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run_cctm.csh
#!/bin/csh -f
# ==================== CCTMv5.2.1 Run Script ========================
# Usage: run.cctm >&! cctm_v52b.log &
#
# To report problems or request help with this script/program:
# http://www.epa.gov/cmaq (EPA CMAQ Website)
# http://www.cmascenter.org (CMAS Website)
# ===================================================================
# ===================================================================
#> Runtime Environment Options
# ===================================================================
#> Choose compiler and set up CMAQ environment with correct
#> libraries using config.cmaq. Options: intel | gcc | pgi
if ( ! $?compiler ) then
setenv compiler gcc
endif
#> Source the config.cmaq file to set the build environment
cd ../..
source ./config_cmaq.csh $compiler
cd CCTM/scripts
#> Set General Parameters for Configuring the Simulation
set VRSN = v521 #> Code Version
set PROC = mpi #> serial or mpi
set MECH = cb6r3_ae6_aq #> Mechanism ID
set EMIS = 2013ef #> Emission Inventory Details
set APPL = CMAQ-ASU1K #> Application Name (e.g. Gridname)
#> Define RUNID as any combination of parameters above or others. By default,
#> this information will be collected into this one string, $RUNID, for easy
#> referencing in output binaries and log files as well as in other scripts.
setenv RUNID ${VRSN}_${compilerString}_${APPL}
#> Set the build directory (this is where the CMAQ executable
#> is located by default).
set BLD = ${CMAQ_HOME}/CCTM/scripts/BLD_CCTM_${VRSN}_${compilerString}
set EXEC = CCTM_${VRSN}.exe
cat $BLD/CCTM_${VRSN}.cfg; echo " "; set echo
#> Set Working, Input, and Output Directories
setenv WORKDIR ${CMAQ_HOME}/CCTM/scripts #> Working Directory. Where the runscript is.
setenv OUTDIR ${CMAQ_DATA}/output_CCTM_${RUNID} #> Output Directory
setenv INPDIR ${CMAQ_DATA}/CMAQ-ASU1K/cctm_input #> Input Directory
setenv LOGDIR ${OUTDIR}/LOGS #> Log Directory Location
setenv NMLpath ${BLD} #> Location of Namelists. Common places are:
#> ${WORKDIR} | ${CCTM_SRC}/MECHS/${MECH} | ${BLD}
# =====================================================================
#> CCTM Configuration Options
# =====================================================================
#> Set Start and End Days for looping
setenv NEW_START TRUE #> Set to FALSE for model restart
set START_DATE = "2015-06-01" #> beginning date (July 1, 2011)
set END_DATE = "2015-06-20" #> ending date (July 14, 2011)
#> Set Timestepping Parameters
set STTIME = 000000 #> beginning GMT time (HHMMSS)
set NSTEPS = 240000 #> time duration (HHMMSS) for this run
set TSTEP = 010000 #> output time step interval (HHMMSS)
#> Horizontal domain decomposition
if ( $PROC == serial ) then
setenv NPCOL_NPROW "1 1"; set NPROCS = 1 # single processor setting
else
@ NPCOL = 3; @ NPROW = 2
@ NPROCS = $NPCOL * $NPROW
setenv NPCOL_NPROW "$NPCOL $NPROW";
endif
#> Vertical extent
set NZ = 35
#setenv LOGFILE $CMAQ_HOME/$RUNID.log #> log file name; uncomment to write standard output to a log, otherwise write to screen
