PTCLM (pronounced either as point clime or Pee-Tee clime) is a Python script to help you set up PoinT CLM
simulations. It runs the CLM tools for you to get datasets set up, and copies them
to a location you can use them according to the
CLM_USRDAT_NAME naming convention. Then
it runs create_newcase for you and modifies the env settings and
namelist appropriately. PTCLM has a simple ASCII text file for storing basic
information for your sites. We also have complete lists for AmeriFlux and Fluxnet-Canada
sites, although we only have the meteorology data for one site. For other sites you
will need to obtain the meteorology data and translate it to a format that the CESM
datm model can use. But, even without meteorology data PTCLM is useful to setup
datasets to run with standard CLM_QIAN data.
The original authors of PTCLM are: Daniel M. Ricciuto, Dali Wang, Peter E. Thornton, Wilfred M. Post all at Environmental Sciences Division, Oak Ridge National Laboratory (ORNL) and R. Quinn Thomas at Cornell University. It was then modified fairly extensively by Erik Kluzek at NCAR. We want to thank all of these individuals for this contribution to the CESM effort. We also want to thank the folks at University of Michigan Biological Stations (US-UMB) who allowed us to use their Fluxnet station data and import it into our inputdata repository, especially Gil Bohrer the PI on record for this site.
To get help on PTCLM1.110726 use the "--help" option as follows.
> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM > ./PTCLM.py --help
The output to the above command is as follows:
Usage: PTCLM.py [options] -d inputdatadir -m machine -s sitename Python script to create cases to run single point simulations with tower site data. Options: --version show program's version number and exit -h, --help show this help message and exit Required Options: -d CCSM_INPUT, --csmdata=CCSM_INPUT Location of CCSM input data -m MYMACHINE, --machine=MYMACHINE Machine, valid CESM script machine (-m list to list valid machines) -s MYSITE, --site=MYSITE Site-code to run, FLUXNET code or CLM1PT name (-s list to list valid names) Configure and Run Options: -c MYCOMPSET, --compset=MYCOMPSET Compset for CCSM simulation (Must be a valid 'I' compset [other than IG compsets], use -c list to list valid compsets) --coldstart Do a coldstart with arbitrary initial conditions --caseidprefix=MYCASEID Unique identifier to include as a prefix to the case name --cesm_root=BASE_CESM Root CESM directory (top level directory with models and scripts subdirs) --debug Flag to turn on debug mode so won't run, but display what would happen --finidat=FINIDAT Name of finidat initial conditions file to start CLM from --list List all valid: sites, compsets, and machines --namelist=NAMELIST List of namelist items to add to CLM namelist (example: --namelist="hist_fincl1='TG',hist_nhtfrq=-1" --QIAN_tower_yrs Use the QIAN forcing data year that correspond to the tower years --rmold Remove the old case directory before starting --run_n=MYRUN_N Number of time units to run simulation --run_units=MYRUN_UNITS Time units to run simulation (steps,days,years, etc.) --quiet Print minimul information on what the script is doing --sitegroupname=SITEGROUP Name of the group of sites to search for you selected site in (look for prefix group names in the PTCLM_sitedata directory) --stdurbpt If you want to setup for standard urban namelist settings --useQIAN use QIAN input forcing data instead of tower site meterology data --verbose Print out extra information on what the script is doing Input data generation options: These are options having to do with generation of input datasets. Note: When running for supported CLM1PT single-point datasets you can NOT generate new datasets. For supported CLM1PT single-point datasets, you MUST run with the following settings: --nopointdata And you must NOT set any of these: --soilgrid --pftgrid --owritesrf --nopointdata Do NOT make point data (use data already created) --owritesrf Overwrite the existing surface datasets if they exist (normally do NOT recreate them) --pftgrid Use pft information from global gridded file (rather than site data) --soilgrid Use soil information from global gridded file (rather than site data) Main Script Version Id: $Id: PTCLM.py 47576 2013-05-29 19:11:16Z erik $ Scripts URL: $HeadURL: \ https://svn-ccsm-models.cgd.ucar.edu/PTCLM/trunk_tags/PTCLM1_130529/PTCLM.py $:
Here we give a simple example of using PTCLM1 for a straightforward case of running at the US-UMB Fluxnet site on yellowstone where we already have the meteorology data on the machine. Note, see the Section called Converting AmeriFlux Data for use by PTCLM for permission information to use this data.
Example 6-1. Example of running PTCLM1 for US-UMB on yellowstone
> setenv CSMDATA $CESMDATAROOT/inputdata > setenv MYCSMDATA $HOME/inputdata > setenv SITE US-UMB > setenv MYMACH yellowstone_intel > setenv MYCASE testPTCLM # First link the standard input files to a location you have write access > cd scripts > ./link_dirtree $CSMDATA $MYCSMDATA # Next build all of the clm tools you will need > cd ../models/lnd/clm/tools/clm4_5/mksurfdata_map > gmake > gmake clean > cd ../../../../../../tools/mapping/gen_domain_files/src > ../../../../scripts/ccsm_utils/Machines/configure -mach yellowstone -compiler intel > gmake > gmake clean # next run PTCLM (NOTE -- MAKE SURE python IS IN YOUR PATH) > cd ../../../../../scripts/ccsm_utils/Tools/lnd/clm/PTCLM > ./PTCLM.py -m $MYMACH --case=$MYCASE --site=$SITE --csmdata=$MYCSMDATA \ --aerdepgrid --ndepgrid # NOTE: we use --aerdepgrid --ndepgrid so that you use the global # aerosol and Nitrogen deposition files rather than site-specific ones. > cd ../../../../../$MYCASE # Finally setup, build, and run the case as normal