sdanalysis 0.9.3

Statistical dynamics analysis of molecular dynamics trajectories.

Statdyn Analysis

This is a set of scripts that use Hoomd to perform the Molecular dynamics simulations of a glass forming molecular liquid. There is a particular focus on understanding the dynamic properties of these molecules.

Note that this is still very early alpha software and there are likely to be large breaking changes that occur.

Installation

The simplest method of installation is using conda. To install

conda install -c malramsay statdyn-analysis

It is also possible to set the repository up as a development environment, in which case cloning the repository and installing is possible by running

git clone https://github.com/malramsay64/statdyn-analysis.git
cd statdyn-analysis
conda env create
source activate sdanalysis-dev
python setup.py develop

Once the environment is setup the tests can be run with

pytest

Running Analysis

Dynamics of a trajectory can be computed using the command

sdanalysis comp-dynamics trajectory-Trimer-13.50-1.20.gsd

which will generate an hdf5 file of the same name containing a single table, dynamics which has all the dynamic quantities tabulated. This also includes a start index, over which statistics can be computed.

Finally the command

sdanalysis figure

will open up a bokeh server which will allow for the interactive visualisation of all dump-*.gsd files in the current directory.