for applying profiles does not work As such only a single speciation profile can be applied to each pollutant in a gridded inventory Similarly a single temporal profile will be applied uniformly across all of the grid cells in a gridded inventory The speciation and temporal cross reference and profile files used with gridded inventories MUST CONTAIN ONLY A SINGLE ENTRY Only one set of profiles per cross reference and profile file is allowed for processing gridded inventories The SCC field of the cross reference files must contain the fallback or default code of all zeros 0000000000 To process multiple gridded inventories 1 e biomass burning commercial shipping industrial area on road mobile etc you must run each inventory through SMOKE sep
28. cise After making these changes save the run script Exercise 3 4 What are the three variables that you changed in the MEGAN run script for this exercise What are the new settings of these variables Answer 3 4 B Run the MEGAN run script to create biogenic emissions calculated with ambient air temperatures gt run megan train lt initials gt csh C After confirming that MEGAN completed successfully run the biogenic speciation program mg2mech to create new CMAQ emissions calculated with the alternate temperature variable Remember to change the name of the input MGERFILE and output files OUTPFILE to read the MEGAN emissions computed with ambient air temperatures and to create an output file that is named differently from the file created in step 1 D Run the MEGAN run script to create biogenic emissions calculated with ambient air temperatures gt run megan train lt initials gt csh Community Modeling and Analysis System 3 4 2013 3 SMOKE Training Biogenic Sources 3 5 Compare the MEGAN results in PAVE 4 Loadthe MEGAN results calculated with both the 2 m temperature and the ambient temperature variables into PAVE and compare the results Check the results that you generated against the results in the SANSWERS biog step 3 directory Exercise 3 5 In general how does changing from the 2 m temperatures to the ambient temperatures change the monoterpene TERP emissions calculated by MEGAN An
29. ck the MEGAN log file in the directory LOGS megan for clues about what went wrong Fix any errors reported in the log and rerun the script before proceeding to the next step Community Modeling and Analysis System 3 2 2013 3 SMOKE Training Biogenic Sources M The utility mg2mech converts the MEGAN output variables to the chemical species required by an air quality modeling system This utility is the analogue of the SMOKE program Spcmat Copy the MEGAN run script to one that uses your initials Examine the new script The first section of the script sets the name and location of the Assigns file and input output directories The second section of the script sets the dates of the MEGAN output files that will be speciated with the utility The next part of the script sets the necessary environment variables for running and configuring mg2mech Within this section of the script the input and output files are defined along with the photochemical mechanism name to be used for the output emissions N Change the Assigns file name to use the Assigns file that you created for the UAE36 grid in the Overview lab Configure the script to create emissions using the CBOSSOA mechanism Exercise 3 2 Which environment variable did you change to set the photochemical mechanism and how did you set this variable for this exercise Answer 3 2 O Save the script and execute it at the command line gt run mg2mech train lt initials gt csh
30. creen This same information is written to the log file for each program C If you need to rerun a program the script will rename your old log files rather than deleting them This behavior is controlled by the AUTO DELETE LOG setting in the point sources run script 44 Examine the log files and output files 3 After the programs have finished you will need to examine the log files for notes warnings and errors We will also look at the report file created by Smkmerge and examine the output emissions in PAVE A Go to the directory containing the log files gt 51065 B Confirm that all of the point source programs completed successfully The logs for the point source programs will include the abbreviation in their names C View the log file for the Grdmat program gt gedit grdmat pt train initials UAE12 1log amp Exercise 4 4 What are the three notes that appear in this log file Hint Search for the word either in gedit or using the Linux command grep 2013 4 3 Community Modeling and Analysis System 4 SMOKE Training Point Sources Answer 4 4 Close the log file Go to the reports directory REPSCEN to examine the report created by Smkmerge Make sure that it is only a state totals report and compare it to the results in SANSWERS point step 3 using either gedit or the Linux command diff Open a new xterm window and start PAVE Load the gridded speciated hourly
31. e 12 km grid name e Change the log file name in the mg2ioapi script to create file tagged with uael2 instead of uae36 e Change the name of the Assigns file in the MEGAN script to the 12 km file 3 6 Change the names of the input ECMAP and output EROUT files in the MEGAN script to refer to the 12 km grid e Change the temperature file TMPFILE to use the METCRO2D file in the MEGAN script e Change the air temperature variable to 2 m temperatures TEMP2 in the MEGAN script Change the log file name in the MEGAN script to create file tagged with uael2 instead of uae36 e Change the name of the Assigns file in the mg2mech script to the 12 km file e Change the names of the input MGERFILE PFTFFILE and output OUTPFILE files in the mg2mech script to refer to the 12 km grid Change the log file name in the mg2mech script to create file tagged with uael2 instead of 36 4 1 1 RUN SMKINVEN 2 RUN GRDMAT 3 RUN SPCMAT 4 RUN TEMPORAL 5 RUN LAYPOINT 6 RUN SMKMERGE 4 2 Variable OUTZONE Value 0 4 3 Variable PLUME GTEMP NAME Value TEMP2 1 Grid settings initialized using UAEI2LCC 78X72 in grid description file 4 4 2 Output grid UAEI2LCC 78X72 set described as 3 Number of sources excluded from grid was 0 5 1 ag bb gfedv2 UAE36LCC 148X134 2007153 8 ncf 5 2 GSREF gsref bioburn txt GSPRO gspro bioburn txt 5 3 25 2000 m 5 4 Layer 19 0 031 moles s Solution for the problem to create a new ver
