Tag: academia

Review of 2017

Happy New Year

2017 has come and gone. 2018 eagerly awaits getting acquainted. But first we look back one last time, trying to turn this into a old tradition. What have I done during the last year of some academic merit.

Publications: +4

Completed refereeing tasks: +8

  • The Journal of Physical Chemistry (2x)
  • Journal of Physics: Condensed Matter (3x)
  • Diamond and Related Materials (3x)

Conferences & workshops: +5 (Attended) 

  • Int. Conference on Diamond and Carbon Materials (DCM) 2017, Gothenburg, Sweden, September 3rd-7th, 2017 [oral presentation]
  • Summerschool: “Upscaling techniques for mathematical models involving multiple scales”, Hasselt, Belgium, June 26th-29th, 2017 [poster presentation]
  • VSC-user day, Brussels, Belgium, June 2nd, 2017 [poster presentation]
  • E-MRS 2017 Spring Meeting, Strasbourg, France, May 22nd-26th, 2017 [1 oral + 2 poster presentations]
  • SBDD XXII, Hasselt University, Belgium, March 8th-10th, 2017 [poster presentation]

PhD-students: +1

  • Mohammadreza Hosseini (okt.-… ,Phd student physical chemistry, Tarbiat Modares University, Teheran, Iran)

Bachelor-students: +2

Current size of HIVE:

  • 48.5K lines of program (code: 70 %)
  • ~70 files
  • 45 (command line) options

Hive-STM program:

And now, upward and onward, a new year, a fresh start.

Review of 2016

2016 has come and gone. 2017 eagerly awaits getting acquainted. But first we look back one last time, trying to turn this into a tradition. What have I done during the last year of some academic merit.

Publications: +4

Completed refereeing tasks: +5

  • ACS Sustainable Chemistry & Engineering
  • The Journal of Physical Chemistry
  • Journal of Physics: Condensed Matter (2x)
  • Diamond and Related Materials

Conferences: +4 (Attended) & + 1 (Organized)

PhD-students: +2

  • Arthur De Vos : (Jan.-Mar., Ghent University, Ghent, Belgium )
  • Mohammadreza Hosseini (okt.-… ,Phd student physical chemistry, Tarbiat Modares University, Teheran, Iran)

Current size of HIVE:

  • 47K lines of program (code: 70 %)
  • 70 files
  • 44 (command line) options

Hive-STM program:

And now, upward and onward, a new year, a fresh start.

Bachelor projects @ UHasselt/IMO

Black arts of computational materials science.

Today the projects for the third year bachelor students in physics were presented at UHasselt. I also contributed two projects, giving the students the opportunity to choose for a computational materials science project. During these projects, I hope to introduce them into the modern (black) arts of High-Performance Computing and materials modelling beyond empirical models.

The two projects focus each on a different aspect of what it is to be a computational materials scientist. One project focuses on performing quantum mechanical calculations using the VASP program, and analyzing the obtained results with existing software. This student will investigate the NV-defect complex in diamond in all its facets. The other project focuses on the development of new tools to investigate the data generated by simulation software like VASP. This student will extend the existing phonon module in the HIVE-toolbox and use it to analyse a whole range of materials, varying from my favourite Metal-Organic Framework to a girl’s best friend: diamond.

Calculemus solidi


A description of the projects in Dutch can be found here.

New sidekick

“One ring to rule them all, one ring to find them, one ring to bring them all, and in the darkness bind them” – J.R.R. Tolkien

“One ring to rule them all, one ring to find them, one ring to bring them all, and in the darkness bind them” – J.R.R. Tolkien

With the start of my new chapter, I also decided to finally buy a new laptop. It’s intended to replace the machine I used at work for the past six years, my desktop at home and my current little netbook. Of these the latter has been my true sidekick for the better part of the last decade. Although nearly all my calculations have been performed on various supercomputers in Belgium and The Netherlands, my little Asus Eee-pc 1000H, being one of the last vestiges of windows XP, was the one which I used to write nearly all of my publications, a PhD in Physics and in Chemistry, my FWO project proposal on MOFs, developed most of the HIVE toolbox, wrote the better part of this blog and website, developed and tested the agent-tutorials, and much more. In short, I did (and still do) protect it with my life.

