Hi ! hope you are well, thanks for the video, I want to ask if this kind of heterostructures can be used for Crystal23, if so, how can I put it into the input, because I am trying to run the optimization of geometry and the structure is failing, thanks again.
Respected professor, when I am going to make a slab model with graphene and a transition metal complex, the graphene become extended to infinity. How can I control it? If you have any suggestion please let me know. Thank you in advance.
I have build sucessfully strcuture like you but when I export data in .vasp it not the same like I designed. Can you help me about this. Thank you very much.
Hi, for the supercell, does it has to be 1x3x1 for gold and 2x2x1 for the graphene sheet? The way I understand is we are finding the common multiplier for a and b - sides. Then make the supercell and adjust the lattice parameters to be the average between 2 supercells. I would like to confirm the math behind your method since I want to make Bcc-Fe(001)/graphene heterostructure for DFT run, if I use 1x3x1 for Fe and 2x2x1 for graphene, my slab is quite large and it takes too long to run. I would like to have smaller slab but not sure if it is correct. Thank you for your time!
Hi. Thanks for the thoughtful questions. Yes you have to try to get the best lattice match, typically this means finding the common multiplier typically.
Thank you so much for helping the learner like me trough your videos. Really am enjoying your tutorials. Anyway, which editing software you are using for editing the text. I use notepad. But I see, you can delete the atoms from the left column easily. But I can not do that in the notepad. Would you please which notepad or software you use for this. Thank you sir.
Hi Cihat - I apologize for the late reply. I am unfamiliar ilar with materials studio. I think if you want to save as a .cif you would have to save the space group as well. Have you tried saving as a .vasp and loading it into materials studio?
Hi, the whole process was explained nicely. Could you make a video on graphene/hexagonal boron nitride in-plane heterostructure with a zigzag interface?
@@nickelandcopper5636 Please refer to Figure 1(a) of this paper: Ding, Ning, Xiangfeng Chen, and Chi-Man Lawrence Wu. "Mechanical properties and failure behaviors of the interface of hybrid graphene/hexagonal boron nitride sheets." Scientific reports 6, no. 1 (2016): 1-9.
Kindly help me in making Li/Ge/Li junction in vesta. I am trying from several days and I tried your method of heterostructure, but I am unable to make such structure. Can you please help me in this regard. Thank you
Hi. So sorry for the late reply. I’m just now getting to these older comments from when I was away. So you still need help for this one? Hope all is well.
Hi, really nice tutorial, it is useful for everybody. I want u to show CaSiO3 (wollastonite) crystal structure. Actually, I want to model the matching crystallography wollastonite find in XRD. Thank you very much
@@nickelandcopper5636 In crystallography, I need to depict the locations of calcium, silicon, and oxygen in the wollastonite structure. Can you assist me with drawing them in detail?
@@nickelandcopper5636 Its always my pleasure. This tutorial series is becoming more like a complete tutorial series day by day. You are doing great!! It will help a lot of people. I heard that it is possible to visualize charge density and charge density difference (CHGCAR) directly in vesta. but is it possible for a certain energy range? I'm a little confused with the color and isosurface. How to indicate charge transfer or something like that. is it possible to visualize bonding/anti-bonding? I use 'vaspkit' to convert WAVECAR into vesta readable format. But I'm still confused about the prediction mainly that made just by charge density visualization. Maybe an example would be appreciable. Thanks again :D
Thanks. I also keep meaning to make the python tutorials but people keep having great ideas for Vesta. So I sort of am just playing it by ear. For the charge density - these are the cube files generated by electronic structure programs. Here’s the deal with them. Assuming DFT , they are typically for a single Kohn sham orbital. Therefore, they are single electron wavefunctions. For example, let’s say we have a quantum dot with a ligand. And the homo ks orbitals is localized on the quantum dot and the lumo is localized on the ligand. So, what you would do is do an excited states calculation, say tddft, and realize that the first excitation is a homo - lumo transition in the KS space. Assuming this is the only transition in the superposition that is the true excited state for this particular excitation, this state is a single slater determinant. Now, you can visualize these KS orbitals in Vesta. If the homo orbital is localized on the core of the dot and the lumo on the ligand, this can be characterized as a charge transfer state. Actually, charge transfer states are typically Ill-defined. And technically, all excitation are charge transfer. But people usually reserve this terminology to refer to excitations between KS orbitals in which the charge density of these orbitals are localized on different parts of the systems. Please let me know if I am being clear enough. So to indicate charge transfer you would just need to show significant localization between the donor and acceptor states. But be warned. Charge transfer states are notoriously mischaracterized in DFT with pure functionals. You ideally should use range separated hybrid functional, if affordable. For the color, two colors is the phase of the wave function. Positive and negative. If only one color, this is like the total charge density - abs value of the wavefunction squared
Ah I see. I am not sure if Linux can support Vesta. I really am not sure by which means Linux can create these. Do you mean using a visualization software supported on the Linux platform?
