DOCSLIB.ORG

ALCF-2 Early Science Program Technical Reports

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
ALCF-2 Early Science Program Technical Reports ANL/ALCF/ESP-13/17 ALCF-2 Early Science Program Technical Reports Compendium of Individual Technical Reports for the 16 ESP Projects Argonne Leadership Computing Facility About Argonne National Laboratory Argonne is a U.S. Department of Energy laboratory managed by UChicago Argonne, LLC under contract DE-AC02-06CH11357. The Laboratory’s main facility is outside Chicago, at 9700 South Cass Avenue, Argonne, Illinois 60439. For information about Argonne and its pioneering science and technology programs, see www.anl.gov. Availability of This Report This report is available, at no cost, at http://www.osti.gov/bridge. It is also available on paper to the U.S. Department of Energy and its contractors, for a processing fee, from: U.S. Department of Energy Office of Scientific and Technical Information P.O. Box 62 Oak Ridge, TN 37831-0062 phone (865) 576-8401 fax (865) 576-5728 [email protected] 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 UChicago Argonne, LLC, nor any of their employees or officers, 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 process 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 document authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof, Argonne National Laboratory, or UChicago Argonne, LLC. ANL/ALCF/ESP-13/17 ALCF-2 Early Science Program Technical Reports Compendium of Individual Technical Reports for the 16 ESP Projects Edited by Timothy J. Williams Argonne Leadership Computing Facility, Argonne National Laboratory July 18, 2013 ALCF-2 Early Science Program Technical Reports Editor: Timothy J. Williams, Argonne Leadership Computing Facility July 2013 1 Contents ALCF-2 Early Science Program Technical Reports Contents 1 The Early Science Program 3 1.1 These Technical Reports . .3 2 Acknowledgements 3 3 Climate-Weather Modeling Studies Using a Prototype Global Cloud-System Re- solving Model 5 4 Materials Design and Discovery: Catalysis and Energy Storage 11 5 Direct Numerical Simulation of Autoignition in a Jet in a Cross-Flow 23 6 High Accuracy Predictions of the Bulk Properties of Water 39 7 Cosmic Structure Probes of the Dark Universe 45 8 Accurate Numerical Simulations Of Chemical Phenomena Involved in Energy Production and Storage with MADNESS and MPQC 57 9 Petascale, Adaptive CFD 71 10 Using Multi-scale Dynamic Rupture Models to Improve Ground Motion Esti- mates 85 11 High-Speed Combustion and Detonation (HSCD) 91 12 Petascale Simulations of Turbulent Nuclear Combustion 97 13 Lattice Quantum Chromodynamics 119 14 Petascale Direct Numerical Simulations of Turbulent Channel Flow 129 15 Ab-initio Reaction Calculations for Carbon-12 141 16 NAMD - The Engine for Large-Scale Classical MD Simulations of Biomolecular Systems Based on a Polarizable Force Field 157 17 Global Simulation of Plasma Microturbulence at the Petascale & Beyond 161 18 Multiscale Molecular Simulations at the Petascale 175 Title Page Photos: Top: Mira|one of three rows of 16 IBM Blue Gene/Q racks. Bottom: Attendees at the ALCF Early Science Program Kick-Off Workshop, 18-19 October 2010, in front of Argonne National Laboratory's TCS Conference Center. 2 The ESP ALCF-2 Early Science Program Technical Reports 1 The Early Science Program The Early Science Program (ESP) is managed for the Department of Energy by the Argonne Leadership Computing Facility (ALCF). ESP was funded to prepare key scientific applications for the architecture and scale of Mira, a 48K-node IBM Blue Gene/Q system that went into production at ALCF in April 2013, and to solidify libraries and infrastructure that will pave the way for other production applications. To distinguish it from past and future Early Science Programs, we denote this one as the ALCF-2 ESP (ALCF-2 is the project name associated with procurement of Mira). The 16 Early Science projects are the result of a call for proposals in 2010, and were chosen based on computational and scientific reviews. The projects, in addition to promising delivery of exciting new science, are all based on state-of-the-art, petascale, parallel applications. Starting in October 2010, the project teams, in collaboration with ALCF staff and IBM, have undertaken intensive efforts to adapt their software to take advantage of Mira's Blue Gene/Q architecture, which, in a number of ways, is a precursor to future HPC architectures. Together, the 16 projects span a diverse range of scientific fields, numerical methods, programming models, and computational approaches. The latter include particle-mesh methods, adaptive meshes, spectral methods, Monte Carlo, molecular dynamics, and ab initio computational chemistry methods. These applications also represent a large portion of the ALCFs current and projected production computational workload. The official Early Science period lasted only about three months (between machine acceptance and commencement of production), during which the ESP had dedicated use of Mira. Projects have about 2 billion core-hours to use on Mira, as much as possible during that 3 month period, so It was essential that the projects were "ready to run" when the clock started ticking. The long lead time of the Program, and dedicated postdoctoral appointees for most projects, working with ALCF staff, helped make that possible. 