AtomViewer
Display and analyse atomistic simulations

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 License (GPL)

Features

• 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 supported)
  

See examples what can be done using with AtomViewer

System requirements
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)

Examples

Download

• 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)

Literature and references

(1) http://dx.doi.org/10.1016/j.actamat.2010.10.016
(2) http://dx.doi.org/10.1016/j.jmps.2011.12.005

Contact

christoph.begau@rub.de

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