Key Concepts in Density Functional Theory from the Many Body Problem to the Kohn-Sham Scheme

Total Page:16

File Type:pdf, Size:1020Kb

Key Concepts in Density Functional Theory from the Many Body Problem to the Kohn-Sham Scheme The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Key concepts in Density Functional Theory From the many body problem to the Kohn-Sham scheme Silvana Botti ILM (LPMCN) CNRS, Universit´eLyon 1 - France European Theoretical Spectroscopy Facility (ETSF) December 12, 2012 { Lyon Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Outline 1 The many-body problem 2 Earlier solutions: Hartree, Hartree-Fock, Thomas-Fermi 3 The solution: density functional theory 4 Hohenberg-Kohn theorems 5 Practical implementations: the Kohn-Sham scheme 6 Summary Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Outline 1 The many-body problem 2 Earlier solutions: Hartree, Hartree-Fock, Thomas-Fermi 3 The solution: density functional theory 4 Hohenberg-Kohn theorems 5 Practical implementations: the Kohn-Sham scheme 6 Summary Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary The many-body problem Schr¨odingerequation for a quantum system of N interacting particles: How to deal with N ≈ 1023 particles? H^ Ψ(fRg ; frg) = EΨ(fRg ; frg) ^ ^ ^ Ne electrons H = Tn (fRg) + Vnn (fRg) + Nn nuclei T^e (frg) + V^ee (frg) + U^en (fRg ; frg) Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary The many-body Hamiltonian ^ ^ ^ ^ ^ ^ H = Tn (fRg) + Vnn (fRg) + Te (frg) + Vee (frg) + Uen (fRg ; frg) Nn 2 Ne 2 X rI X ri T^n = − ; T^e = − ; 2MI 2m I =1 i=1 Nn Ne 1 X ZI ZJ 1 X 1 V^nn = ; V^ee = ; 2 jRI − RJ j 2 jri − rj j I ;J;I 6=J i;j;i6=j Ne;Nn X ZJ U^en = − jRJ − rj j j;J Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Starting approximations Born-Oppenheimer separation In the adiabatic approximation the nuclei are frozen in their equilibrium positions. Example of equilibrium geometries Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Starting approximations Pseudopotential and pseudowavefunction Concept of pseudopotentials The chemically intert core electrons are frozen in their atomic configuration and their effect on chemically active valence electrons is incorporated in an effective potential. Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Pseudopotentials: generation criteria A pseudopotential is not unique, several methods of generation also exist. 1 The pseudo-electron eigenvalues must be the same as the valence eigenvalues obtained from the atomic wavefunctions. 2 Pseudo-wavefunctions must match the all-electron wavefunctions outside the core (plus continuity conditions). 3 The core charge produced by the pseudo-wavefunctions must be the same as that produced by the atomic wavefunctions (for norm-conserving pseudopotentials). 4 The logaritmic derivatives and their first derivatives with respect to the energy must match outside the core radius (scattering properties). 5 Additional criteria for different recipes. Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Pseudopotentials: quality assessment It is important to find a compromise between 1 Transferability: ability to describe the valence electrons in different environments. 2 Efficiency: softness { few plane waves basis functions. Moreover: Which states should be included in the valence and which states in the core? Problem of semicore states. Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary The many-body Hamiltonian Applying the Born-Oppenheimer separation::: Nn 2 Ne 2 X rI X ri 0 = T^n = − ; T^e = − ; 2MI 2m I =1 i=1 Nn Ne 1 X ZI ZJ 1 X 1 constant!V^nn = ; V^ee = ; 2 jRI − RJ j 2 jri − rj j I ;J;I 6=J i;j;i6=j Ne;Nn Ne X ZJ X U^en = − = v (rj ) jRJ − rj j j;J j Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary The many-body problem Schr¨odingerEquation for a quantum-system of Ne interacting electrons: 23 Still, how to deal with Ne ≈ 10 particles? H^ Ψ(frg) = EeΨ(frg) Ne 2 Ne X ri 1 X 1 H^ = − + v (ri ) + Ne electrons 2m 