> 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.md).

# Software Features

The tools listed here cover the usual SWZ simulation chain from structure preparation to analysis. In most projects, the work moves through them in a fairly ordinary order: Atomsk for building or modifying structures, LAMMPS for the simulations themselves, and OVITO or Python-based analysis once the output needs to be inspected and interpreted.

## Core Tools

| Tool                                                                                                    | Purpose                                      | License                         |
| ------------------------------------------------------------------------------------------------------- | -------------------------------------------- | ------------------------------- |
| [LAMMPS](/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/lammps.md) | Molecular dynamics simulation engine         | GPL (open source)               |
| [Atomsk](/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/atomsk.md) | Atomic system builder and file converter     | GPL (open source)               |
| [OVITO](/good-research-practice-in-md-simulations-tuc-swz/infrastructures/software-features/ovito.md)   | Visualization and analysis of atomistic data | Free (Basic) / Commercial (Pro) |

## Additional Software on the SWZ Cluster

The following software is also installed on the [SWZ Rechencluster](/good-research-practice-in-md-simulations-tuc-swz/infrastructures/hardware-options/computing-cluster-at-tu-clausthal.md):

* **OpenMPI** -- message passing interface for parallel LAMMPS runs
* **Anaconda** -- Python distribution for data analysis and scripting
* **Singularity** -- container platform for reproducible computing environments
* **MatLab** -- numerical computing (campus license)
* **Mathematica** -- symbolic computation (campus license)
* **Abaqus** -- finite element analysis
* **Ansys** -- multiphysics simulation