Make a heterostructure or interface using Vesta - pt. 2

[@edanbainglass5567]

Very nice. I've recently discovered this VESTA capability, though I go about it in a slightly different manner. I'll detail it here, in case it helps. I use VASP, if that matters. 1) Calculate strained lattice parameters (averages between the two materials) 2) Open material A in VESTA -> adjust lattice parameters to reflect (1) -> export as .vasp in Cartesian 3) Import material B -> adjust lattice parameters to reflect (1) -> settle on a global position for material B w.r.t A 4) Calculate the long-axis parameter for the supercell (sum up the length of materials A & B, and twice the separation between the two determined in (3)) 5) Open material A in a text-editor and set its long-axis parameter to the value calculated in (4) - note that this will not affect the atomic coordinates due to the Cartesian system 6) Reopen material A in VESTA 7) Import material B and place it in the previously established global position (3) -> you may need to again adjust its interface lattice parameters to the averages 8) Export as .vasp In step 8, the exported coordinates now include all atoms, as the new long unit cell of material A now encompasses both materials, as well as the separation on either end. Hope this helps. Ask questions in the comments. As for my question, do you think a single unit cell layer of each material is sufficient to capture any information? When we calculate surfaces, a slab is employed, generally of enough layers to reproduce/simulate a "bulk" region. When I work with interfaces, I essentially join two slabs. Any thoughts?

[@nickelandcopper5636]

Edan Bainglass, thoughtful comment. Your procedure sounds good. It would be nice if you could make a video for your channel and link it to a reply comment for the viewers out there, and for myself. For your question, I think it is not enough to use only 1 unit cell thick. Usually, you would need many many layers. Like 3-4 each at a minimum. Also, one needs to consider the possibility of an induced dipole. However, typically it is computationally too expensive to consider the many layers. In this situation, we just do what we can with the few layers. Perhaps, fix the atoms on the outer part to not move during MD or relaxation. Be sure to have he vacuum between periodic images large enough to make negligible the interaction with the periodic image. In this video I don’t think I include the vacuum, but ideally one should. In any case, these are tough questions, and I think research done in these areas is super important for the field of computational modeling as a whole.

[@edanbainglass5567]

@@nickelandcopper5636 Sounds like we're on the same page then. And yes, this type of research is 100% crucial. Keep and eye out for my work if you're interested. Several heterostructures are currently in the works over here. As for a tutorial video... yes, I should make one. Soon... :)

[@nickelandcopper5636]

Edan Bainglass, will do. Thanks for letting me know.

[@seemab_fatima]

Assalam o alaikum I am very thankful to you for providing helpful vedio. I have explored lot of channels, but to no use. In this vedio my concepts have been cleared. And now I am able to deal with my structure. Again thank u so much. May Allah kareem bless u 🙂

[@nickelandcopper5636]

Thank you!!

[@shokouhhaghdani3334]

Hi Nickel and Copper, I would like to appreciate your efforts. Your videos (lessons) are really unique!!! Thank you very much!

[@nickelandcopper5636]

Hi Shokouh Haghdani, Thank you so very much! We hope to keep bringing you valuable content!

[@kuangyialee4838]

Hi, thanks for very nice video. I'm wondering if you could make a tutorial to build the interface of two different oxides, e.g. typical perovskite oxides. Also, I like pretty much the vim editor you used in data manipulation.

[@khangkgb2924]

Hi, your demonstration is excellent, thanks!

[@rinuiyer4152]

will you please upload a video regarding the construction of clusters for a ternary system using VESTA

[@nickelandcopper5636]

Sorry for the late reply - I have a video up for a binary system, but this can be applied to ternary. Just may need some additional cutting in that case after making the cluster

[@Amir_Mofrad]

Thank you for such an informative video. I was wondering if you could also explain a scenario where you have dangling bonds between layers and how that should be incorporated in periodic model. Thank you

[@loigiap6082]

Thank you for making this tutorial! Could you please consider making a video on making a monolayer material like MoS2 or Bi2Te3 and multilayers of these materials? Thank you ( in case you only have time to answer this question, please tell me briefly how to do so) Thanks again

[@nickelandcopper5636]

Hi, thanks for the question, and you are welcome! You want to know how to make monolayer MoS2? I am under the impression that many layer MoS2 is actually just a surface slab with vacuum of MoS2. Is that what you need help with?

[@loigiap6082]

@@nickelandcopper5636 Thank you for taking your time to answer my question, problem solved!

[@dr.azharscienceandtech.9352]

Can we make such layer with steel down and water up? Thanks for video

[@kimialotfian6794]

this video helped me a lot, thanks

[@shivampandey-yg4bc]

Can we make heterostructure, using one high density crystalline phase and amorphous phase.

