An Overview on the Libxc Library of Density Functional Approximations
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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. -
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. -
Living at the Top of the Top500: Myopia from Being at the Bleeding Edge
Living at the Top of the Top500: Myopia from Being at the Bleeding Edge Bronson Messer Oak Ridge Leadership Computing Facility & Theoretical Astrophysics Group Oak Ridge National Laboratory Department of Physics & Astronomy University of Tennessee Friday, July 1, 2011 Outline • Statements made without proof • OLCF’s Center for Accelerated Application Readiness • Speculations on task-based approaches for multiphysics applications in astrophysics (e.g. blowing up stars) 2 Friday, July 1, 2011 Riffing on Hank’s fable... 3 Friday, July 1, 2011 The Effects of Moore’s Law and Slacking 1 on Large Computations Chris Gottbrath, Jeremy Bailin, Casey Meakin, Todd Thompson, J.J. Charfman Steward Observatory, University of Arizona Abstract We show that, in the context of Moore’s Law, overall productivity can be increased for large enough computations by ‘slacking’orwaiting for some period of time before purchasing a computer and beginning the calculation. According to Moore’s Law, the computational power availableataparticular price doubles every 18 months. Therefore it is conceivable that for sufficiently large numerical calculations and fixed budgets, computing power will improve quickly enough that the calculation will finish faster if we wait until the available computing power is sufficiently better and start the calculation then. The Effects of Moore’s Law and Slacking 1Figureon Large 1: Computations Chris Gottbrath, Jeremy Bailin, Casey Meakin, Todd Thompson, J.J. Charfman 1 The Effects of Moore’sSteward Observatory, Law and University Slacking of Arizona on Large astro-ph/9912202 Computations Abstract Chris Gottbrath, Jeremy Bailin, Casey Meakin, Todd Thompson, We show that, in the context of Moore’s Law, overall productivity can be increased forJ.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. -
A Deep Dive Into ASUS Solutions
From DataCenters to Supercomputers A Deep Dive Into ASUS Solutions Christopher Liang / Server/WS Product manager ASUS is a global technology leader in the Who is ASUS? digital era. We focus on the mastery of technological innovation and design perfection. We’re very critical of our own work when it comes to only delivering consumers our very best. ASUS Worldwide ASUS has a strong presence in over 50 countries, with offices in Europe, Asia, Australia and New Zealand, the Americas, and South Africa. • > 11,000 employees worldwide (source : HR dept ) • > 3,100 R&D employees (source : HR dept ) • 900+ support centers worldwide (source : TSD dept ) Business Update 11 (estimated) ASUS closed 2011 on a high, with revenues around US$11.8 billion. As of September 2010, the brand is estimated to be worth US$1.285 billion*. 10.1 *2010 Top Taiwan Global Brand (Interbrand) ** Due to Q1-Q2 worldwide economy crisis 8.21 7.66** 6.99 5.087 3.783 3.010 2.081 Revenue US$ (billions) Leader in Performance and Reliability #1 Motherboard Since 1989, ASUS has shipped over 420 million motherboards. Placed end to end, they can form a chain long enough to circumnavigate the globe more than three times. #1 Windows-based Desktop PC Reliability Ranked most reliable Window’s based PC brand 2 years in a row by PCWorld. The 2011 PCWorld Reliability and Service survey was conducted with 63,000 PCWorld readers. 1. Though design thinking to provide cutting Why ASUS ? edge SPEC 2. BIOS – superior performance through increased functionality and upgradeability 3. -
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. -
Density-Functional Theory of Atoms and Molecules • W
