Recent Posts

More Posts

A piece of software I have been using in my reasearch is Hoomd, a ‘relatively’ new package for running Molecular Dynamics (MD) simulations. These MD simulations have the basic premise of throwing hundreds of balls into a box and shaking it to find out what happens. The relative newness of Hoomd is in comparison to other software packages like LAMMPS and GROMACS which have been around for decades, while the initial release of Hoomd was in 2012.

CONTINUE READING

Competition is a strange thing making you suddenly interested in the most unusual of problems It has become a tradition of The Lancer Band, of which I am a member, to produce a video as part of our ANZAC Day commemorations. These videos have been highly successful garnering millions of views on Facebook and with some choice communications throughout the rest of the year have resulted in a commendable social media following.

CONTINUE READING

In the right (or wrong) hands ssh is a powerful tool for the remote management of a Unix system. Most desktop, or workstation distributions of Linux disable remote access over ssh by default. The simplest method to check if you have ssh server running on your machine is to run $ ssh localhost If ssh is not installed or running this will print out a message ssh: connect to host localhost port 22: Connection refused most likely indicating that the ssh server is not running.

CONTINUE READING

Calling the current python visualisation landscape fragmented would probably be an understatement, since itself requires a visualisation to even begin to comprehend. For various reasons I have been unhappy with the tool I was using for visualisation at that time and I have been searching for the one visualisation package to rule them all (spoiler: it doesn’t exist) About a year ago I was using Matplotlib for all my figures, which enabled me to create anything I wanted, usually with a stackoverflow answer giving me a working example to adapt.

CONTINUE READING

You may have heard of a zip bomb or other decompression ‘bombs’, which have the basic premise of containing a large volume of highly redundant data that when decompressed takes up more resources than the system can handle. Within the HDF5 file format there is support for compression, an excellent tool for reducing file sizes, however also ripe for exploitation. This ‘issue’1 of a file containing far more data expected, whether accidental or malicious, is not limited to HDF5 files, any filetype supporting compression is susceptible.

CONTINUE READING