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SEAMM LAMMPS Plug-in

A SEAMM plug-in for LAMMPS, a forcefield-based molecular dynamics code.

This plug-in provides a graphical user interface (GUI) for setting up complex simulations using LAMMPS. It uses a sub-flowchart that provides steps such as constant pressure and temperature (NPT) dynamics which give access to the functionality in LAMMPS in a more consistent and understandable way than the inscrutable fixes that LAMMPS uses.

These sub-flowcharts mirror the main flowchart in form and function and can use the same variables such as temperature and pressure that are accessible anywhere in the flowcharts. This allows “programming” a LAMMPS workflow in the same familiar way that SEAMM uses to represent the overall workflow.

Features

  • Use of any forcefield supported by the forcefield plug-in:

    • PCFF

    • OpenKIM: EAM, MEAM, LJ, ReaxFF

  • Molecular statics: minimization

  • Molecular dynamics: NVE, NVT, and NPT with any of the approaches supported in LAMMPS

  • Automatic statistical analysis of averages from MD

    • Detection of equilibration

    • Mean and standard error of the mean for the sampling after equilibration

    • Autocorrelation function and time

    • Statistical inefficiency

    • Plotting of results in the Dashboard

  • Using property values to drive MD. Rather than running MD for a length of time, automatically run long enough to determine a set of properties within given error bars.

Acknowledgements

This package was created with Cookiecutter and the molssi-seamm/cookiecutter-seamm-plugin project template.

Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under award ACI-1547580

Development Team

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