Tracer config file and other run configuration files

CHIMERE/TRACERS.data

+# Name Type    Lon.   Lat.   First date  Last date    Mass(ton)   Zmin(m)  Zmax(m)   MolMass
+GTRC1   1     -72.2   -40.5  2011060419    2011060500 	5.21e+4   8000.    11000.     64.
+GTRC1   1     -72.2   -40.5  2011060500    2011060507 	8.33e+4   8000.    11000.     64.
+GTRC1   1     -72.2   -40.5  2011060508    2011060519 	5.50e+4   8000.    11000.     64.
+GTRC1   1     -72.2   -40.5  2011060520    2011060600 	1.00e+4   8000.    11000.     64.
+GTRC1   1     -72.2   -40.5  2011060600    2011060607 	2.00e+4   8000.    11000.     64.
+GTRC1   1     -72.2   -40.5  2011060608    2011060619 	3.00e+4   8000.    11000.     64.
+GTRC1   1     -72.2   -40.5  2011060620    2011060700 	1.00e+4   8000.    11000.     64.

CHIMERE/chimere.par.puyehue

+#------------------------------------------------------------------------------------
+#    CHIMERE parameter file
+#       Separate parameters for multiple runs with commas, e.g., Nested... : no, yes
+#       Only use absolute paths for files and directories
+#------------------------------------------------------------------------------------
+   runs :  1
+#------------------------------------------------------------------------------------
+# Analysis or forecast
+ [$forecast]         Forecast(1) or analysis(0) run          : 0
+
+# CHIMERE simulation domain, time-step
+ [$nested]           Nested run? (yes/no)                    : no
+ [$dom]              CHIMERE domain                          : PUY60
+ [$ntotprocs]        Number of available processors          : 45
+ [$ratioproc]        Ratio procs #chimere/#wrf (real)        : 1
+ [$nlevels]          Number of vertical layers               : 40
+ [$top_chimere_pressure] Top layer pressure                  : 120
+ [$first_layer_pressure] First layer pressure                : 998
+
+# Simulation output parameters
+ [$online]           on-line [1] or off-line [0] modeling    : 0
+ [$cpl_case]         coupling case                           : 1
+ [$lab]              Simulation label                        : PUY60-tier1
+ [$clab]             Coarse domain label                     : none
+ [$sim]              Current run label                       : ${idatestart}_${nhours}_${lab}
+ [$simuldir]         Simulation output directory             : /ccc/scratch/cont003/shr10274/maillers/CHIMOUT-${lab}
+ [$outloc]           Write outfiles locally during run (0/1) : 0
+
+# Output parameters
+ [$accur]            Output species detailed (low/full)      : full
+ [$nsconcs]          Conc. save freq. (hr), file end...      : 24
+ [$nsdepos]          Deposition save freq. (hr), file dep... : 6
+ [$accurmet]         Meteo detailed (low/medium/full)        : medium
+
+#------------------------------------------------------------------------------------
+# CHIMERE mandatory databases
+ [$bigfilesdir]      Big files (AEROMIN.bin, etc)            : /ccc/work/cont003/shr10274/shr10274/BIGFILES
+ [$luname]            Land Cover GLCF/GLOBCOVER/USGS         : USGS
+ [$landcover_dir]    Land Cover directory                    : ${bigfilesdir}/LANDCOVER
+ [$megan_data]       MEGAN data root                         : ${bigfilesdir}/MEGAN
+ [$imegan]           MEGAN database choice (1=2.5', 2=30")   : 2
+ [$emissdir]         Anthropogenic emission Dir (stage 1)    : /data/PLT8/pub/menut/EMISURF_OUT/DCWAc2_htap/EMI_2010
+ [$fire_emissdir]    Fire emission Dir (stage 1)             : /data/PLT8/pub/menut/outemiFIRES_DCWAc2/2016
+
+#------------------------------------------------------------------------------------
+# Emissions
+ [$emistyp]          Anthropogenic emission format type      : emisurf
+ [$asurfemis]        anthro surface emissions? (1/0)         : 0
+ [$apointemis]       anthro point emissions?   (1/0)         : 0
+ [$iuse_firemis]     Fire emissions?   (1/0)                 : 0
+ [$ifirevprof]       Fire vertical profile shape (1/2/3)     : 1
+ [$iusebemis]        Biogenic emissions? (1/0)               : 0
+ [$iusedms]          DMS marine emissions? ([1-4]/0)         : 0
+ [$iusedust]         Mineral dust emissions? (0-3)           : 0
+ [$icuth]            u* threshold scheme                     : 1
+ [$ifluxv]           vertical dust flux scheme               : 2
+ [$ifecan]           Use of soil moisture [1] or not [0]     : 1
+ [$iusesalt]         Sea salts emissions? (0/1/2/3/4)        : 0
+ [$ilinox]           NOx lightning                           : 0
+
+#------------------------------------------------------------------------------------
+# Sensitivity factors 
+ [$factaemis]        Factor on anthro surface emissions      : 1.0
+ [$factfemis]        Factor on fire emissions (real)         : 1.0
+ [$factbemis]	     Factor on biogenic emissions (real)     : 1.0
+ [$factdms]          Factor on DMS emissions (real)          : 1.0
+ [$factdemis]        Factor on dust emissions (real)         : 1.0
+ [$factsemis]        Factor on salt emissions (real)         : 1.0
