MDMC package

Subpackages

Module contents

MDMC is a Python 3 package for optimising classical molecular dynamics (MD) potential parameters by refining against experimental data, particularly dynamical data such as the dynamic structure factor. The refinement uses derivative free optimisation algorithms, e.g. Monte Carlo (MC).

Documentation

MDMC has three different forms of documentation:

docstrings provided within the code, such as this one. These can viewed from the Python command shell (REPL) by calling the help() function on the class, function, method or object. In an interactive (ipython) command shell, ? can also be used after a class, function, method or object.
Online documentation, built from /doc, and available on the MDMC homepage.
Interactive (Jupyter notebook) tutorials, available within /doc/tutorials, which provide in dept descriptions and examples of specific features of MDMC.

Available subpackages

common: Functions and classes common to all subpackages
control: Uses refinement and MD subpackages to control MDMC parameter optimisation
gui: Provides GUI functionality
MD: Molecular dynamics tools and engine interfaces
readers: Atomic configuration and experimental observable file readers
refinement: Algorithms for refining parameters
trajectory_analysis: Tools related to creating trajectories and calculating observables from them

Logging

By default MDMC will log a single process regardless of whether it is being run in serial or parallel. The process will log to ‘MDMC.log’.