setenv GRID_NAME CMAQ-ASU1K #> check GRIDDESC file for GRID_NAME options
setenv GRIDDESC $INPDIR/GRIDDESC #> grid description file
#> Output Species and Layer Options
#> CONC file species; comment or set to "ALL" to write all species to CONC
#setenv CONC_SPCS "O3 NO ANO3I ANO3J NO2 FORM ISOP ANH4J ASO4I ASO4J"
#setenv CONC_BLEV_ELEV " 1 4" #> CONC file layer range; comment to write all layers to CONC
#> ACONC file species; comment or set to "ALL" to write all species to ACONC
#setenv AVG_CONC_SPCS "O3 NO CO NO2 ASO4I ASO4J NH3"
setenv AVG_CONC_SPCS "ALL"
setenv ACONC_BLEV_ELEV " 1 1" #> ACONC file layer range; comment to write all layers to ACONC
setenv AVG_FILE_ENDTIME N #> override default beginning ACON timestamp [ default: N ]
setenv EXECUTION_ID $EXEC #> define the model execution id
#> Sychronization Time Step and Tolerance Options
setenv CTM_MAXSYNC 300 #> max sync time step (sec) [ default: 720 ]
setenv CTM_MINSYNC 60 #> min sync time step (sec) [ default: 60 ]
setenv SIGMA_SYNC_TOP 0.7 #> top sigma level thru which sync step determined [ default: 0.7 ]
#setenv ADV_HDIV_LIM 0.95 #> maximum horiz. div. limit for adv step adjust [ default: 0.9 ]
setenv CTM_ADV_CFL 0.95 #> max CFL [ default: 0.75]
#setenv RB_ATOL 1.0E-09 #> global ROS3 solver abs tol [ default: 1.0E-07 ]
#> Science Options
setenv CTM_WB_DUST N #> use inline windblown dust emissions [ default: Y ]
setenv CTM_ERODE_AGLAND Y #> use agricultural activity for windblown dust
#> [ default: N ]; ignore if CTM_WB_DUST = N
setenv CTM_WBDUST_BELD BELD3 #> landuse database for identifying dust source regions
#> [ default: BELD3 ]; ignore if CTM_WB_DUST = N
setenv CTM_LTNG_NO N #> turn on lightning NOx [ default: N ]
setenv CTM_WVEL Y #> save derived vertical velocity component to conc
#> file [ default: N ]
setenv KZMIN Y #> use Min Kz option in edyintb [ default: Y ],
#> otherwise revert to Kz0UT
setenv CTM_ILDEPV Y #> calculate in-line deposition velocities [ default: Y ]
setenv CTM_MOSAIC N #> landuse specific deposition velocities [ default: N ]
setenv CTM_FST N #> mosaic method to get land-use specific stomatal flux
#> [ default: N ]
setenv CTM_ABFLUX N #> ammonia bi-directional flux for in-line deposition
#> velocities [ default: N ]; ignore if CTM_ILDEPV = N
setenv CTM_HGBIDI N #> mercury bi-directional flux for in-line deposition
#> velocities [ default: N ]; ignore if CTM_ILDEPV = N
setenv CTM_SFC_HONO Y #> surface HONO interaction [ default: Y ]; ignore if CTM_ILDEPV = N
setenv CTM_GRAV_SETL Y #> vdiff aerosol gravitational sedimentation [ default: Y ]
setenv CTM_BIOGEMIS N #> calculate in-line biogenic emissions [ default: N ]
setenv CTM_PT3DEMIS N #> calculate in-line plume rise for elevated point emissions
#> [ default: N ]
setenv CTM_ZERO_PCSOA N #> turn off the emissions of the VOC precursor to pcSOA.
#> The CMAQ dev team recommends leaving pcSOA mass in the
#> model for production runs. [ default: N ]
#> Process Analysis Options
setenv CTM_PROCAN N #> use process analysis [ default: N]
#> process analysis global column, row and layer ranges
#> user must check GRIDDESC for validity!
