Analytic MR-CISD and MR-AQCC Gradients and MR-AQCC-LRT for Excited States, GUGA Spin–Orbit CI and Parallel CI Density¤
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The Molecular Sciences Software Institute
The Molecular Sciences Software Institute T. Daniel Crawford, Cecilia Clementi, Robert Harrison, Teresa Head-Gordon, Shantenu Jha*, Anna Krylov, Vijay Pande, and Theresa Windus http://molssi.org S2I2 HEP/CS Workshop at NCSA/UIUC 07 Dec, 2016 1 Outline • Space and Scope of Computational Molecular Sciences. • “State of the art and practice” • Intellectual drivers • Conceptualization Phase: Identifying the community and needs • Bio-molecular Simulations (BMS) Conceptualization • Quantum Mechanics/Chemistry (QM) Conceptualization • Execution Phase. • Structure and Governance Model • Resource Distribution • Work Plan 2 The Molecular Sciences Software Institute (MolSSI) • New project (as of August 1st, 2016) funded by the National Science Foundation. • Collaborative effort by Virginia Tech, Rice U., Stony Brook U., U.C. Berkeley, Stanford U., Rutgers U., U. Southern California, and Iowa State U. • Total budget of $19.42M for five years, potentially renewable to ten years. • Joint support from numerous NSF divisions: Advanced Cyberinfrastructure (ACI), Chemistry (CHE), Division of Materials Research (DMR), Office of Multidisciplinary Activities (OMA) • Designed to serve and enhance the software development efforts of the broad field of computational molecular science. 3 Computational Molecular Sciences (CMS) • The history of CMS – the sub-fields of quantum chemistry, computational materials science, and biomolecular simulation – reaches back decades to the genesis of computational science. • CMS is now a “full partner with experiment”. • For an impressive array of chemical, biochemical, and materials challenges, our community has developed simulations and models that directly impact: • Development of new chiral drugs; • Elucidation of the functionalities of biological macromolecules; • Development of more advanced materials for solar-energy storage, technology for CO2 sequestration, etc. -
SCF and CI Studies on Ground State of Water Molecule
Ab initio SCF and CI studies on the ground state of the water molecule. II. Potential energy and property surfaces Bruce J. Rosenberg, Walter C. Ermler, and Isaiah Shavitt Citation: J. Chem. Phys. 65, 4072 (1976); doi: 10.1063/1.432861 View online: http://dx.doi.org/10.1063/1.432861 View Table of Contents: http://jcp.aip.org/resource/1/JCPSA6/v65/i10 Published by the American Institute of Physics. Additional information on J. Chem. Phys. Journal Homepage: http://jcp.aip.org/ Journal Information: http://jcp.aip.org/about/about_the_journal Top downloads: http://jcp.aip.org/features/most_downloaded Information for Authors: http://jcp.aip.org/authors Downloaded 29 Apr 2013 to 134.76.213.205. This article is copyrighted as indicated in the abstract. Reuse of AIP content is subject to the terms at: http://jcp.aip.org/about/rights_and_permissions Ab initio SCF and CI studies on the ground state of the water molecule. II. Potential energy and property surfaces Bruce J. Rosenberg* and Walter C. Ermlert Department of Chemistry. The Ohio State University. Columbus. Ohio 43210 Isaiah Shavitt Department of Chemistry. The Ohio State University. Columbus. Ohio 43210 and Battelle Memorial Institute. Columbus. Ohio 43201 (Received 29 June 1976) Self-consistent field and configuration interaction calculations for the energy and one-electron properties of the ground state of the water molecule were carried out with a (5s4p2d/3s1p) 39-function STO basis set. The CI treatment included all single and double excitation configurations (SD) relative to the SCF configuration. and a simple formula due to Davidson was used to estimate the energy contribution of quadruple excitations and thus produce a set of corrected (SDQ) energies. -
Arxiv:1911.06836V1 [Physics.Chem-Ph] 8 Aug 2019 A