32. e section of the script that controls the Smkmerge program Change the following settings for Smkmerge Output a gridded file state totals and county totals Output the gridded emissions and the state and county totals in tons day Do not produce temporally allocated output O Do not produce speciated output Exercise 2 2 List the environment variables that you changed or checked the values of Answer 2 2 G Save the run script Community Modeling and Analysis System 2 2 2013 2 SMOKE Training Area Sources 2 3 Running the area sources inventory import gridding and intermediate merge 2 Inthis step you will import the area sources inventory create the gridding matrix and merge the results to create a gridded inventory The gridded inventory merge is not an essential step for creating model ready input files which need to be hourly and have chemical speciation However the intermediate merge step can be used as a quality assurance step and we will use it as part of the learning process A Run the area sources run script gt smk ar train initials csh While the script is running various messages from each of the programs will scroll by on the screen This same information is written to the log file for each program If you need to rerun a program the run script is set up to create backup copies of existing log files rather than deleting them The setting AUTO DELETE LOG in the Script Setti
33. e the previous SMOKE output file gt cd SOUTPUT Community Modeling and Analysis System 6 2 2013 6 SMOKE Training Merging gt mv egts 1 20070601 1 UAE36 train initials ncf egts 1 20070601 1 UAE36 train initials ncf bb C Return to the SSCRIPTS run directory and execute the merge script cd SSCRIPTS run gt smk mrgall train initials csh 6 6 Compare the SMOKE output files in PAVE 5 Start PAVE if it is not already running Load the SEGTS L files with and without biomass burning emissions from the output directories Create a formula for NO that subtracts the emissions without biomass burning sources from the emissions file that includes these sources You can also load in the biomass burning data file from the A OUT directory into PAVE and compare the NO emissions in this file with the NO difference between the merged files The merged file difference and the biomass burning only data should be exactly the same O 2013 6 3 Community Modeling and Analysis System 6 SMOKE Training Merging Page left intentionally blank Community Modeling and Analysis System 6 4 2013 7 SMOKE Training Quality Assurance 7 SMOKE Training Quality Assurance 7 1 Introduction During this quality assurance training you will Turn on the quality assurance options in some of the scripts you have already run Review quality assurance reports to check processing Buildanew quality assurance con
34. emissions file SPGTS3D pgts3d_1 20070601 1 UAE12 train_ lt initials gt ncf from the P OUT directory You may want to use a log scale to display the emissions data you can do this with a formula such as LOG CO 0 0001 You can also compare your results with the file in SANSWERS point step 3 4 5 Projecting point source emissions to a future year 4 In this section you will configure the point sources script to grow the point source inventory to a future year and create model ready emissions A Go to the SSCRIPTS run directory B Copy the future year point sources script to one that uses your initials gt cp smk pt mideast07 18 csh smk pt train initials 18 csh Edit your future year point sources script gt gedit smk pt train initials 18 csh Change the Assigns file name to use the uae12 Assigns file that you created in the Overview lab Edit the script to Run the growth matrix creation program Cntlmat Run the program to apply the growth matrix to the inventory Grwinven Run Temporal Run Smkmerge Use the same Smkmerge settings as used in Step 2 remember to set Smkmerge to output 3 D gridded speciated hourly emissions and state totals L1 DL D DL LI Community Modeling and Analysis System 4 4 2013 4 SMOKE Training Point Sources O 2013 Save the script and exit Invoke the point sources script gt smk pt train initials 18 csh While the programs are running you can look
35. es that were input as 100 5 Some base year rule effectiveness values that were input as 096 2 4 546 the number of sources in the inventory 2 5 Layer 5 Solution for problem Area Source with new 12 km grid 1 Change 36km Assign file to the 12km Assigns file name that you created in the Overview Lab 2 RUN GRDMAT Y Since it is for 12km you need to re run GRDMAT but there is no need to run Smkinven Spcmat or Temporal 3 Run SMKMERGE Y 2 6 e SPCMAT YN Y MRG TEMPORAL YN Y MRG GRDOUT YN Y REPCNY YN N MRG REPSTA YN N e MRG GRDOUT UNIT moles hr e TOTOUT UNIT moles yr 3 1 TEMPVAR 3 2 MECHANISM CB05SOA 3 3 78 691 moles s at hour 12 00 in cell 3 24 2009 8 1 Community Modeling and Analysis System SMOKE Training Answers EROUT INTDIR ER MEGAN UAE36k 148X134 SDATE TA ncf 3 4 TMPFILE METDIR METCRO3D SDATE TEMPVAR TA 3 5 The 2 m temperatures produce higher emissions estimates during day while the ambient temperatures produce higher emissions estimates at night Solution for problem Biogenic sources on the 12 km grid e Change the name of the Assigns file in the mg2ioapi script to the 12 km file e Check the name of the 12 km grid in the DAT GRIDDESC file Set the GDNAM3D variable in the mg2ioapi script to UAEI2LCC 78X72 e Change the names of the input INPFILE and output OUTFILE files in the mg2ioapi script to refer to th
