CCSM Research Tools: CLM4.0 User's Guide Documentation

Erik Kluzek

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Dedicated to the Land Model Working Group, winners of the 2008 CCSM Distinguished Achievement Award. May you continue to collaborate together well, and continue to drive the science of land surface modeling forward with your diligent and persistent efforts.

Table of Contents
Introduction to the CLM4 User's Guide
Important Notes and Best Practices for Usage of CLM4
How to Use This Document
What is new with CLM4 since CLM3.5?
What is new with CLM4 Science?
Biogeophysics and Hydrology
Snow Model
Surface Datasets
Miscellaneous Changes
Summary of Science Changes
What is new with CLM4 Software Infrastructure?
What are The New Configuration Options?
What are The New Namelist Options?
What are The New History Fields?
Quickstart to using CLM4
What is scientifically validated and functional in CLM4?
Standard Configuration and Namelist Options that are Validated
Configure Modes NOT scientifically validated, documented, supported or, in some cases, even advised to be used:
Namelist options that should NOT be exercised:
Build-Namelist options that should NOT be exercised:
Namelist items that should NOT be exercised:
What are the UNIX utilities required to use CLM?
Other resources to get help from
The CCSM User's-Guide
The CCSM Bulletin Board
The CLM web pages
Reporting bugs in CLM4
1. How to customize the configuration for a case with CLM
Choosing a compset using CLM
Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets)
Compsets coupled to active atmosphere with data ocean
Fully coupled compsets with fully active ocean, sea-ice, and atmosphere
Conclusion to choosing a compset
Customizing the CLM configuration
CLM Script configuration items
Configure time User Namelist
Other noteworthy configuration items
Customizing via the template files
More information on the CLM configure script
Customizing the CLM namelist
Definition of Namelist items and their default values
Examples of using different namelist features
Conclusion to customizing chapter
2. Using the CLM tools to create your own input datasets
Common environment variables and options used in building the FORTRAN tools
The File Creation Process
Using the cprnc tool to compare two history files
Using interpinic to interpolate initial conditions to different resolutions
Using mkgriddata to create grid datasets
mkgriddata namelist
Convert CCSM domain files to CLM grid files
Create single point or regional area grid files
Convert CAM files to CLM grid files
Using mkdatadomain to create domain datasets for datm or docn from CLM grid datasets
Using mksurfdata to create surface datasets from grid datasets
Running mksurfdata by Hand
Using NCL scripts ndepregrid.ncl and aerdepregrid.ncl to interpolate aerosol deposition datasets
Using ndepregrid.ncl to interpolate Nitrogen deposition datasets
Using aerdepregrid.ncl to interpolate Aerosol deposition datasets
How to Customize Datasets for particular Observational Sites
Conclusion of tools description
3. Adding New Resolutions or New Files to the build-namelist Database
Adding Resolution Names
Adding or Changing Default Filenames
What are the required files?
4. How to run some special cases
Spinning up the Satellite Phenology Model (CLMSP spinup)
Spinning up the biogeochemistry Carbon-Nitrogen Model (CN spinup)
Spinning up the Carbon-Nitrogen Dynamic Global Vegetation Model (CNDV spinup)
Doing perturbation error growth tests
Running stand-alone CLM with transient historical CO2 concentration
5. How to run Single-Point/Regional cases
Running PTS_MODE configurations
Running Supported Single-point/Regional Datasets
Creating your own single-point/regional surface datasets
Using to get a complete suite of single-point/regional surface datasets from global ones
A. Editing Template Files Before Configure
B. Using the Script runinit_ibm.csh to both Run CLM and Interpolate Datasets
C. Scripts for testing CLM
Testing CLM Using the CCSM Test Scripts
Testing CLM Using the CLM Stand-Alone Testing Scripts
List of Tables
3-1. Required Files for Different Configurations and Simulation Types
List of Figures
4-1. Sample Perturbation Error Growth Curve
List of Examples
1-1. Example user_nl_clm namelist file
1-2. Default CLM Namelist
1-3. Example user_nl_clm namelist adding and removing fields on primary history file
1-4. Example user_nl_clm namelist adding auxiliary history files and changing output frequency
1-5. Example user_nl_clm namelist removing all history fields
1-6. Example user_nl_clm namelist with various ways to average history fields
1-7. Example user_nl_clm namelist outputting some files in 1D Vector format
2-1. Example of running CLM to create a template file for interpinic to interpolate to
2-2. Example of building and running interpinic to interpolate a 1-degree finidat dataset to 10x15
2-3. Example mkgriddata namelist to convert CCSM 4x5 domain files to CLM grid files
2-4. Example mkgriddata namelist to create regional grid over Amazon
2-5. Example mkdatadomain namelist to create a domain file from CLM frac and grid data files
2-6. Example of running to create a 4x5 resolution fsurdat for a 1850 simulation year
2-7. Getting the raw datasets for mksurfdata to your local machine using the check_input_data script
4-1. Example AD_SPINUP Simulation
4-2. Example EXIT_SPINUP Simulation
4-3. Example Final CN Spinup Simulation
4-4. Example CNDV Spinup Simulation
4-5. Example non-perturbed error growth simulation
4-6. Example perturbed error growth simulation
4-7. Example Transient Simulation with Historical CO2