+ [$factlinox]        NOx lightning factor                    : 1.0
+ 
+#------------------------------------------------------------------------------------
+# Meteorology Driver
+# Meteo grib files in either offline or online runs (WRF/ecm)
+ [$dgrb]             Dir for input meteo grib files          : /ccc/work/cont003/gen10274/maillers/IFS
+
+# in case of offline
+ [$meteo]            What is your meteo driver (WRF,ecm)     : ecm
+ [$metdom]           Meteo driver domain                     : GLOB
+ [$meteo_DIR]        Where are your meteo files              : /ccc/work/cont003/gen10274/maillers/IFS
+ [$meteo_file]       Prefix of meteo files                   : 
+ [$wrf_geog]         If WRF, where is the geo_em file        : 
+
+# in case of online
+ [$geodata]          Static input data for WPS               : /ccc/work/cont003/shr10274/shr10274/geog_data_v4.1
+ [$wrfrestart]       WRF restart param (true / false)        : optional
+ [$wrf_restart_dir]  WRF restart dir                         : ${simuldir}
+ [$wrf_tstep_grid]   WRF default is 6 in 6*dx                : 1
+
+#------------------------------------------------------------------------------------
+# Chemical boundary conditions
+#    0 - do not use
+#    1 - use and build
+#    2 - check if files exist and build only
+ [$iusebound]        Use and build bound conditions? (0/1/2) : 0
+ [$iuseini]          Use and build init. conditions? (0/1/2) : 1
+ [$nest_topconc]     Use global top conc?                    : 1
+ [$inibc3d]          Output 3D fields from init. conditions? : 0
+ [$bcdir]            Boundary conditions                     : ${bigfilesdir}
+ [$bcgas]            BC Gaseous Species                      : LMDz4_INCA3_96x95x19_v2013c
+ [$bcgasdt]          Use of gas bc (0/1/2)                   : 1
+ [$bcaer]            BC non-dust  Aerosols                   : LMDz4_INCA3_96x95x19_v2013c
+ [$bcaerdt]          use of aer bc (0/1/2)                   : 1
+ [$bcdust]           BC Dust                                 : GOCART
+ [$bcdustdt]         Use of dust bc (0/1/2)                  : 1
+
+# Chemistry and deposition / resuspension options
+ [$mecachim]         Chemistry mechanism (0..2)              : 0
+ [$aero]             Chemically-active aerosols (1/0)        : 0
+ [$nbins]            Number of aerosol size sections         : 10
+ [$carb]      	     Include carboneceous species?           : 0
+ [$soatyp]    	     Secondary organic aerosol scheme (0..2) : 0
+ [$trc]       	     Include tracers?                        : 1
+ [$nequil]    	     ISORROPIA coupling (1) / tabulation (0) : 0
+ [$npeq]      	     equilibrium calc freq (phys steps, < 5) : 1
+ [$ithermo]   	     Choice of SOA thermodynamics  (0..3)    : 1
+ [$iadrydep]  	     Aero dry deposition (1=Wesely, 2=Zhang) : 2
+ [$resusp]    	     Resuspension [1] or not [0]             : 0
+
+# Numerical solution parameters
+ [$dtphys]           Physical time steps (in mn)             : 20
+ [$dtchem]           Chemical time step (in mn)              : 20
+ [$ngs]              Number of Gauss-Seidel iterations       : 2
+ [$nsu]                - during spinup                       : 3
+ [$irs]                - number of spinup hours              : 1
+ [$iadv]             Advection scheme (0..2)                 : 2
+ [$iadvv]            Vertical advection scheme (0..2)        : 1
+ [$imethod]          twostep[0] or splitting[1]              : 0
+ [$splitcfl]     (if splitting) use CFL for trsp only (0..1) : 1
+ [$is_diagwinw]      Diagnose w from u and v                 : .false.
+ [$cflmax]           Maximal permitted CFL value             : .8
+
+# CHIMERE Subgrid Processes
+ [$ideepconv]        Deep convection activation (1/0)        : 1
+ [$urbancorr]        Urban correction [1] or not [0]         : 0
+ [$ilidar]           Lidar profiles [1] or not [0]           : 0
+ [$idiagblh]     Use BLH of meteo driver (0) or diagnose (1) : 0
+ [$idiagustar]   Use u* of meteo driver (0) or diagnose (1)  : 0
+ [$idiagshf]     Use Surf.Heat Flux of meteo (0) or diag (1) : 0
+ [$sgmodel]      Subgrid scale model for anthropogenic emi   : 0
+
+#------------------------------------------------------------------------------------
+# Flags whether to run individual dynamic interfaces and the Core
+ [$imakechemprep]    Make chemical input data (0:2)          : 1
+ [$istopchemprep]    Make chemical input data and exit       : 0
+ [$istopdom]         Make domains and exit                   : 0
+ [$imakemeteo]       Run meteo interface? (0-2)              : 1
+ [$imakeaemis]       Build anthropogenic emissions? (0-2)    : 1
+ [$imakefemis]       Build fire emissions? (0-2)             : 1
+ [$imakerun]         Run Chimere Core? (0-1)                 : 1
+ [$runwrfonly]       Run WRF without CHIMERE                 : 0
+ [$chimverb]         Print on screen verbose or not [0:5]    : 2
+ [$timeverb]         Print exec time on screen [0:5]         : 0
+
+# Miscellaneous
+ [$do_clean]	     Clean mode (full, light, or none)       : none
+