36. figuration file with explicit instructions Buildanew quality assurance configuration file as a problem solving exercise NOTE To proceed with this lab you must have created an Assigns file for the uae36 grid as described in the SMOKE Overview Exercise Use the following command to source your Assigns file gt source SMKROOT assigns ASSIGNS train lt initials gt cmaqg5 cb05p25 uae36 7 2 The quality assurance script options 1 Turn on the area source quality assurance script options A Go to the SSCRIPTS run directory B View your area sources script gt gedit smk ar train initials csh amp C Configure the script to O Use the 36 km Assigns file Do not rerun any area source processing steps L Run the emissions reporting program Smkreport Create inventory reports by setting QA TYPE to part1 The following settings are valid for the TYPE setting all part1 part2 part3 part4 and custom Note that part3 and part4 are used only for point source quality assurance The qa run csh script sets which reports will be created for each QA TYPE setting D Save the run script 2013 7 1 Community Modeling and Analysis System 7 SMOKE Training Quality Assurance 7 3 Run the reporting program for area sources 2 Now you will run the script that you created in the previous step and then look at the reports generated from this
37. ill be zero emissions up to 184 meters from the surface 8 of the emissions will be between 184 and 324 meters 46 of the emissions between 324 and 522 meters etc The program Layalloc maps the emission heights in meters contained in the layers file to the layers defined by the input meteorology data to produce vertically resolved emissions using a sigma p coordinate Layalloc requires a METCRO3D file as an input to define the vertical layer structure B Run the energy sector area sources script from the SSCRIPTS run directory gt smk areng train initials csh Look for the following to confirm that Layalloc completed gt gt Normal Completion of program LAYALLOC 2 7 Examine the final model ready files Start PAVE gt PAVE Load the AGTS L files from the step 5 and step 6 output directories OUT and compare your results to SAGTS L files in SANSWERS area step 5 and SANSWERSJ area step 6 directories respectively Tip You can use PAVE command line arguments to load the input files when you start up PAVE For example the following command loads the SAGTS L file from step 4 and the AGTS L file in the answers directory Note that each file name must be preceded by gt pave f SA OUT agts areng f SANSWERS area step 4 agts areng In addition to comparing the files that you created during this lab with the answers use PAVE to compare the 2 d and 3 d energy sector area source output files Commu
38. in SINVDIR and GE DAT A Go to the inventory input directory and look at the contents of the directory gt cd SINVDIR gt ls Within the INVDIR directory are the area biog gridded mobile nonroad point and other directories where the raw emissions land use data and Smkreport configuration files are stored These directories correspond to the SARDAT BGDAT GDDAT MBDAT NRDAT and PTDAT environment variables set by the Assigns file Look in these directories and view some the inventory files that are there Note that the mobile and nonroad directories are empty Below is a sample of the input inventory logical file names and their physical file counterparts as set in the Assigns file ARINV area arinv ar lst area source inventory file ARINV area arinv areng st industrial area source inventory file PTINV point ptinv lst point source inventory file The arinv ar lst arinv areng lst and ptinv lst files are list files that contain the file names of actual raw inventory files for this training we are using both IDA and ORL formatted raw inventory files The area source inventory ar lists two raw inventory files while the area energy sector inventory areng and point source inventories list only one raw inventory file each You can use list files to combine as many raw inventory files as you need You may also set the input logical file names e g ARINV to an ORL or IDA formatted file directly if you have only
39. ll be displayed and the Linux prompt will then return F Find out what directory you are currently in The pwd command allows you to see the directory currently available at the Linux prompt Depending on the configuration of your computer this may also be displayed along with the Linux prompt Type the following command to see your directory gt pwd Community Modeling and Analysis System 1 2 2013 1 SMOKE Training Overview G Copy a file The ep command is used to make a copy of a file and give that copy a different name The syntax of the copy command is cp from filename lt to filename You will practice copying files when setting up for a new SMOKE run in step 4 1 3 The SMOKE system directories 2 The main SMOKE system directory is SSMK HOME From the xterm window go to the main SMOKE system directory and look at its contents by typing gt cd SMK HOME changes the directory gt ls shows directory contents Several directory names will be displayed in your window The data directory location of all SMOKE input and output data Thescripts directory location of SMOKE administrative scripts The subsys directory location of SMOKE system libraries and scripts Change directories into the subsys smoke directory and look at the contents by typing gt cd subsys smoke gt ls Several directory names will be displayed in your window The assigns directory location for the Assigns files
