51 results for diamond

Jun 27 2016

Folding Phonons

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June 27, 2016

Game-diamonds About a year ago, I discussed the possibility of calculating phonons (the collective vibration of atoms) in the entire Brillouin zone for Metal-Organic Frameworks. Now, one year later, I return to this topic, but this time the subject matter is diamond. In contrast to Metal-Organic Frameworks, the unit-cell of diamond is very small (only 2 atoms). Because a phonon spectrum is calculated through the gradients of forces felt by one atom due to all other atoms, it is clear that within one diamond unit-cell these forces will not be converged. As such, a supercell will be needed to make sure the contribution, due to the most distant atoms, to the experienced forces, are negligible.

Using such a supercell has the unfortunate drawback that the dynamical matrix (which is $3N \times 3N$ , for N atoms) explodes in size, and, more importantly, that the number of eigenvalues, or phonon-frequencies also increases ( $3N$ ) where we only want to have 6 frequencies ( $3 \times 2$ atoms) for diamond. For an $M \times M \times M$ supercell we end up with $24M^3 -6$ additional phonon bands which are the result of band-folding. Or put differently, $24M^3 -6$ phonon bands coming from the other unit-cells in the supercell. This is not a problem when calculating the phonon density of states. It is, however, a problem when one is interested in the phonon band structure.

The phonon spectrum at a specific q-point in the first Brillouin zone is given by the square root of the eigenvalues of the dynamical matrix of the system. For simplicity, we first assume a finite system of n atoms (a molecule). In that case, the first Brillouin zone is reduced to a single point q=(0,0,0) and the dynamical matrix looks more or less like the hessian:

With $\varphi (N_a,N_b) = [\varphi_{i,j}(N_a , N_b)]$ $3 \times 3$ matrices $\varphi_{i,j}(N_a,N_b)=\frac{\partial^2\varphi}{\partial x_i(N_a) \partial x_j(N_b)} = - \frac{\partial F_i (N_a)}{\partial x_j (N_b)}$ with i, j = x, y, z. Or in words, $\varphi_{i,j}(N_a , N_b)$ represents the derivative of the force felt by atom $N_a$ due to the displacement of atom $N_b$ . Due to Newton’s second law, the dynamical matrix is expected to be symmetric.

When the system under study is no longer a molecule or a finite cluster, but an infinite solid, things get a bit more complicated. For such a solid, we only consider the symmetry in-equivalent atoms (in practice this is often a unit-cell). Because the first Brillouin zone is no longer a single point, one needs to sample multiple different points to get the phonon density-of-states. The role of the q-point is introduced in the dynamical matrix through a factor $e^{iq \cdot (r_{N_a} - r_{N_b}) }$ , creating a dynamical matrix for a single unit-cell containing n atoms:

Because a real solid contains more than a single unit-cell, one should also take into account the interactions of the atoms of one unit-cell with those of all other unit-cells in the system, and as such the dynamical matrix becomes a sum of matrices like the one above:

Where the sum runs over all unit-cells in the system, and N_i indicates an atom in a specific reference unit-cell, and M^R_i an atom in the R^th unit-cells, for which we give index 1 to the reference unit-cell. As the forces decay with the distance between the atoms, the infinite sum can be truncated. For a Metal-Organic Framework a unit-cell will quite often suffice. For diamond, however, a larger cell is needed.

An interesting aspect to the dynamical matrix above is that all matrix-elements for a sum over n unit-cells are also present in a single dynamical matrix for a supercell containing these n unit-cells. It becomes even more interesting if one notices that due to translational symmetry one does not need to calculate all elements of the entire supercell dynamical matrix to construct the full supercell dynamical matrix.

Assume a 2D 2×2 supercell with only a single atom present, which we represent as in the figure on the right. A single periodic copy of the supercell is added in each direction. The dynamical matrix for the supercell can now be constructed as follows: Calculate the elements of the first column (i.e. the gradient of the force felt by the atom in the reference unit-cell, in black, due to the atoms in each of the unit-cells in the supercell). Due to Newton’s third law (action = reaction), this first column and row will have the same elements (middle panel).

Translational symmetry on the other hand will allow us to determine all other elements. The most simple are the diagonal elements, which represent the self-interaction (so all are black squares). The other you can just as easily determine by looking at the schematic representation of the supercell under periodic boundary conditions. For example, to find the derivative of the force on the second cell (=second column, green square in supercell) due to the third cell (third row, blue square in supercell), we look at the square in the same relative position of the blue square to the green square, when starting from the black square: which is the red square (If you read this a couple of times it will start to make sense). Like this, the dynamical matrix of the entire supercell can be constructed.

This final supercell dynamical matrix can, with the same ease, be folded back into the sum of unit-cell dynamical matrices (it becomes an extended lookup-table). The resulting unit-cell dynamical matrix can then be used to create a band structure, which in my case was nicely converged for a 4x4x4 supercell. The bandstructure along high symmetry lines is shown below, but remember that these are actually 3D surfaces. A nice video of the evolution of the first acoustic band (i.e. lowest band) as function of its energy can be found here.

The phonon density of states can also be obtained in two ways, which should, in contrast to the band structure, give the exact same result: (for an $M \times M \times M$ supercell with n atoms per unit-cell)

Generate the density of states for the supercell and corresponding Brillouin zone. This has the advantage that the smaller Brillouin zone can be sampled with fewer q-points, as each q-point acts as M³ q-points in a unit-cell-approach. The drawback here is the fact that for each q-point a (3nM³)x(3nM³) dynamical matrix needs to be solved. This solution scales approximately as O(N³) ~ (3nM³)³ =(3n)³M⁹. Using linear algebra packages such as LAPACK, this may be done slightly more efficient (but you will not get O(N²) for example).
Generate the density of states for the unit-cell and corresponding Brillouin zone. In this approach, the dynamical matrix to solve is more complex to construct (due to the sum which needs to be taken) but much smaller: 3nx3n. However to get the same q-point density, you will need to calculate M³ times as many q-points as for the supercell.

In the end, the choice will be based on whether you are limited by the accessible memory (when running a 32-bit application, the number of q-point will be detrimental) or CPU-time (solving the dynamical matrix quickly becomes very expensive).

Permanent link to this article: https://dannyvanpoucke.be/folding-phonons/

May 29 2016

One more digit of importance

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May 29, 2016

Over the past few weeks I have bumped into several issues each tracing back to numerical accuracy. Although I have been programming for almost two decades I never had to worry much about this, making these events seem as-if the universe is trying to tell me something.