2 jri − rj j i=1 i;j;i6=j Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Why we don't like the electronic wavefunction How many DVDs are necessary to store a wavefunction? Classical example: Oxygen atom (8 electrons) Ψ(r1;:::; r8) depends on 24 coordinates Rough table of the wavefunction: 10 entries per coordinate: =) 1024 entries 1 byte per entry : =) 1024 bytes 5 × 109 bytes per DVD: =) 2 × 1014 DVDs 10 g per DVD: =) 2 × 1015 g DVDs = ×109 t DVDs Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Outline 1 The many-body problem 2 Earlier solutions: Hartree, Hartree-Fock, Thomas-Fermi 3 The solution: density functional theory 4 Hohenberg-Kohn theorems 5 Practical implementations: the Kohn-Sham scheme 6 Summary Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary The Hartree equations: Hartree potential Hartree introduced in 1927 a procedure, which he called the self-consistent field method, to approximate the Schr¨odingerequation variational principle to an ansatz (trial wave function) as a product of single-particle functions:ΨH = φ1 (r1) φ2 (r2) : : : φN (rN ) 2 3 Z 0 2 1 X jφj (r )j − r2 + v (r) + d3r 0 φ (r) = " φ (r) 4 2 i ext jr − r0j 5 i i i j If we do not restrict the sum to j 6= i: self-interaction problem and the antisymmetry of the wavefunction? Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary The Hartree equations: Hartree potential Hartree introduced in 1927 a procedure, which he called the self-consistent field method, to approximate the Schr¨odingerequation variational principle to an ansatz (trial wave function) as a product of single-particle functions:ΨH = φ1 (r1) φ2 (r2) : : : φN (rN ) 2 3 Z 0 2 1 X jφj (r )j − r2 + v (r) + d3r 0 φ (r) = " φ (r) 4 2 i ext jr − r0j 5 i i i j If we do not restrict the sum to j 6= i: self-interaction problem and the antisymmetry of the wavefunction? Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary The approach of the \best wavefunction" In 1930 Slater and Fock independently pointed out that the Hartree method did not respect the principle of antisymmetry. A Slater determinant trivially satisfies the antisymmetry of the exact solution and hence is a suitable ansatz for applying the variational principle The original Hartree method can then be viewed as an approximation to the Hartree-Fock method by neglecting exchange. The Hartree-Fock method was little used until the advent of electronic computers in the 1950s (need of self-consistency!). Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary The Hartree-Fock equations: exchange potential The Hartree-Fock method determines the set of (spin) orbitals which minimizes the energy and give us the best single-determinant: ˛ ˛ ˛φ1(x1) φ2(x1) ··· φN (x1)˛ ˛ ˛ 1 ˛φ1(x2) φ2(x2) ··· φN (x2)˛ Ψ (x ; x ;:::; x ) = p ˛ ˛ HF 1 2 N ˛ . ˛ N! ˛ . ˛ ˛ ˛ ˛φ1(xN ) φ2(xN ) ··· φN (xN )˛ 2 3 Z 0 2 1 X jφj (r )j − r2 + v (r) + d3r 0 φ (r) 4 2 i ext jr − r0j 5 i j Z ∗ 0 X φj (r) φi (r ) − δ d3r 0 = " φ (r) σi σj jr − r0j i i j Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Some remarks on Hartree-Fock The HF potential is self-interaction free. Ignoring relaxation (i.e. the change in the self-consistent potential) the first ionization energy is equal to the negative of the energy of the HOMO: Koopman's theorem. The approximate solution of the HF equations cannot be exact because the true many-body wavefunction is not a single-determinant. In quantum chemistry the correlation energy is defined as the difference between the HF energy and the exact ground-state energy. To go beyond HF a trial wavefunction can be built as a linear combination of HF orbitals, including excited orbitals: configuration interaction (CI). Key concepts in Density Functional Theory Silvana Botti The many-body problem From Hartree to Thomas Fermi DFT HK theorems KS scheme and bands Summary Thomas-Fermi theory Formulated in 1927 in terms of the electronic density alone, the TF theory is viewed as a precursor to density functional theory.