40. lue in the map legend using the plot Configure menu From the Control pull down menu in the plot window select Configure and Tile Enter a new number in the Max legend range box and hit enter For example plot CO emissions and change the maximum scale to 50 Also try different formulas species and zoom functions within PAVE Exit from PAVE when you are finished 2 5 Community Modeling and Analysis System 2 SMOKE Training Area Sources 2 5 Running the area sources speciation temporal allocation and merge 4 In this step you will configure the run script to run area source speciation temporal alloca tion and merge Then you will run the modified script Note that we could have run all of these steps during the previous exercise but by running these steps incrementally we re demonstrating the modularity of SMOKE In this exercise we will not need to rerun the inventory import and gridding steps because they were successfully completed in the previous exercise A Navigate back to the run scripts directory gt cd SCRIPTS run B Edit the smk_ar_train_ lt initials gt csh script to Run the speciation program Spcmat Run the temporal allocation program Temporal Run the merge program Smkmerge Do not run the inventory import Smkinven or gridding programs Grdmat Configure Smkmerge to produce temporally allocated and speciated output Configure Smkmerge to output gridded emissions in moles s
41. lve to select elevated sources NOTE To proceed with this lab you must have created an Assigns file for the uae36 grid as described in the SMOKE Overview Exercise Use the following command to source your Assigns file gt source SMKROOT assigns ASSIGNS train initials cmaq5 cb05p25 uae36 4 2 Therun script and script options 1 Inthis step you will copy the point sources run script and configure it to use your Assigns file and run various point source programs A Start an xterm window if one is not already available B Go to the directory that contains the SMOKE run scripts gt cd SCRIPTS run C Copy the point sources script to one that uses your initials Remember that you can use the tab key to complete file names gt cp smk_pt_mideast07 csh smk_pt_train_ lt initials gt csh D View your point sources script gt gedit smk pt train lt initials gt csh amp E Examine the script At the top of the script the SMK SOURCE environment variable is set to P indicating that point sources will be processed Below that the RUN_ variables control which programs will be run Next the program specific and multiple program environment variables are listed These variables control the behavior of single programs and of two or more programs respectively Finally the Assigns file is sourced and the programs are run 2013 4 Community Modeling and Analysis System 4 SMOKE Training Point Sources
42. nate Weather Research and Forecasting model Community Modeling and Analysis System iv 2013 SMOKE Training Version 3 1i Day 1 8 30 9 15 9 15 10 00 10 00 10 15 10 15 11 00 11 00 12 00 12 00 1 00 1 00 2 00 2 00 3 15 3 15 3 30 3 30 4 15 4 15 5 15 Day 2 8 30 8 45 8 45 9 45 9 45 10 30 10 30 10 45 10 45 11 45 11 45 12 45 12 45 3 00 3 00 3 15 3 15 5 15 Day 3 8 30 8 45 8 45 10 15 10 15 10 30 10 30 12 30 O 2013 COURSE AGENDA Emissions processing basics SMOKE basics Break SMOKE assigns file and scripts Hands on SMOKE overview Lunch Hands on SMOKE overview continued SMOKE programs and options Break SMOKE problem solving Hands on area source processing Review Hands on area source processing continued Hands on biogenic processing with MEGAN Break Hands on biogenic processing continued Lunch Hands on point source processing Break Hands on gridded inventory processing Review Hands on merge processing Break Hands on quality assurance Community Modeling and Analysis System 1 SMOKE Training Overview 1 SMOKE Training Overview 1 1 Introduction During this training overview you will Learn basic Linux commands needed for running SMOKE Learn how to navigate around the main SMOKE directories Learn how to use the Assigns file to set file and directory names needed b
43. ng this problem Think about what steps need to be rerun and which steps do not Discuss with your classmates or your instructor if you are unsure This completes the SMOKE area sources exercise You are now ready to move on to the third exercise which addresses biogenic sources 2013 2 9 Community Modeling and Analysis System 2 SMOKE Training Area Sources Page left intentionally blank Community Modeling and Analysis System 2 10 2013 3 SMOKE Training Biogenic Sources 3 SMOKE Training Biogenic Sources 3 1 Introduction During this biogenic emissions training you will Copy the biogenic sources run scripts examine the scripts and change options Estimate biogenic emissions for CMAQ with the MEGAN model Process using a different temperature variable from the gridded meteorology data Examine biogenic emissions files in PAVE NOTE To proceed with this lab you must have created an Assigns file for the uae36 grid as described in the SMOKE Overview Exercise Use the following command to source your Assigns file gt source SMKROOT assigns ASSIGNS train lt initials gt cmaqg5 cb05p25 uae36 3 2 The run script and script options 1 Inthis step you will copy the biogenic sources run scripts and configure them to use your Assigns file convert gridded emissions factor and leaf area index data to netCDF files run the MEGAN model and speciate the MEGAN output for CMAQ A Sta