Now, let me try to give a proper start to this story; Computational (materials) research is generally perceived as a subset of theoretical (materials) research, and it is true that such a case can be made. It is, however, also true that such thinking can trap us (i.e. the average computational physicist/chemist/mathematician/… programming his/her own code) with numerical accuracy problems. While theoretical equations use exact values for numbers, a computer program is limited by the numerical precision of the variables (e.g. single, double or quadruple precision for real numbers) used in the program. This means that actual numbers with a larger precision are truncated or rounded to the precision of the variable (e.g. 1/3 becomes 0.3333333 instead of 0.333… with an infinite series of 3’s). Most of the time, this is sufficient, and nothing strange will happen. Even more, most of the time, the additional digits would only increase the computational cost while not improving the results in a significant fashion.

Interstellar disc

To understand the importance, or the lack thereof, of additional significant digits, let us first have a look at the precision of $\pi$ and the circumference and surface area of a disc. We will be looking at a rather large disc, one with a radius equal to the distance between the sun, and the nearest star, Alpha Centauri, which is 39 900 000 000 000 km away. The circumference of this disc is given by $2r\pi$ (or $2.5 \times 10^{14}$ km ). As a single precision variable $\pi$ will have about 7-8 significant digits. This means the calculated circumference will have an accuracy of about 1 000 000 km (or a few times the distance between the earth and the moon). Using a double precision $\pi$ variable, which has a precision of 16 decimal digits, the circumference will be accurately calculated to within a few meters. At quadrupal precision, the $\pi$ variable would have 34 significant decimal digits, and we would even be able to calculate the surface of the disc ( $r^2\pi$ or $5.0 \times 10^{33}$ m² ) to within 1 m². Even the surface of a disc the size of our milky way could be calculated with an accuracy of a few hundred square km (or ± the size of Belgium ).

Knowing this, our mind is quickly put at easy regarding possible issues regarding numerical accuracy. However, once in a while we run into one exceptional case (or three, in my case).

1. Infinitesimal finite elements

Temperature profile in the insulating layer of a cylindrical wire.

While looking into the theory behind finite elements, I had some fun implementing a simple program which calculated the temperature distribution due to heat transport in an insulating layer. The finite element approach performed rather nicely, leading to good approximate results, already for a few dozen elements. However, I wanted to push the implementation a bit (the limit of infinite elements should give the exact solution). Since the set of equations was solved by a LAPACK subroutine, using 10 000 elements instead of 10 barely impacted the required time (writing the results took most of 2-3 seconds anyway). The results on the other hand were quite funny as you can see in the picture. The initial implementation, with single precision variables, breaks down even worse already at 1000 elements. Apparently the elements had become too small leading to too small variations of the properties in the stiffness-matrix, resulting in the LAPACK subroutine returning nonsense.

So it turns out that you can have too many elements in a finite elements method.

2. Small volumes: A few more digits please

Optimized volume in Equation of State fit, as function of the range of the fitting data, and step size between data-points. green diamonds, blue triangles and black discs: 1% , 0.5% and 0.25% volume steps respectively.

Recently, I started working at the Wide Band Gap Materials group at the University of Hasselt. So in addition to MOFs I am also working on diamond based materials. While setting up a series of reference calculations, using scripts which already suited me well during my work on MOFs, I was trying to figure out for which volume range, and step size I would get a sufficient convergence in my Equation-of-States Fitting procedure. For the MOFs this is a computationally rather expensive (and tedious) exercise, which, fortunately, gives clear results. For the 2-atom diamond unit cell the calculations are ridiculously fast (in comparison), but the results were confusing. As you can see in the picture, the values I obtained from the different fits seem to oscillate. Checking my E(V) data showed nothing out of the ordinary. All energies and volumes were clearly distinguishable, with the energies given with a precision of 0.001 meV, and the volumes with a precision of 0.01 Å³. However, as you can see in the figure, the volume-oscillations are of the order of 0.001 Å³, ten times smaller than our input precision. Calculating the volumes based on the lattice parameters to get a precision of 10^-6 Å³ for the input volumes stabilizes the convergence behavior of the fits (open symbols in the figure). This problem was not present with the MOFs since these have a unit cell volume which is one hundred times larger, so a precision of 0.01 Å³makes the relative error on the volumes one hundred times smaller than was the case for diamond.

In essence, I was trying to get more accurate output than the input I provided, which will never give sensible results (even if they actually look sensible).

3. Many grains of sand really start to pile up after a while

The last one is a bit embarrassing as it lead to a bug in the HIVE-toolbox, which is fixed in the mean time.

One of the HIVE-toolbox users informed me that the dosgrabber routine had crashed because it could not find the Fermi-level in the output of a VASP calculation. Although VASP itself gives a value for the Fermi-level, I do not use it in the above sub-program, since this value tend to be incorrect for spin-polarized systems with different minority and majority spins. However, in an attempt to be smart (and efficient) I ended up in trouble. The basic idea behind my Fermi-level search is just running through the entire Density of States-spectrum until you have counted for all the electrons in the system. Because the VASP estimate for the Fermi-level is not that far of, you do not need to run through the entire list of several thousand entries, but you could just take a subset-centered around the estimated Fermi-level and check in that subset, speeding this up by a factor of 10 to 100. Unfortunately I calculated the energy step size between density of states entries as the difference between the first two entries, which are given to with an accuracy of 0.001 eV. I guess you already have a feeling what will be the problem. When the index of the estimated Fermi-level is 1000, the error will be of the order of 1 eV, which is much larger than the range I took into account. Fortunately, the problem is easily solved by calculating the energy step size as the difference between the first and last index, and divide by the number of steps, making the error in the particular case more than a thousand times smaller.

So, trying to be smart, you always need to make sure you really are being smart, and remember that small number can become very big when there are a lot of them.

Permanent link to this article: https://dannyvanpoucke.be/one-more-digit-of-importance-en/

Mar 09 2016

SBDD XXI

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March 9, 2016

SBDD XXI logo 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

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March 8, 2016

“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.

academia, change, computers, HPC, workaround
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Permanent link to this article: https://dannyvanpoucke.be/new-sidekick-en/

Mar 01 2016

Helium flash: the beginning of a new chapter.

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March 1, 2016

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/

Sep 10 2015

IAP-meeting 2015: poster

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September 10, 2015

Models for Ti clusters in the COK-69(Ti) MOF.

Falling ill is always a bummer. It’s even more annoying when you just finished preparing a poster for a conference you intended to attend (in the current case this is the annual IAP meeting). Per doctor’s orders I am not allowed to be patient zero at the above conference, so my poster will end up alone at the site (luckily my nice colleagues will take it along and put it up). Because misery loves company (or it’s just a personal skill to pick the wrong moment) I had also decided to make this poster a bit more interactive through a spartan setup: As little text as possible, only a trail of images through which I would tell the story of the research…As you can see I was asking for trouble.

