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  • ASE ManualRelease 3.9.0.3484

    CAMd

    January 19, 2014

  • CONTENTS

    1 Atomic Simulation Environment 31.1 News . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

    2 Overview 7

    3 Installation requirements 9

    4 Download 114.1 Latest stable release . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114.2 Latest development release . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

    5 Installation 135.1 Installation on OS X . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135.2 Installation with package manager on Linux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135.3 Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145.4 Manual installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155.5 Run the tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165.6 Video tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

    6 Tutorials 176.1 Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176.2 ASE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206.3 NumPy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466.4 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 486.5 Videos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

    7 Documentation for modules in ASE 537.1 The Atoms object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 537.2 The Atom object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657.3 Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 677.4 The ase.data module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 677.5 File input and output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 677.6 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 707.7 ASE-GUI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 727.8 Command line tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 797.9 Creating atomic structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 837.10 Structure optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 977.11 Parallel calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1027.12 Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1037.13 ASE-VTK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1077.14 Calculators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1107.15 Constraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1497.16 Nudged elastic band . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1557.17 Vibration analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

    i

  • 7.18 Phonon calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1597.19 Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1597.20 Infrared intensities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1627.21 Molecular dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1647.22 Density Functional Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1687.23 Electron transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1777.24 The data module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1787.25 Trajectory files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1817.26 Utillity functions and classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1847.27 Thermochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1857.28 Building neighbor-lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1917.29 Setting up an OPLS force field calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1927.30 A database for atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193

    8 Frequently Asked Questions 1998.1 ASE-GUI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1998.2 General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1998.3 Download . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200

    9 Glossary 201

    10 Mailing Lists 20310.1 Internet Relay Chat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203

    11 License 20511.1 Human-readable version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20511.2 Legal version of the license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20511.3 What happens when ASE Calculators are under another license? . . . . . . . . . . . . . . . . . . 205

    12 ASE development 20712.1 Development topics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20712.2 Creating an encrypted password for SVN access . . . . . . . . . . . . . . . . . . . . . . . . . . 234

    13 Bugs! 23513.1 Bug report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23513.2 Known bugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235

    14 Porting old ASE-2 code to version 3 23714.1 The ASE2ase tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237

    Bibliography 239

    Python Module Index 241

    Index 243

    ii

  • ASE Manual, Release 3.9.0.3484

    Introduction to ASE - what is it?

    Download and installation instructions

    Tutorials

    Documentation for modules in ASE

    Frequently Asked Questions

    Mailing Lists

    Glossary

    License

    ASE development

    Bugs!

    Porting old ASE-2 code to version 3

    The complete table of contents:

    CONTENTS 1

  • ASE Manual, Release 3.9.0.3484

    2 CONTENTS

  • CHAPTER

    ONE

    ATOMIC SIMULATION ENVIRONMENT

    The Atomic Simulation Environment (ASE) is the common part of the simulation tools developed at CAMd. ASEprovides Python modules for manipulating atoms, analyzing simulations, visualization etc.

    Note: The old ASE-2 webpage has moved to http://wiki.fysik.dtu.dk/ase2.

    Supported calculators:

    Gaussian

    3

  • ASE Manual, Release 3.9.0.3484

    Mopac

    1.1 News

    ASE version 3.8.0 released (22 October 2013).

    ASE version 3.7.0 released (13 May 2013).

    ASE version 3.6.0 released (24 February 2012).

    Bugfix release: ASE version 3.5.1 (24 May 2011).

    ASE version 3.5.0 released (13 April 2011).

    ASE version 3.4.1 released (11 August 2010).

    ASE version 3.4 released (23 April 2010).

    ASE version 3.3 released (11 January 2010).

    ASE version 3.2 released (4 September 2009).

    ASE has reached revision 1000 (16 July 2009).

    ASE version 3.1.0 released (27 March 2009).

    Improved vibrations module: More accurate and possibility to calculate infrared intensities(13 March 2009).

    ASE version 3.0.0 released (13 November 2008).

    4 Chapter 1. Atomic Simulation Environment

  • ASE Manual, Release 3.9.0.3484

    Asap version 3.0.2 released (15 October 2008).

    An experimental abinit interface released (9 June 2008).

    Thursday April 24 will be ASE documentation-day. Ten people from CAMd/Cinf will do a doc-sprintfrom 9 to 16. (17 Apr 2008)

    The new ASE-3.0 Sphinx page is now up and running! (2 Apr 2008)

    A beta version of the new ASE-3.0 will be used for the electronic structure course at CAMd. (10 Jan 2008)

    1.1. News 5

  • ASE Manual, Release 3.9.0.3484

    6 Chapter 1. Atomic Simulation Environment

  • CHAPTER

    TWO

    OVERVIEW

    ASE is an Atomistic Simulation Environment written in the Python programming language with the aim of settingup, steering, and analyzing atomistic simulations. The ASE has been constructed with a number of design goalsthat make it:

    Easy to use:

    Setting up an atomistic total energy calculation or molecular dynamics simulation with ASE is simple andstraightforward. ASE can be used via a graphical user interface, a Command line tool and thePython language. Python scripts are easy to follow (see What is Python? for a short introduction). It issimple for new users to get access to all of the functionality of ASE.

    Flexible:

    Since ASE is based on the Python scripting language it is possible to perform very complicated simulationtasks without any code modifications. For example, a sequence of calculations may be performed with theuse of simp