How to run SIESTA. Introduction to input & output files
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1 How to run SIESTA Introduction to input & output files
2 Linear-scaling DFT based on Numerical Atomic Orbitals (NAOs) Born-Oppenheimer DFT Pseudopotentials Numerical atomic orbitals relaxations, MD, phonons. LDA, GGA norm conserving, factorised. finite range Numerical evaluation of matrix elements P. Ordejon, E. Artacho & J. M. Soler, Phys. Rev. B 53, R10441 (1996) J. M.Soler et al, J. Phys.: Condens. Matter 14, 2745 (2002)
3 What do we need? Access to the executable file: siesta An input file Flexible Data Format (fdf) (A. García & J.M. Soler). A psedopotential file for each kind of element in the input file. Unformatted binary (vps) Formatted ASCII (.psf): more transportable and readable
4 Siesta package: (under( license) Src: Sources of the Siesta code Docs: Documentation and user conditions User s Guide (siesta.tex) Pseudo: ATOM program to generate and test pseudopotentials Examples: fdf and pseudopotentials input files for simple systems Utils: Programs or scripts to analyze the results
5 The input file Main input file: Flexible Data Format (FDF) Physical data of the system Variables to control the approximations
6 FDF characteristics (II) Data can be given in any order Data can be omitted in favour of default values. Labels are case insensitive and characters `-, `_, `. are ignored: LatticeConstant is equivalent to lattice_constant Text following # are comments You may include other FDF files or redirect the search to another file
7 FDF characteristics (II) Syntax: data label followed by its value Character string: SystemLabel h2o Integer: NumberOfAtoms 3 Real: PAO.SplitNorm 0.15 Logical: SpinPolarized.false. Physical magnitudes LatticeConstant 5.43 Ang Physical magnitudes: followed by their units. Many units are valid for the same magnitude (m, cm, nm, Ang, Bohr). There is an automatic conversion to the units required internally. Character strings, NOT in apostrophes
8 FDF characteristics (III) Logical values: T /.true. / true / yes F /.false. / false / no Complex data structures: blocks %block label %endblock label
9 Basic input variables a) General system descriptors b) Structural and geometrical variables c) Functional and solution mehod d) Convergence of the results e) Self-consistency f) Basis set generation related variables.
10 General System description SystemName: descriptive name of the system SystemName Si bulk, diamond structure SystemLabel: nickname to label output files SystemLabel silicon After a succesful run, you should have files like silicon.dm : Density matrix silicon.xv : Final positions and velocities silicon.eig : Eigen-energies...
11 Geometrical and structural variables NumberOfAtoms: number of atoms in the simulation NumberOfAtoms 2 NumberOfSpecies: number of different atomic species NumberOfSpecies 1 ChemicalSpeciesLabel: specify the different chemical species. %block ChemicalSpeciesLabel 1 14 Si %endblock ChemicalSpeciesLabel ALL THESE VARIABLES ARE MANDATORY!!
12 Lattice Vectors LatticeConstant: length to define the scale of the lattice vectors LatticeConstant 5.43 Ang LatticeParameters: Crystallograhic way %block LatticeParameters %endblock LatticeParameters LatticeVectors: read as a matrix, each vector being a line %block LatticeVectors %endblock LatticeVectors
13 Periodic Boundary Conditions (PBC) Atoms in the unit cell are periodically repeated throughout space along the lattice vectors Periodic systems and crystalline solids: Aperiodic systems: Supercell approximation Defects Molecules Surfaces
14 Atomic Coordinates AtomicCoordinatesFormat: format of the atomic positions in input: Bohr: cartesian coordinates, in bohrs Ang: cartesian coordinates, in Angstroms ScaledCartesian: cartesian coordinates, units of the lattice constant Fractional: referred to the lattice vectors AtomicCoordinatesFormat AtomicCoordinatesAndAtomicSpecies: Fractional %block AtomicCoordinatesAndAtomicSpecies Si Si %endblock AtomicCoordinatesAndAtomicSpecies
