Category: blog

Sep 04 2019

Workshop Machine Learning for Coatings: First Machine Learning (day 3)

Gartner hype cycle. Courtesy of Kevin Cremanns.

Gartner hype cycle. Courtesy of Kevin Cremanns.

Today the workshop shifted gears a bit. We left the experimental side of the story and moved fully into the world of machine learning. This change went hand-in-hand with a doubling of the number of participants, showing how a hot-topic machine learning really is.  Kevin Cremanns, who is presenting this part of the workshop, started by putting things into perspective a bit, and warned everyone not to hope for magical solutions (ML and AI have their problems), while at the same time presenting some very powerful examples of what is possible. A fun example is the robotic arm learning to flip pancakes:



During the introduction, all the usual suspects of machine learning passed the stage. And although you can read about them in every ML-book, it is nice to hear them discussed by someone who uses them on a daily basis. This mainly because practical details (often omitted in text-books) are also mentioned, helping one to avoid the same mistakes many have made before you. Furthermore, the example codes provided are extremely well documented, making them an interesting source of teaching material (the online manuals for big libraries like sci-kit learn or pandas tend to be too abstract, too big, and too intertwined for new users).

All-in-all a very interesting day. I look forward to tomorrow, as then we will be introduced into the closed source machine learning library developed at the University Hochschule Niederrhein.

Sep 03 2019

Workshop Machine Learning for Coatings: Magical Humans (day 2)

Today was the second day of the machine learning workshop on coatings. After having focused on the components of coatings, today our focus went to characterization and deposition. The set of available characterization techniques is as extensive as the possible components to use. There was, however, one thing which grabbed my attention: “The magical human observer”. Several characterization techniques were presented to heavily rely on the human observer’s opinion and Fingerspitzengefühl.  Sometimes this even came with the suggestion that such a human observer outperforms the numerical results of characterization machinery. This makes me wonder if this isn’t an indication of a poor translation of the human concept to the experiment intended to perform the same characterization. Another important factor to keep in mind when building automation frameworks and machine learning models.

In the afternoon, we again put on our lab coats and goggles. The task of the day: put our raspberry pink lacquer on different substrates and characterize the glossiness (visually) and the pendulum hardness.

Tomorrow the machine learning will kick in.

Sep 02 2019

Workshop Machine Learning for Coatings (day 1)

Today was the first day of school…not only for my son, but for me as well. While he bravely headed for the second grade of primary school, I was en route to the first day of a week-long workshop on Machine Learning and Coatings technology at the Hochschule Niederrhein in Krefeld. A workshop combining both the practical art of creating coating formulations and the magic of simulation, more specifically machine learning.

During my career as a computational materials researcher, I have worked with almost every type of material imaginable (from solids to molecules, including the highly porous things in between called MOFs), and looked into every aspect available, be it configuration (defects , surfaces, mixtures,…) or materials properties (electronic structure, charge transfer, mechanical behavior and spin configurations). But each and every time, I did this from a purely theoretical perspective*. As a result, I have not set foot in a lab (except when looking for a colleague) since 2002 or 2003, so you can imagine my trepidation at the prospect of having to do “real” lab-work during this workshop.

Participating in such a practical session— even such a ridiculously simple and safe one— is a rather interesting experience. The safety-goggles, white-coat and gloves are cool to wear, true, but from my perspective as a computational researcher who wants to automate things, this gives me a better picture of what is going on. For example, we** carefully weigh 225.3 grams of a liquid compound and add 2.2 grams of another (each with an accuracy of about 0.01 gram). In another cup, we collect two dye compounds (powders), again trying our best to perfectly match the prescribed quantities. But when the two are combined in the mixer it is clear that a significant quantity (multiple grams) are lost, just sticking to the edge of the container and spatula. So much for carefully weighing (of course a pro has tricks and skills to deal with this better than we did, but still). Conclusion: (1)Error bars are important, but hard to define. (2) Mixtures made by hand or by a robot should be quite different in this regard.