@@nickelandcopper5636 thanks a lot for your prompt response. Yes I believe that Vesta works in linux (Ubuntu). And my question is can you please make a tutorials similar to those u did in windows but for linux users.
Ok. I see what you are asking now. I unfortunately cannot. I do not have a Linux platform to work on. That being said, I don’t see why anything would be different. Just use Linux based text files to manipulate the atomic coordinates. I use the Far3 viewer to manage text files on windows. But you can also just use regular text files on linux. The information you learn on my channel about how to use Vesta should transfer directly to using Vesta on Linux. What will be different is how you edit the various files saved by Vesta.
![VESTA Software - Cu [111] / Graphene Heterostructure Part 2](http://i.ytimg.com/vi/-HGpX1snrlE/mqdefault.jpg)
![VESTA Software - Cu [111] / Graphene Heterostructure Part 2](/img/tr.png)
Your videos are truly amazing! Please don’t stop making these videos. You are sure to grow exponentially. I really wish you the best of luck!
Really nice!
A Video of Al terminated corundum (0001) and Au(111) would be nice to visualize the moiré resulting from the mismatch
Great video. Very useful for everyone.
Thank you sir.
Hi ! hope you are well, thanks for the video, I want to ask if this kind of heterostructures can be used for Crystal23, if so, how can I put it into the input, because I am trying to run the optimization of geometry and the structure is failing, thanks again.
Hi, I want to make a heterostructure of h-BN adsorbed on the Ru(0001) surface. Can you please suggest how to do it?
Respected professor, when I am going to make a slab model with graphene and a transition metal complex, the graphene become extended to infinity. How can I control it? If you have any suggestion please let me know. Thank you in advance.
I have build sucessfully strcuture like you but when I export data in .vasp it not the same like I designed. Can you help me about this. Thank you very much.
Hi, for the supercell, does it has to be 1x3x1 for gold and 2x2x1 for the graphene sheet? The way I understand is we are finding the common multiplier for a and b - sides. Then make the supercell and adjust the lattice parameters to be the average between 2 supercells. I would like to confirm the math behind your method since I want to make Bcc-Fe(001)/graphene heterostructure for DFT run, if I use 1x3x1 for Fe and 2x2x1 for graphene, my slab is quite large and it takes too long to run. I would like to have smaller slab but not sure if it is correct. Thank you for your time!
Hi. Thanks for the thoughtful questions. Yes you have to try to get the best lattice match, typically this means finding the common multiplier typically.
Hi @@nickelandcopper5636 does your method work with different cell shape? ex. Bcc_Fe-110 and graphene?
Thank you so much for helping the learner like me trough your videos. Really am enjoying your tutorials. Anyway, which editing software you are using for editing the text. I use notepad. But I see, you can delete the atoms from the left column easily. But I can not do that in the notepad. Would you please which notepad or software you use for this. Thank you sir.
Is it a blue screen? That’s the far3 viewer
@@nickelandcopper5636 Yes, I said this. Thank you sir a lot.
after building heterostructure, i want to open this cif file with another visualizer i.e: material studio, but it could not open.
Hi Cihat - I apologize for the late reply. I am unfamiliar ilar with materials studio. I think if you want to save as a .cif you would have to save the space group as well. Have you tried saving as a .vasp and loading it into materials studio?
Hi, the whole process was explained nicely. Could you make a video on graphene/hexagonal boron nitride in-plane heterostructure with a zigzag interface?
Can you provide a picture? I don’t quite know what you mean
@@nickelandcopper5636 Please refer to Figure 1(a) of this paper: Ding, Ning, Xiangfeng Chen, and Chi-Man Lawrence Wu. "Mechanical properties and failure behaviors of the interface of hybrid graphene/hexagonal boron nitride sheets." Scientific reports 6, no. 1 (2016): 1-9.