Not being able to be there physically, and knowing that most people nowadays own a smart-phone, I came up with the following solution: One of my colleagues will also put up a QR-code, sending the interested reader to this blog-post, where he/she will be able to read the story of the poster. (Questions can be put in the comments, and the full size version of the poster can be reached by clicking on the picture below.)

Abstract

Poster created for the 2015 IAP meeting on september 11<SUP>th</SUP>, 2015 in Hasselt, Belgium.

Poster created for the 2015 IAP meeting on September 11^th, 2015 in Hasselt, Belgium.

Metal-Organic Frameworks (MOFs) are a versatile class of crystalline materials showing great promise in a wide range of applications. Recently, light-based applications, with a focus on luminescence and photo-catalysis, have become of interest. Although new luminescent MOFs are readily synthesized, a fundamental understanding of the underlying mechanisms in the electronic structure is often lacking.

First principles, or ab initio simulations of these MOFs can be used both for validating the experimentally proposed atomistic model of the MOF and for elucidating its luminescent behavior. On this poster, two different MOF-topologies are investigated. In the first case, we consider the well-known UiO-66(Zr) MOF. For this MOF, it is known that functionalization of the linkers modifies its luminescent behavior. As our second case, we consider the very recently created/synthesized COK-69(Ti) MOF. This new MOF is both flexible and luminescent, making it of interest for various applications.

The Old: UiO-66(Zr)-X

Atomic Structure

In our work on the UiO-66, we made use of the primitive unit cell, which contains only a single node and six linker molecules. This cell still contains about 120 atoms (in contrast to about 480 atoms for the conventional cubic cell) making it a rather large system from the point of view of ab initio calculations. The relation between this primitive unit cell and the conventional cubic cell is indicated by comparison to the diamond primitive and cubic cell (top left corner).

The functionalized versions of this MOF were created by manually replacing some of the H atoms of the BDC-linker (benzene-1,4-dicarboxylic acid) by the functional group of interest (OH or SH) and then optimizing the entire structure.

Ball-and-stick model of a primitive unit cell of UiO-66(Zr). Linker functionalization is indicated on the right. Primitive and conventional unit cells for diamond are given as reference.

Electronic Structure

Electronic band structure and DOS of UiO-66(Zr)-2,5SH

The calculated electronic band structure (left) and density of states (right) of the double SH-functionalized UiO-66(Zr). The conduction band is colored in blue, while the gap states related to the functional groups are colored green. The “old” valence band is colored yellow. This picture is a modified version of the published one.(Ref 1)

Starting from the optimized geometrical structures, the electronic structure is investigated. Taking three high-symmetry lines of the first Brillouin zone, the band structure was generated for all the functionalized MOFs.

The first aspect that drew my attention was the fact that the bottom conduction bands (indicated in blue) remained unchanged while part of the top of the valence band (indicated in green) splits off and moved upward into the band gap. At this point, nomenclature also becomes a bit of a problem. In a doped semi-conductor, the green bands would be called gap states, which would mean that the band gap of the host-material remains unchanged (which is actually also the case here, the distance between the yellow valence band and the blue conduction band is exactly the same for all functionalized UiO-66(Zr) systems we investigated). However, unlike those semiconductors, these gap states are entirely filled, and contain a significant electron occupation (in doped semi-conductors, these states often appear due to ppm doping). Because of this, they take the role of the valence band leading to a measured band gap equal to the distance between the top green bands and the conduction band (blue). So we end up with two band gaps. To have a clear link with experiments on MOFs, we will call the latter the band gap, while we will call the distance between the yellow and blue bands the “super band gap” (super, to indicate that we go beyond the size of the band gap, but it can still be considered a band gap. If that were not the case, we should call it the “supra band gap”).

The discussion of the super band gap can be rather short: it remains unchanged from the value of the unfunctionalized UiO-66(Zr): roughly 4 eV. In contrast, the band gap depends on both the functional group, and the number of functional groups present on each linker. In case of the double SH-functionalized linkers, each functional group leads to a gap state that is being split of from the valence band (cf. two green bands in the right picture).

Orbital character of valence and conduction band.

Orbital character of gap states, and valence and conduction bands for OH functionalized linkers in UiO-66(Zr).

Analysis of the orbital character shows that the splitting of the valence band can be taken quite literal. Where the valence band (or HOMO if you use molecular terminology) of the unfunctionalized UiO-66(Zr) mainly consists of the π-orbital of the BDC linker, this orbital is split upon functionalization. The conduction band orbital (or LUMO) on the other hand is barely modified.

Because LDA and GGA functionals are well-known to underestimate the experimental band gaps (even though the band structure is qualitatively well represented), we have also used a hybrid functional (HSE06, which was developed for solids) to calculate the band gap, and as expected, we find that the qualitative picture of the electron density of states (DOS) is retained, and the resulting calculated band gap is in perfect agreement with the experimentally measured values (experiments performed by Kevin Hendrickx of the Centre for Ordered Materials, Organometallics and Catalysis at Ghent University).

In conclusion, our ab initio calculations have shown us that functionalization of the linkers leads to a splitting of the valence band and the creation of a gap state, and that the band gap can be predicted with great accuracy for these materials.

The New: COK-69(Ti)

Atomic Structure

Ball-and-stick model of the COK-69(Ti) MOF. A single triangular Ti cluster is shown in more detail.

The COK-69(Ti) MOF is a newly developed MOF by the Center for Surface Chemistry and Catalysis of the university of Leuven. It is one of the few Ti containing MOFs that have already been synthesized. Because of this, the initial model provided was not sufficiently accurate to perform good electronic structure calculations. The weak point of the model was the uncertainty of the actual structure of the triangular Ti-O clusters. The original model (figure a) was not charge balanced. As a result, the electronic structure of this model showed it to be a metal (or a very narrow band gap semiconductor), in clear disagreement with experiment. Charge balance could be obtained in several ways: removal of O atoms, formation of H₂O bound to the cluster (e.g. figure c) or the formation of OH groups (e.g. figure b). By investigating different models, we found that the removal of O atoms is highly unfavorable, while the formation of OH groups and a bound H₂O molecule are comparable in stability. As a result of the latter observation, it is not unreasonable to assume that under experimental conditions the bound H₂O molecule dissociates and lead to the formation of two OH groups, and that this process is also reversed, leading to a constant moving back and forth between the two models.