For the theoretical part of my brain, mixing 10 compounds is just putting them in the same box and stir, mix or shake. Practice can be quite different, especially if you need 225 grams of compound A, and 2.2 grams of compound B. This means that for the experimentalist there is a “natural order” for doing things. This order does not exist at the theoretical side of the spectrum***, where I build my automation and machine learning. This, in addition to the implicit interdependence of combined compounds, gives the high-dimensional space of possible mixtures a rather contorted shape. This gives rise to several questions begging for answers, such as: how important is this order, and can we (ab)use all this to make our search space smaller (but still efficient to sample).

At the end of the day, I learned a lot of interesting things and our team of three ended up with a nice raspberry pink varnish.

Next, day two, where we will characterize our raspberry pink varnish.

 

Footnotes

* Yes, I do see how strange this may appear for someone whose main research focus is aimed at explaining and predicting experiments. 🙂
** We were divided in teams of 2-3 people, so there were people with actual lab skills nearby to keep me safe. However, if this makes you think I was just idly present in the background, I have to disappoint you. I am brave enough to weigh inanimate powders and slow flowing resins 😉 .
*** Computational research in its practice uses aspects of both the experimental and theoretical branches of research. We think as theoreticians when building models and frameworks, and coax our algorithms to a solution with a gut-feeling and Fingerspitzengefühl only experimentalists can appreciate.

Jul 02 2019

Start to science-communicate

Today and tomorrow, there is a 2-day summer school on science communication held at the University of Antwerp: Let’s Talk Science! During this summer school there are a large number of workshops to participate in, and lectures to attend, dealing with all aspects of science communication.

Wetenschapsbattle Trophy: Hat made by the children for the contestants of the wetenschapsbattle. Mine has diamonds and computers. 🙂

I was invited to represent Hasselt University (and science communication done by its members) during the plenary panel session starting the summer school. The goal of this plenary session was to share our experiences and thoughts on science communication. The contributions varied from hands-on examples to more abstract presentations of what to keep in mind, including useful tips. The central aim of my presentation was directed at identifying the boundary between science communication and scientific communication. Or more precisely, showing that this border may be more artificial than we are aware of. By showing that everyone’s unique in his/her expertise and discipline, I provided the link between conference presentations and presentations for the general public. I traveled through my history of science communication, starting in the middle: with the Science Battle. An event, I wrote about before, where you are asked to explain your work in 15 minutes to an audience of 6-to 12-year-olds. Then I worked my way back via my blog and contributions to “Ik heb been vraag” (such as: if you drop a penny from the Eiffel tower, will this kill someone on the ground?) to the early beginning of my research: simulating STM images. In the latter case, although I was talking to experts in their field (experimental growth and characterization), their total lack of experience in modelling and quantum mechanical simulations transformed my colleagues into “general public”. This is an important aspect to realize, not only for science communication, but also for scientific communication. As a consequence this also means that most of the tips and tricks applicable to science communication are also applicable to scientific communication.

For example: tell a coherent story. As noted by one of my favorite authors – Terry Pratchett – the human species might have better been called “Pan Narrans”, the storytelling ape. We tell stories and we remember by stories. This is also a means to make your scien(ce/tific) communication more powerful. I told the story of my passion during science explained and my lecture for de Universiteit van Vlaanderen.

A final point I touched is the question of “Why?”. Why should you do science communication? Some may note that is our duty as scientists, since we are payed with taxpayer money. But personally I believe this is not a good incentive. Science communication should originate from your own passion. It should be because you want to, instead of because you have to. If you want to, it is much easier to show you passion, show your interest, and also take the time to do it.

This brought me back to my central theme: Science communication can be simple and small. E.g. projecting simulated STM images on the wall’s of the medieval castle in Ghent (Gravensteen) during a previous edition of the Ghent Light Festival.

