Tag: Conceptual DFT

Materiomics Chronicles: week 11 & 12

After the exam period in weeks nine and ten, the eleventh and twelfth week of the academic year bring the second quarter of our materiomics program at UHasselt for the first master students. Although I’m not coordinating any courses in this quarter, I do have some teaching duties, including being involved in two of the hands-on projects.

As in the past 10 weeks, the bachelor students in chemistry had lectures for the courses introduction to quantum chemistry and quantum and computational chemistry. For the second bachelor this meant they finally came into contact with the H atom, the first and only system that can be exactly solved using pen and paper quantum chemistry (anything beyond can only be solved given additional approximations.) During the exercise class we investigated the concept of aromatic stabilization in more detail in addition to the usual exercises with simple Schrödinger  equations and wave functions. For the third bachelor, their travel into the world of computational chemistry continued, introducing post-Hartree-Fock methods with also include the missing correlation energy. This is the failure of Hartree-Fock theory, making it a nice framework, but of little practical use for any but the most trivial molecules (e.g. H2 for example already being out of scope). We also started looking into molecular systems, starting with simple diatomic molecules like H2+.

SnV split vacancy defect in diamond.

SnV split vacancy defect in diamond.

In the master materiomics, the course Machine learning and artificial intelligence in modern materials science hosted a guest lecture on Large Language Models, and their use in materials research as well as an exercise session during which the overarching ML study of the QM9 dataset was extended. During the course on  Density Functional Theory there was a second lab, this time on conceptual DFT. For the first master students, the hands-on project kept them busy. One group combining AI and experiments, and a second group combining DFT modeling of SnV0 defects in diamond with their actual lab growth. It was interesting to see the enthusiasm of the students. With only some mild debugging, I was able to get them up and running relatively smoothly on the HPC. I am also truly grateful to our experimental colleagues of the diamond growth group, who bravely set up these experiments and having backup plans for the backup plans.

At the end of week 12, we added another 12h of classes, ~1h of video lecture, ~2h of HPC support for the handson project and 6h of guest lectures, putting our semester total at 118h of live lectures. Upwards and onward to weeks 13 & 14.

Materiomics Chronicles: week 9 & 10

With the end of the first quarter in week eight, the nine and tenth week of the academic year were centered around the first batch of exams for the first master students of our materiomics program at UHasselt. For the other students in the second master and bachelor, academic life continued with classes.

Coefficients of the 63-1G basis set for the H and He atom.

Coefficients of the 63-1G basis set for the H and He atom.

The course introduction to quantum chemistry starts to hone in on the first actual fully realistic system: the H atom. But before we get there, the students of the second bachelor chemistry extended their particle on a ring model system to an infinite number of ring systems: i.e. discs, spheres, and balls. Separation of variables has no longer any secrets for them. Now they are ready for reality after many weeks of abstract toy models. The third bachelor students on the other hand had their first ever contact with real practical quantum chemistry (i.e. computational chemistry) during the course quantum and computational chemistry. They learned about Hartree-Fock, the self-consistent field method, basis sets and slater orbitals. They entered this new world with a practical exercise class where, using jupyter notebooks and the psi4 package, they performed their first even quantum chemical calculations. Starting with the trivial H and He atom systems as a start, since for these we have calculated exact solutions during the classes of this course. This way, we learned about the quality of different basis sets and the time of calculations.

In the master materiomics, the first master students had their exams on Fundamentals of materials modeling, and Properties of functional materials, where all showed they understood the topics presented to sufficient degree making them ready for the second quarter. For the second master students, the course on Density Functional Theory held a lecture on the limitations of DFT and a guest lecture on conceptual DFT.

With week 10 drawing to a close, we added another 15h of classes, ~1h of video lecture and 2h of guest lectures, putting our semester total at 106h of live lectures. Upwards and onward to weeks 11 & 12.

Reply to ‘Comment on “Extending Hirshfeld-I to bulk and periodic materials” ‘

Authors: Danny E. P. Vanpoucke, Isabel Van Driessche, and Patrick Bultinck
Journal: J. Comput. Chem. 34(5), 422-427 (2013)
doi: 10.1002/jcc.23193
IF(2013): 3.601
export: bibtex
pdf: <J.Comput.Chem.> <arXiv>
Graphical Abstract: Hirshfeld-I atoms-in-molecules atoms in Ti doped CeO2. Graphical Abstract:The issues raised in the preceding comment are addressed. It is shown why Hirshfeld-I is, from a theoretical point of view, a good method for defining AIM and obtaining charges. Charges for a set of ionic systems are calculated using our presented method and shown to be chemically feasable. Comparison of pseudo-density to all-electron based results shows the pseudo-densities to be sufficient to obtain all-electron quality results. Timing results for systems containing hundreds of atoms.

Abstract

The issues raised in the comment by Manz are addressed through the presentation of calculated atomic charges for NaF, NaCl, MgO, SrTiO3, and La2Ce2O7, using our previously presented method for calculating Hirshfeld-I charges in solids (Vanpoucke et al., J. Comput. Chem. doi: 10.1002/jcc.23088). It is shown that the use of pseudovalence charges is sufficient to retrieve the full all-electron Hirshfeld-I charges to good accuracy. Furthermore, we present timing results of different systems, containing up to over 200 atoms, underlining the relatively low cost for large systems. A number of theoretical issues are formulated, pointing out mainly that care must be taken when deriving new atoms in molecules methods based on “expectations” for atomic charges.

Extending Hirshfeld-I to bulk and periodic materials

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: Hirshfeld-I atoms-in-molecules carbon atoms in a graphene sheet. 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.