Tutorials & Miscellaneous

  • VASP tutorial (2010-2014) :    A short tutorial for novice VASP users. I presented this tutorial as a seminar on several occasions. It should get you started doing the most standard (simple) calculations: e.g. a relaxation, a self consistent calculation, a DOS or band structure calculation…
  • d-orbitals and f-orbitals : The result of some exercises from the exercise-sessions of the course “Introductory Quantum Mechanics” I supported at the University of Twente. They show some 3D images and animations of certain d-and f-orbitals as generated using Maple and gnuplot. In addition to presenting nice pictures of these orbitals, they serve as an example showing what may go wrong when you use software as black box magic.

Useful/Interesting Links

  • wikipedia : The well-known online encyclopedia and worthy counterpart of Encyclopædia Britannica. A comparative study by nature showed both to be comparable with regard to their accuracy. Next to being an interesting source to start your search for information, it is also a location where you can share your gathered/specialized knowledge with the rest of the world.
  • arXiv : Since articles in highly regarded and peer reviewed journals tend to stay hidden behind expensive subscriptions, and because the time between submission and publication often takes multiple months, it is always interesting to have a look at what is being published on a preprint server such as ArXiv. Also, already published articles can be found here, making them a valuable source of reference material, when subscriptions block your access to the paper you are looking for.
  • Researchgate : The linkedin/facebook of the modern scientist. This social medium allows you to create a profile and tracks down your publications. Based on your interaction with other scientists (publications/answering and posing questions/…) a scientific reputation index is calculated. Although it is interesting to have if you plan a long term scientific career, it also provides an alternate way of getting your hands on the newest publications since many scientists post full-text versions of their work here, or you can ask the author of an interesting publication privately for a copy  if none are available.
  • Math world :  This is what happens when a mathematician has nothing to do and gets bored. Math world is a sort of Wikipedia of mathematics. If you cannot find what you are looking for there can be three reasons. (1) you are looking for it the wrong way, (2) it isn’t present (yet), and (3) “You are out of your league, now the real fun begins.”
  • Science world :  This is the parent webpage for the above Math world. Next to the mathematics webpages there are also pages on Physics, Astronomy, Chemistry and biographies of scientists.
  • Simulations :   This webpage, of the University of Colorado, hosts a set of Java-applets which allow you to investigate some of the basic principles of Physics. There is, for example, a simple model of how an MRI works, but also an example explaining the Photo-electric effect (for which Albert Einstein got the 1921 physics Nobel price).
    There are also some applets which allow you to play with potential barriers and the tunneling of wave packets through these barriers.
  • :  Online journal (IOP) containing clear articles on the latest in Physics research. Links to the original articles are present, as are links to similar older articles.
  • Stukjes onderzoek : The blog (in Dutch) of Sylvia Wenmackers, a physicist and philosopher of science, where she discusses both physics and philosophy of science related to her life and work.
  • UGentBloggers : Blogs of other researchers at UGent.


Surviving Unix/Linux/HPC environments:

  • Midnight Commander:

    Midnight Commander (or mc) is a very useful tool which allows you to browse *nix folder-structures with a system akin to the windows file-explorer. Especially if you have extensive folder-structures this tool will come in handy, as it makes switching folders and copying data extremely easy. There is also an easy to use text-editor (a true WYSIWYG text editor, unlike the horror vi(m), which for some reason continues existence.)  To get access to this tool on the TIER-1 /TIER-2 systems installed at UGent you need to do nothing as it is a default part of their installation. To get access to this tool on TIER-1/TIER-2 systems installed at KULeuven you need to module load mc (Unfortunately the install isn’t automatically linked to the script so you keep getting thrown back to the directory you started from. This can be solved by adding a cluster specific alias (i.e. an alias inside a case loop targeting different clusters).
    For Breniac you need to use following alias mc=’. /apps/leuven/broadwell/2016a/software/mc/4.8.13-GCCcore-4.9.3/libexec/mc/’, while for
    Thinking you need to use alias mc=’. /apps/leuven/thinking/2014a/software/mc/4.6.1/share/mc/bin/’  ).

  • XmGrace:

    XmGrace is a useful and simple WYSIWYG graphics program which allows you to create 2D plots of your data. You get extensive control over the layout of the graphs and multiple output formats (both raster and vector formats). In addition, it is possible to script this program, allowing for the creation of identical graphs for a large set of data. This program can be installed within a cygwin installation. Grace is available at UGent through module load grace, at KULeuven no grace module is available.