Schematic representation of possible triangular Ti clusters for the CO-69(Ti) MOF.

Electronic Structure

Also, the calculated electronic structure for both models is reasonably comparable: similar sized band gaps, and the same character for the valence (mainly O states) and the conduction (mainly Ti states) bands. Making it hard to give preference to one model over the other as being the actual ground state structure of this MOF, without further study.

Irradiated COK-69

More interestingly, we found the cluster with three OH groups (cf. figure d) to be most stable. In such a model, two of the Ti atoms should have an oxidation number of 4, while one has an oxidation number of 3. Looking into the electronic structure of this specific model of the COK-69 shows some amazing features. Firstly, the band gap is much reduced to about the size associated with a semiconductor, and secondly, the states of the Ti³⁺ atom show a valence to conduction transition of 3.2 eV, which roughly coincides with the blue color obtained for the irradiated COK-69 MOF.

Two samples of the COK-69(Ti) MOF. The normal COK-69 at the top, and the irradiated COK-69 MOF at the bottom. Figure taken from Ref 2.

Ti³⁺ centers are known to provide a blue color in other materials, and it is now also shown to be the case for this MOF. In addition, experiments on the irradiated COK-69 MOF also showed that no more than 1/3 of the Ti atoms could be Ti³⁺, which is also the maximum indicated by our model (one Ti per Ti-cluster).

Another interesting bonus provided by this last model is from the theoretical perspective. Due to the symmetry of the cluster and the strong correlation of the Ti-d states, standard DFT is not able to differentiate between the Ti⁴⁺ and Ti³⁺ atoms. As such, the atomic charge is the same for all. By adding an additional Hubbard U potential on the Ti-d states (the so-called DFT+U approach) it is possible to differentiate between the different Ti oxidation states, as is shown by the nice bifurcation diagram.

Differentiation of Ti species as function of the U value used in a DFT+U approach. Atomic charges are calculated using the Hirshfeld-I partitioning scheme[3]. Figure taken from Ref 2.

In conclusion, our ab initio calculations allowed us to build a more accurate model of the COK-69 MOF and provide a model for the irradiated COK-69 MOF. In case of the latter, the calculated electronic structure can be used to elucidate the blue color of the irradiated COK-69.

References

[1] “Understanding intrinsic light absorption properties of UiO-66 frameworks”, K. Hendrickx, D.E.P. Vanpoucke, K. Leus, et al. Inorganic Chemistry (in revision)

[2] “A Flexible Photoactive Titanium MOF based on a [TiIV3(µ3-O)O2(COO)6]-Cluster”, B. Beuken, F. Vermoortele, D.E.P. Vanpoucke, et al. Angewandte Chemie (accepted)

[3] D.E.P. Vanpoucke, P. Bultinck, and I. Van Driessche, J. Comput. Chem. 34 405-417 (2013) & J. Comput. Chem. 34 422-427 (2013)

Permanent link to this article: https://dannyvanpoucke.be/iap-meeting-poster-2015-en/

Jun 19 2015

Phonons: shake those atoms

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June 19, 2015

In physics, a phonon is a collective excitation in a periodic, elastic arrangement of atoms or molecules in condensed matter, like solids and some liquids. Often designated a quasi-particle, it represents an excited state in the quantum mechanical quantization of the modes of vibrations of elastic structures of interacting particles.

— source: wikipedia

Or for simplicity: sound waves; the ordered shaking of atoms or molecules. When you hit a metal bell with a (small) hammer, or make a wineglass sing by rubbing the edges, you experience the vibrations of the object as sound. All objects in nature (going from atoms to stars) can be made to vibrate, and they do this at one or more specific frequencies : their eigenfrequencies or normal frequencies.

Also single molecules, if they are hit (for example by another molecule bumping into them) or receive extra energy in another way, start to vibrate. These vibrations can take many forms (elongating and shortening of bonds, rotating of parts of the molecule with respect to other parts, flip-flopping of loose ends, and so forth) and give a unique signature to the molecule since each of these vibrations (so-called eigen-modes) corresponds with a certain energy given to the molecule. As a result, if you know all the eigen-modes of a molecule, you also know which frequencies of infrared light they should absorb, which is very useful, since in experiment we do not “see” molecules (if we see them at all) as nice ball-and-stick objects.

From the computational point of view, this is not the only reason why in molecular modeling the vibrational frequencies of a system (i.e. the above eigen-modes) are calculated. In addition, they also tell if a system is in its ground state (which is what one is looking for most of the time) or not. Although this tool has wide-spread usage in molecular modeling, it is seldom used in ab initio solid state physics because of the associated computational cost. In addition, because of the finite size of the unit cell, the reciprocal space in which phonons live also has a finite size, in contrast to the single point for a molecule…making life complex. 😎

Permanent link to this article: https://dannyvanpoucke.be/phonons-shake-those-atoms-en/

Publication list

Full publication list: 2008 (1), 2009 (1), 2010 (3), 2011 (2), 2012 (4),2013 (3), 2014 (6), 2015 (5), 2016 (4), 2017 (4),2018 (1),2019 (3),2020 (5), 2021 (2), 2022 (4),2023 (2), 2024 (2) In Preparation (1), and Editorial work
PhD-thesis’es: 2009, 2012
Covers: 2013,2015,2022,2024

In Preparation/Press/Accepted

The role of atomic reference models in the Hirshfeld-I atoms-in-molecules partitioning scheme

Danny E. P. Vanpoucke, Sofie Van Damme, Veronique Van Speybroeck and Patrick Bultinck,

XX, YY (2015), (on hold)
doi: {IF(2014)=IIII}

2024

First-principles investigation of hydrogen-related reactions on (100)–(2×1)∶H diamond surfaces

Emerick Y. Guillaume, Danny E. P. Vanpoucke, Rozita Rouzbahani, Luna Pratali Maffei, Matteo Pelucchi, Yoann Olivier, Luc Henrard, and Ken Haenen,

Carbon 222, 118949 (2024),
doi: 10.1016/j.carbon.2024.118949 {IF(2022)=10.9}
Cover Nature Reviews Physics