1.1 These Technical Reports The purpose of the Technical Reports gathered here is to document and publicly circulate what the ESP projects have done and learned in preparing their application codes for Mira. This includes, for example, approaches for better use of in-node thread parallelism, accessing the BG/Q's QPX functionality (4-way SIMD vectorization), use of BG/Q specific libraries such as the low-level PAMI communication system, and using ESSL and Mass libraries. We hope that these examples will inform and help our production users on Mira, and those working on optimization applications en route to applying for computer time grants on ALCF systems via the INCITE and ALCC programs. 2 Acknowledgements For all projects in these reports: This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357. 3 The ESP ALCF-2 Early Science Program Technical Reports 4 GFDL esp ALCF-2 Early Science Program Technical Reports 3 Climate-Weather Modeling Studies Using a Prototype Global Cloud-System Resolving Model PI: V. Balaji (Geophysical Fluid Dynamics Laboratory) Project Summary We expect our understanding of the role of clouds in climate to undergo a qualitative change as the resolutions of global models begin to encompass clouds. At these resolutions, non-hydrostatic dynamics become significant and deep convective processes are resolved. We are poised at the threshold of being able to run global scale simulations that include direct, non-parameterized, simulations of deep convective clouds. The goal of this project is to use Mira to explore the frontier of weather prediction and climate modeling with the newly developed Geophysical Fluid Dynamics Laboratory (GFDL) global cloud-resolving model. A single, unified atmospheric modeling system with a cubed-sphere dynamical core and bulk cloud microphysics running at hydrostatic ( 10 km) and non-hydrostatic ( 5 km) resolutions will be run with the goal of capturing the climatology∼ of clouds and severe storms≤ in a warming world. The ability to reproduce historical tropical storm statistics will be used as a test of this ground-breaking model. The purpose of the experiments proposed is to validate the global cloud-resolving climate model via hurricane hindcasts. For this purpose, we will perform hurricane verification studies for the 2008 Atlantic Season. Storms in 2008 lasted a total of 100 days; performing 5-day forecasts on each of the days would give a total of 500 forecast days for the season. Report originally released as ANL/ALCF-ESP-13/1 5 GFDL esp ALCF-2 Early Science Program Technical Reports Climate-Weather Modeling Studies Using a Prototype Global Cloud-System Resolving Model Research Team Members: V. Balaji – Computational Scientist, Princeton University Shian-Jiann Lin – Physical Scientist, GFDL Christopher Kerr – Computational Scientist, GFDL Executive Summary: Clouds remain the largest source of uncertainty in our understanding of global climate change. Different aspects of the planetary cloud field can provide positive and negative feedback to the Earth’s energy balance, and clouds of course are directly implicated in changes to the planetary distribution of precipitation. A fundamental problem in our current understanding of the role of clouds in the dynamics of climate are that current resolutions do not resolve the fundamental length scales associated with clouds. We expect our understanding of the role of clouds in climate to undergo a qualitative change as the resolutions of global models begin to encompass clouds. At these resolutions (which
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C
    Jaguar 5.5 User Manual Copyright © 2003 Schrödinger, L.L.C. All rights reserved. Schrödinger, FirstDiscovery, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Prime, QSite, and QikProp are trademarks of Schrödinger, L.L.C. MacroModel is a registered trademark of Schrödinger, L.L.C. To the maximum extent permitted by applicable law, this publication is provided “as is” without warranty of any kind. This publication may contain trademarks of other companies. October 2003 Contents Chapter 1: Introduction.......................................................................................1 1.1 Conventions Used in This Manual.......................................................................2 1.2 Citing Jaguar in Publications ...............................................................................3 