44. ngs section of the run script controls whether old logs are deleted or renamed For the training you will save your old log files so that you or the instructor can look back at previous log files 2 4 Examine the log files and output files 3 Animportant part of running SMOKE is examining the log files for notes warnings and errors For notes and warnings you must decide whether they indicate problems or can be ignored If there are errors you must fix them because the programs will not complete successfully if an error occurs We will examine the log files and also look at the gridded inventory and state and county totals A B C O 2013 Go to the directory containing the log files for area sources gt 51065 Confirm that all programs completed successfully When a SMOKE program completes successfully it will write the following message to the log file gt gt Normal Completion of program PROGRAM NAME gt You can check the end of a log file using the tail command gt tail smkinven ar train initials log Use this command to make sure that all of your log files end with the Normal Completion message View the log file for Smkinven using gedit gt gedit smkinven ar train lt initials gt log amp 2 3 Community Modeling and Analysis System 2 SMOKE Training Area Sources Exercise 2 3 What are the five major types of warnings that appear in this log file Tip You can use the Linux c
45. nity Modeling and Analysis System 2 8 2013 2 SMOKE Training Area Sources You can cycle through the time steps of your SAGTS L file using the Animate option in the Control menu To slow down the animation select Set Minimum Frame Time from the Graphics menu in the main window A value of 5 is a good speed Exercise 2 5 What is the number of the first model layer that contains emissions in the 3 d energy sector area source output file Answer 2 5 2 8 Problem solving 7 Inthis problem solving exercise you will configure SMOKE to run area sources for another grid and using some additional options Instead of having step by step instructions you will need to figure out what files and settings are necessary If you encounter errors along the way you will need to figure out solutions with the help of your instructor You can compare your results to the answers in SANSWERSJ area step 7 Exercise 2 6 Configure the script and run SMOKE for area sources with the following settings O Process area source emissions on the UAE12 grid Ll Create the gridded speciated and temporally allocated emission files in moles hr Use cmaq5 cb05p25 speciation O Do not create the state or county totals reports Tip s you have already completed all of the basic SMOKE processing steps in the previous exercises e g inventory import speciation you only need to rerun the steps that are required for completi
46. ntory program logs Examine biomass burning emissions files in PAVE NOTE To proceed with this lab you must have created an Assigns file for the uae36 grid as described in the SMOKE Overview Exercise Use the following command to source your Assigns file gt source SMKROOT assigns ASSIGNS train initials cmaq5 cb05p25 uae36 5 2 The run script and script options 1 Copy the biomass burning sources bb run script and configure it to use your Assigns file and to run inventory import gridding and merge A Start an xterm window if needed B Go to the directory containing the SMOKE run scripts gt cd SCRIPTS run C Copy the biomass burning sources script to one that uses your initials Remember that you can use the tab key to complete file names gt cp smk bb mideast07 csh smk bb train initials csh D Edit your biomass burning sources script gt gedit smk bb train initials csh amp E Examine the run script At the top of the script the SMK SOURCE environment variable is set to A indicating that the gridded inventory will be processed as an area source Below that the RUN variables control which programs will be run Next the program specific and multiple program environment variables are listed These variables control the behavior of single programs and of two or more programs respectively Finally the Assigns file is sourced and the programs are run 2013 5 1 Community Modeling and
47. o list the contents of a directory use the Is command followed by the Enter key gt ls 2013 1 1 Community Modeling and Analysis System 1 SMOKE Training Overview C Change directories To change to a different directory use the ed command The syntax of this command is cd directory name gt For example to change to the subsys directory from your home directory type the following command gt cd smoke subsys To back out of a directory type the following command gt cd To back out two directory levels type the following command cd D Usean environment variable The following example uses the environment variable SSMKROOT to change to the root directory of the SMOKE system To use an environment variable the dollar sign must precede the environment variable with no space between the dollar sign and the environ ment variable Type the following command to change to the SMOKE root directory we will use capital letters for all environment variables gt cd SMK HOME NOTE For the training SSMK HOME has been set for you in your environment This will not be true for the SMOKE release case that you can download E Determine the value of an environment variable The echo command permits you to see the value of an environment variable For example to see the value of the SSMK HOME environment variable type the following gt echo SMK HOME The contents of the variable wi
