Just a tip if you re-add your 111 lattice plane before applying the transformation matrix, it should transform the plane as well. This is an easy way to figure out which of your new unit cell faces is the correct one. Otherwise great video, I found it super useful.
Hi Michael, sorry for the late reply. This sounds great but I can’t quite imagine what you say. Can you please try to elaborate or describe it again for me? Thank you 🙏
@@nickelandcopper5636 At 6:40 you delete the lattice planes, instead you can delete 2-4 but keep the first one and just hide it for now (in the "Objects section uncheck slices). Then after you transform the unit cell at 10:00 the transformation should also apply to the hidden lattice plane, now if you view enable it again it will see it should line up with one of the faces of the transformed unit cell ... Actually now that I look at this again I think there was a small error in the video, I think the rotation matrix you made needs to be transposed i.e. ((1,0,1),(-1,-1,0),(0,1,1)). If you use the transposed rotation matrix as I just wrote then the (111) plane will transform into a (002) plane indicating that the c face is the pre-tranformed (111) face.
@@michaellacount7626 thanks so much. Is there some way I can contact you outside of TH-cam comments? It’s been a while but if I recall the correct the surface I show is indeed the 111 surface, right?
@@nickelandcopper5636 Based on the fact that my previous 2 comments aren't showing up it seems trying to put any contact info here will get it instant flagged ... and youtube doesn't seem to have a way to private message someone. So best idea at the moment is keep doing this and if we get it all sorted delete the back and forth at a later date. Terrible way to communicate but I don't see another way. As far as whether you got the correct 111 surface I can't say for certain one way or the other. It's possible you did and I'm mistaken, it's also possible you happened upon something that just looks like the 111 surface, despite being monoclinic there is enough symmetry that its conceivable multiple faces are indistinguishable from one another. The only idea I have to distinguish it would be to edit the atoms so they are all different types so that there is more visual information to make a conclusion.
Hi Nickel and Copper, thank you very much. I am learning a lot from your videos. Can you please make a video on the B2O3 surface with 101 plane? I think it's an interesting example to show,.
Hi Nickel and Copper, I am trying to study the hydrogen evolution reaction on the (111), (110), (100) and (011) surface planes of Cobalt (III) Phosphide (COP). I want create a slab model of the different facets from the bulk CoP, add vacuum and the adsorbate (hydrogen) so I can carry out my calculations. Could you please make a comprehensive tutorial on that as I don't even know where to start from. Hope to hear from you soon. Thank you
Hi Esther, can you please send me the materials project ID for the CoP system you wish to study? I will look into this system next week. I am away this week
Like the eye on your face ...little did NandC know they were adding comedy to this channel :p I know how you feel ...in the moment, thinking you need to make sure to explain something and then the explanation seems trivial :) great video!! I really want to be able to take a POSCAR output and given the lattice constants and the new plane you want, apply rotation matrices to the lattice .....I'm still kind of stumped on this one though ...this method in VESTA works nicely
I have a program I am making called latticeTransformer that does that exact thing. You start with the POSCAR, give desired plane, and it gives you a bunch of rotation matrices as output. I have it made, actually …. Hehe. But it’s in a really rough state
very very good, this is great, Building slab geometries for catalysis or any application , I admire your effort, thank friend. I'm going to study your method of making my slab . congratulations
It’s possible that maybe the b or c dimension may be the 111 surface. It may still be the a dimension like I thought though, so make sure to double check this. One of the dimensions is though!
@@nickelandcopper5636 Yes, I've been analyzing your method. i want to build a slab with 72 atoms . the slab i found is 36 atoms ZrO2(111) is small . i want to put nickel on ZrO2(111) support . i will study your method
@@nickelandcopper5636 i have paper pubs.acs.org/doi/pdf/10.1021/acs.jpcc.8b11279?rand=2yxhn2av shows information on models of slabs for ZrO2 with 72 atoms. when you have time available it would be useful to read this paper
Hi Nickel and Copper, thank you for making the helpful video. One question: at 10:00, where you transform the matrix, there is a warning of changing the coordinate system from right- to left-handed one. Is it because that you chose the wrong sequence of the atoms for constructing new unit vectors of a’ and b’? Will it affect the result? Should we keep the right-handed system? Thanks
Hi Copper, thanks for your very nice videos. I have reviewed this video for many times and enjoyed a lot. According to your new video on CoP (111) surface, (111)*(transformation matrix) should equal to (00 1*constant), right? But I found this is not the case for the transformation matrix in this video. Could you tell me why? Also, you calculate the transformation matrix by aligning the coordinates laterally in some videos but vertically in other videos, which way is better?
