DOCSLIB.ORG

NEWTON-X a Package for Newtonian Dynamics Close to the Crossing Seam

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
NEWTON-X a Package for Newtonian Dynamics Close to the Crossing Seam www.newtonx.org NEWTON-X a package for Newtonian dynamics close to the crossing seam Documentation based on NEWTON-X version 2.0 build 17 (release March 7, 2017) Return to Table of Contents ii NEWTON-X: Newtonian dynamics close to the crossing seam Return to Table of Contents iii 1 Table of contents 1 TABLE OF CONTENTS ................................................................................................................................ III 2 ABOUT NEWTON-X ................................................................................................................................ 1 2.1 General Information ............................................................................................................................ 1 2.2 Contact Information ............................................................................................................................. 1 2.3 What is new in this version .................................................................................................................. 2 3 MIXED QUANTUM-CLASSICAL DYNAMICS SIMULATIONS ........................................................................... 3 4 DEVELOPERS AND CONTRIBUTORS ............................................................................................................ 5 5 HOW TO REFERENCE NEWTON-X ............................................................................................................ 6 6 QUICK START ............................................................................................................................................. 7 6.1 NEWTON-X Tutorial............................................................................................................................ 7 6.2 The NXINP tool .................................................................................................................................... 7 6.3 Initial conditions generation ................................................................................................................ 8 6.4 Dynamics Input .................................................................................................................................... 8 6.4.1 Adiabatic dynamics (dynamics on one surface) .......................................................................................... 8 6.4.2 Nonadiabatic dynamics (Surface hopping) ................................................................................................. 9 6.4.3 Mixed adiabatic and nonadiabatic dynamics .............................................................................................. 9 6.5 Creating the trajectory inputs .............................................................................................................. 9 6.6 Running the dynamics ........................................................................................................................ 10 6.7 Where are the results? ....................................................................................................................... 10 6.8 Overview of the file structure ............................................................................................................. 10 6.8.1 Dynamics simulations ............................................................................................................................... 10 7 CAPABILITIES .......................................................................................................................................... 12 7.1 General features ................................................................................................................................. 12 7.2 Overview of the available interfaces .................................................................................................. 13 8 HOW TO GET NEWTON-X ...................................................................................................................... 14 9 HOW TO INSTALL NEWTON-X ............................................................................................................... 15 9.1 Binary distribution ............................................................................................................................. 15 9.2 To install NEWTON-X you need ........................................................................................................ 15 9.3 To run NEWTON-X you need ............................................................................................................. 15 9.4 Setup of third-party programs ............................................................................................................ 15 9.5 Verification of installation ................................................................................................................. 16 10 INITIAL CONDITIONS GENERATION ........................................................................................................... 17 10.1 How to execute INITICOND ......................................................................................................... 17 10.2 Input parameters ........................................................................................................................... 17 10.3 What you need to execute .............................................................................................................. 22 10.3.1 Additional files and directories ................................................................................................................. 22 10.3.2 The JOB_AD directory ............................................................................................................................. 23 10.3.3 The JOB_N and JOB_N-1 directories ...................................................................................................... 24 10.3.4 Save files option ....................................................................................................................................... 24 10.4 Output ............................................................................................................................................ 25 10.5 Running in several computers ....................................................................................................... 26 11 TRAJECTORY-INPUT GENERATION, INITIAL CONDITIONS FOR MULTIPLE STATES, AND SPECTRA ............... 27 11.1 INPUT FOR SPECTRUM AND TRAJECTORIES ........................................................................ 27 11.2 Absorption and emission spectra .................................................................................................. 29 11.3 Photoelectron spectra ................................................................................................................... 30 11.4 Initial conditions for multiple states .............................................................................................. 32 11.5 Managing several trajectories ....................................................................................................... 32 11.6 About energy restrictions .............................................................................................................. 33 12 DYNAMICS INPUTS ................................................................................................................................... 34 12.1 What is necessary to run the jobs .................................................................................................. 34 12.1.1 control.dyn ................................................................................................................................................ 34 12.1.2 Geometry .................................................................................................................................................. 36 12.1.3 Velocity .................................................................................................................................................... 36 12.1.4 Freezing atoms .......................................................................................................................................... 37 12.1.5 Specific input for quantum-chemistry electronic-structure calculations ................................................... 37 12.1.5.1 Which electronic method to use ..................................................................................................... 37 12.1.5.2 Using analytical models ................................................................................................................. 37 12.1.5.3 COLUMBUS ................................................................................................................................. 39 NEWTON-X: Newtonian dynamics close to the crossing seam Return to Table of Contents iv 12.1.5.4 TURBOMOLE ............................................................................................................................... 40 12.1.5.5 DFTB ............................................................................................................................................. 42 12.1.5.6 GAUSSIAN ................................................................................................................................... 42 12.1.5.7 TINKER ......................................................................................................................................... 47 12.1.5.8 DFTB+ ..........................................................................................................................................