Emanuele Bosoni, Louis Beal, Marnik Bercx, Peter Blaha, Stefan Blügel, Jens Bröder, Martin Callsen, Stefaan Cottenier, Augustin Degomme, Vladimir Dikan, Kristjan Eimre, Espen Flage-Larsen, Marco Fornari, Alberto Garcia, Luigi Genovese, Matteo Giantomassi, Sebastiaan P. Huber, Henning Janssen, Georg Kastlunger, Matthias Krack, Georg Kresse, Thomas D. Kühne, Kurt Lejaeghere, Georg K. H. Madsen, Martijn Marsman, Nicola Marzari, Gregor Michalicek, Hossein Mirhosseini, Tiziano M. A. Müller, Guido Petretto, Chris J. Pickard, Samuel Poncé, Gian-Marco Rignanese, Oleg Rubel, Thomas Ruh, Michael Sluydts, Danny E.P. Vanpoucke, Sudarshan Vijay, Michael Wolloch, Daniel Wortmann, Aliaksandr V. Yakutovich, Jusong Yu, Austin Zadoks, Bonan Zhu, and Giovanni Pizzi,

Nat. Rev. Phys. 6(1), (2024),
doi: na (web) {IF(2021)=36.273}
How to verify the precision of density-functional-theory implementations via reproducible and universal workflows

Emanuele Bosoni, Louis Beal, Marnik Bercx, Peter Blaha, Stefan Blügel, Jens Bröder, Martin Callsen, Stefaan Cottenier, Augustin Degomme, Vladimir Dikan, Kristjan Eimre, Espen Flage-Larsen, Marco Fornari, Alberto Garcia, Luigi Genovese, Matteo Giantomassi, Sebastiaan P. Huber, Henning Janssen, Georg Kastlunger, Matthias Krack, Georg Kresse, Thomas D. Kühne, Kurt Lejaeghere, Georg K. H. Madsen, Martijn Marsman, Nicola Marzari, Gregor Michalicek, Hossein Mirhosseini, Tiziano M. A. Müller, Guido Petretto, Chris J. Pickard, Samuel Poncé, Gian-Marco Rignanese, Oleg Rubel, Thomas Ruh, Michael Sluydts, Danny E.P. Vanpoucke, Sudarshan Vijay, Michael Wolloch, Daniel Wortmann, Aliaksandr V. Yakutovich, Jusong Yu, Austin Zadoks, Bonan Zhu, and Giovanni Pizzi,

Nat. Rev. Phys. 6(1), 45-58 (2024),
doi: 10.1038/s42254-023-00655-3 {IF(2021)=36.273}

2023

Hydration sphere structure of architectural molecules: polyethylene glycol and polyoxymethylene oligomers

Ahmed M. Rozza, Danny E. P. Vanpoucke, Eva-Maria Krammer, Julie Bouckaert, Ralf Blossey, Marc F. Lensink, Mary Jo Ondrechen, Imre Bakó, Julianna Oláh, and Goedele Roos,

J. Mol. Liq. 384, 122172 (2023),
doi: 10.1016/j.molliq.2023.122172 {IF(2021)=6.633}
Elucidating the optimized P2 type Na_0.67Mn_1−xCu_xO₂ cathode active material via operando XAS

S. Altin, S. Altundag, E. Altin, D. E. P. Vanpoucke, S. Avci, and M. N. Ates,

J. Alloys Compd. 936, 168138 (2023),
doi: 10.1016/j.jallcom.2022.168138 {IF(2021)=6.371}

2022

Cover Polymer International

Danny E.P. Vanpoucke, Marie A.F. Delgove, Jules Stouten, Jurrie Noordijk, Nils De Vos, Kamiel Matthysen, Geert G.P. Deroover, Siamak Mehrkanoon, and Katrien V. Bernaerts,

Polymer International 71(8), i-i (2022),
doi: 10.1002/pi.6434 {IF(2021)=3.213}
A machine learning approach for the design of hyperbranched polymeric dispersing agents based on aliphatic polyesters for radiation curable inks

Danny E.P. Vanpoucke, Marie A.F. Delgove, Jules Stouten, Jurrie Noordijk, Nils De Vos, Kamiel Matthysen, Geert G.P. Deroover, Siamak Mehrkanoon, and Katrien V. Bernaerts,

Polymer International 71(8), 966-975 (2022),
doi: 10.1002/pi.6378 {IF(2021)=3.213}
Localized vibrational modes of GeV-centers in diamond: Photoluminescence and first-principles phonon study

Kirill N. Boldyrev, Vadim S. Sedov, Danny E.P. Vanpoucke, Victor G. Ralchenko, and Boris N. Mavrin

Diam. Relat. Mater. 126, 109049 (2022),
doi: 10.1016/j.diamond.2022.109049 {IF(2021)=3.806}
On the influence of water on THz vibrational spectral features of molecular crystals

Sergey Mitryukovskiy, Danny E. P. Vanpoucke, Yue Bai, Théo Hannotte, Mélanie Lavancier, Djamila Hourlier, Goedele Roos and Romain Peretti,

PhysChemChemPhys 24(10), 6107-6125 (2022),
doi: 10.1039/D1CP03261E {IF(2021)=3.945}
Deep Eutectic Solvents as Nonflammable Electrolytes for Durable Sodium-Ion Batteries

Dries De Sloovere, Danny E. P. Vanpoucke, Andreas Paulus, Bjorn Joos, Lavinia Calvi, Thomas Vranken, Gunter Reekmans, Peter Adriaensens, Nicolas Eshraghi, Abdelfattah Mahmoud, Frédéric Boschini, Mohammadhosein Safari, Marlies K. Van Bael, An Hardy

Advanced Energy & Sustainability Research 3(3), 2100159 (2022),
doi: 10.1002/aesr.202100159 {IF(2022)=NA}

2021

Assigning probabilities to non-Lipschitz mechanical systems

Danny E. P. Vanpoucke, and Sylvia Wenmackers

Chaos 31(12), 123131 (2021), [Editor’s Pick]
doi: 10.1063/5.0063388 {IF(2021)=3.741}
Impact of methane concentration on surface morphology and boron incorporation of heavily boron-doped single crystal diamond layers

Rozita Rouzbahani, Shannon S. Nicley, Danny E. P. Vanpoucke, Fernando Lloret, Paulius Pobendinskas, Daniel Araujo, and Ken Haenen,

Carbon 172, 463-473 (2021),
doi: 10.1016/j.carbon.2020.10.061 {IF(2021)=11.307}

2020

Small Data Materials Design with Machine Learning: When the Average Model Knows Best

Danny E. P. Vanpoucke, Onno S. J. van Knippenberg, Ko Hermans, Katrien V. Bernaerts, and Siamak Mehrkanoon

J. Appl. Phys. 128 (5), 054901 (2020), [Featured Article][Scilight]
doi: 10.1063/5.0012285 {IF(2021)=2.877}
Partitioning the vibrational spectrum: Fingerprinting defects in solids

