A Review on Non-Relativistic, Fully Numerical Electronic Structure Calculations on Atoms and Diatomic Molecules
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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. -
1 9729/01/TJC Prelim/2018 [Turn Over
1 CHEMISTRY 9729/01 Paper 1 Multiple Choice 15th September 2018 1 hour Additional materials: Multiple Choice Answer Sheet Data Booklet READ THESE INSTRUCTIONS FIRST Write in soft pencil. Do not use staples, paper clips, glue or correction fluid. Write your name and Civics Group Write and shade your index number There are thirty questions on this paper. Answer all questions. For each question there are four possible answers A, B, C and D. Choose the one you consider correct and record your choice in soft pencil on the separate Answer Sheet. Read the instructions on the Answer Sheet very carefully. Each correct answer will score one mark. A mark will not be deducted for a wrong answer. Any rough working should be done in this booklet. The use of an approved scientific calculator is expected, where appropriate. This document consists of 13 printed pages. 9729/01/TJC Prelim/2018 [Turn Over 2 Section A For each question there are four possible answers, A, B, C and D. Choose the one you consider correct and record your choice in soft pencil on the separate Answer Sheet (OMS). 1 Some isotopes are unstable and undergo nuclear (radioactive) reactions. In one type of reaction, an unstable nucleus assimilates an electron from an inner orbital of its electron cloud. The net effect is the conversion of a proton and an electron into a neutron. Which of the following describes this type of reaction? A 11C 12C B 111I 111Te C 76Br 75Br D 76Kr 75Br 2 Sodium hydrogencarbonate can be prepared from sodium sulfate by a three-step process: Na2SO4(s) + 4C(s) -
Inorganic Chemistry
AS-Level INORGANIC CHEMISTRY Q1 A mixture of the oxides of two elements of the third period is dissolved in water. The solution is approximately neutral. What could be the constituents of the mixture? A Al2O3 and MgO B Na2O and MgO C Na2O and P4O10 D SO3 and P4O10 Q2 Aluminium chloride catalyses certain reactions by forming carbocations (carbonium ions) with chloroalkanes as shown. Which property makes this reaction possible? A AlCl3 is a covalent molecule. B AlCl3 exists as the dimer Al2Cl6 in the vapour. C The aluminium atom in AlCl3 has an incomplete octet of electrons. D The chlorine atom in RCl has a vacant p orbital. Q3 What are the products of the thermal decomposition of magnesium nitrate? A magnesium nitride and oxygen B magnesium oxide and nitrogen C magnesium oxide, nitrogen and oxygen D magnesium oxide, nitrogen dioxide and oxygen Q4 Chlorine compounds show oxidation states ranging from –1 to +7. What are the reagent(s) and conditions necessary for the oxidation of elemental chlorine into a compound containing chlorine in the +5 oxidation state? A AgNO3(aq) followed by NH3(aq) at room temperature B concentrated H2SO4 at room temperature C cold dilute NaOH(aq) D hot concentrated NaOH(aq) Q5 Which gaseous hydride most readily decomposes into its elements on contact with a hot glass rod? A ammonia B hydrogen chloride C hydrogen iodide D steam Q6 Which reagent, when mixed and heated with ammonium sulphate, liberates ammonia? A aqueous bromine B dilute hydrochloric acid C limewater D acidified potassium dichromate(VI) Q7 Which pollutant -
Core Software Blocks in Quantum Chemistry: Tensors and Integrals Workshop Program
