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Danny Vanpoucke
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Apr 12 2016
Call for Abstracts: Condensed Matter Science in Porous Frameworks: On Zeolites, Metal- and Covalent-Organic Frameworks
Together with Ionut Tranca (TU Eindhoven, The Netherlands) and Bartłomiej Szyja (Wrocław University of Technology, Poland) I am organizing a colloquium “Condensed Matter Science in Porous Frameworks: On Zeolites, Metal- and Covalent-Organic Frameworks” which will take place during the 26th biannual Conference & Exhibition CMD26 – Condensed Matter in Groningen (September 4th – 9th, 2016). During our colloquium, we hope to bring together experimental and theoretical researchers working in the field of porous frameworks, providing them the opportunity to present and discuss their latest work and discoveries.
Zeolites, Metal-Organic Frameworks, and Covalent-Organic Frameworks are an interesting class of hybrid materials. They are situated at the boundary of research fields, with properties akin to both molecules and solids. In addition, their porosity puts them at the boundary between surfaces and bulk materials, while their modular nature provides a wealthy playground for materials design.
We invite you to submit your abstract for oral or poster contributions to our colloquium. Poster contributions participate in a Best Poster Prize competition.
The deadline for abstract submission is April 30th, 2016.
The extended deadline for abstract submission is May 14th, 2016.
CMD26 – Condensed Matter in Groningen is an international conference, organized by the Condensed Matter Division of the European Physical Society, covering all aspects of condensed matter physics, including soft condensed matter, biophysics, materials science, quantum physics and quantum simulators, low temperature physics, quantum fluids, strongly correlated materials, semiconductor physics, magnetism, surface and interface physics, electronic, optical and structural properties of materials. The scientific programme will consist of a series of plenary and semi-plenary talks and Mini-colloquia. Within each Mini-colloquium, there will be invited lectures, oral contributions and posters.
Feel free to distribute this call for abstracts and our flyer and we hope to see you in Groningen!
Permanent link to this article: https://dannyvanpoucke.be/cmd26-call-2016-en/
Apr 06 2016
Animated Primes
Optimus Prime, the most prime of all autobots.[source]
2, 3, 5, 7, 11, 13, 17, 19, 23, …and on toward infinity. Prime numbers are a part of mathematics which seduce most of us at some point in our lives to try and “solve them”. There is structure in them, but too little to be easily understandable, and too much to let go and consider them chaos.
Recently, my girlfriend got sucked into this madness. Luckily she is not trying to generate the next largest prime (which would need to have more than 22 Million digits, although I might have jinxed it now). Instead she is looking for order into chaos; leading to pen and paper graphs, evolving into excel worksheets being abused as ordinary bitmap pictures and finally mathematica applications for even more heavy lifting.
These last exercises came to a somewhat grinding halt when mathematica refused to generate a gif-animation (it just failed to do the job without providing any warning that something might have gone awry). However, because it could generate the separate frames without any issues, I was tempted to dig up an old fortran module which allowed me to generate gif images and animations. I remembered correctly that it was able to both read and write gif-images, and so, after 10 minutes of writing a small program (9 minutes remembering how things worked) and another 10 linking in all dependencies and fixing some inconsistencies, I had a working program for generating a gif animation from separate gif images.
[codesyntax lang=”fortran” title=”Small program for reading single gif images and storing them as gif-animation.” blockstate=”collapsed”]
program GifCombo
use GIFImageModule; use typesmodule;
implicit none
character(len=255):: filename,basename
integer :: imin, imax, nr, ios
type(TGif):: AniGif, StatGif
write(*,*) "Small program to combine a set of GIFs to make one animated gif."
write(*,*) "Gif-filenames should be structured as GIFNAME_XX.gif ,"
write(*,*) "With GIFNAME the basename, and XX an integer number (without preceding zero's)."
write(*,*) " > Provide the basename:"
read(*,*) basename
write(*,*) " > Provide the lower index:"
read(*,*) imin
write(*,*) " > Provide the higher index:"
read(*,*) imax
!The actual work
call AniGif%initialize()
do nr=imin,imax
write(filename,'(I0)') nr
filename=trim(basename)//"_"//trim(filename)//".gif"
if (nr>imin) then
call StatGif%initialize()
call StatGif%read(filename,1,ios,.true.)
call AniGif%addImage(int(StatGif%image(:,:,1),I_int))
call StatGif%free()
else
call AniGif%read(filename,1,ios,.true.)
end if
end do
call AniGif%setGlobalDelayTime(30)
!writing the result
filename=trim(basename)//"_Animated.gif"
call AniGif%write(filename)
write(*,*) "This should have written an animated Gif to:",trim(filename)
end program GifCombo
[/codesyntax]
The initial test went smoothly. Using some simple gif images I created in paint, the resulting 4 frame animation is the one on the left (which is probably giving you a headache as you read this ;-).
