SIESTA manual ../version

1 U s e r s G u i d eS I E S T A 27, 2021 Committee:Emilio ArtachoCIC-Nanogune and University of CambridgeJos Mar a CelaBarcelona Supercomputing CenterJulian D. GaleCurtin University of Technology, PerthAlberto Garc aInstitut de Ci ncia de Materials, CSIC, BarcelonaJavier JunqueraUniversidad de Cantabria, SantanderRichard M. MartinUniversity of Illinois at Urbana-ChampaignPablo Ordej nCentre de Investigaci en Nanoci nciai Nanotecnologia, (CSIC-ICN), BarcelonaNick R bner PapiorTechnical University of DenmarkDaniel S nchez-PortalUnidad de F sica de Materiales,Centro Mixto CSIC-UPV/EHU, San Sebasti nJos M. SolerUniversidad Aut noma de MadridSIESTAis Copyright 1996-2021 by The SIESTA GroupContributors to SIESTAThe SIESTA project was initiated by Pablo Ordejon (then at the Univ.)

2 De Oviedo), and Jose and Emilio Artacho (Univ. Autonoma de Madrid, UAM). The development team was thenjoined by Alberto Garcia (then at Univ. del Pais Vasco, Bilbao), Daniel Sanchez-Portal (UAM),and Javier Junquera (Univ. de Oviedo and later UAM), and sometime later by Julian Gale (then atImperial College, London). In 2007 Jose M. Cela (Barcelona Supercomputing Center, BSC) becamea core developer and member of the Steering originalTranSIESTA module was developed by Pablo Ordejon and Jose L. Mozos (thenat ICMAB-CSIC), and Mads Brandbyge, Kurt Stokbro, and Jeremy Taylor (Technical Univ. ofDenmark).The currentTranSIESTA module within SIESTA is developed by Nick R. Papior and Mads Brand-byge. Nick R. Papior became a core developer and member of the Steering Committee in contributors (we apologize for any omissions):Eduardo Anglada, Thomas Archer, Luis C.

3 Balbas, Xavier Blase, Ramon Cuadrado, Michele Ceriotti,Fabiano Corsetti, Raul de la Cruz, Gabriel Fabricius, Marivi Fernandez-Serra, Jaime Ferrer, Chu-Chun Fu, Sandra Garcia, Victor M. Garcia-Suarez, Rogeli Grima, Rainer Hoft, Georg Huhs, JorgeKohanoff, Richard Korytar, In-Ho Lee, Lin Lin, Nicolas Lorente, Miquel Llunell, Eduardo Machado,Maider Machado, Jose Luis Martins, Volodymyr Maslyuk, Juana Moreno, Frederico Dutilh Novaes,Micael Oliveira, Magnus Paulsson, Oscar Paz, Andrei Postnikov, Roberto Robles, Tristana Sondon,Andrew Walker, Andrew Walkingshaw, Toby White, Francois Willaime, Chao Sankey, Niklewski and Drabold made the FIREBALL code available to P. we no longer use the routines in that code, it was essential in the initial development ofSIESTA, which still uses many of the algorithms developed by to SIESTA21 INTRODUCTION82 The build directory.

4 Multiple-target compilation .. The file .. Debug options .. Parallel .. MPI .. OpenMP .. Library dependencies .. 143 EXECUTION OF THE Specific execution options .. 204 THE FLEXIBLE DATA FORMAT (FDF)205 PROGRAM Standard output .. Output to dedicated files .. 236 DETAILED DESCRIPTION OF PROGRAM General system descriptors .. Pseudopotentials .. Basis set and KB projectors .. Overview of atomic-orbital bases implemented inSIESTA.. 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 block.

5 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 .. sampling .. Output of k-point information .. Exchange-correlation functionals .. Spin polarization .. Spin Orbit coupling .. The self-consistent-field loop.

6 Harris functional .. Mixing options .. Mixing of the Charge Density .. Initialization of the density-matrix .. Initialization of the SCF cycle with charge densities .. Output of density matrix and Hamiltonian .. 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 .. Orbital minimization method (OMM) .. Order(N) calculations .. The PEXSI solver .. Pole handling .. Parallel environment and control options.

7 Electron tolerance and the PEXSI solver .. Inertia-counting .. Re-use of information accross iterations .. Calculation of the density of states by inertia-counting .. Calculation of the LDOS by selected-inversion .. Band-structure analysis .. Format of the .bands file .. Output of wavefunctions associated to bands .. Output of selected 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 .. Voronoi and Hirshfeld atomic population analysis .. Crystal-Orbital overlap and hamilton populations (COOP/COHP).

8 Optical properties .. Macroscopic polarization .. Maximally Localized Wannier Functions .. 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, CPU-time, and Wall time accounting options .. The catch-all option UseSaveData .. Output of information for Denchar .. NetCDF (CDF4) output file .. 11357 STRUCTURAL RELAXATION, PHONONS, AND MOLECULAR Compatibility with pre-v4 versions .. Structural relaxation .. Conjugate-gradients optimization .. Broyden optimization .. FIRE relaxation.

9 Target stress options .. Molecular dynamics .. Output options for dynamics .. Restarting geometry optimizations and MD runs .. Use of general constraints .. Phonon calculations .. 1258 DFT+U1259 External control of Examples of Lua programs .. External MD/relaxation methods .. 13010 Source code structure .. Compilation .. Brief description .. Electrodes .. Matching coordinates .. Principal layer interactions .. Convergence of electrodes and scattering regions .. Quick and dirty .. General options .. Algorithm specific options .. Poisson solution for fixed boundary conditions .. Electrode description options .. Chemical potentials.

10 Complex contour integration options .. Bias contour integration options .. Output .. Utilities for analysis:TBtrans.. 15611 ANALYSIS TOOLS15612 SCRIPTING15613 PROBLEM Error and warning messages .. 15714 REPORTING BUGS15715 ACKNOWLEDGMENTS15716 APPENDIX: Physical unit names recognized by FDF15917 APPENDIX: XML Controlling XML output .. Converting XML to XHTML .. 16118 APPENDIX: Selection of precision for storage16219 APPENDIX: Data structures and reference counting163 Bibliography164 Index16671 INTRODUCTIONThis Reference manual contains descriptions of all the input, output and execution features ofSIESTA, but is not really a tutorial introduction to the program. Interested users can find tu-torial material prepared forSIESTA schools and workshops at the project s web : See the description of changes in the logic of the SCF loopSIESTA(Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a methodand its computer program implementation, to perform electronic structure calculations andab initiomolecular dynamics simulations of molecules and solids.