siesta

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U S E R' S G U I D E

S I E S T A 3.1

August 26, 2011

Emilio Artacho	University of Cambridge

José María Cela	Barcelona Supercomputing Center

Julian D. Gale	Curtin University of Technology, Perth

Alberto García	Institut de Ciència de Materials, CSIC, Barcelona

Javier Junquera	Universidad de Cantabria, Santander

Richard M. Martin	University of Illinois at Urbana-Champaign

Pablo Ordejón	Centre de Investigació en Nanociència
	i Nanotecnologia, (CSIC-ICN), Barcelona

Daniel Sánchez-Portal	Unidad de Física de Materiales,
	Centro Mixto CSIC-UPV/EHU, San Sebastián

José M. Soler	Universidad Autónoma de Madrid

http://www.uam.es/siesta

Contents
INTRODUCTION
COMPILATION
- The building directory
  - Multiple-target compilation
- 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
  - Overview of atomic-orbital bases implemented in SIESTA
  - Type of basis sets
  - Size of the basis set
  - Range of the orbitals
  - Generation of multiple-zeta orbitals
  - Soft-confinement options
  - Kleinman-Bylander projectors
  - The PAO.Basis block
  - Filtering
  - Saving and reading basis-set information
  - Tools to inspect the orbitals and KB projectors
  - Basis optimization
  - Low-level options regarding the radial grid
- Structural information
  - Traditional structure input in the fdf file
  - Z-matrix format and constraints
  - Output of structural information
  - Input of structural information from external files
  - Input from a FIFO file
  - Precedence issues in structural input
  - Interatomic distances
- -point sampling
  - Output of k-point information
- Exchange-correlation functionals
- Spin polarization
- The self-consistent-field loop
  - Mixing options
  - Initialization of the density-matrix
  - Initialization of the SCF cycle with charge densities
  - Output of density matrix
  - Convergence criteria
- The real-space grid and the eggbox-effect
- Matrix elements of the Hamiltonian and overlap
  - The auxiliary supercell
- Calculation of the electronic structure
  - Diagonalization options
  - Output of eigenvalues and wavefunctions
  - Occupation of electronic states and Fermi level
  - Order(N) calculations
- Band-structure analysis
  - Format of the .bands file
- Output of wavefunctions
- Densities of states
  - Total density of states
  - Partial (projected) density of states
  - Local density of states
- Options for chemical analysis
  - Mulliken charges and overlap populations
  - Crystal-Orbital overlap and hamilton populations (COOP/COHP)
- 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
  - Parallel decompositions for O(N)
- 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.
  - Compiling TBTtrans
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
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2011-11-16