Chapter 2: The Maestro Graphical User Interface...........................................5 2.1 Starting Maestro...................................................................................................5 2.2 The Maestro Main Window .................................................................................7 2.3 Maestro Projects ..................................................................................................7 2.4 Building a Structure.............................................................................................9 2.5 Atom Selection ..................................................................................................10 2.6 Toolbar Controls ................................................................................................11
    [Show full text]
  • Electronic Structure Calculations in Quantum Chemistry
    Electronic Structure Calculations in Quantum Chemistry Alexander B. Pacheco User Services Consultant LSU HPC & LONI [email protected] HPC Training Louisiana State University Baton Rouge Nov 16, 2011 Electronic Structure Calculations in Quantum Chemistry Nov 11, 2011 HPC@LSU - http://www.hpc.lsu.edu 1 / 55 Outline 1 Introduction 2 Ab Initio Methods 3 Density Functional Theory 4 Semi-empirical Methods 5 Basis Sets 6 Molecular Mechanics 7 Quantum Mechanics/Molecular Mechanics (QM/MM) 8 Computational Chemistry Programs 9 Exercises 10 Tips for Quantum Chemical Calculations Electronic Structure Calculations in Quantum Chemistry Nov 11, 2011 HPC@LSU - http://www.hpc.lsu.edu 2 / 55 Introduction What is Computational Chemistry? Computational Chemistry is a branch of chemistry that uses computer science to assist in solving chemical problems. Incorporates the results of theoretical chemistry into efficient computer programs. Application to single molecule, groups of molecules, liquids or solids. Calculates the structure and properties of interest. Computational Chemistry Methods range from 1 Highly accurate (Ab-initio,DFT) feasible for small systems 2 Less accurate (semi-empirical) 3 Very Approximate (Molecular Mechanics) large systems Electronic Structure Calculations in Quantum Chemistry Nov 11, 2011 HPC@LSU - http://www.hpc.lsu.edu 3 / 55 Introduction Theoretical Chemistry can be broadly divided into two main categories 1 Static Methods ) Time-Independent Schrödinger Equation H^ Ψ = EΨ ♦ Quantum Chemical/Ab Initio /Electronic Structure Methods ♦ Molecular Mechanics 2 Dynamical Methods ) Time-Dependent Schrödinger Equation @ { Ψ = H^ Ψ ~@t ♦ Classical Molecular Dynamics ♦ Semi-classical and Ab-Initio Molecular Dynamics Electronic Structure Calculations in Quantum Chemistry Nov 11, 2011 HPC@LSU - http://www.hpc.lsu.edu 4 / 55 Tutorial Goals Provide a brief introduction to Electronic Structure Calculations in Quantum Chemistry.
    [Show full text]
  • The Aomix Manual and the FAQ Webpage, You Cannot Resolve Your Problem, Contact the Aomix Developer with the Detailed Description of Your Problem
    AOMix version 6.94 Software Manual Dr. S. I. Gorelsky, AOMix manual (www.sg-chem.net) Updated on January 21, 2021 AOMix is a user-friendly, comprehensive package for the molecular orbital analysis. AOMix calculates percentage contributions of different molecular fragments (atoms, ligands, groups of atomic orbitals / basis functions, groups of fragment molecular orbitals, etc.) to molecular orbitals from output files generated by different computational chemistry packages and produces data tables (in the ASCII text format) with relevant MO information, condensed Fukui functions, etc. In addition, it generates total, partial and overlap population density-of-states (DOS) plots and can be used for MO composition analysis in systems with many fragments. It also calculates the MO compositions in the basis of fragment molecular orbitals (FOs), occupation numbers for FOs and atomic orbitals (AOs), and, if the number of fragments is greater than 1, the amounts of electron donation / back-donation between molecular fragments (charge decomposition analysis, CDA), electronic polarizations of fragments, and generates plot data for MO interaction diagrams. In addition, it can be used for Morokuma’s energy decomposition analysis (EDA) and to generate a guess wave function of multi-fragment molecular systems from the wave functions of fragments. The software calculates total and free valence indices of fragments, 2-center (Wiberg, Löwdin, and Mayer) and 3-, 4-, 5- and 6-center bond orders between molecular fragments (which can be defined as atoms, groups of atoms, or groups of atomic orbitals) and performs the Löwdin population analysis. The software can be also used for recovery of the initial guess (as the converged wave function) and the analysis of spin-unrestricted MO calculations: the program projects β-spin molecular orbitals on to -spin molecular orbitals and prints the overlap matrix i j .
