User's Guide S I E S T A 4.0 June 23, 2016 Emilio Artacho CIC-Nanogune and University of Cambridge Jos´eMar´ıaCela Barcelona Supercomputing Center Julian D. Gale Curtin University of Technology, Perth Alberto Garc´ıa Institut de Ci`enciade Materials, CSIC, Barcelona Javier Junquera Universidad de Cantabria, Santander Richard M. Martin University of Illinois at Urbana-Champaign Pablo Ordej´on Centre de Investigaci´oen Nanoci`encia i Nanotecnologia, (CSIC-ICN), Barcelona Daniel S´anchez-Portal Unidad de F´ısica de Materiales, Centro Mixto CSIC-UPV/EHU, San Sebasti´an Jos´eM. Soler Universidad Aut´onomade Madrid http://www.uam.es/siesta Copyright c The Siesta Group, E.Artacho, J.M. Cela, J.D.Gale, A.Garc´ıa,J.Junquera, P.Ordej´on,D.S´anchez-Portal and J.M.Soler, 1996-2016 Contents 1 INTRODUCTION 6 2 COMPILATION 8 2.1 The building directory . 8 2.1.1 Multiple-target compilation . 9 2.2 The arch.make file . 9 3 EXECUTION OF THE PROGRAM 10 4 THE FLEXIBLE DATA FORMAT (FDF) 12 5 PROGRAM OUTPUT 13 5.1 Standard output . 13 5.2 Output to dedicated files . 14 6 DETAILED DESCRIPTION OF PROGRAM OPTIONS 14 6.1 General system descriptors . 15 6.2 Pseudopotentials . 16 6.3 Basis set and KB projectors . 17 6.3.1 Overview of atomic-orbital bases implemented in Siesta . 17 6.3.2 Type of basis sets . 21 6.3.3 Size of the basis set . 22 6.3.4 Range of the orbitals . 22 6.3.5 Generation of multiple-zeta orbitals . 22 6.3.6 Soft-confinement options . 24 6.3.7 Kleinman-Bylander projectors . 25 6.3.8 The PAO.Basis block . 26 6.3.9 Filtering . 29 6.3.10 Saving and reading basis-set information . 30 6.3.11 Tools to inspect the orbitals and KB projectors . 30 6.3.12 Basis optimization . 30 6.3.13 Low-level options regarding the radial grid . 31 6.4 Structural information . 32 6.4.1 Traditional structure input in the fdf file . 32 1 6.4.2 Z-matrix format and constraints . 35 6.4.3 Output of structural information . 39 6.4.4 Input of structural information from external files . 40 6.4.5 Input from a FIFO file . 41 6.4.6 Precedence issues in structural input . 41 6.4.7 Interatomic distances . 42 6.5 k-point sampling . 42 6.5.1 Output of k-point information . 43 6.6 Exchange-correlation functionals . 44 6.7 Spin polarization . 46 6.8 The self-consistent-field loop . 46 6.8.1 Mixing options . 47 6.8.2 Mixing of the Charge Density . 51 6.8.3 Initialization of the density-matrix . 53 6.8.4 Initialization of the SCF cycle with charge densities . 55 6.8.5 Output of density matrix . 56 6.8.6 Convergence criteria . 56 6.9 The real-space grid and the eggbox-effect . 57 6.10 Matrix elements of the Hamiltonian and overlap . 61 6.10.1 The auxiliary supercell . 61 6.11 Calculation of the electronic structure . 62 6.11.1 Diagonalization options . 63 6.11.2 Output of eigenvalues and wavefunctions . 64 6.11.3 Occupation of electronic states and Fermi level . 64 6.11.4 Orbital minimization method (OMM) . 65 6.11.5 Order(N) calculations . 68 6.12 Band-structure analysis . 71 6.12.1 Format of the .bands file . 72 6.12.2 Output of wavefunctions associated to bands . 73 6.13 Output of selected wavefunctions . 73 6.14 Densities of states . 74 6.14.1 Total density of states . 74 6.14.2 Partial (projected) density of states . 75 6.14.3 Local density of states . 76 2 6.15 Options for chemical analysis . 76 6.15.1 Mulliken charges and overlap populations . 76 6.15.2 Voronoi and Hirshfeld atomic population analysis . 77 6.15.3 Crystal-Orbital overlap and hamilton populations (COOP/COHP) . 78 6.16 Optical properties . 79 6.17 Macroscopic polarization . 81 6.18 Maximally Localized Wannier Functions. Interface with the wannier90 code . 83 6.19 Systems with net charge or dipole, and electric fields . 86 6.20 Output of charge densities and potentials on the grid . 87 6.21 Auxiliary Force field . 90 6.22 Parallel options . 91 6.22.1 Parallel decompositions for O(N) . 92 6.23 Efficiency options . 93 6.24 Memory, CPU-time, and Wall time accounting options . 93 6.25 The catch-all option UseSaveData . 94 6.26 Output of information for Denchar . 94 7 STRUCTURAL RELAXATION, PHONONS, AND MOLECULAR DY- NAMICS 94 7.1 Compatibility with pre-v4 versions . 96 7.2 Structural relaxation . 96 7.2.1 Conjugate-gradients optimization . 98 7.2.2 Broyden optimization . 98 7.2.3 FIRE relaxation . 99 7.2.4 Quenched MD . 99 7.3 Target stress options . 100 7.4 Molecular dynamics . 101 7.5 Output options for dynamics . 103 7.6 Restarting geometry optimizations and MD runs . 104 7.7 Use of general constraints . 104 7.8 Phonon calculations . 106 8 TRANSIESTA 107 8.1 Brief description . 107 3 8.2 Source code structure . 108 8.3 Compilation . 108 8.4 Running a fast example . 109 8.5 Brief explanation . 110 8.6 Electrodes . 111 8.6.1 Repetition . 112 8.7 TranSiesta Options . 113 8.7.1 General options . 113 8.7.2 Electrode description options . 114 8.7.3 Complex contour integration options . 116 8.7.4 Bias contour integration options . 116 8.8 Matching TranSiesta coordinates: basic rules . 117 8.9 Output . 117 8.10 Utilities for analysis: tbtrans. ............................118 8.10.1 Output . 121 8.10.2 Compiling TBTtrans . 121 9 ANALYSIS TOOLS 121 10 SCRIPTING 121 11 PROBLEM HANDLING 122 11.1 Error and warning messages . 122 11.2 Known but unsolved problems and bugs . 122 12 REPORTING BUGS 122 13 ACKNOWLEDGMENTS 123 14 APPENDIX: Physical unit names recognized by FDF 124 15 APPENDIX: NetCDF 126 16 APPENDIX: Parallel Siesta 128 17 APPENDIX: File Formats 131 18 APPENDIX: XML Output 133 4 18.1 Controlling XML output . ..