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.
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
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.