Appendix

Table of Contents

• Parallel calculations using ATK
  • Introduction
  • System requirements
    • Hardware considerations
    • Library requirements
  • License
  • Launching a parallel job using MPICH2
  • Upgrade from MPICH 1.2
  • I/O in parallel NanoLanguage scripts
  • Controlling threading in MKL
  • How is ATK parallelized?
  • Benchmarks
  • Summary
• Using ATK interactively
  • Prerequisites
  • Entering interactive mode
  • Command history
  • Exiting an interactive ATK session
  • Analysis mode
  • Importing files
  • Auto-completion
  • Command history
  • Additional resources
• Saving data
  • Saving data
  • NetCDF files
  • VNL files
  • Alternatives
    • Pickling in Python
    • Pickling
    • Unpickling
    • Note
• Tips
  • Restarting calculations
    • Restarting a finished job
    • Restarting an aborted calculation
  • Overwriting VNLFile samples
  • Specifying different basis sets for several different atoms
  • Extracting data points from a transmission spectrum
  • Generating VNL files from parallel runs
  • Importing an XYZ-file
  • Timing a calculation
  • Convergence of two-probe calculations
    • Choosing the appropriate parameters
    • Setting up the initial electron density from an equivalent bulk calculation
    • Constrained calculations
  • Convergence of light-element atoms
• Atomic data
• Bibliography