setenv PA_BCOL_ECOL "10 320"
setenv PA_BROW_EROW "10 195"
setenv PA_BLEV_ELEV "1 4"
#> I/O Controls
setenv IOAPI_LOG_WRITE F #> turn on excess WRITE3 logging [ options: T | F ]
setenv FL_ERR_STOP N #> stop on inconsistent input files
setenv PROMPTFLAG F #> turn on I/O-API PROMPT*FILE interactive mode [ options: T | F ]
setenv IOAPI_OFFSET_64 NO #> support large timestep records (>2GB/timestep record) [ options: YES | NO ]
setenv CTM_EMISCHK N #> Abort CMAQ if missing surrogates from emissions Input files
#> Aerosol Diagnostic Controls
setenv CTM_AVISDIAG N #> Aerovis diagnostic file [ default: N ]
setenv CTM_PMDIAG Y #> Instantaneous Aerosol Diagnostic File [ default: Y ]
setenv CTM_APMDIAG Y #> Hourly-Average Aerosol Diagnostic File [ default: Y ]
setenv APMDIAG_BLEV_ELEV "1 3" #> layer range for average pmdiag
setenv APMDIAG_BLEV_ELEV "" #> layer range for average pmdiag = NLAYS
#> Diagnostic Output Flags
setenv CTM_CKSUM Y #> cksum report [ default: Y ]
setenv CLD_DIAG N #> cloud diagnostic file [ default: N ]
setenv CTM_AERDIAG Y #> aerosol diagnostic file [ default: N ]
setenv CTM_PHOTDIAG Y #> photolysis diagnostic file [ default: N ]
setenv CTM_SSEMDIAG N #> sea-salt emissions diagnostic file [ default: N ]
setenv CTM_DUSTEM_DIAG Y #> windblown dust emissions diagnostic file [ default: N ]; ignore if CTM_WB_DUST = N
setenv CTM_DEPV_FILE Y #> deposition velocities diagnostic file [ default: N ]
setenv VDIFF_DIAG_FILE Y #> vdiff & possibly aero grav. sedimentation diagnostic file [ default: N ]
setenv LTNGDIAG N #> lightning diagnostic file [ default: N ]
setenv CTM_AOD Y #> AOD diagnostic file [ default: N ]
setenv B3GTS_DIAG Y #> beis mass emissions diagnostic file [ default: N ]
setenv PT3DDIAG N #> optional 3d point source emissions diagnostic file [ default: N]; ignore if CTM_PT3DEMIS = N
setenv PT3DFRAC N #> optional layer fractions diagnostic (play) file(s) [ default: N]; ignore if CTM_PT3DEMIS = N
setenv REP_LAYER_MIN -1 #> Minimum layer for reporting plume rise info [ default: -1 ]
set DISP = delete #> [ delete | keep ] existing output files
# =====================================================================
#> Input Directories and Filenames
# =====================================================================
set ICpath = $INPDIR/icbc #> initial conditions input directory
set BCpath = $INPDIR/icbc #> boundary conditions input directory
set EMISpath = $INPDIR/emis #> surface emissions input directory
set IN_PTpath = $INPDIR/emis #> elevated emissions input directory (in-line point only)
set IN_LTpath = $INPDIR/lightning #> lightning NOx input directory
set METpath = $INPDIR #> meteorology input directory
#set JVALpath = $INPDIR/jproc #> offline photolysis rate table directory
set OMIpath = $BLD #> ozone columne data for the photolysis model
set LUpath = $INPDIR/land #> BELD landuse data for windblown dust model
set SZpath = $INPDIR/land #> surf zone file for in-line seasalt emissions
set ICBC_CASE = 2013ef_v6_13g_s07 #> Version label for the ICBCs
set EMIS_CASE = 2013ef_v6_13g_s07_hg #> Version Label for the Emissions
