Density Functional Theory (DFT) and the Concepts of the Augmented-Plane-Wave Plus Local Orbital (L)APW+Lo Method
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Free and Open Source Software for Computational Chemistry Education
Free and Open Source Software for Computational Chemistry Education Susi Lehtola∗,y and Antti J. Karttunenz yMolecular Sciences Software Institute, Blacksburg, Virginia 24061, United States zDepartment of Chemistry and Materials Science, Aalto University, Espoo, Finland E-mail: [email protected].fi Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. We point out the existence of a variety of free and open source software (FOSS) packages for computational chemistry that offer a wide range of functionality all the way from approximate semiempirical calculations with tight- binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. By their very definition, FOSS packages allow usage for whatever purpose by anyone, meaning they can also be used in industrial applications without limitation. Also, FOSS software has no limitations to redistribution in source or binary form, allowing their easy distribution and installation by third parties. Many FOSS scientific software packages are available as part of popular Linux distributions, and other package managers such as pip and conda. Combined with the remarkable increase in the power of personal devices—which rival that of the fastest supercomputers in the world of the 1990s—a decentralized model for teaching computational chemistry is now possible, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device 1 (BYOD) scheme. In addition to the programs’ use for various applications, open access to the programs’ source code also enables comprehensive teaching strategies, as actual algorithms’ implementations can be used in teaching. -
Basis Sets Running a Calculation • in Performing a Computational
Session 2: Basis Sets • Two of the major methods (ab initio and DFT) require some understanding of basis sets and basis functions • This session describes the essentials of basis sets: – What they are – How they are constructed – How they are used – Significance in choice 1 Running a Calculation • In performing a computational chemistry calculation, the chemist has to make several decisions of input to the code: – The molecular geometry (and spin state) – The basis set used to determine the wavefunction – The properties to be calculated – The type(s) of calculations and any accompanying assumptions 2 Running a calculation •For ab initio or DFT calculations, many programs require a basis set choice to be made – The basis set is an approx- imate representation of the atomic orbitals (AOs) – The program then calculates molecular orbitals (MOs) using the Linear Combin- ation of Atomic Orbitals (LCAO) approximation 3 Computational Chemistry Map Chemist Decides: Computer calculates: Starting Molecular AOs determine the Geometry AOs O wavefunction (ψ) Basis Set (with H H ab initio and DFT) Type of Calculation LCAO (Method and Assumptions) O Properties to HH be Calculated MOs 4 Critical Choices • Choice of the method (and basis set) used is critical • Which method? • Molecular Mechanics, Ab initio, Semiempirical, or DFT • Which approximation? • MM2, MM3, HF, AM1, PM3, or B3LYP, etc. • Which basis set (if applicable)? • Minimal basis set • Split-valence • Polarized, Diffuse, High Angular Momentum, ...... 5 Why is Basis Set Choice Critical? • The -
Solid-State NMR Techniques for the Structural Characterization of Cyclic Aggregates Based on Borane–Phosphane Frustrated Lewis Pairs
molecules Review Solid-State NMR Techniques for the Structural Characterization of Cyclic Aggregates Based on Borane–Phosphane Frustrated Lewis Pairs Robert Knitsch 1, Melanie Brinkkötter 1, Thomas Wiegand 2, Gerald Kehr 3 , Gerhard Erker 3, Michael Ryan Hansen 1 and Hellmut Eckert 1,4,* 1 Institut für Physikalische Chemie, WWU Münster, 48149 Münster, Germany; [email protected] (R.K.); [email protected] (M.B.); [email protected] (M.R.H.) 2 Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland; [email protected] 3 Organisch-Chemisches Institut, WWU Münster, 48149 Münster, Germany; [email protected] (G.K.); [email protected] (G.E.) 4 Instituto de Física de Sao Carlos, Universidad de Sao