:mod:`mdhandle` is a post-processing framework for molecular dynamics simulation, particularly fluid mechanics, materials science and other non-macromolecule simulation.
Currently, :mod:`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.
- Linux:
- Requires
Python 2.6
or higher in the2.x
series. Not compatible withPython 3.x
due to dependancy withNumPy
. Python
package dependencies:NumPy
SciPy
matplotlib
PyTables
IPython
sphinx
andnumpydoc
for documentation.- Python dependancies are downloaded automatically during install
by
easy_install
orpip
.
- OS X: See Linux.
- Windows: Windows support is unknown. As shipped, :mod:`mdhandle` is developed for POSIX systems and may operate using the
cygwin
environment.
To install :mod:`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
Systemwide settings are contained within :mod:`mdhandle.settings`. They can be modified within the file, or at runtime during program/script execution.
Example scripts can be found in the bin
directory, which is installed along with the :mod:`mdhandle` module by the python setup.py install
.
Additional scripts can be found at http://github.com/dtlussier/mdhandle_more_scripts
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. :mod:`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/.
- Dan Lussier, Fluidics and Biocomplexity Group, Oxford University (dtlussier@gmail.com, http://github.com/dtlussier)
Related Packages:
MMTK
, http://dirac.cnrs-orleans.fr/MMTK/MD-Tracks
, http://molmod.ugent.be/code/wiki/MD-Tracksmdanalysis
, http://code.google.com/p/mdanalysis/Pizza
, http://www.sandia.gov/~sjplimp/pizza.html
Thanks:
- Yiannis Ventikos, Fluidics and Biocomplexity Group, Oxford University