# =====================================================================
#> Begin Loop Through Simulation Days
# =====================================================================
set TODAYG = ${START_DATE}
set TODAYJ = `date -ud "${START_DATE}" +%Y%j` #> Convert YYYY-MM-DD to YYYYJJJ
set STOP_DAY = `date -ud "${END_DATE}" +%Y%j` #> Convert YYYY-MM-DD to YYYYJJJ
while ($TODAYJ <= $STOP_DAY ) #>Compare dates in terms of YYYYJJJ
#> Retrieve Calendar day Information
set YYYYMMDD = `date -ud "${TODAYG}" +%Y%m%d` #> Convert YYYY-MM-DD to YYYYMMDD
set YYMMDD = `date -ud "${TODAYG}" +%y%m%d` #> Convert YYYY-MM-DD to YYMMDD
set YYYYJJJ = $TODAYJ
#> Calculate Yesterday's Date
set YESTERDAY = `date -ud "${TODAYG}-1days" +%Y%m%d` #> Convert YYYY-MM-DD to YYYYJJJ
# =====================================================================
#> Input Files (Some are Day-Dependent)
# =====================================================================
#> Initial conditions
if ($NEW_START == true || $NEW_START == TRUE ) then
# setenv ICFILE ICON_20110630_bench.nc
setenv ICFILE ICON_v52_CMAQ-ASU1K_profile.nc
setenv INITIAL_RUN Y #related to restart soil information file
rm -rf $LOGDIR/CTM_LOG*${RUNID}* # Remove all Log Files Since this is a new start
mkdir -p $OUTDIR
else
set ICpath = $OUTDIR
setenv ICFILE CCTM_CGRID_${RUNID}_${YESTERDAY}.nc
setenv INITIAL_RUN N
endif
#> Boundary conditions
# set BCFILE = BCON_${YYYYMMDD}_bench.nc
set BCFILE = BCON_v52_CMAQ-ASU1K_profile.nc
#> Off-line photolysis rates
#set JVALfile = JTABLE_${YYYYJJJ}
#> Ozone column data
set OMIfile = OMI_1979_to_2015.dat
#> Optics file
set OPTfile = PHOT_OPTICS.dat
#> MCIP meteorology files
# setenv GRID_BDY_2D $METpath/GRIDBDY2D_${YYMMDD}
# setenv GRID_CRO_2D $METpath/GRIDCRO2D_${YYMMDD}
# setenv GRID_CRO_3D $METpath/GRIDCRO3D_${YYMMDD}
# setenv GRID_DOT_2D $METpath/GRIDDOT2D_${YYMMDD}
# setenv MET_CRO_2D $METpath/METCRO2D_${YYMMDD}
# setenv MET_CRO_3D $METpath/METCRO3D_${YYMMDD}
# setenv MET_DOT_3D $METpath/METDOT3D_${YYMMDD}
# setenv MET_BDY_3D $METpath/METBDY3D_${YYMMDD}
setenv GRID_BDY_2D $METpath/GRIDBDY2D_ASU1K
setenv GRID_CRO_2D $METpath/GRIDCRO2D_ASU1K
setenv GRID_CRO_3D $METpath/GRIDCRO3D_ASU1K
setenv GRID_DOT_2D $METpath/GRIDDOT2D_ASU1K
setenv MET_CRO_2D $METpath/METCRO2D_ASU1K
setenv MET_CRO_3D $METpath/METCRO3D_ASU1K
setenv MET_DOT_3D $METpath/METDOT3D_ASU1K
setenv MET_BDY_3D $METpath/METBDY3D_ASU1K
setenv LAYER_FILE $MET_CRO_3D # Deprecated: MET_CRO_3D is now read directly in CCTM
#> Emissions files
if ( $CTM_PT3DEMIS == 'N' ) then
#> Offline 3d emissions file name
#set EMISfile = emis_mole_all_${YYYYMMDD}_cb6_bench.nc
set EMISfile = HERMESv3_par_${YYYYMMDD}.nc
else
#> In-line emissions configuration
set STKCASEG = 12US1_2011ek_cb6cmaq_v6_11g # Stack Group Version Label
set STKCASEE = 12US1_cmaq_cb6e51_2011ek_cb6cmaq_v6_11g # Stack Emission Version Label
set EMISfile = HERMESv3_par_${YYYYMMDD}.nc #> Surface emissions
setenv NPTGRPS 5 #> Number of elevated source groups
# setenv STK_GRPS_01 $IN_PTpath/stack_groups/stack_groups_ptnonipm_${STKCASEG}.nc
setenv STK_GRPS_01 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/stack_groups/stack_groups_ptnonipm_12US1_2011ek_cb6cmaq_v6_11g.nc