Kindly help me in making Li/Ge/Li junction in vesta. I am trying from several days and I tried your method of heterostructure, but I am unable to make such structure. Can you please help me in this regard. Thank you
Hi. So sorry for the late reply. I’m just now getting to these older comments from when I was away. So you still need help for this one? Hope all is well.
Can you please tell me how to use Graphene as a substrate on CdS monolayer
Hi, really nice tutorial, it is useful for everybody.
I want u to show CaSiO3 (wollastonite) crystal structure. Actually, I want to model the matching crystallography wollastonite find in XRD.
Thank you very much
Hi. I apologize for the late reply. What would you like to do with this structure?
@@nickelandcopper5636 In crystallography, I need to depict the locations of calcium, silicon, and oxygen in the wollastonite structure. Can you assist me with drawing them in detail?
Hi, really nice tutorial, it is useful for me, keep up the good work.
I want u to show the multilayer Mo2S3 crystal structure.
Thank you very much
Hi thanks for nice comment. What exactly do you mean? Can you show me a picture?
Ah! Awesome!! 😁😁
I really like this fractional method. Very nice method you found! Thank you again for sharing it
@@nickelandcopper5636 Its always my pleasure. This tutorial series is becoming more like a complete tutorial series day by day. You are doing great!! It will help a lot of people. I heard that it is possible to visualize charge density and charge density difference (CHGCAR) directly in vesta. but is it possible for a certain energy range? I'm a little confused with the color and isosurface. How to indicate charge transfer or something like that. is it possible to visualize bonding/anti-bonding? I use 'vaspkit' to convert WAVECAR into vesta readable format. But I'm still confused about the prediction mainly that made just by charge density visualization. Maybe an example would be appreciable.
Thanks again :D
Thanks. I also keep meaning to make the python tutorials but people keep having great ideas for Vesta. So I sort of am just playing it by ear. For the charge density - these are the cube files generated by electronic structure programs. Here’s the deal with them. Assuming DFT , they are typically for a single Kohn sham orbital. Therefore, they are single electron wavefunctions. For example, let’s say we have a quantum dot with a ligand. And the homo ks orbitals is localized on the quantum dot and the lumo is localized on the ligand. So, what you would do is do an excited states calculation, say tddft, and realize that the first excitation is a homo - lumo transition in the KS space. Assuming this is the only transition in the superposition that is the true excited state for this particular excitation, this state is a single slater determinant. Now, you can visualize these KS orbitals in Vesta. If the homo orbital is localized on the core of the dot and the lumo on the ligand, this can be characterized as a charge transfer state. Actually, charge transfer states are typically Ill-defined. And technically, all excitation are charge transfer. But people usually reserve this terminology to refer to excitations between KS orbitals in which the charge density of these orbitals are localized on different parts of the systems. Please let me know if I am being clear enough. So to indicate charge transfer you would just need to show significant localization between the donor and acceptor states. But be warned. Charge transfer states are notoriously mischaracterized in DFT with pure functionals. You ideally should use range separated hybrid functional, if affordable. For the color, two colors is the phase of the wave function. Positive and negative. If only one color, this is like the total charge density - abs value of the wavefunction squared
@@nickelandcopper5636 Thanks a lot! Now it is clear to me!! I got it
hello.. plz show us how to make slab of 001 surface of Mn3O4, its becoming very difficult. Help plz. !! thank you.
Hi Saransha - I see you other comment on another video regarding Mn3O4. Do you still need help with this one? I apologize for the late reply
@@nickelandcopper5636 Hello Sir, yes please. It will be of great help Sir. :)
In linux please
Hi. I am not quite sure what you mean
@@nickelandcopper5636 i am sorry. I was wondering if you can make a tutorials on how to create heterostructure for users in Linux
Ah I see. I am not sure if Linux can support Vesta. I really am not sure by which means Linux can create these. Do you mean using a visualization software supported on the Linux platform?
@@nickelandcopper5636 thanks a lot for your prompt response.
Yes I believe that Vesta works in linux (Ubuntu).
And my question is can you please make a tutorials similar to those u did in windows but for linux users.
Ok. I see what you are asking now. I unfortunately cannot. I do not have a Linux platform to work on. That being said, I don’t see why anything would be different. Just use Linux based text files to manipulate the atomic coordinates. I use the Far3 viewer to manage text files on windows. But you can also just use regular text files on linux. The information you learn on my channel about how to use Vesta should transfer directly to using Vesta on Linux. What will be different is how you edit the various files saved by Vesta.