15 XC-functional DFT XC.Functional LDA GGA XC.authors CA PW92 PBE SpinPolarized PZ CA Ceperley-Alder PZ Perdew-Zunger PW92 Perdew-Wang-92 PBE Perdew-Burke-Ernzerhof
16 Solution method Two options to solve the electronic problem (Kohn-Sham equations) From the atomic coordinates and the unit cell r R, r a { } Order N operations ( H ε S ) C = 0 Hamiltonian, H, and Overlap, S, matrices SolutionMethod diagon ordern
17 Spetial set of k-points: Accurate results for a small # k-points: Baldereschi, Chadi-Cohen, Monkhorst-Pack kgrid_cutoff: Kgrid_cutoff kgrid_monkhorst_pack: K-point sampling 10.0 Ang %block kgrid_monkhorst_pack %endblock kgrid_monkhorst_pack
18 ρ( r )= ρ atom ( r ) Initial guess V ( r ) V ( r ) ρ( r )= ρ µ,ν φ µ φ ν µ,ν out in ρ µ,, ρ, Mixing ν µ ν Linear: DM.MixingWeigth NonLinear (Pulay): DM.NumberPulay H v, xc Self-consistent iterations r ρ out µ, ν Ĥψ = ε ψ MaxSCFIterations ρ out in µ ν ρµ, ν <, DM.Tolerance Total energy Charge density Forces
19 Toruntheserial version: How to run siesta [path]/siesta < input.fdf > output & To see the information dumbed in the output file while it runs tail f output Alternatively: [path]/siesta < input.fdf tee ouput
20 Analysing the output (I) The output header Siesta version Fortran compiler
21 Analysing the output (II) dumping the input file
22 processing the input
23 coordinates and k-sampling
24 Output: First MD step
25 Output: Self-consistency
26 Output: Eigenvalues, forces, stress
27 Output: Total energy
28 Output: timer
29 Saving & reading information (I) Some information is stored by Siesta and can be used to restart the simulations from previous a run: Density matrix: Localized wave functions (Order-N): Atomic positions and velocities: CG history (minimizations): DM.UseSaveDM ON.UseSaveLWF MD.UseSaveXV MD.UseSaveCG All of them are logical variables (and save lots of time!!)
30 Saving & reading information (II) Information needed as input for various post-processing programs, for example, to visualize: Total charge density: Deformation charge density: Electrostatic potential: Total potential: Local density of states: Charge density contours: Atomic coordinates: SaveRho SaveDeltaRho SaveElectrostaticPotential SaveTotalPotential LocalDensityOfStates WriteDenchar WriteCoorXmol and WriteCoorCerius All of them are logical variables
31 Analyzing the electronic structure (I) Band structure along the high symetry lines of the BZ BandLineScale: scale of the k vectors in BandLines BandLinesScale pi/a BandLines: lines along with band energies are calculated. %block BandLines L \Gamma X \Gamma %endblock BandLines
32 Analyzing the electronic structure (II) Density Of States: total and projected on the atomic orbitals Compare with experimental spectroscopy Bond formation ProjectedDensityOfStates: %block ProjectedDensityOfStates ev %endblock ProjectedDensityOfStates Lower energy Higher energy width # points
33 Analyzing the electronic structure (III) Population analysis: Mulliken prescription Amounts of charge on an atom or in an orbital inside the atom Bond formation Be careful, very dependent on the basis functions WriteMullikenPop 0 = None 1 = Atomic and orbitals charges 2 = 1 + atomic overlap pop. 3 = 2 + orbital overlap pop.
34 Utilities (I) Various post-processing tools: PHONONS: Finite differences: VIBRA (P. Ordejón) Linear response: LINRES ( M. Pruneda et al.) Interphase with Phonon program (Parlinsky) Visualization of the CHARGE DENSITY and POTENTIALS -3D: PLRHO (J. M. Soler), grid2cube, grid2xfs, -2D: CONTOUR (E. Artacho) -2D: DENCHAR (J. Junquera)
35 Utilities (II) TRANSPORT PROPERTIES: TRANSIESTA (M. Brandbydge et al.), SMEAGOL (S. Sanvito et. al.) PSEUDOPOTENTIAL and BASIS information: PyAtom (A. García). XML output: Visualization of the ouput (J. Wakelin & A. García). PDOS-xml tool (A. García) ATOMIC COORDINATES: Sies2arc (J. Gale)
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