Slab Cutting using Vesta pt. 1 - Au(111)

[@jianjeong3674]

Your tutorial video is really helpful to vesta beginner! I fully understand with watching ur video. Thank you :))

[@nickelandcopper5636]

Hyunah Jeong, thank you for the kind words. Hope to make more videos soon. Hope you are staying safe.

[@MRF77]

13:20 We're still waiting for this video haha! Please do this if possible. (I checked but couldn't find it on your channel). Thanks!

[@nickelandcopper5636]

Ah yes - thanks for reminding me

[@tufanroy9117]

Excellent video. Thank you for your great effort.

[@venierolenzi2529]

Very nice video, thanks for sharing!

[@nickelandcopper5636]

My pleasure

[@abd-elrahmanali2509]

thank you Nickel For your useful explanation can you please help me of how to make a cut of Cu (100) beside that i dont know how to find the input file for Cu to use in Vesta

[@souravmondal1815]

I am trying to expose the (111) plane in Au-Ag(50-50) alloy structure. After giving the last transformation it contains only the gold atoms and there are no silver atoms. Can you explain, please?

[@gabrielvinicius9855]

Really amazing tuto! How does the matrix looks like if I wanted the 111 phase of an FCC Co structure? Using the transformation matrix of this tuto, Co atoms get very close and problems arise during the ground state calc. I tried to apply the concepts discussed here and I got something really messy :(

[@eric_welch]

is there a more systematic way to determine the 3rd lattice plane?? you seemed to just know that the -110 plane was normal to the 111 plane ...is there a way to know this without going through the calculus or did you at some point just do the maths to determine a plane normal to 111?? thanks!!

[@nickelandcopper5636]

Hey, see if this video of mine helps. Watch the whole thing but the math is around 3 min mark or shortly after. The transformation isn’t orthogonal here for all axes but for cubic system it would be: kzbin.info/www/bejne/rJWUZIl6nMeJldU

[@eric_welch]

@@nickelandcopper5636 thanks!!

[@ahmedomran2054]

@Nickel and Copper Thank you and really it is a nice job.In your video for Au (111) you constructed the supercell by using the boundry option but for Ru 111 you said that wrong and we should transform.Can you explain the difference?

[@nickelandcopper5636]

Ahmed Sherif Omran, thanks for the thoughtful comment. In the video for Au, I first needed to transform the unit cell such that the 111 curvaceous was exposed. For this, it is ok to use the boundary option. When we do the boundary option and then save the coordinates, we only save the primitive unit cell coordinates, whatever they may be. For the Ru video, I wanted to make a super cell. So, I need to transform the unit cell coordinates into the super cell coordinates. In this case, the boundary option won’t work because if I just did the boundary option and saved I would get back only the primitive unit cell. For the Au case, I only transformed the unit cell into another type of unit cell. No super cell there, and hence I used just the boundary option. Overall, I plan on making more videos soon. Also, I wish you safety in these uncertain times.

[@nickelandcopper5636]

Surface* not curvaceous

[@ahmedomran2054]

​@@nickelandcopper5636 Thank you for your reply and I hope you safety too.I did not get the point clearly but -correct me if I am wrong-I understand that in Au 111 you got slab for another unit cell (because that was the purpose)and for Ru 111 you get a slab from supercell coordinates which is more comprehensive (general approach) that should apply in all cases for purpose of periodic calculations..Thanks again and you are doing amazing job!

[@nickelandcopper5636]

Ahmed Sherif Omran, thanks, I think there is still some misunderstanding though. For the Au case, I just transform one type of unit cell into another. No super cell. Therefore, I use boundary option. For Ru, I make turn one type of unit cell into a super cell or the same type. Therefore, no boundary option

[@nickelandcopper5636]

Of* the same type

[@atefehtarokh9586]

Thank you! It is possible to show how a Co(111) can be made?

[@FabriSlv]

HI, really helpful video, I'd done this before but this way is indeed much faster. However, I was wondering how you calculate the miller indexes of the perpendicular plane, and if there's any quick trick other than doing all the maths in it... can you help?

[@nickelandcopper5636]

So sorry for the late response. Yes there is a way you can easily calculate lattice planes in Vesta

[@josedanielgutierrezlondono1274]

Excellent, thank you!!

[@MiroslavIlias]

Hello ! Can you please place an adsorbate on the constructed Au(111) slab via VESTA ? If not, what other free software would you use ?

[@koriro1000]

Thanks, quite helpful

[@f1chtl]

What a cool channel! i am a Student and it is hard to find good resources on some of this stuff.

[@anikfaisal]

This was very helpful. I made a similar unit cell for BCC Ta following your instruction. I have question: if I want to create a stacking fault by translating a few upper atoms while keeping the bottom atoms fixed, would that be possible in Vesta?

[@nickelandcopper5636]

It would be possible for sure. Do you have an article that shows how such a structure looks? An image?