Recommended publications
  • Accessing the Accuracy of Density Functional Theory Through Structure
    This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. Letter Cite This: J. Phys. Chem. Lett. 2019, 10, 4914−4919 pubs.acs.org/JPCL Accessing the Accuracy of Density Functional Theory through Structure and Dynamics of the Water−Air Interface † # ‡ # § ‡ § ∥ Tatsuhiko Ohto, , Mayank Dodia, , Jianhang Xu, Sho Imoto, Fujie Tang, Frederik Zysk, ∥ ⊥ ∇ ‡ § ‡ Thomas D. Kühne, Yasuteru Shigeta, , Mischa Bonn, Xifan Wu, and Yuki Nagata*, † Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan ‡ Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany § Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States ∥ Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098 Paderborn, Germany ⊥ Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan ∇ Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan *S Supporting Information ABSTRACT: Density functional theory-based molecular dynamics simulations are increasingly being used for simulating aqueous interfaces. Nonetheless, the choice of the appropriate density functional, critically affecting the outcome of the simulation, has remained arbitrary. Here, we assess the performance of various exchange−correlation (XC) functionals, based on the metrics relevant to sum-frequency generation spectroscopy. The structure and dynamics of water at the water−air interface are governed by heterogeneous intermolecular interactions, thereby providing a critical benchmark for XC functionals.
    [Show full text]
  • Density Functional Theory
    Density Functional Approach Francesco Sottile Ecole Polytechnique, Palaiseau - France European Theoretical Spectroscopy Facility (ETSF) 22 October 2010 Density Functional Theory 1. Any observable of a quantum system can be obtained from the density of the system alone. < O >= O[n] Hohenberg, P. and W. Kohn, 1964, Phys. Rev. 136, B864 Density Functional Theory 1. Any observable of a quantum system can be obtained from the density of the system alone. < O >= O[n] 2. The density of an interacting-particles system can be calculated as the density of an auxiliary system of non-interacting particles. Hohenberg, P. and W. Kohn, 1964, Phys. Rev. 136, B864 Kohn, W. and L. Sham, 1965, Phys. Rev. 140, A1133 Density Functional ... Why ? Basic ideas of DFT Importance of the density Example: atom of Nitrogen (7 electron) 1. Any observable of a quantum Ψ(r1; ::; r7) 21 coordinates system can be obtained from 10 entries/coordinate ) 1021 entries the density of the system alone. 8 bytes/entry ) 8 · 1021 bytes 4:7 × 109 bytes/DVD ) 2 × 1012 DVDs 2. The density of an interacting-particles system can be calculated as the density of an auxiliary system of non-interacting particles. Density Functional ... Why ? Density Functional ... Why ? Density Functional ... Why ? Basic ideas of DFT Importance of the density Example: atom of Oxygen (8 electron) 1. Any (ground-state) observable Ψ(r1; ::; r8) 24 coordinates of a quantum system can be 24 obtained from the density of the 10 entries/coordinate ) 10 entries 8 bytes/entry ) 8 · 1024 bytes system alone. 5 · 109 bytes/DVD ) 1015 DVDs 2.
    [Show full text]
  • Robust Determination of the Chemical Potential in the Pole
    Robust determination of the chemical potential in the pole expansion and selected inversion method for solving Kohn-Sham density functional theory Weile Jia, and Lin Lin Citation: The Journal of Chemical Physics 147, 144107 (2017); doi: 10.1063/1.5000255 View online: http://dx.doi.org/10.1063/1.5000255 View Table of Contents: http://aip.scitation.org/toc/jcp/147/14 Published by the American Institute of Physics THE JOURNAL OF CHEMICAL PHYSICS 147, 144107 (2017) Robust determination of the chemical potential in the pole expansion and selected inversion method for solving Kohn-Sham density functional theory Weile Jia1,a) and Lin Lin1,2,b) 1Department of Mathematics, University of California, Berkeley, California 94720, USA 2Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA (Received 14 August 2017; accepted 24 September 2017; published online 11 October 2017) Fermi operator expansion (FOE) methods are powerful alternatives to diagonalization type methods for solving Kohn-Sham density functional theory (KSDFT). One example is the pole expansion and selected inversion (PEXSI) method, which approximates the Fermi operator by rational matrix functions and reduces the computational complexity to at most quadratic scaling for solving KSDFT. Unlike diagonalization type methods, the chemical potential often cannot be directly read off from the result of a single step of evaluation of the Fermi operator. Hence multiple evaluations are needed to be sequentially performed to compute the chemical potential to ensure the correct number of electrons within a given tolerance. This hinders the performance of FOE methods in practice. In this paper, we develop an efficient and robust strategy to determine the chemical potential in the context of the PEXSI method.