With the unfortunate and in the end terminal shutdown of WIn XP (i.e. some people discovered how to detect the OS and link this to a kill event…just because XP no longer receives updates, and therefore suddenly becomes as leaky as a sieve 🙄 ) a new OS was needed. In addition, I also wanted some more resources for development (and just running a browser…It feels like programming skills are quickly deteriorating these days if you see how memory intensive even trivial applications are), so the new OS ended up being a new computer altogether. After some searching, I found the laptop which I hope to be using for the next decade: an Acer Predator 15. It has a nice intel skylake cpu (dual-threaded quad-core with 6Mb L3 cache, the 8Mb version was not to be found with the 32Gb of RAM I was looking for). The contrast with my netbook could not be greater, so I’ll be checking and comparing performance of my HIVE-code on this new machine to that on my old Asus netbook (dual-threaded atom cpu, with 1Gb of RAM) . This should give some interesting results.

Not having installed a new windows OS since 2007, windows 10 came as quite a shock (and the aftershocks are still coming.) It seems like privacy is a thing of the past. Anything you say, watch, type, draw is by default send to the home office, and distributed to third parties which may be interested in providing you “user specific content” (i.e. commercials 😥 ) This is in stark contrast to the days where people often installed several antivirus programs and firewalls to protect their data from hackers…now we just seem to throw that same information out for grabs. Then to say there are people who believe we are on the verge of the end of capitalism. I’m afraid they either are misreading the signs, or some are reading the signs very accurately and are collecting the new gold before it has been declared gold. I feel like I’m getting old, or just old-school.

One of the advantages of having lived through those early years where fear of internet-hackers and piracy were defaults, is that we also learned to get around all the same protections. Maybe you remember the irony of having to rip a CD to be able to simply listen to it because of all protection-software (and hardware when you rented it at the local library)? It seems those days are back. While installing some old games, I ran into a piracy-protection software (which is no longer supported due to security leaks) which blocked both playing and even installing the game. So you end up either buying the game through steam (as many will suggest you…why should I do that if I bought the game already…twice?) or installing it on an older machine, just brute-force copying the entire installed game, copying/installing missing dll’s and finding a no-cd crack (Yes, it is claimed as illegal, but since most machines these days come without optical drives I beg to differ), or figure out another way to play old games. In the end, you start with a feeling of victory before even playing a new round of Civilizations 4…which is nice and sad at the same time (it should not have been necessary).

Another interesting experience was the transfer of my emails from my UGent address to the UHasselt one. Mail-clients like Outlook and Thunderbird seem not that well adapted to easily handle such exercises (missing folders and emails upon copy-actions, which needed to be fixed manually), especially if you have a very extensive folder-structure. The most nasty problem I encountered when setting up accounts was the fact that the new UHasselt (gmail) account could not be linked to the thunderbird installation (even though the intermediate gmail-account for transferring my UGent mail was not that problematic). Apparently there was also a cookies option embedded in thunderbird itself, which should be switched on, woeps.

Two weeks after the start of my new chapter, most hurdles have been overcome. Nearly all necessary software has been installed (with or without the cooperation of the windows 10 OS  👿 ), my e-mail has been transferred, as well as 4Tb of data on the HPC systems (for which I am infinitely grateful to both the HPC teams of the UGent and UHasselt). Now it is time to start working again. Tomorrow, the diamond conference starts at the UHasselt, giving me the opportunity to quickly get involved in a new, additional field of materials.


Review of 2015

With 2015 having past on moving quickly toward oblivion, and 2016 freshly knocking at our door, it is time to look back and contemplate what we have done over the course of the previous year.

