Contents

• INTRODUCTION
• COMPILATION
  • The building directory
  • The arch.make file
  
  
• EXECUTION OF THE PROGRAM
• THE FLEXIBLE DATA FORMAT (FDF)
• PROGRAM OUTPUT
  • Standard output
  • Output to dedicated files
  
  
• DETAILED DESCRIPTION OF PROGRAM OPTIONS
  • General system descriptors
  • Pseudopotentials
  • Basis set and KB projectors
  • Structural information
  • -point sampling
  • Exchange-correlation functionals
  • Spin polarization
  • The self-consistent-field loop
  • The real-space grid and the eggbox-effect
  • Matrix elements of the Hamiltonian and overlap
  • Calculation of the electronic structure
  • Band-structure analysis
  • Output of wavefunctions
  • Densities of states
  • Options for chemical analysis
  • Optical properties
  • Macroscopic polarization
  • Systems with net charge or dipole, and electric fields
  • Output of charge densities and potentials on the grid
  • Auxiliary Force field
  • Parallel options
  • Efficiency options
  • Memory accounting options
  • The catch-all option UseSaveData
  • Output of information for Denchar
  
  
• STRUCTURAL RELAXATION, PHONONS, AND MOLECULAR DYNAMICS
  • Structural relaxation
  • Target stress options
  • Molecular dynamics
  • Output options for dynamics
  • Restarting geometry optimizations and MD runs
  • Use of general constraints
  • Phonon calculations
  • Interface to the PHONON program
  
  
• TRANSIESTA
  • Brief description
  • Source code structure
  • Compilation
  • Running a fast example
  • Brief explanation
  • Electrodes
  • TRANSIESTA Options
  • Matching TRANSIESTA coordinates: basic rules
  • Output
  • Utilities for analysis: tbtrans.
  
  
• ANALYSIS TOOLS
• SCRIPTING
• PROBLEM HANDLING
  • Error and warning messages
  • Known but unsolved problems and bugs
  
  
• REPORTING BUGS
• ACKNOWLEDGMENTS
• APPENDIX: Physical unit names recognized by FDF
• APPENDIX: NetCDF
• APPENDIX: Parallel SIESTA
• APPENDIX: File Formats
• APPENDIX: XML Output
  • Controlling XML output
  • Converting XML to XHTML
  
  
• APPENDIX: Selection of precision for storage
• Index