    [Show full text]
  • Octopus: a First-Principles Tool for Excited Electron-Ion Dynamics
    octopus: a first-principles tool for excited electron-ion dynamics. ¡ Miguel A. L. Marques a, Alberto Castro b ¡ a c, George F. Bertsch c and Angel Rubio a aDepartamento de F´ısica de Materiales, Facultad de Qu´ımicas, Universidad del Pa´ıs Vasco, Centro Mixto CSIC-UPV/EHU and Donostia International Physics Center (DIPC), 20080 San Sebastian,´ Spain bDepartamento de F´ısica Teorica,´ Universidad de Valladolid, E-47011 Valladolid, Spain cPhysics Department and Institute for Nuclear Theory, University of Washington, Seattle WA 98195 USA Abstract We present a computer package aimed at the simulation of the electron-ion dynamics of finite systems, both in one and three dimensions, under the influence of time-dependent electromagnetic fields. The electronic degrees of freedom are treated quantum mechani- cally within the time-dependent Kohn-Sham formalism, while the ions are handled classi- cally. All quantities are expanded in a regular mesh in real space, and the simulations are performed in real time. Although not optimized for that purpose, the program is also able to obtain static properties like ground-state geometries, or static polarizabilities. The method employed proved quite reliable and general, and has been successfully used to calculate linear and non-linear absorption spectra, harmonic spectra, laser induced fragmentation, etc. of a variety of systems, from small clusters to medium sized quantum dots. Key words: Electronic structure, time-dependent, density-functional theory, non-linear optics, response functions PACS: 33.20.-t, 78.67.-n, 82.53.-k PROGRAM SUMMARY Title of program: octopus Catalogue identifier: Program obtainable from: CPC Program Library, Queen’s University of Belfast, N.
    [Show full text]
  • 1-DFT Introduction
    MBPT and TDDFT Theory and Tools for Electronic-Optical Properties Calculations in Material Science Dott.ssa Letizia Chiodo Nano-bio Spectroscopy Group & ETSF - European Theoretical Spectroscopy Facility, Dipartemento de Física de Materiales, Facultad de Químicas, Universidad del País Vasco UPV/EHU, San Sebastián-Donostia, Spain Outline of the Lectures • Many Body Problem • DFT elements; examples • DFT drawbacks • excited properties: electronic and optical spectroscopies. elements of theory • Many Body Perturbation Theory: GW • codes, examples of GW calculations • Many Body Perturbation Theory: BSE • codes, examples of BSE calculations • Time Dependent DFT • codes, examples of TDDFT calculations • state of the art, open problems Main References theory • P. Hohenberg & W. Kohn, Phys. Rev. 136 (1964) B864; W. Kohn & L. J. Sham, Phys. Rev. 140 , A1133 (1965); (Nobel Prize in Chemistry1998) • Richard M. Martin, Electronic Structure: Basic Theory and Practical Methods, Cambridge University Press, 2004 • M. C. Payne, Rev. Mod. Phys.64 , 1045 (1992) • E. Runge and E.K.U. Gross, Phys. Rev. Lett. 52 (1984) 997 • M. A. L.Marques, C. A. Ullrich, F. Nogueira, A. Rubio, K. Burke, E. K. U. Gross, Time-Dependent Density Functional Theory. (Springer-Verlag, 2006). • L. Hedin, Phys. Rev. 139 , A796 (1965) • R.W. Godby, M. Schluter, L. J. Sham. Phys. Rev. B 37 , 10159 (1988) • G. Onida, L. Reining, A. Rubio, Rev. Mod. Phys. 74 , 601 (2002) codes & tutorials • Q-Espresso, http://www.pwscf.org/ • Abinit, http://www.abinit.org/ • Yambo, http://www.yambo-code.org • Octopus, http://www.tddft.org/programs/octopus more info at http://www.etsf.eu, www.nanobio.ehu.es Outline of the Lectures • Many Body Problem • DFT elements; examples • DFT drawbacks • excited properties: electronic and optical spectroscopies.