Paulo, Sao Carlos SP 13566-590, Brazil * Correspondence: [email protected] Academic Editor: Mattias Edén Received: 20 February 2020; Accepted: 17 March 2020; Published: 19 March 2020 Abstract: Modern solid-state NMR techniques offer a wide range of opportunities for the structural characterization of frustrated Lewis pairs (FLPs), their aggregates, and the products of cooperative addition reactions at their two Lewis centers. This information is extremely valuable for materials that elude structural characterization by X-ray diffraction because of their nanocrystalline or amorphous character, (pseudo-)polymorphism, or other types of disordering phenomena inherent in the solid state. Aside from simple chemical shift measurements using single-pulse or cross-polarization/magic-angle spinning NMR detection techniques, the availability of advanced multidimensional and double-resonance NMR methods greatly deepened the informational content of these experiments. In particular, methods quantifying the magnetic dipole–dipole interaction strengths and indirect spin–spin interactions prove useful for the measurement of intermolecular association, connectivity, assessment of FLP–ligand distributions, and the stereochemistry of adducts. -
An Introduction to Hartree-Fock Molecular Orbital Theory
An Introduction to Hartree-Fock Molecular Orbital Theory C. David Sherrill School of Chemistry and Biochemistry Georgia Institute of Technology June 2000 1 Introduction Hartree-Fock theory is fundamental to much of electronic structure theory. It is the basis of molecular orbital (MO) theory, which posits that each electron's motion can be described by a single-particle function (orbital) which does not depend explicitly on the instantaneous motions of the other electrons. Many of you have probably learned about (and maybe even solved prob- lems with) HucÄ kel MO theory, which takes Hartree-Fock MO theory as an implicit foundation and throws away most of the terms to make it tractable for simple calculations. The ubiquity of orbital concepts in chemistry is a testimony to the predictive power and intuitive appeal of Hartree-Fock MO theory. However, it is important to remember that these orbitals are mathematical constructs which only approximate reality. Only for the hydrogen atom (or other one-electron systems, like He+) are orbitals exact eigenfunctions of the full electronic Hamiltonian. As long as we are content to consider molecules near their equilibrium geometry, Hartree-Fock theory often provides a good starting point for more elaborate theoretical methods which are better approximations to the elec- tronic SchrÄodinger equation (e.g., many-body perturbation theory, single-reference con¯guration interaction). So...how do we calculate molecular orbitals using Hartree-Fock theory? That is the subject of these notes; we will explain Hartree-Fock theory at an introductory level. 2 What Problem Are We Solving? It is always important to remember the context of a theory. -
User Manual for the Uppsala Quantum Chemistry Package UQUANTCHEM V.35
User manual for the Uppsala Quantum Chemistry package UQUANTCHEM V.35 by Petros Souvatzis Uppsala 2016 Contents 1 Introduction 6 2 Compiling the code 7 3 What Can be done with UQUANTCHEM 9 3.1 Hartree Fock Calculations . 9 3.2 Configurational Interaction Calculations . 9 3.3 M¨ollerPlesset Calculations (MP2) . 9 3.4 Density Functional Theory Calculations (DFT)) . 9 3.5 Time Dependent Density Functional Theory Calculations (TDDFT)) . 10 3.6 Quantum Montecarlo Calculations . 10 3.7 Born Oppenheimer Molecular Dynamics . 10 4 Setting up a UQANTCHEM calculation 12 4.1 The input files . 12 4.1.1 The INPUTFILE-file . 12 4.1.2 The BASISFILE-file . 13 4.1.3 The BASISFILEAUX-file . 14 4.1.4 The DENSMATSTARTGUESS.dat-file . 14 4.1.5 The MOLDYNRESTART.dat-file . 14 4.1.6 The INITVELO.dat-file . 15 4.1.7 Running Uquantchem . 15 4.2 Input parameters . 15 4.2.1 CORRLEVEL ................................. 15 4.2.2 ADEF ..................................... 15 4.2.3 DOTDFT ................................... 16 4.2.4 NSCCORR ................................... 16 4.2.5 SCERR .................................... 16 4.2.6 MIXTDDFT .................................. 16 4.2.7 EPROFILE .................................. 