Multireference electron correlation methods: Journeys along potential energy surfaces Jae Woo Park,1, ∗ Rachael Al-Saadon,2 Matthew K. MacLeod,3 Toru Shiozaki,2, 4 and Bess Vlaisavljevich5, y 1Department of Chemistry, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Korea. 2Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208, USA. 3Workday, 4900 Pearl Circle East, Suite 100, Boulder, CO 80301, USA. 4Quantum Simulation Technologies, Inc., 625 Massachusetts Ave., Cambridge, MA 02139, USA. 5Department of Chemistry, University of South Dakota, 414 E. Clark Street, Vermillion, SD 57069, USA. (Dated: November 19, 2019) Multireference electron correlation methods describe static and dynamical electron correlation in a balanced way, and therefore, can yield accurate and predictive results even when single-reference methods or multicon- figurational self-consistent field (MCSCF) theory fails. One of their most prominent applications in quantum chemistry is the exploration of potential energy surfaces (PES). This includes the optimization of molecular ge- ometries, such as equilibrium geometries and conical intersections, and on-the-fly photodynamics simulations; both depend heavily on the ability of the method to properly explore the PES. Since such applications require the nuclear gradients and derivative couplings, the availability of analytical nuclear gradients greatly improves the utility of quantum chemical methods. This review focuses on the developments and advances made in the past two decades. To motivate the readers, we first summarize the notable applications of multireference elec- tron correlation methods to mainstream chemistry, including geometry optimizations and on-the-fly dynamics. Subsequently, we review the analytical nuclear gradient and derivative coupling theories for these methods, and the software infrastructure that allows one to make use of these quantities in applications. -
Perturbational Treatment of Spin-Orbit Coupling for Generally Applicable High-Level Multi-Reference Methods
Perturbational treatment of spin-orbit coupling for generally applicable high-level multi-reference methods Sebastian Mai1, Thomas Müller2,a), Felix Plasser3, Philipp Marquetand1, Hans Lischka and Leticia González1 1Institute of Theoretical Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria 2Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany 3Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany 4Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA Abstract An efficient perturbational treatment of spin-orbit coupling within the framework of high-level multi-reference techniques has been implemented in the most recent version of the COLUMBUS quantum chemistry package, extending the existing fully variational two-component (2c) multi-reference configuration interaction singles and doubles (MRCISD) method. The proposed scheme follows related implementations of quasi-degenerate perturbation theory (QDPT) model space techniques. Our model space is built either from uncontracted, large-scale scalar relativistic MRCISD wavefunctions or based on the scalar-relativistic solutions of the linear-response-theory-based multi-configurational averaged quadratic coupled cluster method (LRT-MRAQCC). The latter approach allows for a consistent, approximatively size-consistent and size-extensive treatment of spin-orbit coupling. The approach is described in -
Curriculum Vitae Rodney J
Revised 4/29/2017 CURRICULUM VITAE RODNEY J. BARTLETT GRADUATE RESEARCH PROFESSOR OF CHEMISTRY AND PHYSICS QUANTUM THEORY PROJECT DEPARTMENTS OF CHEMISTRY AND PHYSICS UNIVERSITY OF FLORIDA PO BOX 118435 GAINESVILLE, FLORIDA USA 32611-8435 Phone: 352-392-6974 Email: [email protected] Web Page: http://www.clas.ufl.edu/users/rodbartl BIRTH DATE: March 31, 1944 CV INDEX AREA OF SPECIALIZATION Quantum chemistry, molecular electronic structure and spectra, ab initio many-electron methods Following the initial formulation of Jiri Cizek of coupled-cluster theory with double excitations, CCD, Rod Bartlett pioneered the development of coupled-cluster (CC) theory in quantum chemistry to offer highly accurate solutions of the Schroedinger equation for molecular structure and spectra. He introduced the term ‘size-extensivity’ for many-body methods like CC that scale properly with the number of electrons; now viewed as an essential element in quantum chemistry approximations. He and his co-workers were the first to formulate and implement CC theory with all single and double excitations (CCSD), to add triples non- iteratively (CCSD[T]), iteratively, CCSDT-1, and fully, CCSDT; followed by quadruple (CCSDTQ) and pentuple excitations (CCSDTQP). He also presented a density matrix formulation for the analytical gradients (forces) for the non- variational CC method, a necessity for any widely used method in quantum chemistry. This led to the CC functional, E=0|(1+)exp(-T)Hexp(T)|0 where the forces on an atom, , become E/X=0|(1+)exp(-T)(H/X)exp(T)|0. This functional also defines the CC response and relaxed density matrices for all properties, a non-Hermitian generalization of the conventional density matrices. -