CHIMERE/mylaunch.sh

+#!/bin/bash
+
+#MSUB -r dom                                      #Request name
+#MSUB -n 45                                       #Number of procs
+#MSUB -q skylake                                  #Partition
+#MSUB -T 86400                                    #86400 Elapsed time limit in seconds (max=24 hours)
+#MSUB -o Job_OUT/chimere_%I.out                   #Standard output
+#MSUB -e Job_OUT/chimere_%I.err                   #Error output
+#MSUB -A gen10274                                 #Nom du projet qui sera comptabilise
+#MSUB -@ sylvain.mailler@lmd.polytechnique.fr
+#MSUB -x                                          #requests for exclusive use of the allocated nodes
+#MSUB -m work,scratch
+
+set -x
+
+cd ${BRIDGE_MSUB_PWD}
+
+cat chimere.par.puyehue-tier2 | sed 's/_IUSEINI_/0/g' > chimere.par.puyehue-tier2.first
+cat chimere.par.puyehue-tier2 | sed 's/_IUSEINI_/1/g' > chimere.par.puyehue-tier2.next
+
+# ./chimere.sh chimere.par.puyehue-tier2.first f 2011060400 24
+# ./chimere.sh chimere.par.puyehue-tier2.next  f 2011060500 24
+# ./chimere.sh chimere.par.puyehue-tier2.next  f 2011060600 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011060700 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011060800 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011060900 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011061000 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011061100 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011061200 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011061300 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011061400 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011061500 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011061600 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011061700 24
+./chimere.sh chimere.par.puyehue-tier2.next  f 2011061800 24