[@anikfaisal]

@@nickelandcopper5636 thanks for replying! Here is an article: ro.uow.edu.au/cgi/viewcontent.cgi?referer=&httpsredir=1&article=5307&context=eispapers

[@nickelandcopper5636]

@@anikfaisal great - thanks! This looks do-able. I’ll try to have it done sometimes next week. I’ll let you know when I make the video, and I am going to need you to tell me if my procedure looks correct. I actually don’t know too much about these stacking faults, but it looks like I can just make a cell with the appropriate planes (111, etc) and then shift the atoms after.

[@anikfaisal]

@@nickelandcopper5636 thanks for taking the time! I can do the shifting with the knowledge of Burgers vector but I would prefer to have a visual way to do the shift in order to create a twinning fault in the crystal

[@nickelandcopper5636]

@@anikfaisal sure. This is an interesting problem and I look forward to working with you on it. It looks like this is what we’ll need to do: 1. Reformulate the cell such that the (111), (11-2), and (1-10) surfaces are exposed. 2. Shift the middle two layers to make the different stacking fault configurations. I’ll be able to tell when I work on it next week if 1. can be done, which I think it should be able to be done.

[@haripokhrel3701]

Can you please do it for Al2O3 from the beginning with the cif input file. I am getting a problem with it.

[@rupeshtiwari567]

Hii, Nickel. Very nice video first of all. I'm wondering that in the case of Au(111), the repeat unit cell should be hexagonal instead of FCC cubic. Could you please explain how to make the FCC Au(111) hexagonal unit cell that would be really helpful?

[@omermutasim1200]

Amazing. Thank you a bunch

[@jonathancampeggio1045]

Sorry, but the 100 plane in the new unit cell (aka the old 111 plane) is not the one that contains 4 gold atoms? I have a similar problem with palladium. Thank you

[@markryanr.tripolevsu7028]

Hey thanks for the tutorials. Just curious, would I be able to export the cut slab to make calculations, like in BURAI, for example? Need to do calculations on surface energies.

[@nickelandcopper5636]

Hi - I have some videos where I show this. See the molecule / gold interface video

[@Hirokoi4226]

Very interesting and useful. Thanks a lot. Still, I wonder if VESTA is able to create surface automatically based on the symmetry of the crystal. Let's say I want to generate a surface with low Miller indexes (or any arbitrary face) from the primitive cell of crystalline material. Do you know how I can generate the surface (with vacuum) even if I don't know what is the most exposed surface?

[@nickelandcopper5636]

Hi. Not that I know of, you would need to know which surface you want first I think.

[@Hirokoi4226]

@@nickelandcopper5636 Ok. Pity. I have another question. Imagine I have a cubic spinel Co3O4 structure, for which the most exposed surface is the (1 1 0), which is not parallel to ab, ac or bc plane. If I want to create a new slab structure with that surface in contact with vacuum, then I will need to rotate the whole structure after "cutting" my bulk unit cell, isn't it? However, I don't how to make a 2D surface without missing or overlapping atoms. Do you have any suggestions for that?

[@nickelandcopper5636]

Jian Xiang Lian, I have a bunch of videos where I do 2d structures with vacuum. Send me some information about the structure and I’ll see if I can make it, maybe it will be my next video

[@Hirokoi4226]

@@nickelandcopper5636 Well, let me first check your KZbin channel. Perhaps I can find the solution already. If not, then I'll be glad to propose you a challenge. :D

[@Hirokoi4226]

@Nickel and Copper I found the video I needed: kzbin.info/www/bejne/Z5DXf3iPg5iKjKs Thanks a lot for your great work. Very useful. Btw, do you also make videos on how to use GDIS? :D

[@heartking101]

Sir, is the method suitable for all fcc crystal lattice of another molecule ?

[@PedroRodriguez-ui8sx]

Thank you very much again for the video. It would be very interesting if you can show how to use the files generated in quantum expresso, for example for the relax task.

[@nickelandcopper5636]

Hi Pedro, You got it! My next video will be how to use the coordinates from this video to do a relax calculation using quantum espresso. Thank you again for your kind words.

[@PedroRodriguez-ui8sx]

Perfect. Thanks in advance.

[@omermutasim1200]

@@nickelandcopper5636 did you make that video for quantum espresso?

[@Jhonatan86526]

Thanks ! really helpful!

[@bilalkhan-ly6ym]

Hi! Can you help me create a (TiO2)38 cluster with 101 plane?

[@payalwadhwa7993]

Awesome Video! Many thanks for the same. I havaery. I have cut (111) plane of similar FCC structure of Lead. I want to create its 2D structure with a vacuum. In some way, (111) plane looks like hexagonal, but which 2 atoms need to be considered from 6 atoms obtained in (111) plane, please suggest me the same. Also, once i keep 2 atoms and change the vacuum in z-direction, distance between the two atoms drastically changed, so should we then dependent on the optimization. Kindly put some light on the same. Thanks a lot!