# setenv STK_GRPS_02 $IN_PTpath/stack_groups/stack_groups_ptegu_${STKCASEG}.nc
setenv STK_GRPS_02 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/stack_groups/stack_groups_ptegu_12US1_2011ek_cb6cmaq_v6_11g.nc
# setenv STK_GRPS_03 $IN_PTpath/stack_groups/stack_groups_othpt_${STKCASEG}.nc
setenv STK_GRPS_03 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/stack_groups/stack_groups_othpt_12US1_2011ek_cb6cmaq_v6_11g.nc
# setenv STK_GRPS_04 $IN_PTpath/stack_groups/stack_groups_ptfire_${YYYYMMDD}_${STKCASEG}.nc
setenv STK_GRPS_04 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/stack_groups/stack_groups_ptfire_${YYYYMMDD}_12US1_2011ek_cb6cmaq_v6_11g.nc
# setenv STK_GRPS_05 $IN_PTpath/stack_groups/stack_groups_pt_oilgas_${STKCASEG}.nc
setenv STK_GRPS_05 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/stack_groups/stack_groups_pt_oilgas_12US1_2011ek_cb6cmaq_v6_11g.nc
setenv LAYP_STTIME $STTIME
setenv LAYP_NSTEPS $NSTEPS
# setenv STK_EMIS_01 $IN_PTpath/ptnonipm/inln_mole_ptnonipm_${YYYYMMDD}_${STKCASEE}.nc
setenv STK_EMIS_01 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/ptnonipm/inln_mole_ptnonipm_${YYYYMMDD}_12US1_2011ek_cb6cmaq_v6_11g.nc
# setenv STK_EMIS_02 $IN_PTpath/ptegu/inln_mole_ptegu_${YYYYMMDD}_${STKCASEE}.nc
setenv STK_EMIS_02 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/ptegu/inln_mole_ptegu_${YYYYMMDD}_12US1_2011ek_cb6cmaq_v6_11g.nc
# setenv STK_EMIS_03 $IN_PTpath/othpt/inln_mole_othpt_${YYYYMMDD}_${STKCASEE}.nc
setenv STK_EMIS_03 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/othpt/inln_mole_othpt_${YYYYMMDD}_12US1_2011ek_cb6cmaq_v6_11g.nc
# setenv STK_EMIS_04 $IN_PTpath/ptfire/inln_mole_ptfire_${YYYYMMDD}_${STKCASEE}.nc
setenv STK_EMIS_04 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/ptfire/inln_mole_ptfire_${YYYYMMDD}_12US1_2011ek_cb6cmaq_v6_11g.nc
# setenv STK_EMIS_05 $IN_PTpath/pt_oilgas/inln_mole_pt_oilgas_${YYYYMMDD}_${STKCASEE}.nc
setenv STK_EMIS_05 /root/CMAQ-5.2.1/data/SE52BENCH/emis/inln_point/pt_oilgas/inln_mole_pt_oilgas_${YYYYMMDD}_12US1_2011ek_cb6cmaq_v6_11g.nc
setenv LAYP_STDATE $YYYYJJJ
endif
#> Lightning NOx configuration
if ( $CTM_LTNG_NO == 'Y' ) then
setenv LTNGNO "InLine" #> set LTNGNO to "Inline" to activate in-line calculation
#> In-line lightning NOx options
setenv USE_NLDN N #> use hourly NLDN strike file [ default: Y ]
if ( $USE_NLDN == Y ) then
setenv NLDN_STRIKES $INPDIR/lightning/NLDN.12US1.${YYYYMMDD}_bench.nc
else
setenv LOG_START 2.0 #> RC value to transit linear to log linear
endif
#setenv LTNGPARMS_FILE $INPDIR/lightning/LTNG_AllParms_12US1_bench.nc #> lightning parameter file
endif
#> In-line biogenic emissions configuration
if ( $CTM_BIOGEMIS == 'Y' ) then
set IN_BEISpath = ${INPDIR}/land
set GSPROpath = ${IN_BEISpath}
setenv GSPRO $GSPROpath/gspro_biogenics_1mar2017.txt
setenv B3GRD $IN_BEISpath/b3grd_bench.nc
setenv BIOG_SPRO B10C6 #> speciation profile to use for biogenics
setenv BIOSW_YN Y #> use frost date switch [ default: Y ]
