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ReaxKit Examples

This directory contains runnable scripts that demonstrate current ReaxKit usage.

Directory structure

examples/
    data/
        control
        sample_tabular_data.csv
        small_fort.7
        small_xmolout
    xmolout_basic_example.py
    connectivity_multifile_example.py
    gen_plot_presentation_example.py
    multi_engine_get_msd_cli_blueprint.py
    README.md
    lifs_box_pipeline/
        data/
            fort.90
        prepare_lis_box.py
        run_fort90_to_xmolout.py
        README.md
    romp_active_control/
        data/
            fort.90
            monomer.bgf
        config.yaml
        romp_edit_ops.py
        run_active_step.py
        README.md

Example scripts

xmolout_basic_example.py

Demonstrates direct Python-task usage on xmolout data: - load trajectory via XmoloutHandler - extract coordinate series - compute MSD - extract cell dimensions - export CSV outputs

connectivity_multifile_example.py

Demonstrates multi-file connectivity/charge analysis with xmolout + fort.7: - load ConnectivityData and ChargeData - extract charge and sum-bond-order features - build connection lists/tables/stats - detect bond events - compute coordination status

Related tutorial: 02_atom_property_and_video_workflows.md

gen_plot_presentation_example.py

Demonstrates file-agnostic plotting utilities on tabular data: - single and multi-series plots - directed plots - dual y-axis plots - 3D scatter - 2D heatmap projection

Related tutorial: 04_gen_plot_workflow.md

multi_engine_get_msd_cli_blueprint.py

Demonstrates a task-first, multi-engine architecture blueprint for reaxkit get_msd style flows.

LiFS box pipeline/

Demonstrates a reusable workflow for generating packed Li/S structures from ReaxFF/XTLGRF fort.90 files. It coordinates several reusable ReaxKit modules and produces new files from an input structure.

ROMP active-control/

Demonstrates a config-driven simulation controller that reads a ReaxFF fort.90 state, removes selected molecular fragments, inserts a monomer with overlap checks, and writes next-step geo plus report files.

Notes

  • These examples are for learning and exploration, not formal tests.
  • For conceptual walkthroughs, use tutorials.