Chapter 6. How to run PTCLM1.110726

Table of Contents
Introduction to PTCLM
Guide to the options of PTCLM
Examples using PTCLM
Adding data for use by PTCLM
A bit about the structure of PTCLM, what it does, and how it works

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.

Introduction to PTCLM

To get help on PTCLM1.110726 use the "--help" option as follows.

> cd scripts/ccsm_utils/Tools/lnd/clm/PTCLM
> ./ --help

The output to the above command is as follows:

Usage: [options] -d inputdatadir -m machine -s sitename

Python script to create cases to run single point simulations with tower site data.

  --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
    -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
                        Unique identifier to include as a prefix to the case name
                        Root CESM directory (top level directory with models and scripts
    --debug             Flag to turn on debug mode so won't run, but display what would
    --finidat=FINIDAT   Name of finidat initial conditions file to start CLM from
    --list              List all valid: sites, compsets, and machines
                        List of namelist items to add to CLM namelist (example:
    --QIAN_tower_yrs    Use the QIAN forcing data year that correspond to the tower
    --rmold             Remove the old case directory before starting
    --run_n=MYRUN_N     Number of time units to run simulation
                        Time units to run simulation (steps,days,years, etc.)
    --quiet             Print minimul information on what the script is doing
                        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
    --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
    --soilgrid          Use soil information from global gridded file (rather than site

  Main Script Version Id: $Id: 47576 2013-05-29 19:11:16Z erik $ Scripts URL: $HeadURL:  \ $:

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
> ./ -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