    [Show full text]
  • Electronic Structure of Molecules and Materials from Quantum Simulations
    THE UNIVERSITY OF CHICAGO ELECTRONIC STRUCTURE OF MOLECULES AND MATERIALS FROM QUANTUM SIMULATIONS A DISSERTATION SUBMITTED TO THE FACULTY OF THE DIVISION OF THE PHYSICAL SCIENCES IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF CHEMISTRY BY HE MA CHICAGO, ILLINOIS DECEMBER 2020 ProQuest Number:28153743 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent on the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. ProQuest 28153743 Published by ProQuest LLC (2020). Copyright of the Dissertation is held by the Author. All Rights Reserved. This work is protected against unauthorized copying under Title 17, United States Code Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 Copyright c 2020 by He Ma All Rights Reserved To my family TABLE OF CONTENTS LIST OF FIGURES . vi LIST OF TABLES . xiii ACKNOWLEDGMENTS . xvii ABSTRACT . xviii 1 INTRODUCTION . 1 2 THEORETICAL BACKGROUND . 5 2.1 The electronic structure problem . 5 2.2 Density functional theory . 7 2.3 Many-body perturbation theory . 9 3 FINITE FIELD ALGORITHM FOR MANY-BODY PERTURBATION THEORY 12 3.1 Finite field calculation of response functions . 13 3.1.1 Introduction . 13 3.1.2 The finite-field approach . 16 3.1.3 GW calculations . 24 3.1.4 Technical details . 35 3.1.5 Conclusions . 48 3.2 Bethe-Salpeter equation .
    [Show full text]
  • Methods for the Electronic Structure of Large Chemical Systems Hong-Zhou Ye
    Methods for the Electronic Structure of Large Chemical Systems by Hong-Zhou Ye B.S., Peking University (2015) Submitted to the Department of Chemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemistry at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY May 2020 ○c Massachusetts Institute of Technology 2020. All rights reserved. Author............................................................................ Department of Chemistry May 7, 2020 Certified by. Troy Van Voorhis Haslam and Dewey Professor of Chemistry Thesis Supervisor Accepted by....................................................................... Robert W. Field Haslam and Dewey Professor of Chemistry Chairman, Department Committee on Graduate Theses 2 This doctoral thesis has been examined by a Committee of the Department of Chemistry as follows: Professor Adam P. Willard. Chairman, Thesis Committee Associate Professor of Chemistry Professor Troy Van Voorhis . Thesis Supervisor Haslam and Dewey Professor of Chemistry Professor Heather J. Kulik . Member, Thesis Committee Associate Professor of Chemical Engineering 4 Methods for the Electronic Structure of Large Chemical Systems by Hong-Zhou Ye Submitted to the Department of Chemistry on May 7, 2020, in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Chemistry Abstract An accurate description of the electronic structure of chemical systems is crucial to under- standing the atomistic mechanisms of many functional materials and designing new ones. In this thesis, we present methods that can potentially be used to computationally study the electronic structure of large chemical systems. The thesis can be roughly divided into two parts. In the first part, we focus on using quantum embedding (QE) theory to reduce the scaling of traditional electron correlation methods while maintaining their accuracy.