Publications: +5


Journal covers:+1Cover image CrystEngComm 2015 Vol 17 Issue 45


Completed refereeing tasks: +11

  • ACS Catalysis
  • Frontiers in Physics (2x)
  • Journal of Physics: Condensed Matter
  • Proceedings for 39th International Conference & Exposition on Advanced Ceramics & Composites
  • Applied Physics Letters (2x)
  • Materials Science in Semiconductor Processing
  • Journal of Superconductivity and Novel Magnetism (2x)
  • Surface Science


Conferences: +3 (Attended) & + 1 (Organized)


Master-students: +1

  • Arthur De Vos : Combined theoretical-experimental study of chromium doped zinc gallate phosphor


Jury member of PhD-thesis committee: +1

  • Ir. Yuanyuan Guan
    Title: Development of a method to determine the solubility ranges of intermetallic compounds in metal-metal connections
    PhD candidate at KU Leuven with Prof. Dr. Ir. Nele Moelans
    Department of Materials Engineering

Current size of HIVE:

  • 44K lines of program (code: 71 %)
  • 64 files
  • 40 (command line) options

Hive-STM program:


And now, upward and onward, a new year, a fresh start.

HIVE-STM: A simple post-processing tool for simulating STM

While I was working on my PhD-thesis on Pt nanowires at the university of Twente, one of the things I needed was a method for simulating scanning-tunneling microscopy (STM) images in a quick and easy way. This was because the main experimental information on on these nanowires was contained in STM-images.

Because I love programming, I ended up writing a Delphi-program for this task. Delphi, being an Object Oriented version of the Pascal-programming language containing a Visual Components Library, was ideally suited for writing an easy to use program with a graphical user interface (GUI). The resulting STM-program was specifically designed for my personal needs and the system I was working on at that time.

In August 2008, I was contacted by two German PhD students, with the request if it would be possible for them to use my STM program. In October, an American post-doc and a South-Korean graduate student followed with similar requests, from which point onward I started getting more and more requests from researchers from all over the world. Now, seven years later, I decided to put all “HIVE-users” in a small data-base just to keep track of their number and their affiliation. I already knew I send the program to quite a lot of people, but I was still amazed to discover that it were 225 people from 34 countries.

Hive Requests December 2015

Bar-graph showing the evolution in requests for the HIVE-STM program.

There is a slow but steady increase in requests over the years, with currently on average about one request every week. It is also funny to see there was a slight setback in requests both times I started in a new research-group. For 2015, the data is incomplete, as it does not include all requests of the month December. Another way to distribute the requests is by the month of the year. This is a very interesting graph, since it clearly shows the start of the academic year (October). There are two clear minima (March and September), for which the later is probably related due to the fact that it is the last month of before the start of the academic year (much preparation for new courses) and, in case of the solid state community, this month is also filled with conferences. The reason why there is a minimum in March, however, escapes me ( 💡 all suggestions are welcome 💡 ).

Hive requests per month.

Distribution of requests for the HIVE-STM program on a monthly basis.

The geographic distribution of affiliations of those requesting the STM-program shows Europe, Azia and America to take roughly equal shares, while African affiliations are missing entirety. Hopefully this will change after the workshop on visualization and analysis of VASP outputs delivered at the Center for High Performance Computing‘s 9th National Meeting in South Africa by Dr. David Carballal. By far the most requests come from the USA (57), followed by China(23) and then Germany(15). South-Korea(14) unexpectedly takes the fourth place, while the fifth place is a tie between the UK, Spain and India(12 each).

Hive requests demographics 2015

Distribution of Hive requests per country and continent.

All in all, the STM program seems to be of interest to many more researchers than I would have ever expected, and has currently been cited about 25 times, so it is time to add a page listing these papers as examples of what can be done with HIVE(which has in the mean time been done, check out useful link n°2).