Load more

Recommended publications
  • 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.
    [Show full text]
  • The Landau-Zener Transition and the Surface Hopping Method for the 2D Dirac Equation for Graphene
    Commun. Comput. Phys. Vol. 21, No. 2, pp. 313-357 doi: 10.4208/cicp.020515.250716a February 2017 The Landau-Zener Transition and the Surface Hopping Method for the 2D Dirac Equation for Graphene 1,2 3,4, Ali Faraj and Shi Jin ∗ 1 Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, P.R. China. 2 Grenoble INP, ESISAR, 26902 Valence Cedex 9, France. 3 Department of Mathematics, Institute of Natural Sciences, MOE-LSEC and SHL-MAC, Shanghai Jiao Tong University, Shanghai 200240, P.R. China. 4 Department of Mathematics, University of Wisconsin, Madison, WI 53706, USA. Received 2 May 2015; Accepted (in revised version) 25 July 2016 Abstract. A Lagrangian surface hopping algorithm is implemented to study the two dimensional massless Dirac equation for Graphene with an electrostatic potential, in the semiclassical regime. In this problem, the crossing of the energy levels of the system at Dirac points requires a particular treatment in the algorithm in order to describe the quantum transition—characterized by the Landau-Zener probability— between different energy levels. We first derive the Landau-Zener probability for the underlying problem, then incorporate it into the surface hopping algorithm. We also show that different asymptotic models for this problem derived in [O. Morandi, F. Schurrer, J. Phys. A: Math. Theor. 44 (2011) 265301] may give different transition prob- abilities. We conduct numerical experiments to compare the solutions to the Dirac equation, the surface hopping algorithm, and the asymptotic models of [O. Morandi, F. Schurrer, J. Phys. A: Math. Theor. 44 (2011) 265301]. AMS subject classifications: 35Q41, 37M05, 65M70, 65Z05, 81-08, 81Q20, 81V99 Key words: Dirac equation, Wigner transform, semiclassical model, band crossing, Landau-Zener formula, surface hopping algorithm, spectral methods.
    [Show full text]
  • Performance of Trajectory Surface Hopping Method in the Treatment of Ultrafast Intersystem Crossing Dynamics
    Performance of trajectory surface hopping method in the treatment of ultrafast intersystem crossing dynamics Jiawei Peng1,2,4, Yu Xie1, Deping Hu3, and Zhenggang Lan1,a) 1SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China 2Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 2066101, China 3MOE Key Laboratory of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, China 4University of Chinese Academy of Sciences, Beijing 100049, P. R. China We carried out extensive studies to examine the performance of the fewest-switches surface hopping method in the description of the ultrafast intersystem crossing dynamic of various singlet-triplet (S-T) models by comparison with the results of the exact full quantum dynamics. Different implementation details and some derivative approaches were examined. As expected, it is better to perform the trajectory surface hopping calculations in the spin-adiabatic representation or by the local diabatization approach, instead of in the spin-diabatic representation. The surface hopping method provides reasonable results for the short-time dynamics in the S-T model with weak spin-orbital coupling (diabatic coupling), although it does not perform well in the models with strong spin-orbital coupling (diabatic coupling). When the system accesses the S-T potential energy crossing with rather high kinetic energy, the trajectory surface hopping method tends to produce the good description of the nonadiabatic intersystem crossing dynamics. The impact of the decoherence correction on the performance of the trajectory surface hopping is system dependent.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • Lecture 6: Introduction to Surface Hopping and to Sharc
    Introduction Ehrenfest Surface Hopping Sharc Example Lecture 6: Introduction to Surface Hopping and to Sharc Sebastian Mai Sharc Workshop Vienna, October 3rd–7th, 2016 Sebastian Mai Lecture 6:Introduction to Surface Hopping and to Sharc 1 / 34 Introduction Ehrenfest Surface Hopping Sharc Example Introduction What we already have heard during the last days: I Classical nuclear dynamics I Ab initio dynamics I Born-Oppenheimer approximation I Excited states Goal: Perform excited-state dynamics with classical nuclei. We need to consider the Born-Oppenheimer approximation: I The electronic wavefunction can change during dynamics. I The electronic wavefunction has an eect on the nuclear motion. Sebastian Mai Lecture 6:Introduction to Surface Hopping and to Sharc 3 / 34 Introduction Ehrenfest Surface Hopping Sharc Example Electronic wavefunction evolution Classical nuclear dynamics No nuclear wavefunction! ) Electronic wavefunction as linear combination of basis functions: X Ψ(t) = c (t) ϕ (1) j i α j α i α Inserting this into the TDSE: @ i~ Ψ(t) = Hˆ el Ψ(t) (2) @t j i j i and premultiplying with ϕ gives: h β j * + X @c (t) D E @ X D E i~ α ϕ ϕ + c (t) ϕ ϕ = c (t) ϕ Hˆ el ϕ (3) @t β α α β @t α α β α 2 α 3 α 6 7 6 7 46 57 Sebastian Mai Lecture 6:Introduction to Surface Hopping and to Sharc 4 / 34 Introduction Ehrenfest Surface Hopping Sharc Example Electronic equation of motion From last slide: * + X @c (t) D E @ X D E i~ α ϕ ϕ + c (t) ϕ ϕ = c (t) ϕ Hˆ el ϕ (4) @t β α α β @t α α β α 2 α 3 α 6 7 6 7 Defining46 matrix elements: 57 X @c (t) X i~ α δ + c (t) T = c (t) H (5) @t βα α βα α βα 62 α 73 α 6 7 Rearranging:46 57 @cβ (t) X i = c (t) H + T (6) @t − α ~ βα βα α As matrix equation with atomic units: @ c(t) = [iH + T] c(t) (7) @t − Sebastian Mai Lecture 6:Introduction to Surface Hopping and to Sharc 5 / 34 Introduction Ehrenfest Surface Hopping Sharc Example Electronic wavefunction interpretation Complex electronic wavefunction represented through vector c(t).
