Basic introduction to SIESTA
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1 Basic introduction to SIESTA Emilio Artacho Department of Earth Sciences University of Cambridge 1
2 The method Linear-scaling DFT based on NAOs (Numerical Atomic Orbitals) 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) Born-Oppenheimer (relaxations, mol.dynamics) DFT (LDA, GGA) Pseudopotentials (norm conserving,factorised) Numerical atomic orbitals as basis (finite range) Numerical evaluation of matrix elements (3Dgrid) Implemented in the SIESTA program
3 Siesta resources (I) Web page: Pseudos and basis database Tutorials Mailing list User guide and reference manual Mailing list archives (Wiki)
4 Siesta resources (2) Andrei Postnikov Siesta utils page: Lev Kantorovich Siesta utils page: 4
5 Siesta software package: Src: Sources of the Siesta code. Src/Sys: makefiles for the compilation Obj: default directory where compilation goes Tests: A collection of tests. Docs: Documentation and user conditions: User s Guide (siesta.tex) Pseudo: ATOM program to generate and test pseudos. Examples: fdf and pseudos input files for simple systems. Tutorials: Tutorials for basis and pseudo generation. Utils: Programs or scripts to analyze the results.
6 To run Siesta you need: 1.- Access to the executable file 2.- An input file: written in ascii (plain text) using: Flexible Data Format (FDF) (A. García and J. M. Soler) 3.- A pseudopotential file for each kind of element in the input file. Two different formats: Unformatted binary (.vps) Formatted ASCII (.psf) (more transportable and easy to look at)
7 Running siesta Siesta has no windows, it is run from a UNIX terminal or from a MSDOS console. Main input file: name.fdf Contents: Physical data of the system Variables to control the aproximations Format: Flexible Data Format (FDF)
8 FDF (I) Data can be given in any order Data can be omitted in favor of default values 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
9 FDF (II) Labels are case insensitive and characters -_. are ignored LatticeConstant is equivalent to lattice_constant Text following # are comments Logical values: T,.true., yes, F,.false., no By default logicals are true: DM.UseSaveDM Character strings, NOT in apostrophes Complex data structures: blocks %block label %endblock label
10 FDF (III) Physical magnitudes: followed by its units. Many physical units are recognized for each magnitude (Length: m, cm, nm, Ang, bohr) Automatic conversion to the ones internally required. You may include other FDF files or redirect the search to another file, so for example in the main fdf it s possible: AtomicCoordinatesFormat < system_xyz.fdf AtomicCoordinatesAndAtomicSpecies < system_xyz.fdf
11 Basic input variables 1.- General system descriptors 2.- Structural and geometrical variables 3.- Functional and solution mehod (Order-N/diagonalization) 4.- Convergence of the results 5.- Self-consistency 6.- Basis set generation related variables 7.- Molecular dynamics 8.- Electron transport (TranSIESTA)
12 General system descriptor: output SystemName: descriptive name of the system SystemName Si bulk, diamond structure SystemLabel: nickname of the system to name output files SystemLabel bulksi (After a successful run, you should have files like bulksi.dm : Density matrix bulksi.xv: Final positions and velocities...)
13 Structural and geometrical 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 BLOCK %endblock ChemicalSpeciesLabel ALL THESE VARIABLES ARE MANDATORY
14 Geometry: Lattice Vectors Surfaces PBC: Atoms in the unit cell always are periodically repeated throughout space along the lattice vectors LatticeConstant: real length to define the scale of the lattice vectors LatticeConstant 5.43 Ang LatticeParameters: Crystallographic way %block LatticeParameters %endblock LatticeParameters LatticeVectors: read as a matrix, each vector on a line %block LatticeVectors %endblock LatticeVectors
15 AtomicCoordinatesFormat: Atomic Coordinates Bohr: cartesian coordinates, in bohrs Ang: cartesian coordinates, in Angstroms ScaledCartesian: cartesian coor scaled by lattice constant Fractional: referred to the lattice vectors AtomicCoordinatesFormat Fractional AtomicCoordinatesAndAtomicSpecies: %block AtomicCoordinatesAndAtomicSpecies %endblock AtomicCoordinatesAndAtomicSpecies
16 Functional DFT XC.Functional LDA GGA SpinPolarized XC.authors CA PW92 PZ DFT Density Functional Theory LDA Local Density Approximation GGA Generalized Gradient Approximation VDW van der Waals PBE CA Ceperley-Alder PZ Perdew-Zunger PW92 Perdew-Wang-92 PBE Perdew-Burke-Ernzerhof DRSLL Dion et al (VdW)
17 Benzene sandwich Not perfect, but a pragmatic possibility, still from first-principles and within KS-DFT 17 Efficient implementation (Roman & Soler PRL 09)
18 Solution method 0: Start from the atomic coordinates and the unit cell 1: Compute H, S (Order N ): Hamiltonian (H), Overlap (S) matrices Execution time 2: SolutionMethod diagon Order-N
19 k-sampling Many magnitudes require integration of Bloch functions over Brillouin zone (BZ) ( ) = dk r n( k r r # ) $ i k! r i " BZ ( ) 2 In practice: integral sum over a finite uniform grid Real space Reciprocal space Essential for: Small periodic systems Metals Magnetic systems Good description of the Bloch states at the Fermi level Even in same insulators: Perovskite oxides