16 4.2.8 DOABSSPECTRUM ............................... 17 4.2.9 NEPERIOD .................................. 17 4.2.10 EFIELDMAX ................................. 17 4.2.11 EDIR ..................................... 17 4.2.12 FIELDDIR .................................. 18 4.2.13 OMEGA .................................... 18 2 CONTENTS 3 4.2.14 NCHEBGAUSS ................................. 18 4.2.15 RIAPPROX .................................. 18 4.2.16 LIMPRECALC (Only openmp-version) . 19 4.2.17 DIAGDG ................................... 19 4.2.18 NLEBEDEV .................................. 19 4.2.19 MOLDYN ................................... 19 4.2.20 DAMPING ................................... 19 4.2.21 XLBOMD .................................. -
TBTK: a Quantum Mechanics Software Development Kit
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Copenhagen University Research Information System TBTK A quantum mechanics software development kit Bjornson, Kristofer Published in: SoftwareX DOI: 10.1016/j.softx.2019.02.005 Publication date: 2019 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Bjornson, K. (2019). TBTK: A quantum mechanics software development kit. SoftwareX, 9, 205-210. https://doi.org/10.1016/j.softx.2019.02.005 Download date: 09. apr.. 2020 SoftwareX 9 (2019) 205–210 Contents lists available at ScienceDirect SoftwareX journal homepage: www.elsevier.com/locate/softx Original software publication TBTK: A quantum mechanics software development kit Kristofer Björnson Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK–2100, Copenhagen, Denmark article info a b s t r a c t Article history: TBTK is a software development kit for quantum mechanical calculations and is designed to enable the Received 7 August 2018 development of applications that investigate problems formulated on second-quantized form. It also Received in revised form 21 February 2019 enables method developers to create solvers for tight-binding, DFT, DMFT, quantum transport, etc., that Accepted 22 February 2019 can be easily integrated with each other. Both through the development of completely new solvers, Keywords: as well as front and back ends to already well established packages. TBTK provides data structures Quantum mechanics tailored for second-quantization that will encourage reusability and enable scalability for quantum SDK mechanical calculations. C++ ' 2019 The Author. -
An Overview on the Libxc Library of Density Functional Approximations
An overview on the Libxc library of density functional approximations Susi Lehtola Molecular Sciences Software Institute at Virginia Tech 2 June 2021 Outline Why Libxc? Recap on DFT What is Libxc? Using Libxc A look under the hood Wrapup GPAW 2021: Users' and Developers' Meeting Susi Lehtola Why Libxc? 2/28 Why Libxc? There are many approximations for the exchange-correlation functional. But, most programs I ... only implement a handful (sometimes 5, typically 10-15) I ... and the implementations may be buggy / non-standard GPAW 2021: Users' and Developers' Meeting Susi Lehtola Why Libxc? 3/28 Why Libxc, cont'd This leads to issues with reproducibility I chemists and physicists do not traditionally use the same functionals! Outdated(?) stereotype: B3LYP vs PBE I how to reproduce a calculation performed with another code? GPAW 2021: Users' and Developers' Meeting Susi Lehtola Why Libxc? 4/28 Why Libxc, cont'd The issue is compounded by the need for backwards and forwards compatibility: how can one I reproduce old calculations from the literature done with a now-obsolete functional (possibly with a program that is proprietary / no longer available)? I use a newly developed functional in an old program? GPAW 2021: Users' and Developers' Meeting Susi Lehtola Why Libxc? 5/28 Why Libxc, cont'd A standard implementation is beneficial! I no need to keep reinventing (and rebuilding) the wheel I use same collection of density functionals in all programs I new functionals only need to be implemented in one place I broken/buggy functionals only need to be fixed in one place I same implementation can be used across numerical approaches, e.g. -
Introduction to DFT and the Plane-Wave Pseudopotential Method
