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
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/MD-Molecules-Hoomd.git
cd MD-Molecules-Hoomd
conda env create
source activate statdyn-dev
python setup.py develop
Once the environment is setup the tests can be run with
pytest
Interaction with the program is currently through the command line, using the command line arguments to specify the various parameters.
To create a crystal structure for a simulation run
sdrun create --space-group p2 -s 1000 test.gsd
which will generate a file which has a trimer molecule with a p2 crystal structure. The simulation will be run for 1000 steps at a default low temperature to relax any stress.
For other options see
sdrun create --help
This output file we created can then be equilibrated using
sdrun equil -t 1.2 -s 1000 test.gsd test-1.2.gsd
which will gradually bring the temperature from the default to 1.2 over 1000
steps with the final configuration output to test-1.2.gsd. This is unlikely
to actually equilibrate this configuration, but it will run fast.
A production run can be run with the prod sub-command
sdrun prod -t 1.2 -s 1000 test-1.2.gsd
This has a different series of options including outputting a series of
timesteps optimised for the analysis of dynamics quantities in the file
prefixed with trajectory-. This dynamics optimised file can be analysed
with
sdrun 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
sdrun figure
will open up a bokeh server which will allow for the interactive visualisation
of all dump-*.gsd files in the current directory.