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https://github.com/molssi-seamm/lammps_step

A SEAMM plug-in for LAMMPS, a forcefield-based molecular dynamics code.
https://github.com/molssi-seamm/lammps_step

computational-chemistry computational-materials-science lammps molssi molssi-seamm

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

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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.



* Free software: BSD license

* Documentation: https://molssi-seamm.github.io/lammps_step/index.html

* Code: https://github.com/molssi-seamm/lammps_step



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.



.. _Cookiecutter: https://github.com/audreyr/cookiecutter

.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin



Developed by the Molecular Sciences Software Institute (MolSSI_),

which receives funding from the `National Science Foundation`_ under

award ACI-1547580



.. _MolSSI: https://www.molssi.org

.. _`National Science Foundation`: https://www.nsf.gov