Bonan Zhu Computational Materials Scientist at UCL

Access the internet (for good) on login nodes behind firewalls

On some computing clusters the login nodes do not have internet access. This is a pain for installing software that requires pulling data from a repository, e.g. Python, Julia and many others. Lucky, there is a simple way to bypass this limitation without hacking through the firewall - SOCKS5 proxy with ssh reverse tunnelling. This allows the... Read more

enabling data compression in AiiDA 2.0

AiiDA 2.0 introduces the new storage format. Rather than placing files individually shard folders, an object storage is used. It includes storage backend stores the data and allows efficient retrival of the data using the hash computed from its content. By default, the disk-objectstore is used for this. The filenames and folder structures are n... Read more

DFT parallelisation rule of thumb

TL.DR for VASP Maximise k point parallelisation whenever possible keep number of bands per band group > 10 for GGA calculation use as little lower plane wave parallelisation as possible for hybrid calculations, but keep bands per band group > 4 do not over parallelise by using too many core - you can end in the wrong side of the ... Read more

Parallel efficiencies of (small) plane wave DFT calculations

Plane wave DFT calculations are often known as “cubic-scaling” where the cost grows as the number of atoms (more precisely the number of electrons) cubed. Thankfully, they can be parallelised over many (possibly very large number of cores) to accelerate the calculations. This is often done at multiple levels: the plane wave coefficients, the ban... Read more

Hello World!

This my first post using Jekyll - so hello world. The aim of this site is to provide a peronal space for sharing my research and also act as a blog. From time to time, I will post contents related to computational materials science and programming. Hopefully, they will be of the interests of my fellow researchers and peers! Read more