20

B3LYP is still a decent functional at its level of theory (single-hybrid functional), but you're right that there's a general criticism of it, which I largely hear in the form of people saying things like "all they did was B3LYP/6-31G*" to criticize non-experts that blindly use this combination which became the "default" in chemistry for ...


18

You can see it with VESTA software. For example, we can see the different lattice planes of NaCl crystal. [001] plane of NaCl: [101] plane of NaCl: [111] plane of NaCl:


17

I think this review¹ by Head-Gordon is a useful supplement to Nike's answer. Its combines a review of functional development, a benchmarking of various functionals, and an explanation of the design process for the $\omega$B97 functionals. Its also open access, so its a great resource if you are interested in DFT functionals in general. They benchmarked 200 ...


16

I don't have too much to add to the answers of Nike Dattani and Tyberius, but I think the crux is that its capabilities have been historically overestimated. One particular failing of B3LYP is that it tends to underestimate bond energies. However, since the small (and fast) 6-31G* basis set will lead to overbinding, the famous combination B3LYP/6-31G* ended ...


13

Assuming a generic chemistry background I wouldn't assume that knowledge of crystal structure would be too in depth at an undergraduate level. It is definitely encountered, but depending on the type of chemistry you want to go into, you probably never deal with solid state chemistry. I would first explain briefly how crystals are described by periodic ...


8

There is currently no tool built into ASE to do this sort of detective work on surface terminations. I highly suggest that you take the approach of trying to eliminate dangling bonds first (for example, Se atoms with only 1 neighbor). This will give you a more reasonable termination, but may not give you the desired Ni-Se ratio. With a complex unit cell ...


7

Generally, if you want to perform simulations with some force field, you will have to search the literature for published FFs tailored for your problem. The Stillinger-Weber (SW) model is very popular to describe bulk (diamond) silicon, for which it was designed in the first place. But several reparametrizations have also been published. If you happen to ...


5

This may be a bit of a rough answer, so apologies in advance... Since the eigenvalues obtained using non-energy-consistent pseudopotentials (i.e. the situation in VASP as far as I know) do not themselves have physical meaning, we typically use a slab system with an explicit vacuum, in order to make reference to vacuum. A more common situation is calculating ...


5

I would propably explain that there are different planes within a crystal, show some of them in an animation or pyhsical prop and depending on the depth of the presentation just omit the numbering and details.


5

The reconstructed $(\sqrt{3} \times \sqrt{3})R30$ surface unit cell can be obtained by first applying the rotation matrix $ \begin{pmatrix} 1.0 & 2.0 & 0.0 \\ -1.0 & 1.0 & 0.0 \\ 0.0 & 0.0 & 1.0 \end{pmatrix}$ to the primitive bulk unit cell, and then the reconstructed $(001)$ surface can be cleaved from this unit cell, or ...


4

To answer your first question: the theory has certainly been worked out in some detail. The most accurate approach (a) would involve a quantum transport calculation in the non-equilibrium Green function formalism, describing the tip (L) and the sample (R) as semi-infinite leads, connected by a central region (C), and using the Meir-Wingreen formula to ...


4

Wannier90 might not be good at preserving the symmetry. But they probably include a few new methods to enforce symmetry in Wannier90.v.3.1.0. Maybe you can check this. http://www.wannier.org/features/ Also, WannierTools can symmetrize the hr.dat, but from my personal experience it sometimes gives you worse results than the original hr.dat. http://www....


4

Just some thoughts... All depends on what type of study do you want to do. An aside note: studying the interaction or behavior of a ligand attached to a surface is different to study the passivation of that surface with the same ligand. For only one ligand, you can search the surface for symmetry sites and then, manually (just adding it to a distance lower ...


4

Take care in the figure posted by Jack that the [hkl] notation actually represents the vector plane, that is the direction perpendicular to the plane. The plane are indexed as (hkl). for example, the first figure should be read as (001) plane of NaCl, whereas [001] represents the direction along the c-axis.


3

ASE is not aware of which layer things are on when you use the surface function to build an arbitrary surface. However, the indices should be in order of z height I believe. You can use the following to assign the tags, just be aware that this will not work for more complex surfaces very well (which is why it is not done by default I believe). slab = ...


3

There are two different perspectives here. The first one is the creation of the SQS structure itself accomplished through the ATAT package, for example. The second one is the calculation of the slab properties. The SQS procedure returns the smaller structure that resembles the periodic structure properties. For alloys, for instance, the inputs are the ...


3

I would just like to point out that the question explicitly mentions adsorbing atomic oxygen rather than $\mathrm{O_{2}}$ (without mentioning the oxygen source or the surface). One can therefore somewhat simplify the question to: what is the strongest bond the oxygen atom can form? In molecules, the strongest bond is the C≡O triple bond in carbon monoxide at ...


2

I found the answer already. As the inconsistent calculation between the bulk and the thin film in the DFT calculation process. A small error term will generate a diverge behaviour in the surface energy as I increase the thickness of the slab. One way to fix this issue is to use the data from my thin film calculation to extrapolate the bulk energy without ...


1

As Anibal points in his answer, generating the SQS and using it for a surface calculation are two separate things, and shouldn't affect each other. You would still take all precautions as usual while performing the DFT calculation. That being said, there could be scenarios where you may want to restrict/prefer certain atom types amassing at edges or corners ...


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