Supercell construction and adding Vacuum in Vesta - Ruthenium

[@MrNeeess]

How would you do it if you wanted to add vacuum on both sides in the direction? So that the structure would be in the middle of the unit cell

[@nickelandcopper5636]

Henrik Ness , add N angstrom more vacuum and then shift the coordinates all by N in that direction

[@suwathaav7706]

Thank you for this video, a great timely help. Can you please explain me how to increase or decrease the interlayer space in the layered crystal structure.

[@jabeddh]

How to make a 2D periodic cell by adding vacuum in (111) direction?

[@abraraminkhan1384]

hey, I am currently working on supercapacitors for which i have a create a model of electrolytes confined between two electrodes. electrode material would be grpahene and any metal oxide composite. Can i use Vesta to model the whole system? what do you recommend?

[@nickelandcopper5636]

Yes you could but you would need two slab models with the electrolyte in-between and vacuum on the other sides of the slabs. Is it single layer graphene or many layer?

[@abraraminkhan1384]

@@nickelandcopper5636 no it would be many layer...then upto it some later of metal oxide would be there

[@nickelandcopper5636]

abraramin khan so the metal oxide would be in contact with the many layer graphene? Where would the ions go? Would some be touching the oxide and some touching the graphene? Would any ions be within the graphene layers or metal oxide layers, or only in the space between them

[@GoutamNarayan]

@@nickelandcopper5636 Is there any specific reason for the 2 slab model? Like I have always seen researchers using that.

[@hb8540]

Thanks for the nice tutorial. A basic question about far software: How to select the column (@ 7:16). Also to input the file you made at the end to QE, should we choose ibrav = 0 ? Also some people make the vaccuum up and down (the monolayer for example in the middle) which should be equivalent to the vaccuum you did. How to to do that in vesta? I saw people doing that using burai

[@nickelandcopper5636]

Hi H B, to select the column @7:16, use "alt", then highlight. And yes, choose ibrav = 0. It does not matter where the vacuum is, it is equivalent. Check my videos on dipole correction I put the cell in the middle of the vacuum as you mentioned. Cheers, N&C

[@sraddhaagrawal2714]

Hi, can you please help me with building a non-integer supercell of a 2D material? Something like 1.5x1.5x1. I am facing some issue with the periodic boundary images. Atoms get duplicated, which is not the case in integer supercells.

[@nickelandcopper5636]

Hi. I am not sure how to make what you describe. If you mean a structure with unit vectors with Root (2), something like this - this is equivalent to exposing the 111 face of a cubic crystal

[@nickelandcopper5636]

Hi. Please create a new comment that is not posted as a reply to another persons initial comment. Please start your question as an individual comment

[@sraddhaagrawal2714]

@@nickelandcopper5636 Hi, no, actually just like you showed in the video to generate a supercell of 2x2x2, I want a supercell of, say, sqrt(3)xsqrt(3)x1. Is this possible to do through Vesta?

[@nickelandcopper5636]

Sraddha Agrawal - what i am saying is that having a cubic super cell of root integer is equivalent to the super cell which the internal 111 plane is exposed

[@sraddhaagrawal2714]

@@nickelandcopper5636 Okay, I get it. Thanks!

[@si19da21]

Sir can ZnO and Ti heterostructure can be created

[@vivekpendharkar5152]

Hi, could you please help me with modelling a stacking fault in Ni(FCC) super cell?

[@nickelandcopper5636]

Hi. Thanks for the comment. I am not sure how to properly model a stacking fault. I don’t know much about geology

[@omermutasim1200]

very useful. For quantum espresso input file , can i use the vasp file directly without deleting atoms (second procedure) ? or i have to follow the first procedure you mentioned i.e. deleting atoms, then save xyz file then vasp file ?

[@nickelandcopper5636]

Hi Omer. Thanks for all of the questions. Use the vasp file at the very end. The one that gives the structure with the vacuum

[@omermutasim1200]

Nickel and Copper Do you mean the vasp file in the second procedure , ? i.e. without deleting atoms , right. ?

[@nickelandcopper5636]

The video was a long time ago, so I am not sure. But just figure out which vasp file corresponds to the structure with vacuum towards the end

[@omermutasim1200]

Nickel and Copper thanks a lot 👌

[@nickelandcopper5636]

Yup!

