Tag: academic life

Oct 22 2023

Materiomics Chronicles: week 5

After week four, this fifth week of the academic year is most arguably the most intense and hectic week of teaching. With 22h of classes and still two classes that needed to be prepared from scratch (even including weekends time was running out), I’m tired but happy it is over. However, all the effort is worth it, and I was happy to hear the students of our materiomics program at UHasselt appreciate the effort put into creating their classes, during an evaluation meeting.

The corral is an artificial structure created from 48 iron atoms (the sharp peaks) on a copper surface. The wave patterns in this scanning tunneling microscope image are formed by copper electrons confined by the iron atoms. Don Eigler and colleagues created this structure in 1993 by using the tip of a low-temperature scanning tunneling microscope (STM) to position iron atoms on a copper surface, creating an electron-trapping barrier. This was the first successful attempt at manipulating individual atoms and led to the development of new techniques for nanoscale construction.source: https://www.nisenet.org/catalog/scientific-image-quantum-corral-top-view

The corral is an artificial structure created from 48 iron atoms (the sharp peaks) on a copper surface. The wave patterns in this scanning tunneling microscope image are formed by copper electrons confined by the iron atoms. Don Eigler and colleagues created this structure in 1993 by using the tip of a low-temperature scanning tunneling microscope (STM) to position iron atoms on a copper surface, creating an electron-trapping barrier. This was the first successful attempt at manipulating individual atoms and led to the development of new techniques for nanoscale construction.
source: https://www.nisenet.org/catalog/scientific-image-quantum-corral-top-view

For the second bachelor students in chemistry the introduction to quantum chemistry finally put them into contact with some “real” quantum mechanics when they were introduced into the world of potential barriers, steps, and wells. Though these are still abstract and toy-model in nature, they provide a first connection with reality, where they can be seen as crude approximations of the potential experienced by valence electrons near the surface, or STM experiments. They were also introduced to my favorite quantum system related to this course: the quantum corral. Without any effort it can be used in half a dozen situations with varying complexity to show and learn basic quantum mechanics. For the third bachelor chemistry students the course quantum and computational chemistry finally provided them the long promised first example of a non-trivial quantum chemical object: The Helium atom. With it’s two electrons, we break free of the H-atom(-like)  world. Using perturbation theory and Slater determinant wave functions, we made our first approximations of its energy. In addition, these students also had a seminar for their course Introductory lectures in preparation to the bachelor project (Kennismakingstraject m.b.t. stage en eindproject, in Dutch). During this lecture I gave a brief introduction and overview of the work I did in the past and the work we do in our research group QuATOMs, which although “quantum” is quite different of what the students experience during their courses on quantum chemistry.

In the materiomics program, the first master students continued their travels into the basics of force-fields during the lecture of the course Fundamentals of materials modelling. The exercise class of this week upped the ante by moving from ASE to LAMMPS for practical modeling of alkane chains, which was also the topic of their second lab session. In the course Properties of functional materials, we investigated the ab initio modelling of vibrations. During the exercise classes we investigated precalculated phonon spectra in the materials-project database, as well as calculated our own vibrational spectrum at the gamma-point of the first Brillouin zone. During the second master course Machine learning and artificial intelligence in modern materials science the central theme was GIGO (Garbage-In-Garbage-Out). How can we make sure our data is suitable and good enough for our models to return useful results. We therefore looked into data-preparation & cleaning, as well as  clustering methods.

At the end of this week, we have added another 22h of live lectures and ~1h of video lectures, putting our semester total at 74h of live lectures. Upwards and onward to week 6.

Oct 15 2023

Materiomics Chronicles: week 4

Week four of the academic year at the chemistry and materiomics programs of UHasselt, we are stepping up the pace a bit…at least for me. The students continue to dive deeper into the various subjects furthering their knowledge gained in the previous weeks.

In the bachelor chemistry program, the third bachelor chemistry extended their knowledge of variational theory to excited states, in the course quantum and computational chemistry. They also saw some first glimpses of the mathematical setup which makes the use of computational methods so important and powerful in quantum chemistry.  Finally they proved the Hellmann-Feynman Theorem which makes structure optimization in quantum chemistry practically feasible. For the second bachelor chemistry, the course introduction to quantum chemistry was focused on the time-dependent Schrödinger equation and the uncertainty principle.

In the first master materiomics, I was the  main player this week (and will also be so next week) teaching the classes of two of the three courses. In the course Properties of functional materials, the second module started, which is centered on the computational (quantum mechanical) modeling of materials properties. Here the students build on their recently acquired expertise in DFT to gain further insights into electronic structure calculations both in theory and in practice. In addition, the students also had their first seminar presentation where they present their understanding after studying two papers within the context of the concepts presented during the first module of the course. In the course Fundamentals of materials modelling, we moved to a new level of modeling: atomistic modeling using force-fields. The freshly gained knowledge was also here directly applied through the modeling of bulk aluminum using the ASE library in a jupyter notebook. (For many a first contact with python.) Finally, the students of the second master learned about “dynamical” modeling, in the course on Density Functional Theory, covering NEB calculations for energy barriers as well as basic molecular dynamics (with examples such as the water molecule below).