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. -
Nwchem User Documentation Release 4.0.1
NWChem User Documentation Release 4.0.1 High Performance Computational Chemistry Group W.R. Wiley Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory P.O. Box 999, Richland, WA 99352 January 2001 2 DISCLAIMER This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR RESPON- SIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY INFORMATION, APPARA- TUS, PRODUCT, SOFTWARE, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS. LIMITED USE This software (including any documentation) is being made available to you for your internal use only, solely for use in performance of work directly for the U.S. Federal Government or work under contracts with the U.S. Department of Energy or other U.S. Federal Government agencies. This software is a version which has not yet been evaluated and cleared for commercialization. Adherence to this notice may be necessary for the author, Battelle Memorial Institute, to successfully assert copyright in and commercialize this software. This software is not intended for duplication or distribution to third parties without the permission of the Manager of Software Products at Pacific Northwest National Laboratory, Richland, Washington, 99352. ACKNOWLEDGMENT This software and its documentation were produced with Government support under Contract Number DE-AC06- 76RLO-1830 awarded by the United States Department of Energy. The Government retains a paid-up non-exclusive, irrevocable worldwide license to reproduce, prepare derivative works, perform publicly and display publicly by or for the Government, including the right to distribute to other Government contractors. -
Mathematics and Computer Science
ANL/MC S-TM-219 Workshop Report on Large-Scale Matrix Diagonalization Methods in Chemistry Theory Institute held at Argonne National Laboratory May 20-22, 1996 edited by Cliristian H. Bischof, Ron L. Shepard, and Steven Huss-Lederman MATHEMATICS AND COMPUTER SCIENCE DIVISION Argonne Xational Laboratory, with facilities in the states of Illinois and Idaho, is owned by the United States government, and operated by The University of Chicago under the provisions of a contract with the Department of Energy. DISCLAIMER This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of theiiemployees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or pro- cess disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. .. I. Reproduced from the best available copy. Available to and DOE contractors from the Office of ScientificDOE and Technical Information P.O.Box 62 Oak Ridge, TN 3783 1 Prices available from (423) 576-8401 Available to the public from the National Technical information Service U.S. Department of Commerce 5285 Port Royal Road Springfield. -
Information to Users
INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand corner and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. University Microfilms International A Bell & Howell Information Company 300 North Zeeb Road, Ann Arbor, Ml 48106-1346 USA 313/761-4700 800/521-0600 Order Number 9211227 Application of multireference-based correlation methods to the study of weak bonding interactions Stahlberg, Eric Alan, Ph.D. The Ohio State University, 1991 UMI 300 N. -
Computational Chemistry: a Practical Guide for Applying Techniques to Real-World Problems
Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems. David C. Young Copyright ( 2001 John Wiley & Sons, Inc. ISBNs: 0-471-33368-9 (Hardback); 0-471-22065-5 (Electronic) COMPUTATIONAL CHEMISTRY COMPUTATIONAL CHEMISTRY A Practical Guide for Applying Techniques to Real-World Problems David C. Young Cytoclonal Pharmaceutics Inc. A JOHN WILEY & SONS, INC., PUBLICATION New York . Chichester . Weinheim . Brisbane . Singapore . Toronto Designations used by companies to distinguish their products are often claimed as trademarks. In all instances where John Wiley & Sons, Inc., is aware of a claim, the product names appear in initial capital or all capital letters. Readers, however, should contact the appropriate companies for more complete information regarding trademarks and registration. Copyright ( 2001 by John Wiley & Sons, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic or mechanical, including uploading, downloading, printing, decompiling, recording or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without the prior written permission of the Publisher. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY 10158-0012, (212) 850-6011, fax (212) 850-6008, E-Mail: PERMREQ @ WILEY.COM. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold with the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional person should be sought. -