3.320: Lecture 7 (Feb 24 2005) DENSITYDENSITY--FUNCTIONALFUNCTIONAL THEORY,THEORY, ANDAND DENSITYDENSITY--FUNCTIONALFUNCTIONAL PRACTICEPRACTICE Feb 24 2005 3.320 Atomistic Modeling of Materials -- Gerbrand Ceder and Nicola Marzari Hartree-Fock Equations r rr ϕϕαβ()rr11() L ϕν()r1 ϕϕ()rrr ()rrϕ()r rr r 1 αβ22L ν2 ψ (,rr12,...,rn )= n! MMOM r rr ϕϕαβ()rrnn()L ϕν()rn ⎡⎤1 2 r r r ⎢⎥−∇iI+∑VR()−riϕλ ()ri + ⎣⎦2 I ⎡⎤1 ϕϕ* ()rrrr()drrϕ ()rr − ⎢⎥∑ ∫ µµjjr r jλ i ⎣⎦⎢⎥µ ||rrji− ⎡⎤1 ϕϕ* ()rdrrϕϕ()rrr r(rr)= ε(r) ∑ ⎢⎥∫ µµj rrλ j j i λ i µ ⎣⎦⎢⎥||rrj − i Feb 24 2005 3.320 Atomistic Modeling of Materials -- Gerbrand Ceder and Nicola Marzari Image removed for copyright reasons. Screenshot of online article. “Nobel Focus: Chemistry by Computer.” Physical Review Focus, 21 October 1998. http://focus.aps.org/story/v2/st19 Feb 24 2005 3.320 Atomistic Modeling of Materials -- Gerbrand Ceder and Nicola Marzari The Thomas-Fermi approach • Let’s try to find out an expression for the energy as a function of the charge density • E=kinetic+external+el.-el. • Kinetic is the tricky term: how do we get the curvature of a wavefunction from the charge density ? • Answer: local density approximation Feb 24 2005 3.320 Atomistic Modeling of Materials -- Gerbrand Ceder and Nicola Marzari Local Density Approximation • We take the kinetic energy density at every point to correspond to the kinetic energy density of the homogenous electron gas 5 T(rr) = Aρ 3 (rr) 5 1 ρ(rr)ρ(rr ) E [ρ] = A ρ 3 (rr)drr + ρ(rr)v (rr)drr + 1 2 drrdrr Th−Fe ∫ ∫ ext ∫∫ r r 1 2 2 | r1 − r2 | Feb 24 2005 -
ADP-Ribose) Polymerase-1 Catalytic Pocket Using Autogrow4, a Genetic Algorithm for De Novo Design
Targeting the Poly (ADP-Ribose) Polymerase-1 Catalytic Pocket Using AutoGrow4, a Genetic Algorithm for De Novo Design by Jacob Oscar Spiegel Bachelor of Engineering in Biomedical Engineering, State University of New York at Stony Brook, 2013 Submitted to the Graduate Faculty of the Dietrich School of Arts and Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2020 Committee Page UNIVERSITY OF PITTSBURGH DIETRICH SCHOOL OF ARTS AND SCIENCES This dissertation was presented by Jacob Oscar Spiegel It was defended on March 10, 2020 and approved by Dr. Andrew VanDemark, Associate Professor, Department of Biological Sciences Dr. Jeffrey Lawrence, Professor and Chair, Department of Biological Sciences Dr. Bennett Van Houten, Professor, Department of Pharmacology and Chemical Biology Dissertation Director: Dr. Jacob Durrant, Assistant Professor, Department of Biological Sciences ii Copyright © by Jacob Oscar Spiegel 2020 iii Targeting the Poly (ADP-Ribose) Polymerase-1 Catalytic Pocket Using AutoGrow4, a Genetic Algorithm for De Novo Design Jacob Oscar Spiegel, Ph.D. University of Pittsburgh, 2020 AutoGrow4 is a free and open-source program for de novo drug design that uses a genetic algorithm (GA) to create novel predicted small-molecule ligands for a given protein target without the constraints of a finite, pre-defined virtual library. By leveraging recent computational and cheminformatic advancements, AutoGrow4 is faster, more stable, and more modular than previous versions. Features such as docking-software compatibility, chemical filters, multithreading options, and selection methods have been expanded to support a wide range of user needs. This dissertation will cover the development and validation of AutoGrow4, as well as its application to poly (ADP-ribose) polymerase-1 (PARP-1). -
Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8- Oxoguanine Glycosylase, Hogg1
Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8- Oxoguanine Glycosylase, hOGG1 The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Crenshaw, Charisse M., Kwangho Nam, Kimberly Oo, Peter S. Kutchukian, Brian R. Bowman, Martin Karplus, and Gregory L. Verdine. 2012. “Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, HOGG1.” Journal of Biological Chemistry287 (30): 24916–28. https:// doi.org/10.1074/jbc.M111.316497. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:41511240 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 30, pp. 24916–24928, July 20, 2012 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1*□S Received for publication, October 25, 2011, and in revised form, March 17, 2012 Published, JBC Papers in Press, April 16, 2012, DOI 10.1074/jbc.M111.316497 Charisse M. Crenshaw‡¶, Kwangho Nam§¶, Kimberly Oo§, Peter S. Kutchukian§¶, Brian R. Bowman§¶, Martin Karplus§ʈ, and Gregory L. Verdine§¶**1 From the Departments -
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.