> For the complete documentation index, see [llms.txt](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://tu-clausthal.gitbook.io/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/atomsk.md).

# Atomsk

A tool for building and manipulating atomic systems for MD simulations

[Atomsk](https://atomsk.univ-lille.fr/) is a practical tool for preparing structures before they ever reach LAMMPS. At SWZ, it is most useful when a project needs something more deliberate than a hand-edited data file: building a supercell, introducing a defect, converting between formats, or generating a starting structure that will later be relaxed and simulated elsewhere.

## Key Features

Atomsk is especially helpful for four kinds of jobs: creating regular atomic systems such as unit cells and supercells, introducing defects such as vacancies or dislocations, converting between file formats, and making geometric changes to an existing system without rewriting everything by hand. That combination makes it a good bridge between structure preparation and the rest of an MD workflow.

## Common Usage Examples

Create an FCC copper supercell:

```bash
atomsk --create fcc 3.615 Cu orient [110] [1-10] [001] -duplicate 10 10 10 Cu_supercell.lmp
```

Generate a polycrystalline sample:

```bash
atomsk --polycrystal Cu_unitcell.xsf polycrystal.txt Cu_polycrystal.lmp
```

Convert between file formats:

```bash
atomsk input.xyz output.lmp
```

Introduce an edge dislocation:

```bash
atomsk Cu_supercell.lmp -dislocation 0.5*BOX 0.5*BOX edge z y 2.556 0.33 dislocation.lmp
```

## Installation

Atomsk is open source and can be installed from the [official website](https://atomsk.univ-lille.fr/dl.php) or compiled from source. Pre-compiled binaries are available for Linux, macOS, and Windows. In practice, it is often enough to keep a local installation on the workstation where structures are prepared and then move the resulting files into the main project directory.

## Resources

The [Atomsk documentation](https://atomsk.univ-lille.fr/doc.php) is concise and worth reading directly. The [tutorials](https://atomsk.univ-lille.fr/tutorial.php) are particularly useful when working with dislocations, grain boundaries, or polycrystals, and the [GitHub repository](https://github.com/pierrehirel/atomsk) is the right place to check source code and release information.