Simulated STM of nanowires projected on the Gravensteen (Ghent) during the 2012 Light Festival). Courtesy of Glenn Pollefeyt

Simulated STM of nanowires projected on the Gravensteen (Ghent) during the 2012 Light Festival). Courtesy of Glenn Pollefeyt

Jun 06 2019

VSC-users day 2019

It is becoming an interesting yearly occurrence: the VSC user day. During this 5th edition, HPC users of the various Flemish universities gather together at the Belgian Royal Academy of Science (KVAB) to present their state-of-the-art work using the Flemish Tier-1 and Tier-2 supercomputers. This is done during a poster-presentation session. This year, I presented my work with regard to vibrational spectra in solids and periodic systems. In contrast to molecules, vibrational spectra in solids are rarely investigated at the quantum mechanical level due to their high cost. I show that imaginary modes are not necessarily a result of structural instabilities, and I present a method for identifying the vibrational spectrum of a defect.

Poster for the VSC user day 2019.

In addition, international speakers discuss recent (r)evolutions in High Performance Computing, and during workshops, the participants are introduced in new topics such as GPU-computing, parallelization, and the VSC Cloud and data platform. The possibilities of GPU were presented by Ehsan, of the VSC, showing extreme speedups of 10x to 100x, strongly depending on the application, the graphics card. It is interesting to see that simple CUDA prama’s can be used to obtain such effects…maybe I should have a go at them for the Hirshfeld and phonon parts of my HIVE code…if they can deal with quadruple precision, and very large arrays. During the presentation of Joost Vandevondele (ETH Zürich) we learned what the future holds with regard to next generation HPC machines. As increasing speed becomes harder and harder to obtain, people are again looking into dedicated hardware systems, a situation akin to the founding days of HPC. Whether this is a situation we should applaud remains to be seen, as it means that we are moving back to codes written for specific machines. This decrease in portability will probably be alleviated by high level scripting languages (such as python), which at the same time result in a significant loss of the initial gain. (Think of the framework approach to modern programming which leads to trivial applications requiring HPC resources to start.)

In addition, this year the HPC-team of the TIER-1 machine is present for a panel discussion, presenting the future of the infrastructure. The machine nearly doubled in size which is great news. Let us hope that in addition for financing hardware, there is also a significant budget considered for a serious extension of a dedicated HPC support team. Running a Tier-1 machine is not something one does as a side-project, but which requires a constant vigilance of a dedicated team to deal with software updates, resulting compatibility issues, conflicting scripts and just hardware and software running haywire because they can.

With this hope, I look toward the future. A future where computational research is steadily are every quickly is becoming common place in the fabric om academic endeavors.

May 23 2019

Annual Meeting of the Belgian Physical Society 2019

Yesterday, it was the annual meeting of the Belgian Physical Society, a nice event where Belgian physicists come together to present their latest work. It also provides a good opportunity for junior scientist to present their work (e.g. through the young speaker contest, an event I won in 2011).

The three students competing for the young speaker award presented three very interesting topics going from the creation of Aharonov-Bohm cages over the observation of high energy cosmic rays with detectors of several thousand square kilometers to the temperature determination of clusters. This years young speaker award went very deservedly to Daniela Mockler for her work on the measurement of cosmic rays.

Before lunch there was the usual conference picture (can you spot me? 😎 )

BPS 2019 conference group picture

After our lunch there was the poster session. This year, I decided only to present a poster of my work on vibrational spectra. It combined work on Eu defects in diamond, the vibrational spectrum of Lactose and water and a method for fingerprinting defects in diamond.

During the parallel sessions, I attended the parallel session on physics education. Domien Van der Elst highlighted the daunting task of dealing with a serious shortage in Physics and Mathematics teachers. He suggest the creation of an online platform to (replace/)supplement physics teachers. Despite the possible benefits (and the fact that some big companies are looking into similar setups) I remain skeptical. My main worry being GDPR (privacy) wise and the growing trend that software users are more and more considered as sources providing data and private information to mine and use for a companies benefit (not the software user). The second talk by Bart Huyskens was very inspiring. From his practical experience as a high school teacher, he develops, together with a colleague, hardware, software and courseware for STEM projects. And when he says STEM projects he means it: projects containing ALL parts of a STEM education. Hearing him talk, it is not hard to start dreaming up possible projects, both short and long term. The third and final presentation of the session was by Phillipe Leonard on the concept of “Challenge Labs“. During these labs, teams of students get a “simple problem” to solve. However, while trying to solve the the problem, they discover nothing is what it seems, and they need to learn to think outside the box. This definitely is an interesting method of teaching (assuming good support by the teacher involved) which has the possibility to lift students to a higher level.