 

At the end of this week, we have added another 17h of live lectures and ~1h of video lectures, putting our semester total at 52h of live lectures. Upwards and onward to week 5.

Oct 07 2023

Materiomics Chronicles: week 3

In week three of the academic year at the chemistry and materiomics programs of UHasselt, the students started to put their freshly gained new knowledge of weeks 1 and 2 into practice with a number of exercise classes.

For the second bachelor chemistry students, this meant performing their first calculations within the context of the course introduction to quantum chemistry. At this point this is still very mathematical (e.g., calculating commutators) and abstract (e.g., normalizing a wave function or calculating the probability of finding a particle, given a simple wave function), but this will change, and chemical/physical meaning will slowly be introduced into the mathematical formalism. For the third bachelor chemistry, the course quantum and computational chemistry continued with perturbation theory, and we started with the variational method as well. The latter was introduced through the example of the H atom, for which the exact variational ground state was recovered starting from a well chosen trial wave function.

Infinite polymethylene glycol (POM) chain.

Ball-and-stick representation of an infinite polymethylene glycol (POM) chain.

In the master materiomics, the first master course fundamentals of materials modelling, dove into the details underpinning DFT introducing concepts like pseudo-potentials, the frozen-core approximation, periodic boundary conditions etc. This knowledge was then put into practice during a second exercise session working on the supercomputer, as a last preparation for the practical lab exercise the following day. During this lab, the students used the supercomputer to calculate the Young modulus of two infinite linear polymers. An intense practical session which they all executed with great courage (remember 2 weeks ago they never heard of DFT, nor had they accessed a supercomputer). Their report for this practical will be part of their grade.

For the second master materiomics, the course focused on Density Functional Theory consisted of a discussion lecture, covering the topics the students studied during their self study assignments. In addition, I recorded two video lectures for the blended learning part of the course. For the course Machine learning and artificial intelligence in modern materials science self study topics were covered in such a discussion lecture as well. In addition, the QM9 data set was investigated during an exercise session, as preparation for further detailed study.

At the end of this week, we have added another 16h of live lectures and ~1h of video lectures, putting our semester total at 35h of live lectures. Upwards and onward to week 4.

Sep 30 2023

Materiomics Chronicles: week 2

After the more gentle introductions last week during the first lectures at UHasselt, this week we dove into the deep end.

For the students of the second bachelor chemistry  the course introduction to quantum chemistry dove into the postulates of quantum chemistry. They learned about the wave-function and operators, had their first contact with the mystics notation of quantum chemistry: the bra-ket notation. For the third bachelor chemistry, the course quantum and computational chemistry was centered around perturbation theory. In addition to the theory, we applied the method to the simple system of the infinite square potential.

The electron density in the primitive diamond unit cell.

In the master materiomics the course fundamentals of materials modeling was kicked into high gear, not only did the students learn the theory behind quantum mechanical modelling, they also had their fist experience on the supercomputers of the VSC. So in addition to the road from the standard Schrödinger equation to the Hohenberg-Kohn-Sham equations of DFT, they also traveled their first steps along the road from their somewhat familiar windows OS to the bash command-line environment of the HPC unix system.

Finally, as the course introduction into quantum chemistry is part of the preparatory program of the master materiomics, I started creating the narrated versions of those lectures as well (2h worth recording, corresponding to 4h of live lectures). As the available time is limited, we are going for single shot recordings which makes things exciting in that department as well.

At the end of this week, we have added another 7h of live lectures and 2h of video lectures, putting our semester total at 19h of lectures. Upwards and onward to week 3.

Sep 24 2023

Materiomics Chronicles: week 1

The first week of the academic year at UHasselt has come to an end, while colleagues at UGent and KULeuven are still preparing for the start of their academic year next week. Good luck to all of you.

This week started full throttle for me, with classes for each of my six courses. After introductions in classes with new students (for me) in the second bachelor chemistry and first master materiomics, and a general overview in the different courses, we quickly dove into the subject at hand.

The second bachelor students (introduction to quantum chemistry) got a soft introduction into (some of) the historical events leading up to the birth of quantum mechanics such as the black body radiation, the atomic model and the nature of light. They encountered the duck-rabbit of particle-wave duality and awakened their basic math skills with the standing wave problem. For the third bachelor students, the course on quantum and computational chemistry started with a quick recap of the course introduction to quantum mechanics, making sure they are all again up to speed with concepts like braket-notation and commutator relations.

For the master materiomics it was also a busy week. We kicked of the 1st Ma course Fundamentals of materials modeling, which starts of calm and easy with a general picture of the role of computational research as third research paradigm. We discussed in which fields computational research can be found (flabbergasting students with an example in Theology: a collaboration between Sylvia Wenmackers & Helen De Cruz),  approximation vs idealization, examples of materials research at different scales, etc. As a homework assignment the students were introduced into the world of algorithms through the lecture of Hannah Fry (Should computers run the world). For the  2nd Ma, the courses on Density Functional Theory and Machine learning and artificial intelligence in modern materials science both started. The lecture of the former focused on the nuclear wave function and how we (don’t) deal with it in DFT, but still succeed in optimizing structures. During the lecture on AI we dove into the topics of regularization and learning curves, and extended on different types of ensemble models.

