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INTRODUCTION
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siesta
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siesta
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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
2011-11-16