48. of the week to use for setting day of week and diurnal temporal profiles procdates txt time periods to be processed by Temporal GE DAT UAE36 SRGDESC txt GE DAT UAEI2 SRGDESC txt the codes descriptions and location of the surrogate files Community Modeling and Analysis System 1 8 2013 1 SMOKE Training Overview SCCDESC scc desc txt the source category code descriptions SICDESC sic desc txt the standard industrial classification SIC code descriptions 7 Take look at each of the primary intermediate and final output directories SSCENARIO STATIC OUTPUT REPSCEN and REPSTAT Note how the value of SEBASE variable 1 train_ lt initials gt is used in these paths Exercise 1 3 What environment variable is common to the values of the output directory environ ment variables listed above Hint Use the set dirs scr script in the Assigns direc tory to determine this 1 6 Setting up for a new grid 8 Now you will step through the various tasks needed for setting up a new grid In this case we will set up an 8 km grid that also focuses on Nashville Tennessee USA A Copy your Assigns file to a file with a different grid name as the final part of the file name gt cd SASSIGNS gt cp ASSIGNS train initials cmaq5 cb05p25 uae36 ASSIGNS train initials cmaq5 cb05p25 uael2 B Use gedit to edit the 12 km Assigns file Change the GRID environment variable value to the grid
49. ommand grep to find words in a text file For example the following command will find all instances of the word WARNING in the Smkinven log file and then sort the unique lines gt grep WARNING smkinven ar train initials log sort u Answer 2 3 D Exit from the gedit window E Now go to the inventory output directory to examine the output files from Smkinven gt cd SINVOPD gt less asrc ar txt use the space bar to scroll and the q key to quit gt less area map ar train initials txt ncdump area ar ncf less NOTE ncdump is a netCDF utility that allows you to view binary netCDF files as text While in ncdump you can scroll forward with the space bar backward with lt b gt and use lt q gt to quit Exercise 2 4 What is the setting for the number of rows in the header of the area ncf file What does this correspond to in terms of the area source inventory Hint Look in Chap ter 9 of the SMOKE User s Manual for descriptions of the Smkinven output files Answer 2 4 F Youcan also convert the NetCDF file to a text file with the following command gt ncdump area ar ncf gt area ar out txt Community Modeling and Analysis System 2 4 2013 2 SMOKE Training Area Sources G Now go to the reports directory to examine the gridded inventory report gt cd SREPSTAT gt ls gt gedit repag ar UAE36 train lt initials gt rpt You can compare your report file with the
50. or NO that subtracts the component emissions from the combined file and plot this formula The results should be close to zero everywhere You can check other species in the various files and compare them to the SEGTS L file created in Step 2 You can also compare your log files and results with those in SANSWERS merge step 2 6 5 Create a biomass burning emissions sensitivity case 4 In this exercise you will rerun the program Mrggrid program to combine all of the files from the previous step except for biomass burning emissions Removing one emissions sector from an emission simulation is one way to determine the sensitivity of air quality to the emissions from that sector Comparing the result of a pair of air quality model simulations one with and the other without biomass burning emissions will demonstrate the impacts of biomass burning on air quality This exercise demonstrates how to set up a brute force emissions sensitivity for air quality modeling A Edit the merge script that you created in Step 2 to create merged emissions that do not include biomass burning data Set the MRGFILES environment variable to ARGTS_L AENGGTS L BGGTS_L Notice how you removed the variable BBGTS3D from the list created previously Also change the SRCABBR environment variable to reflect that the emissions only contain area and biogenic sources arbg Save the script and exit from the text editor B Go the SOUTPUT directory and renam
51. rcise 5 5 Use the SMOKE utility Layalloc to create new 36 km biomass burning emissions using an alternative vertical allocation profile Things to consider when setting up this case include Creating a new LAYER FRACTION file in the GE DAT directory Changing the LAYER FRACTION file for biomass burning bb in the 36 km Assigns file Renaming the previous biomass burning 3 d emissions file use the Unix command mv to rename the file Community Modeling and Analysis System 5 6 2013 6 SMOKE Training Merging 6 SMOKE Training Merging 6 1 Introduction During this merge processing training you will Copy the merge run script examine the script and change options e Use the SMOKE merge tool Mrggrid to combine model ready files NOTE To proceed with this lab you must have created an Assigns file for the uae36 grid as described in the SMOKE Overview Exercise Use the following command to source your Assigns file gt source SSMKROOT assigns ASSIGNS train initials cmaq5 cb05p25 uae36 6 2 script and script options 1 Copy the merge mrgall run script and configure it to use your Assigns file A Start an xterm window if needed B Go to the SCRIPTS run directory C Copy the merge script to one that uses your initials gt cp smk mrgall mideast07 csh smk_mrgall_train_ lt initials gt csh D Edit your merge script in gedit and change the Assigns file setting to use your 36 km
