Most commented posts
- Start to Fortran — 1 comment
- Phonons: shake those atoms — 3 comments
Dec 09 2015
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.

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 💡 ).

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).

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).
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.
Permanent link to this article: https://dannyvanpoucke.be/hive-stm-db-2015-en/
Dec 05 2015
In the previous posts, I presented my contribution (original Dutch version / English translation) to the Robbert Dijkgraaf essay contest. This year’s theme was on the importance of imagination in science. My girlfriend, Sylvia, also participated in this essay contest. We read each-others contributions as a final check before submission, and at that point it became clear to me I was out of my league 😳 .
During the gala of science in Amsterdam, the winner of the Robbert Dijkgraaf essay contest was made public. And the winner is: Sylvia Wenmackers.
On her blog you can read the winning essay (in Dutch), and you will understand why I immediately knew my essay was outclassed. Congratulations again my dear 😀 .
Permanent link to this article: https://dannyvanpoucke.be/rd-essay-contest-2015-en/
Nov 28 2015
This year I participated in the Robbert Dijkgraaf essay-contest 2015.
The central theme of the contest was imagination, and in my contribution
I presented the role of imagination in computational materials science,
and why it is so important for this field.
The original Dutch version of the essay can be found here.
Imagine a world where you can actually see atoms. Even more, you can use them as LEGOs and manipulate them to do your bidding. Imagine a world in which you can switch off the laws of nature, or create new ones which are more to your liking. In such a world, you are in charge. Welcome to my world: the world of “computational materials science“.
It would be a nice start for a commercial for this research field. The accompanying clip would then show images fading into one another of supercomputers and animations of chemical and biochemical processes at the atomic scale. Moving in a fast-forward pace into our future with science-fiction-like orbital labs where calculated materials are immediately transformed into new medicine, ultra-thin screens and applications for the aerospace industry.
The ever faster flood of images culminates in the final slogan:”Simulate the future” with a subtext urging you to go study computational materials science. I assume that such a clip would tempt peoples imagination. It addresses our human urge to create, and holds the promise that you can do anything you want, as long as you can imagine it. In fact, your imagination becomes the only limiting factor.
As with most commercial, this one also presents reality slightly more beautiful than it actually is. As for any other scientist in any other field, your contribution to progress as a computational materials scientist is rather more limited than you would like it to be. This is a normal aspect of science. The presented divine omnipotence and omniscience, on the other had, are attainable. As a computational scientist you do have absolute control over the atomic positions and the forces at play. In contrast, an experimental scientist is forced to deal with the quirks of nature and his or her machinery. This omnipotence allows you to create any world you can imagine…inside a computer.
As a scientist, you wish to understand the world around you. This limits the freedom you gained through your omnipotence, unless you would choose to join a team of game-designers. It, however, does not mean that your creativity is curtailed in any way. On the contrary. Where the team of game-designers knows the entire story to be told, including rules and laws of nature relevant for the game world, this is not the case for computational materials science. For the latter it is often their quest to discover the story-line as they go, including relevant laws of nature. As a computational materials scientist, you become the narrator, whose task consist of thinking up new stories time and time again. The narrator, who needs to tweak existing plots, extending or confining story-lines, until the final story fits the shape of reality.
Luckily, you are not alone to bring this daunting task to a successful end. You always have the support of your loyal sidekick: your supercomputer. Using its brute force, your sidekick calculates the effects of any intrigue or plot twist you can imagine. Based on your introductory chapter, in which you describe the world and its natural laws, it will allow the story to unfold. By asking him the right questions, and comparing his answers to reality, you learn which parts of your story don’t really fit reality yet.
How you should rewrite your introductory chapter differs every time. Sometimes it is clear what is going on: an essential character is missing (e.g. an impurity atom which is distorting the crystal lattice), or the character lives at the wrong location (not site A, then let us see about site B?). It becomes more difficult when a character refuses to play the role it was dealt (e.g. Pt atoms that remain invisible for STM, so who is going to play the role of the nanowire we observe?). The most difficult situation occurs with the need for a full rewrite of the introductory chapter. This provides too much freedom, since it is our knowledge of the limitations of reality which provides the necessary support and guidance for drafting the story-line. In such a case, you need an inspiring idea which provides you with a new point of view. Inspiration can come in many forms and at any time, often when least expected. A well-known example is this of the theoretical chemist Kekulé who, in a daydream, saw a snake bite its own tail. As a result Kekulé was able to envision the ring-shape of the benzene molecule. Such wonderful problem solving twists-of-mind are rare. They are often the consequence of long and intense study of a single problem, which drive you to the limit, since they require you to imagine something you have never thought of before. In management-circles this is called “thinking-outside-the-box”, which sound a lot easier than it actually is. It does not mean that all of the sudden everything goes, you always have to bear in mind the actual box you started from.