setenv BIOSEASON $IN_BEISpath/bioseason.cmaq.2011_12US1_wetland100.ghrsst_bench.ncf #> ignore season switch file if BIOSW_YN = N
setenv SUMMER_YN Y #> Use summer normalized emissions? [ default: Y ]
setenv PX_VERSION Y #> MCIP is PX version? [ default: N ]
setenv SOILINP $OUTDIR/CCTM_SOILOUT_${RUNID}_${YESTERDAY}.nc
#> Biogenic NO soil input file; ignore if INITIAL_RUN = Y
endif
#> Windblown dust emissions configuration
if ( $CTM_WB_DUST == 'Y' ) then
# Input variables for BELD3 Landuse option
setenv DUST_LU_1 $LUpath/beld3_12US1_459X299_output_a_bench.nc
setenv DUST_LU_2 $LUpath/beld4_12US1_459X299_output_tot_bench.nc
setenv MODIS_FPAR $LUpath/modis_bench.nc
if ( $CTM_ERODE_AGLAND == 'Y' ) then
setenv CROPMAP01 ${INPDIR}/land/BeginPlanting_12km_bench.nc
setenv CROPMAP04 ${INPDIR}/land/EndPlanting_12km_bench.nc
setenv CROPMAP08 ${INPDIR}/land/EndHarvesting_12km_bench.nc
endif
endif
#> In-line sea salt emisisions configuration
setenv OCEAN_1 $SZpath/ocean_file.dummy.CMAQ-ASU1K.nc #> horizontal grid-dependent surf zone file
#> Bidiretional ammonia configuration
if ( $CTM_ABFLUX == 'Y' ) then
setenv E2C_Soilfile ${INPDIR}/land/2011_US1_soil_bench.nc
setenv E2C_Fertfile ${INPDIR}/land/2011_US1_time${YYYYMMDD}_bench.nc
setenv B4LU_file ${INPDIR}/land/beld4_12kmCONUS_2006nlcd_bench.nc
setenv E2C_SOIL ${E2C_Soilfile}
setenv E2C_FERT ${E2C_Fertfile}
setenv BELD4_LU ${B4LU_file}
endif
# =====================================================================
#> Output Files
# =====================================================================
#> set output file name extensions
setenv CTM_APPL ${RUNID}_${YYYYMMDD}
#> set output file names
setenv S_CGRID "$OUTDIR/CCTM_CGRID_${CTM_APPL}.nc" #> 3D Inst. Concenctrations
setenv CTM_CONC_1 "$OUTDIR/CCTM_CONC_${CTM_APPL}.nc -v" #> On-Hour Concentrations
setenv A_CONC_1 "$OUTDIR/CCTM_ACONC_${CTM_APPL}.nc -v" #> Hourly Avg. Concentrations
setenv MEDIA_CONC "$OUTDIR/CCTM_MEDIA_CONC_${CTM_APPL}.nc -v" #> NH3 Conc. in Media
setenv CTM_DRY_DEP_1 "$OUTDIR/CCTM_DRYDEP_${CTM_APPL}.nc -v" #> Hourly Dry Deposition
setenv CTM_DEPV_DIAG "$OUTDIR/CCTM_DEPV_${CTM_APPL}.nc -v" #> Dry Deposition Velocities
setenv CTM_PT3D_DIAG "$OUTDIR/CCTM_PT3D_${CTM_APPL}.nc -v" #>
setenv B3GTS_S "$OUTDIR/CCTM_B3GTS_S_${CTM_APPL}.nc -v" #> Biogenic Emissions
setenv SOILOUT "$OUTDIR/CCTM_SOILOUT_${CTM_APPL}.nc" #> Soil Emissions
setenv CTM_WET_DEP_1 "$OUTDIR/CCTM_WETDEP1_${CTM_APPL}.nc -v" #> Wet Dep From All Clouds
setenv CTM_WET_DEP_2 "$OUTDIR/CCTM_WETDEP2_${CTM_APPL}.nc -v" #> Wet Dep From SubGrid Clouds
setenv CTM_VIS_1 "$OUTDIR/CCTM_PMVIS_${CTM_APPL}.nc -v" #> On-Hour Visibility
setenv CTM_AVIS_1 "$OUTDIR/CCTM_APMVIS_${CTM_APPL}.nc -v" #> Hourly-Averaged Visibility
setenv CTM_PMDIAG_1 "$OUTDIR/CCTM_PMDIAG_${CTM_APPL}.nc -v" #> On-Hour Particle Diagnostics
setenv CTM_APMDIAG_1 "$OUTDIR/CCTM_APMDIAG_${CTM_APPL}.nc -v" #> Hourly Avg. Particle Diagnostic
setenv CTM_RJ_1 "$OUTDIR/CCTM_PHOTDIAG1_${CTM_APPL}.nc -v" #> Photolysis Rxn Diagnostics
setenv CTM_RJ_2 "$OUTDIR/CCTM_PHOTDIAG2_${CTM_APPL}.nc -v" #> Photolysis Rates Output
setenv CTM_SSEMIS_1 "$OUTDIR/CCTM_SSEMIS_${CTM_APPL}.nc -v" #> Sea Spray Emissions
