Kohn-Sham Scheme, Band Structure and Optical Spectra
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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. -
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. -
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. -
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. -
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. -
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. -
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 . -
The Impact of Density Functional Theory on Materials Research
www.mrs.org/bulletin functional. This functional (i.e., a function whose argument is another function) de- scribes the complex kinetic and energetic interactions of an electron with other elec- Toward Computational trons. Although the form of this functional that would make the reformulation of the many-body Schrödinger equation exact is Materials Design: unknown, approximate functionals have proven highly successful in describing many material properties. Efficient algorithms devised for solving The Impact of the Kohn–Sham equations have been imple- mented in increasingly sophisticated codes, tremendously boosting the application of DFT methods. New doors are opening to in- Density Functional novative research on materials across phys- ics, chemistry, materials science, surface science, and nanotechnology, and extend- ing even to earth sciences and molecular Theory on Materials biology. The impact of this fascinating de- velopment has not been restricted to aca- demia, as DFT techniques also find application in many different areas of in- Research dustrial research. The development is so fast that many current applications could Jürgen Hafner, Christopher Wolverton, and not have been realized three years ago and were hardly dreamed of five years ago. Gerbrand Ceder, Guest Editors The articles collected in this issue of MRS Bulletin present a few of these suc- cess stories. However, even if the compu- Abstract tational tools necessary for performing The development of modern materials science has led to a growing need to complex quantum-mechanical calcula- tions relevant to real materials problems understand the phenomena determining the properties of materials and processes on are now readily available, designing a an atomistic level. -
Practice: Quantum ESPRESSO I
MODULE 2: QUANTUM MECHANICS Practice: Quantum ESPRESSO I. What is Quantum ESPRESSO? 2 DFT software PW-DFT, PP, US-PP, PAW FREE http://www.quantum-espresso.org PW-DFT, PP, PAW FREE http://www.abinit.org DFT PW, PP, Car-Parrinello FREE http://www.cpmd.org DFT PP, US-PP, PAW $3000 [moderate accuracy, fast] http://www.vasp.at DFT full-potential linearized augmented $500 plane-wave (FLAPW) [accurate, slow] http://www.wien2k.at Hartree-Fock, higher order correlated $3000 electron approaches http://www.gaussian.com 3 Quantum ESPRESSO 4 Quantum ESPRESSO Quantum ESPRESSO is an integrated suite of Open- Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. Core set of codes, plugins for more advanced tasks and third party packages Open initiative coordinated by the Quantum ESPRESSO Foundation, across Italy. Contributed to by developers across the world Regular hands-on workshops in Trieste, Italy Open-source code: FREE (unlike VASP...) 5 Performance Small jobs (a few atoms) can be run on single node Includes determining convergence parameters, lattice constants Can use OpenMP parallelization on multicore machines Large jobs (~10’s to ~100’s atoms) can run in parallel using MPI to 1000’s of cores Includes molecular dynamics, large geometry relaxation, phonons Parallel performance tied to BLAS/LAPACK (linear algebra routines) and 3D FFT (fast Fourier transform) New GPU-enabled version available 6 Usability Documented online: -
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. -
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. -
Dr. David Danovich
Dr. David Danovich ! 14 January 2021 (h-index: 34; 124 publications) Personal Information Name: Contact information Danovich David Private: Nissan Harpaz st., 4/9, Jerusalem, Date of Birth: 9371643 Israel June 29, 1959 Mobile: +972-54-4768669 E-mail: [email protected] Place of Birth: Irkutsk, USSR Work: Institute of Chemistry, The Hebrew Citizenship: University, Edmond Safra Campus, Israeli Givat Ram, 9190401 Jerusalem, Israel Marital status: Phone: +972-2-6586934 Married +2 FAX: +972-2-6584033 E-mail: [email protected] Current position 1992- present: Senior computational chemist and scientific programmer in the Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel Scientific skills Very experienced scientific researcher with demonstrated ability to implement ab initio molecular electronic structure and valence bond calculations for obtaining insights into physical and chemical properties of molecules and materials. Extensive expertise in implementation of Molecular Orbital Theory based on ab initio methods such as Hartree-Fock theory (HF), Density Functional Theory (DFT), Moller-Plesset Perturbation theory (MP2-MP5), Couple Cluster theories [CCST(T)], Complete Active Space (CAS, CASPT2) theories, Multireference Configuration Interaction (MRCI) theory and modern ab initio valence bond theory (VBT) methods such as Valence Bond Self Consistent Field theory (VBSCF), Breathing Orbital Valence Bond theory (BOVB) and its variants (like D-BOVB, S-BOVB and SD-BOVB), Valence Bond Configuration Interaction theory (VBCI), Valence Bond Perturbation theory (VBPT). Language skills Advanced Conversational English, Russian Hebrew Academic background 1. Undergraduate studies, 1978-1982 Master of Science in Physics, June 1982 Irkutsk State University, USSR Dr. David Danovich ! 2. Graduate studies, 1984-1989 Ph.