Skip to content

ReaxKit Examples

This directory contains runnable example scripts that demonstrate how to use ReaxKit in practice. These examples are intended to be:

  • minimal,
  • reproducible,
  • easy to modify,
  • executable without Jupyter notebooks.

They complement the tutorials in tutorials by showing working code rather than detailed explanations.

Directory structure

examples/
    data/
        control
        sample_tabular_data.csv
        small_fort.7
        small_xmolout

    xmolout_basic_example.py
    xmolout_fort7_example.py
    plotter_meta_example.py
    README.md

Data files (examples/data/)

The data/ subfolder contains small, truncated sample files used by the example scripts.

These files are intentionally small so that examples: - run quickly, - do not require large downloads, - are suitable for local testing.

Included files

  • small_xmolout
    Minimal xmolout trajectory for geometry-based analysis.

  • small_fort.7
    Minimal fort.7 file containing per-atom and bond-order information.

  • control
    Example ReaxFF control file (used for reference or input generation examples).

  • sample_tabular_data.csv
    Generic tabular data used by the meta plotting example.

Example scripts

xmolout_basic_example.py

Demonstrates direct Python usage of ReaxKit analyzers on an xmolout file.

Shows how to: - load xmolout with XmoloutHandler, - extract atom trajectories, - compute derived quantities (e.g. MSD), - inspect box and thermodynamic information, - export results to CSV.

This example mirrors the logic used in CLI workflows (as explained by 01_understanding_quickstart.md), but uses analyzers directly.

xmolout_fort7_example.py

Demonstrates multi-file analysis using both xmolout and fort.7.

Shows how to: - load geometry (xmolout) and chemical data (fort.7), - extract per-atom properties (charges, sum of bond orders), - construct connectivity graphs, - track bond-order time series and bond events, - compute coordination status using atom types and valences, - export results for further analysis or plotting.

This example corresponds to the concepts explained in 02_xmolout_fort7_coordination.md.

plotter_meta_example.py

Demonstrates use of ReaxKit’s meta plotting utilities on arbitrary tabular data.

Shows how to: - read a generic CSV file, - generate single-curve and multi-curve plots, - create directed plots, - generate dual y-axis plots, - visualize 3D scatter data, - project 3D data into 2D heatmaps.

This example is file-agnostic and does not rely on ReaxFF-specific semantics. A CLI tutorial for this existes in 04_plotter_meta_workflow.

Notes

  • These examples are not tests.
  • They are meant for learning, exploration, and validation.
  • For conceptual explanations, see tutorials.
  • For extending ReaxKit, see templates.

If you encounter issues running an example, verify that ReaxKit is installed correctly and that paths to the data/files are unchanged.