Thanks so much … ya … your are right it should transform according to your equations … it’s possible that there is a mistake here! I’ve thought about swapping it out for a fix … but haven’t had the time Edit - see the discussion under “Michael LaCount’s” comment. He explains the nature of the error
Very helpful. I have a question: if i have crystal with FCC structure , i’m interested in 100 surface (natural exposed), so i should add vaccum in x-axis direction, right ? , Can i Add vaccum in z-axis direction instead of x-axis ? Is that correct ?
Another question: i see in some other websites, they destroy periodicity in x, y & z direction before saving in xyz format then transfer to vasp as you normally do . In your cases you destroy periodicity in x & y when you add vaccum in Z-direction. So please explain this to me. Thanks in advance
One needs to have the entire unit cell in the dimension on which they add vacuum. So you must not destroy periodicity in this dimension. That’s why I don’t destroy in x and y when adding vacuum to z
Nickel and Copper Thanks a lot . Regarding FCC , for100 surface, vaccum is added to X-axis direction, is it possible to add it to z-axis ? Which direction is the correct one ?
Making 110 surface for alpha-MnO2 (Tetragonal) seems so difficult. I could not find the plane for selected atoms (3rd and 4th plane). Can you please try this material?
How do you remove bond visualization while having 'ball and stick model' selected? I find the bonds to be very confusing when I'm trying to find periodicity.
Just a tip if you re-add your 111 lattice plane before applying the transformation matrix, it should transform the plane as well. This is an easy way to figure out which of your new unit cell faces is the correct one. Otherwise great video, I found it super useful.
Hi Michael, sorry for the late reply.
This sounds great but I can’t quite imagine what you say. Can you please try to elaborate or describe it again for me? Thank you 🙏
@@nickelandcopper5636 At 6:40 you delete the lattice planes, instead you can delete 2-4 but keep the first one and just hide it for now (in the "Objects section uncheck slices). Then after you transform the unit cell at 10:00 the transformation should also apply to the hidden lattice plane, now if you view enable it again it will see it should line up with one of the faces of the transformed unit cell ... Actually now that I look at this again I think there was a small error in the video, I think the rotation matrix you made needs to be transposed i.e. ((1,0,1),(-1,-1,0),(0,1,1)). If you use the transposed rotation matrix as I just wrote then the (111) plane will transform into a (002) plane indicating that the c face is the pre-tranformed (111) face.
@@michaellacount7626 thanks so much. Is there some way I can contact you outside of TH-cam comments? It’s been a while but if I recall the correct the surface I show is indeed the 111 surface, right?
@@nickelandcopper5636 Based on the fact that my previous 2 comments aren't showing up it seems trying to put any contact info here will get it instant flagged ... and youtube doesn't seem to have a way to private message someone. So best idea at the moment is keep doing this and if we get it all sorted delete the back and forth at a later date. Terrible way to communicate but I don't see another way. As far as whether you got the correct 111 surface I can't say for certain one way or the other. It's possible you did and I'm mistaken, it's also possible you happened upon something that just looks like the 111 surface, despite being monoclinic there is enough symmetry that its conceivable multiple faces are indistinguishable from one another. The only idea I have to distinguish it would be to edit the atoms so they are all different types so that there is more visual information to make a conclusion.
Hi Nickel and Copper, thank you very much. I am learning a lot from your videos. Can you please make a video on the B2O3 surface with 101 plane? I think it's an interesting example to show,.
Hi Nickel and Copper, I am trying to study the hydrogen evolution reaction on the (111), (110), (100) and (011) surface planes of Cobalt (III) Phosphide (COP). I want create a slab model of the different facets from the bulk CoP, add vacuum and the adsorbate (hydrogen) so I can carry out my calculations. Could you please make a comprehensive tutorial on that as I don't even know where to start from. Hope to hear from you soon. Thank you
Hi Esther, can you please send me the materials project ID for the CoP system you wish to study? I will look into this system next week. I am away this week
Wow fantastic! i like the way to 'find the plane for selected atoms' ! it is really useful. thanks
Like the eye on your face ...little did NandC know they were adding comedy to this channel :p I know how you feel ...in the moment, thinking you need to make sure to explain something and then the explanation seems trivial :) great video!! I really want to be able to take a POSCAR output and given the lattice constants and the new plane you want, apply rotation matrices to the lattice .....I'm still kind of stumped on this one though ...this method in VESTA works nicely
I have a program I am making called latticeTransformer that does that exact thing.