    [Show full text]
  • Jaguar User's Guide
    JAGUAR USER’S GUIDE Version 4.2 March 2002 Julie R. Wright © 1998, 2000, 2001, 2002 Schrödinger, Inc. All Rights Reserved. JAGUAR USER’S GUIDE Version 4.2 March 2002 Julie R. Wright Schrödinger, Inc. 1500 SW First Avenue, Suite 1180 Portland, OR 97201 Telephone: (503) 299-1150 Fax: (503) 299-4532 Email: [email protected] © 1998, 2000, 2001, 2002 Schrödinger, Inc. All rights reserved. Copyright © 1998, 2000, 2001, 2002 Schrödinger, Inc. All rights reserved. Schrödinger, Inc. provides this publication “as is” without warranty of any kind, either expressed or implied. NBO 4.0 is copyright © 1996 Board of Regents of the University of Wisconsin System on behalf of the Theoretical Chemistry Institute. Babel 1.3 is copyright © 1992-96 W. Patrick Walters and Matthew T. Stahl. SPARTAN is a trademark owned by Wavefunction, Inc. BIOGRAF and Cerius2 are trademarks of Molecular Simulations, Inc. Gaussian, Gaussian 90, Gaussian 92, and Gaussian 94 are federally registered trademarks of Gaussian, Inc. Silicon Graphics, IRIX, and OpenGL are trademarks of Silicon Graphics, Inc. IBM is a registered trademark of International Business Machines Incorporated. DEC is a trademark of Digital Equipment Corporation. UNIX is a registered trademark of UNIX Systems Laboratories, Inc. X Window System is a registered trademark of Massachusetts Institute of Technology. All other brand or product names are trademarks or registered trademarks of their respective companies or organizations. 420067032002 Table of Contents Jaguar User’s Guide Table of Contents 1. Introduction....................................................................................... 1 1.1. Overview of this User’s Guide................................................................................ 1 1.2. Citing Jaguar in Publications ................................................................................ 3 1.3. Technical Support..................................................................................................
    [Show full text]
  • Arxiv:2002.12531V1 [Physics.Chem-Ph] 28 Feb 2020
    Recent developments in the PySCF program package Qiming Sun,1 Xing Zhang,2 Samragni Banerjee,3 Peng Bao,4 Marc Barbry,5 Nick S. Blunt,6 Nikolay A. Bogdanov,7 George H. Booth,8 Jia Chen,9, 10 Zhi-Hao Cui,2 Janus Juul Eriksen,11 Yang Gao,12 Sheng Guo,13 Jan Hermann,14, 15 Matthew R. Hermes,16 Kevin Koh,17 Peter Koval,18 Susi Lehtola,19 Zhendong Li,20 Junzi Liu,21 Narbe Mardirossian,22 James D. McClain,23 Mario Motta,24 Bastien Mussard,25 Hung Q. Pham,16 Artem Pulkin,26 Wirawan Purwanto,27 Paul J. Robinson,28 Enrico Ronca,29 Elvira Sayfutyarova,30 Maximilian Scheurer,31 Henry F. Schurkus,2 James E. T. Smith,25 Chong Sun,2 Shi-Ning Sun,12 Shiv Upadhyay,32 Lucas K. Wagner,33 Xiao Wang,34 Alec White,2 James Daniel Whitfield,35 Mark J. Williamson,36 Sebastian Wouters,37 Jun Yang,38 Jason M. Yu,39 Tianyu Zhu,2 Timothy C. Berkelbach,28, 34 Sandeep Sharma,25 Alexander Sokolov,3 and Garnet Kin-Lic Chan2 1)AxiomQuant Investment Management LLC, Shanghai, 200120, China 2)Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA 3)Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA 4)Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences,Beijing 100190, China 5)Simbeyond B.V., P.O. Box 513, NL-5600 MB Eindhoven, The Netherlands 6)Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, United Kingdom 7)Max Planck Institute for Solid
    [Show full text]
  • Jaguar User Manual
    Jaguar User Manual Jaguar 7.9 User Manual Schrödinger Press Jaguar User Manual Copyright © 2012 Schrödinger, LLC. All rights reserved. While care has been taken in the preparation of this publication, Schrödinger assumes no responsibility for errors or omissions, or for damages resulting from the use of the information contained herein. BioLuminate, Canvas, CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike, and WaterMap are trademarks of Schrödinger, LLC. Schrödinger and MacroModel are registered trademarks of Schrödinger, LLC. MCPRO is a trademark of William L. Jorgensen. DESMOND is a trademark of D. E. Shaw Research, LLC. Desmond is used with the permission of D. E. Shaw Research. All