Danny E. P. Vanpoucke,

Comput. Mater. Sci. 181, 109736 (2020),
doi: 10.1016/j.commatsci.2020.109736 {IF(2021)=3.572}
Influence of diamond crystal orientation on the interaction with biological matter

Viraj Damle, Kaiqi Wu, Oreste De Luca, Natalia Ortí-Casañ, Neda Norouzi, Aryan Morita, Joop de Vries, Hans Kaper, Inge Zuhorn, Ulrich Eisel, Danny E.P. Vanpoucke, Petra Rudolf, and Romana Schirhagl,

Carbon 162, 1-12 (2020),
doi: 10.1016/j.carbon.2020.01.115 {IF(2021)=11.307}
UV-Curable Biobased Polyacrylates Based on a Multifunctional 2 Monomer Derived from Furfural

Jules Stouten, Danny E. P. Vanpoucke, Guy Van Assche, and Katrien V. Bernaerts,

Macromolecules 53(4), 1388-1404 (2020),
doi: 10.1021/acs.macromol.9b02659 {IF(2021)=6.051}
Investigation of structural, electronic and magnetic properties of breathing metal–organic framework MIL-47(Mn): a first principles approach

Mohammadreza Hosseini, Danny E.P. Vanpoucke, Paolo Giannozzi, Masoud Berahman, Nasser Hadipour,

RSC Adv. 10, 4786-4794 (2020),
doi: 10.1039/C9RA09196C {IF(2021)=4.036}

2019

Can Europium Atoms form Luminescent Centres in Diamond: A combined Theoretical-Experimental Study

Danny E. P. Vanpoucke, Shannon S. Nicley, Jorne Raymakers, Wouter Maes, and Ken Haenen,

Diam. Relat. Mater. 94, 233-241 (2019),
doi: 10.1016/j.diamond.2019.02.024 {IF(2019)=2.650}
Synthesis, characterization and thermodynamic stability of nanostructured ε-iron carbonitride powder prepared by a solid-state mechanochemical route

Seyyed Amin Rounaghi, Danny E. P. Vanpoucke, Elaheh Esmaeili, Sergio Scudino, and Jürgen Eckert

J. Alloys Compd. 778, 327-336 (2019),
doi: 10.1016/j.jallcom.2018.11.007 {IF(2019)=4.650 }
Predicting Partial Atomic Charges in Siliceous Zeolites

Jarod J. Wolffis, Danny E. P. Vanpoucke, Amit Sharma, Keith V. Lawler, and Paul M. Forster,

Microporous and Mesoporous Materials 277, 184-196 (2019),
doi: 10.1016/j.micromeso.2018.10.028 {IF(2019)=4.551}

2018

Bookchapter:”Computational Chemistry Experiment Possibilities”

Bartłomiej M. Szyja and Danny E. P. Vanpoucke

Zeolites and Metal-Organic Frameworks. From Lab to Industry., Chapter 9, p 235-264 (2018),
ISBN : 978-94-629-8556-8
Amsterdam University Press

2017

Revisiting the Neutral C-Vacancy in Diamond: Localization of Electrons through DFT+U

Danny E. P. Vanpoucke, and Ken Haenen

Diam. Relat. Mater. 79, 60-69 (2017),
doi: 10.1016/j.diamond.2017.08.009 {IF(2017)=2.232}
A combined experimental and theoretical investigation of the Al-Melamine reactive milling system: a mechanistic study towards AlN-based ceramics

Seyyed A. Rounaghi, Danny E. P. Vanpoucke, Hossein Eshghi, Sergio Scudino, Elaheh Esmaeili, Steffen Oswald, and Jürgen Eckert

J. Alloys Compd. 729, 240-248 (2017),
doi: 10.1016/j.jallcom.2017.09.168 {IF(2017)=3.779}
Mechanochemical synthesis of nanostructured metal nitrides, carbonitrides and carbon nitride: A combined theoretical and experimental study

Seyyed Amin Rounaghi, Danny E. P. Vanpoucke, Hossein Eshghi, Sergio Scudino, Elaheh Esmaeili, Steffen Oswald, and Jürgen Eckert,

Phys. Chem. Chem. Phys. 19, 12414-12424 (2017),
doi: 10.1039/C7CP00998D {IF(2017)=3.906}
Linker Functionalization in MIL-47(V)-R Metal–Organic Frameworks: Understanding the Electronic Structure

Danny E. P. Vanpoucke,

J. Phys. Chem. C 121(14), 8014-8022 (2017),
doi: 10.1021/acs.jpcc.7b01491 {IF(2017)=4.484}

2016

Mechanochemical route to the synthesis of nanostructured Aluminium nitride

Seyyed Amin Rounaghi, Hossein Eshghi, Sergio Scudino, Anastasia Vyalikh, Danny E. P. Vanpoucke, Wolfgang Gruner, Steffen Oswald, Ali-Reza Kiani-Rashid, Mohsen Samadi-Khoshkhoo, Ulrich Scheler, and Jürgen Eckert

Scientific Reports 6, 33375 (2016),
doi: 10.1038/srep33375 {IF(2016)=4.259}
First-Principles Study of Antisite Defect Configurations in ZnGa₂O₄:Cr Persistent Phosphors

Arthur De Vos, Kurt Lejaeghere, Danny E.P. Vanpoucke, Jonas J. Joos, Philippe F. Smet, and Karen Hemelsoet,

Inorg. Chem. 55(5), 2402–2412 (2016),
doi: 10.1021/acs.inorgchem.5b02805 {IF(2016)=4.857}
Computational Materials Science: Where Theory Meets Experiments

Danny E. P. Vanpoucke,

ICACC 2015 conference proceeding, Developments in Strategic Ceramic Materials: Ceramic Engineering and Science Proceedings 36(8), 323-334 (2016),
ISBN: 978-1-119-21173-0
Doping of CeO₂ as a Tunable Buffer Layer for Coated Superconductors: A DFT Study of Mechanical and Electronic Properties

Danny E. P. Vanpoucke,

ICACC 2015 conference proceeding, Developments in Strategic Ceramic Materials: Ceramic Engineering and Science Proceedings 36(8), 169-177 (2016),
ISBN: 978-1-119-21173-0

2015

Understanding intrinsic light absorption properties of UiO-66 frameworks: A combined theoretical and experimental study

Kevin Hendrickx, Danny E.P. Vanpoucke, Karen Leus, Kurt Lejaeghere, Andy Van Yperen-De Deyne, Veronique Van Speybroeck, Pascal Van Der Voort, and Karen Hemelsoet