A Case Study with Nwchem
CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE Concurrency Computat.: Pract. Exper. 2010; 00:1–17 Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cpe Performance Characterization of Global Address Space Applications: A Case Study with NWChem Jeff R. Hammond∗, Sriram Krishnamoorthy+, Sameer Shende‡ Nichols A. Romero∗, Allen D. Malony‡ ∗ Argonne National Laboratory + Pacific Northwest National Laboratory ‡ University of Oregon SUMMARY The use of global address space languages and one-sided communication for complex applications is gaining attention in the parallel computing community. However, lack of good evaluative methods to observe multiple levels of performance makes it difficult to isolate the cause of performance deficiencies and to understand the fundamental limitations of system and application design for future improvement. NWChem is a popular computational chemistry package which depends on the Global Arrays / ARMCI suite for partitioned global address space functionality to deliver high-end molecular modeling capabilities. A workload characterization methodology was developed to support NWChem performance engineering on large-scale parallel platforms. The research involved both the integration of performance instrumentation and measurement in the NWChem software, as well as the analysis of one-sided communication performance in the context of NWChem workloads. Scaling studies were conducted for NWChem on Blue Gene/P and on two large-scale clusters using different generation Infiniband interconnects and x86 processors. The performance analysis and results show how subtle changes in the runtime parameters related to the communication subsystem could have significant impact on performance behavior. The tool has successfully identified several algorithmic bottlenecks which are already being tackled by computational chemists to improve NWChem performance. -
Adiabatic and Nonadiabatic Molecular Dynamics with Multireference Ab
Columbus in Rio: univie.ac.at/columbus/rio Rio de Janeiro, Nov. 27- Dec. 02, 2005 AdiabaticAdiabatic andand nonadiabaticnonadiabatic molecularmolecular dynamicsdynamics withwith multireferencemultireference abab initioinitio methodsmethods Mario Barbatti Institute for Theoretical Chemistry University of Vienna Outline First Lecture: An introduction to molecular dynamics 1. Dynamics, why? 2. Overview of the available approaches Second Lecture: Towards an implementation of surface hopping dynamics 1. Practical aspects to be addressed 2. The NEWTON-X program 3. Some applications: theory and experiment PartPart IIII TowardsTowards anan implementationimplementation ofof surfacesurface hoppinghopping dynamicsdynamics PracticalPractical aspectsaspects toto bebe addressedaddressed InitialInitial conditionsconditions 2 2 (0) 1 ⎡− 2α(R − Re ) ⎤ ⎡− P ⎤ PW (R, P) = exp⎢ ⎥exp⎢ ⎥ E πh ⎣ h ⎦ ⎣ 2αh ⎦ mω α = HO 2 E0 ± ∆E Sn Wigner distribution S0 accept R,P don’t accept ClassicalClassical dynamics:dynamics: integratorintegrator Any standard method can be used in the integration of the Newton equations. A good one is the Velocity Verlet (Swope et al. JCP 76, 637 (1982)): For each nucleus I 1 R (t + ∆t) = R (t) + v (t)∆t + a (t)∆t 2 I I I 2 I ⎛ ∆t ⎞ 1 vI ⎜t + ⎟ = vI (t) + aI (t)∆t ⎝ 2 ⎠ 2 1 aI (t) = − ∇R E[]R I (t + ∆t) Quantum chemistry calculation M I ⎛ ∆t ⎞ 1 vI (t + ∆t) = vI ⎜t + ⎟ + aI (t + ∆t)∆t ⎝ 2 ⎠ 2 TimeTime-step-step forfor thethe classicalclassicalequationsequations Schlick, Barth and Mandziuk, Annu. Rev. Biophys. Struct. 26, 181 (1997). TimeTime-step-step forfor thethe classicalclassicalequationsequations Time step should not be larger than 1 fs (1/10v). ∆t = 0.5 fs assures a good level of conservation of energy most of the time.