Slab Cutting using Vesta pt. 2 - CaF2

In this video, we expose the (111) plane of CaF2, and make a new unit cell such that the (111) plane is now a naturally exposed face. The presence of the F anions make this cutting more complicated than a single atom FCC unit cell. Finally, we apply a further transformation to the unit cell to create a slab.
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[@juliangeiger3195]

These are definitely the most useful VESTA-tutorials on KZbin! Thank you for making them!

[@nickelandcopper5636]

Thanks Julian - the more recent ones one surface reconstruction are better imo these these old ones

[@jonathancampeggio1045]

Thank you so much. In my opinion, VESTA should hire you to promote their product. Excellent job!

[@nickelandcopper5636]

Haha - thank you!!

[@동진쎄미켐-v5w]

I really appreciate your dedication to this education for the people worldwide. Thank you from S. Korea

[@nickelandcopper5636]

Thank you so much for your kind words!

[@hastihojabr]

I really needed this tutorial for my university project. Thanks A lot.

[@nickelandcopper5636]

Glad it was helpful!

[@YTantirungrotechai]

thank you very much for very excellent, very clear videos.

[@PedroRodriguez-ui8sx]

Fantastic video. Very nice job. Thanks a lot

[@nickelandcopper5636]

Hi Pedro,Thank you so much for the kind words. I hope to make more helpful videos soon!

[@merrywatch6261]

Thanks Nickel for this informative tutorial. I was able to reproduced exactly what you did to the end. However, when I opened the CaF2 (111) plane and checked the lattice plane I found out that (111) plane is not exposed as it's supposed to be. Kindly shed more light on this.

[@nickelandcopper5636]

Ah this is because Vesta treats whatever you give it as being in the original setting. You have to just see by eye. On matter what Vesta will think the 111 plane is internal for this type of system

[@МарияГолосная-д5л]

Thanks a lot for detailed instructions! CeO2 111 surface will be built in the same way?

[@sahibhasan7095]

Thank you very much, really you are a great person

[@nickelandcopper5636]

Thank you for watching!

[@indrapardede3750]

@Nickel and Copper Thank you very much for your video. It's very helpful. So, in this case, the thickness of CaF2 is 1 ML (monolayer). Thank you for your kind answer.

[@nickelandcopper5636]

Yes! Although, there is a mistake in this video, it is not hard to fix. I should have gone more one of the directions for checking the periodicity. Small error. But ya - I am pretty sure that 1 unit fell thick = 1 ML

[@Deepak.physicist]

I have a small doubt, on changing the slab to (201) plane, using matrix values, the crystal becomes somewhat like compressed and kind of sandwiched, is that okay for the slab? FYI, the structure I have chosen is WP2, monoclinic structure from Materials project (ID: mp-11329).

[@harshitagangwar4196]

Quite a helpful tutorial. But I am still struggling when trying to cut 101 surface of Anatase TiO2. Can you guide for this case?

[@nickelandcopper5636]

I can hopefully look into it. Are you sure that’s a stable surface?

[@harshitagangwar4196]

@@nickelandcopper5636 In my knowledge, when any molecule is introduced in close vicinity of TiO2, (101) surface seems to display most reaction. Therefore I am trying to expose (101) surface so as to observe the effects of the molecule over it.

[@nickelandcopper5636]

@@harshitagangwar4196 ah, I see. I’ll look into it

[@jugantaroy6723]

Nice tutorial! Can you make tutorial for Rutile TiO2 (101) surface. This video looks like appropriate for TiO2(101) surface but the tricky part is the third corner can't be define. Thanks

[@nickelandcopper5636]

Would you happen to know what the cell axes angles would be for that system? Surely someone has studied this before and knows them. Also maybe which planes the lattice vectors are? I’ve looked into this briefly and it seems that to get the third corner actually requires one to use an angle in your cell. Check out my video on ZnO where I do am forced to do something similar in order to get the third corner

[@bilalahmadshiekh9943]

Very nice video. I love it. Kindly make a video for how to construct organic molecule surface slab. I will be much thankful to you.

[@nickelandcopper5636]

Hi Bilal, I have actually already made several such videos. Please check the play list. If there is a particular system you wish me to make. Please suggest it.

[@muhammadhassan-uk2ml]

How we can obtain the monolayer from it?

[@kkm5384]

hi if i delete some atoms and save it or export it as VASP and reopen, then again the deleted atoms are shwoing up. how to delete them permanantly and save whatever i want?

