Display and analyse
AtomViewer is a visualization and analysis tool for atomistic
simulations, primarily molecular dynamics simulations.
By characterization of the atomic configuration it can display or filter
certain atoms, making crystal structures or other properties visible.
Plastic deformation in crystalline solids are mainly related to the
creation and movement of dislocations. These entities are not directly
part of atomistic simulations, but instead they need to be extracted from
the atomistic configuration. The detection and characterization of
dislocations and their Burgers vector is one of the main features of
AtomViewer, since it includes reference implementations for the
dislocation network detection and classification methods as published by
Begau et al. (1,2).
AtomViewer is open source and available free of charge under the terms of
the GNU General Public
- Dislocation analysis in FCC and BCC crystals
- Calculation of lattice rotation patterns
- Calculation of dislocation densities
- Import and rendering of any scalar values per atom
- Import of files in IMD format (Link)
or LAMMPS (Link) (partially
See examples what can be done using with AtomViewer
AtomViewer is cross-plattform software and should run on many different
plattforms as long as the following requirements are fullfilled
- installed Java SE 6 Runtime Enviroment or newer
- OpenGL 3.2 compatible graphic device (OpenGL 3.3 recommended)
- at least 1 GB of free RAM (the more the better)
- One of the following operating systems either in 32- or 64 bit version
(not all plattforms are tested, there is no guarantee for full support)
- Microsoft Windows (XP or later)
- MacOS X (10.7 or later)
- Linux (Ubuntu 11 or later, OpenSuse 10 or later, ...)
- Solaris (OpenSolaris 2009.06 or later)
The archive contains libraries for all supported plattforms.
AtomViewer is started by executing the scripts AtomViewer.bat (Windows) or
AtomViewer.sh (Linux, Mac).
AtomViewers sources are embedded into the file "AtomViewer.jar"
The most current versions are available on Github. Sources can be compiled using the included ant-build script.
Version 2.1 (January 23rd, 2015)
Atom Viewer 2.1
Developer build of Version 3 (March 13th, 2016)
Atom Viewer 3.0 preview
The developer version of an upcoming release that will include several major updates on AtomViewer. The jar file is compatible with the release 2.1.
Replace the file "AtomViewer.jar" in AtomViewer's directory with this one to update. Although still under development, this is the recommend version of AtomViewer.
Feature requests or recommendations are welcome to improve the usability.
Currently the following features are planned for the next version.
- A highly increased number of analysis routines that can be applied interactively on data sets including the following options (Partially implemented)
- Centrosymmetry analyis (done)
- Coordination number and atomic density (done)
- Spatial smoothing of any atomic quantity (done)
- Slip vector analysis (done)
- Computation of displacement and differences between snapshots (done)
- Approximation of surfaces (done)
- Common neighbor analysis (TBD)
- New user interface that is suited for a wider range of applications (Partially)
- Support for high-DPI displays (done)
- New rendering features, including the possibilty to display vector and tensor fields (Vector field renderer implemented, user interface incomplete)
- Customizable tool-chain in which a series of analysis steps can be defined and applied to sets of files either during opening the files or as standalone postprocessing (partially, still experimental. Only available if started using the argument "-exp")
- User-friendly way to modify several aspects of the analysis routines which are crystal-structure dependent without the need to write a plugin (Partially)
- Improved analysis capabilities for polycrystalline samples (TBD)
- Support for reading/writing further file-formats
- read XYZ/ExtXYZ (done)
- read CFG (done)
- write LAMMPS formats (TBD)
- write IMD (done)
Atom Viewer 1.2 final (Last build supporting OpenGL 2.0, released November 21th, 2013)
Please send questions and bug reports to