CESM1.2.0 tutorial: WACCM and CAM-ChemMike Mills Simone TilmesWACCM Liaison CAM-Chem Liaisonmmills@ucar.edu tilmes@ucar.eduAugust 16, 2012CESM-WACCM and CAM-Chem component configurationsQuickstart guide for present-day compsetsHow to change model outputHow to change a reaction ratePost-processing data analysisValidating CESM/WACCMWACCM & CAM-Chem customer supportNCAR is supported by the National Science Foundation

WACCM /CAMChem component configurationsCAM

atmosphereoceanlandsea ice

WACCM/CAMChem

specified chemistryfree-runningspecified dynamics

static (pre-industrial or present-day)transient

free-runningdata

observationsclimatology

free-runningdata

observationsclimatology

free-runningdata

observationsclimatology

WACCM /CAMChem component configurationsCO2 (ppmv)1850 Control20th Century1955-2005RCPsRCP8.5RCP4.5RCP2.6Present DaySpecified Dynamics

WACCM component configurationsScientifically validatedin CESM1.1.1Scientifically validatedin CESM1.1.1Find scientifically validated compsets here: http://www2.cesm.ucar.edu/models/scientifically-supported

CESM1.2.0(WACCM) CompsetsSupported GridsComponents / MeteorologyFull ocean, static:B_1850_WACCM_CN (B1850WCN)B_2000_WACCM_CN (BWCN)

Full ocean, transient:B_1850-2005_WACCM_CN (B20TRWCN)B_1955-2005_WACCM_CN (B55TRWCN)B_RCP2.6_WACCM_CN (BRCP26WCN)B_RCP4.5_WACCM_CN (BRCP45WCN)B_RCP8.5_WACCM_CN (BRCP85WCN)

Data ocean, static:F_1850_WACCM (F1850W)F_2000_WACCM (FW)F_2000_WACCM_SC (FWSC)F_2000_WACCMX (FWX)F_1996_WACCMX (FWX1996)

Data ocean, transient:F_1955-2005_WACCM_CN (F55WCN)FGEOS_C4WCM_L40CN (FSDW)f19_g16

f19_g16

f19_f19, f45_f45

f19_f19, f45_f45CLM4.0/CNpre-industrialpresent day

CLM4.0/CNannual solar variabilitydaily solar variabilitydaily solar variabilitydaily solar variabilitydaily solar variability

CLM4.0pre-industrialpresent dayspecified chemistrythermosphere extension, solar maxthermosphere extension, solar min

CLM4.0/CN, daily solar variability

GEOS5 nudging

CAMChem component configurationsFind scientifically validated compsets here: http://www2.cesm.ucar.edu/models/scientifically-supported

Compsets: CESM1.2.0 CAM-Chem, grid:1.9x2.5Model (phys)/radiation/gridChemistryComponents /MeteorologyCAM4, static ocean:B_2000_TROP_MOZART (BMOZ)B_2000_MOZSOA (BMOZSOA)F_2000_TROP_MOZART (FMOZ)F_2000_MOZSOA (FMOZSOA)F2000_C4SSOA_L40 (FSOA)

CAM4, specified dynamics:FGEOS_C4BAM_L40CN (FSDBAM)FGEOS_C4MOZ_L40CN (FSDCHM)

CAM5, static ocean:B_2000_MOZMAM_CN (BMOZMAM)B_2000_STRATMAM3_CN (BSTRATMAM3) B_2000_STRATMAM7_CNF_2000_MOZMAM_CN (FMOZMAM)F_2000_STRATMAM3_CNF_2000_STRATMAM7_CN

CAM4 superfast chemistryB_2000_CN_CHEM (B2000CNCHM) B_1850_CN_CHEM (B1850CNCHM) B_1850-2000_CN_CHEM(B20TRCNCHM) F_1850_CN_CHEM (F1850CNCHM) CAM4, activef19_g16

f19_f19

CAM4, passivef19_f19

CAM5, activef19_g16

f19_f19

CAM4, activef19_g16

f19_f19trop_mozart+soa chemistrytrop_mozart, soatrop_mozart, soatrop/strat soa

trop_bamtrop_mozart

trop_mozart,mamtrop/strat mam

trop/strat mam7trop mamtrop/strat mamtrop/strat mam7

super_fast_llnlFull ocn/ice, CLM4.0 +MEGANdata ocn/ice, CLM4.0 +MEGAN+MEGAN+MEGAN

transient data ocn/ice, CLM4.0/CN, GEOS5

Full ocn/ice CLM4.0/CN

data ocn/ice, CLM4.0_CN

MEGAN VOC CLM4.0/CNtransient full ocn/ice

static full ocn/ice

Quickstart guide for present-day WACCM/CAMChem compsetGo to the script directory in your source code >cd /glade/p/cesm/tutorial/cesm1_2_0.tutorial/scripts >create_newcase list compsets