[@dimashd8256]

Thank you for making a wonderful lecture video. Could you guide me on the following. If I am to use this structure for surface calculation in quantum espresso, could I use the cell parameters and coordinates from this as input file for quantum espresso. Or does some modification is needed for atomic position. Thanks

[@nickelandcopper5636]

Thanks for the nice comment! Use the coordinates in the .vasp file for a quantum espresso calculation. You just have to add in the atomic labels that’s all. Ex) “Ru”

[@dimashd8256]

@@nickelandcopper5636 Thank you so much. I will go ahead and work on it.

[@nickelandcopper5636]

Nice! I would first do a large amount of reading on Ru surfaces if this is what you want to do. If you want to use a different system, you can still follow the same procedure. I have other videos for other systems too. Take care.

[@dimashd8256]

@@nickelandcopper5636 It definitely helped. However the number of atoms seems too many. I feel some of these are redundant but don't know how to choose those . I was going through a tutorial of slab coagulation using quantum espresso of Al001 with 5 layers. The number of atoms is 5 in this case with tetragonal symmetry and atomic positions of 5 Al atoms are given in input file. However supercell Al001 made from Vesta has more than 23 atoms. I am not getting how to reduce it to 5.

[@nickelandcopper5636]

You may be confusing the xyz structure with the .vasp. Also I believe the model here is a super cell

[@shaheengulshanah448]

can you please do the same for SnO2? It will be really helpful.

[@sherifdeenbolarinwa3296]

Hi, thank you for the videos. I am new to crystal structure manipulations and computational physics as a whole. I am trying to lay my hand on various crystal building examples. I am currently working on PtSe2 and I am unable to proceed as my structure is not similar to what's obtainable in literature. More importantly how to export these coordinates for QE calculations. Thanks in advance

[@nickelandcopper5636]

Hey. First off, for someone just getting started, the best advice I can give is to be patient with yourself. The key is to learn as often as possible. Knowledge builds like compound interest. The more you know, the easier it becomes to acquire new knowledge. Although I find this to be true generally, it is especially critical in science. For QE, or any electronic structure software package, typically you would just upload the atomic coordinates saved in the .xyz or .vasp files. Now, saving your data using VESTA as a .vasp or .xyz will give different atomic coordinates, so it is best here to watch a bunch of videos to get a feel for the difference between them. Typically, a .vasp file will give you coordinates in which periodic atoms are deleted automatically. A .xyz file typically saves every atom on the screen. For PtSe2 - what do you mean your structure is not in the literature? If you need help building a structure, let me know what it is an hopefully I can do it.

[@bolarinwasherifdeenoluwase8228]

Thank you for the response. Truly, I’ve been ensuring I watch your videos daily and also read the vesta manual just to ensure I consolidate the art of structure building and manipulation. What I meant regarding my structure was that I ended up with a structure that I cannot find it’s similitude one literature. I would be glad if you can help build PtSe monolayer supercell and detail how to extract it for QE ESP

[@nickelandcopper5636]

Sure. Please provide me the lattice type and space group of your particular PtSe crystal. Also please provide me what exactly you would like? When I read monolayer supercell this means to me to be a supercell of a unit cell of a monolayer. By the way - which crystal face is the layer?

[@bolarinwasherifdeenoluwase8228]

Tribunal PtSe2. H M P -3m1. [Space group164]. Exactly, I meant that the unit cell should be transformed to a monolayer then the supercell of such should be obtained. This new coordinates should now be extracted such that I can view the exact new shape (monolayer supercell) using either vesta or any other visualization software. Also it should be suitable for QE calculations. Thanks and many cheers

[@nickelandcopper5636]

Which crystal face should the monolayer be?

[@mustafaaeea2722]

Thank you for your wonderful work. I am learning it. if I have to make an interface Al (101)//Al2o3(01110). How to adjust lattice mismatch along c axis and how I use it as a saving data file for Lammps simulation. Thanks Please

[@josephkaore5809]

Why can't you just create a supercell then open the supercell using vi-editor and add a vacuum in the desired direction?

