Lecture 8 Gaussian Basis Sets CHEM6085: Density Functional
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Atomic Orbitals
Visualization of Atomic Orbitals Source: Robert R. Gotwals, Jr., Department of Chemistry, North Carolina School of Science and Mathematics, Durham, NC, 27705. Email: [email protected]. Copyright ©2007, all rights reserved, permission to use for non-commercial educational purposes is granted. Introductory Readings Where are the electrons in an atom? There are a number of Models - a description of models that look to describe the location and behavior of some physical object or electrons in atoms. It is important to know this information, as behavior in nature. Models it helps chemists to make statements and predictions about are often mathematical, describing the behavior of how atoms will react with other atoms to form molecules. The some event. model one chooses will oftentimes influence the types of statements one can make about the behavior – that is, the reactivity – of an atom or group of atoms. Bohr model - states that no One model, the Bohr model, describes electrons as small two electrons in an atom can billiard balls, rotating around the positively charged nucleus, have the same set of four much in the way that planets quantum numbers. orbit around the Sun. The placement and motion of electrons are found in fixed and quantifiable levels called orbits, Orbits- where electrons are or, in older terminology, shells. believed to be located in the There are specific numbers of Bohr model. Orbits have a electrons that can be found in fixed amount of energy, and are identified with the each orbit – 2 for the first orbit, principle quantum number 8 for the second, and so forth. -
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 -
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 .................................. -
Chemical Bonding & Chemical Structure
Chemistry 201 – 2009 Chapter 1, Page 1 Chapter 1 – Chemical Bonding & Chemical Structure ings from inside your textbook because I normally ex- Getting Started pect you to read the entire chapter. 4. Finally, there will often be a Supplement that con- If you’ve downloaded this guide, it means you’re getting tains comments on material that I have found espe- serious about studying. So do you already have an idea cially tricky. Material that I expect you to memorize about how you’re going to study? will also be placed here. Maybe you thought you would read all of chapter 1 and then try the homework? That sounds good. Or maybe you Checklist thought you’d read a little bit, then do some problems from the book, and just keep switching back and forth? That When you have finished studying Chapter 1, you should be sounds really good. Or … maybe you thought you would able to:1 go through the chapter and make a list of all of the impor- tant technical terms in bold? That might be good too. 1. State the number of valence electrons on the following atoms: H, Li, Na, K, Mg, B, Al, C, Si, N, P, O, S, F, So what point am I trying to make here? Simply this – you Cl, Br, I should do whatever you think will work. Try something. Do something. Anything you do will help. 2. Draw and interpret Lewis structures Are some things better to do than others? Of course! But a. Use bond lengths to predict bond orders, and vice figuring out which study methods work well and which versa ones don’t will take time. -
Electron Configurations, Orbital Notation and Quantum Numbers
5 Electron Configurations, Orbital Notation and Quantum Numbers Electron Configurations, Orbital Notation and Quantum Numbers Understanding Electron Arrangement and Oxidation States Chemical properties depend on the number and arrangement of electrons in an atom. Usually, only the valence or outermost electrons are involved in chemical reactions. The electron cloud is compartmentalized. We model this compartmentalization through the use of electron configurations and orbital notations. The compartmentalization is as follows, energy levels have sublevels which have orbitals within them. We can use an apartment building as an analogy. The atom is the building, the floors of the apartment building are the energy levels, the apartments on a given floor are the orbitals and electrons reside inside the orbitals. There are two governing rules to consider when assigning electron configurations and orbital notations. Along with these rules, you must remember electrons are lazy and they hate each other, they will fill the lowest energy states first AND electrons repel each other since like charges repel. Rule 1: The Pauli Exclusion Principle In 1925, Wolfgang Pauli stated: No two electrons in an atom can have the same set of four quantum numbers. This means no atomic orbital can contain more than TWO electrons and the electrons must be of opposite spin if they are to form a pair within an orbital. Rule 2: Hunds Rule The most stable arrangement of electrons is one with the maximum number of unpaired electrons. It minimizes electron-electron repulsions and stabilizes the atom. Here is an analogy. In large families with several children, it is a luxury for each child to have their own room. -
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 -
Lecture 3. the Origin of the Atomic Orbital: Where the Electrons Are