Review options for create_newcase command: >create_newcase res RESOLUTION case CASENAME -compset COMPSET mach MACHINE

RESOLUTIONS: name (shortname): 1.9x2.5_1.9x2.5 (f19_f19) 1.9x2.5_gx1v6 (f19_g16)

CASENAME: your directory/casename

COMPSET: longname (shortname): F_2000_WACCM (FW) / F_2000_TROP_MOZART (FMOZSOA)

MACHINES: name (description): yellowstone (NCAR IBM, os is Linux, 16 pes/node, batch system is LSF)

Quickstart guide for present-day WACCM/CAMChem compsetCreate a new F_2000_WACCM or F_2000_TROP_MOZART case in $CASEROOT = ~/f2000.FW.f19_f19.001 or ~/f2000.FMOZSOA.f19_f19.001 >create_newcase res f19_f19 case ~/f2000.FW.f19_f19.001 compset FW mach yellowstone or >create_newcase res f19_f19 case ~/f2000.FMOZSOA.f19_f19.001 compset FMOZSOA mach yellowstone

go to your case directory >cd ~/f2000.FW.f19_f19.001 or >cd ~/f2000.FMOZSOA.f19_f19.001 setup the model >cesm_setupnamelists (atm_in, ice_in, lnd_in, docn_in) will appear in the CaseDocs subdirectory, as well as in your $rundirbuild the model >*.build

Quickstart guide for present-day WACCM/CAMChem compsetCheck the newly generated namelist prior run >ls CaseDocs/*

atm_in: atmospheric namelist varliables chem_mech.in: chemical mechanism file drv_flds_in: dry deposition variables, MEGAN variables (if used) lnd_in: land namelist variables

Quickstart guide for present-day WACCM/CAMChem compset >less CaseDocs/atm_in (for the WACCM case):

Quickstart guide for present-day WACCM/CAMChem compsetcheck the charge accounts and wall time in your run script: >less *run

submit the job to the batch queue (default 5-day run): >*submitCheck the status of your job: >bjobs (if you need to kill the job: >bkill )queue: small (only 2 hours), regular (up to 8 hours)

send email when job endsMaximum wall time for jobCharge account numberTip: You can set your default charge account by creating a text file called .ccsm_proj in your home directory, with the account ID.

Quickstart guide for present-day WACCM/CAMChem compsetfind your model output in your run dir ($run_dir) after finished: >ls /glade/scratch///run

find our model output in the short-time archive >ls /glade/scratch//archive// (note: there will be no monthly values available if you just run for 5 days)long-time archive your job if needed (do not archive what you dont need for a long time ) >*.l_archive

namelist informationrestart information

How do I change model output?Review list of current CAM history variablesCurrently >2300 existing CAM history variablesComplete list is printed in atm.log.* file generated during each run in $rundir/run or in ~/$case_name/logs/atm.log* if run completedSearch log file for MASTER FIELD LIST to review.

How do I change model output?Create a user_nl_cam file in your $casediravgflag_pertape: averaging flag for all variables on history files (h0, h1, h2, etc.). Valid values are A (Average), I (Instantaneous), X (Maximum), M (Minimum), B (GMT 00:00:00 average), and L for local time history averaging.fincl1, fincl2, etc: list of variables added to default output on h0, h1, etc. Appended ":" sets averaging flag for the field.fexcl1, fexcl2, etc: list of variables excluded from default output on h0, h1, etc.

How do I change model output?Create a user_nl_cam file in your $casedirfincl[12345]lonlat: List of columns or contiguous columns at which the fincl[12345] fields will be output. '10e_20n' would pick the model column closest to 10E longitude by 20N latitude. '10e:20e_15n:20n' would select the model columns which fall with in the longitude range from 10-20E and the latitude range from 15-20N.mfilt: maximum number of time samples written to h0, h1, etc. nhtfrq: write frequencies for history files in timesteps (if positive) or hours (if negative). The h0 files may be monthly averages if nhtfrq(1) = 0.

Update the user_nl_cam file in your $casedir and add/change the fincl2 output > nedit user_nl_cam

Preview namelists and make sure changes are in your CaseDocs/atm_in file >preview_namelistsCheck your CaseDocs/atm_in >less CaseDocs/atm_inResubmit your job >*.submitHow do I change model output?