    [Show full text]
  • Camcasp 5.9 Alston J. Misquitta† and Anthony J
    CamCASP 5.9 Alston J. Misquittay and Anthony J. Stoneyy yDepartment of Physics and Astronomy, Queen Mary, University of London, 327 Mile End Road, London E1 4NS yy University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW September 1, 2015 Abstract CamCASP is a suite of programs designed to calculate molecular properties (multipoles and frequency- dependent polarizabilities) in single-site and distributed form, and interaction energies between pairs of molecules, and thence to construct atom–atom potentials. The CamCASP distribution also includes the programs Pfit, Casimir,Gdma 2.2, Cluster, and Process. Copyright c 2007–2014 Alston J. Misquitta and Anthony J. Stone Contents 1 Introduction 1 1.1 Authors . .1 1.2 Citations . .1 2 What’s new? 2 3 Outline of the capabilities of CamCASP and other programs 5 3.1 CamCASP limits . .7 4 Installation 7 4.1 Building CamCASP from source . .9 5 Using CamCASP 10 5.1 Workflows . 10 5.2 High-level scripts . 10 5.3 The runcamcasp.py script . 11 5.4 Low-level scripts . 13 6 Data conventions 13 7 CLUSTER: Detailed specification 14 7.1 Prologue . 15 7.2 Molecule definitions . 15 7.3 Geometry manipulations and other transformations . 16 7.4 Job specification . 18 7.5 Energy . 23 7.6 Crystal . 25 7.7 ORIENT ............................................... 26 7.8 Finally, . 29 8 Examples 29 8.1 A SAPT(DFT) calculation . 29 8.2 An example properties calculation . 30 8.3 Dispersion coefficients . 34 8.4 Using CLUSTER to obtain the dimer geometry . 36 9 CamCASP program specification 39 9.1 Global data .
    [Show full text]
  • The CECAM Electronic Structure Library and the Modular Software Development Paradigm
    The CECAM electronic structure library and the modular software development paradigm Cite as: J. Chem. Phys. 153, 024117 (2020); https://doi.org/10.1063/5.0012901 Submitted: 06 May 2020 . Accepted: 08 June 2020 . Published Online: 13 July 2020 Micael J. T. Oliveira , Nick Papior , Yann Pouillon , Volker Blum , Emilio Artacho , Damien Caliste , Fabiano Corsetti , Stefano de Gironcoli , Alin M. Elena , Alberto García , Víctor M. García-Suárez , Luigi Genovese , William P. Huhn , Georg Huhs , Sebastian Kokott , Emine Küçükbenli , Ask H. Larsen , Alfio Lazzaro , Irina V. Lebedeva , Yingzhou Li , David López- Durán , Pablo López-Tarifa , Martin Lüders , Miguel A. L. Marques , Jan Minar , Stephan Mohr , Arash A. Mostofi , Alan O’Cais , Mike C. Payne, Thomas Ruh, Daniel G. A. Smith , José M. Soler , David A. Strubbe , Nicolas Tancogne-Dejean , Dominic Tildesley, Marc Torrent , and Victor Wen-zhe Yu COLLECTIONS Paper published as part of the special topic on Electronic Structure Software Note: This article is part of the JCP Special Topic on Electronic Structure Software. This paper was selected as Featured ARTICLES YOU MAY BE INTERESTED IN Recent developments in the PySCF program package The Journal of Chemical Physics 153, 024109 (2020); https://doi.org/10.1063/5.0006074 An open-source coding paradigm for electronic structure calculations Scilight 2020, 291101 (2020); https://doi.org/10.1063/10.0001593 Siesta: Recent developments and applications The Journal of Chemical Physics 152, 204108 (2020); https://doi.org/10.1063/5.0005077 J. Chem. Phys. 153, 024117 (2020); https://doi.org/10.1063/5.0012901 153, 024117 © 2020 Author(s). The Journal ARTICLE of Chemical Physics scitation.org/journal/jcp The CECAM electronic structure library and the modular software development paradigm Cite as: J.