52. rectory gt smk areng train initials csh After the programs have finished confirm that all of the programs completed successfully using the tail command on the log files in the LOGS directory You can compare your log files to the answers in SANSWERS area step 5 6 Now open the energy sector area sources run script and configure it to run the 2 d layer allocation program Do not run the inventory import program Smkinven Do not run the speciation program Spcmat Do not run the gridding program Grdmat Do not run the temporal allocation program Temporal Do not run the merge program Smkmerge Run the 2 layer allocation program Layalloc O 2013 2 7 Community Modeling and Analysis System 2 SMOKE Training Area Sources Save and exit from the energy sector area sources run script A Examine the Layalloc input file in the SGE DAT directory Use a text editor to view the file layers areng txt This file contains four comma separated columns in each row The rows in this file correspond to different emission altitude bands The first column represents the emission altitude band number this is not related to the meteorology layers The second and third columns contain the bottom and top emission heights respectively in meters from the surface for each emission layer The fourth column is the fraction of emissions to allocate to each emission layer The file layers areng txt specifies that there w
53. rt an xterm window if one is not already available B Go to the directory that contains the SMOKE run scripts gt cd SCRIPTS run C Copy the mg2ioapi run script to one that uses your initials In the instructions below fill in your initials where indicated Remember that you can use the tab key to complete file names gt cp run mg2ioapi mideast07 csh run mg2ioapi train lt initials gt csh D View the mg2ioapi run script gt gedit run mg2ioapi train lt initials gt csh amp E The utility mg2ioapi is used to convert a text file of gridded emissions factors for biogenic sources and monthly mean leaf area index values to a binary netCDF file Examine the script This is a fairly simple script that sets the Assigns file grid information and input output file names before calling the executable file F Change the Assigns file name to use the Assigns file that you created for the UAE36 grid in the Overview lab 2013 3 1 Community Modeling and Analysis System 3 SMOKE Training Biogenic Sources G Save the script and execute it at the command line gt run mg2ioapi train initials csh H Confirm that the program completed successfully by looking for the following message on your terminal window after running the script gt gt Normal Completion of program MG2IOAPI If this message does not appear check the mg2ioapi log file in the directory LOGS megan for clues about what went wrong Fix any errors repor
54. rted by SMOKE Answer 7 2 Examine and compare the reports in the SREPSTAT and REPSCEN directories Exercise 7 3 Look in the report by SCC and by hour in the SREPSCEN directory How many tons hr of NOx are emitted by SCC 20100201 on hour 17 Answer 7 3 7 5 Run the quality assurance step for area sources using a custom configuration 4 nthis step you will follow a specific set of instructions to create a REPCONFIG input file that you will use to create a custom area sources report To create the REPCONFIG file you may need to review the format of this file in Section 7 3 of the SMOKE User s Manual You can also look at existing REPCONFIG files in the INVDIR other directory A Return to the SSCRIPTS run directory and open the mobile sources script that you created previously gt cd SCRIPTS run gt gedit smk ar train initials csh B Configure the script to O Use the 36 km Assigns file Do not rerun any area source processing steps Run the reporting program 2013 7 3 Community Modeling and Analysis System 7 SMOKE Training Quality Assurance O Set QA TYPE to custom Make a new environment variable REPORTI under the Script settings section of the script and set it to REPSCEN ar custom rpt C Save the area sources script D Create a new file in the SARDAT directory called repconfig area txt E In this REPCONFIG file enter the commands to Run for area sources Create
55. run B Copy the area sources script to one that uses your initials In the instructions below fill in your initials where indicated as you did for the Assigns file Remember that you can use the tab key to complete file names gt cp smk_ar_mideast07 csh smk_ar_train_ lt initials gt csh C View your area sources script using the following command gt gedit smk ar train lt initials gt csh amp D Examine the script Note that at the top of the script the SMK SOURCE environment variable is set to A indicating that area sources should be processed Below that the script sets which programs to run using the RUN_ variables Next the program specific 2013 2 1 Community Modeling and Analysis System 2 SMOKE Training Area Sources and then the multiple program environment variables are listed These variables control individual program behavior and the behavior of two or more programs respectively Finally the Assigns file is sourced and the programs are run E Change the Assigns file name to use the Assigns file that you created for the uae36 grid in the Overview lab F Change the appropriate RUN environment variables to configure the script to run the programs for Run the inventory import program Smkinven Run the gridding program Grdmat Run the merge program Smkmerge Answer 2 1 Exercise 2 1 What were the names of the RUN environment variables that were set to Y l Find th
56. swer 3 5 3 6 Problem solving 5 In this problem solving exercise you will configure MEGAN to create biogenic emissions for another grid Instead of having step by step instructions you will need to figure out what files and settings are necessary If you encounter errors along the way you will need to figure out solutions with the help of your instructor You can compare your results to the answers in SANSWERS biog step 5 Exercise 3 6 Configure the MEGAN scripts to calculate biogenic emission on the UAE12 grid O Convert the UAE12 emissions factor and leaf area index CSV file to netCDF Compute biogenic emissions for the UAE12 grid with MEGAN Use 2 m temperatures and solar radiation reaching the surface to calculate these emissions Speciate the MEGAN emissions using the CBOSSOA photochemical mechanism 2013 3 5 Community Modeling and Analysis System 3 SMOKE Training Biogenic Sources Page left intentionally blank Community Modeling and Analysis System 3 6 2013 4 SMOKE Training Point Sources 4 SMOKE Training Point Sources 4 1 Introduction During this point sources training you will Copy the point sources run script examine the script and change options Process point source emissions for CMAQ Project a point source inventory to a future year Examine point source program logs and reports Examine point source emissions files in PAVE e Problem so