Core Software Blocks in Quantum Chemistry: Tensors and Integrals Workshop Program Start: Sunday, May 7, 2017 afternoon. Resort check-in at 4:00 pm. Finish: Wednesday, May 10, noon Lectures are in Scripps, posters are in Heather. Sunday 6:00-7:00: Dinner 7:30-9:00 Opening session 7:30–7:45 Anna Krylov (USC): “MolSSI and some lessons from previous workshop, goals of the workshop” 7:45-8:00 Theresa Windus (Iowa): “Mission of the Molecular Science Consortium” 8:00-9:00 Introduction of participants: 2 min presentation, can have one slide (send in advance) 9:00-10:30 Reception and posters Monday Breakfast: 7:30-9:00 9:00-11:45 Session I: Overview of tensors projects and current developments (moderator Daniel Smith) 9:00-9:10 Daniel Smith (MolSSI): Overview of tensor projects 9:10-9:30 Evgeny Epifanovsky (Q-Chem): Overview of Libtensor 9:30-9:50 Ed Solomonik: "An Overview of Cyclops Tensor Framework" 9:50-10:10 Ed Valeev (VT): "TiledArray: A composable massively parallel block-sparse tensor framework" 10:10-10:30 Coffee break 10:30-10:50 Devin Matthews (UT Austin): "Aquarius and TBLIS: Orthogonal Axes in Multilinear Algebra" 10:50-11:10 Karol Kowalskii (PNNL, NWChem): "NWChem, NWChemEX , and new tensor algebra systems for many-body methods" 11:10-11:30 Peng Chong (VT): "Many-body toolkit in re-designed Massively Parallel Quantum Chemistry package" 11:30-11:55 Moderated discussion: "What problems are we *still* solving?” Lunch: 12:00-1:00 Free time for unstructured discussions 5:00 Posters (coffee/tea) Dinner: 6-7:00 7:15-9:00 Session II: Computer -
WO 2016/074683 Al 19 May 2016 (19.05.2016) W P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/074683 Al 19 May 2016 (19.05.2016) W P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12N 15/10 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/DK20 15/050343 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 11 November 2015 ( 11. 1 1.2015) KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (25) Filing Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (26) Publication Language: English SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: PA 2014 00655 11 November 2014 ( 11. 1 1.2014) DK (84) Designated States (unless otherwise indicated, for every 62/077,933 11 November 2014 ( 11. 11.2014) US kind of regional protection available): ARIPO (BW, GH, 62/202,3 18 7 August 2015 (07.08.2015) US GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, (71) Applicant: LUNDORF PEDERSEN MATERIALS APS TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, [DK/DK]; Nordvej 16 B, Himmelev, DK-4000 Roskilde DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, (DK). -
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. -
Trends in Atomistic Simulation Software Usage [1.3]
A LiveCoMS Perpetual Review Trends in atomistic simulation software usage [1.3] Leopold Talirz1,2,3*, Luca M. Ghiringhelli4, Berend Smit1,3 1Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingenierie Chimiques, Valais, École Polytechnique Fédérale de Lausanne, CH-1951 Sion, Switzerland; 2Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l’Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 3National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 4The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany This LiveCoMS document is Abstract Driven by the unprecedented computational power available to scientific research, the maintained online on GitHub at https: use of computers in solid-state physics, chemistry and materials science has been on a continuous //github.com/ltalirz/ rise. This review focuses on the software used for the simulation of matter at the atomic scale. We livecoms-atomistic-software; provide a comprehensive overview of major codes in the field, and analyze how citations to these to provide feedback, suggestions, or help codes in the academic literature have evolved since 2010. An interactive version of the underlying improve it, please visit the data set is available at https://atomistic.software. GitHub repository and participate via the issue tracker. This version dated August *For correspondence: 30, 2021 [email protected] (LT) 1 Introduction Gaussian [2], were already released in the 1970s, followed Scientists today have unprecedented access to computa- by force-field codes, such as GROMOS [3], and periodic tional power. -
Lawrence Berkeley National Laboratory Recent Work