After the coffee break, I attended the remainder of the condensed matter session. During this session Michael Sluydts presented his Machine-Learning work on dopants in Si and Ge. An approach which should be very suitable for diamond as well.

 

All in all a very interesting day.

Apr 01 2019

Universiteit Van Vlaanderen

A bit over 1 month ago, I told you about my adventure at the film studio of “de Universiteit Van Vlaanderen“. Today is the day the movie is officially released. You can find it at the website of de Universiteit Van Vlaanderen: Video. The video is in Dutch as this is a science-communication platform aimed at the local population, presenting the expertise available at our local universities.

 

In addition to this video, I was asked by Knack magazine to write a piece on the topic presented. As computational research is my central business I wrote a piece on the subject introducing the general public to the topic. The piece can be read here (in Dutch).

And of course, before I forget, this weekend there was also the half-yearly daylight saving exercise with our clocks.[and in Dutch]

 

Mar 18 2019

SBDD XXIV: Diamond workshop

The participants to SBDD XXIV of 2019.  (courtesy of Jorne Raymakers, SBDD XXIV secretary) 

 

Last week the 24th edition of the Hasselt diamond workshop took place (this year chaired by Christoph Becher). It’s already the fourth time, since 2016, I have attended this conference, and each year it is a joy to meet up with the familiar faces of the diamond research field. The program was packed, as usual. And this year the NV-center was again predominantly present as the all-purpose quantum defect in diamond. I keep being amazed at how much it is used (although it has a rather low efficiency) and also about how many open question remain with regard to its incorporation during growth. With a little luck, you may read more about this in the future, as it is one of a few dozen ideas and questions I want to investigate.

A very interesting talk was given by Yamaguchi Takahide, who is combining hexagonal-BN and H-terminated diamond for high performance electronic devices. In such a device the h-BN leads to the formation of a 2D hole-gas at the interface (i.e., surface transfer doping), making it interesting for low dimensional applications. (And it of course hints at the opportunities available with other 2D materials.) The most interesting fact, as well as the most mind-boggling to my opinion, was the fact that there was no clear picture of the atomic structure of the interface. But that is probably just me. For experiments, nature tends to make sure everything is alright, while we lowly computational materials artificers need to know where each and every atom belongs. I’ll have to make some time to find out.

A second extremely interesting presentation was given by Anke Krueger (who will be the chair of the 25th edition of SBDD next year), showing of her groups skill at creating fluorine terminated diamond…without getting themselves killed. The surface termination of diamond with fluorine comes with many different hazards, going from mere poisoning, to fire and explosions. The take-home message: “kids don’t try this at home”. Despite all this risky business, a surface coverage of up to 85% was achieved, providing a new surface termination for diamond, with a much stronger trapping of negative charges near the surface, ideal for forming negatively charged NV centers.

On the last day, Rozita Rouzbahani presented our collaboration on the growth of B doped diamond. She studied the impact of growth conditions on the B concentration and growth speed of B doped diamond surfaces. My computational results corroborate her results and presents the atomic scale mechanism resulting in an increased doping concentration upon increased growth speed. I am looking forward to the submission of this nice piece of research.

And now, we wait another year for the next edition of SBDD, the celebratory 25th edition with a focus on diamond surfaces.

Feb 20 2019

Universiteit Van Vlaanderen: Will we be able to design new materials using our smartphone in the future?

Yesterday, I had the pleasure of giving a lecture for the Universiteit van Vlaanderen, a science communication platform where Flemish academics are asked to answer “a question related to their research“. This question is aimed to be highly clickable and very much simplified. The lecture on the other hand is aimed at a general lay public.