As a computational materials scientist you have to combine your omnipotence over your virtual world with your power to imagine new worlds, hoping to see a glimmer of reality in the reflections of your silicon chips.
Permanent link to this article: https://dannyvanpoucke.be/sidekick-en/
Nov 28 2015
Met dit essay nam ik deel aan de Robbert Dijkgraaf essay-prijs 2015.
Dit jaar was het thema verbeelding, en in mijn bijdrage doe ik een
poging de rol van verbeelding naar voren te brengen binnen
computationeel materiaalonderzoek. Ik probeer eveneens uit te
leggen hoe ik computationeel onderzoek zie als onderzoeksdomein.
Een vertaling naar het Engels kan hier gevonden worden.
Stel je een wereld voor waarin je atomen kunt zien. Meer nog, je kunt ze stapelen als legoblokken en manipuleren naar eigen goeddunken. Stel je een wereld voor waarin je de natuurwetten kunt aan- of afzetten, een wereld waar je zelf nieuwe natuurwetten kunt schrijven. In zo een wereld heb jij het voor het zeggen. Welkom in mijn wereld, de wereld van het “computationele materiaalonderzoek“.
Het zou een mooi begin zijn van een reclamespot voor dit onderzoeksgebied. In de bijhorende clip krijg je in elkaar overgaande beelden te zien van supercomputers enerzijds en animaties van chemische en biochemische processen op de atomaire schaal anderzijds. Het geheel wordt dan doorgelinkt aan onze eigen toekomst met sciencefictionachtige laboratoria waar de berekende materialen direct worden omgezet tot nieuwe medicijnen, flinterdunne beeldschermen en toepassing voor de ruimtevaart. De steeds sneller elkaar opvolgende beelden
culmineren dan in de slotslogan: “Simuleer de toekomst!” met als onderschrift de aansporing om computationeel materiaalonderzoek te gaan studeren. Ik stel me voor dat zo’n reclameclip wel tot de verbeelding zou spreken. Het spreekt onze menselijke drang om te creëren aan met de belofte dat je alles kunt, als je het je maar kunt voorstellen. Je verbeelding is de enige beperkende factor.
Zoals bij de meeste reclamespots wordt ook in deze de werkelijkheid iets mooier voorgesteld dan ze is. Zoals voor elke andere wetenschapper geldt immers dat je bijdrage aan de vooruitgang beperkter is dan je zou willen. De gepresenteerde goddelijke almacht en alwetendheid liggen wel binnen handbereik. Als computationeel onderzoeker heb je immers absolute controle over de plaatsing van atomen en de inwerkende krachten, iets waar een experimenteel onderzoeker deels is overgelaten aan de grillen van de natuur en zijn of haar apparatuur. Deze controlevrijheid laat je toe, binnen een computer, elke wereld te creëren die je maar kunt bedenken.
Als wetenschapper wil je de wereld om je heen begrijpen, wat bovenstaande vrijheden inperkt, tenzij je ervoor kiest om in een team van computergame-designers aan de slag gaan. Dit betekent niet dat je creativiteit wordt beknot, integendeel. Waar bij het ontwerpteam het volledige verhaal bekend is, inclusief de regels en natuurwetten van de wereld waarin je speelt, is dat niet het geval bij computationeel materiaalonderzoek. Meer nog, vaak is het net je opdracht het verhaal gaandeweg te ontdekken, inclusief de natuurwetten die relevant zijn. Je wordt als het ware een verteller die telkens nieuwe verhalen moet bedenken, of bestaande plots moet aanpassen, uitbreiden of beperken, tot de verhaallijn past in de vorm van de werkelijkheid.
