mdhandle - README - v0.9

Introduction

mdhandle is a post-processing framework for molecular dynamics simulation, particularly fluid mechanics, materials science and other non-macromolecule simulation.

Currently, mdhandle is focused on interacting with result produced by the LAMMPS (http://lammps.sandia.gov) software package, but could be extended to handle the results from other software packages.

System Requirements

1. Linux:

• Requires Python 2.6 or higher in the 2.x series. Not compatible with Python 3.x due to dependancy with NumPy.

• Python package dependencies:

  • NumPy
  • SciPy
  • matplotlib
  • PyTables
  • IPython
  • sphinx and numpydoc for documentation.
  • Python dependancies are downloaded automatically during install by easy_install or pip.

2. OS X: See Linux.
3. Windows: Windows support is unknown. As shipped, mdhandle is developed for POSIX systems and may operate using the cygwin environment.

Install

To install mdhandle, run :

>>> python setup.py install

This command will install Python modules, and build the LAMMPS library extension. It is advisable to install the module rather than using it in place within the source tree. To avoid polluting the system site-packages directory, virtualenv should be used.

Source and binary distributions can also be created by :

>>> python setup.py sdist

or :

>>> python setup.py bdist

Configuration

Systemwide settings are contained within mdhandle.settings. They can be modified within the file, or at runtime during program/script execution.

Scripts

Example scripts can be found in the bin directory, which is installed along with the mdhandle module by the python setup.py install.

Additional scripts can be found at http://github.com/dtlussier/mdhandle_more_scripts

Documentation

After installation is complete, documentation can be found within the doc folder.

Sphinx (http://sphinx.pocoo.org/) is required to build the documentation via: :

% cd doc
% make html

The resulting docs are then at doc/_build/html/index.html. Other available build formats can be seen by invoking: :

% cd doc
% make

Building the documentation at the local level reflects any changes made at the local level. mdhandle must be in your PYTHONPATH to build docs using sphinx.

A persistent version of the documentation reflecting the github version is at http://dtlussier.github.com/mdhandle/.

Authors

• Dan Lussier, Fluidics and Biocomplexity Group, Oxford University (dtlussier@gmail.com, http://github.com/dtlussier)

Acknowledgements

Related Packages:

• MMTK, http://dirac.cnrs-orleans.fr/MMTK/
• MD-Tracks, http://molmod.ugent.be/code/wiki/MD-Tracks
• mdanalysis, http://code.google.com/p/mdanalysis/
• Pizza, http://www.sandia.gov/~sjplimp/pizza.html

Thanks:

• Yiannis Ventikos, Fluidics and Biocomplexity Group, Oxford University