Welcome to Molecular Dynamics Analysis for IPython (ipyMD)!

This package aims to provide a means of producing reusable analysis of Molecular Dynamics (MD) output in the IPython Notebook.

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Analysis of the atomic coordination of Na, wrt Cl, for an NaCl nano-crystal.

There are many programs for 3D visualisation of MD output (my favourite being Ovito). However, there lacks a means to produce a more thorough, documented analysis of the data. IPython Notebooks are ideal for this type of analysis and so the objective of ipymd is to produce a Python package that can be used in conjuction with programmes like Ovito, to produce documented and reuseable analysis.

The aim of ipymd is to produce IPython Notebooks that include:

  • Static images of the simulations
  • Analysis of simulation data, including graphical plots

It has been created with the goal to be:

  • Easy to use
  • Easy to extend

chemlab It builds primarily on the chemlab package, that is an API layer on top of OpenGL. Data is parsed in standard formats, such as [pandas](http://pandas.pydata.org/) dataframes, which are easy to create and use independantly from this package, in order to extend its functionality.

Author Chris Sewell
Project Page https://github.com/chrisjsewell/ipymd


ipymd is released under the GNU GPL3 or GNU LGPL license, if the PyQt parts are omitted (in ipymd.visualise.opengl) and the ipymd.data_input.spacegroup package is omitted, ipyMD is released under the GNU GPLv3 and its main developer is Chris Sewell.