Je staat er gelukkig niet alleen voor om een goede afloop te regelen. Je wordt bijgestaan door je trouwe sidekick: je supercomputer. Deze is in staat met brute kracht de gekste plotwendingen door te rekenen. Op basis van jouw inleidende hoofdstuk, waarin je de wereld en haar natuurwetten schetst, zal hij het verhaal verder laten ontplooien. Door dan de juiste vragen te stellen en de antwoorden met de werkelijkheid te vergelijken kom je erachter waar je verhaal nog niet helemaal in de werkelijkheid past.
Hoe je je inleidende hoofdstuk daarop moet aanpassen verschilt per geval. Soms is het duidelijk wat er aan de hand is: er ontbreekt een cruciaal personage (bijvoorbeeld een onzuiverheidsatoom dat het kristaalrooster verstoord) of het personage woont op de foute plaats (toch niet op de plaats van atoom A, atoom B dan maar?). Moeilijker wordt het als sommige personages weigeren de hun toebedeelde rol te spelen (Die platina-atomen zijn onzichtbaar voor de rastertunnelmicroscoop, wie speelt nu de rol van de zichtbare nanodraad?).
De lastigste situatie is wanneer een volledige herschrijving van het inleidende hoofdstuk nodig is. Hierdoor krijg je te veel vrijheid in handen, terwijl het net de gekende beperkingen zijn die je houvast geven bij het opstellen van het verhaal. Je hebt dan een idee nodig dat je een link geeft met de werkelijkheid. Inspiratie kan hier velerlei vormen aannemen en op willekeurig moment komen. Een bekende anekdote is deze van de theoretische chemicus Kekulé, die in een dagdroom een slang zichzelf in de staart zag bijten en daardoor de ringvormige structuur van de benzeenmolecule uitdokterde. Zulke wonderlijk probleemoplossende gedachtenkronkels komen zelden spontaan, maar zijn veeleer het gevolg van lang en intens werk op eenzelfde vraagstuk. Dergelijke situaties drijven je tot het uiterste, je moet je immers iets voorstellen waar je nooit eerder aan gedacht hebt. In managementkringen wordt zoiets “buiten het kader denken” genoemd, wat bedrieglijk eenvoudig klinkt. Je mag immers niet vergeten dat voor onderzoek dit niet betekent dat alles plots toegelaten is (met andere woorden, je mag het kader zeker niet uit het oog verliezen bij het dagdromen).
Als computationeel materiaalonderzoeker moet je dus je almacht over je virtuele wereld combineren met je eigen vermogen nieuwe werelden in gedachten te scheppen, in de hoop zo onderweg een glimp van de buitenwereld in je siliciumchip op te vangen.
Permanent link to this article: https://dannyvanpoucke.be/sidekick-nl/
Nov 26 2015
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 ).
The 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).
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.)
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?
ou thought of the quality of those papers. You can also ask your colleagues what they think of the quality.*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.
Permanent link to this article: https://dannyvanpoucke.be/oa-scams-en/
Permanent link to this article: https://dannyvanpoucke.be/paper2015_aniecok69-en/
Nov 13 2015
| Authors: | Thomas Bogaerts, Louis Vanduyfhuys, Danny E.P. Vanpoucke, Jelle Wieme, Michel Waroquier, Pascal Van Der Voort, and Veronique Van Speybroeck, |
| Journal: | CrystEngComm. 17(45), 8565 (2015) |
| doi: | 10.1039/C5CE90198G |
| IF(2015): | 3.849 |
| export: | bibtex |
| pdf: | <CrystEngComm> |
The cover image depicts an X-ray beam hitting a sample of MIL-47(V) Metal-Organic Framework (reddish powder), resulting in an X-ray diffraction pattern. This leads to the atomic structure on the left, Where the spin-densities are indicated for the anti-ferromagnetic ground state. (The related paper can be found here.)
Permanent link to this article: https://dannyvanpoucke.be/paper2015_xrdthomasdannycover-en/
Permanent link to this article: https://dannyvanpoucke.be/paper2015_inorgchemuio66-en/
Permanent link to this article: https://dannyvanpoucke.be/paper2015_accuratemofs-en/
Permanent link to this article: https://dannyvanpoucke.be/experimental-truths-en/