Lawrence Berkeley National Laboratory Recent Work Title From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape. Permalink https://escholarship.org/uc/item/4sm897jh Journal Chemical reviews, 121(8) ISSN 0009-2665 Authors Kowalski, Karol Bair, Raymond Bauman, Nicholas P et al. Publication Date 2021-04-01 DOI 10.1021/acs.chemrev.0c00998 Peer reviewed eScholarship.org Powered by the California Digital Library University of California From NWChem to NWChemEx: Evolving with the computational chemistry landscape Karol Kowalski,y Raymond Bair,z Nicholas P. Bauman,y Jeffery S. Boschen,{ Eric J. Bylaska,y Jeff Daily,y Wibe A. de Jong,x Thom Dunning, Jr,y Niranjan Govind,y Robert J. Harrison,k Murat Keçeli,z Kristopher Keipert,? Sriram Krishnamoorthy,y Suraj Kumar,y Erdal Mutlu,y Bruce Palmer,y Ajay Panyala,y Bo Peng,y Ryan M. Richard,{ T. P. Straatsma,# Peter Sushko,y Edward F. Valeev,@ Marat Valiev,y Hubertus J. J. van Dam,4 Jonathan M. Waldrop,{ David B. Williams-Young,x Chao Yang,x Marcin Zalewski,y and Theresa L. Windus*,r yPacific Northwest National Laboratory, Richland, WA 99352 zArgonne National Laboratory, Lemont, IL 60439 {Ames Laboratory, Ames, IA 50011 xLawrence Berkeley National Laboratory, Berkeley, 94720 kInstitute for Advanced Computational Science, Stony Brook University, Stony Brook, NY 11794 ?NVIDIA Inc, previously Argonne National Laboratory, Lemont, IL 60439 #National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373 @Department of Chemistry, Virginia Tech, Blacksburg, VA 24061 4Brookhaven National Laboratory, Upton, NY 11973 rDepartment of Chemistry, Iowa State University and Ames Laboratory, Ames, IA 50011 E-mail: [email protected] 1 Abstract Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. -
Openmolcas: from Source Code to Insight Ignacio Fdez
Article Cite This: J. Chem. Theory Comput. XXXX, XXX, XXX−XXX pubs.acs.org/JCTC OpenMolcas: From Source Code to Insight Ignacio Fdez. Galvan,́ 1,2 Morgane Vacher,1 Ali Alavi,3 Celestino Angeli,4 Francesco Aquilante,5 Jochen Autschbach,6 Jie J. Bao,7 Sergey I. Bokarev,8 Nikolay A. Bogdanov,3 Rebecca K. Carlson,7,9 Liviu F. Chibotaru,10 Joel Creutzberg,11,12 Nike Dattani,13 Mickael̈ G. Delcey,1 Sijia S. Dong,7,14 Andreas Dreuw,15 Leon Freitag,16 Luis Manuel Frutos,17 Laura Gagliardi,7 Fredé rić Gendron,6 Angelo Giussani,18,19 Leticia Gonzalez,́ 20 Gilbert Grell,8 Meiyuan Guo,1,21 Chad E. Hoyer,7,22 Marcus Johansson,12 Sebastian Keller,16 Stefan Knecht,16 Goran Kovacevič ,́ 23 Erik Kallman,̈ 1 Giovanni Li Manni,3 Marcus Lundberg,1 Yingjin Ma,16 Sebastian Mai,20 Joaõ Pedro Malhado,24 Per Åke Malmqvist,12 Philipp Marquetand,20 Stefanie A. Mewes,15,25 Jesper Norell,11 Massimo Olivucci,26,27,28 Markus Oppel,20 Quan Manh Phung,29 Kristine Pierloot,29 Felix Plasser,30 Markus Reiher,16 Andrew M. Sand,7,31 Igor Schapiro,32 Prachi Sharma,7 Christopher J. Stein,16,33 Lasse Kragh Sørensen,1,34 Donald G. Truhlar,7 Mihkel Ugandi,1,35 Liviu Ungur,36 Alessio Valentini,37 Steven Vancoillie,12 Valera Veryazov,12 Oskar Weser,3 Tomasz A. Wesołowski,5 Per-Olof Widmark,12 Sebastian Wouters,38 Alexander Zech,5 J. Patrick Zobel,12 and Roland Lindh*,2,39 1Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. -
Arxiv:2006.14956V1 [Physics.Comp-Ph]
NECI: N-Electron Configuration Interaction with an emphasis on state-of-the-art stochastic methods Kai Guther,1, a) Robert J. Anderson,2 Nick S. Blunt,3 Nikolay A. Bogdanov,1 Deidre Cleland,4 Nike Dattani,5 Werner Dobrautz,1 Khaldoon Ghanem,1 Peter Jeszenski,6 Niklas Liebermann,1 Giovanni Li Manni,1 Alexander Y. Lozovoi,1 Hongjun Luo,1 Dongxia Ma,1 Florian Merz,7 Catherine Overy,3 Markus Rampp,8 Pradipta Kumar Samanta,1 Lauretta R. Schwarz,1, 3 James J. Shepherd,9 Simon D. Smart,3 Eugenio Vitale,1 Oskar Weser,1, 2 George H. Booth,2 and Ali Alavi1,3, b) 1)Max Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart, Germany 2)Department of Physics, King’s College London, Strand, London WC2R 2LS, United Kingdom 3)Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom 4)CSIRO Data61, Docklands VIC 3008, Australia 5)Department of Electrical and Computer Engineering, University of Waterloo, 200 University Avenue, Waterloo, Canada 6)Centre for Theoretical Chemistry and Physics, NZ Institute for Advanced Study, Massey University, New Zealand arXiv:2006.14956v1 [physics.comp-ph] 26 Jun 2020 7)Lenovo HPC&AI Innovation Center, Meitnerstr. 