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. Copy bldit.bcon.pgf as bldit_bcon_pgf.default. Edit the compilation options in the bldit script (see MMAQ CMAQ Options). Copy the new bldit.bcon.pgf as ~/ Documents/bldit_bcon_MMAQ{period}.txt. c. Invoke the build script to create an executable: “./bldit.bcon.pgf”. The same compilation will be used for all ensembles. d. Copy the run.bcon file as run_bcon.default. Edit run.bcon script (see MMAQ CMAQ Options). Copy the new run.bcon as ~/Documents/ run_bcon_MMAQ{period}.txt. e. Execute ./run.bcon in emacs compile mode. For longer runs, enter “./run.bcon > ~/Documents/bcon_{period}_ens{#}.txt” Run BCON for each ensemble. Between each run, change the OUTDIR to the next ensemble subdirectory. f. Check bcon.log. You should see “Program BCON completed successfully.” Copy the log as ~/Documents/bcon_{period}_ens{#}.txt”. g. You should see something like the following output in $M3DATA/bcon/ens{#}: BCON_cb05_M_36_2001_profile h. Examine BCON output files using ncdump or ncview. i. This step must be repeated for a new time period. 6. JPROC calculates chemical-mechanism-specific clear-sky photolysis rates at fixed altitudes, hour angles, and latitude bands from tabulated absorption cross-section and quantum yield (CSQY) data. a. Make sure you have the following inputs: M3BLD, ET, PROFILES, CSGY, TOMS, O2ABS, and O3ABS. b. Copy bldit.jproc.pgf as bldit_jproc_pgf.default. Edit the compilation options in the bldit script (see MMAQ CMAQ Options). Copy the new bldit.jproc.pgf as ~/ Documents/bldit_jproc_MMAQ{period}.txt. c. Invoke the build script to create an executable: “./bldit.jproc.pgf”. The same compilation will be used for all ensembles. d. Copy the run.jproc file as run_jproc.default. Edit run.jproc script (see MMAQ CMAQ Options). Copy the new run.jproc as ~/Documents/ run_jproc_MMAQ{period}.txt. e. Execute ./run.jproc in emacs compile mode. For longer runs, enter “./run.jproc > ~/Documents/jproc_{period}.txt” Run JPROC once for all ensemble. f. Check jproc.log. (JPROC does not have any notice like “Program JPROC completed successfully”.) Copy the log as ~/Documents/jproc_{period}.txt”. g. You should see the following output in $M3DATA/jrpoc: JTABLE_{date}. h. Examine JPROC output files using TextEdit. i. This step must be repeated for a new time period. 7. PACP generates FORTRAN INCLUDE files for building a version of the CCTM that can calculate integrated process rates and/or integrated reactive rates for diagnosing CMAQ simulations. a. Create "PACP_INFILE" to configure PACP (see MMAQ PACP Input File). Save it as ~/Documents/pacp_infile_{period}.txt. b. Make sure you have the following inputs: M3BLD and PACP_INFILE. c. Go to $M3WORK/scripts/procan. Copy bldit.pacp.pgf as bldit_pacp_pgf.default. Edit the compilation options in the bldit script (see MMAQ CMAQ Options). Copy the new bldit.pacp.pgf as ~/Documents/bldit_pacp.txt. Invoke the build script to 2
create an executable: “./bldit.pacp.pgf”. This program only needs to be compiled once. d. Copy the run.pacp file as run_pacp.default. Edit run.pacp script (see MMAQ CMAQ Options). Copy the new run.pacp as ~/Documents/ run_pacp_MMAQ{period}.txt. e. Execute ./run.pacp in emacs compile mode. For longer runs, enter “./run.pacp > ~/Documents/pacp_{period}.txt” Run PACP once for all ensembles. (The {period} in the log file is necessary in case I choose to change PACP_INFILE). f. Check pacp.log. You should see “Program PACP completed successfully”. Copy the log as ~/Documents/pacp_{period}.txt”. g. You should see the following outputs in $M3DATA/pacp/: PA_CTL.EXT, PA_CMN.EXT, PA_DAT.EXT, and PA_REPORT. h. Examine PACP output files using TextEdit. i. This step is only done once for all periods and all ensembles. 8. PDM is the plume-in-grid preprocessor, which generates plume dynamics, such as dimensions and location, from special emissions input files generated by an emissions model for plume-in-grid simulations. a. Make sure you have the following inputs: GRIDCRO2D, GRIDDOT2D, METCRO2D, METDOT3D, METCRO3D, and GRIDDESC from MCIP, STACK_MEPSE from SMOKE, and PDM_PING_O if restarting the simulation. PACP should already be run if you want optional diagnostic output. b. Copy bldit.pdm.pgf as bldit_pdm_pgf.default. Edit the path directories. Copy the new bldit.pdm.pgf as ~/Documents/bldit_pdm.txt. c. Invoke the build script to create an executable: “./bldit.pdm.pgf”. This program only has to be compiled once. d. Copy the run.pdm file as run_pdm.default. Edit run.pdm script (see MMAQ CMAQ Options). Copy the new run.pdm as ~/Documents/ run_pdm_MMAQ{period}.txt. e. Execute ./run.pdm in emacs compile mode. For longer runs, enter “./run.pdm > ~/ Documents/pdm_{period}_ens{#}.txt” Run PDM for each ensemble. Between each run, change the OUTDIR to the next ensemble subdirectory. f. Check pdm.log. You should see “Program PDM completed successfully”. Copy the log as ~/Documents/pdm_{period}_ens{#}.txt”. g. You should see the following outputs in $M3DATA/pdm/ens{#}: PDM_PING_1 and NFOUT_3 (Optional diagnostic plume rise output). If optional diagnostic files are requested: NFOUT_2 (plume paramters) and NFOUT_1 (plume rise). h. Examine PDM output files using ncdump or ncview. i. This step must be repeated for a new time period and for each ensemble. 9. CCTM integrates the output from all of the preprocessing programs, including the emissions and meteorology models, to simulate continuous atmospheric chemical conditions. a. Make sure you have the following inputs: M3BLD, OCEAN_1 (from $M3HOME/ data/emis/2001/), EMIS_1 and MEPSE_1 (from SMOKE), PDM_PING_1 (from PDM), ICON_{filename} (from ICON), BCON_{filename} (from BCON), JTABLE_{date} (from JPROC), and GRID_CRO_2D, GRID_CRO_3D, GRID_DOT_2D, GRID_BDY_2D, MET_CRO_2D, MET_DOT_3D, 3
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