setenv CTM_DUST_EMIS_1 "$OUTDIR/CCTM_DUSTEMIS_${CTM_APPL}.nc -v" #> Dust Emissions
setenv CTM_IPR_1 "$OUTDIR/CCTM_PA_1_${CTM_APPL}.nc -v" #> Process Analysis
setenv CTM_IPR_2 "$OUTDIR/CCTM_PA_2_${CTM_APPL}.nc -v" #> Process Analysis
setenv CTM_IPR_3 "$OUTDIR/CCTM_PA_3_${CTM_APPL}.nc -v" #> Process Analysis
setenv CTM_IRR_1 "$OUTDIR/CCTM_IRR_1_${CTM_APPL}.nc -v" #> Chem Process Analysis
setenv CTM_IRR_2 "$OUTDIR/CCTM_IRR_2_${CTM_APPL}.nc -v" #> Chem Process Analysis
setenv CTM_IRR_3 "$OUTDIR/CCTM_IRR_3_${CTM_APPL}.nc -v" #> Chem Process Analysis
setenv CTM_DRY_DEP_MOS "$OUTDIR/CCTM_DDMOS_${CTM_APPL}.nc -v" #> Dry Dep
setenv CTM_DRY_DEP_FST "$OUTDIR/CCTM_DDFST_${CTM_APPL}.nc -v" #> Dry Dep
setenv CTM_DEPV_MOS "$OUTDIR/CCTM_DEPVFST_${CTM_APPL}.nc -v" #> Dry Dep Velocity
setenv CTM_DEPV_FST "$OUTDIR/CCTM_DEPVMOS_${CTM_APPL}.nc -v" #> Dry Dep Velocity
setenv CTM_VDIFF_DIAG "$OUTDIR/CCTM_VDIFF_DIAG_${CTM_APPL}.nc -v" #> Vertical Dispersion Diagnostic
setenv CTM_VSED_DIAG "$OUTDIR/CCTM_VSED_DIAG_${CTM_APPL}.nc -v" #> Particle Grav. Settling Velocity
setenv CTM_AOD_1 "$OUTDIR/CCTM_AOD_DIAG_${CTM_APPL}.nc -v" #> Aerosol Optical Depth Diagnostic
setenv CTM_LTNGDIAG_1 "$OUTDIR/CCTM_LTNGHRLY_${CTM_APPL}.nc -v" #> Hourly Avg Lightning NO
setenv CTM_LTNGDIAG_2 "$OUTDIR/CCTM_LTNGCOL_${CTM_APPL}.nc -v" #> Column Total Lightning NO
#> set floor file (neg concs)
setenv FLOOR_FILE ${OUTDIR}/FLOOR_${CTM_APPL}.txt
#> create output directory
if ( ! -d "$OUTDIR" ) mkdir -p $OUTDIR
#> look for existing log files and output files
set log_test = `ls CTM_LOG_???.${CTM_APPL}`
set OUT_FILES = (${FLOOR_FILE} ${S_CGRID} ${CTM_CONC_1} ${A_CONC_1} ${MEDIA_CONC} \
${CTM_DRY_DEP_1} $CTM_DEPV_DIAG $CTM_PT3D_DIAG $B3GTS_S $SOILOUT $CTM_WET_DEP_1\
$CTM_WET_DEP_2 $CTM_VIS_1 $CTM_AVIS_1 $CTM_PMDIAG_1 $CTM_APMDIAG_1 \
$CTM_RJ_1 $CTM_RJ_2 $CTM_SSEMIS_1 $CTM_DUST_EMIS_1 $CTM_IPR_1 $CTM_IPR_2 \
$CTM_IPR_3 $CTM_IRR_1 $CTM_IRR_2 $CTM_IRR_3 $CTM_DRY_DEP_MOS \
$CTM_DRY_DEP_FST $CTM_DEPV_MOS $CTM_DEPV_FST $CTM_VDIFF_DIAG $CTM_VSED_DIAG \
$CTM_AOD_1 $CTM_LTNGDIAG_1 $CTM_LTNGDIAG_2)
set OUT_FILES = `echo $OUT_FILES | sed "s; -v;;g" `
echo $OUT_FILES
set out_test = `ls $OUT_FILES`
#> delete previous output if requested
if ( $DISP == 'delete' ) then
#> remove previous log files
echo " ancillary log files being deleted"
foreach file ( $log_test )
echo " deleting $file"
/bin/rm -f $file
end
#> remove previous output files
echo " output files being deleted"
foreach file ( $out_test )
echo " deleting $file"
/bin/rm -f $file
end
else
#> error if previous log files exist
if ( "$log_test" != "" ) then
echo "*** Logs exist - run ABORTED ***"
echo "*** To overide, set $DISP == delete in run_cctm.csh ***"
echo "*** and these files will be automatically deleted. ***"
exit 1
endif
#> error if previous output files exist
if ( "$out_test" != "" ) then
echo "*** Output Files Exist - run will be ABORTED ***"
foreach file ( $out_test )
echo " cannot delete $file"
end
echo "*** To overide, set $DISP == delete in run_cctm.csh ***"
echo "*** and these files will be automatically deleted. ***"
exit 1
endif
endif
#> for the run control ...