9, 70563 Stuttgart 8)Max Planck Computing and Data Facility (MPCDF), Gießenbachstr. 2, 85748 Garching, Germany 9)Department of Chemistry & Informatics Institute, University of Iowa (Dated: 29 June 2020) 1 We present NECI, a state-of-the-art implementation of the Full Configuration Inter- action Quantum Monte Carlo algorithm, a method based on a stochastic application of the Hamiltonian matrix on a sparse sampling of the wave function. -
Characterization of At- Species in Simple and Biological Media by High Performance Anion Exchange Chromatography Coupled to Gamma Detector
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by HAL-Univ-Nantes Characterization of At- species in simple and biological media by high performance anion exchange chromatography coupled to gamma detector. A. Sabati´e-Gogova, Julie Champion, Sandrine Huclier, N. Michel, F. Pottier, N. Galland, Z. Asfari, M. Ch´erel,Gilles Montavon To cite this version: A. Sabati´e-Gogova, Julie Champion, Sandrine Huclier, N. Michel, F. Pottier, et al.. Charac- terization of At- species in simple and biological media by high performance anion exchange chromatography coupled to gamma detector.. Analytica Chimica Acta, Elsevier Masson, 2012, 721, pp.182. <10.1016/j.aca.2012.01.052>. <in2p3-00681129> HAL Id: in2p3-00681129 http://hal.in2p3.fr/in2p3-00681129 Submitted on 20 Mar 2012 HAL is a multi-disciplinary open access L'archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destin´eeau d´ep^otet `ala diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publi´esou non, lished or not. The documents may come from ´emanant des ´etablissements d'enseignement et de teaching and research institutions in France or recherche fran¸caisou ´etrangers,des laboratoires abroad, or from public or private research centers. publics ou priv´es. 1 Characterization of At- species in simple and biological media by high performance 2 anion exchange chromatography coupled to gamma detector. 3 4 5 A. Sabatié-Gogovaa, J. Championa, S. Hucliera, N. Michela, F. Pottiera, N. Gallandb, Z. 6 Asfaric, M. Chéreld, G. Montavona* 7 8 9 a Laboratoire SUBATECH, UMR CNRS 6457 IN2P3 Ecole des Mines de Nantes, 4 rue A. -
Efficient Open-Source Implementations of Linear-Scaling
Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees Maximilian Scheurer,∗,y,x Peter Reinholdt,∗,z,x Jógvan Magnus Haugaard Olsen,{ Andreas Dreuw,y and Jacob Kongstedz yInterdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany zDepartment of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark {DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark xContributed equally to this work E-mail: [email protected]; [email protected] Abstract We present open-source implementations of the linear-scaling Fast Multipole Method (FMM) within the Polarizable Embedding (PE) model for efficient treatment of large polarizable environments in computational spectroscopy simulations. The implementa- tions are tested for accuracy, efficiency, and usability on model systems as well as more realistic biomolecular systems. We explain how FMM parameters affect the calculation of molecular properties and show that PE calculations employing FMM can be carried out in a black-box manner. The efficiency of the linear-scaling approach is demonstrated by simulating the UV/Vis spectrum of a chromophore in an environment of more than 1 one million polarizable sites. Our implementations are interfaced to several open-source quantum chemistry programs, making computational spectroscopy simulations within the PE model and FMM available to a large variety of methods and a broad user base. 1 Introduction