CLM 6.1 Introduction to PTCLM - erika72/clm-docs GitHub Wiki

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
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