[@nickelandcopper5636]

Ah. Save it as an .xyz

[@nickelandcopper5636]

Saving as a .xyz saves the atoms on the screen, no matter what

[@kkm5384]

@@nickelandcopper5636 ok. then another issue in my case. (1) if i do so in XYZ, and reopen i am losing the lattice shape and parameters, and (2) due to periodic boundary situation, some atoms are displaying outside the lattice, visually. now i am not very sure which atoms to delete, before exporting to XYZ. or if i delete exactly those outside lattice boundary, even then its not sure, if some of the edge atoms are part PBC. So when i reopn the XYZ file, i am finding extra atoms and that too losing lattice boundary marking

[@nickelandcopper5636]

Ok. This exact problem is what I show in many videos. This is why I am constantly saving as an xyz to put the coordinates into the vasp. I talk many times about having to delete certain atoms to retain the periodicity. Please watch all of my surface reconstruction videos and I guarantee you will understand after that

[@nickelandcopper5636]

I must have 10 surface reconstruction videos. In each video I talk exactly about this issue. Many different systems too! So please watch those and then let me know. Be sure to check the more recent ones, starting a few months back

[@zhl4545]

i tried creating rutile (110) using the similar approach but I couldn't do it. The stoichiometry is wrong each time when I try. Do you have any tips for that?

[@nickelandcopper5636]

Rutile what ... TiO2?

[@nickelandcopper5636]

Hi Evan, check the new video - made it for you.

[@zhl4545]

@@nickelandcopper5636 thank you very much! Can't believe you made a video about it. I saw it and it helps a lot.

[@kkm5384]

this is good. i trying to do for a hybrid structure with two materials. quantum dots with ligands and wish to create a unit cell along with ligand strcutre, is it possble? i tried to follow your method, but did some thing wrong i think, it created a huge bulky cel.

[@nickelandcopper5636]

It is possible if you use a large vacuum in all directions. I can make a video to show you if you would like. Basically, it would be a quantum dot with ligands sitting in the center of a giant unit cell. Essentially, the cell would be so big that the neighboring QDs do not interact. Is this what you would like me to share?

[@kkm5384]

@@nickelandcopper5636 thanks for reply. But not exactly the way you explained. What i am looking for is: - say, there is a QD formed with many unit cells combined. And i attach the ligands in Z direction. but part of the QD only visible it means in X and Y directions it shows a periodic boundary. and more over i wish to add two such QDs opposite to each other and from this combined structure (i.e.with 1 QDS+ligands on only Z-direction) , i wish to select a unit structure and cut the rest. May be difficult to perceive. If you give email, i can draw a structure and share.

[@nickelandcopper5636]

One cannot have many unit cells - you only have one unit cell by definition. One should not have the QD be periodic, because if it was periodic, then it would be "bulk" in those directions. That's why you need to add the vacuum in all directions to get the isolated (0d) QD

[@kkm5384]

@@nickelandcopper5636 Thank you. i understand. In such case kindly share the video as per your earlier reply. But with an extension to that, i wish to include two such QDs in the system, so that, i will submit for relaxing the geometry and submit for Molecular dynamics. Its will be very helpful to me and others as well. Thank you. :)

[@nickelandcopper5636]

K K Sram sure. I’ll be away for a few weeks but will be back after that. I will tell you though that having two quantum dots with ligands will be literally thousands of atoms. One would not use a periodic computation for that, but rather a localized basis. Which software do you plan to use for MD?

[@rahulsuresh373]

Can you post a video on construction of (2√3 × 2√3)R30° phase of Au(111) supercell?

[@nickelandcopper5636]

Hi Rahul. My course on heterostructures may be able to answer this question. I show how to make root integer supercells there.

[@rahulsuresh373]

@@nickelandcopper5636 Thank you. it was helpful

[@abhishekthakur7931]

Nice video. Very helpful. Is the stoichiometry of CaF2 is being taken care of?

[@nickelandcopper5636]

I have an error in this video actually. You could extend some more in the c dimension. But if you do this it will be. I apologize for the error. I hope soon I will post the correction.

[@nickelandcopper5636]

But yes - if you take care of the one error the stoichiometry will be taken care of

[@nickelandcopper5636]

Actually, on second thought, maybe it’s fine. I’d have to revisit this one to see if there is an error. In any case, you can save the new unit cell as a .vasp file and then check the stoichiometry to see. If you do this, please let me know what you get

[@abhishekthakur7931]

​@@nickelandcopper5636 If I save the unit cell as .vasp then the stoichiometry is correct. But if I save the same unit cell as .xyz file then stoichiometry is incorrect. Can you explain this? Which one is correct .xyz file or .vasp file?

[@nickelandcopper5636]

Depends on what you want to use it for. If you save it as a Vasp, it gives you coordinates to enter into an electronic structure package. In other words, saving as a .vasp deletes repeating atoms. Saving as an .xyz saves all atoms, even those that repeat.

[@mahmudulislam3872]

can you create a slab by exposing the 104 surface of calcite ?

[@nickelandcopper5636]

104? I don't believe I have heard of this!