    [Show full text]
  • Accelerating Performance and Scalability with NVIDIA Gpus on HPC Applications
    Accelerating Performance and Scalability with NVIDIA GPUs on HPC Applications Pak Lui The HPC Advisory Council Update • World-wide HPC non-profit organization • ~425 member companies / universities / organizations • Bridges the gap between HPC usage and its potential • Provides best practices and a support/development center • Explores future technologies and future developments • Leading edge solutions and technology demonstrations 2 HPC Advisory Council Members 3 HPC Advisory Council Centers HPC ADVISORY COUNCIL CENTERS HPCAC HQ SWISS (CSCS) CHINA AUSTIN 4 HPC Advisory Council HPC Center Dell™ PowerEdge™ Dell PowerVault MD3420 HPE Apollo 6000 HPE ProLiant SL230s HPE Cluster Platform R730 GPU Dell PowerVault MD3460 10-node cluster Gen8 3000SL 36-node cluster 4-node cluster 16-node cluster InfiniBand Storage (Lustre) Dell™ PowerEdge™ C6145 Dell™ PowerEdge™ R815 Dell™ PowerEdge™ Dell™ PowerEdge™ M610 InfiniBand-based 6-node cluster 11-node cluster R720xd/R720 32-node GPU 38-node cluster Storage (Lustre) cluster Dell™ PowerEdge™ C6100 4-node cluster 4-node GPU cluster 4-node GPU cluster 5 Exploring All Platforms / Technologies X86, Power, GPU, FPGA and ARM based Platforms x86 Power GPU FPGA ARM 6 HPC Training • HPC Training Center – CPUs – GPUs – Interconnects – Clustering – Storage – Cables – Programming – Applications • Network of Experts – Ask the experts 7 University Award Program • University award program – Universities / individuals are encouraged to submit proposals for advanced research • Selected proposal will be provided with: – Exclusive computation time on the HPC Advisory Council’s Compute Center – Invitation to present in one of the HPC Advisory Council’s worldwide workshops – Publication of the research results on the HPC Advisory Council website • 2010 award winner is Dr.
    [Show full text]
  • Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C
    Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C. All rights reserved. Schrödinger, FirstDiscovery, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Prime, QSite, and QikProp are trademarks of Schrödinger, L.L.C. MacroModel is a registered trademark of Schrödinger, L.L.C. To the maximum extent permitted by applicable law, this publication is provided “as is” without warranty of any kind. This publication may contain trademarks of other companies. October 2003 Contents Chapter 1: Introduction.......................................................................................1 1.1 Conventions Used in This Manual.......................................................................2 1.2 Citing Jaguar in Publications ...............................................................................3 Chapter 2: The Maestro Graphical User Interface...........................................5 2.1 Starting Maestro...................................................................................................5 2.2 The Maestro Main Window .................................................................................7 2.3 Maestro Projects ..................................................................................................7 2.4 Building a Structure.............................................................................................9 2.5 Atom Selection ..................................................................................................10 2.6 Toolbar Controls ................................................................................................11
    [Show full text]
  • Thomas–Fermi–Dirac–Von Weizsäcker Models in Finite Systems Garnet Kin-Lic Chan, Aron J
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Caltech Authors - Main Thomas–Fermi–Dirac–von Weizsäcker models in finite systems Garnet Kin-Lic Chan, Aron J. Cohen, and Nicholas C. Handy Citation: 114, (2001); doi: 10.1063/1.1321308 View online: http://dx.doi.org/10.1063/1.1321308 View Table of Contents: http://aip.scitation.org/toc/jcp/114/2 Published by the American Institute of Physics JOURNAL OF CHEMICAL PHYSICS VOLUME 114, NUMBER 2 8 JANUARY 2001 Thomas–Fermi–Dirac–von Weizsa¨cker models in finite systems Garnet Kin-Lic Chan,a) Aron J. Cohen, and Nicholas C. Handy Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom ͑Received 7 June 2000; accepted 8 September 2000͒ To gain an understanding of the variational behavior of kinetic energy functionals, we perform a numerical study