3. Standalone User Guide

• 3.1. Implementation
  • 3.1.1. Directory structure
  • 3.1.2. Grid and boundary conditions
  • 3.1.3. Initialization and Forcing
  • 3.1.4. Choosing an appropriate time step
  • 3.1.5. Model output
    • 3.1.5.1. Diagnostic files
    • 3.1.5.2. Restart files
    • 3.1.5.3. History files
    • 3.1.5.4. Biogeochemistry History Fields
• 3.2. Running Icepack
  • 3.2.1. Scripts
    • 3.2.1.1. Overview
    • 3.2.1.2. Command Line Options
    • 3.2.1.3. Preset Options
    • 3.2.1.4. Examples
    • 3.2.1.5. C Preprocessor (CPP) Macros
    • 3.2.1.6. Model Version Control
    • 3.2.1.7. Other Scripts Tools
  • 3.2.2. Porting
    • 3.2.2.1. Machine variables
    • 3.2.2.2. Cross-compiling
    • 3.2.2.3. Machine Account Settings
    • 3.2.2.4. Machine Queue Settings
  • 3.2.3. Porting to Laptop or Personal Computers
    • 3.2.3.1. Installing Miniconda
    • 3.2.3.2. Initializing your shell for use with conda
    • 3.2.3.3. Initializing your shell for conda manually
    • 3.2.3.4. Creating Icepack directories and the conda environment
    • 3.2.3.5. Using the conda configuration
  • 3.2.4. Forcing data
  • 3.2.5. Horizontal ice advection
  • 3.2.6. Run Directories
  • 3.2.7. Local modifications
• 3.3. Testing Icepack
  • 3.3.1. Individual Tests
    • 3.3.1.1. Individual Test Examples
  • 3.3.2. Test suites
    • 3.3.2.1. Test Suite Examples
  • 3.3.3. Test Reporting
  • 3.3.4. Code Coverage Testing
  • 3.3.5. Test Plotting
• 3.4. Case Settings, Model Namelist, and CPPs
  • 3.4.1. Table of C Preprocessor (CPP) Macros
  • 3.4.2. Table of Icepack Settings
  • 3.4.3. Tables of Namelist Options
    • 3.4.3.1. setup_nml
    • 3.4.3.2. grid_nml
    • 3.4.3.3. tracer_nml
    • 3.4.3.4. thermo_nml
    • 3.4.3.5. dynamics_nml
    • 3.4.3.6. shortwave_nml
    • 3.4.3.7. ponds_nml
    • 3.4.3.8. snow_nml
    • 3.4.3.9. forcing_nml
    • 3.4.3.10. zbgc_nml
  • 3.4.4. BGC Tuning Parameters
• 3.5. Troubleshooting
  • 3.5.1. Initial setup
  • 3.5.2. Restarts
  • 3.5.3. Debugging hints
  • 3.5.4. Known bugs and other issues
  • 3.5.5. Interpretation of albedos
  • 3.5.6. Interpretation of general results
  • 3.5.7. Proliferating subprocess parameterizations