Inorg. Chem. 54(22), 10701-10710 (2015),
doi: 10.1021/acs.inorgchem.5b01593 {IF(2015)=4.820}
A Flexible Photoactive Titanium Metal-Organic Framework Based on a [Ti^IV₃(μ₃-O)(O)₂(COO)₆] Cluster

Bart Bueken, Frederik Vermoortele, Danny E. P. Vanpoucke, Helge Reinsch, Chih-Chin Tsou, Pieterjan Valvekens, Trees De Baerdemaeker, Rob Ameloot, Christine E. A. Kirschhock, Veronique
Van Speybroeck, James M. Mayer and Dirk De Vos,

Angew. Chem. Int. Ed. 54(47), 13912-13917 (2015),
doi: 10.1002/anie.201505512 {IF(2015)=11.705}
Cover Image of CrystEngComm

Thomas Bogaerts, Louis Vanduyfhuys, Danny E.P. Vanpoucke, Jelle Wieme, Michel Waroquier, Pascal Van Der Voort, and Veronique Van Speybroeck,

Cryst. Eng. Comm. 17(45), 8565 (2015),
doi: 10.1039/C5CE90198G {IF(2015)=3.849}
Fine-tuning the theoretically predicted structure of MIL-47(V) with the aid of powder X-ray diffraction

Thomas Bogaerts, Louis Vanduyfhuys, Danny E.P. Vanpoucke, Jelle Wieme, Michel Waroquier, Pascal Van Der Voort, and Veronique Van Speybroeck,

Cryst. Eng. Comm. 17(45), 8612-8622 (2015),
doi: 10.1039/C5CE01388G {IF(2015)=3.849}
Mechanical Properties from Periodic PlaneWave Quantum Mechanical Codes: The Challenge of the Flexible Nanoporous MIL-47(V) Framework

Danny E. P. Vanpoucke, Kurt Lejaeghere, Veronique Van Speybroeck, Michel Waroquier, and An Ghysels,

J. Phys. Chem. C 119(41), 23752-23766 (2015),
doi: 10.1021/acs.jpcc.5b06809 {IF(2015)=4.509}
Convergence of Atomic Charges with the Size of the Enzymatic Environment

Danny E. P. Vanpoucke, Julianna Oláh, Frank De Proft, Veronique Van Speybroeck, and Goedele Roos

J. Chem. Inf. Model. 55(3), 564-571 (2015),
doi: 10.1021/ci5006417 {IF(2015)=3.657}

2014

Comment on ‘Europium doping induced symmetry deviation and its impact on the second harmonic generation of doped ZnO nanowires’

Danny E. P. Vanpoucke,

Nanotechnology 25(45), 458001 (2014),
doi: 10.1088/0957-4484/25/45/458001 {IF(2014)=3.821}
Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles

Danny E. P. Vanpoucke, Jan W. Jaeken, Stijn De Baerdemacker, Kurt Lejaeghere
and Veronique Van Speybroeck

Beilstein J. Nanotechnol. 5, 1738-1748 (2014),
doi: 10.3762/bjnano.5.184 {IF(2014)=2.670}
Aliovalent Doping of CeO₂: DFT study of oxidation state and vacancy effects

Danny E. P. Vanpoucke, Patrick Bultinck, Stefaan Cottenier, Veronique Van Speybroeck, and Isabel Van Driessche

J. Mater. Chem. A 2, 13723-13737 (2014),
doi:10.1039/C4TA02449D {IF(2014)=7.443}
Rationality: A Social-Epistemology Perspective

Sylvia Wenmackers, Danny E. P. Vanpoucke, and Igor Douven,

Front. Psychol. 5, 581 (14 pages) (2014),
doi: 10.3389/fpsyg.2014.00581 {IF(2014)=2.560}
Modeling 1D structures on semiconductor surfaces: Synergy of theory and experiment

Danny E. P. Vanpoucke,

J. Phys.: Condens. Matter 26(13), 133001 (2014), (commissioned Topical Review)
doi: 10.1088/0953-8984/26/13/133001 {IF(2014)=2.346}
Tetravalent Doping of CeO₂: The impact of valence electron character on group IV dopant influence

Danny E. P. Vanpoucke, Stefaan Cottenier, Veronique Van Speybroeck, Isabel Van Driessche, and Patrick Bultinck,

J. Am. Ceram. Soc. 97(1), 258-266 (2014),
doi:10.1111/jace.12650 {IF(2014)=2.610}

2013

New Functionalized Metal-Organic Frameworks MIL-47-X (X = -Cl, -Br, -CH₃, -CF₃, -OH, -OCH₃): Synthesis, Characterization and CO₂ Adsorption Properties

Shyam Biswas, Danny E. P. Vanpoucke, Toon Verstraelen, Matthias Vandichel, Sarah Couck, Karen Leus, Ying-Ya Liu, Michel Waroquier, Veronique Van Speybroeck, Joeri F. M. Denayer, and Pascal Van Der Voort,

J. Phys. Chem. C 117(44), 22784-22796 (2013),
doi: 10.1021/jp406835n {IF(2013)=4.835}
Cover Image of Journal of Computational Chemistry

Danny E. P. Vanpoucke,

J. Comput. Chem. 34(5), i-ii (2013),
doi:10.1002/jcc.23239 {IF(2013)=3.601}
Reply to ‘Comment on “Extending Hirshfeld-I to bulk and periodic materials” ‘

Danny E. P. Vanpoucke, Isabel Van Driessche, and Patrick Bultinck,

J. Comput. Chem. 34(5), 422-427 (2013),
doi:10.1002/jcc.23193 {IF(2013)=3.601}
Extending Hirshfeld-I to bulk and periodic materials

Danny E. P. Vanpoucke, Patrick Bultinck, and Isabel Van Driessche,

J. Comput. Chem. 34(5), 405-417 (2013),
doi:10.1002/jcc.23088 {IF(2013)=3.601}

2012

Investigation of tunable buffer layers for coated superconductors:from solid state physics to quantum chemistry

Danny E. P. Vanpoucke,

Ph.D. Thesis at University of Ghent, Belgium (2012),
Aqueous CSD approach for the growth of novel, lattice-tuned La_xCe_1-xO_d epitaxial layers

Vyshnavi Narayanan, Petra Lommens, Klaartje De Buysser, Danny E.P. Vanpoucke, Ruben Huehne,
Leopoldo Molina, Gustaaf Van Tendeloo , Pascal Van Der Voort, Isabel Van Driessche,

J. Mater. Chem. 22, 8476 (2012),
doi:10.1039/C2JM15752G {IF(2012)=6.101}
Models and simulations in material science: two cases without error bars

Sylvia Wenmackers and Danny E. P. Vanpoucke,

Statistica Neerlandica 66, 339-355 (2012),
doi: 10.1111/j.1467-9574.2011.00519.x {IF(2012)=0.585}
Tuning of CeO₂ buffer layers for coated superconductors through doping

Danny E. P. Vanpoucke, Stefaan Cottenier, Veronique Van Speybroeck, Patrick Bultinck, and Isabel Van Driessche,

Appl. Surf. Sci. 260, 32-35 (2012),
doi: 10.1016/j.apsusc.2012.01.032, {IF(2012)=2.112}
Probability of inconsistencies in theory revision, A multi-agent model for updating logically interconnected beliefs under bounded confidence

S. Wenmackers, D. E. P. Vanpoucke and I. Douven,

Eur. Phys. J. B 85:44(2012),
doi: 10.1140/epjb/e2011-20617-8 {IF(2012)=1.282}

2011

Pt Nanowires on Ge(001): Sheep in Wolf’s Clothing?