rights reserved. This publication may contain the trademarks of other companies. Schrödinger software includes software and libraries provided by third parties. For details of the copyrights, and terms and conditions associated with such included third party software, see the Legal Notices, or use your browser to open $SCHRODINGER/docs/html/third_party_legal.html (Linux OS) or %SCHRODINGER%\docs\html\third_party_legal.html (Windows OS). This publication may refer to other third party software not included in or with Schrödinger software ("such other third party software"), and provide links to third party Web sites ("linked sites"). References to such other third party software or linked sites do not constitute an endorsement by Schrödinger, LLC or its affiliates. Use of such other third party software and linked sites may be subject to third party license agreements and fees. Schrödinger, LLC and its affiliates have no responsibility or liability, directly or indirectly, for such other third party software and linked sites, or for damage resulting from the use thereof.
    [Show full text]
  • A View of Covalent and Ionic Bonding from Maximum Probability Domains M
    A view of covalent and ionic bonding from Maximum Probability Domains M. Menéndez, A. Martín Pendás, Benoît Braïda, A. Savin To cite this version: M. Menéndez, A. Martín Pendás, Benoît Braïda, A. Savin. A view of covalent and ionic bonding from Maximum Probability Domains. Computational and Theoretical Chemistry, Elsevier, 2015, 1053, pp.142-149. 10.1016/j.comptc.2014.10.004. hal-01627697 HAL Id: hal-01627697 https://hal.archives-ouvertes.fr/hal-01627697 Submitted on 21 Nov 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. A view of covalent and ionic bonding from Maximum Probability Domains a,b a b,c, b,c M. Menéndez , A. Martín Pendás , B. Braïda ⇑, A. Savin a Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain b Sorbonne Universités, UPMC Univ. Paris 06, UMR 7616, LCT, F-75005 Paris, France c CNRS, UMR 7616, LCT, F-75005 Paris, France abstract Connecting the accurate Quantum Mechanics to the chemical view is the first of foremost purposes of interpretative methods in general, and topological analysis in particular. In this field of methods, the Maximum Probability Domains (MPD) analysis, is conceptually appealing but has not been extensively applied yet.
    [Show full text]
  • Jaguar User Manual
    Jaguar User Manual Jaguar 7.7 User Manual Schrödinger Press Jaguar User Manual Copyright © 2010 Schrödinger, LLC. All rights reserved. While care has been taken in the preparation of this publication, Schrödinger assumes no responsibility for errors or omissions, or for damages resulting from the use of the information contained herein. Canvas, CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike, and WaterMap are trademarks of Schrödinger, LLC. Schrödinger and MacroModel are registered trademarks of Schrödinger, LLC. MCPRO is a trademark of William L. Jorgensen. Desmond is a trademark of D. E. Shaw Research. Desmond is used with the permission of D. E. Shaw Research. All rights reserved. This publication may contain the trademarks of other companies. Schrödinger software includes software and libraries provided by third parties. For details of the copyrights, and terms and conditions associated with such included third party software, see the Legal Notices for Third-Party Software in your product installation at $SCHRODINGER/docs/html/third_party_legal.html (Linux OS) or %SCHRODINGER%\docs\html\third_party_legal.html (Windows OS). This publication may refer to other third party software not included in or with Schrödinger software ("such other third party software"), and provide links to third party Web sites ("linked sites"). References to such other third party software or linked sites do not constitute an endorsement by Schrödinger, LLC. Use of such other third party software and linked sites may be subject to third party license agreements and fees. Schrödinger, LLC and its affiliates have no responsibility or liability, directly or indirectly, for such other third party software and linked sites, or for damage resulting from the use thereof.
    [Show full text]