57. ted in the log and rerun the script before proceeding to the next step I The program MEGAN calculates biogenic emissions using gridded emissions factors leaf area index land cover and meteorology data Copy the MEGAN run script to one that uses your initials In the instructions below fill in your initials where indicated gt cp run megan mideast07 csh run megan train initials csh J View the MEGAN run script The first section of the script sets the name and location of the Assigns file and input output directories The second section of the script sets the dates for running the model Note that MEGAN 15 dependent on input meteorology data The availability of hourly meteorology will determine the time periods and spatial extent ofa MEGAN simulation The next part of the script sets the necessary environment variables for running and configuring the model Within this section of the script the input and output files are defined including the meteorology variables to use for calculating emissions Exercise 3 1 Which environment variable controls the temperature variable to use in the MCIP output Answer 3 1 K Save the script and execute it at the command line gt run megan train initials csh L Confirm that the program completed successfully by looking for the following message on your terminal window after running the script gt gt Normal Completion of program MEGAN If this message does not appear che
58. tical distribution profile for biomass burning emissions 5 5 e Create anew LAYER FRACTION file with the layer distribution information provided for this exercise e Change the LAYER FRACTION environment variable on line 108 of the 36 km Assigns file to point to the new file Community Modeling and Analysis System 8 2 2009 SMOKE Training Answers Rename the biomass burning 3 d output file in the A OUT directory to a new file name so that this file does not get overwritten during this exercise e Run the biomass burning script with only the RUN LAY ALLOC variable set to Y All other RUN variables should be set to N SCC 99CIRCERES Name CIRCE Residential 7 2 Smkreport ran 3 times and it completed 2 runs there was an error in the elevpoint report that SMOKE could not open the input file PELV 7 3 11 077 tons hour 7 1 2009 8 3 Community Modeling and Analysis System
59. view Page left intentionally blank Community Modeling and Analysis System 1 12 2013 2 SMOKE Training Area Sources 2 SMOKE Training Area Sources 2 1 Introduction During this area sources training you will the area sources run script examine the script and change options e Process 2 d and 3 d area source emissions for the CMAQ model Examine area source program logs and reports Examine area source emissions files in PAVE Problem solve for processing area sources on a new grid The symbol gt is used throughout the training materials to represent the Linux prompt When this symbol appears as the first entry on a line in these instructions you do not need to type it Also Courier font is used to indicate text that you should type at the prompt as you work through the exercises NOTE To proceed with this lab you must have created an Assigns file for the uae36 grid as described in the SMOKE Overview Exercise Use the following command to source your Assigns file gt source SMKROOT assigns ASSIGNS train lt initials gt cmaqg5 cb05p25 uae36 2 2 The run script and script options 1 Inthis step you will copy the area sources run script and configure it to use your Assigns file and to run SMOKE for inventory import gridding and merge The following steps will guide you through this process A Go to the directory that contains the SMOKE run scripts gt cd SCRIPTS
60. y SMOKE e Explore the input and output directories Review the locations of important SMOKE input files and see examples of them Learn how to set up SMOKE for a new grid or episode The symbol gt is used throughout the training materials to represent the Linux prompt When this symbol appears as the first entry on a line in these instructions you do not need to type it Also Courier font is used to indicate text that you should type at the prompt as you work through the exercises The login information for your training laptop is provided below Keep this information handy for reference throughout the class Login Password 1 2 Linux commands and information needed for training 1 The following is a brief tutorial of basic Linux commands needed for the SMOKE exercises NOTE In Linux the case is important lowercase and uppercase are not interpreted the same way so please follow the instructions carefully From the Main Menu bottom left corner open a terminal window by selecting Applications and then Accessories There is also a Terminal icon on the toolbar A Please read through the document titled SMOKE Training Linux Basics if you have not already done so It gives a quick overview of some important Linux concepts and also provides a list of most of the commands you will need for this class In the next steps we will try out some of the commands B Get a list of the contents of a directory T

(SMOKE) Modeling System

Contents

Download Pdf Manuals

Related Search

Related Contents