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.

• Free software: BSD license
• Documentation: https://molssi-seamm.github.io/lammps_step/index.html
• Code: https://github.com/molssi-seamm/lammps_step

• 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.

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