The real test, with the single frame gifs Sylvia had prepared, was rather interesting: It failed miserably. Fortunately it also taught us the origin of the problem: mathematica was generating frames of different dimensions. And although this does not give rise to problems in the workbook or generated avi, it does kill an animated gif. After fixing this, also mathematica successfully generated the animated gif Sylvia wanted to see. Also my own small program was now able to perform the intended trick, although it showed that a different color-map was created for each frame by mathematica, something my own implementation did not handle well (we’ll fix that somewhere in the future).
The executable (including prerequisite dll’s) can be downloaded here.
If you do not suffer from epileptic seizures (or not yet), you could check out the results in the spoiler below.
Permanent link to this article: https://dannyvanpoucke.be/animated-primes-en/
Mar 09 2016
SBDD XXI
Today was the first day of the three-day long diamond conference at the university of Hasselt. And although this sounds as-if it is a mere small-scale local conference, it is actually one of the two main international conferences in the field. The Surface and Bulk Defects in Diamond (SBDD) workshop grew in twenty years from a small event with only a few dozen participants to the current event with over 200 participants. As such, it is the place to be, for one as me, who is dipping into a new field of materials.
One thing that already became quite clear today, is the fact that there are many opportunities in this field for the computational materials scientist, as the large majority of the researchers are experimentalists. Of the >120 posters presented, I have only discovered about 5 theoretical ones. Having had very nice chats with their presenters I already learned a lot of what I will have to keep in mind when studying diamond. But so far, I have not come across any issues that are impossible to resolve, which is good news :-).
Permanent link to this article: https://dannyvanpoucke.be/sbdd-xx1-en/
Mar 08 2016
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
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.
Permanent link to this article: https://dannyvanpoucke.be/new-sidekick-en/
Mar 01 2016
Helium flash: the beginning of a new chapter.
During the past two and a half years, part of being a delocalized physicist has meant for me that I had to work at one end of the country while my girlfriend and son lived at the other. Today this situation drastically changed, as I moved with my FWO-postdoctoral project from my alma mater to the University of Hasselt, where I started in the Wide Band Gap Materials group of Prof. Ken Haenen.
My delocalization will now take the form of Metal-Organic Frameworks on the one side and Diamond based materials on the other. As the sole computational solid state physicist in an otherwise entirely experimental group (and even institute) I seem to have returned to a well known configuration (At Ghent university I was initially the house-theoretician of the SCRiPTS group). Also the idea of performing calculations on diamond brings back memories, since this allotrope of carbon lives two levels above the germanium on which Pt nanowires grow. All-in-all I look forward to an exciting time. But first things first: getting my HPC credentials and data safely transported from the one end of the country to the other.
Permanent link to this article: https://dannyvanpoucke.be/a-new-chapter-en/
Feb 11 2016
First-Principles Study of Antisite Defect Configurations in ZnGa2O4:Cr Persistent Phosphors
| Authors: | Arthur De Vos, Kurt Lejaeghere, Danny E. P. Vanpoucke, Jonas J. Joos, Philippe F. Smet, and Karen Hemelsoet |
| Journal: | Inorg. Chem. 55(5), 2402-2412 (2016) |
| doi: | 10.1021/acs.inorgchem.5b02805 |
| IF(2016): | 4.857 |
| export: | bibtex |
| pdf: | <Inorg.Chem> |
 |
| Graphical Abstract: First-principles simulations on zinc gallate solid phosphors (ZGO) containing a chromium dopant and antisite defects (left) rationalize the attractive interactions between the various elements. A large number of antisite pair configurations is investigated and compared with isolated antisite defects. Defect energies point out the stability of the antisite defects in ZGO. Local structural distortions are reported, and charge transfer mechanisms are analyzed based on theoretical density of states (right) and Hirshfeld-I charges. |
Abstract
Zinc gallate doped with chromium is a recently developed near-infrared emitting persistent phosphor, which is now extensively studied for in vivo bioimaging and security applications. The precise mechanism of this persistent luminescence relies on defects, in particular, on antisite defects and antisite pairs. A theoretical model combining the solid host, the dopant, and/or antisite defects is constructed to elucidate the mutual interactions in these complex materials. Energies of formation as well as dopant, and defect energies are calculated through density-functional theory simulations of large periodic supercells. The calculations support the chromium substitution on the slightly distorted octahedrally coordinated gallium site, and additional energy levels are introduced in the band gap of the host. Antisite pairs are found to be energetically favored over isolated antisites due to significant charge compensation as shown by calculated Hirshfeld-I charges. Significant structural distortions are found around all antisite defects. The local Cr surrounding is mainly distorted due to a ZnGa antisite. The stability analysis reveals that the distance between both antisites dominates the overall stability picture of the material containing the Cr dopant and an antisite pair. The findings are further rationalized using calculated densities of states and Hirshfeld-I charges.
