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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:
Atomic Simulation Environment
News
Overview
Installation guide
Installation with package manager on Linux
Installation on OS X
Installation on Windows
Manual installation
Requirements
Installation process
Download
Latest stable release
Latest development release
Run the tests
Video tutorial
Tutorials
Python
What is Python?
Executing Python code
Types
Loops
Functions and classes
Importing modules
ASE
Introduction: Nitrogen on copper
Atoms
Calculators
Structure relaxation
Input-output
Visualization
Molecular dynamics
Manipulating atoms
Atomization energy
Finding lattice constants
HCP
Analysis
Using the stress tensor
Equation of state
Diffusion of gold atom on Al(100) surface (constraint)
Self-diffusion on the Al(110) surface (NEB + Dimer method exercise)
Diffusion of gold atom on Al(100) surface (NEB)
Restarting NEB
Parallelizing over images with MPI
Image Dependent Pair Potential for improved interpolation of NEB initial guess
Example 1: Ethane
Example 2: N diffusion over a step edge
Dissociation tutorial
Using the spacegroup subpackage
Examples of setting up bulk structures
Aluminium (fcc)
Iron (bcc)
Magnesium (hcp)
Diamond
Sodium chloride
Rutile
CoSb3 skutterudite
The Spacegroup class
Molecular dynamics
Constant temperature MD
Isolated particle MD
Partly occupied Wannier Functions
Constrained minima hopping (global optimization)
Optimization with a Genetic Algorithm
A Brief Overview of the Implementation
A Basic Example
Running the GA in Parallel
Relaxations in Parallel on the Same Computer
Running the GA together with a queing system
GA Search for stable FCC alloys
Basic outline of the search
Setting up reference database
Initial population
Run the algorithm
Extending the algorithm
Extra mutation operators
Prevent identical calculations from being performed
Reuse of calculations between algorithm runs
NumPy
Numeric arrays in Python
Further reading
Exercises
Siesta 1: Basis Sets
Part 1: Standard basis sets
Part 2: Optimized basis sets
Tips
Siesta 2: Molecular Dynamics
Videos
Documentation for modules in ASE
The Atoms object
Working with the array methods of Atoms objects
Unit cell and boundary conditions
Special attributes
Adding a calculator
List-methods
Other methods
List of all Methods
The Atom object
Getting an Atom from an Atoms object
Units
The
ase.data
module
File input and output
Examples
ase-gui
ase-gui basics and command line options
General use
Files
Selecting part of a trajectory
Writing files
Interactive use
NEB calculations
Plotting data from the command line
Defaults for ase-gui
High contrast settings for ase-gui
Edit
Add atoms
Modify
Copy/Paste
View
Repeat
Rotate
Colors
Settings
Tools
Graphs
Movie
Expert mode
Constraints
Render scene
Move atoms
Rotate atoms
Orient atoms
NEB
Bulk Modulus
Setup
Calculate
Set calculator
Energy and forces
Energy minimization
Scale system
Command line tools in ASE
Help
Bash completion
Creating atomic structures
Molecules
Common bulk crystals
Nanotubes
Graphene nanoribbons
Surfaces
Common surfaces
Example
Utility functions for setting up surfaces
The following functions are provided
Adding new utility functions
Adding adsorbates
Create specific non-common surfaces
Example
General crystal structures and surfaces
Example
Available crystal lattices
Usage
Defining new lattices
Lattices with more than one element
Structure optimization
Local optimization
BFGS
LBFGS
FIRE
MDMin
SciPy optimizers
BFGSLineSearch
Global optimization
Basin hopping
Minima hopping
Parallel calculations
Visualization
Mayavi
VTK
PrimiPlotter
FieldPlotter
ASE-VTK
Representing atoms
Atom-centered data
Predefined shapes
Calculators
Supported calculators
Calculator keywords
QMMM
Calculator interface
Electronic structure calculators
Constraints
The FixAtoms class
The FixBondLength class
The FixBondLengths class
The FixedLine class
The FixedPlane class
The FixedMode class
The Hookean class
The FixInternals class
Combining constraints
Making your own constraint class
The Filter class
The UnitCellFilter class
The StrainFilter class
Nudged elastic band
The NEB class
Interpolation
Trajectories
Restarting
Climbing image