20 k-sampling Special set of k-points: Accurate results for a small # k-points: kgrid_cutoff (1): kgrid_cutoff 10.0 Ang kgrid_monkhorst_pack (2): %block kgrid_monkhorst_pack %endblock kgrid_monkhorst_pack 1 Moreno and Soler, PRB 45, (1992). 2 Monkhorst and Pack, PRB 13, 5188 (1997)
21 Selfconsistency (SCF) Initial guess: "!( r ) =! atom ( r )!( r ) = $! µ," # µ # " µ," No Tolerance MaxSCFIterations? Yes Properties: Total energy, Charge density Forces
22 Hard confining potentials A single parameter Energy shift E. Artacho et al. Phys. Stat. Solidi (b) 215, 809 (1999) Fireballs O. F. Sankey & D. J. Niklewski, Phys. Rev. B 40, 3979 (1989) Convergence vs Energy shift of Bond lengths Bond energies BUT: A different cut-off radius for each orbital 22
23 Soft confining potentials r (a.u.) r (a.u.) Better basis, variationally, & other results Removes the discontinuity in the derivative J. Junquera, O. Paz, D. Sanchez-Portal & E. Artacho, Phys. Rev. B, 64, (2001) E. Anglada, J. M. Soler, J. Junquera & E. Artacho, Phys. Rev. B 66, (2002)
24 Multiple-zeta E. Artacho et al., Phys. Stat. Solidi (b) 215, 809 (1999). 24
25 Polarization E. Artacho et al., Phys. Stat. Solidi (b) 215, 809 (1999). 25
26 Basis set: Main controls Explicit control within block PAO.Basis %block PAO.Basis Sr n=4 0 1 E n=5 0 2 E n=4 1 1 E n=5 1 1 E n=4 2 1 E %EndBlock PAO.Basis Otherwise, automatic: PAO.BasisSize DZP // PAO.EnergyShift 50 mev etc Rules of thumb in Artacho et al, JPCM 2008
27 How to run Siesta To run the serial version, from a unix/terminal: Basic run, output in the screen: % siesta < Fe.fdf Output redirected to a file: % siesta < Fe.fdf > Fe.out Screen and file output: % siesta < Fe.fdf tee Fe.out (assuming the siesta binary is in your PATH)
28 Output: the header
29 Output: dumping the input file
30 Output: processing the input
31 Output: coordinates and k-sampling
32 Output: First MD step
33 Output: Self-consistency
34 Output: Eigenvalues, forces, stress
35 Output: Total energy
36 Output: timer (real and cpu times)
37 Saving and reading information (I) Some information is stored by Siesta to restart simulations from: Density matrix: DM.UseSaveDM Localized wave functions (Order-N): ON.UseSaveLWF Atomic positions and velocities: MD.UseSaveXV Conjugate gradient history (minimizations): MD.UseSaveCG All of them are logical variables EXTREMELY USEFUL TO SAVE A LOT OF TIME!
38 Saving and reading information (II) Information needed as input for various post-processing programs, for example, to visualize: Total charge density: SaveRho Deformation charge density: SaveDeltaRho Electrostatic potential: SaveElectrostaticPotential Total potential: SaveTotalPotential Local density of states: LocalDensityOfStates Charge density contours: WriteDenchar Atomic coordinates: WriteCoorXmol and WriteCoorCerius All of them are logical variables
39 Analyzing the electronic structure (I) Band structure along the high symetry lines of the BZ BandLineScale: scale of the k vectors in BandLines BandLineScale pi/a BandLines: lines were band energies are calculated. %block BandLines L \Gamma X \Gamma %endblock BandLines
40 Analyzing the electronic structure (II) Density of states: total and projected on the atomic orbitals ProjectedDensityOfStates: %block ProjectedDensityOfStates ev %endblock ProjectedDensityOfStates
41 Analyzing the electronic structure (III) Population analysis: Mulliken prescription - Charge associated to basis orbital or atom - Careful, badly defined, arbitrary and very dependent on the basis functions WriteMullikenPop WriteMullikenPop 0 = None 1 = Atomic and orbitals charges 2 = 1 + atomic overlap pop. 3 = 2 + orbital overlap pop. Others (Voronoi, Hirschfeld, Maier)
42 Tools (I) Various post-processing programs and utilities: - Phonons: Finite differences: VIBRA (P. Ordejón) Linear response: LINRES ( J. M. Pruneda et al.) - Interface with Phonon program (Parlinsky) -Visualisation of CHARGE DENSITY and POTENTIALS -3D: PLRHO (J. M. Soler) -2D: CONTOUR (E. Artacho) -2D: DENCHAR (J. Junquera) -3D: sies2xsf (Xcrysden) (A. Postnikov) -3D: grid2cube (Gaussian) (P. Ordejón) -3D: rho2grd (Materials Studio) (O. Paz)
43 Tools (II) -TRANSPORT PROPERTIES: TRANSIESTA (M. Brandbydge et al.) -PSEUDOPOTENTIAL and BASIS information: PyAtom (A. García) -ATOMIC COORDINATES: Sies2arc (J. Gale) -DOS, PDOS, Bands: PlotUtils (O. Paz) - Others (STM etc)
44 Some things we have not covered Polarisation Optical properties Variety of GGAs Z-matrix Tuning performance, output and parallelisation Alternative basis sets (Ghosts, Bessels,, user provided, variational ) 44
45 Releases 2.0 STABLE (2.0.2.) 3.0 beta (present version ) Development 45
46 3.0 Several minor modifications DFT-D and similar molecular mechanics COOP, COHP Virtual crystal approximation Wu-Cohen GGA, PBEsol Scripting and Siesta as a server Fire quench (optimiser) 2 x faster diagon 46
47 3.0 and beyond Improved parallelisation Filtering Transiesta LDA+U, pseudo-sic Spin-Orbit TD-DFT VdW Langreth s functional Divide and conquer & LNV O(N) solvers Multigrid Poisson solver; mixed BC (and a very substantial internal reshape) 47
48 Back home Get academic licence (free): gives you ID & password Compile: lets of shared experience for different platforms in mailing list and its archive Architecture dependent file: arch.make Try with./configure first 48
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