Introduction to DFT and the plane-wave pseudopotential method Keith Refson STFC Rutherford Appleton Laboratory Chilton, Didcot, OXON OX11 0QX 23 Apr 2014 Parallel Materials Modelling Packages @ EPCC 1 / 55 Introduction Synopsis Motivation Some ab initio codes Quantum-mechanical approaches Density Functional Theory Electronic Structure of Condensed Phases Total-energy calculations Introduction Basis sets Plane-waves and Pseudopotentials How to solve the equations Parallel Materials Modelling Packages @ EPCC 2 / 55 Synopsis Introduction A guided tour inside the “black box” of ab-initio simulation. Synopsis • Motivation • The rise of quantum-mechanical simulations. Some ab initio codes Wavefunction-based theory • Density-functional theory (DFT) Quantum-mechanical • approaches Quantum theory in periodic boundaries • Plane-wave and other basis sets Density Functional • Theory SCF solvers • Molecular Dynamics Electronic Structure of Condensed Phases Recommended Reading and Further Study Total-energy calculations • Basis sets Jorge Kohanoff Electronic Structure Calculations for Solids and Molecules, Plane-waves and Theory and Computational Methods, Cambridge, ISBN-13: 9780521815918 Pseudopotentials • Dominik Marx, J¨urg Hutter Ab Initio Molecular Dynamics: Basic Theory and How to solve the Advanced Methods Cambridge University Press, ISBN: 0521898633 equations • Richard M. Martin Electronic Structure: Basic Theory and Practical Methods: Basic Theory and Practical Density Functional Approaches Vol 1 Cambridge University Press, ISBN: 0521782856 -
Electronic Structure Study of Copper-Containing Perovskites
Electronic Structure Study of Copper-containing Perovskites Mark Robert Michel University College London A thesis submitted to University College London in partial fulfilment of the requirements for the degree of Doctor of Philosophy, February 2010. 1 I, Mark Robert Michel, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Mark Robert Michel 2 Abstract This thesis concerns the computational study of copper containing perovskites using electronic structure methods. We discuss an extensive set of results obtained using hybrid exchange functionals within Density Functional Theory (DFT), in which we vary systematically the amount of exact (Hartree-Fock, HF) exchange employed. The method has enabled us to obtain accurate results on a range of systems, particularly in materials containing strongly correlated ions, such as Cu2+. This is possible because the HF exchange corrects, at least qualitatively, the spurious self-interaction error present in DFT. The materials investigated include two families of perovskite-structured oxides, of potential interest for technological applications due to the very large dielectric constant or for Multi-Ferroic behaviour. The latter materials exhibit simultaneously ferroelectric and ferromagnetic properties, a rare combination, which is however highly desirable for memory device applications. The results obtained using hybrid exchange functionals are highly encouraging. Initial studies were made on bulk materials such as CaCu3Ti4O12 (CCTO) which is well characterised by experiment. The inclusion of HF exchange improved, in a systematic way, both structural and electronic results with respect to experiment. The confidence gained in the study of known compounds has enabled us to explore new compositions predictively. -
Pyscf: the Python-Based Simulations of Chemistry Framework
PySCF: The Python-based Simulations of Chemistry Framework Qiming Sun∗1, Timothy C. Berkelbach2, Nick S. Blunt3,4, George H. Booth5, Sheng Guo1,6, Zhendong Li1, Junzi Liu7, James D. McClain1,6, Elvira R. Sayfutyarova1,6, Sandeep Sharma8, Sebastian Wouters9, and Garnet Kin-Lic Chany1 1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125, USA 2Department of Chemistry and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA 3Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA 4Department of Chemistry, University of California, Berkeley, California 94720, USA 5Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom 6Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA 7Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P. R. China 8Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80302, USA 9Brantsandpatents, Pauline van Pottelsberghelaan 24, 9051 Sint-Denijs-Westrem, Belgium arXiv:1701.08223v2 [physics.chem-ph] 