Danny E. P. Vanpoucke

Belgian Physical Society Magazine 3, 11-16 (2011), (Featured Article for the BF)
Density functional theory study of La₂Ce₂O₇: disordered fluorite vs pyrochlore structure

Danny E. P. Vanpoucke, Patrick Bultinck, Stefaan Cottenier, Veronique Van Speybroeck and Isabel Van Driessche,

Phys. Rev. B 84, 054110 (2011),
doi: 10.1103/PhysRevB.84.054110 {IF(2011)=3.691}

2010

CO adsorption on Pt-induced Ge nanowires

Danny E. P. Vanpoucke and G. Brocks,

Phys. Rev. B 81, 235434 (2010),
doi: 10.1103/PhysRevB.81.235434 {IF(2010)=3.774}
Pt-induced nanowires on Ge(001): A density functional theory study

Danny E. P. Vanpoucke and G. Brocks,

Phys. Rev. B 81, 085410 (2010),
doi: 10.1103/PhysRevB.81.085410 {IF(2010)=3.774}
Density functional theory study of Pt-induced Ge(001) reconstructions

Danny E. P. Vanpoucke and G. Brocks,

Phys. Rev. B 81, 035333 (2010),
doi: 10.1103/PhysRevB.81.035333 {IF(2010)=3.774}

2009

Ab Initio study of Pt Induced Nanowires on Ge(001)

Danny E. P. Vanpoucke,

Ph.D. Thesis at University of Twente, The Netherlands (2009),
doi: 10.3990/1.9789036528733

ISBN : 978-90-365-2873-3
The formation of Self-Assembled Nanowire Arrays on Ge(001): a DFT study of Pt Induced Nanowire Arrays

Danny E. P. Vanpoucke and G. Brocks,

Mater. Res. Soc. Symp. Proc. 1177, 1177-Z03-09 (2009),
doi: 10.1557/PROC-1177-Z03-09

2008

Formation of Pt-induced Ge atomic nanowires on Pt/Ge(001): A density functional theory study

Danny E. P. Vanpoucke and G. Brocks,

Phys. Rev. B 77, 241308(R) (2008),
doi: 10.1103/PhysRevB.77.241308 {IF(2008)=3.322}

Editorial work

Computational Nanoscience – How to Exploit Synergy Between Predictive Simulations and Experiment

Curran Associates, Inc. ( Jun 2010 )
series: Materials Research Society Symposium Proceedings Volume 1177
ISBN: 9781617383960
Editor: Vanpoucke D.

proceedings.com

Permanent link to this article: https://dannyvanpoucke.be/publication-list-en/

Oct 28 2014

Extending Hirshfeld-I to bulk and periodic materials

Filed under 2013, publications
October 28, 2014

Authors:	Danny E. P. Vanpoucke, Patrick Bultinck, and Isabel Van Driessche,
Journal:	J. Comput. Chem. 34(5), 405-417 (2013)
doi:	10.1002/jcc.23088
IF(2013):	3.601
export:	bibtex
pdf:	<J.Comput.Chem.> <arXiv>

Graphical Abstract: The Hirshfeld-I method is extended to solids, allowing for the partitioning of a solid density into constituent atoms. The use of precalculated density grids makes the implementation code independent, and the use of pseudo-potential based electron density distributions is shown to give qualitatively the same results as all electron densities. Results for some simple solids/periodic systems like cerium oxide and graphene are presented.

Abstract

In this work, a method is described to extend the iterative Hirshfeld-I method, generally used for molecules, to periodic systems. The implementation makes use of precalculated pseudopotential-based electron density distributions, and it is shown that high-quality results are obtained for both molecules and solids, such as ceria, diamond, and graphite. The use of grids containing (precalculated) electron densities makes the implementation independent of the solid state or quantum chemical code used for studying the system. The extension described here allows for easy calculation of atomic charges and charge transfer in periodic and bulk systems. The conceptual issue of obtaining reference densities for anions is discussed, and the delocalization problem for anionic reference densities originating from the use of a plane wave basis set is identified and handled.

Conceptual DFT, Hirshfeld-I, JComputChem, Materials Science, PhD thesis 2

Permanent link to this article: https://dannyvanpoucke.be/paper2013_hipaper-en/

Oct 28 2014

Models and simulations in material science: two cases without error bars

Filed under 2012, publications
October 28, 2014

Authors:	Sylvia Wenmackers and Danny E. P. Vanpoucke
Journal:	Statistica Neerlandica 66, 339-355 (2012)
doi:	10.1111/j.1467-9574.2011.00519.x
IF(2012):	0.585
export:	bibtex
pdf:	<Stat.Neer.> <arXiv>

Abstract

We discuss two research projects in material science in which the results cannot be stated with an estimation of the error: a spectroscopic ellipsometry study aimed at determining the orientation of DNA molecules on diamond and a scanning tunneling microscopy study of platinum-induced nanowires on germanium. To investigate the reliability of the results, we apply ideas from the philosophy of models in science. Even if the studies had reported an error value, the trustworthiness of the result would not depend on that value alone.

Materials Science, Model Development, Philosophy, Pt Nanowires, StatNeer

Permanent link to this article: https://dannyvanpoucke.be/paper2012_modelswrong-en/

51 results for diamond

Interstellar disc

1. Infinitesimal finite elements

2. Small volumes: A few more digits please

3. Many grains of sand really start to pile up after a while

Abstract

The Old: UiO-66(Zr)-X

Atomic Structure

Electronic Structure

The New: COK-69(Ti)

Atomic Structure

Electronic Structure

Irradiated COK-69

References

In Preparation/Press/Accepted

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Abstract

Abstract

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