[@y3rzhan]

I think we should press remove duplicated atoms button after creating the supercell. Author of the video was doing manually

[@gabrielvinicius9855]

Thanks for sharing such a nice tutorial - appreciate it. A quick question: Does the order in which you introduce the vacuum matter? I mean, you introduced the vacuum layer from the unit cell. Could you first make a 111 structure out of your unit cell and then introduce the vacuum? Thank you in advance :-)

[@nickelandcopper5636]

Of course! I have a ton of videos where I first make the 111 surface and then add vacuum. If you need a specific example done let me know

[@gabrielvinicius9855]

@@nickelandcopper5636 Thanks so much for replying. Nice, then the order doesn't matter. Another question, how to get the primitive 111 out of the FCC structure using VESTA? Do you have videos about it? Thank you in advance :- )

[@nickelandcopper5636]

@@gabrielvinicius9855 sure. Check my more recent video on copper 111 surface. I start with primitive cell and do the 111 surface transformation. This gives primitive 111 cubic surface. If you start with conventional standard cell and do 111 transformation, you get the congenital standard 111 surface. Both are equivalent but of different sizes and angles

[@omermutasim1200]

How can i create supercell:sqrt(3) X sqrt(3) X 1 transformation to my unit cell using VESTA ?,

[@nickelandcopper5636]

For example, just cut the 111 surface from a cubic crystal. This is the root3 (or root2 depending on the initial crystal) structure

[@zhl4545]

How do I know which atoms to remove in other surfaces? For example I was trying to make a supercell using the gold 111 surface according to your previous video and it turns out that the c/b view has a different uniform structure than the c/a view and when I tried to delete only the first column of atoms from the right according to the video here, the resulting structure is wrong. Btw thanks for the tutorial :)

[@nickelandcopper5636]

Hi Evan, not sure what you mean. I think I have some videos on the channel where I cut slabs of 111 surfaces.

[@salmamoussadeq9074]

thank u soo much but i can't find cif file for Ag 100

[@nickelandcopper5636]

Just find the cif file for Ag. If you can’t find it using the crystallographic database type this into google: Silver cubic unit cell materials project. The link should be on that page somewhere.

[@davidansi1683]

Thanks for the video. How can i know if my cell violates the periodic boundary condition? You said the same set of atoms at one side is the same at the other side. Did you know that from the GUI? I'm a beginner

[@nickelandcopper5636]

It’s the gui that populates the repeated atoms. The actual atoms in your system are those contained in the input file (.vasp, POSCAR, etc)

[@davidansi1683]

​@@nickelandcopper5636 thanks. I later understood it from the beginner videos on your channel. In your udemy course did you cover how to dope and also introduce vacancies?

[@mouh2009]

how about a hexagonal structure, how can we make a circuit supercell with vacuum

[@nickelandcopper5636]

Hi Mouhamed, I am not sure what you mean. Which hexagonal structure do you refer to in specific? Also, what is a "circuit" supercell? How does it differ from the one I make here?

[@mouh2009]

@@nickelandcopper5636 Sir, I thank you for your message First of all I have no idea how the word circuit was introduced in my original message, my question was simple I am trying to make a supercell with the structure SmCo5 which has the symmetry P6/mmm using your approach.

[@mouh2009]

@@nickelandcopper5636 The structure of (SmCo5.Vesta) is completely défirent from what you have in your Ru example, so I find it so difficult to find where to make changes.

[@nickelandcopper5636]

Hi Mouhamed. No worries about the circuit mis-spell. I will take a look at the structure and try to do the unit cell. At first glance, it looks like you need a basis transformation. See my video on Au and CaF2, where I do a similar basis transformation to expose a (111) plane. In your case, you would reformulate the unit cell such that the internal planes are outward facing, which would give you a unit cell with 90 degree angles between cell axes.

[@nickelandcopper5636]

Hi Mouhamed. I was able to add vacuum with you structure. I will make a video and upload it tonight. It can be done both with and without a change of basis. I will show both ways. Cheers, Nickel and Copper.

[@zhiyongzhang8747]

sir,how to change one atom color of a cell,thanks @Nickel and Copper

[@nickelandcopper5636]

Hi Zhiyong Zhang, thank you for the comment. Can you please revise your question? I am not sure what you mean by atoms color of a cell. Do you mean, how to change the atomic identity of an atom within my unit cell? For example, how to change one of my Ru atoms to a Gold (Au) atom?

[@zhiyongzhang8747]

Nickel and Copper yes, change only one atom to another atom

[@zhiyongzhang8747]

Nickel and Copper For example,when I change Ru to Au by edit data ,all the Ru atoms become to Au. But what I need is only one Ru atom becomes Au. Thanks to answering my question

[@nickelandcopper5636]

@@zhiyongzhang8747 , Thank you for your reply. This is a simple fix. I will make a short video tonight about how to do such a thing. Take care, Nickel and Copper.

[@nickelandcopper5636]

Hi Zhiyong Zhang, I have had some things come up and have no been able to make the video. I will make it soon as I can though. Take care.

[@y3rzhan]

rhombohedral unit cell users: WASTED