2 Mar 2017 Abstract PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, so as to facilitate new method development and enable flexible ∗[email protected] [email protected] 1 computational workflows. The package provides a wide range of tools to support simulations of finite-size systems, extended systems with periodic boundary conditions, low-dimensional periodic systems, and custom Hamiltonians, using mean-field and post-mean-field methods with standard Gaussian basis functions. To ensure ease of extensibility, PySCF uses the Python language to implement almost all of its features, while computationally critical paths are implemented with heavily optimized C routines. -
Arxiv:2005.05756V2
“This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Oliveira, M.J.T. [et al.]. The CECAM electronic structure library and the modular software development paradigm. "The Journal of Chemical Physics", 12020, vol. 153, núm. 2, and may be found at https://aip.scitation.org/doi/10.1063/5.0012901. The CECAM Electronic Structure Library and the modular software development paradigm Micael J. T. Oliveira,1, a) Nick Papior,2, b) Yann Pouillon,3, 4, c) Volker Blum,5, 6 Emilio Artacho,7, 8, 9 Damien Caliste,10 Fabiano Corsetti,11, 12 Stefano de Gironcoli,13 Alin M. Elena,14 Alberto Garc´ıa,15 V´ıctor M. Garc´ıa-Su´arez,16 Luigi Genovese,10 William P. Huhn,5 Georg Huhs,17 Sebastian Kokott,18 Emine K¨u¸c¨ukbenli,13, 19 Ask H. Larsen,20, 4 Alfio Lazzaro,21 Irina V. Lebedeva,22 Yingzhou Li,23 David L´opez-Dur´an,22 Pablo L´opez-Tarifa,24 Martin L¨uders,1, 14 Miguel A. L. Marques,25 Jan Minar,26 Stephan Mohr,17 Arash A. Mostofi,11 Alan O'Cais,27 Mike C. Payne,9 Thomas Ruh,28 Daniel G. A. Smith,29 Jos´eM. Soler,30 David A. Strubbe,31 Nicolas Tancogne-Dejean,1 Dominic Tildesley,32 Marc Torrent,33, 34 and Victor Wen-zhe Yu5 1)Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany 2)DTU Computing Center, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark 3)Departamento CITIMAC, Universidad de Cantabria, Santander, Spain 4)Simune Atomistics, 20018 San Sebasti´an,Spain 5)Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA 6)Department of Chemistry, Duke University, Durham, NC 27708, USA 7)CIC Nanogune BRTA and DIPC, 20018 San Sebasti´an,Spain 8)Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain 9)Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom 10)Department of Physics, IRIG, Univ. -
Electronic Structure, Atomic Forces and Structural Relaxations by Wien2k
Electronic structure, atomic forces and structural relaxations by WIEN2k Peter Blaha Institute of Materials Chemistry TU Vienna, Austria R.Laskowski, F.Tran, K.Schwarz (TU Vienna) M.Perez-Mato (Bilbao) K.Parlinski (Krakow) D.Singh (Oakridge) M.Fischer, T.Malcherek (Hamburg) Outline: General considerations when solving H=E DFT APW-based methods (history and state-of-the-art) WIEN2k program structure + features forces, structure relaxation Applications Phonons in matlockite PbFI Phase transitions in Aurivillius phases Structure of Pyrochlore Y2Nb2O7 phase transitions in Cd2Nb2O7 Concepts when solving Schrödingers-equation Treatment of Form of “Muffin-tin” MT spin Non-spinpolarized potential atomic sphere approximation (ASA) Spin polarized pseudopotential (PP) (with certain magnetic order) Full potential : FP Relativistic treatment of the electrons exchange and correlation potential non relativistic Hartree-Fock (+correlations) semi-relativistic Density functional theory (DFT) fully-relativistic Local density approximation (LDA) Generalized gradient approximation (GGA) Beyond LDA: e.g. LDA+U, Hybrid-DFT 1 2 k k k V (r) i i i Schrödinger - equation 2 Basis functions Representation plane waves : PW, PAW augmented plane waves : APW non periodic of solid atomic oribtals. e.g. Slater (STO), Gaussians (GTO), (cluster, individual MOs) LMTO, numerical basis periodic (unit cell, Blochfunctions, “bandstructure”) DFT Density Functional Theory Hohenberg-Kohn theorem: (exact) The total energy of an interacting inhomogeneous electron gas in the presence of an external potential Vext(r ) is a functional of the density E V (r) (r)dr F [ ] ext Kohn-Sham: (still exact!) 1 (r)(r) E T [] V (r)dr drdr E [] o ext 2 | r r | xc Ekinetic Ene Ecoulomb Eee Exc exchange-correlation non interacting hom.