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:

Here we give a simple example of using PTCLM1 for a straightforward case of running at the US-UMB Fluxnet site on bluefire 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 bluefire

setenv CSMDATA   /fis/cgd/cseg/csm/inputdata
setenv MYCSMDATA $HOME/inputdata
setenv SITE      US-UMB
setenv MYMACH    bluefire
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/mksurfdata
gmake clean
cd ../mkdatadomain
gmake clean
cd ../mkgriddata
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 configure, build, and run the case as normal