Happy Hiving to all of you, and thank you for your trust.


Useful link:
[1] More information on the HIVE-STM program and how to acquire it.

[2] List of publications using and citing the HIVE-STM program.

Publish or perish: of predatory journals and open-access scams


In the current academic world, there are two often heard mantra’s: publish more and publish open access. In a world where there are ever more researchers competing for limited financial resources, distribution of these resources needs persistent justification. While funding agencies seem to be in a relentless quest for ‘excellence‘ in research (or just more publications, because that is easily quantifiable), a new side-quest has emerged: ‘open access publication’. This side-quest can either be considered as a move against scientific publishers requesting huge subscription fees from universities or as a further way of justifying what is being done with tax-payer money (with open access the tax-payer can go find out him-/herself ).


predator by sweens07, http://cyrax-494.deviantart.com/art/Predator-410150978The publish or perish culture has lead to the birth of predatory journals and publishers. These journals more and more act as regular journals (e.g. promising/claiming peer review). However, in the end, as long as a publishing fee is paid your paper will get published. Researchers of ill intend can easily get their work published in such journals and as such inflate their CV. Unfortunately, also poorly informed researchers, with no ill intend, can be trapped by such journals. These journals use rather aggressive mailing campaigns (I generally get a few of these e-mails every week on my academic mail account) and present journals with names rather similar to well established journals. Luckily, after a while you start to recognize the usual predatory publishers such as scirp, bentham science publishers or hindawi publishing. The setup of their mailings are rather similar. There are two main types: the professional journal type and the personal interest type. The first setup starts by presenting their journal as brand new and of high interest to field, indicating that the journal is indexed in several listings (giving it the impression of validity) and finally that there is a publishing charge (which generally isn’t that steep, 100-200$). The second type approaches you noting they have read one of your recent publications, and consider it to be of great quality and interest to the world. After sufficient flattery you are then invited to publish new work with them (which can be done at a special discount).

Predators v2.0

Lately, with the recent quest for open-access publishing (funding agencies/universities requiring of their researchers to publish open access*) these predatory journals moved on. Nowadays, you do not need to pay for publication any longer, you now pay for the “open access” of your work. In my case, the most recent invitation was by intechopen. I was invited to write a chapter in a book on Metal-Organic Frameworks, and since it is open access, it would only cost 670€ in processing charges. No thank you. After a reminder by the publishing process manager I put in the effort to check if they are already blacklisted as a predatory journal/publisher, and yes they are: Jeffrey Beal’s list of predatory publishers. (For the record, if you are invited to write a paper/book-chapter there should be no page/processing charges at all, on the contrary you should actually get a (small) fee.)

How to discern a legitimate journal from a predatory journal?

This question is becoming harder to answer every year. With open access, also regular publishers have discovered a new gold-mine which they are rather eager to excavate. Also with the huge flood of publications that all need to be reviewed by multiple referees, quality in that area starts to degrade slightly but steadily. So what to do?

  1. First, check if it is a journal you have been reading papers from, and remind yourself what ybealls-listou thought of the quality of those papers. You can also ask your colleagues what they think of the quality.
  2. Second, check if the journal actually has an impact factor on for example web of science (if that is the usual practice in your field). This is similar as checking with a credit rating agencies about the status of a country…which may in the long run not be as flawless as expected.
  3. Third, check if the journal/publisher has been blacklisted in the ever expanding list of predatory publishers by Jeffrey Beall. (Although there is some discussion on the validity of the list itself, I believe it to be a good starting point if you are in doubt.)

*They, however, tend to have conflicting standards in this regard. You are on the one hand encouraged to publish in high impact journals and you are required to publish open access. On the other hand however, no additional funding is provided to pay for the open access costs in high impact journals. These costs are often several thousand euros for one publication, or more than half an FWO bench-fee which is to be used for visiting conferences, buying lab equipment or computational resources.