Parallelization over images
Analysis of output
Vibration analysis
Phonon calculations
Example
Phase diagrams and Pourbaix diagrams
Pourbaix diagrams
Thermochemistry
Ideal-gas limit
Example
Harmonic limit
Crystals
Example
Background
Infrared intensities
Molecular dynamics
Choosing the time step
File output
Logging
Constant NVE simulations (the microcanonical ensemble)
Velocity Verlet dynamics
Constant NVT simulations (the canonical ensemble)
Langevin dynamics
Nosé-Hoover dynamics
Berendsen NVT dynamics
Constant NPT simulations (the isothermal-isobaric ensemble)
Berendsen NPT dynamics
Density Functional Theory
Brillouin zone sampling
Monkhorst-Pack
Chadi-Cohen
Special points in the Brillouin zone
Maximally localized Wannier functions
Introduction
The Wannier class
Density of states
More details
Band gap
STM images
Bader Analysis
Electron transport
The data module
Atomic data
Molecular data
S22, s26, and s22x5 data
Trajectory files
Trajectory
Examples
The TrajectoryReader and TrajectoryWriter objects
PickleTrajectory
Converting old PickleTrajectory files to new Trajectory files
BundleTrajectory
See also
Utillity functions and classes
Equation of state
Geometry tools
Symmetry analysis
Phonons
Building neighbor-lists
Setting up an OPLS force field calculation
Modified xyz
Defining the force field
A database for atoms
What’s in the database?
ase-db
Querying
Integration with other parts of ASE
Browse database with your web-browser
Python Interface
Dictionary representation of rows
Extracting Atoms objects from the database
Add additional data
Row objects
More details
Genetic Algorithm
Optimization with a Genetic Algorithm
A Brief Overview of the Implementation
A Basic Example
Running the GA in Parallel
Relaxations in Parallel on the Same Computer
Running the GA together with a queing system
GA Search for stable FCC alloys
Basic outline of the search
Setting up reference database
Initial population
Run the algorithm
Extending the algorithm
Extra mutation operators
Prevent identical calculations from being performed
Reuse of calculations between algorithm runs
Dimer method
Frequently Asked Questions
ASE-GUI
How do I export images from a trajectory to png or pov files?
General
Citation: how should I cite ASE?
Download
Glossary
Mailing Lists
Internet Relay Chat
License
Human-readable version
Legal version of the license
What happens when ASE Calculators are under another license?
ASE development
Development topics
Release notes
Development version in trunk
Version 3.9.0
Version 3.8.0
Version 3.7.0
Version 3.6.0
Version 3.5.1
Version 3.5.0
Version 3.4.1
How to contribute
SVN access
Committers
Using version control (SVN)
Coding Conventions
Importing modules
Python Coding Conventions
General advice
Writing documentation in the code
Run pep8 and pyflakes on your code
Run autopep8.py on your code
Using pylint to check your code
Run epydoc on your code
Writing documentation
Installing Docutils and Sphinx
Other requirements
Using Sphinx
Extensions to Sphinx
Running Python code to create figures
reStructedText in emacs
Updating Sphinx
Setting up development environment with Vagrant
Adding new calculators
Description of base-classes
The Calculator base-class
The FileIOCalculator class
Making movies
using recordmydesktop
using avconf to collect png files
New release
Testing the code
How to fail successfully
Buildbot
Configuration of buildmaster
Installation and configuration of buildslaves
Installation
Fedora
OS X
RHEL5
RHEL6
RHEL7
Windows
Configuration
Translate ASE
How to translate
Check and commit your translation
Maintaining translations
To do
Documentation
Code
Python 3 strategy
ASE enhancement proposals
Calculator interface proposal
Behavior
Standards parameters
ABC calculator example
Implementation
Testing
Command line tools
Current status
Proposed set of command line tools
Comments
Naming convention
Implementation details
Creating an encrypted password for SVN access
Bugs!
Bug report
Known bugs
Porting old ASE-2 code to version 3
The ASE2ase tool
ASE
Overview
Installation
Tutorials
Documentation
FAQ
Mailing lists
Release notes
License info
Development
Development
Epydoc
Source code (svn)
Bugs!
Bug Tracker
BuildBot
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