Author Topic: Overlapping issue on mxene nanoribbon  (Read 134 times)

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Offline khariyahA

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Overlapping issue on mxene nanoribbon
« on: June 5, 2022, 03:28 »
Hi everyone, I really need help, im having issue about overlapping.
Im currently studying about mxene nanoribbon, Ti2CO2. To form Ti2CO2 nanoribbon, i tried to build it separately, which first i build C-Ti nanoribbon and then C-O nanoribbon. After that, i drag C-Ti nanoribbon onto C-O nanoribbon. The structure will look like below.

Before i proceed for running, there is prompt appears saying some atoms overlap and some atoms closer. Sir, is there any way for me to solve this overlap issue ? I want to produce bandstructure.

I really appreciate if you can help me on this.

Offline Anders Blom

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Re: Overlapping issue on mxene nanoribbon
« Reply #1 on: June 8, 2022, 07:58 »
I guess you need to separate the layers in the X direction?

Offline khariyahA

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Re: Overlapping issue on mxene nanoribbon
« Reply #2 on: June 8, 2022, 09:30 »
Thankyou so much Dr Blom for your reply   :)

Dr Blom, can you explain further how to separate the layers ?
If i separate the layers, it will become 2 different layers and will not form the intended material.

Offline Anders Blom

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Re: Overlapping issue on mxene nanoribbon
« Reply #3 on: June 8, 2022, 09:58 »
Well, the layers are surely not supposed to be on top of each other, as they probably are now (same x-coordinate for all atoms)? So you will need to select the atoms in one layer, make a translation of say 2 Å up or down to make a bi-layer structure. Or, if that is not what you want, some other transformation that brings the system to correct form.

Offline khariyahA

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Re: Overlapping issue on mxene nanoribbon
« Reply #4 on: June 8, 2022, 10:59 »
Dr Blom, I think i finally understand it. The structure is not supposed to be on top of each other or either in bi-layer structure, as in the reference paper attachment below. Mxene nanoribbon, Ti2CO2 is structure that consists of 3 atoms which are Ti, C and O. I tried to find Ti2CO2 in the database files, but the structure is not there. How can i build 3 atoms to one structure ? From the plugin features, it only can build 2 atoms at one time.

I hope you can help me figure out this. Thank you Dr Blom.

Offline Anders Blom

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Re: Overlapping issue on mxene nanoribbon
« Reply #5 on: June 9, 2022, 00:25 »
Ah, it's a lot easier to help when you state what you want the end result to be :-)

The important thing to note is that MXenes don't consist of a collection of flat layers with a 2-atom basis in a hexagonal lattice (like graphene). So your method to combine different nanosheets will not work.

There are a lot of scientific papers showing the structure of MXenes, even specifically Ti2CO2, such as eg. https://doi.org/10.1039/C9TA09185H, so I think you would be wise to study the topic more generally,

To build the specific structure you are interested in, I would start with the MAX phase of AlCCr2 which actually is included as a template in the Crystal Builder plugin (under the P63/mmc space group). Just change Cr to Ti and you get Ti2CAl. Once you have built this, remove all atoms except the 3 middle ones (in the Z direction), and you actually end up with the MXene Ti2C.

Now you just have to oxygenate it. My method for this is to select both Ti atoms, and make a duplicate copy of them (menu Edit, Copy and then Paste). The pasted atoms will overlap the original Ti atoms, for now. Change these pasted atoms to oxygen using the Periodic Table button. Then open the Coordinate list and move the two oxygen atoms to the opposite side, respectively. So, the one at z=5.6 goes to z=9 or so, and the one at 7.9 goes to z=4.5 (exact values don't matter for now).

The structure built in this way corresponds to the CBACB stacking in Fig 1 (a) of https://doi.org/10.1039/c4cp05140h, and making the other versions is straightforward as well, by just shifting one or both oxygen to x=y=0. Note that there is also an alternative structure with ABA stacking for the 3 middle layers, but that is not covered here or in that paper.

Finally, you can use the Quick Optimizer with UFF; the structure I built in this way is attached, and is hopefully a good starting geometry for a proper DFT geometry optimization and further studies.
« Last Edit: June 9, 2022, 06:52 by Anders Blom »

Offline khariyahA

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Re: Overlapping issue on mxene nanoribbon
« Reply #6 on: June 9, 2022, 16:37 »
Thank you so much for helping me Dr Blom. I sincerely appreciate it  :)

Offline khariyahA

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Re: Overlapping issue on mxene nanoribbon
« Reply #7 on: June 9, 2022, 19:50 »
Dr Blom, I got confused a little bit about the type of this structure, is it armchair edge or zigzag edge nanoribbon?

And I also got a problem to come out with the transmission spectrum and I-V characteristics of that material since there is problem at device tools (device from bulk). Then, after getting the output, how to vary the width and length of that structure?(I need to compare their band structures with various lengths and widths). I hope you could help me to overcome all the issues. Thank you in advance Dr Blom!

Offline Anders Blom

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Re: Overlapping issue on mxene nanoribbon
« Reply #8 on: June 9, 2022, 23:04 »
I don't have time or space to provide a whole course in running these calculations here, but I recommend our tutorials.

To your specific questions, a MATERIAL does not have a transmission spectrum or I-V curve, for that you need to create a device, which has some scattering region that makes it a non-trivial system, not just a repetition of the bulk material.

The structure I sent is neither zigzag nor armchair because it's not a nanoribbon. It's the periodic unitcell of the oxygenated MXene, so it's periodic in two directions, like a graphene sheet (not a graphene nanoribbon). You could make a nanoribbon using the same ideas as for graphene or MoS2 I suppose, but surface termination will definitely be tricky. The width of such a ribbon would influence its band structure, the length however does not.