iki.fi Euler
Introduction
Euler is a command line tool for processing and analysing atomic data, for example from molecular dynamics simulations. The idea of the program is that one read's in a system from a file, or constructs one from a basis, and then all commands given as command line arguments are executed on the system in the order in which they're given, so various combinations can be used flexibly to achieve more than any single command could.
The program currently supports well xyz-files and constructing a system using a basis with a simple file format. It works especially well with the xyz-files produced by the MD-code Parcas, but also has for example LAMMPS-functionality.
Features include basic manipulation, clustering, removing atoms based on different criteria, and different analysis methods such as common neighbour analysis, identifying liquid/solid atoms, identifying bonds, hydrogen bonds and molecules, searching for vacancies, etc.
Licence
Euler is licenced under GPL v2, except that it contains the Mersenne Twister random number generator, the licence of which is here.
News
- 2013-04-19 New version available (r276). Also included a tool to create nanocrystalline systems using a Voronoi construction (such as the one in the picture above). This is based on the same components as euler so carries the same versioning.
- 2012-03-22 New version available (r244), see below for changes.
- 2011-07-12 Made the program available here. The current version is r216.
Download
The program is standard C++ and should be easy enough to compile. GSL is needed, though. For help on usage, run without arguments and see the man-file.
The versions will be identified by the Subversion revision.
- euler & voronoi r276
- Euler source .tar.bz2
- Voronoi source .tar.bz2
- Several small improvements and bug fixes.
- euler r244
- Source .tar.bz2
- Changes include:
- File formats: better LAMMPS support including identification and output of bonds/angles/dihedrals, output of Siesta .fdf files.
- Small improvements and bug fixes.
- New commands, including adjusting scaling of units (length, time), simulating AFM tip images, tracking atomic displacement.
- euler r216