Tag: Materials Science

Today was the fifth and last day of our spring school on computational tools for materials science. However, this was no reason to sit back and relax. After having been introduced into VASP (day-2) and ABINIT (day-3) for solids, and into Gaussian (day-4) for molecules, today’s code (CP2K) is one which allows you to study both when focusing on dynamics and solvation.

If ensembles were coffee…

The introduction into the Swiss army knife called CP2K was provided by Dr. Andy Van Yperen-De Deyne. He explained to us the nature of the CP2K code (periodic, tools for solvated molecules, and focus on large/huge systems) and its limitations. In contrast to the codes of the previous days, CP2K uses a double basis set: plane waves where the properties are easiest and most accurate described with plane waves and gaussians where it is the case for gaussians. By means of some typical topics of calculations, Andy explained the basic setup of the input and output files, and warned for the explosive nature of too long time steps in molecular dynamics simulations. The possible ensembles for molecular dynamics (MD) were explained as different ways to store hot coffee. Following our daily routine, this session was followed by a hands-on session.

In the afternoon, the advanced session was presented by a triumvirate:  Thierry De Meyer, who discussed QM/MM simulations in detail, Dr. Andy Van Yperen-De Deyne, who discused vibrational finger printing and Lennart Joos, who, as the last presenter of the week, showed how different codes can be combined within a single project, each used where they are at the top of their strength, allowing him to unchain his zeolites.

CP2K, all lecturers: Andy Van Yperen-De Deyne (top left), Thierry De Meyer (top right), Lennart Joos (bottom left). All spring school participants hard at work during the hands-on session, even at this last day (bottom right).

The spring school ended with a final hands-on session on CP2K, where the CMM team was present for the last stretch, answering questions and giving final pointers on how to perform simulations, and discussing which code to be most appropriate for each project. At 17h, after my closing remarks, the curtain fell over this spring school on computational tools for materials science. It has been a busy week, and Kurt and I are grateful for the help we got from everyone involved in this spring school, both local and external guests. Tired but happy I look back…and also a little bit forward, hoping and already partially planning a next edition…maybe in two years we will return.

Our external lecturers from the VASP group (Martijn Marsman, top left) and the ABINIT group (Xavier Gonze, top right, Matteo Giantomassi, bottom left, Gian-Marco Rignanese, bottom right)

After having focused on solids during the previous two days of our spring school, using either VASP (Tuesday) or ABINIT (Wednesday), today’s focus goes to molecules, and we turn our attention to the Gaussian code.

Dietmar Hertsen introduced us into the Gaussian code, and immediately showed us why this code was included in our spring school set: it is the most popular code (according to google). He also explained this code is so popular (among chemists) because it can do a lot of the chemistry chemists are interested in, and because of the simplicity of the input files for small molecules. After pointing out the empty lines quirks of Gaussian it was time to introduce some of the possible editors to use with Gaussian. The remainder of his lecture, Dietmar showed us how simple (typical) Gaussian calculations are run, pointing out interesting aspects of the workflow, and the fun of watching vibrations in molden. He ended his lecture giving us some tips and tricks for the investigation of transition states, and the study of chemical reactions, as a mental preparation for the first hands-on session which followed after the coffee-break.

Lecturers for the Gaussian code: Dietmar Hertsen (left) introducing the basics of the code, while Patrick Bultinck (right) discuses more advanced wave function techniques in more detail.

In the afternoon it was time to take out the big guns. Prof. Patrick Bultinck, of the Ghent Quantum Chemistry Group, was so kind to provide the advanced session. In this session, we were reminded, after two days of using the density as a central property, that wave functions are the only way to obtain perfect results. Unfortunately, practical limitations hamper the application to the systems of interest from a practical physical point of view. Patrick, being a quantum chemist to the bone, at several points stepped away from his slides and showed on the blackboard how several approximations to full configuration interaction (full-CI) can be obtained. He also made us aware of the caveats of such approaches; Such as size consistency and basis(-type) dependence for truncated CI, and noted that although CASSCF is a powerful method (albeit not for the fainthearted), it is somewhat a black art that should be used with caution. As such, CASSCF was not included in the advanced hands-on sessions guided by Dr. Sofie Van Damme (but who knows what may happen in a future edition of this spring school).

Today is the third day of our spring school. After the introduction to VASP yesterday, we now turn our attention to another quantum mechanical level solid state code: ABINIT. This is a Belgian ab initio code (mainly) developed at the Université Catholique de Louvain (UCL) in Wallonia.