At the end of week 1, this brings me to a total of 12h of lectures. Upwards and onward to week 2.

Jun 02 2023

E-MRS Spring meeting 2023

In march 2019, Belgium went into COVID-lock down while I attended the yearly diamond conference (SBDD25). Since then, I have been in a bit of a conference lock down myself as well. By visiting the 2023 spring meeting of E-MRS, this lock down has been lifted for international conferences (outside Belgium). Inside Belgium, there was already the DFT-2022 in Brussels, where I was also part of the National Scientific Committee, and of course SBDD26 & SBDD27, which as a diamond researcher you can not miss.

Coming back to Strassbourg for E-MRS brings back some memories, and generated some nice new ones. This year there was a nice Symposium called “Computations for materials – discovery, design and the role of data“[program] which got my full attention. During the first session on AI-accelerated Materials discovery, I had the pleasure to present some of my own work on the Machine Learning of small data sets (cf. papers on the average model, and UV-curable inks). The symposium was nicely coinciding with much of my interest, and showed two (not unexpected, and maybe symposium biased) trends:

  1.  There is an important evolution toward lab-automation and use of robotics (people don’t want to manually build dozens of battery cells or perform hundreds of repetitive synthesis experiments for materials optimization. This shows the future materials scientist, be it a chemist, physicist or engineer will have to become a robotics and/or programming expert as well. This only strengthens me in my vision for our materiomics [NL] students at UHasselt. These skills will be essential for their future scientific career development.
  2. Machine Learning and Artificial Intelligence will play an important role in future materials design. However, we need a better understanding of what we are doing, and not just use any method and accept it as “excellent” because the R² value is high. For now, we can still get away with the latter, but this will not last much longer. It will become more important to have a simple but interpretable model, rather than a complex (over-fitting) Deep Learning Neural Network without understanding of the underlying physics and chemistry. Also here we will have to put in some effort within the materiomics program.

 

So after an interesting International conference, and making some new contacts…it is time to return home, four more courses need to be prepared from scratch for coming academic year.

Mar 14 2020

SBDD 25 (aka the COVID19 edition)

Last Wednesday, the 25th edition of the Hasselt Diamond workshop started. The central topic of this celebratory edition was focused on surfaces, perfectly suited to present some of my more recent diamond based work.[1][2] Just as the previous years, the program was packed with interesting talks on anything diamond. Phosphorous doped diamond seemed to be the “new thing” this year, but I could be biased, as I was speaking on phosphorous adsorption myself. Due to a cancellation, I found myself being asked on Monday afternoon to present my work as a talk 😎 , on Wednesday morning 😯 . Because I had been a bit too ambitious in my conference abstract, this talk ended up being nicely complementary to my poster.

Poster SBDD 25 conference, Hasselt 2020

Unfortunately, this celebratory edition also fell victim to the COVID-19 crisis. In addition to being the most popular conversation topic—a close second to diamond research—, it also had a very real impact on the conference itself. The COVID-19 crisis resulted in a drop of attendance from 238 people in 2019 to 143 this year.  In addition, the quickly changing situation worldwide lead to last minute cancellations due to travel restrictions. On Thursday evening, the conference site went into lock down. Furthermore, that evening, the Belgian federal government also decided that schools and higher education should be closed, as well as pubs and restaurants, until April 3rd. There was also the urgent request for people to work from home as much as possible. (Consider this a good example of acting NOW aimed at saving people.)

Consider this computational scientist in lock down in his home lab until further notice.

Nov 30 2019

Casting Keynotes: The Virtual Lab

Last Tuesday? I had the pleasure of competing in the casting keynotes competition of the TEDx UHasselt chapter. An evening filled with interesting talks on subjects ranging from the FAIR principles of open-data (by Liebet Peeters)  to the duty not stay silent in the face of “bad ideas” and leading a life of purpose. An interesting presentation was the one by Ann Bessemans on visual prosody to improve reading skills in young children as well as reading experience, more specifically the transfer of non-literal-content, for non-native speakers. There was also time for some humor, with the dangerous life of Tim Biesmans, who suffers from peanut-allergies. For him, death lurks around every corner, even in a first-date’s kiss. During my talk, I traced the evolution of computational research as the third paradigm of scientific discovery, showing you can find computational research in every field, and why it is evolving at its break-neck speed.

During the event, both the public and a jury voted on the best presentation, which would then have to present at the TEDx UHasselt in 2020.

And the Winner is …drum roll… Danny Vanpoucke!

So this story will continue during the 2020 TEDx event at UHasselt, and I hope to see you there 🙂

Casting Keynotes

top: Full action shots of my presentation. Moore’s Law as driving force behind computational research, and pondering the meaning of Artificial Intelligence. Bottom: Yes, I won 🙂

 

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.

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]