[@MRF77]

what's the text editor you're using? Can please you show how eliminate those line numbers (after copying atom coordinates from xyz to vasp file)?

[@haseebahmad3500]

Dear, thank you for this helpful video. We can make a heterostructure from 2 bulk structures using this technique. But I want to know what will be high symmetry points for the band calculations of a heterostructure? I want to use the Quantum Espresso as a DFT code.

[@nickelandcopper5636]

Hi haseeb ahmad, thank you for your kind words and great question. We actually do have the knowledge of how to perform such a calculation, but do not have the time as of right now to much such a video. In the near future (1-2 months) it is possible that we could make this video. In the meantime if you figure out how to do it, we suggest that you compute he band structure first for each structure individually, and then compute the band structure for the heterostructure. I personally would suggest practicing how to compute the band structure for a computationally inexpensive crystal first, such as bulk silicon, in which much documentation is available.

[@haseebahmad3500]

@@nickelandcopper5636 Thanks, and the question persists, after individual bands calculations I will move to heterostructure ultimately. Then the high symmetry points will remain the same as the individual crystal structure?

[@nickelandcopper5636]

haseeb ahmad , this is a great question. Ultimately, I do not know the answer. I think your question actually is an active areas of research in material science. The fermi level will be changed for sure, the high symmetry points may blend into each other. I suggest you spend a week and do an in depth literature search on this topic. There is a saying I like to quote in these situations “3 months of work will save you 1 week in the library” - which of course is a sarcastic statement. It means that a lot of question you have now are already answered in the literature. If you happen to do an in-depth literature search and still cannot find an answer to your question - then you have yourself a great research topic! I wish you call the best, and thanks for viewing the channel.

[@haseebahmad3500]

@@nickelandcopper5636 Thank you very much for your help.

[@hannahjeniffer7269]

Nice video. I am trying to make an interface between 111 face of a monoclinic CuO and 202 face of NiO. can you explain how can I do this in vesta??

[@abraraminkhan1384]

Is this process applicable for making mixture of nacl and h20? If not how can i do this?

[@vubaokhanhkieu]

Great work, thanks

[@nickelandcopper5636]

My pleasure

[@rodolfoaguirre5292]

Hey Nickel and Copper, thanks for the nice video. Do you know how to rotate one of the crystals so that say for example the 111 plane is parallel to the 001 plane of the other crystal ? Thanks

[@nickelandcopper5636]

Rodolfo Aguirre, one can write a simple python script for this. Not sure how to do it in Vesta. Sorry for the late reply, been crazy busy last 6 months. Hoping to get back here soon. Maybe I can show how to start with writing such a script.

[@shashank8098]

Hi, will it work when one of the phases is monoclinic and other graphene?

[@nickelandcopper5636]

You would have to transform the graphene to monoclinic or the monoclinic to hexagonal. Or, transform both to orthorhombic.

[@parthkhandelwal43]

Your video is very helpful, could you explain to me how to rotate one crystal with respect to other about an axis.

[@nickelandcopper5636]

Thanks for the question. That's tricky. I will think about it, but it may take me several weeks to come to a notion of how it can be done.

[@achintya2425]

can you please upload a video on making bulk from monolayer and vice versa

[@nickelandcopper5636]

I’ll try my best!

[@kkm5384]

hi, good video. How did you select a combined unit cell in the hetero-structure? and second question is that, in this example, its lucky that both individual cells has almost compatible lattice match. there are some situations, unless we expand say 9x6 and the other as 4x4 and then only they would match to minimum extent. in such lasrge hybrid cells, after creating how do you select a combined unit cell again?

[@nickelandcopper5636]

Thank you for the kind words. You are correct. Lucky choice. Sometimes, one needs to expand to very large sizes to get it to match, like you say. Nice catch!

[@nickelandcopper5636]

For combined unit cell, just take the smallest axes that work. If one is 2 and needs to expand by 6, then it’s 12. The other will be 3 and need to be expanded by 4. Therefore, use 12 for the combined. Something like this.

[@ishworkhadka2550]

Thank you very much for your nice tutorial. I want to know about creating twisted bilayer heterostructure (and homostructure too) using VESTA with some angle rotated another. How can we do that in VESTA? Please I am grateful to your reply.

[@nickelandcopper5636]

Ishwor Khadka, same with the comment reply a few down. One needs an external python script for this. I think I’ll show how when I can. Hope all is well.

[@stanley3259]

@@nickelandcopper5636 please do

[@_THUIFIQUEALAM]

How to select the multiplying factor when the crystals are not cubic?