Since no-one at CMM has practical experience with this code and several of us are interested to learn more about this code, we were very pleased that the group of Prof. Xavier Gonze was willing to support this day in its entirety. During the morning introductory session Prof. Xavier Gonze introduced us into the world of the ABINIT code, for which the initial ideas stem from 1997. Since then, the program has grown to about 800.000 lines of fortran code(!) and a team of 50 people worldwide currently contribute to its development. Also in recent years, a set of python scripts have been developed providing a more user friendly interface (abipy) toward the users of the code. The main goal of the development of this interface, is to shift interest back to the physics instead of trying to figure out which keywords do the trick. We also learned that the ABINIT code is strongly inspired by the ‘free software’ model, and as such Prof. Xavier Gonze prefers to refer to the copyright of ABINIT as copyleft. This open source mentality seems also to provide strength to the code; leading to its large number of developers/contributors; which in turn leads to the implementation of a wide variety of basis-sets, functionals and methodologies.

After the general introduction, Dr. Matteo Giantomassi introduced the abipy python package. This package was especially developed for automating post-processing of ABINIT results, and automatically generating input files. In short, to make interaction with ABINIT easier. Matteo, however, also warned that this approach which makes the use of ABINIT much more black box, might confuse beginners, since a lot of magic is going on under the hood of the abipy scripts. However, his presence, and that of the rest of the ABINIT delegation made sure confusion was kept to a minimum during the hands-on sessions, for which we are very grateful.

After the lunch break, Prof.  Gian-Marco Rignanese and Prof. Xavier Gonze held a duo seminar on more advanced topics covering Density Functional Perturbation Theory and based on this spectroscopy and phonon calculations beyond the frozen phonon approach. Of these last aspects I really am interested in seeing how they cope with my Metal Organic Frameworks…

On this second day of our spring school, the first ab initio solid state code is introduced: VASP, the Vienna Ab initio Simulation Package.

Having worked with this code for almost a full decade, some consider me an expert, and as such I had the dubious task of providing first contact with this code to our participants. Since all basic aspects and methods had already been introduced on the first day, I mainly focused on presenting the required input files and parameters, and showing how these should be tweaked for some standard type solid state calculations. Following this one-hour introduction, in which I apparently had not yet scared our participants too much, all participants turned up for the first hands-on session, where they got to play with the VASP program.

In the afternoon, we were delighted to welcome our first invited speaker, straight from the VASP-headquarters: Dr. Martijn Marsman. He introduced us to advanced features of VASP going beyond standard DFT. He showed the power (and limitations) of hybrid-functionals and introduced the quasi-particle approach of GW. We even went beyond GW with the Bethe-Salpeter equations (which include electron-hole interactions). Unfortunately, these much more accurate approaches are also much more expensive than standard DFT, but there is work being done on the implementation of a cubic scaling RPA implementation, which will provide a major step forward in the field of solid state science. Following this session, a second hands-on session took place where exercises linked to these more advanced topic were provided and eagerly tried by many of the more advanced participants.

Today our one-week spring school on computational tools for materials science kicked off. During this week, Kurt Lejaeghere and I host this spring school, which we have been busily organizing the last few months, intended to introduce materials scientists into the use of four major ab-initio codes (VASP, ABINIT, Gaussian and CP2K). During this first day, all participants are immersed in the theoretical background of molecular modeling and solid state physics.

Prof. Karen Hemelsoet presented a general introduction into molecular modeling, showing us which computational techniques are useful to treat problems of varying scales, both in space and time. With the focus going to the modeling of molecules she told us everything there is to know about the potential energy surface, (PES)  how to investigate it using different computational methods. She discussed the differences between localized (i.e. gaussian) and plane wave basis sets and taught us how to accurately sample the PES using both molecular dynamics and normal mode analysis. As a final topic she introduced us to the world of computational spectroscopy, showing how infrared spectra can be simulated, and the limitations of this type of simulations.

With the, somewhat mysterious, presentations of Prof. Stefaan Cottenier we moved from the  realm of molecules to that of solids. In his first session, he introduced density functional theory, a method ideally suited to treat extended systems at the quantum mechanical level. And showed that as much information is present in the electron density of a system as is in its wave function. In his second session, we fully plunged in the world of solids, and we were guided, step by step, towards a full understanding of the technical details generally found in the methods section of (ab-initio) computational materials science work. Throughout this session, NaCl was used as an ever present example, and we learned that our simple high-school picture of bonding in kitchen salt is a lie-to-children. In reality, Cl doesn’t gain an extra electron by stealing it away from Na, instead it is rather the Na 3s electron which is living to far away from the Na nucleus it belongs to.