I build my lecture around the topic of materials simulations at the atomic scale. This task ended up being rather challenging, as my computational research has very little direct overlap with the everyday life of the average person. I deal with supercomputers (which these days tend to be bench-marked in terms of smartphone power) and the quantum mechanical simulation of materials at the atomic scale, two other topics which may ring a bell…but only as abstract topics people may have heard of.

Therefor, I crafted a story taking people on a fast ride down the rabbit hole of my work. Starting from the almost divine power of the computational materials scientist over his theoretical sample, over the reality of nano-scale materials in our day-to-day lives, past the relative size of atoms and through the game nature of simulations and the salvation of computational research by grace of Moore’s Law…to the conclusion that in 25 years, we may be designing the next generation of CPU materials on our smartphone instead of a TIER-1 supercomputer. …did I say we went down the rabbit hole?

The television experience itself was very exhilarating for me. Although my actual lecture took only 15 minutes, the entire event took almost a full day. Starting with preparations and a trial run in the afternoon (for me and my 4 colleagues) followed by make-up (to make me look pretty on television 🙂 … or just to reduce my reflectance). In the evening we had a group diner meeting the people who would be in charge of the technical aspects and entertainment of the public. And then it was 19h30. Tensions started to grow. The public entered the studio, and the show was ready to start. Before each lecture, there was a short interview to test sound and light, and introduce us to the public. As the middle presenter, I had the comfortable position not to be the first, so I could get an idea of how things went for my colleagues, and not to be the last, which can really be destructive on your nerves.

At 21h00, I was up…

…and down the rabbit hole we went. 

 

 

Full periodic table, with all elements presented with their relative size (if known)

Full periodic table, with all elements presented with their relative size (if known) created for the Universiteit van Vlaanderen lecture.

 

Feb 06 2019

Roots of Science

Today VLIR (Flemish Inter-university Council) and the Young Academy had a conference on the future of fundamental research in Flanders: Roots of Science. We live in a world where we rely on science more and more to resolve our problems (think climate change, disease control, energy generation, …). In our bizarre world of alternative facts and fake news, science can be utterly ignored in one sentence and proposed as a magical solution in the next.

Although I am happy with the faith some have in the possibilities of science, it is important to remember that it is not magic. This has a very important consequence:

Things do not happen simply because you want them to happen.

 

Many important breakthroughs in science are what one would call serendipity (e.g., the discovery of penicillin by Fleming, development of the WWW as a side-effect of researchers wanting to share their data

at CERN in 1991,…) . In Flanders the Royal Flemish Academy and the Young Academy have written a Standpoint (an evidence-based advisory text)

discussing the need for more researcher-driven research in contrast to agenda-driven research, as they believe this is a conditio sine qua non for a healthy scientific future.

Where government-driven research focuses on resolving questions from society, researcher-driven research allows the researcher to follow his or her personal interest. This not with the primal aim of having short-te

rm return of investment, but with the aim of providing the fundamental knowledge and expertise which some day may be needed for the former. In researcher-driver research, the journey is the goal as this is where scientific progress is made by finding solutions for problems not imagined before.

Do we have to pay for this with our tax-payers money? I think we do. No-one imagined optical drives (CD, DVD, blue-ray) to become a billion euro industry while the laser was being developed in a lab. Who would have thought the transistor would play such an important role in our every-day life? And what about the first computer? Thomas Watson, President of IBM, has allegedly said in 1943: “I think there is a world market for maybe 5 computers.” And, yet, now many of us have more than 5 computers at home (including tables, smartphones,…)! The researchers working on these “inventions” did not do this with your Blue-ray player or smartphone in mind. These high impact applications are “merely” side-products of their fundamental scientific research. No-one at the time could predict this, so why should we be able to do this today? In this sense, you should see funding of fundamental research as a long term investment. Tax-money is being invested in our future, and the future of children and grandchildren. Although we do not know what will be the outcome, we know from the past that it will have an impact on our lives.

Its difficult to make predictions, especially about the future.

Let us therefor support more researcher-driven research.

 

In addition to the Standpoint, there is also a very nice video explaining the situation (with subtitles in English or Dutch, use the cogwheel to select your preference).