    [Show full text]
  • Molecular Dynamics Beyond the Born-Oppenheimer Approximation: Mixed Quantum–Classical Approaches
    John von Neumann Institute for Computing Molecular Dynamics Beyond the Born-Oppenheimer Approximation: Mixed Quantum–Classical Approaches Nikos L. Doltsinis published in Computational Nanoscience: Do It Yourself!, J. Grotendorst, S. Bl¨ugel, D. Marx (Eds.), John von Neumann Institute for Computing, J¨ulich, NIC Series, Vol. 31, ISBN 3-00-017350-1, pp. 389-409, 2006. c 2006 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher mentioned above. http://www.fz-juelich.de/nic-series/volume31 Molecular Dynamics Beyond the Born-Oppenheimer Approximation: Mixed Quantum–Classical Approaches Nikos L. Doltsinis Chair of Theoretical Chemistry Ruhr-Universit¨at Bochum 44780 Bochum, Germany E-mail: [email protected] This contribution takes a closer look at the foundations of conventional molecular dynamics simulations such as the Born-Oppenheimer approximation and the treatment of atomic nuclei according to the laws of classical mechanics. Regimes of validity of the adiabatic approximation are defined and models that take into account nonadiabatic effects in situations where the Born- Oppenheimer approximation breaks down are introduced. We focus on two mixed quantum- classical methods that differ only in the way the forces on the — classical — atomic nuclei are determined from the solutions to the time-independent electronic Schr¨odinger equation. In the Ehrenfest approach, the system moves on a single potential energy surface obtained by weighted averaging over all adiabatic states, whereas the ’surface hopping’ method allows transitions between pure adiabatic potential energy surfaces according to their weights.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Frozen Gaussian Approximation with Surface Hopping for Mixed Quantum-Classical Dynamics: a Mathematical Justification of Fewest Switches Surface Hopping Algorithms
    FROZEN GAUSSIAN APPROXIMATION WITH SURFACE HOPPING FOR MIXED QUANTUM-CLASSICAL DYNAMICS: A MATHEMATICAL JUSTIFICATION OF FEWEST SWITCHES SURFACE HOPPING ALGORITHMS JIANFENG LU AND ZHENNAN ZHOU ABSTRACT. We develop a surface hopping algorithm based on frozen Gaussian approximation for semiclassical matrix Schrödinger equations, in the spirit of Tully’s fewest switches surface hopping method. The algorithm is asymptoti- cally derived from the Schrödinger equation with rigorous approximation error analysis. The resulting algorithm can be viewed as a path integral stochastic representation of the semiclassical matrix Schrödinger equations. Our results provide mathematical understanding to and shed new light on the important class of surface hopping methods in theoretical and computational chemistry. 1. INTRODUCTION The surface hopping algorithms, in particular the celebrated Tully’s fewest switches surface hopping (FSSH) al- gorithm [7,29], are widely used in theoretical and computational chemistry for mixed quantum-classical dynamics in the non-adiabatic regime. The Schrödinger equation, which is often high dimensional in chemistry applications, is impractical to solve directly due to curse of dimensionality. Thus, development of algorithms based on semiclassical approximation, which only involve solving ODEs, is necessary. Within the Born-Oppenheimer approximation, the resulting algo- rithm from the semiclassical approximation is the familiar ab initio molecular dynamics and related semiclassical algorithms. However, in many applications,
    [Show full text]