Atomsk
Description
Atomsk is an Open Source command-line program dedicated to the creation, manipulation, and conversion of atomic systems. It supports the file formats used by many programs, including:
- Visualization softwares: Atomeye, OVITO, VESTA, XCrySDen;
- Ab initio calculation softwares: Quantum Espresso, VASP, SIESTA;
- Classical force-field simulation softwares: DL_POLY, GULP, IMD, LAMMPS, XMD;
- TEM image simulation softwares: Dr Probe, JEMS, QSTEM.
Atomsk can be used to transform and shape atomic systems: duplicate, rotate, deform, insert dislocations, merge several systems, create bicrystals and polycrystals, etc.
Licencs
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of atomsk and load default version of atomsk as
module avail atomsk/ # list available modules module load atomsk # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail atomsk
and choose explicit version you want to use.