[@nickelandcopper5636]

Try to find multiplying factor that leads to a set of cell vectors that minimize the lattice mismatch

[@_THUIFIQUEALAM]

Can you elaborate it please?

[@_THUIFIQUEALAM]

Is it possible to make a video on GaN -Graphene hetero-structure to explain it clearly?

[@_THUIFIQUEALAM]

Thanks in advance

[@nickelandcopper5636]

@@_THUIFIQUEALAM sure. Each cell gets a multiplying factor, that changes the unit cell to a super cell. Your goal is to find a multiplying factor for each unit cell such that the size of their supercells are very similar, and different inly by a few perfect of in length. Cubic or non cubic - it is the same

[@ashishdhole443]

How to create a supercell showing interface of two bulk solids (Say an interface between In and Ru bulk slabs)?

[@nickelandcopper5636]

Hi Ashish, I think showed something similar in this video, right?

[@liamzou1277]

very nice videos! Could you give a lecture on how to build twin boundary structure? Another question is how to determine the distance between two crystal structures for calculations?

[@nickelandcopper5636]

Hi Liam Zou, What exactly do you mean by twin boundary structure? Could you please provide me with a few links and/or describe what you mean? Once I know what it is - I am sure I can do it .... anything is possible! Also, For the distance. Usually, a few Angstoms (3-5) is fine, because what you will do is eventually optimize the geometry of your structure, and that will position the different crystal slabs at their optimal distance apart, ... hopefully!

[@liamzou1277]

@@nickelandcopper5636 Thank you for the prompt reply, it is helpful! Please see the link below for one of the examples for twin boundary (Fig.1), I feel it is difficult to modify the interface using vesta. Thank you. www.nature.com/articles/s41524-017-0010-6

[@nickelandcopper5636]

Hi Liam Zou, Thank you for the link and for your kinds words in your first post. So, if I have this correct (not my field of research) - the twin boundary structure would be a single crystal in which the twin boundary separates two mirror image slabs? These slabs, would be hpc packed crystals, in which the twin boundaries most readily forms upon a phase transition from high to low symmetry, usually via thermal means. Is my thinking correct? The twin boundary seems to be a shared plane amongst the two crystals. If so, I think I can make such a structure, and I can upload the video next Wednesday or Thursday (3/27) or (3/28).

[@liamzou1277]

@@nickelandcopper5636 Exactly! That would be great and I am looking forward to watching the video!

[@salmamoussadeq9074]

were i can found cif file for Ag(100)

[@nickelandcopper5636]

See my beginner tutorial series video on how to find a cif file

[@rongwu8005]

Which software are you using for the VASP? Thanks. I can neither open the vasp files or the .xy files.... Thank you

[@nickelandcopper5636]

Far3 software. Open and close with F3. When opened, save with F2

[@ibukunolaniyan1072]

@@nickelandcopper5636 I also have a problem with this. I downloaded the far manager, but it doesn't open the file. Can i use notepad to open it also?

[@nickelandcopper5636]

Ibukun Olaniyan - open with F4 save with F2 before exiting with escape. And yes notepad works too but is more difficult for deleting at certain times

[@seemab_fatima]

Assalam o alaikum! Sir i need to plot 3d hetrostructure of three materials. Please help me to build this structure at vesta. will you please share any link for my support. i shall b very thankful to u.

[@nickelandcopper5636]

Which structures?

[@seemab_fatima]

@@nickelandcopper5636 I want to make MTJ.. it is the combination of An alloy and ZnO

[@nickelandcopper5636]

@@seemab_fatima do you have a reference to a paper? Maybe it is shown somewhere? I would need the crystal lattice types, and what surfaces facets are touching in the heterostructure

[@rinuiyer4152]

Is it possible to make a heterostructure with tetragonal and orthorhombic heterostructure?

[@nickelandcopper5636]

It should be. You may have to do some sort of basis transformation though

[@rinuiyer4152]

@@nickelandcopper5636 Can you tell me how to do it with minimal lattice mismatch?

[@nickelandcopper5636]

@@rinuiyer4152 I may be able to make a video on it soon … been thinking about coming back to the channel nowadays - but it is too long to type. Do you have the systems you want to make into a heterostructure?

[@rinuiyer4152]

@@nickelandcopper5636 Thanks a lot. In the materials project database there is a system BaCu2Se2 with two different phases. One is tetragonal and one is orthorhombic. If you can make it on this it will be helpful. Thanks for making these videos.

[@nickelandcopper5636]

Can you link them to me pls? Pls send links

[@tanmaydas2799]

Thank you so much