LECTURE 3. THE ORIGIN OF THE ATOMIC ORBITAL: WHERE THE ELECTRONS ARE In one sentence I will tell you the most important idea in this lecture: Wave equation solutions generate atomic orbitals that define the electron distribution around an atom. To start we need to simplify the math by switching to spherical polar coordinates (everything = spherical) rather than Cartesian coordinates (everything = at right angles). So the wave equations generated will now be of the form ψ(r, θ, Φ) = R(r)Y(θ, Φ) where R(r) describes how far out on a radial trajectory from the nucleus you are. r is a little way out and is small Now that we are extended radially on ψ, we need to ask where we are on the sphere carved out by R(r). Think of blowing up a balloon and asking what is going on at the surface of each new R(r). To cover the entire surface at projection R(r), we need two angles θ, Φ that get us around the sphere in a manner similar to knowing the latitude & longitude on the earth. These two angles yield Y(θ, Φ) which is the angular wave function A first solution: generating the 1s orbit So what answers did Schrodinger get for ψ(r, θ, Φ)? It depended on the four quantum numbers that bounded the system n, l, ml and ms. So when n = 1 and = the solution he calculated was: 1/2 -Zr/a0 1/2 R(r) = 2(Z/a0) *e and Y(θ, Φ) = (1/4π) . -
Powerpoint Presentation
Session 2 Basis Sets CCCE 2008 1 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 CCCE 2008 2 Running a Calculation • In performing ab initio and DFT computa- tional chemistry calculations, 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 CCCE 2008 3 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 CCCE 2008 4 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 CCCE 2008 5 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 -
Towards Efficient Data Exchange and Sharing for Big-Data Driven Materials Science: Metadata and Data Formats
www.nature.com/npjcompumats PERSPECTIVE OPEN Towards efficient data exchange and sharing for big-data driven materials science: metadata and data formats Luca M. Ghiringhelli1, Christian Carbogno1, Sergey Levchenko1, Fawzi Mohamed1, Georg Huhs2,3, Martin Lüders4, Micael Oliveira5,6 and Matthias Scheffler1,7 With big-data driven materials research, the new paradigm of materials science, sharing and wide accessibility of data are becoming crucial aspects. Obviously, a prerequisite for data exchange and big-data analytics is standardization, which means using consistent and unique conventions for, e.g., units, zero base lines, and file formats. There are two main strategies to achieve this goal. One accepts the heterogeneous nature of the community, which comprises scientists from physics, chemistry, bio-physics, and materials science, by complying with the diverse ecosystem of computer codes and thus develops “converters” for the input and output files of all important codes. These converters then translate the data of each code into a standardized, code- independent format. The other strategy is to provide standardized open libraries that code developers can adopt for shaping their inputs, outputs, and restart files, directly into the same code-independent format. In this perspective paper, we present both strategies and argue that they can and should be regarded as complementary, if not even synergetic. The represented appropriate format and conventions were agreed upon by two teams, the Electronic Structure Library (ESL) of the European Center for Atomic and Molecular Computations (CECAM) and the NOvel MAterials Discovery (NOMAD) Laboratory, a European Centre of Excellence (CoE). A key element of this work is the definition of hierarchical metadata describing state-of-the-art electronic-structure calculations. -
APW+Lo Basis Sets
Computer Physics Communications 179 (2008) 784–790 Contents lists available at ScienceDirect Computer Physics Communications www.elsevier.com/locate/cpc Force calculation for orbital-dependent potentials with FP-(L)APW + lo basis sets ∗ Fabien Tran a, , Jan Kuneš b,c, Pavel Novák c,PeterBlahaa,LaurenceD.Marksd, Karlheinz Schwarz a a Institute of Materials Chemistry, Vienna University of Technology, Getreidemarkt 9/165-TC, A-1060 Vienna, Austria b Theoretical Physics III, Center for Electronic Correlations and Magnetism, Institute of Physics, University of Augsburg, Augsburg 86135, Germany c Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnická 10, CZ-162 53 Prague 6, Czech Republic d Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208, USA article info abstract Article history: Within the linearized augmented plane-wave method for electronic structure calculations, a force Received 8 April 2008 expression was derived for such exchange–correlation energy functionals that lead to orbital-dependent Received in revised form 14 May 2008 potentials (e.g., LDA + U or hybrid methods). The forces were implemented into the WIEN2k code and Accepted 27 June 2008 were tested on systems containing strongly correlated d and f electrons. The results show that the Availableonline5July2008 expression leads to accurate atomic forces. © PACS: 2008 Elsevier B.V. All rights reserved. 61.50.-f 71.15.Mb 71.27.+a Keywords: Computational materials science Density functional theory Forces Structure optimization Strongly correlated materials 1. Introduction The majority of present day electronic structure calculations on periodic solids are performed with the Kohn–Sham (KS) formulation [1] of density functional theory [2] using the local density (LDA) or generalized gradient approximations (GGA) for the exchange–correlation energy.