of the Thomas–Fermi–Dirac–von Weizsa¨cker theory in finite systems. A general purpose Gaussian-based code is constructed to perform energy and geometry optimizations on polyatomic systems to high accuracy. We carry out benchmark studies on atomic and diatomic systems. Our results indicate that the Thomas–Fermi–Dirac–von Weizsa¨cker theory can give an approximate description of matter, with atomic energies, binding energies, and bond lengths of the correct order of magnitude, though not to the accuracy required of a qualitative chemical theory. We discuss the implications for the development of new kinetic functionals. © 2001 American Institute of Physics. ͓DOI: 10.1063/1.1321308͔ I. INTRODUCTION
    [Show full text]
  • Quantum Chemical Calculations of NMR Parameters
    Quantum Chemical Calculations of NMR Parameters Tatyana Polenova University of Delaware Newark, DE Winter School on Biomolecular NMR January 20-25, 2008 Stowe, Vermont OUTLINE INTRODUCTION Relating NMR parameters to geometric and electronic structure Classical calculations of EFG tensors Molecular properties from quantum chemical calculations Quantum chemistry methods DENSITY FUNCTIONAL THEORY FOR CALCULATIONS OF NMR PARAMETERS Introduction to DFT Software Practical examples Tutorial RELATING NMR OBSERVABLES TO MOLECULAR STRUCTURE NMR Spectrum NMR Parameters Local geometry Chemical structure (reactivity) I. Calculation of experimental NMR parameters Find unique solution to CQ, Q, , , , , II. Theoretical prediction of fine structure constants from molecular geometry Classical electrostatic model (EFG)- only in simple ionic compounds Quantum mechanical calculations (Density Functional Theory) (EFG, CSA) ELECTRIC FIELD GRADIENT (EFG) TENSOR: POINT CHARGE MODEL EFG TENSOR IS DETERMINED BY THE COMBINED ELECTRONIC AND NUCLEAR WAVEFUNCTION, NO ANALYTICAL EXPRESSION IN THE GENERAL CASE THE SIMPLEST APPROXIMATION: CLASSICAL POINT CHARGE MODEL n Zie 4 V2,k = 3 Y2,k ()i,i i=1 di 5 ATOMS CONTRIBUTING TO THE EFG TENSOR ARE TREATED AS POINT CHARGES, THE RESULTING EFG TENSOR IS THE SUM WITH RESPECT TO ALL ATOMS VERY CRUDE MODEL, WORKS QUANTITATIVELY ONLY IN SIMPLEST IONIC SYSTEMS, BUT YIELDS QUALITATIVE TRENDS AND GENERAL UNDERSTANDING OF THE SYMMETRY AND MAGNITUDE OF THE EXPECTED TENSOR ELECTRIC FIELD GRADIENT (EFG) TENSOR: POINT CHARGE MODEL n Zie 4 V2,k = 3 Y2,k ()i,i i=1 di 5 Ze V = ; V = 0; V = 0 2,0 d 3 2,±1 2,±2 2Ze V = ; V = 0; V = 0 2,0 d 3 2,±1 2,±2 3 Ze V = ; V = 0; V = 0 2,0 2 d 3 2,±1 2,±2 V2,0 = 0; V2,±1 = 0; V2,±2 = 0 MOLECULAR PROPERTIES FROM QUANTUM CHEMICAL CALCULATIONS H = E See for example M.
    [Show full text]
  • Use of Mo”Ller-Plesset Perturbation Theory in Molecular Calculations: Spectroscopic Constants of First Row Diatomic Molecules
    JOURNAL OF CHEMICAL PHYSICS VOLUME 108, NUMBER 12 22 MARCH 1998 Use of Mo”ller-Plesset perturbation theory in molecular calculations: Spectroscopic constants of first row diatomic molecules Thom H. Dunning, Jr. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 Kirk A. Peterson Department of Chemistry, Washington State University and the Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 ~Received 9 December 1997; accepted 17 December 1997! The convergence of Mo”ller–Plesset perturbation expansions ~MP2–MP4/MP5! for the spectroscopic constants of a selected set of diatomic molecules ~BH, CH, HF, N2, CO, and F2! has been investigated. It was found that the second-order perturbation contributions to the spectroscopic constants are strongly dependent on basis set, more so for HF and CO than for BH. The MP5 contributions for HF were essentially zero for the cc-pVDZ basis set, but increased significantly with basis set illustrating the difficulty of using small basis sets as benchmarks for correlated calculations. The convergence behavior of the exact Mo”ller–Plesset perturbation expansions were investigated using estimates of the complete basis set limits obtained using large correlation consistent basis sets. For BH and CH, the perturbation expansions of the spectroscopic constants converge monotonically toward the experimental values, while for HF, N2, CO, and F2, the expansions oscillate about the experimental values. The perturbation expansions are, in general, only slowly converging and, for HF, N2, CO, and F2, appear to be far from convergence at MP4. In fact, for HF, N2, and CO, the errors in the calculated spectroscopic constants for the MP4 method are larger than those for the MP2 method ~the only exception is De!.
    [Show full text]