Hi Sajid, I haven't actually reduced anything at the end 10:04 . The POSCAR did not have those infinite atoms, to begin with. It's just a VESTA visualization artefact. When I tell VESTA to not display the extra atoms beyond the cell, that is not affecting the number of atoms in the structure file. It is only for Vesta's visualization.
9:59 You can see that when I imported the POSCAR to VESTA, it already said that it has 53 atoms (look in the output window in the lower portion). The only problem was that VESTA has this setting where it will additionally display extra atoms (not in our structure). So I fixed that.
@@PhysWhizthanks very much for this informative video. I have few questions? I want to make some Oxide functional group on Graphene, if I do the same process that you have done but every time we open the file we have infinite atoms. 1- Does not it make problem in poscar file and optimization running? 2- I can see the boundaries but for investigation on surface effects of G like adsorption , I didn’t see this boundary in z direction, could you please help me? Thank you so much.
1. I showed in the video how to export the POSCAR properly. Then when we visualized it with VESTA, there was an issue of extra atoms being displayed. I showed that the POSCAR only had 53 atoms as we had intended it to have. It was just a stupid VESTA visualization issue, nothing else. VESTA is not the only visualization tool out there. There are many more tools like Jmol, CrysX-3D Viewer, etc. You can visualize the file there and see for yourself. The problem would be there if your POSCAR also has those extra atoms. But I already showed in the video about how to get rid of the extra atoms at the boundary and beyond the boundary and then save the structure. One should always check that the POSCAR only has the same number of atoms that they expect and not extra atoms. In my case the graphene unit cell has two atoms. So a 5x5 super cell has 5x5x2 = 50 atoms. Then 3 additional atoms from water to make it 53.
Hi Sajid, In my latest video I discuss the issue of these spurious extra atoms and how they won't affect the calculation: ruclips.net/video/yP1BREWv6u0/видео.html
Hi @Phys Whiz, I want to adsorb Li ion above the graphene monolayer 3 Angtstrom on multiple sites for batteries studies. I haven't to import Li from the outside, could you please discuss how to to do this.
You can simply create an XYZ file with the Li ion and then follow the steps in the tutorial. Save the following text as Li.xyz using any text editor: 1 Comment: Li ion Li 0.0000 0.0000 0.0000
![How to model hexagonal boron nitride (hBN) monolayer using VESTA? [TUTORIAL]](http://i.ytimg.com/vi/mNssTAuseRY/mqdefault.jpg)
![How to model hexagonal boron nitride (hBN) monolayer using VESTA? [TUTORIAL]](/img/tr.png)
![How to Create a Graphene Monolayer using VESTA? [TUTORIAL]](http://i.ytimg.com/vi/yP1BREWv6u0/mqdefault.jpg)
![How to Calculate Adsorption Energy using Quantum ESPRESSO and DFT? [TUTORIAL]](http://i.ytimg.com/vi/GiyluHexTzA/mqdefault.jpg)
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![How to place an Adsorbate (water) Molecule on hBN Surface? [TUTORIAL]](/img/1.gif)
Can you please upload a video for making bc3 monolayer? And also need information how we add volume here?
This is not exactly for BC3 but should be useful to you
ruclips.net/video/mNssTAuseRY/видео.html
Don't we need to save it at the end again after reducing the huge graphene monolayer as per our requirement?
Hi Sajid, I haven't actually reduced anything at the end 10:04 . The POSCAR did not have those infinite atoms, to begin with. It's just a VESTA visualization artefact. When I tell VESTA to not display the extra atoms beyond the cell, that is not affecting the number of atoms in the structure file. It is only for Vesta's visualization.
9:59 You can see that when I imported the POSCAR to VESTA, it already said that it has 53 atoms (look in the output window in the lower portion). The only problem was that VESTA has this setting where it will additionally display extra atoms (not in our structure). So I fixed that.
@@PhysWhizthanks very much for this informative video. I have few questions? I want to make some Oxide functional group on Graphene, if I do the same process that you have done but every time we open the file we have infinite atoms. 1- Does not it make problem in poscar file and optimization running?
2- I can see the boundaries but for investigation on surface effects of G like adsorption , I didn’t see this boundary in z direction, could you please help me? Thank you so much.
1. I showed in the video how to export the POSCAR properly. Then when we visualized it with VESTA, there was an issue of extra atoms being displayed. I showed that the POSCAR only had 53 atoms as we had intended it to have. It was just a stupid VESTA visualization issue, nothing else. VESTA is not the only visualization tool out there. There are many more tools like Jmol, CrysX-3D Viewer, etc. You can visualize the file there and see for yourself. The problem would be there if your POSCAR also has those extra atoms. But I already showed in the video about how to get rid of the extra atoms at the boundary and beyond the boundary and then save the structure. One should always check that the POSCAR only has the same number of atoms that they expect and not extra atoms. In my case the graphene unit cell has two atoms. So a 5x5 super cell has 5x5x2 = 50 atoms. Then 3 additional atoms from water to make it 53.
Hi Sajid, In my latest video I discuss the issue of these spurious extra atoms and how they won't affect the calculation: ruclips.net/video/yP1BREWv6u0/видео.html
Hi @Phys Whiz, I want to adsorb Li ion above the graphene monolayer 3 Angtstrom on multiple sites for batteries studies. I haven't to import Li from the outside, could you please discuss how to to do this.
You can simply create an XYZ file with the Li ion and then follow the steps in the tutorial. Save the following text as Li.xyz using any text editor:
1
Comment: Li ion
Li 0.0000 0.0000 0.0000
@@PhysWhiz that's wonderful. Thanx