Changing a reaction rateThe chemistry preprocessor: generates CAM Fortran source code to solve chemistry.Input: a simple ASCII file listing chemical reactions and rates.The chemistry preprocessor input file used in your previous run is in your $CASEROOT/CaseDocs/chem_mech.inAdditional input files for default chemical mechanisms are in each source code subdirectory for mechanisms under $CCSMROOT/models/atm/cam/src/chemistry/pp_* (i.e. pp_waccm_mozart)

Open $CASEROOT/CaseDocs/chem_mech.inTemperature-independent rates: k [cm3 molec1 s1]= a0 O1D + O3 -> O2 + O2 ; 1.20e-10Arrhenius type: k = a0 * exp (b0/T), where b0 = (-E/R) O1D + H2O -> 2*OH ; 1.63e-10, 60.Troe rate constant: k = ax / (1 2), where: = k0*M/k, = log10(), M= air density (molec cm-3), T = temperature (K) k0 = a0*(300/T)**a1, k = b0*(300/T)**b1, x= exponential factor CLO + NO2 + M -> CLONO2 + M ; 1.80e-31, 3.4, 1.5e-11, 1.9, 0.6User-specific reactions: [usr_O_O2] O + O2 + M -> O3 + M Rate defined in routine mo_usrrxt.F90Modifying the chemical preprocessor input filea0b0a0b0a1b1x

Building the model with new chemistryCopy a sample preprocessor input file to the case directory and edit it: >cd $CASEROOT >cp CaseDocs/chem_mech.in my_chem_mech.in >nedit my_chem_mech.in & (use any editor to edit your script)

Modify the temperature-dependence of the reaction O + O3 2*O2, changing the exponent term from -2060 to -2050: [cph_O_O3,cph] O + O3 -> 2*O2 ; 8.00e-12, -2050.

Edit the file env_build.xml in the case directory to add the CAM configure option -usr_mech_infile pointing to the new preprocessor input file:

Re-setup and rebuild your run: >cesm_setup clean >cesm_setup >*.clean_build >*. build

Post-processing data analysisCESM history files are in standard netCDF format, and may be analyzed with standard analysis tools, including Matlab, IDL, NCL, and NCO.GEOV is an IDL-based viewer for geophysical history files created by NCAR's CAM, WACCM and MOZART models. GEOV can be downloaded from the WACCM webpagehttp://www.cesm.ucar.edu/working_groups/WACCM/ Or install geov on yellowstone:Logon to yellowstone (or caldara or geyser): > ssh -X yellowstone.ucar.edu

Edit .cshrc file. Add line: setenv IDL_STARTUP ~fvitt/idl_startup~fvitt/idl_startup sets the idl path to include GEOV: idl_path = expand_path('+~fvitt/geov') !path=!path+':'+idl_path >source .cshrc >idl geov

View model output on yellowstone: > cd /glade/scratch/$USER/archive > idl geov

Post-processing data analysisCESM history files are in standard netCDF format, and may be analyzed with standard analysis tools, including Matlab, IDL, NCL, and NCO.GEOV is an IDL-based viewer for geophysical history files created by NCAR's CAM, WACCM and MOZART models. GEOV can be downloaded from the WACCM webpagehttp://www.cesm.ucar.edu/working_groups/WACCM/

Post-processing data analysisCESM history files are in standard netCDF format, and may be analyzed with standard analysis tools, including Matlab, IDL, NCL, and NCO.GEOV is an IDL-based viewer for geophysical history files created by NCAR's CAM, WACCM and MOZART models. GEOV can be downloaded from the WACCM webpagehttp://www.cesm.ucar.edu/working_groups/WACCM/

Post-processing data analysisCAM diagnostic packages are described under CAM Post-Processing Utilities on the CAM documentation page at http://www.cgd.ucar.edu/amp/amwg/diagnostics/.

Post-processing data analysisDiagnostic packages for all model components (atmosphere, land, ice, and ocean) can be found from the component post-processing utilities page (http://www.cesm.ucar.edu/models/cesm1.2/model_diagnostics/).Ocean ENSOSea Ice Thickness

Validating CESM/WACCMUsers may validate their implementation of CESM/WACCM by repeating experiments we have done at NCAR, and using the component post-processing utilities to compare the climate generated to output we have made available publicly on the Earth System Grid (http://www.earthsystemgrid.org). Please visit our CESM 1.0 experiments and diagnostics page (http://www.cesm.ucar.edu/experiments/cesm1.0/) for an updated list of experiments with links to output data locations. Output from additional experiments will be made available on a timeline in accordance with the CMIP5 data policy.

WACCM and CAM-Chem Customer SupportCGD Forum: http://bb.cgd.ucar.edu/

Mike MillsWACCM Liaisonmmills@ucar.edu(303) 497-1425

Simone TilmesCAM-Chem Liaisontilmes@ucar.edu(303) 497-1445

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