Permanent link to this article: https://dannyvanpoucke.be/paper2016_inorgchemzgodoping-en/
Feb 04 2016
Virtual Winterschool 2016: Computational Solid State Physics & Chemistry
In just an hour, I’ll be presenting my talk at the virtual winterschool 2016. In an attempt to tempt fate as much as possible I will try to give/run real-time examples on our HPC in Gent, however at this moment no nodes are available yet to do so. Let’s keep our fingers crossed and see if it all works out.
Abstract
Modern materials research has evolved to the point where it is now common practice to manipulate materials at nanometer scale or even at the atomic scale (e.g. Intel’s skylake architecture with 14nm features, atomic layer deposition and surface structure manipulations with an STM-tip). At these scales, quantum mechanical effects become ever more relevant, making their prediction important for the field of materials science.
In this session, we will discuss how advanced quantum mechanical calculations can be performed for solids and indicate some differences with standard quantum chemical approaches. We will touch upon the relevant concepts for performing such calculations (plane-wave basis-sets, pseudo-potentials, periodic boundary conditions,…) and show how the basic calculations are performed with the VASP-code. You will familiarize yourself with the required input files and we will discuss several of the most important output-files and the data they contain.
At the end of this session you should be able to set up a single-point calculation, a structure optimization, a density of states and band structure calculation.
Additional Files/Info
Permanent link to this article: https://dannyvanpoucke.be/virtwinter2016-en/
Permanent link to this article: https://dannyvanpoucke.be/paper2016_icacc_gyif-en/
Feb 01 2016
Doping of CeO2 as a Tunable Buffer Layer for Coated Superconductors: A DFT Study of Mechanical and Electronic Properties
| Authors: | Danny E. P. Vanpoucke, |
| Journal: | Developments in Strategic Ceramic Materials: Ceramic Engineering and Science Proceedings 36(8), 169-177 (2016) (ICACC 2015 conference proceeding) |
| Editors: | Waltraud M. Kriven, Jingyang Wang, Dongming Zhu,Thomas Fischer, Soshu Kirihara |
| ISBN: | 978-1-119-21173-0 |
| webpage: | Wiley-VCH |
| export: | bibtex |
| pdf: | <preprint> |
Abstract
In layered ceramic superconductor architectures, CeO2 buffer layers are known to form micro cracks during the fabrication process. To prevent this crack formation, doping of the CeO2 layer has been suggested. In this theoretical study, the influence of dopants (both tetravalent and aliovalent) on the mechanical and structural properties of CeO2 is investigated by means of density functional theory. Group IVa and IVb dopants show clearly distinct stability, with the former favouring interface and surface doping, while the latter favour uniform bulk doping. This behaviour is linked to the dopant electronic structure. The presence of charge compensating vacancies is shown to complicate the mechanical and structural picture for aliovalent dopants. We find that the vacancies often counteract the dopant modifications of the host material. In contrast, all dopants show an inverse relation between the bulk modulus and thermal expansion coefficient, independent of their valency and the presence of oxygen vacancies. Based on the study of these idealized systems, new dopants are suggested for applications.
Permanent link to this article: https://dannyvanpoucke.be/paper2016_icacc_virtmater-en/
Jan 29 2016
Winterschool on computational chemistry
Starting next week from February 3rd up to February 9th the second virtual winterschool on computational chemistry will take place. This week-long winter school is packed with interesting webinars given by experts from all over the world (among others Kieron Burke and John Perdew, jep those of the DFT-functionals we are using) and me. I’ll be presenting an introductory tutorial in solid state calculations and how to use VASP for this task.
Registration for this winter school is free, and since it takes place on the world wide web, there is still room at the back :-). (In addition to a lack of worries whether or not you will be able to get your hands on a last minute plane-ticket or hotel-room and which funding agency might reimburse those tickets.) I’ll be running example-calculations real time, and hope my sidekick will perform to expectation.
Permanent link to this article: https://dannyvanpoucke.be/winterschoolcc2016-en/