This package aims to provide a means of producing reusable analysis of Molecular Dynamics (MD) output in the IPython Notebook.
See http://ipymd.rtfd.io for the full documentation!
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
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 dataframes, which are easy to create and use independantly from this package, in order to extend its functionality.
Anaconda is recommended to create a Python environment within which to use ipymd:
conda create -n ipymd -c cjs14 ipymd
source activate ipymd
jupyter notebook
Currently the conda package is only available for OSX. For other operating systems, or to use the latest version from Github, the following environment should work:
conda create -n ipymd python=2.7.11=0 numpy scipy matplotlib pandas ipython ipython-notebook pillow pyopengl pyqt six
If there are any issues, see the known working package dependancies list: https://github.com/chrisjsewell/ipymd/blob/master/working_dependencies_list_osx.txt
In the IPython Notebook, the ipymd package can then be imported.
import ipymdipymd 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 as well. See license_lgpl.txt and license_gpl.txt files attached.