setenv CTM_STDATE $YYYYJJJ
setenv CTM_STTIME $STTIME
setenv CTM_RUNLEN $NSTEPS
setenv CTM_TSTEP $TSTEP
setenv EMIS_1 $EMISpath/$EMISfile
setenv INIT_GASC_1 $ICpath/$ICFILE
setenv INIT_AERO_1 $INIT_GASC_1
setenv INIT_NONR_1 $INIT_GASC_1
setenv INIT_TRAC_1 $INIT_GASC_1
setenv BNDY_GASC_1 $BCpath/$BCFILE
setenv BNDY_AERO_1 $BNDY_GASC_1
setenv BNDY_NONR_1 $BNDY_GASC_1
setenv BNDY_TRAC_1 $BNDY_GASC_1
setenv OMI $OMIpath/$OMIfile
setenv OPTICS_DATA $OMIpath/$OPTfile
#setenv XJ_DATA $JVALpath/$JVALfile
set TR_DVpath = $METpath
set TR_DVfile = $MET_CRO_2D
#> species defn & photolysis
setenv gc_matrix_nml ${NMLpath}/GC_$MECH.nml
setenv ae_matrix_nml ${NMLpath}/AE_$MECH.nml
setenv nr_matrix_nml ${NMLpath}/NR_$MECH.nml
setenv tr_matrix_nml ${NMLpath}/Species_Table_TR_0.nml
#> check for photolysis input data
setenv CSQY_DATA ${NMLpath}/CSQY_DATA_$MECH
if (! (-e $CSQY_DATA ) ) then
echo " $CSQY_DATA not found "
exit 1
endif
if (! (-e $OPTICS_DATA ) ) then
echo " $OPTICS_DATA not found "
exit 1
endif
# ===================================================================
#> Execution Portion
# ===================================================================
#> Print attributes of the executable
ls -l $BLD/$EXEC; size $BLD/$EXEC
#unlimit
#limit
date
#> Executable call for single PE, uncomment to invoke
# /usr/bin/time $BLD/$EXEC
#> Executable call for multi PE, configure for your system
# set MPI = /usr/local/intel/impi/3.2.2.006/bin64
# set MPIRUN = $MPI/mpirun
#time mpirun -r ssh -np $NPROCS $BLD/$EXEC
time mpirun -np $NPROCS $BLD/$EXEC
date
# ===================================================================
#> Finalize Run for This Day and Loop to Next Day
# ===================================================================
#> Save Log Files and Move on to Next Simulation Day
if (! -e $LOGDIR ) then
mkdir $LOGDIR
endif
mv CTM_LOG_???.${CTM_APPL} $LOGDIR
#> The next simulation day will, by definition, be a restart
setenv NEW_START false
#> Increment both Gregorian and Julian Days
set TODAYG = `date -ud "${TODAYG}+1days" +%Y-%m-%d` #> Add a day for tomorrow
set TODAYJ = `date -ud "${TODAYG}" +%Y%j` #> Convert YYYY-MM-DD to YYYYJJJ
end #Loop to the next Simulation Day
exit
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