You start with the POSCAR, give desired plane, and it gives you a bunch of rotation matrices as output. I have it made, actually …. Hehe. But it’s in a really rough state
@@nickelandcopper5636 I find that I have to tranpose the final rotation matrix to get it to work correctly in VESTA
@@eric_welch yes I think you are correct. I think there is a small error here.
@@nickelandcopper5636 do you know why this is?? is it the way VESTA treats the rotation??
very very good, this is great, Building slab geometries for catalysis or any application , I admire your effort, thank friend. I'm going to study your method of making my slab . congratulations
It’s possible that maybe the b or c dimension may be the 111 surface. It may still be the a dimension like I thought though, so make sure to double check this. One of the dimensions is though!
@@nickelandcopper5636 Yes, I've been analyzing your method. i want to build a slab with 72 atoms . the slab i found is 36 atoms ZrO2(111) is small . i want to put nickel on ZrO2(111) support . i will study your method
Try to vary the slab size with edit - unit cell - transform. Then scale the diagonal elements only
@@nickelandcopper5636 thanks
@@nickelandcopper5636 i have paper pubs.acs.org/doi/pdf/10.1021/acs.jpcc.8b11279?rand=2yxhn2av shows information on models of slabs for ZrO2 with 72 atoms. when you have time available it would be useful to read this paper
Hi Nickel and Copper, thank you for making the helpful video. One question: at 10:00, where you transform the matrix, there is a warning of changing the coordinate system from right- to left-handed one. Is it because that you chose the wrong sequence of the atoms for constructing new unit vectors of a’ and b’? Will it affect the result? Should we keep the right-handed system? Thanks
Hi Copper, thanks for your very nice videos. I have reviewed this video for many times and enjoyed a lot. According to your new video on CoP (111) surface, (111)*(transformation matrix) should equal to (00 1*constant), right? But I found this is not the case for the transformation matrix in this video. Could you tell me why? Also, you calculate the transformation matrix by aligning the coordinates laterally in some videos but vertically in other videos, which way is better?
Thanks so much … ya … your are right it should transform according to your equations … it’s possible that there is a mistake here!
I’ve thought about swapping it out for a fix … but haven’t had the time
Edit - see the discussion under “Michael LaCount’s” comment. He explains the nature of the error
Thanks a lot for your interesting tutorials !
Please, which text editor you are using here?
The Far3 editor
Soo goood
Hi Nickel and Copper, Can you
help me to build CeO2 111 surface slab ??
I want to draw crystal structure of surface 104 of LiNiO2 by Vesta. Can I help you?
I want to create interface between monoclinic system and cubic system, can you make the tutorial please
By the way, how do you know that the a direction is the cleaved (111)face, not the c direction? How could we confirm which direction is what we want?
How do you find out which atoms to remove along any axis
I remove the ones that are the periodic image along that axis
Very helpful. I have a question: if i have crystal with FCC structure , i’m interested in 100 surface (natural exposed), so i should add vaccum in x-axis direction, right ? , Can i Add vaccum in z-axis direction instead of x-axis ? Is that correct ?
Another question: i see in some other websites, they destroy periodicity in x, y & z direction before saving in xyz format then transfer to vasp as you normally do . In your cases you destroy periodicity in x & y when you add vaccum in Z-direction. So please explain this to me. Thanks in advance
One needs to have the entire unit cell in the dimension on which they add vacuum. So you must not destroy periodicity in this dimension. That’s why I don’t destroy in x and y when adding vacuum to z
Yes - see my old video on Ru surface. I only add vacuum to the naturally exposed surface
Nickel and Copper Thanks a lot . Regarding FCC , for100 surface, vaccum is added to X-axis direction, is it possible to add it to z-axis ? Which direction is the correct one ?
Also , what is direction for adding vaccum if i’m interested in 010 surface ? Sorry for the inconvenience
Making 110 surface for alpha-MnO2 (Tetragonal) seems so difficult. I could not find the plane for selected atoms (3rd and 4th plane). Can you please try this material?
What is alpha? Cubic? Can you send materials project number
How do you remove bond visualization while having 'ball and stick model' selected? I find the bonds to be very confusing when I'm trying to find periodicity.
Question is resolved later in the video: Edit/Bonds/Delete
Alternatively under the objects pane you can uncheck bonds to temporarily hide the bonds.