Run CMAQ

Run CMAQ
1. Run MCIP to process the meteorology input for CMAQ (see Run MCIP). You should
have the following files: GRIDDESC, GRID_CRO_2D, GRID_DOT_2D,
GRID_BDY_2D, MET_CRO_2D, MET_DOT_3D, MET_CRO_3D, AND
MET_BDY_3D. Run SMOKE to process emission files for CMAQ (see Run
SMOKE). You should have the following files: EMIS_1 and, if you are using plumein-grid,
MEPSE_1.
2. Go to /phd/data and create a project directory: MMAQ{period}. Within it, create the
following input subdirectories: icin, bcin, phot, procan, and emis and the following
output subdirectories: icon, bcon, jproc, pdm, pacp, and cctm. Within each output
subbdirectory (except jproc and pacp), create file folders for all 8 ensembles
(ens{#}). Change the $M3DATA environmental variables to /phd/data/MMAQ{period}.
3. Edit .tcshrc “Setting environmental variables for this model run” section so that
M3DATA set to “/phd/data/MMAQ{period}”. Make sure this line is uncommented and
comment out settings for other models.
4. ICON generates a gridded binary netCDF file of the chemical conditions in the
modeling domain for the first hour of a simulation.
a. Make sure you have the following inputs: M3BLD, IC_PROFILE OR
CTM_CONC_1, GRIDDESC, MET_CRO_3D, MECH_CONV_FILE if conversion
from a different chem mechanism is required and CTM_PING_1, PING_PDM_1,
and MET_CRO_3D_CRS if plume-in-grid is used.
b. Copy bldit.icon.pgf as bldit_icon_pgf.default. Edit the compilation options in the
bldit script (see MMAQ CMAQ Options). Copy the new bldit.icon.pgf as ~/
Documents/bldit_icon_MMAQ{period}.txt.
c. Invoke the build script to create an executable: “./bldit.icon.pgf”. The same
compilation will be used for all ensembles.
d. Copy the run.icon file as run_icon.default. Edit run.icon script (see MMAQ CMAQ
Options). Copy the new run.icon as ~/Documents/run_icon_MMAQ{period}.txt.
e. Execute ./run.icon in emacs compile mode. For longer runs, enter “./run.icon > ~/
Documents/icon_{period}_ens{#}.txt” Run ICON for each ensemble. Between
each run, change the OUTDIR to the next ensemble subdirectory.
f. Check icon.log. You should see “Program ICON completed successfully”. Copy
the log as ~/Documents/icon_{period}_ens{#}.txt”.
g. You should see something like the following output in $M3DATA/icon/ens{#}:
ICON_cb05_M_36_2001_profile
h. Examine ICON output files using ncdump or ncview.
i. This step must be repeated for a new time period.
5. BCON generates a gridded binary netCDF file of the chemical conditions along the
horizontal boundaries of the modeling domain.
a. Make sure you have the following inputs: M3BLD, BC_PROFILE or
CTM_CONC_1, GRIDDESC, MET_CRO_3D, MECH_CONV_FILE if conversion
from a different chem mechanism is required and CTM_PING_1, PING_PDM_1,
and MET_CRO_3D_CRS if plume-in-grid is used.
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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
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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,
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MET_CRO_3D, and MET_BDY_3D (from MCIP). PACP should already be run if
you want process analysis output.
b. Copy bldit.cctm.pgf as bldit_cctm_pgf.default. Edit the compilation options in the
bldit script (see MMAQ CMAQ Options). Copy the new bldit.cctm.pgf as ~/
Documents/bldit_cctm_MMAQ{period}.txt.
c. Invoke the build script to create an executable: “./bldit.cctm.pgf”. The same
compilation will be used for all ensembles.
d. Copy the run.cctm file as run_cctm.default. Edit run.cctm script (see MMAQ
CMAQ Options). Copy the new run.cctm as ~/Documents/
run_cctm_MMAQ{period}.txt.
e. Execute ./run.cctm in emacs compile mode. For longer runs, enter “./run.cctm >
~/Documents/cctm_{period}_ens{#}.txt” Run CCTM for each ensemble. Between
each run, change the OUTDIR to the next ensemble subdirectory.
f. Check cctm.log. You should see “Program CCTM completed successfully. Copy
the log as ~/Documents/cctm_{period}_ens{#}.txt”.
g. You should see the following outputs in $M3DATA/cctm/ens{#}:
(1) CCTM_CONC (hourly instantaneous concentration)
(2) CCTM_ACONC (hourly average concentration)
(3) CCTM_CGRID (restart file)
(4) CCTM_DRYDEP (hourly cumulative dry deposition)
(5) CCTM_WETDEP (hourly cumulative wet deposition)
(6) CCTM_AEROVIS (hourly instantaneous visibility)
(7) CCTM_DIAM (instantaneous hourly aerosol diameter)
(8) CCTM_PING (plume-in-grid unmerged plume data)
(9) CCTM_PING_DIAM (plume-in-grid hourly aerosol diameter)
(10) CCTM_PING_DDEP (plume-in-grid dry deposition)
(11) CCTM_IPR_[1-3] (process analysis integrated process rate)
(12) CCTM_IRR_[1-3] (process analysis integrated reaction rate)
h. Examine CCTM output files using ncdump or ncview.
i. This step must be repeated for a new time period and for each ensemble.
Thursday, June 19, 2008
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