[@VanDjikFanInfectedxftbl]

Thank you so much for this video..I like all the videos of Nickel and Cooper. I want to ask how to take a supercell with root3xroot3 for 2-D structures. Can you please explain sir?

[@nickel6913]

🤗

[@darshilchodvadiya7572]

How to make (1 0 4) plane ? Can you explain to me?

[@simonoctaviobahamondez8616]

you saved my life

[@omermutasim1200]

I think there is no videos in youtube that shows the adsorption energy calculation (molecule/metal) using quantum espresso (vc-relax..) , it would really help a lot of people if you can make video for it. BTW , your videos are truly helpful. thanks.

[@nickelandcopper5636]

Thanks. I may make a series in the future but I am in the middle of making another series and I am busy with other things too. Thanks for the suggestion though

[@nickelandcopper5636]

My video on dipole correction in quantum espresso talks about adsorption energy though. Check out the playlist

[@newaybelachew8376]

Thank you for your interesting tutor. If you have time please, show me one example of how to draw the adsorption or overlaying of a molecule ( such as, CO2) over (111) surface of Au.

[@nickelandcopper5636]

Hi Neway Belachew, it’s been a long time since I’ve been able to come to the channel. But I will have some time soon. In any case, I thought I should respond to your comment now. Please see the entire playlist of videos. I show such a setup in one of them.

[@newaybelachew8376]

@@nickelandcopper5636 Thank you. I got the sample lecture.

[@nehakatoch9616]

Thank you sir. Can you please share how to make 001 surface out of complicated systems?

[@nickelandcopper5636]

Hi Neha Katoch, Certainly. In fact, the 001 surface is a commonly exposed surface to begin with. So it is much simpler. Do you have an example I could use for demonstration?

[@nehakatoch9616]

@@nickelandcopper5636 Fe2O3

[@nickelandcopper5636]

Hi Neha Katoch, I apologize for the late reply. Are you talking about the Fe2O3 unit cell with a R-3cR space group? Please specify the space group.

[@nehakatoch9616]

@@nickelandcopper5636 yes R-3c

[@nickelandcopper5636]

Ok. For this one, the 001 surface is already exposed. Do you need to see how to make a slab model with added vacuum for this one?

[@omermutasim1200]

I tried to follow the same procedure for Pt (111 and Cu(111) (FCC ), but it gave different structure than shown in these two papers shown below, Even though , they have cubic crystal. periodicity

[@omermutasim1200]

Please clarify it to me. Cu: www.researchgate.net/publication/235480501_Facet-insensitive_graphene_growth_on_copper Pt : www.researchgate.net/publication/282812946_Molecular_adsorption_at_Pt111_How_accurate_are_DFT_functionals

[@nickelandcopper5636]

I have a video where I cut copper 111 check it out

[@nickelandcopper5636]

Also soon to release part 2 of that video

[@omermutasim1200]

does that mean i shouldn't look for periodicity in the normal direction to plane 111 for all FCC structutre I'm stucked in this issue for the whole past week. Please help me What is the criteria ?

[@nickelandcopper5636]

Yes you must find the periodicity. Please watch the video where I cut the cell for copper it will help

[@dwaipayanchakraborty8501]

Thank you for the beautiful video. However, in some paper, I got some different configurations of the Au (111) plane constructed from 29 Au atoms. It confused me, can you please share your email id so that I can send you the paper.

[@nickelandcopper5636]

Hi. Thanks. I won’t share my email here. Please just everything public so everyone can benefit. It’s possible that they constructed a 111 surface using a different type of gold unit cell. Gold can come in a few different space groups. It is also possible that they have a super cell, and not a unit cell. 29 atoms sounds like a lot.

[@nickelandcopper5636]

But what you speak of shows a larger issue in the field of computational chemistry / physics / material science. I think people need to start better explaining how they do things. Not just the end result.

[@dwaipayanchakraborty8501]

​@@nickelandcopper5636 NANO LETTERS 2002 Vol. 2, No. 8 Page 877-880 I was referring to this paper. Yes, they may take supercell not the unit cell. For the case of the fcc unit cell of Au what you have used in the video, the top and the bottom layer along the z-axis will be the (111) plane. Now if I wish to have only a layer of 111 plane, then should I delete all the other atoms and put the vacuum there?

[@nickelandcopper5636]

Yes. Now, check out my videos on making monolayer. Start with the 111 unit cell I make and follow the procedure for making the monolayer I show in the monolayer videos

[@dwaipayanchakraborty8501]

@@nickelandcopper5636 Thank you for your suggestions. I have watched your WSe2 and GaAs monolayer videos and the ZrO2 111 slab model and bulk silicon surface slab videos. In the ZrO2 you put the vacuum on the whole 111 unit cell in the a direction and for silicon in the c direction. But if I want only the atoms of the top layer should I follow the WSe2 and GaAs monolayer videos?