CESM Research Tools: CLM4 in CESM1.1.1 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 in CESM1.1.1 since previous public releases?
Quickstart to using CLM4
What is scientifically validated and functional in CLM4 in CESM1.1.1?
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 CESM User's-Guide
The CESM Bulletin Board
The CLM web pages
Reporting bugs in CLM4
Some Acronymn's We'll be Using
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 setup
CLM Script configuration items
User Namelist
Precedence of Options
Setting Your Initial Conditions File
Other noteworthy configuration items
Downloading DATM Forcing Data
Customizing via the build script 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
Customizing the DATM Namelist and Streams files
CLM_QIAN mode and it's DATM settings
CLM1PT mode and it's DATM settings
CPLHIST3HrWx mode and it's DATM settings
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
General information on running the FORTRAN tools
Running FORTRAN tools with namelists
Running FORTRAN tools with command line options
Running FORTRAN tools built with SMP=TRUE
Using NCL scripts
The File Creation Process
Using the cprnc tool to compare two history files
Using interpinic to interpolate initial conditions to different resolutions
Creating an output SCRIP grid file at a resolution to run the model on
Using mknocnmap.pl to create grid and maps for single-point regional grids
Creating mapping files that mksurfdata_map will use
Creating a domain file for CLM and DATM
Creating a set of regional datasets from existing global datasets
Using mksurfdata_map to create surface datasets from grid datasets
Running mksurfdata.pl
Running mksurfdata_map by Hand
Converting unstructured grid output to gridded datasets for post processing
How to Customize Datasets for particular Observational Sites
Conclusion of tools description
3. Adding New Resolutions or New Files to the build-namelist Database
Managing Your Own Data-files
Adding Resolution Names
Adding or Changing Default Filenames
What are the required files?
4. How to run some special cases
Running with the prognostic crop model on
Running with the irrigation model on
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)
Running with MOAR data as atmospheric forcing to spinup the model
Running with your own previous simulation as atmospheric forcing to spinup the model
Running stand-alone CLM with transient historical CO2 concentration
5. How to run Single-Point/Regional cases
Which Single Point Option Should I choose?
Running PTS_MODE configurations
Warning about Running with a Single-Processor on a Batch Machine
Running Supported Single-point/Regional Datasets
Running Supported Single-point Datasets that have their own Atmospheric Forcing
Creating your own single-point/regional surface datasets
Using getregional_datasets.pl to get a complete suite of single-point/regional surface datasets from global ones
Running with your own atmosphere forcing
6. Trouble Shooting Problems
Trouble with Setup
Trouble with Building
Trouble with Running
Tracking Problems by Querying Log Files
General Advice on Debugging Run time Problems
7. Scripts for testing CLM
Testing CLM Using the CESM Test Scripts
Testing CLM Using the CLM Specific Stand-Alone Tools Testing Scripts
Testing CLM tools using the CLM Stand-Alone Tools Testing Scripts
A. Building the Users-Guide Documentation for CLM
List of Tables
1-1. CLM History Fields
3-1. Required Files for Different Configurations and Simulation Types
5-1. Atmosphere Forcing Fields
List of Figures
2-1. Data Flow for Creation of Surface Datasets from Raw SCRIP Grid Files
2-2. Legend for Data Flow Figures
2-3. Global Domain file creation
2-4. Domain file creation using mknoocnmap.pl
2-5. Details of running mksurfdata_map
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 of running mksurfdata.pl to create a 4x5 resolution fsurdat for a 1850 simulation year
2-4. Getting the raw datasets for mksurfdata_map to your local machine using the check_input_data script
4-1. Example Crop Simulation
4-2. Example Irrigation Simulation
4-3. Example AD_SPINUP Simulation
4-4. Example EXIT_SPINUP Simulation
4-5. Example Final CN Spinup Simulation
4-6. Example CNDV Spinup Simulation
4-7. Example Simulation with MOAR Data on yellowstone
4-8. Example Fully Coupled Simulation to Create Data to Force Next Example Simulation
4-9. Example Simulation Forced with Data from the Previous Simulation
4-10. Example Transient Simulation with Historical CO2
5-1. Example of running CLM over a single-point test site in Brazil with the default Qian atmosphere data forcing.
5-2. Example of running CLM over the single-point of Mexicocity Mexico with the default Qian atmosphere data forcing.
5-3. Example of running CLM over the single-point of Vancouver Canada with supplied atmospheric forcing data for Vancouver.
5-4. Example of running getregional_datasets.pl to get datasets for a specific region over Alaska
5-5. Example of using CLM_USRDAT_NAME to run a simulation using user datasets for a specific region over Alaska
5-6. Example of setting up a case with your own atmosphere forcing
5-7. Example of DATM streams files with your own forcing for 3-hourly data
6-1. Example of cesm_setup problem with missing datasets